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authorAndreas Maunz <andreas@maunz.de>2012-02-20 14:45:20 +0100
committerAndreas Maunz <andreas@maunz.de>2012-02-20 14:45:20 +0100
commite77cc376aaff8ca481fdace6d5795c5b5feb0e87 (patch)
tree7414410257818a6f52e64fc720827766b05ed70a
parentec9256dc1b29a3203d6e987244d2aeacbd3dda1a (diff)
Added pc descriptor calc service
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-rw-r--r--java/joelib2/util/types/BasicStackType.classbin0 -> 629 bytes
-rw-r--r--java/joelib2/util/types/BasicStringInt.classbin0 -> 1089 bytes
-rw-r--r--java/joelib2/util/types/BasicStringObject.classbin0 -> 698 bytes
-rw-r--r--java/joelib2/util/types/BasicStringPattern.classbin0 -> 731 bytes
-rw-r--r--java/joelib2/util/types/BasicStringString.classbin0 -> 1268 bytes
-rw-r--r--java/joelib2/util/types/BondBoolean.classbin0 -> 159 bytes
-rw-r--r--java/joelib2/util/types/BondDouble.classbin0 -> 157 bytes
-rw-r--r--java/joelib2/util/types/BondInt.classbin0 -> 151 bytes
-rw-r--r--java/joelib2/util/types/BondString.classbin0 -> 157 bytes
-rw-r--r--java/joelib2/util/types/BondWrapper.classbin0 -> 175 bytes
-rw-r--r--java/joelib2/util/types/BooleanValue.classbin0 -> 147 bytes
-rw-r--r--java/joelib2/util/types/DoubleDouble.classbin0 -> 632 bytes
-rw-r--r--java/joelib2/util/types/DoubleInt.classbin0 -> 153 bytes
-rw-r--r--java/joelib2/util/types/DoubleType.classbin0 -> 202 bytes
-rw-r--r--java/joelib2/util/types/DoubleValue.classbin0 -> 253 bytes
-rw-r--r--java/joelib2/util/types/FactoryInfo.classbin0 -> 298 bytes
-rw-r--r--java/joelib2/util/types/IntInt.classbin0 -> 284 bytes
-rw-r--r--java/joelib2/util/types/IntIntInt.classbin0 -> 305 bytes
-rw-r--r--java/joelib2/util/types/IntValue.classbin0 -> 238 bytes
-rw-r--r--java/joelib2/util/types/StackType.classbin0 -> 209 bytes
-rw-r--r--java/joelib2/util/types/StringDouble.classbin0 -> 159 bytes
-rw-r--r--java/joelib2/util/types/StringInt.classbin0 -> 153 bytes
-rw-r--r--java/joelib2/util/types/StringObject.classbin0 -> 257 bytes
-rw-r--r--java/joelib2/util/types/StringPattern.classbin0 -> 274 bytes
-rw-r--r--java/joelib2/util/types/StringString.classbin0 -> 319 bytes
-rw-r--r--java/joelib2/util/types/StringValue.classbin0 -> 264 bytes
-rw-r--r--java/jtt/docbook/DocBookArticles.classbin0 -> 3836 bytes
-rw-r--r--java/jtt/docbook/DocBookEquations.classbin0 -> 6052 bytes
-rw-r--r--java/jtt/docbook/DocBookMolecules.classbin0 -> 6460 bytes
-rw-r--r--java/jtt/docbook/Jade.classbin0 -> 2021 bytes
-rw-r--r--java/jtt/latex/bibtex/Bibitem.classbin0 -> 9802 bytes
-rw-r--r--java/jtt/latex/bibtex/BibitemHolder.classbin0 -> 3168 bytes
-rw-r--r--java/jtt/util/Executable.classbin0 -> 2620 bytes
-rw-r--r--java/junit-3.8.1.jarbin0 -> 121070 bytes
-rw-r--r--java/linux/title2databin0 -> 14514 bytes
-rw-r--r--java/linux/title2data.cpp79
-rw-r--r--java/log4j.jarbin0 -> 350525 bytes
-rw-r--r--java/log4j.properties104
-rw-r--r--java/mm.mysql-2.0.14-bin.jarbin0 -> 125901 bytes
-rw-r--r--java/optional.jarbin0 -> 654735 bytes
-rw-r--r--java/resources/CML2SDF.sdf58
-rw-r--r--java/resources/aspirin2D.mol31
-rw-r--r--java/resources/aspirin2D.numeric.mol56381
-rw-r--r--java/resources/aspirin3D.mol47
-rw-r--r--java/resources/cis_butene.mol12
-rw-r--r--java/resources/contigous.mol150
-rw-r--r--java/resources/hexamethylbenzen.mol29
-rw-r--r--java/resources/logP.mr.txt1
-rw-r--r--java/resources/multiple.mol296
-rw-r--r--java/resources/patty.txt4
-rw-r--r--java/resources/psa.txt20
-rw-r--r--java/resources/renumbered.sdf120
-rw-r--r--java/resources/smartsEvaluation/2-phenylnaphtho-oxazole.mol46
-rw-r--r--java/resources/smartsEvaluation/2H-chromen-2-one.mol28
-rw-r--r--java/resources/smartsEvaluation/3-hydroxy-4-iminocyclohexa-2,5-dien-1-one.mol23
-rw-r--r--java/resources/smartsEvaluation/4-(methylimino)cyclohexa-2,5-dien-1-one.mol23
-rw-r--r--java/resources/smartsEvaluation/4-chlorpyrimidin.mol19
-rw-r--r--java/resources/smartsEvaluation/4-chlorpyrimidin_h.mol25
-rw-r--r--java/resources/smartsEvaluation/5-[1-cyclobutyl-2-[(hydroxythio)oxy]-1-(3-methylaziridin-2-yl)propyl]-1,3-azaphosphinane.mol49
-rw-r--r--java/resources/smartsEvaluation/5-cyclobutyl-2-cycloheptylphosphinane.mol41
-rw-r--r--java/resources/smartsEvaluation/6-iminocyclohexa-1,4-diene-1,3-diol.mol23
-rw-r--r--java/resources/smartsEvaluation/8-amino-3H-phenoxazin-3-ol.mol59
-rw-r--r--java/resources/smartsEvaluation/8-amino-3H-phenoxazin-3-one.mol41
-rw-r--r--java/resources/smartsEvaluation/9,10-dihydroxyphenanthrene.mol39
-rw-r--r--java/resources/smartsEvaluation/TEST_1.mol31
-rw-r--r--java/resources/smartsEvaluation/TEST_1_H.mol40
-rw-r--r--java/resources/smartsEvaluation/TEST_2.mol36
-rw-r--r--java/resources/smartsEvaluation/TEST_3.mol41
-rw-r--r--java/resources/smartsEvaluation/ab_unsat_carbonyl.mol16
-rw-r--r--java/resources/smartsEvaluation/ab_unsat_carbonyl_h.mol32
-rw-r--r--java/resources/smartsEvaluation/actinides.mol53
-rw-r--r--java/resources/smartsEvaluation/alkali_elements.mol17
-rw-r--r--java/resources/smartsEvaluation/boron_group.mol15
-rw-r--r--java/resources/smartsEvaluation/butan.mol12
-rw-r--r--java/resources/smartsEvaluation/butene.mol12
-rw-r--r--java/resources/smartsEvaluation/cis_butene.mol12
-rw-r--r--java/resources/smartsEvaluation/di_halogen_ethyl.mol42
-rw-r--r--java/resources/smartsEvaluation/earth_alkanline.mol12
-rw-r--r--java/resources/smartsEvaluation/ethan.mol8
-rw-r--r--java/resources/smartsEvaluation/evaluation.txt130
-rw-r--r--java/resources/smartsEvaluation/he_group.mol11
-rw-r--r--java/resources/smartsEvaluation/hydroxylamin.mol12
-rw-r--r--java/resources/smartsEvaluation/hydroxylamin_H.mol27
-rw-r--r--java/resources/smartsEvaluation/knockout65.mol29
-rw-r--r--java/resources/smartsEvaluation/lanthanides.mol48
-rw-r--r--java/resources/smartsEvaluation/lanthanides2.mol22
-rw-r--r--java/resources/smartsEvaluation/peroxide.mol10
-rw-r--r--java/resources/smartsEvaluation/phenol.mol19
-rw-r--r--java/resources/smartsEvaluation/propan.mol10
-rw-r--r--java/resources/smartsEvaluation/pyrene-4,5-diol.mol44
-rw-r--r--java/resources/smartsEvaluation/pyridine.mol17
-rw-r--r--java/resources/smartsEvaluation/pyrimidin_derivat.mol78
-rw-r--r--java/resources/smartsEvaluation/recap.mol155
-rw-r--r--java/resources/smartsEvaluation/trans_butene.mol12
-rw-r--r--java/resources/smartsEvaluation/water.mol10
-rw-r--r--java/resources/smartsEvaluation/{(Z)-1-(1-hydrazinopropyl)-2-[(hydroxythio)oxy]-2-sulfinovinyl}(oxo)sulfonium.mol35
-rw-r--r--java/resources/smartsEvaluation/{[[hydroxy(oxetan-3-yl)amino](oxaziridin-3-yl)methyl]dithio}methanetriol.mol38
-rw-r--r--java/resources/test.mol66
-rw-r--r--java/resources/test2.mol46
-rw-r--r--java/resources/test3.mol66
-rw-r--r--java/resources/trans_butene.mol12
-rw-r--r--java/sgt.jarbin0 -> 827708 bytes
-rw-r--r--java/vecmath.jarbin0 -> 325572 bytes
-rw-r--r--java/weka.jarbin0 -> 2324032 bytes
-rw-r--r--java/windows/title2data.cpp82
-rw-r--r--java/wsi/ra/database/DatabaseConnection.classbin0 -> 3196 bytes
-rw-r--r--java/wsi/ra/image/BMPFile.classbin0 -> 2822 bytes
-rw-r--r--java/wsi/ra/io/BasicBatchFileUtilities.classbin0 -> 2098 bytes
-rw-r--r--java/wsi/ra/io/BasicBatchScriptReplacer.classbin0 -> 3148 bytes
-rw-r--r--java/wsi/ra/io/BasicRegExpFilenameFilter.classbin0 -> 1029 bytes
-rw-r--r--java/wsi/ra/io/BatchFileUtilities.classbin0 -> 366 bytes
-rw-r--r--java/wsi/ra/io/BatchScriptReplacer.classbin0 -> 369 bytes
-rw-r--r--java/wsi/ra/io/RegExpFilenameFilter.classbin0 -> 188 bytes
-rw-r--r--java/wsi/ra/taglets/Author.classbin0 -> 2903 bytes
-rw-r--r--java/wsi/ra/taglets/CVSVersion.classbin0 -> 2938 bytes
-rw-r--r--java/wsi/ra/taglets/Cite.classbin0 -> 13051 bytes
-rw-r--r--java/wsi/ra/taglets/License.classbin0 -> 2516 bytes
-rw-r--r--java/wsi/ra/taglets/ListTag$ListType.classbin0 -> 1158 bytes
-rw-r--r--java/wsi/ra/taglets/ListTag.classbin0 -> 5476 bytes
-rw-r--r--java/wsi/ra/taglets/TagPrefs.classbin0 -> 1230 bytes
-rw-r--r--java/wsi/ra/taglets/ToDo.classbin0 -> 522 bytes
-rw-r--r--java/wsi/ra/taglets/WikipediaEN.classbin0 -> 1666 bytes
-rw-r--r--java/wsi/ra/text/DecimalFormatHelper.classbin0 -> 2812 bytes
-rw-r--r--java/wsi/ra/text/DecimalFormatter.classbin0 -> 121 bytes
-rw-r--r--java/wsi/ra/text/DocBookEquations.classbin0 -> 1957 bytes
-rw-r--r--java/wsi/ra/text/UnicodeHelper.classbin0 -> 1799 bytes
-rw-r--r--java/wsi/ra/tool/ArrayBinning.classbin0 -> 3474 bytes
-rw-r--r--java/wsi/ra/tool/ArrayBinningInterface.classbin0 -> 443 bytes
-rw-r--r--java/wsi/ra/tool/ArrayStatistic.classbin0 -> 3759 bytes
-rw-r--r--java/wsi/ra/tool/ArrayStatisticInterface.classbin0 -> 472 bytes
-rw-r--r--java/wsi/ra/tool/BasicPropertyHolder.classbin0 -> 8141 bytes
-rw-r--r--java/wsi/ra/tool/BasicResourceLoader.classbin0 -> 4082 bytes
-rw-r--r--java/wsi/ra/tool/Deque.classbin0 -> 2299 bytes
-rw-r--r--java/wsi/ra/tool/DequeInterface.classbin0 -> 633 bytes
-rw-r--r--java/wsi/ra/tool/DequeIterator.classbin0 -> 671 bytes
-rw-r--r--java/wsi/ra/tool/DequeIteratorInterface.classbin0 -> 171 bytes
-rw-r--r--java/wsi/ra/tool/DequeNode.classbin0 -> 898 bytes
-rw-r--r--java/wsi/ra/tool/DequeNodeInterface.classbin0 -> 82 bytes
-rw-r--r--java/wsi/ra/tool/HashedDoubleArray.classbin0 -> 3415 bytes
-rw-r--r--java/wsi/ra/tool/HashedIntArray.classbin0 -> 2883 bytes
-rw-r--r--java/wsi/ra/tool/PropertyHolder.classbin0 -> 754 bytes
-rw-r--r--java/wsi/ra/tool/ResourceLoaderInterface.classbin0 -> 151 bytes
-rw-r--r--java/wsi/ra/tool/SortedHashedIntArray.classbin0 -> 2376 bytes
-rw-r--r--java/wsi/ra/tool/SortedVector.classbin0 -> 2996 bytes
-rw-r--r--java/wsi/ra/tool/SortedVectorInterface.classbin0 -> 935 bytes
-rw-r--r--java/wsi/ra/tool/StatisticUtils.classbin0 -> 3026 bytes
-rw-r--r--java/wsi/ra/tool/Statistics.classbin0 -> 8435 bytes
-rw-r--r--java/wsi/ra/tool/StopWatch.classbin0 -> 942 bytes
-rw-r--r--java/wsi/ra/tool/StopWatchInterface.classbin0 -> 224 bytes
-rw-r--r--java/xerces.jarbin0 -> 933730 bytes
1211 files changed, 76941 insertions, 0 deletions
diff --git a/application.rb b/application.rb
index e4f5044..f806271 100644
--- a/application.rb
+++ b/application.rb
@@ -1,7 +1,19 @@
+ENV["JAVA_HOME"] = "/usr/lib/jvm/java-6-sun" unless ENV["JAVA_HOME"]
+ENV["JOELIB2"] = File.join File.expand_path(File.dirname(__FILE__)),"java"
+deps = []
+deps << "#{ENV["JAVA_HOME"]}/lib/tools.jar"
+deps << "#{ENV["JAVA_HOME"]}/lib/classes.jar"
+deps << "#{ENV["JOELIB2"]}"
+jars = Dir[ENV["JOELIB2"]+"/*.jar"].collect {|f| File.expand_path(f) }
+deps = deps + jars
+ENV["CLASSPATH"] = deps.join(":")
+
+
require 'rubygems'
gem "opentox-ruby", "~> 3"
require 'opentox-ruby'
require 'profiler'
+require 'rjb'
set :lock, true
@@ -340,6 +352,29 @@ post '/:id' do
halt 202,task.uri.to_s+"\n"
end
+
+# Create PC descriptors
+#
+# @param [String] pc_type
+# @return [text/uri-list] Task ID
+post '/:id/pcdesc' do
+ response['Content-Type'] = 'text/uri-list'
+ raise "No PC type given" unless params["pc_type"]
+
+ task = OpenTox::Task.create("PC descriptor calculation for dataset ", @uri) do
+ types = params[:pc_type].split(",")
+ if types.include?("joelib")
+ Rjb.load(nil,["-Xmx64m"])
+ s = Rjb::import('JoelibFc')
+ end
+ OpenTox::Algorithm.pc_descriptors( { :dataset_uri => @uri, :pc_type => params[:pc_type], :rjb => s } )
+ end
+ raise OpenTox::ServiceUnavailableError.newtask.uri+"\n" if task.status == "Cancelled"
+ halt 202,task.uri.to_s+"\n"
+end
+
+
+
# Delete a dataset
# @return [text/plain] Status message
delete '/:id' do
diff --git a/java/Acme/IntHashtable.class b/java/Acme/IntHashtable.class
new file mode 100644
index 0000000..d589d5e
--- /dev/null
+++ b/java/Acme/IntHashtable.class
Binary files differ
diff --git a/java/Acme/IntHashtableEntry.class b/java/Acme/IntHashtableEntry.class
new file mode 100644
index 0000000..68e61d2
--- /dev/null
+++ b/java/Acme/IntHashtableEntry.class
Binary files differ
diff --git a/java/Acme/IntHashtableEnumerator.class b/java/Acme/IntHashtableEnumerator.class
new file mode 100644
index 0000000..094c480
--- /dev/null
+++ b/java/Acme/IntHashtableEnumerator.class
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diff --git a/java/Acme/JPM/Encoders/GifEncoder.class b/java/Acme/JPM/Encoders/GifEncoder.class
new file mode 100644
index 0000000..333716a
--- /dev/null
+++ b/java/Acme/JPM/Encoders/GifEncoder.class
Binary files differ
diff --git a/java/Acme/JPM/Encoders/GifEncoderHashitem.class b/java/Acme/JPM/Encoders/GifEncoderHashitem.class
new file mode 100644
index 0000000..98abe62
--- /dev/null
+++ b/java/Acme/JPM/Encoders/GifEncoderHashitem.class
Binary files differ
diff --git a/java/Acme/JPM/Encoders/GrayJPEG.class b/java/Acme/JPM/Encoders/GrayJPEG.class
new file mode 100644
index 0000000..218329b
--- /dev/null
+++ b/java/Acme/JPM/Encoders/GrayJPEG.class
Binary files differ
diff --git a/java/Acme/JPM/Encoders/ImageEncoder.class b/java/Acme/JPM/Encoders/ImageEncoder.class
new file mode 100644
index 0000000..6a987ea
--- /dev/null
+++ b/java/Acme/JPM/Encoders/ImageEncoder.class
Binary files differ
diff --git a/java/Acme/JPM/Encoders/PpmEncoder.class b/java/Acme/JPM/Encoders/PpmEncoder.class
new file mode 100644
index 0000000..ec98b4d
--- /dev/null
+++ b/java/Acme/JPM/Encoders/PpmEncoder.class
Binary files differ
diff --git a/java/Jmol.jar b/java/Jmol.jar
new file mode 100644
index 0000000..2c7e5aa
--- /dev/null
+++ b/java/Jmol.jar
Binary files differ
diff --git a/java/JoelibFc.class b/java/JoelibFc.class
new file mode 100644
index 0000000..5e68988
--- /dev/null
+++ b/java/JoelibFc.class
Binary files differ
diff --git a/java/ant.jar b/java/ant.jar
new file mode 100644
index 0000000..3a67607
--- /dev/null
+++ b/java/ant.jar
Binary files differ
diff --git a/java/bin2hex.pl b/java/bin2hex.pl
new file mode 100644
index 0000000..f419c3e
--- /dev/null
+++ b/java/bin2hex.pl
@@ -0,0 +1,35 @@
+o = lo0; //Zeiger auf die Elemente unterhalb des partitionElement
+ int hi = hi0; //Zeiger auf die Elemente oberhalb des partitionElement
+ double pElem; //partitionElement. It divide the data array in two parts.
+ int noRecPar = 20; //Ist der zu sortierende Teilbereich kleiner als (hier:20) x Elemente, so ueberspringe
+ //die Rekursion. Am Ende aller (mit QuickSort) vorsortierten Elemente wird nun
+ //InsertSoert angewendet. Man koennte auch die einzelnen Teilbereiche mit InsertSort
+ //sortieren, jedoch ist die Anwendung auf das gesamte vorsortierte Array effektiver.
+
+ if ( (hi0 - lo0) >= noRecPar)
+ {
+
+ //nimmt einfach das mittlere Element als teilendes Element.
+ pElem = xy.x[ ( lo0 + hi0 ) / 2 ];
+
+ //wiederholt die Schleife bis sich die Zeiger schneiden.
+ while( lo <= hi )
+ {
+ //suche das erste Element, das groeSer oder gleich dem teilenden Element (partitionElement)
+ //ist, beginnend mit dem kleinsten Index (Zeiger).
+ while( ( lo < hi0 ) && ( xy.x[lo] < pElem )) ++lo;
+
+ //suche das erste Element, das kleiner oder gleich dem teilenden Element (partitionElement)
+ //ist, beginnend mit dem groeStem Index (Zeiger).
+ while( ( hi > lo0 ) && ( xy.x[hi] > pElem )) --hi;
+
+ // vertausche die gefundenen Werte, wenn die Zeiger noch nicht vertauscht sind.
+ if( lo <= hi )
+ {
+ xy.swap(lo, hi);
+ ++lo;
+ --hi;
+ }
+ }
+
+ //Wenn \ No newline at end of file
diff --git a/java/cformat/PrintfFormat$DecDouble.class b/java/cformat/PrintfFormat$DecDouble.class
new file mode 100644
index 0000000..1b80656
--- /dev/null
+++ b/java/cformat/PrintfFormat$DecDouble.class
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diff --git a/java/cformat/PrintfFormat$OutBuffer.class b/java/cformat/PrintfFormat$OutBuffer.class
new file mode 100644
index 0000000..0f25b29
--- /dev/null
+++ b/java/cformat/PrintfFormat$OutBuffer.class
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diff --git a/java/cformat/PrintfFormat.class b/java/cformat/PrintfFormat.class
new file mode 100644
index 0000000..3b05ba1
--- /dev/null
+++ b/java/cformat/PrintfFormat.class
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diff --git a/java/cformat/PrintfFormatTest$TestException.class b/java/cformat/PrintfFormatTest$TestException.class
new file mode 100644
index 0000000..93b3194
--- /dev/null
+++ b/java/cformat/PrintfFormatTest$TestException.class
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diff --git a/java/cformat/PrintfFormatTest.class b/java/cformat/PrintfFormatTest.class
new file mode 100644
index 0000000..6ea2158
--- /dev/null
+++ b/java/cformat/PrintfFormatTest.class
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diff --git a/java/cformat/PrintfStream.class b/java/cformat/PrintfStream.class
new file mode 100644
index 0000000..b2253a2
--- /dev/null
+++ b/java/cformat/PrintfStream.class
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diff --git a/java/cformat/PrintfWriter.class b/java/cformat/PrintfWriter.class
new file mode 100644
index 0000000..655110a
--- /dev/null
+++ b/java/cformat/PrintfWriter.class
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diff --git a/java/cformat/ScanfFormat$Cmatch.class b/java/cformat/ScanfFormat$Cmatch.class
new file mode 100644
index 0000000..ec11d0d
--- /dev/null
+++ b/java/cformat/ScanfFormat$Cmatch.class
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diff --git a/java/cformat/ScanfFormat.class b/java/cformat/ScanfFormat.class
new file mode 100644
index 0000000..2b15ef5
--- /dev/null
+++ b/java/cformat/ScanfFormat.class
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diff --git a/java/cformat/ScanfFormatTest.class b/java/cformat/ScanfFormatTest.class
new file mode 100644
index 0000000..bea49e6
--- /dev/null
+++ b/java/cformat/ScanfFormatTest.class
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diff --git a/java/cformat/ScanfMatchException.class b/java/cformat/ScanfMatchException.class
new file mode 100644
index 0000000..4226d27
--- /dev/null
+++ b/java/cformat/ScanfMatchException.class
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diff --git a/java/cformat/ScanfReader.class b/java/cformat/ScanfReader.class
new file mode 100644
index 0000000..f633f0e
--- /dev/null
+++ b/java/cformat/ScanfReader.class
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diff --git a/java/cformat/ScanfReaderTest.class b/java/cformat/ScanfReaderTest.class
new file mode 100644
index 0000000..36fbaff
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diff --git a/java/com/obrador/DCT.class b/java/com/obrador/DCT.class
new file mode 100644
index 0000000..4113413
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+++ b/java/com/obrador/DCT.class
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diff --git a/java/com/obrador/Huffman.class b/java/com/obrador/Huffman.class
new file mode 100644
index 0000000..ce910f4
--- /dev/null
+++ b/java/com/obrador/Huffman.class
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diff --git a/java/com/obrador/Jpeg.class b/java/com/obrador/Jpeg.class
new file mode 100644
index 0000000..95e93a5
--- /dev/null
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new file mode 100644
index 0000000..848ff71
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diff --git a/java/com/obrador/JpegInfo.class b/java/com/obrador/JpegInfo.class
new file mode 100644
index 0000000..f84d191
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diff --git a/java/com/vladium/utils/ClassScope$1.class b/java/com/vladium/utils/ClassScope$1.class
new file mode 100644
index 0000000..7449d2c
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+++ b/java/com/vladium/utils/ClassScope$1.class
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diff --git a/java/crimson.jar b/java/crimson.jar
new file mode 100644
index 0000000..0536ae1
--- /dev/null
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diff --git a/java/docs/algo/APropertyBFS.html b/java/docs/algo/APropertyBFS.html
new file mode 100644
index 0000000..df26fb7
--- /dev/null
+++ b/java/docs/algo/APropertyBFS.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.APROPERTYBFS"
+></A
+>Valence</H2
+><P
+>Breadth first search calculating the distance only between boolean atom properties (default: Atom in conjugated environment).</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/algo/BreadthFirstSearch.html b/java/docs/algo/BreadthFirstSearch.html
new file mode 100644
index 0000000..47c782c
--- /dev/null
+++ b/java/docs/algo/BreadthFirstSearch.html
@@ -0,0 +1,122 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.ALGORITHMS.BREADTHFIRSTSEARCH"
+></A
+>Breadth First Search (BFS)</H1
+><P
+>&#13;The BFS method performs a breadth-first search [<A
+HREF="bibliography.html#CLR98"
+>clr98</A
+>] of a graph.
+A breadth-first search visits vertices that are closer to the
+source before visiting vertices that are further away. In this
+context `distance' is defined as the number of edges in the
+shortest path from the source vertex.
+<DIV
+CLASS="FIGURE"
+><A
+NAME="JOELIB.ALGORITHMS.BREADTHFIRSTSEARCH.PSEUDOCODE"
+></A
+><P
+><B
+>Figure 1. Pseudocode for the BFS algorithm</B
+></P
+><PRE
+CLASS="PROGRAMLISTING"
+>paint all vertices white;
+paint the source grey, set its distance to 0 and enqueue it;
+repeat
+ dequeue vertex v;
+ if v is the target, we're done - exit this algorithm;
+ paint v black;
+ for each white neighbor w of v
+ paint w grey;
+ set distance w to (distance v + 1);
+ set parent w to v;
+ enqueue w
+until the queue is empty
+if we haven't yet exited, we didn't find the target</PRE
+></DIV
+>
+The time complexity is <IMG
+SRC="formulas/o_e+v.gif"> [<A
+HREF="bibliography.html#CLR98"
+>clr98</A
+>].</P
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/algo/DepthFirstSearch.html b/java/docs/algo/DepthFirstSearch.html
new file mode 100644
index 0000000..a4afe64
--- /dev/null
+++ b/java/docs/algo/DepthFirstSearch.html
@@ -0,0 +1,137 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.ALGORITHMS.DEPTHFIRSTSEARCH"
+></A
+>Depth First Search (DFS)</H1
+><P
+>The DFS method performs a depth--first search [<A
+HREF="bibliography.html#CLR98"
+>clr98</A
+>] of a graph.
+A depth--first search visits vertices that are further to the
+source before visiting vertices that are closer away. In this
+context `distance' is defined as the number of edges in the
+shortest path from the source vertex.
+<DIV
+CLASS="FIGURE"
+><A
+NAME="JOELIB.ALGORITHMS.DEPTHFIRSTSEARCH.PSEUDOCODE"
+></A
+><P
+><B
+>Figure 1. Pseudocode for the DFS algorithm</B
+></P
+><PRE
+CLASS="PROGRAMLISTING"
+>DFS(G)
+ {
+ For each v in V,
+ {
+ color[v]=white;
+ pred[u]=NULL
+ }
+
+ time=0;
+ For each u in V
+ If (color[u]=white) DFSVISIT(u)
+ }
+
+
+ DFSVISIT(u)
+ {
+ color[u]=gray;
+ d[u] = ++time;
+
+ For each v in Adj(u) do
+ If (color[v] = white)
+ {
+ pred[v] = u;
+ DFSVISIT(v);
+ }
+
+ color[u] = black; f[u]=++time;
+ }</PRE
+></DIV
+>
+The time complexity is <IMG
+SRC="formulas/o_e+v.gif"> [<A
+HREF="bibliography.html#CLR98"
+>clr98</A
+>].</P
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/algo/DistanceMatrix.html b/java/docs/algo/DistanceMatrix.html
new file mode 100644
index 0000000..6a745e7
--- /dev/null
+++ b/java/docs/algo/DistanceMatrix.html
@@ -0,0 +1,102 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.ALGORITHMS.DISTANCEMATRIX"
+></A
+>Topological distance matrix</H1
+><P
+>Calculates the topological distances between all atom pairs.
+Here a simple Breadth First Search (BFS )
+is used to calculate these distances, which causes a running time of
+<SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>O(A<SUP
+>3</SUP
+>)</B
+></SPAN
+>, where
+<SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>A</B
+></SPAN
+> is the number of atoms.</P
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/algo/GeomDistanceMatrix.html b/java/docs/algo/GeomDistanceMatrix.html
new file mode 100644
index 0000000..76488d9
--- /dev/null
+++ b/java/docs/algo/GeomDistanceMatrix.html
@@ -0,0 +1,84 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.ALGORITHMS.GEOMDISTANCEMATRIX"
+></A
+>Geometrical distance matrix</H1
+><P
+>The geometrical distance matrix calculates the euklidian distance between the 3D coordinates of all atom pairs.</P
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/algo/Morgan.html b/java/docs/algo/Morgan.html
new file mode 100644
index 0000000..0a20be3
--- /dev/null
+++ b/java/docs/algo/Morgan.html
@@ -0,0 +1,157 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.ALGORITHMS.MORGAN"
+></A
+>Morgan: Unique atom numbering</H1
+><P
+>Algorithm to get a unique numbering for molecules (graphs) [<A
+HREF="bibliography.html#MOR65"
+>mor65</A
+>].
+<DIV
+CLASS="FIGURE"
+><A
+NAME="JOELIB.ALGORITHMS.MORGAN.LABELING.PSEUDOCODE"
+></A
+><P
+><B
+>Figure 1. Pseudocode for the Morgan labeling algorithm</B
+></P
+><PRE
+CLASS="PROGRAMLISTING"
+>label each atom with its degree;
+labels=count the number of different labels;
+hasNTchanged=5;
+for all time
+ label each atom with sum of label+all neighbor labels;
+ actLabels=count the number of different labels;
+ if actLabels equal labels then
+ decrement hasNTchanged;
+ if hasNTchanged is zero break loop;
+ fi
+rof</PRE
+></DIV
+>
+The sloppy breaking criteria is necessary, because it's possible that the number of different labels can be
+constant for only two iterations. But that's not so interesting, let's continue with the
+renumbering part of the Morgan algorithm. As you can see, it's possible, that 'symmetric' atoms in the
+molecule will have same labels. Is there now a possibility to solve these 'labeling/renumbering' ties ?
+Yes, additional informations, like bond order and element number can be used for resolving renumbering ties
+or the suggested Jochum-Gasteiger canonical renumbering [<A
+HREF="bibliography.html#TC00"
+>tc00</A
+>] informations can be used.
+<DIV
+CLASS="FIGURE"
+><A
+NAME="JOELIB.ALGORITHMS.MORGAN.RENUMBERING.PSEUDOCODE"
+></A
+><P
+><B
+>Figure 2. Pseudocode for the Morgan renumbering algorithm</B
+></P
+><PRE
+CLASS="PROGRAMLISTING"
+>calculate the morgan atom labels;
+start breadth first search from this atom;
+choose node with the highest label and set new atom index to 1;
+repeat
+ build deque i of atoms with same BFS traversing number i;
+ if deque i contains no equal labels
+ renumber atoms in order of decreasing atom labels.
+ fi
+ else
+ try to resolve renumbering tie for the equal labels:
+ 1. prefer atom with higher bond order for renumbering
+ 2. prefer atom with higher element number for renumbering
+ 3. ...
+ if tie solved
+ renumber atoms in order of decreasing atom labels.
+ fi
+ else
+ show renumbering tie warning;
+ esle
+ esle
+ increment i;
+until all atoms are numbered</PRE
+></DIV
+>
+The uniquely renumbered molecule can be used to calculate molecule
+hashcodes and canonical/unique SMILES representations (see ).</P
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/algo/bibliography.html b/java/docs/algo/bibliography.html
new file mode 100644
index 0000000..5e0ebd1
--- /dev/null
+++ b/java/docs/algo/bibliography.html
@@ -0,0 +1,782 @@
+<HTML
+><HEAD
+><TITLE
+>Bibliography</TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="HOME"
+HREF="Morgan.html"><LINK
+REL="PREVIOUS"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="BIBLIOGRAPHY"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="NAVHEADER"
+><TABLE
+SUMMARY="Header navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TH
+COLSPAN="3"
+ALIGN="center"
+></TH
+></TR
+><TR
+><TD
+WIDTH="10%"
+ALIGN="left"
+VALIGN="bottom"
+><A
+HREF="bibliography.html"
+ACCESSKEY="P"
+>Prev</A
+></TD
+><TD
+WIDTH="80%"
+ALIGN="center"
+VALIGN="bottom"
+></TD
+><TD
+WIDTH="10%"
+ALIGN="right"
+VALIGN="bottom"
+>&nbsp;</TD
+></TR
+></TABLE
+><HR
+ALIGN="LEFT"
+WIDTH="100%"></DIV
+><A
+NAME="AEN14"
+></A
+><H1
+><A
+NAME="AEN14"
+></A
+>Bibliography</H1
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="BMV84"
+></A
+><P
+>[bmv84]&nbsp;<SPAN
+CLASS="AUTHOR"
+>P. Broto, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>G. Moreau, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and C. Vandycke</SPAN
+>, <I
+CLASS="CITETITLE"
+>Molecular Structures: Perception, Autocorrelation Descriptor and SAR Studies</I
+>, <I
+CLASS="CITETITLE"
+>Eur. J. Med. Chem.</I
+>, 19, 66-70, 1984.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="BS93"
+></A
+><P
+>[bs93]&nbsp;<SPAN
+CLASS="AUTHOR"
+>B. L. Bush </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and R. P. Sheridan</SPAN
+>, <I
+CLASS="CITETITLE"
+>PATTY: A Programmable Atom Typer and Language for Automatic Classification of Atoms in Molecular Databases</I
+>, <I
+CLASS="CITETITLE"
+>J. Chem. Inf. Comput. Sci.</I
+>, 33, 756-762, 1993.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="CLR98"
+></A
+><P
+>[clr98]&nbsp;<SPAN
+CLASS="AUTHOR"
+>T. Cormen, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>C. Leiserson, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and R. L. Rivest</SPAN
+>, 0-262-03141-8, MIT-Press, <I
+>Introduction to Algorithms</I
+>, 1998.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="DL93"
+></A
+><P
+>[dl93]&nbsp;<SPAN
+CLASS="AUTHOR"
+>A. N. Davies </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and P. Lampen</SPAN
+>, <I
+CLASS="CITETITLE"
+>JCAMP-DX for NMR</I
+>, <I
+CLASS="CITETITLE"
+>Appl. Spec.</I
+>, 47, 1093-1099, 1993.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="DW88"
+></A
+><P
+>[dw88]&nbsp;<SPAN
+CLASS="AUTHOR"
+>R. S. Mc Donald </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and P. A. Wilks</SPAN
+>, <I
+CLASS="CITETITLE"
+>JCAMP-DX: A Standard Form for Exchange of Infrared Spectra in Computer Readable Form</I
+>, <I
+CLASS="CITETITLE"
+>Appl. Spec.</I
+>, 42, 151-162, 1988.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="ERS00"
+></A
+><P
+>[ers00]&nbsp;<SPAN
+CLASS="AUTHOR"
+>P. Ertl, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>B. Rohde, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and P. Selzer</SPAN
+>, <I
+CLASS="CITETITLE"
+>Fast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of drug transport properties</I
+>, <I
+CLASS="CITETITLE"
+>J. Med. Chem.</I
+>, 43, 3714-3717, 2000.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="FIG96"
+></A
+><P
+>[fig96]&nbsp;<SPAN
+CLASS="AUTHOR"
+>J. Figueras</SPAN
+>, <I
+CLASS="CITETITLE"
+>Ring Perception Using Breadth-First Search</I
+>, <I
+CLASS="CITETITLE"
+>J. Chem. Inf. Comput. Sci.</I
+>, 36, 986-991, 1996.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="GAS95"
+></A
+><P
+>[gas95]&nbsp;<SPAN
+CLASS="AUTHOR"
+>J. Gasteiger</SPAN
+>, <I
+>Keyword Reference Manual for Gasteiger Clear Text Files</I
+>.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="GBT02"
+></A
+><P
+>[gbt02]&nbsp;<SPAN
+CLASS="AUTHOR"
+>A. Golbraikh, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>D. Bonchev, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and A. Tropsha</SPAN
+>, <I
+CLASS="CITETITLE"
+>Novel Z/E-Isomerism Descriptors Derived from Molecular Topology and Their Application to QSAR Analysis</I
+>, <I
+CLASS="CITETITLE"
+>J. Chem. Inf. Comput. Sci.</I
+>, 42, 769-787, 2002.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="GHHJS91"
+></A
+><P
+>[ghhjs91]&nbsp;<SPAN
+CLASS="AUTHOR"
+>J. Gasteiger, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>B. M. Hendriks, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>P. Hoever, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>C. Jochum, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and H. Somberg</SPAN
+>, <I
+CLASS="CITETITLE"
+>JCAMP-CS: A Standard Format for Chemical Structure Information in Computer Readable Form</I
+>, <I
+CLASS="CITETITLE"
+>Appl. Spec.</I
+>, 45, 4-11, 1991.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="GM78"
+></A
+><P
+>[gm78]&nbsp;<SPAN
+CLASS="AUTHOR"
+>J. Gasteiger </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and M. Marsili</SPAN
+>, <I
+CLASS="CITETITLE"
+>A New Model for Calculating Atomic Charges in Molecules</I
+>, <I
+CLASS="CITETITLE"
+>Tetrahedron Lett.</I
+>, ?, 3181-3184, 1978.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="GT03"
+></A
+><P
+>[gt03]&nbsp;<SPAN
+CLASS="AUTHOR"
+>A. Golbraikh </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and A. Tropsha</SPAN
+>, <I
+CLASS="CITETITLE"
+>QSAR Modeling Using Chirality Descriptors Derived from Molecular Topology</I
+>, <I
+CLASS="CITETITLE"
+>J. Chem. Inf. Comput. Sci.</I
+>, 42, 144-154, 2003.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="GXSB00"
+></A
+><P
+>[gxsb00]&nbsp;<SPAN
+CLASS="AUTHOR"
+>L. Xue, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>F. L. Stahura, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>J. W. Godden, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and J. Bajorath</SPAN
+>, <I
+CLASS="CITETITLE"
+>Searching for molecules with similar biological activity: analysis by fingerprint profiling</I
+>, <I
+CLASS="CITETITLE"
+>Pac. Symp. Biocomput.</I
+>, 8, 566-575, 2000.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="LHDL94"
+></A
+><P
+>[lhdl94]&nbsp;<SPAN
+CLASS="AUTHOR"
+>P. Lampen, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>H. Hillig, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>A. N. Davies, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and M. Linscheid</SPAN
+>, <I
+CLASS="CITETITLE"
+>JCAMP-DX for Mass Spectrometry</I
+>, <I
+CLASS="CITETITLE"
+>Appl. Spec.</I
+>, 48, 1545-1552, 1994.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="MOR65"
+></A
+><P
+>[mor65]&nbsp;<SPAN
+CLASS="AUTHOR"
+>H. L. Morgan</SPAN
+>, <I
+CLASS="CITETITLE"
+>The Generation of a Unique Machine Description for Chemical Structures - A Technique Developed at Chemical Abstracts Service</I
+>, <I
+CLASS="CITETITLE"
+>J. Chem. Doc.</I
+>, 5, 107-113, 1965.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="MR99"
+></A
+><P
+>[mr99]&nbsp;<SPAN
+CLASS="AUTHOR"
+>P. Murray-Rust </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and H. S. Rzepa</SPAN
+>, <I
+CLASS="CITETITLE"
+>Chemical Markup, XML, and the Worldwide Web. 1. Basic Principles</I
+>, <I
+CLASS="CITETITLE"
+>J. Chem. Inf. Comput. Sci.</I
+>, 39, 928-942, 1999.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="MR01A"
+></A
+><P
+>[mr01a]&nbsp;<SPAN
+CLASS="AUTHOR"
+>P. Murray-Rust </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and H. S. Rzepa</SPAN
+>, <I
+CLASS="CITETITLE"
+>Chemical Markup, XML and the World-Wide Web. 2. Information Objects and the CMLDOM</I
+>, <I
+CLASS="CITETITLE"
+>J. Chem. Inf. Comput. Sci.</I
+>, 41, ?-?, 2001.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="MR01B"
+></A
+><P
+>[mr01b]&nbsp;<SPAN
+CLASS="AUTHOR"
+>G. V. Gkoutos, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>P. Murray-Rust, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>H. S. Rzepa, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and M. Wright</SPAN
+>, <I
+CLASS="CITETITLE"
+>Chemical markup, XML, and the world-wide web. 3. toward a signed semantic chemical web of trust</I
+>, <I
+CLASS="CITETITLE"
+>J. Chem. Inf. Comput. Sci.</I
+>, 41, 1295-1300, 2001.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="SDF"
+></A
+><P
+>[sdf]&nbsp;Inc. MDL Information Systems, <I
+><A
+HREF="http://www.mdli.com/downloads/literature/ctfile.pdf"
+TARGET="_top"
+>Structured Data File format</A
+></I
+>.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="SMARTS"
+></A
+><P
+>[smarts]&nbsp;Inc. Daylight Chemical Information Systems, <I
+><A
+HREF="http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html"
+TARGET="_top"
+>Smiles ARbitrary Target Specification (SMARTS)</A
+></I
+>.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="SMILES"
+></A
+><P
+>[smiles]&nbsp;Inc. Daylight Chemical Information Systems, <I
+><A
+HREF="http://www.daylight.com/dayhtml/smiles/smiles-intro.html"
+TARGET="_top"
+>Simplified Molecular Input Line Entry System (SMILES)</A
+></I
+>.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="TC00"
+></A
+><P
+>[tc00]&nbsp;<SPAN
+CLASS="AUTHOR"
+>R. Todeschini </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and V. Consonni</SPAN
+>, 3-52-29913-0, Wiley-VCH, <I
+>Handbook of Molecular Descriptors</I
+>.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="WC99"
+></A
+><P
+>[wc99]&nbsp;<SPAN
+CLASS="AUTHOR"
+>S. A. Wildman </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and G. M. Crippen</SPAN
+>, <I
+CLASS="CITETITLE"
+>Prediction of Physicochemical Parameters by Atomic Contributions</I
+>, <I
+CLASS="CITETITLE"
+>J. Chem. Inf. Comput. Sci.</I
+>, 39, 868-873, 1999.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="WEI88"
+></A
+><P
+>[wei88]&nbsp;<SPAN
+CLASS="AUTHOR"
+>D. Weinenger</SPAN
+>, <I
+CLASS="CITETITLE"
+>SMILES: a Chemical Language for Information Systems. 1. Introduction to Methodology and Encoding Rules</I
+>, <I
+CLASS="CITETITLE"
+>J. Chem. Inf. Comput. Sci.</I
+>, 28, 31-36, 1988.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="WEI89"
+></A
+><P
+>[wei89]&nbsp;<SPAN
+CLASS="AUTHOR"
+>D. Weinenger</SPAN
+>, <I
+CLASS="CITETITLE"
+>SMILES 2: Algorithm for Generation of Unique SMILES Notation</I
+>, <I
+CLASS="CITETITLE"
+>J. Chem. Inf. Comput. Sci.</I
+>, 29, 97-101, 1989.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="WIL01"
+></A
+><P
+>[wil01]&nbsp;<SPAN
+CLASS="AUTHOR"
+>E. L. Willighagen</SPAN
+>, <I
+><A
+HREF="http://www.ijc.com/abstracts/abstract4n4.html"
+TARGET="_top"
+>Processing CML Conventions in Java</A
+></I
+>, <I
+CLASS="CITETITLE"
+>Internet Journal of Chemistry</I
+>, 4, 4, 2001.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="WY96"
+></A
+><P
+>[wy96]&nbsp;<SPAN
+CLASS="AUTHOR"
+>W. P. Walters </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and S. H. Yalkowsky</SPAN
+>, <I
+CLASS="CITETITLE"
+>ESCHER-A Computer Program for the Determination of External Rotational Symmetry Numbers from Molecular Topology</I
+>, <I
+CLASS="CITETITLE"
+>J. Chem. Inf. Comput. Sci.</I
+>, 36, 1015-1017, 1996.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="ZUP89"
+></A
+><P
+>[zup89]&nbsp;<SPAN
+CLASS="AUTHOR"
+>J. Zupan</SPAN
+>, 0-471-92173-4, Wiley-VCH, <I
+>Algorithms for Chemists</I
+>.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="P"
+>Prev</A
+></TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+><A
+HREF="Morgan.html"
+ACCESSKEY="H"
+>Home</A
+></TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>&nbsp;</TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>Bibliography</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>&nbsp;</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/algo/formulas/o_e+v.gif b/java/docs/algo/formulas/o_e+v.gif
new file mode 100644
index 0000000..c2ac4ac
--- /dev/null
+++ b/java/docs/algo/formulas/o_e+v.gif
Binary files differ
diff --git a/java/docs/feature/APropertyBFS.html b/java/docs/feature/APropertyBFS.html
new file mode 100644
index 0000000..dd46d0b
--- /dev/null
+++ b/java/docs/feature/APropertyBFS.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.APROPERTYBFS"
+></A
+>Atom property breadth first search</H2
+><P
+>Breadth first search calculating the distance only between boolean atom properties (default: Atom in conjugated environment).</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/APropertyDistanceMatrix.html b/java/docs/feature/APropertyDistanceMatrix.html
new file mode 100644
index 0000000..056c875
--- /dev/null
+++ b/java/docs/feature/APropertyDistanceMatrix.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.APROPERTYDISTANCEMATRIX"
+></A
+>Atom property distance matrix</H2
+><P
+>Distance matrix calculating the distance only between boolean atom properties (default: Atom in conjugated environment).</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/AcidicGroups.html b/java/docs/feature/AcidicGroups.html
new file mode 100644
index 0000000..1bb2d9e
--- /dev/null
+++ b/java/docs/feature/AcidicGroups.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.ACIDICGROUPS"
+></A
+>Number of acidic groups</H2
+><P
+>Number of acidic groups.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/AliphaticOHGroups.html b/java/docs/feature/AliphaticOHGroups.html
new file mode 100644
index 0000000..f0d8a24
--- /dev/null
+++ b/java/docs/feature/AliphaticOHGroups.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.ALIPHATICOHGROUPS"
+></A
+>Number of aliphatic hydroxy groups</H2
+><P
+>Number of aliphatic hydroxy groups.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/AromaticBonds.html b/java/docs/feature/AromaticBonds.html
new file mode 100644
index 0000000..faa7fa2
--- /dev/null
+++ b/java/docs/feature/AromaticBonds.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.AROMATICBONDS"
+></A
+>Number of aromatic bonds</H2
+><P
+>Number of aromatic bonds.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/AromaticOHGroups.html b/java/docs/feature/AromaticOHGroups.html
new file mode 100644
index 0000000..781c23b
--- /dev/null
+++ b/java/docs/feature/AromaticOHGroups.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.HBD1"
+></A
+>Number of Hydrogen Bond Donors (HBD)</H2
+><P
+>Number of Hydrogen Bond Donors (HBD). The default SMARTS pattern is: [!#6;!H0].</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/AtomBondOrderSum.html b/java/docs/feature/AtomBondOrderSum.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomBondOrderSum.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomENAllredRochow.html b/java/docs/feature/AtomENAllredRochow.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomENAllredRochow.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomENPauling.html b/java/docs/feature/AtomENPauling.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomENPauling.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomENSanderson.html b/java/docs/feature/AtomENSanderson.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomENSanderson.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomElectronAffinity.html b/java/docs/feature/AtomElectronAffinity.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomElectronAffinity.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomExplicitHydrogenCount.html b/java/docs/feature/AtomExplicitHydrogenCount.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomExplicitHydrogenCount.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomFreeElectronsCount.html b/java/docs/feature/AtomFreeElectronsCount.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomFreeElectronsCount.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomFreeOxygenCount.html b/java/docs/feature/AtomFreeOxygenCount.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomFreeOxygenCount.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomHeavyValence.html b/java/docs/feature/AtomHeavyValence.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomHeavyValence.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomHeteroValence.html b/java/docs/feature/AtomHeteroValence.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomHeteroValence.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomHybridisation.html b/java/docs/feature/AtomHybridisation.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomHybridisation.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomImplicitHydrogenCount.html b/java/docs/feature/AtomImplicitHydrogenCount.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomImplicitHydrogenCount.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomImplicitValence.html b/java/docs/feature/AtomImplicitValence.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomImplicitValence.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomInAcceptor.html b/java/docs/feature/AtomInAcceptor.html
new file mode 100644
index 0000000..5785a4f
--- /dev/null
+++ b/java/docs/feature/AtomInAcceptor.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.ATOMINACCEPTOR"
+></A
+>Atom in acceptor</H2
+><P
+>Is this atom a hydrogen acceptor atom.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/AtomInAromaticSystem.html b/java/docs/feature/AtomInAromaticSystem.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomInAromaticSystem.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomInConjEnvironment.html b/java/docs/feature/AtomInConjEnvironment.html
new file mode 100644
index 0000000..2a3289e
--- /dev/null
+++ b/java/docs/feature/AtomInConjEnvironment.html
@@ -0,0 +1,184 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.ATOMINCONJENVIRONMENT"
+></A
+>Atom in conjugated environment</H2
+><P
+>Atom in conjugated environment.
+<DIV
+CLASS="TABLE"
+><A
+NAME="AEN7"
+></A
+><P
+><B
+>Table 1. SMARTS definitions for assigning the conjugated atom property flag</B
+></P
+><TABLE
+BORDER="1"
+CLASS="CALSTABLE"
+><THEAD
+><TR
+><TH
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>SMARTS</TH
+><TH
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Description</TH
+></TR
+></THEAD
+><TBODY
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>a</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Aromatic atoms</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>*=,#*-,=*=,#*</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>All butadien analogues</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>[N,P,O,S]=,#*-[*;!H0]</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>alpha, beta unsaturated (pi effect)</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>*=,#*-[F,Cl,Br,I]</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>alpha, beta unsaturated (sigma effect)</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>*=,#*-[N,P,O,S;!H0]</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>alpha, beta unsaturated (pi effect, tautomer)</TD
+></TR
+></TBODY
+></TABLE
+></DIV
+></P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/AtomInDonAcc.html b/java/docs/feature/AtomInDonAcc.html
new file mode 100644
index 0000000..61b8188
--- /dev/null
+++ b/java/docs/feature/AtomInDonAcc.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.ATOMINDONACC"
+></A
+>Atom in donor or acceptor</H2
+><P
+>Is this atom a hydrogen donor or acceptor atom.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/AtomInDonor.html b/java/docs/feature/AtomInDonor.html
new file mode 100644
index 0000000..399b2f9
--- /dev/null
+++ b/java/docs/feature/AtomInDonor.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.ATOMINDONOR"
+></A
+>Atom in donor</H2
+><P
+>Is this atom a hydrogen donor atom.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/AtomInRing.html b/java/docs/feature/AtomInRing.html
new file mode 100644
index 0000000..79b7741
--- /dev/null
+++ b/java/docs/feature/AtomInRing.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.ATOMINRING"
+></A
+>Atom in ring</H2
+><P
+>Is this atom a ring atom.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/AtomInRingsCount.html b/java/docs/feature/AtomInRingsCount.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomInRingsCount.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomInTerminalCarbon.html b/java/docs/feature/AtomInTerminalCarbon.html
new file mode 100644
index 0000000..23c8b41
--- /dev/null
+++ b/java/docs/feature/AtomInTerminalCarbon.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.ATOMINTERMINALCARBON"
+></A
+>Atom is terminal carbon</H2
+><P
+>Is this atom a terminal carbon atom.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsAlphaBetaUnsaturated.html b/java/docs/feature/AtomIsAlphaBetaUnsaturated.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomIsAlphaBetaUnsaturated.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsAmideNitrogen.html b/java/docs/feature/AtomIsAmideNitrogen.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomIsAmideNitrogen.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsAntiClockwise.html b/java/docs/feature/AtomIsAntiClockwise.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomIsAntiClockwise.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsAromaticNOxide.html b/java/docs/feature/AtomIsAromaticNOxide.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomIsAromaticNOxide.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsAxial.html b/java/docs/feature/AtomIsAxial.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomIsAxial.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsCarbon.html b/java/docs/feature/AtomIsCarbon.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomIsCarbon.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsCarboxylOxygen.html b/java/docs/feature/AtomIsCarboxylOxygen.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomIsCarboxylOxygen.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsChiral.html b/java/docs/feature/AtomIsChiral.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomIsChiral.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsClockwise.html b/java/docs/feature/AtomIsClockwise.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomIsClockwise.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsElectronegative.html b/java/docs/feature/AtomIsElectronegative.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomIsElectronegative.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsHalogen.html b/java/docs/feature/AtomIsHalogen.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomIsHalogen.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsHeteroatom.html b/java/docs/feature/AtomIsHeteroatom.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomIsHeteroatom.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsHydrogen.html b/java/docs/feature/AtomIsHydrogen.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomIsHydrogen.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsNegative.html b/java/docs/feature/AtomIsNegative.html
new file mode 100644
index 0000000..2754ce0
--- /dev/null
+++ b/java/docs/feature/AtomIsNegative.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.ATOMISNEGATIVE"
+></A
+>Atom is negative</H2
+><P
+>Is this atom a negative charged atom.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsNitroOxygen.html b/java/docs/feature/AtomIsNitroOxygen.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomIsNitroOxygen.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsNitrogen.html b/java/docs/feature/AtomIsNitrogen.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomIsNitrogen.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsNonPolarHydrogen.html b/java/docs/feature/AtomIsNonPolarHydrogen.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomIsNonPolarHydrogen.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsOxygen.html b/java/docs/feature/AtomIsOxygen.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomIsOxygen.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsPhosphateOxygen.html b/java/docs/feature/AtomIsPhosphateOxygen.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomIsPhosphateOxygen.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsPhosphorus.html b/java/docs/feature/AtomIsPhosphorus.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomIsPhosphorus.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsPolarHydrogen.html b/java/docs/feature/AtomIsPolarHydrogen.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomIsPolarHydrogen.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsPositive.html b/java/docs/feature/AtomIsPositive.html
new file mode 100644
index 0000000..4f4204d
--- /dev/null
+++ b/java/docs/feature/AtomIsPositive.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.ATOMISPOSITIVE"
+></A
+>Atom is positive</H2
+><P
+>Is this atom a positive charged atom.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsSulfateOxygen.html b/java/docs/feature/AtomIsSulfateOxygen.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomIsSulfateOxygen.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsSulfur.html b/java/docs/feature/AtomIsSulfur.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomIsSulfur.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsUnsaturated.html b/java/docs/feature/AtomIsUnsaturated.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomIsUnsaturated.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomKekuleBondOrderSum.html b/java/docs/feature/AtomKekuleBondOrderSum.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomKekuleBondOrderSum.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomMass.html b/java/docs/feature/AtomMass.html
new file mode 100644
index 0000000..f1a2cde
--- /dev/null
+++ b/java/docs/feature/AtomMass.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.ATOMMASS"
+></A
+>Atom masss</H2
+><P
+>Atom mass.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/AtomPartialCharge.html b/java/docs/feature/AtomPartialCharge.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomPartialCharge.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomType.html b/java/docs/feature/AtomType.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomType.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomValence.html b/java/docs/feature/AtomValence.html
new file mode 100644
index 0000000..dcd6db8
--- /dev/null
+++ b/java/docs/feature/AtomValence.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.ATOMVALENCE"
+></A
+>Valence</H2
+><P
+>Valence.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/AtomValenceSum.html b/java/docs/feature/AtomValenceSum.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/AtomValenceSum.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomVanDerWaalsVolume.html b/java/docs/feature/AtomVanDerWaalsVolume.html
new file mode 100644
index 0000000..bf76e72
--- /dev/null
+++ b/java/docs/feature/AtomVanDerWaalsVolume.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.ATOMVANDERWAALSVOLUME"
+></A
+>Van der Waals volume</H2
+><P
+>Van der Waals volume.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/Autocorrelation.html b/java/docs/feature/Autocorrelation.html
new file mode 100644
index 0000000..53fe464
--- /dev/null
+++ b/java/docs/feature/Autocorrelation.html
@@ -0,0 +1,168 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.AUTOCORRELATION"
+></A
+>Moreau-Broto topological autocorrelation</H2
+><P
+>Moreau-Broto topological autocorrelation [<A
+HREF="bibliography.html#BMV84"
+>bmv84</A
+>].
+<DIV
+CLASS="EQUATION"
+><A
+NAME="AEN8"
+></A
+><P
+><B
+>Equation 1. Moreau-Broto autocorrelation</B
+></P
+><DIV
+CLASS="MEDIAOBJECT"
+><P
+><IMG
+SRC="formulas/autocorrelation.gif"
+ALIGN="CENTER"></P
+></DIV
+></DIV
+>
+where <SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>d<SUB
+>ij</SUB
+></B
+></SPAN
+> is the topological distance between the atoms
+<SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>i</B
+></SPAN
+> and atom <SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>j</B
+></SPAN
+>, <SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>w<SUB
+>i</SUB
+></B
+></SPAN
+>
+and <SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>w<SUB
+>j</SUB
+></B
+></SPAN
+> are the atom properties of the atoms <SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>i</B
+></SPAN
+> and
+<SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>j</B
+></SPAN
+>.</P
+><P
+>It must be mentioned that the autocorrelation is only a special case of the radial distribution function ().</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/BCUT.html b/java/docs/feature/BCUT.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/BCUT.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/BasicGroups.html b/java/docs/feature/BasicGroups.html
new file mode 100644
index 0000000..581d187
--- /dev/null
+++ b/java/docs/feature/BasicGroups.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.BASICGROUPS"
+></A
+>Number of basic groups</H2
+><P
+>Number of basic groups.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/BondInAromaticSystem.html b/java/docs/feature/BondInAromaticSystem.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/BondInAromaticSystem.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/BondInRing.html b/java/docs/feature/BondInRing.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/BondInRing.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/BondIsAmide.html b/java/docs/feature/BondIsAmide.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/BondIsAmide.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/BondIsCarbonyl.html b/java/docs/feature/BondIsCarbonyl.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/BondIsCarbonyl.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/BondIsClosure.html b/java/docs/feature/BondIsClosure.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/BondIsClosure.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/BondIsEster.html b/java/docs/feature/BondIsEster.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/BondIsEster.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/BondIsPrimaryAmide.html b/java/docs/feature/BondIsPrimaryAmide.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/BondIsPrimaryAmide.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/BondIsRotor.html b/java/docs/feature/BondIsRotor.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/BondIsRotor.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/BondKekuleType.html b/java/docs/feature/BondKekuleType.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/BondKekuleType.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/BurdenEigenvalues.html b/java/docs/feature/BurdenEigenvalues.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/BurdenEigenvalues.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/BurdenModifiedEigenvalues.html b/java/docs/feature/BurdenModifiedEigenvalues.html
new file mode 100644
index 0000000..dc6a83b
--- /dev/null
+++ b/java/docs/feature/BurdenModifiedEigenvalues.html
@@ -0,0 +1,96 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.BURDENMODIFIEDEIGENVALUES"
+></A
+>Burden modified eigenvalues</H2
+><P
+>Burden modified eigenvalues [<A
+HREF="bibliography.html#TC00"
+>tc00</A
+>].</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/CompressedFeatureMatrix.html b/java/docs/feature/CompressedFeatureMatrix.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/CompressedFeatureMatrix.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/ConjElectroTopolState.html b/java/docs/feature/ConjElectroTopolState.html
new file mode 100644
index 0000000..bc0369e
--- /dev/null
+++ b/java/docs/feature/ConjElectroTopolState.html
@@ -0,0 +1,173 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.CONJELECTROTOPOLSTATE"
+></A
+>Conjugated electrotopological state</H2
+><P
+>Conjugated electrotopological state [<A
+HREF="bibliography.html#WZ03"
+>wz03</A
+>,<A
+HREF="bibliography.html#WFZ04B"
+>wfz04b</A
+>].
+<DIV
+CLASS="EQUATION"
+><A
+NAME="AEN9"
+></A
+><P
+><B
+>Equation 1. Conjugated electrotopological state</B
+></P
+><DIV
+CLASS="MEDIAOBJECT"
+><P
+><IMG
+SRC="formulas/cets.gif"
+ALIGN="CENTER"></P
+></DIV
+></DIV
+>
+<SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>I<SUB
+>i</SUB
+></B
+></SPAN
+> is the intrinsic state of atom <SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>i</B
+></SPAN
+> ()
+and <SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>k</B
+></SPAN
+> the distance influence. The distance influence is reduced by the conjugated topological distance
+<DIV
+CLASS="EQUATION"
+><A
+NAME="AEN19"
+></A
+><P
+><B
+>Equation 2. Conjugated topological distance</B
+></P
+><DIV
+CLASS="MEDIAOBJECT"
+><P
+><IMG
+SRC="formulas/ctd.gif"
+ALIGN="CENTER"></P
+></DIV
+></DIV
+>
+where <SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>C<SUB
+>i</SUB
+></B
+></SPAN
+> is the conjugated atom <SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>i</B
+></SPAN
+> ()
+of the molecule.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/ConjugatedTopologicalDistance.html b/java/docs/feature/ConjugatedTopologicalDistance.html
new file mode 100644
index 0000000..6deea0d
--- /dev/null
+++ b/java/docs/feature/ConjugatedTopologicalDistance.html
@@ -0,0 +1,117 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.CONJUGATEDTOPOLOGICALDISTANCE"
+></A
+>Conjugated topological distance</H2
+><P
+>Conjugated topological distance [<A
+HREF="bibliography.html#WZ03"
+>wz03</A
+>,<A
+HREF="bibliography.html#WFZ04B"
+>wfz04b</A
+>].
+<DIV
+CLASS="EQUATION"
+><A
+NAME="AEN9"
+></A
+><P
+><B
+>Equation 1. Conjugated topological distance</B
+></P
+><DIV
+CLASS="MEDIAOBJECT"
+><P
+><IMG
+SRC="formulas/ctd.gif"
+ALIGN="CENTER"></P
+></DIV
+></DIV
+></P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/DistanceDistanceMatrix.html b/java/docs/feature/DistanceDistanceMatrix.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/DistanceDistanceMatrix.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/DistanceMatrix.html b/java/docs/feature/DistanceMatrix.html
new file mode 100644
index 0000000..ecd0533
--- /dev/null
+++ b/java/docs/feature/DistanceMatrix.html
@@ -0,0 +1,111 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTORS."
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.DISTANCEMATRIX"
+></A
+>Topological distance matrix</H2
+><P
+>Calculates the topological distances between all atom pairs.
+Here a simple BFS (see also )
+is used to calculate these distances, which causes a running time of
+<SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>O(A<SUP
+>3</SUP
+>)</B
+></SPAN
+>, where
+<SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>A</B
+></SPAN
+> is the number of atoms.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/Dummy.html b/java/docs/feature/Dummy.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/Dummy.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/ElectrogeometricalState.html b/java/docs/feature/ElectrogeometricalState.html
new file mode 100644
index 0000000..d25b39a
--- /dev/null
+++ b/java/docs/feature/ElectrogeometricalState.html
@@ -0,0 +1,139 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.ELECTROGEOMETRICALSTATE"
+></A
+>Electrogeometrical state</H2
+><P
+>Electrogeometrical state [<A
+HREF="bibliography.html#WZ03"
+>wz03</A
+>,<A
+HREF="bibliography.html#WFZ04B"
+>wfz04b</A
+>].
+<DIV
+CLASS="EQUATION"
+><A
+NAME="AEN9"
+></A
+><P
+><B
+>Equation 1. Electrogeometrical state</B
+></P
+><DIV
+CLASS="MEDIAOBJECT"
+><P
+><IMG
+SRC="formulas/egs.gif"
+ALIGN="CENTER"></P
+></DIV
+></DIV
+>
+<SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>I<SUB
+>i</SUB
+></B
+></SPAN
+> is the intrinsic state of atom <SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>i</B
+></SPAN
+> ()
+and <SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>k</B
+></SPAN
+> the distance influence.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/ElectrotopologicalState.html b/java/docs/feature/ElectrotopologicalState.html
new file mode 100644
index 0000000..6de0bf2
--- /dev/null
+++ b/java/docs/feature/ElectrotopologicalState.html
@@ -0,0 +1,139 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.ELECTROTOPOLOGICALSTATE"
+></A
+>Electrotopological state</H2
+><P
+>Electrotopological state [<A
+HREF="bibliography.html#TC00"
+>tc00</A
+>,<A
+HREF="bibliography.html#WFZ04B"
+>wfz04b</A
+>].
+<DIV
+CLASS="EQUATION"
+><A
+NAME="AEN9"
+></A
+><P
+><B
+>Equation 1. Electrotopological state</B
+></P
+><DIV
+CLASS="MEDIAOBJECT"
+><P
+><IMG
+SRC="formulas/ets.gif"
+ALIGN="CENTER"></P
+></DIV
+></DIV
+>
+<SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>I<SUB
+>i</SUB
+></B
+></SPAN
+> is the intrinsic state of atom <SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>i</B
+></SPAN
+> ()
+and <SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>k</B
+></SPAN
+> the distance influence.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/FractionRotatableBonds.html b/java/docs/feature/FractionRotatableBonds.html
new file mode 100644
index 0000000..a34080c
--- /dev/null
+++ b/java/docs/feature/FractionRotatableBonds.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.FRACTIONROTATABLEBONDS"
+></A
+>Fraction of rotatable bonds</H2
+><P
+>Fraction of rotatable bonds.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/GeomDistanceMatrix.html b/java/docs/feature/GeomDistanceMatrix.html
new file mode 100644
index 0000000..ff8cc05
--- /dev/null
+++ b/java/docs/feature/GeomDistanceMatrix.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTORS."
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.GEOMDISTANCEMATRIX"
+></A
+>Geometrical distance matrix</H2
+><P
+>The geometrical distance matrix calculates the euklidian distance between the 3D coordinates of all atom pairs.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/GeometricalDiameter.html b/java/docs/feature/GeometricalDiameter.html
new file mode 100644
index 0000000..242edc6
--- /dev/null
+++ b/java/docs/feature/GeometricalDiameter.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.GEOMETRICALDIAMETER"
+></A
+>Geometrical diameter</H2
+><P
+>Geometrical diameter.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/GeometricalRadius.html b/java/docs/feature/GeometricalRadius.html
new file mode 100644
index 0000000..76a2596
--- /dev/null
+++ b/java/docs/feature/GeometricalRadius.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.GEOMETRICALRADIUS"
+></A
+>Geometrical radius</H2
+><P
+>Geometrical radius.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/GeometricalShapeCoefficient.html b/java/docs/feature/GeometricalShapeCoefficient.html
new file mode 100644
index 0000000..e1401be
--- /dev/null
+++ b/java/docs/feature/GeometricalShapeCoefficient.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.GEOMETRICALSHAPECOEFFICIENT"
+></A
+>Geometrical shape coefficient</H2
+><P
+>Geometrical shape coefficient.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/GlobalTopologicalChargeIndex.html b/java/docs/feature/GlobalTopologicalChargeIndex.html
new file mode 100644
index 0000000..63e2715
--- /dev/null
+++ b/java/docs/feature/GlobalTopologicalChargeIndex.html
@@ -0,0 +1,96 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.GLOBALTOPOLOGICALCHARGEINDEX"
+></A
+>Global topological charge</H2
+><P
+>Global topological charge [<A
+HREF="bibliography.html#TC00"
+>tc00</A
+>].</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/GraphPotentials.html b/java/docs/feature/GraphPotentials.html
new file mode 100644
index 0000000..a192e96
--- /dev/null
+++ b/java/docs/feature/GraphPotentials.html
@@ -0,0 +1,131 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.GRAPHPOTENTIALS"
+></A
+>Graph potentials</H2
+><P
+>Graph potentials [<A
+HREF="bibliography.html#WY96"
+>wy96</A
+>] or rotational symmetry descriptor. Only the connection table
+is needed to calculate the external rotational symmetry, or topological equivalent atoms.
+<DIV
+CLASS="EQUATION"
+><A
+NAME="AEN8"
+></A
+><P
+><B
+>Equation 1. Graph potentials</B
+></P
+><DIV
+CLASS="MEDIAOBJECT"
+><P
+><IMG
+SRC="formulas/graphpotentials_1.gif"
+ALIGN="CENTER"></P
+></DIV
+></DIV
+>
+where <SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>v<SUB
+>i</SUB
+></B
+></SPAN
+> is the valence (vertex degree) of the atom
+<SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>i</B
+></SPAN
+>.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/GraphShapeCoefficient.html b/java/docs/feature/GraphShapeCoefficient.html
new file mode 100644
index 0000000..735e913
--- /dev/null
+++ b/java/docs/feature/GraphShapeCoefficient.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.GRAPHSHAPECOEFFICIENT"
+></A
+>Graph shape coefficient</H2
+><P
+>Graph shape coefficient.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/HBA1.html b/java/docs/feature/HBA1.html
new file mode 100644
index 0000000..6dcb012
--- /dev/null
+++ b/java/docs/feature/HBA1.html
@@ -0,0 +1,94 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.HBA1"
+></A
+>Number of Hydrogen Bond Acceptors (HBA) 1</H2
+><P
+>Number of Hydrogen Bond Acceptors (HBA) 1.
+The default SMARTS pattern is: [$([!#6;+0]);!$([F,Cl,Br,I]);!$([o,s,nX3]);!$([Nv5,Pv5,Sv4,Sv6])].</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/HBA2.html b/java/docs/feature/HBA2.html
new file mode 100644
index 0000000..4ad7747
--- /dev/null
+++ b/java/docs/feature/HBA2.html
@@ -0,0 +1,94 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.HBA2"
+></A
+>Number of Hydrogen Bond Acceptors (HBA) 2</H2
+><P
+>Number of Hydrogen Bond Acceptors (HBA) 2.
+The default SMARTS pattern is: [$([$([#8,#16]);!$(*=N~O);!$(*~N=O);X1,X2]),$([#7;v3;!$([nH]);!$(*(-a)-a)])].</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/HBD1.html b/java/docs/feature/HBD1.html
new file mode 100644
index 0000000..58922cf
--- /dev/null
+++ b/java/docs/feature/HBD1.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.HBD1"
+></A
+>Number of Hydrogen Bond Donors (HBD) 1</H2
+><P
+>Number of Hydrogen Bond Donors (HBD) 1. The default SMARTS pattern is: [!#6;!H0].</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/HBD2.html b/java/docs/feature/HBD2.html
new file mode 100644
index 0000000..a66a20f
--- /dev/null
+++ b/java/docs/feature/HBD2.html
@@ -0,0 +1,94 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.HBD2"
+></A
+>Number of Hydrogen Bond Donors (HBD) 2</H2
+><P
+>Number of Hydrogen Bond Donors (HBD) 2.
+The default SMARTS pattern is: [$([O;H1,-&#38;!$(*-N=O)]),$([S;H1&amp;X2,-&amp;X1]),$([#7;H;!$(*(S(=O)=O)C(F)(F)F);!$(n1nnnc1);!$(n1nncn1)]),$([#7;-])].</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/HeavyBonds.html b/java/docs/feature/HeavyBonds.html
new file mode 100644
index 0000000..c460fba
--- /dev/null
+++ b/java/docs/feature/HeavyBonds.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.HEAVYBONDS"
+></A
+>Number of heavy bonds</H2
+><P
+>Number of heavy bonds.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/HeteroCycles.html b/java/docs/feature/HeteroCycles.html
new file mode 100644
index 0000000..d1e124f
--- /dev/null
+++ b/java/docs/feature/HeteroCycles.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.HETEROCYCLES"
+></A
+>Number of heterocycles</H2
+><P
+>Number of heterocycles.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/HydrophobicGroups.html b/java/docs/feature/HydrophobicGroups.html
new file mode 100644
index 0000000..020d78c
--- /dev/null
+++ b/java/docs/feature/HydrophobicGroups.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.HYDROPHOBICGROUPS"
+></A
+>Number of hydrophobic groups</H2
+><P
+>Number of hydrophobic groups.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/IntrinsicState.html b/java/docs/feature/IntrinsicState.html
new file mode 100644
index 0000000..82c8c76
--- /dev/null
+++ b/java/docs/feature/IntrinsicState.html
@@ -0,0 +1,145 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.INTRINSICSTATE"
+></A
+>Intrinsic topological state</H2
+><P
+>Intrinsic topological state [<A
+HREF="bibliography.html#TC00"
+>tc00</A
+>,<A
+HREF="bibliography.html#WFZ04B"
+>wfz04b</A
+>].
+<DIV
+CLASS="EQUATION"
+><A
+NAME="AEN9"
+></A
+><P
+><B
+>Equation 1. Intrinsic topological state</B
+></P
+><DIV
+CLASS="MEDIAOBJECT"
+><P
+><IMG
+SRC="formulas/istate.gif"
+ALIGN="CENTER"></P
+></DIV
+></DIV
+>
+where <SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>L<SUB
+>i</SUB
+></B
+></SPAN
+> is the principal quantum number,
+<IMG
+SRC="formulas/delta_i_nu.gif"> is the number of valence electrons, and
+<IMG
+SRC="formulas/delta_i.gif"> is the number of sigma electrons of the
+<SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>i</B
+></SPAN
+>th atom <SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>a<SUB
+>i</SUB
+></B
+></SPAN
+>.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/KierShape1.html b/java/docs/feature/KierShape1.html
new file mode 100644
index 0000000..9690413
--- /dev/null
+++ b/java/docs/feature/KierShape1.html
@@ -0,0 +1,176 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.KIERSHAPE1"
+></A
+>Kier Shape 1</H2
+><P
+>The Kier shape
+<IMG
+SRC="formulas/kier1.gif"> descriptor [<A
+HREF="bibliography.html#TC00"
+>tc00</A
+>]
+can be defined as :</P
+><DIV
+CLASS="EQUATION"
+><A
+NAME="AEN10"
+></A
+><P
+><B
+>Equation 1. Kier shape 1</B
+></P
+><DIV
+CLASS="MEDIAOBJECT"
+><P
+><IMG
+SRC="formulas/kier1_1.gif"
+ALIGN="CENTER"></P
+></DIV
+></DIV
+><P
+><SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>P<SUB
+>max</SUB
+></B
+></SPAN
+> is the maximum number of paths of length 1.
+<SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>P<SUB
+>min</SUB
+></B
+></SPAN
+> is the minimum number of paths of length 1 in a molecule graph of same
+atom number.
+<SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>P1</B
+></SPAN
+> is the number of paths in the given molecule of length 1.
+or:</P
+><DIV
+CLASS="EQUATION"
+><A
+NAME="AEN21"
+></A
+><P
+><B
+>Equation 2. Kier shape 1 (alternative formulation)</B
+></P
+><DIV
+CLASS="MEDIAOBJECT"
+><P
+><IMG
+SRC="formulas/kier1_2.gif"
+ALIGN="CENTER"></P
+></DIV
+></DIV
+><P
+><SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>A</B
+></SPAN
+> means the number of nodes in the molecules graph.
+<SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>P1</B
+></SPAN
+> is the number of paths of length 1 in the given molecule.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/KierShape2.html b/java/docs/feature/KierShape2.html
new file mode 100644
index 0000000..d3117b2
--- /dev/null
+++ b/java/docs/feature/KierShape2.html
@@ -0,0 +1,131 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.KIERSHAPE2"
+></A
+>Kier shape 2</H2
+><P
+>The Kier shape
+<IMG
+SRC="formulas/kier2.gif"> descriptor [<A
+HREF="bibliography.html#TC00"
+>tc00</A
+>]
+can be defined as :</P
+><DIV
+CLASS="EQUATION"
+><A
+NAME="AEN10"
+></A
+><P
+><B
+>Equation 1. Kier shape 2</B
+></P
+><DIV
+CLASS="MEDIAOBJECT"
+><P
+><IMG
+SRC="formulas/kier2_1.gif"
+ALIGN="CENTER"></P
+></DIV
+></DIV
+><P
+><SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>A</B
+></SPAN
+> means the number of nodes in the molecules graph.
+<SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>P2</B
+></SPAN
+> is the number of paths of length 2 in the given molecule.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/KierShape3.html b/java/docs/feature/KierShape3.html
new file mode 100644
index 0000000..7b760b5
--- /dev/null
+++ b/java/docs/feature/KierShape3.html
@@ -0,0 +1,131 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.KIERSHAPE3"
+></A
+>Kier shape 3</H2
+><P
+>The Kier shape
+<IMG
+SRC="formulas/kier3.gif"> descriptor [<A
+HREF="bibliography.html#TC00"
+>tc00</A
+>]
+can be defined as :</P
+><DIV
+CLASS="EQUATION"
+><A
+NAME="AEN10"
+></A
+><P
+><B
+>Equation 1. Kier shape 3</B
+></P
+><DIV
+CLASS="MEDIAOBJECT"
+><P
+><IMG
+SRC="formulas/kier3_1.gif"
+ALIGN="CENTER"></P
+></DIV
+></DIV
+><P
+><SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>A</B
+></SPAN
+> means the number of nodes in the molecules graph.
+<SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>P3</B
+></SPAN
+> is the number of paths of length 3 in the given molecule.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/LogP.html b/java/docs/feature/LogP.html
new file mode 100644
index 0000000..914533b
--- /dev/null
+++ b/java/docs/feature/LogP.html
@@ -0,0 +1,96 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.LOGP"
+></A
+>Octanol/Water partition coefficient (logP)</H2
+><P
+>Octanol/Water partition coefficient (logP) or hydrophobicity [<A
+HREF="bibliography.html#WC99"
+>wc99</A
+>].</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/MolarRefractivity.html b/java/docs/feature/MolarRefractivity.html
new file mode 100644
index 0000000..88757de
--- /dev/null
+++ b/java/docs/feature/MolarRefractivity.html
@@ -0,0 +1,96 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.MOLARREFRACTIVITY"
+></A
+>Molar refractivity (MR)</H2
+><P
+>Molar refractivity (MR) [<A
+HREF="bibliography.html#WC99"
+>wc99</A
+>].</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/MolecularWeight.html b/java/docs/feature/MolecularWeight.html
new file mode 100644
index 0000000..e463e1c
--- /dev/null
+++ b/java/docs/feature/MolecularWeight.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.MOLECULARWEIGHT"
+></A
+>Molecular weight (MW)</H2
+><P
+>Molecular weight (MW).</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/MoleculeHashcode.html b/java/docs/feature/MoleculeHashcode.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/MoleculeHashcode.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/NO2Groups.html b/java/docs/feature/NO2Groups.html
new file mode 100644
index 0000000..6fa91d4
--- /dev/null
+++ b/java/docs/feature/NO2Groups.html
@@ -0,0 +1,97 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.NO2GROUPS"
+></A
+>Number of -NO<SUB
+>2</SUB
+> groups</H2
+><P
+>Number of -NO<SUB
+>2</SUB
+> groups.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/NumberOfAtoms.html b/java/docs/feature/NumberOfAtoms.html
new file mode 100644
index 0000000..f79063f
--- /dev/null
+++ b/java/docs/feature/NumberOfAtoms.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.NUMBEROFATOMS"
+></A
+>Number of atoms</H2
+><P
+>Number of atoms.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/NumberOfB.html b/java/docs/feature/NumberOfB.html
new file mode 100644
index 0000000..fd7e2e4
--- /dev/null
+++ b/java/docs/feature/NumberOfB.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.NUMBEROFB"
+></A
+>Number of boron atoms</H2
+><P
+>Number of boron atoms.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/NumberOfBonds.html b/java/docs/feature/NumberOfBonds.html
new file mode 100644
index 0000000..22dfb7e
--- /dev/null
+++ b/java/docs/feature/NumberOfBonds.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.NUMBEROFBONDS"
+></A
+>Number of bonds</H2
+><P
+>Number of bonds.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/NumberOfBr.html b/java/docs/feature/NumberOfBr.html
new file mode 100644
index 0000000..5807bb9
--- /dev/null
+++ b/java/docs/feature/NumberOfBr.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.NUMBEROFBR"
+></A
+>Number of bromine atoms</H2
+><P
+>Number of bromine atoms.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/NumberOfC.html b/java/docs/feature/NumberOfC.html
new file mode 100644
index 0000000..a1b224e
--- /dev/null
+++ b/java/docs/feature/NumberOfC.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.NUMBEROFC"
+></A
+>Number of carbon atoms</H2
+><P
+>Number of carbon atoms.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/NumberOfCl.html b/java/docs/feature/NumberOfCl.html
new file mode 100644
index 0000000..04892d5
--- /dev/null
+++ b/java/docs/feature/NumberOfCl.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.NUMBEROFCL"
+></A
+>Number of chlorine atoms</H2
+><P
+>Number of chlorine atoms.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/NumberOfF.html b/java/docs/feature/NumberOfF.html
new file mode 100644
index 0000000..c12b2f5
--- /dev/null
+++ b/java/docs/feature/NumberOfF.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.NUMBEROFF"
+></A
+>Number of fluorine atoms</H2
+><P
+>Number of fluorine atoms.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/NumberOfHal.html b/java/docs/feature/NumberOfHal.html
new file mode 100644
index 0000000..11df356
--- /dev/null
+++ b/java/docs/feature/NumberOfHal.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.NUMBEROFHAL"
+></A
+>Number of halogen atoms</H2
+><P
+>Number of halogen atoms.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/NumberOfI.html b/java/docs/feature/NumberOfI.html
new file mode 100644
index 0000000..0580e12
--- /dev/null
+++ b/java/docs/feature/NumberOfI.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.NUMBEROFI"
+></A
+>Number of iodine atoms</H2
+><P
+>Number of iodine atoms.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/NumberOfN.html b/java/docs/feature/NumberOfN.html
new file mode 100644
index 0000000..bd65ada
--- /dev/null
+++ b/java/docs/feature/NumberOfN.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.NUMBEROFN"
+></A
+>Number of nitrogen atoms</H2
+><P
+>Number of nitrogen atoms.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/NumberOfO.html b/java/docs/feature/NumberOfO.html
new file mode 100644
index 0000000..7ecbe0a
--- /dev/null
+++ b/java/docs/feature/NumberOfO.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.NUMBEROFO"
+></A
+>Number of oxygen atoms</H2
+><P
+>Number of oxygen atoms.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/NumberOfP.html b/java/docs/feature/NumberOfP.html
new file mode 100644
index 0000000..3669e91
--- /dev/null
+++ b/java/docs/feature/NumberOfP.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.NUMBEROFP"
+></A
+>Number of phosphorus atoms</H2
+><P
+>Number of phosphorus atoms.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/NumberOfS.html b/java/docs/feature/NumberOfS.html
new file mode 100644
index 0000000..b735ee5
--- /dev/null
+++ b/java/docs/feature/NumberOfS.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.NUMBEROFS"
+></A
+>Number of sulfur atoms</H2
+><P
+>Number of sulfur atoms.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/OSOGroups.html b/java/docs/feature/OSOGroups.html
new file mode 100644
index 0000000..ca49ebf
--- /dev/null
+++ b/java/docs/feature/OSOGroups.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.OSOGROUPS"
+></A
+>Number of -OSO atoms</H2
+><P
+>Number of -OSO atoms.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/PolarSurfaceArea.html b/java/docs/feature/PolarSurfaceArea.html
new file mode 100644
index 0000000..357056f
--- /dev/null
+++ b/java/docs/feature/PolarSurfaceArea.html
@@ -0,0 +1,96 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.POLARSURFACEAREA"
+></A
+>Polar surface area (PSA)</H2
+><P
+>Polar surface area (PSA) [<A
+HREF="bibliography.html#ERS00"
+>ers00</A
+>].</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/RadialDistributionFunction.html b/java/docs/feature/RadialDistributionFunction.html
new file mode 100644
index 0000000..09d9600
--- /dev/null
+++ b/java/docs/feature/RadialDistributionFunction.html
@@ -0,0 +1,230 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.RADIALDISTRIBUTIONFUNCTION"
+></A
+>Radial distribution function (RDF)</H2
+><P
+>The radial distribution function (RDF) [<A
+HREF="bibliography.html#MSG99"
+>msg99</A
+>,<A
+HREF="bibliography.html#WFZ04B"
+>wfz04b</A
+>] can be interpreted as the probability distribution of finding an atom in a spherical volume of
+radius <SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>r</B
+></SPAN
+>.
+<DIV
+CLASS="EQUATION"
+><A
+NAME="AEN14"
+></A
+><P
+><B
+>Equation 1. Radial distribution function</B
+></P
+><DIV
+CLASS="MEDIAOBJECT"
+><P
+><IMG
+SRC="formulas/rdf.gif"
+ALIGN="CENTER"></P
+></DIV
+></DIV
+>
+where <SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>r<SUB
+>ij</SUB
+></B
+></SPAN
+> is the geometrical distance between the atoms
+<SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>i</B
+></SPAN
+> and atom <SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>j</B
+></SPAN
+>, <SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>w<SUB
+>i</SUB
+></B
+></SPAN
+>
+and <SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>w<SUB
+>j</SUB
+></B
+></SPAN
+> are the atom properties of the atoms <SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>i</B
+></SPAN
+> and
+<SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>j</B
+></SPAN
+>. <SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>B</B
+></SPAN
+> is the smoothing parameter
+(fuzziness of the distance <SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>r<SUB
+>ij</SUB
+></B
+></SPAN
+>) for the interatomic distance and
+<SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>f</B
+></SPAN
+> the scaling factor.</P
+><P
+>If <SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>B</B
+></SPAN
+> aims to infinity the RDF code approximates to the autocorrelation function () and the fuzziness
+of the distance <SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>r<SUB
+>ij</SUB
+></B
+></SPAN
+> vanishes. So the RDF code can be treated as a generalized
+autocorrelation function.</P
+><P
+>The RDF user parameters can be defined in the <TT
+CLASS="FILENAME"
+>joelib.properties</TT
+>-file, otherwise the default parameters will be used:</P
+><PRE
+CLASS="PROGRAMLISTING"
+>jcompchem.joelib.desc.types.RadialDistributionFunction.minSphericalVolume = 0.2
+joelib.desc.types.RadialDistributionFunction.maxSphericalVolume = 10.0
+joelib.desc.types.RadialDistributionFunction.sphericalVolumeResolution = 0.2
+joelib.desc.types.RadialDistributionFunction.smoothingFactor = 25</PRE
+><P
+>Optional the RDF can be calculated with protonated molecules, but you must be sure that all available atom
+properties are calculated with hydrogens also. Because this is not the standard, this option should be only used by developers.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/RotatableBonds.html b/java/docs/feature/RotatableBonds.html
new file mode 100644
index 0000000..42ef0d9
--- /dev/null
+++ b/java/docs/feature/RotatableBonds.html
@@ -0,0 +1,94 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.ROTATABLEBONDS"
+></A
+>Number of rotatable bonds</H2
+><P
+>Number of rotatable bonds, where the atoms are heavy atoms with bond order one and a hybridization which is not one (no sp).
+Additionally the bond is a non-ring-bond.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/SMILESMolecule.html b/java/docs/feature/SMILESMolecule.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/SMILESMolecule.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/SO2Groups.html b/java/docs/feature/SO2Groups.html
new file mode 100644
index 0000000..e4cd9a7
--- /dev/null
+++ b/java/docs/feature/SO2Groups.html
@@ -0,0 +1,97 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.SO2GROUPS"
+></A
+>Number of -SO<SUB
+>2</SUB
+> atoms</H2
+><P
+>Number of -SO<SUB
+>2</SUB
+> atoms.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/SOGroups.html b/java/docs/feature/SOGroups.html
new file mode 100644
index 0000000..fd3e45a
--- /dev/null
+++ b/java/docs/feature/SOGroups.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.SOGROUPS"
+></A
+>Number of -SO groups</H2
+><P
+>Number of -SO groups.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/SSKey3DS.html b/java/docs/feature/SSKey3DS.html
new file mode 100644
index 0000000..fad741d
--- /dev/null
+++ b/java/docs/feature/SSKey3DS.html
@@ -0,0 +1,779 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.SSKEY3DS"
+></A
+>Pharmacophore fingerprint</H2
+><P
+>Pharmacophore fingerprint [<A
+HREF="bibliography.html#GXSB00"
+>gxsb00</A
+>].
+<DIV
+CLASS="TABLE"
+><A
+NAME="AEN8"
+></A
+><P
+><B
+>Table 1. Pharmacophore fingerprint definition</B
+></P
+><TABLE
+BORDER="1"
+CLASS="CALSTABLE"
+><THEAD
+><TR
+><TH
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Bit position</TH
+><TH
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Set when</TH
+></TR
+></THEAD
+><TBODY
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>1</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Fraction of rotatable bonds &#62; 0.0</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>2</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Fraction of rotatable bonds &#62; 0.1</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>3</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Fraction of rotatable bonds &#62; 0.2</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>4</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Fraction of rotatable bonds &#62; 0.3</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>5</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Fraction of rotatable bonds &#62; 0.4</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>6</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Aromatic bonds in molecule &#62; 2</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>7</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Aromatic bonds in molecule &#62; 8</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>8</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Aromatic bonds in molecule &#62; 16</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>9</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Aromatic bonds in molecule &#62; 20</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>10</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Aromatic bonds in molecule &#62; 26</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>11</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Aromatic bonds in molecule &#62; 32</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>12</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Aromatic bonds in molecule &#62; 38</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>13</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Molecule contains a heterocycle</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>14</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Molecule contains an aromatic hydroxy group</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>15</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Molecule contains an aliphatic hydroxy group</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>16</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Molecule contains an aliphatic secondary amine</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>17</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Molecule contains an aliphatic tertiary amine</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>18</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Molecule contains a phenyl ring</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>19</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Molecule contains a ring containing nitrogen</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>20</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Molecule contains a -SO<SUB
+>2</SUB
+> group</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>21</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Molecule contains a -SO</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>22</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Molecule contains an ester </TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>23</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Molecule contains an amide </TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>24</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Molecule contains a 5-membered non-aromatic ring</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>25</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Molecule contains a 5-membered aromatic ring</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>26</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Molecule contains a 9-membered or larger (fused) ring</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>27</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Molecule contains a fused ring system</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>28</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Molecule contains a fused aromatic ring system</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>29</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Molecule contains a -OSO group</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>30</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Molecule contains a halogen atom</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>31</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Molecule contains a nitrogen atom attached to alpha-carbon of aromatic system</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>32</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Molecule contains a -NO<SUB
+>2</SUB
+> group</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>33</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Molecule contains rings separated by 2-3 non-ring atoms</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>34</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Molecule contains rings separated by 4-5 non-ring atoms</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>35</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Molecule contains a NN group</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>36</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Molecule contains a carbon atom attached to 3 carbons and a hetero atom</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>37</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Molecule contains an oxygen atom separated by 2 atoms</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>38</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Molecule contains a methyl group attached to hetero atom</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>39</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Molecule contains a double bond</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>40</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Molecule contains a non-H atom linked to 3 heteroatoms</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>41</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Molecule contains a quaternary atom</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>42</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Molecule contains 2 methylenes separated by 2 atoms</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>43</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Molecule contains a non-ring oxygen atom attached to aromatic system</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>44</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Molecule contains 2 non-C,H atoms separated by 2 atoms</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>45</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Number of hydrogen bond acceptors &#62;= 1</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>46</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Number of hydrogen bond acceptors &#62;= 2</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>47</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Number of hydrogen bond acceptors &#62;= 3</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>48</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Number of hydrogen bond acceptors &#62;= 4</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>49</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Number of hydrogen bond acceptors &#62;= 5</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>50</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Number of hydrogen bond acceptors &#62;= 6</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>51</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Number of hydrogen bond acceptors &#62;= 7</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>52</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Number of hydrogen bond acceptors &#62;= 8</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>53</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Number of hydrogen bond acceptors &#62;= 9</TD
+></TR
+><TR
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>54</TD
+><TD
+WIDTH="50%"
+ALIGN="LEFT"
+VALIGN="TOP"
+>Number of hydrogen bond acceptors &#62;= 10</TD
+></TR
+></TBODY
+></TABLE
+></DIV
+></P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/TopologicalAtomPair.html b/java/docs/feature/TopologicalAtomPair.html
new file mode 100644
index 0000000..32731b0
--- /dev/null
+++ b/java/docs/feature/TopologicalAtomPair.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.TOPOLOGICALATOMPAIR"
+></A
+>Valence</H2
+><P
+>Atom pair descriptor using topological distances.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/TopologicalDiameter.html b/java/docs/feature/TopologicalDiameter.html
new file mode 100644
index 0000000..660bbb6
--- /dev/null
+++ b/java/docs/feature/TopologicalDiameter.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.TOPOLOGICALDIAMETER"
+></A
+>Topological diameter</H2
+><P
+>Topological diameter.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/TopologicalRadius.html b/java/docs/feature/TopologicalRadius.html
new file mode 100644
index 0000000..07299fa
--- /dev/null
+++ b/java/docs/feature/TopologicalRadius.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.TOPOLOGICALRADIUS"
+></A
+>Topological radius</H2
+><P
+>Topological radius.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/WeightedBurdenEigenvalues.html b/java/docs/feature/WeightedBurdenEigenvalues.html
new file mode 100644
index 0000000..0d10a46
--- /dev/null
+++ b/java/docs/feature/WeightedBurdenEigenvalues.html
@@ -0,0 +1,3 @@
+<HTML>
+Dummy
+</HTML> \ No newline at end of file
diff --git a/java/docs/feature/WeightedBurdenModifiedEigenvalues.html b/java/docs/feature/WeightedBurdenModifiedEigenvalues.html
new file mode 100644
index 0000000..0e93938
--- /dev/null
+++ b/java/docs/feature/WeightedBurdenModifiedEigenvalues.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.WEIGHTEDBURDENMODIFIEDEIGENVALUES"
+></A
+>Weighted burden modified eigenvalues</H2
+><P
+>Accepts six different weighted atom properties to calculate BCUT values.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/ZagrebIndex1.html b/java/docs/feature/ZagrebIndex1.html
new file mode 100644
index 0000000..130990f
--- /dev/null
+++ b/java/docs/feature/ZagrebIndex1.html
@@ -0,0 +1,123 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.ZAGREBINDEX1"
+></A
+>Zagreb index 1</H2
+><P
+>Zagreb index 1 [<A
+HREF="bibliography.html#TC00"
+>tc00</A
+>].</P
+><DIV
+CLASS="EQUATION"
+><A
+NAME="AEN8"
+></A
+><P
+><B
+>Equation 1. Zagreb index 1</B
+></P
+><DIV
+CLASS="MEDIAOBJECT"
+><P
+><IMG
+SRC="formulas/zagreb1.gif"
+ALIGN="CENTER"></P
+></DIV
+></DIV
+><P
+>where <SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>a</B
+></SPAN
+> are all atoms of the hydrogen depleted graph and
+<IMG
+SRC="formulas/delta.gif"> is the vertex degree.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+> \ No newline at end of file
diff --git a/java/docs/feature/ZagrebIndex2.html b/java/docs/feature/ZagrebIndex2.html
new file mode 100644
index 0000000..735a797
--- /dev/null
+++ b/java/docs/feature/ZagrebIndex2.html
@@ -0,0 +1,143 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.ZAGREBINDEX2"
+></A
+>Zagreb index 2</H2
+><P
+>Zagreb index 2 [<A
+HREF="bibliography.html#TC00"
+>tc00</A
+>].</P
+><DIV
+CLASS="EQUATION"
+><A
+NAME="AEN8"
+></A
+><P
+><B
+>Equation 1. Zagreb index 2</B
+></P
+><DIV
+CLASS="MEDIAOBJECT"
+><P
+><IMG
+SRC="formulas/zagreb2.gif"
+ALIGN="CENTER"></P
+></DIV
+></DIV
+><P
+>where <SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>b</B
+></SPAN
+> are all bonds of the hydrogen depleted graph and
+<IMG
+SRC="formulas/delta.gif"> is the vertex degree.
+<SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>i</B
+></SPAN
+> and <SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>j</B
+></SPAN
+> are the atom indices
+of the atoms connected to the bond <SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>b</B
+></SPAN
+>.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
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+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
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+>&nbsp;</TD
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+>Next</A
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diff --git a/java/docs/feature/bibliography.html b/java/docs/feature/bibliography.html
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+<HTML
+><HEAD
+><TITLE
+>Bibliography</TITLE
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+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="HOME"
+HREF="ZagrebIndex2.html"><LINK
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+>Prev</A
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+ALIGN="right"
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+>&nbsp;</TD
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+></TABLE
+><HR
+ALIGN="LEFT"
+WIDTH="100%"></DIV
+><A
+NAME="AEN20"
+></A
+><H1
+><A
+NAME="AEN20"
+></A
+>Bibliography</H1
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="BMV84"
+></A
+><P
+>[bmv84]&nbsp;<SPAN
+CLASS="AUTHOR"
+>P. Broto, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>G. Moreau, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and C. Vandycke</SPAN
+>, <I
+CLASS="CITETITLE"
+>Molecular Structures: Perception, Autocorrelation Descriptor and SAR Studies</I
+>, <I
+CLASS="CITETITLE"
+>Eur. J. Med. Chem.</I
+>, 19, 66-70, 1984.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="BS93"
+></A
+><P
+>[bs93]&nbsp;<SPAN
+CLASS="AUTHOR"
+>B. L. Bush </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and R. P. Sheridan</SPAN
+>, <I
+CLASS="CITETITLE"
+>PATTY: A Programmable Atom Typer and Language for Automatic Classification of Atoms in Molecular Databases</I
+>, <I
+CLASS="CITETITLE"
+>J. Chem. Inf. Comput. Sci.</I
+>, 33, 756-762, 1993.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="CLR98"
+></A
+><P
+>[clr98]&nbsp;<SPAN
+CLASS="AUTHOR"
+>T. Cormen, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>C. Leiserson, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and R. L. Rivest</SPAN
+>, 0-262-03141-8, MIT-Press, <I
+>Introduction to Algorithms</I
+>, 1998.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="DL93"
+></A
+><P
+>[dl93]&nbsp;<SPAN
+CLASS="AUTHOR"
+>A. N. Davies </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and P. Lampen</SPAN
+>, <I
+CLASS="CITETITLE"
+>JCAMP-DX for NMR</I
+>, <I
+CLASS="CITETITLE"
+>Appl. Spec.</I
+>, 47, 1093-1099, 1993.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="DW88"
+></A
+><P
+>[dw88]&nbsp;<SPAN
+CLASS="AUTHOR"
+>R. S. Mc Donald </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and P. A. Wilks</SPAN
+>, <I
+CLASS="CITETITLE"
+>JCAMP-DX: A Standard Form for Exchange of Infrared Spectra in Computer Readable Form</I
+>, <I
+CLASS="CITETITLE"
+>Appl. Spec.</I
+>, 42, 151-162, 1988.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="ERS00"
+></A
+><P
+>[ers00]&nbsp;<SPAN
+CLASS="AUTHOR"
+>P. Ertl, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>B. Rohde, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and P. Selzer</SPAN
+>, <I
+CLASS="CITETITLE"
+>Fast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of drug transport properties</I
+>, <I
+CLASS="CITETITLE"
+>J. Med. Chem.</I
+>, 43, 3714-3717, 2000.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="FIG96"
+></A
+><P
+>[fig96]&nbsp;<SPAN
+CLASS="AUTHOR"
+>J. Figueras</SPAN
+>, <I
+CLASS="CITETITLE"
+>Ring Perception Using Breadth-First Search</I
+>, <I
+CLASS="CITETITLE"
+>J. Chem. Inf. Comput. Sci.</I
+>, 36, 986-991, 1996.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="GAS95"
+></A
+><P
+>[gas95]&nbsp;<SPAN
+CLASS="AUTHOR"
+>J. Gasteiger</SPAN
+>, <I
+>Keyword Reference Manual for Gasteiger Clear Text Files</I
+>.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="GBT02"
+></A
+><P
+>[gbt02]&nbsp;<SPAN
+CLASS="AUTHOR"
+>A. Golbraikh, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>D. Bonchev, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and A. Tropsha</SPAN
+>, <I
+CLASS="CITETITLE"
+>Novel Z/E-Isomerism Descriptors Derived from Molecular Topology and Their Application to QSAR Analysis</I
+>, <I
+CLASS="CITETITLE"
+>J. Chem. Inf. Comput. Sci.</I
+>, 42, 769-787, 2002.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="GHHJS91"
+></A
+><P
+>[ghhjs91]&nbsp;<SPAN
+CLASS="AUTHOR"
+>J. Gasteiger, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>B. M. Hendriks, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>P. Hoever, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>C. Jochum, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and H. Somberg</SPAN
+>, <I
+CLASS="CITETITLE"
+>JCAMP-CS: A Standard Format for Chemical Structure Information in Computer Readable Form</I
+>, <I
+CLASS="CITETITLE"
+>Appl. Spec.</I
+>, 45, 4-11, 1991.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="GM78"
+></A
+><P
+>[gm78]&nbsp;<SPAN
+CLASS="AUTHOR"
+>J. Gasteiger </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and M. Marsili</SPAN
+>, <I
+CLASS="CITETITLE"
+>A New Model for Calculating Atomic Charges in Molecules</I
+>, <I
+CLASS="CITETITLE"
+>Tetrahedron Lett.</I
+>, ?, 3181-3184, 1978.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="GT03"
+></A
+><P
+>[gt03]&nbsp;<SPAN
+CLASS="AUTHOR"
+>A. Golbraikh </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and A. Tropsha</SPAN
+>, <I
+CLASS="CITETITLE"
+>QSAR Modeling Using Chirality Descriptors Derived from Molecular Topology</I
+>, <I
+CLASS="CITETITLE"
+>J. Chem. Inf. Comput. Sci.</I
+>, 42, 144-154, 2003.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="GXSB00"
+></A
+><P
+>[gxsb00]&nbsp;<SPAN
+CLASS="AUTHOR"
+>L. Xue, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>F. L. Stahura, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>J. W. Godden, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and J. Bajorath</SPAN
+>, <I
+CLASS="CITETITLE"
+>Searching for molecules with similar biological activity: analysis by fingerprint profiling</I
+>, <I
+CLASS="CITETITLE"
+>Pac. Symp. Biocomput.</I
+>, 8, 566-575, 2000.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="LHDL94"
+></A
+><P
+>[lhdl94]&nbsp;<SPAN
+CLASS="AUTHOR"
+>P. Lampen, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>H. Hillig, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>A. N. Davies, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and M. Linscheid</SPAN
+>, <I
+CLASS="CITETITLE"
+>JCAMP-DX for Mass Spectrometry</I
+>, <I
+CLASS="CITETITLE"
+>Appl. Spec.</I
+>, 48, 1545-1552, 1994.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="ML91"
+></A
+><P
+>[ml91]&nbsp;<SPAN
+CLASS="AUTHOR"
+>E. C. Meng </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and R. A. Lewis</SPAN
+>, <I
+CLASS="CITETITLE"
+>{D}etermination of {M}olecular {T}opology and {A}tomic {H}ybridisation {S}tates from {H}eavy {A}tom {C}oordinates</I
+>, <I
+CLASS="CITETITLE"
+>J. Comp. Chem.</I
+>, 12, 891-898, 1991.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="MOR65"
+></A
+><P
+>[mor65]&nbsp;<SPAN
+CLASS="AUTHOR"
+>H. L. Morgan</SPAN
+>, <I
+CLASS="CITETITLE"
+>The Generation of a Unique Machine Description for Chemical Structures - A Technique Developed at Chemical Abstracts Service</I
+>, <I
+CLASS="CITETITLE"
+>J. Chem. Doc.</I
+>, 5, 107-113, 1965.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="MR99"
+></A
+><P
+>[mr99]&nbsp;<SPAN
+CLASS="AUTHOR"
+>P. Murray-Rust </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and H. S. Rzepa</SPAN
+>, <I
+CLASS="CITETITLE"
+>Chemical Markup, XML, and the Worldwide Web. 1. Basic Principles</I
+>, <I
+CLASS="CITETITLE"
+>J. Chem. Inf. Comput. Sci.</I
+>, 39, 928-942, 1999.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="MR01A"
+></A
+><P
+>[mr01a]&nbsp;<SPAN
+CLASS="AUTHOR"
+>P. Murray-Rust </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and H. S. Rzepa</SPAN
+>, <I
+CLASS="CITETITLE"
+>Chemical Markup, XML and the World-Wide Web. 2. Information Objects and the CMLDOM</I
+>, <I
+CLASS="CITETITLE"
+>J. Chem. Inf. Comput. Sci.</I
+>, 41, ?-?, 2001.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="MR01B"
+></A
+><P
+>[mr01b]&nbsp;<SPAN
+CLASS="AUTHOR"
+>G. V. Gkoutos, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>P. Murray-Rust, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>H. S. Rzepa, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and M. Wright</SPAN
+>, <I
+CLASS="CITETITLE"
+>Chemical markup, XML, and the world-wide web. 3. toward a signed semantic chemical web of trust</I
+>, <I
+CLASS="CITETITLE"
+>J. Chem. Inf. Comput. Sci.</I
+>, 41, 1295-1300, 2001.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="MSG99"
+></A
+><P
+>[msg99]&nbsp;<SPAN
+CLASS="AUTHOR"
+>M. C. Hemmer, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>V. Steinhauer, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and J. Gasteiger</SPAN
+>, <I
+CLASS="CITETITLE"
+>Deriving the 3D Structure of Organic Molecules from their Infrared Spectra</I
+>, <I
+CLASS="CITETITLE"
+>Vibrat. Spect.</I
+>, 19, 63-67, 1999.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="SDF"
+></A
+><P
+>[sdf]&nbsp;Inc. MDL Information Systems, <I
+><A
+HREF="http://www.mdli.com/downloads/literature/ctfile.pdf"
+TARGET="_top"
+>Structured Data File format</A
+></I
+>.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="SMARTS"
+></A
+><P
+>[smarts]&nbsp;Inc. Daylight Chemical Information Systems, <I
+><A
+HREF="http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html"
+TARGET="_top"
+>Smiles ARbitrary Target Specification (SMARTS)</A
+></I
+>.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="SMILES"
+></A
+><P
+>[smiles]&nbsp;Inc. Daylight Chemical Information Systems, <I
+><A
+HREF="http://www.daylight.com/dayhtml/smiles/smiles-intro.html"
+TARGET="_top"
+>Simplified Molecular Input Line Entry System (SMILES)</A
+></I
+>.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="TC00"
+></A
+><P
+>[tc00]&nbsp;<SPAN
+CLASS="AUTHOR"
+>R. Todeschini </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and V. Consonni</SPAN
+>, 3-52-29913-0, Wiley-VCH, <I
+>Handbook of Molecular Descriptors</I
+>.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="WC99"
+></A
+><P
+>[wc99]&nbsp;<SPAN
+CLASS="AUTHOR"
+>S. A. Wildman </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and G. M. Crippen</SPAN
+>, <I
+CLASS="CITETITLE"
+>Prediction of Physicochemical Parameters by Atomic Contributions</I
+>, <I
+CLASS="CITETITLE"
+>J. Chem. Inf. Comput. Sci.</I
+>, 39, 868-873, 1999.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="WEI88"
+></A
+><P
+>[wei88]&nbsp;<SPAN
+CLASS="AUTHOR"
+>D. Weinenger</SPAN
+>, <I
+CLASS="CITETITLE"
+>SMILES: a Chemical Language for Information Systems. 1. Introduction to Methodology and Encoding Rules</I
+>, <I
+CLASS="CITETITLE"
+>J. Chem. Inf. Comput. Sci.</I
+>, 28, 31-36, 1988.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="WEI89"
+></A
+><P
+>[wei89]&nbsp;<SPAN
+CLASS="AUTHOR"
+>D. Weinenger</SPAN
+>, <I
+CLASS="CITETITLE"
+>SMILES 2: Algorithm for Generation of Unique SMILES Notation</I
+>, <I
+CLASS="CITETITLE"
+>J. Chem. Inf. Comput. Sci.</I
+>, 29, 97-101, 1989.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="WIL01"
+></A
+><P
+>[wil01]&nbsp;<SPAN
+CLASS="AUTHOR"
+>E. L. Willighagen</SPAN
+>, <I
+><A
+HREF="http://www.ijc.com/abstracts/abstract4n4.html"
+TARGET="_top"
+>Processing CML Conventions in Java</A
+></I
+>, <I
+CLASS="CITETITLE"
+>Internet Journal of Chemistry</I
+>, 4, 4, 2001.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="WY96"
+></A
+><P
+>[wy96]&nbsp;<SPAN
+CLASS="AUTHOR"
+>W. P. Walters </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and S. H. Yalkowsky</SPAN
+>, <I
+CLASS="CITETITLE"
+>ESCHER-A Computer Program for the Determination of External Rotational Symmetry Numbers from Molecular Topology</I
+>, <I
+CLASS="CITETITLE"
+>J. Chem. Inf. Comput. Sci.</I
+>, 36, 1015-1017, 1996.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="WZ03"
+></A
+><P
+>[wz03]&nbsp;<SPAN
+CLASS="AUTHOR"
+>J. K. Wegner </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and A. Zell</SPAN
+>, <I
+CLASS="CITETITLE"
+>Prediction of Aqueous Solubility and Partition Coefficient Optimized by a Genetic Algorithm Based Descriptor Selection Method</I
+>, <I
+CLASS="CITETITLE"
+>J. Chem. Inf. Comput. Sci.</I
+>, 43, 1077-1084, 2003.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="WFZ04A"
+></A
+><P
+>[wfz04a]&nbsp;<SPAN
+CLASS="AUTHOR"
+>J. K. Wegner, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>H. Froehlich, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and A. Zell</SPAN
+>, <I
+CLASS="CITETITLE"
+>Feature Selection for Descriptor based Classification Models. 1. Theory and GA-SEC Algorithm</I
+>, <I
+CLASS="CITETITLE"
+>J. Chem. Inf. Comput. Sci.</I
+>, 44, ASAP alert, 2004.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="WFZ04B"
+></A
+><P
+>[wfz04b]&nbsp;<SPAN
+CLASS="AUTHOR"
+>J. K. Wegner, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>H. Froehlich, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and A. Zell</SPAN
+>, <I
+CLASS="CITETITLE"
+>Feature Selection for Descriptor based Classification Models. 2. Human Intestinal Absorption</I
+>, <I
+CLASS="CITETITLE"
+>J. Chem. Inf. Comput. Sci.</I
+>, 44, ASAP alert, 2004.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="ZUP89"
+></A
+><P
+>[zup89]&nbsp;<SPAN
+CLASS="AUTHOR"
+>J. Zupan</SPAN
+>, 0-471-92173-4, Wiley-VCH, <I
+>Algorithms for Chemists</I
+>.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
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+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="P"
+>Prev</A
+></TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+><A
+HREF="ZagrebIndex2.html"
+ACCESSKEY="H"
+>Home</A
+></TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>&nbsp;</TD
+></TR
+><TR
+><TD
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+ALIGN="left"
+VALIGN="top"
+>Bibliography</TD
+><TD
+WIDTH="34%"
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+VALIGN="top"
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+> \ No newline at end of file
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+<b><i>Article</i><a name=\"bk02\"> (bk02)</a></b>, M. B&ouml;hm & G. Klebe, Development of New Hydrogen--Bond Descriptors and Their Application to Comparative Molecular Field Analyses , <em>J. Med. Chem., </em> <b>2002</b> <i>, 45</i> , 1585-1597.
+<b><i>Article</i><a name=\"bmv84\"> (bmv84)</a></b>, P. Broto; G. Moreau & C. Vandycke, Molecular Structures: Perception, Autocorrelation Descriptor and SAR Studies , <em>Eur. J. Med. Chem., </em> <b>1984</b> <i>, 19</i> , 66-70.
+<b><i>Book</i><a name=\"br90\"> (br90)</a></b>, D. Bonchev & D. H. Rouvray, D. Bonchev & D. H. Rouvray <i>(ed.)</i>, Chemical Graph Theory: Introduction and Fundamentals , <em>Gordon and Breach Science Publishers, </em> <b>1990</b> <i>, 1</i>.
+<b><i>Article</i><a name=\"bs93\"> (bs93)</a></b>, B.L.Bush & R.P.Sheridan, PATTY: A Programmable Atom Typer and Language for Automatic Classification of Atoms in Molecular Databases. , <em>J. Chem. Inf. Comput. Sci., </em> <b>1993</b> <i>, 33</i> , 756-762.
+<b><i>Inbook</i><a name=\"clr98bfs\"> (clr98bfs)</a></b>, T. H. Cormen; C. E. Leiserson & R. L. Rivest, Introduction to Algorithms , 23.2, <em>MIT--Press, </em> <b>1998</b> , 469-477.
+<b><i>Inbook</i><a name=\"clr98complexity\"> (clr98complexity)</a></b>, T. H. Cormen; C. E. Leiserson & R. L. Rivest, Introduction to Algorithms , 2, <em>MIT--Press, </em> <b>1998</b> , 23-41.
+<b><i>Inbook</i><a name=\"clr98dfs\"> (clr98dfs)</a></b>, T. H. Cormen; C. E. Leiserson & R. L. Rivest, Introduction to Algorithms , 23.3, <em>MIT--Press, </em> <b>1998</b> , 477-483.
+<b><i>Incollection</i><a name=\"dhl90\"> (dhl90)</a></b>, A.N. Davies; H. Hilling & M. Linscheid, J. Gasteiger <i>(ed.)</i>, JCAMP--DX, a standard ? , <em>Springer--Verlag, </em> <b>1990</b> , 147-156.
+<b><i>Article</i><a name=\"dl93\"> (dl93)</a></b>, A. N. Davies & P. Lampen, JCAMP--DX for NMR , <em>Appl. Spec., </em> <b>1993</b> <i>, 47</i> , 1093-1099.
+<b><i>Article</i><a name=\"dw88\"> (dw88)</a></b>, R. S. Mc Donald & Paul A. Wilks, JCAMP--DX: A Standard Form for Exchange of Infrared Spectra in Computer Readable Form , <em>Appl. Spec., </em> <b>1988</b> <i>, 42</i> , 151-162 . <b><i>Article</i><a name=\"ers00\"> (ers00)</a></b>, P. Ertl; B. Rohde & P. Selzer, Fast Calculation of Molecular Polar Surface Area as a Sum of Fragment-Based Contributions and Its Application to the Prediction of Drug Transport Properties , <em>J. Med. Chem. 2000, 43, 3714-3717, </em> <b>2000</b> <i>, 43</i> , 3714-3717.
+<b><i>Article</i><a name=\"fig96\"> (fig96)</a></b>, J. Figueras, Ring Perception Using Breadth--First Search , <em>J. Chem. Inf. Comput. Sci., </em> <b>1996</b> <i>, 36</i> , 986-991.
+<b><i>Article</i><a name=\"ghhjs91\"> (ghhjs91)</a></b>, J. Gasteiger; B. M. P. Hendriks; P. Hoever; C. Jochum & H. Somberg, JCAMP--CS: A Standard Format for Chemical Structure Information in Computer Readable Form , <em>Appl. Spec., </em> <b>1991</b> <i>, 45</i> , 4-11.
+<b><i>Article</i><a name=\"gm78\"> (gm78)</a></b>, J. Gasteiger & M. Marsili, A New Model for Calculating Atomic Charges in Molecules , <em>Tetrahedron Lett., </em> <b>1978</b> , 3181-3184.
+<b><i>Article</i><a name=\"gmrw01\"> (gmrw01)</a></b>, G. V. Gkoutos; P. Murray--Rust; S. Rzepa & M. Wright, Chemical Markup, XML, and the World--Wide Web. 3. Toward a Signed Semantic Chemical Web of Trust , <em>J. Chem. Inf. Comput. Sci., </em> <b>2001</b> <i>, 41</i> , 1295-1300 . <a href=\"http://dx.doi.org/10.1021/ci000406v\">DOI: 10.1021/ci000406v</a>.
+<b><i>Article</i><a name=\"gwb98\"> (gwb98)</a></b>, J. Gillet; P. Willett & J. Bradshaw, Identification of Biological Activity Profiles Using Substructural Analysis and Genetic Algorithms , <em>J. Chem. Inf. Comput. Sci., </em> <b>1998</b> <i>, 38</i> , 165-179.
+<b><i>Article</i><a name=\"gxsb00\"> (gxsb00)</a></b>, L. Xue; F. L. Stahura; J. W. Godden & J. Bajorath, Searching for molecules with similar biological activity: analysis by fingerprint profiling , <em>Pac. Symp. Biocomput., </em> <b>2000</b> <i>, 8</i> , 566-575.
+<b><i>Misc</i><a name=\"jwd00\"> (jwd00)</a></b>, C. A. James; D. Weininger & J. Delany, Daylight Theory Manual.
+<b><i>Article</i><a name=\"lhdl94\"> (lhdl94)</a></b>, P. Lampen; H. Hillig; A. N. Davies & Michael Linscheid, JCAMP--DX for Mass Spectrometry , <em>Appl. Spec., </em> <b>1994</b> <i>, 48</i> , 1545-1552.
+<b><i>Article</i><a name=\"lldf01\"> (lldf01)</a></b>, C. A. Lipinski; F. Lombardo; B. W. Dominy & P. J. Feeney, Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings , <em>Adv. Drug Delivery Reviews, </em> <b>2001</b> <i>, 46</i> , 3-26.
+<b><i>Misc</i><a name=\"mdlMolFormat\"> (mdlMolFormat)</a></b>, MDL Information Systems, Inc., MDL CTfile Formats.
+<b><i>Article</i><a name=\"ml91\"> (ml91)</a></b>, E. C. Meng & R. A. Lewis, Determination of Molecular Topology and Atomic Hybridisation States from Heavy Atom Coordinates , <em>J. Comp. Chem., </em> <b>1991</b> <i>, 12</i> , 891-898.
+<b><i>Article</i><a name=\"mor65\"> (mor65)</a></b>, H. L. Morgan, The Generation of a Unique Machine Description for Chemical Structures -- A Technique Developed at Chemical Abstracts Service. , <em>J. Chem. Doc., </em> <b>1965</b> <i>, 5</i> , 107-113.
+<b><i>Article</i><a name=\"mr01\"> (mr01)</a></b>, P. Murray--Rust & H. S. Rzepa, Chemical Markup, XML and the World--Wide Web. 2. Information Objects and the CMLDOM , <em>J. Chem. Inf. Comput. Sci., </em> <b>2001</b> <i>, 41</i> , 1113-1123 . <a href=\"http://dx.doi.org/10.1021/ci000404a\">DOI: 10.1021/ci000404a</a>.
+<b><i>Article</i><a name=\"mr03\"> (mr03)</a></b>, P. Murray--Rust & H. S. Rzepa, Chemical Markup, XML and the World--Wide Web. 4. CML Schema , <em>J. Chem. Inf. Comput. Sci., </em> <b>2003</b> <i>, 43</i> , 757-772 . <a href=\"http://dx.doi.org/10.1021/ci0256541\">DOI: 10.1021/ci0256541</a>.
+<b><i>Article</i><a name=\"mrww04\"> (mrww04)</a></b>, P. Murray--Rust; H. S. Rzepa; J. Williamson & E. L. Willighagen, Chemical Markup, XML and the World--Wide Web. 5. Applications of Chemical Metadata in RSS Aggregators , <em>J. Chem. Inf. Comput. Sci., </em> <b>2004</b> <i>, 44</i> , 462-469 . <a href=\"http://dx.doi.org/10.1021/ci034244p\">DOI: 10.1021/ci034244p</a>.
+<b><i>Article</i><a name=\"odtl01\"> (odtl01)</a></b>, T. I. Oprea; A. M. Davis; S. J. Teague & P. D. Leeson, Is There a Difference between Leads and Drugs? A Historical Perspective , <em>J. Chem. Inf. Comput. Sci., </em> <b>2001</b> <i>, 41</i> , 1308-1315 . <a href=\"http://dx.doi.org/10.1021/ci010366a\">DOI: 10.1021/ci010366a</a>.
+<b><i>Misc</i><a name=\"pdbFormat\"> (pdbFormat)</a></b>, Protein Data Bank (PDB) File Format , <b>2002</b>.
+<b><i>Misc</i><a name=\"povray\"> (povray)</a></b>, POV--Team, Persistence of Vision Raytracer (POVRay).
+<b><i>Article</i><a name=\"rr99b\"> (rr99b)</a></b>, P. Murray--Rust & H. S. Rzepa, Chemical Markup, XML, and the Worldwide Web. 1. Basic Principles , <em>J. Chem. Inf. Comput. Sci., </em> <b>1999</b> <i>, 39</i> , 928-942 . <a href=\"http://dx.doi.org/10.1021/ci990052b\">DOI: 10.1021/ci990052b</a>.
+<b><i>Manual</i><a name=\"smarts\"> (smarts)</a></b>, Daylight Chemical Information Systems, Inc., Smiles ARbitrary Target Specification (SMARTS).
+<b><i>Manual</i><a name=\"smilesFormat\"> (smilesFormat)</a></b>, Daylight Chemical Information Systems, Inc., Simplified Molecular Input Line Entry System (SMILES).
+<b><i>Manual</i><a name=\"sybylmol2\"> (sybylmol2)</a></b>, Tripos, Tripos Mol2 File Format.
+<b><i>Inbook</i><a name=\"tc00kiershape\"> (tc00kiershape)</a></b>, R. Todeschini & V. Consonni, Handbook of Molecular Descriptors , K, <em>Wiley--VCH, </em> <b>2000</b> , 248-250.
+<b><i>Inbook</i><a name=\"tc00zagrebgroup\"> (tc00zagrebgroup)</a></b>, R. Todeschini & V. Consonni, Handbook of Molecular Descriptors , Z, <em>Wiley--VCH, </em> <b>2000</b> , 509.
+<b><i>Book</i><a name=\"tri92\"> (tri92)</a></b>, N. Trinajsti, Chemical Graph Theory , <em>CRC Press, Florida, U.S.A., </em> <b>1992</b>.
+<b><i>Article</i><a name=\"wc99\"> (wc99)</a></b>, S. A. Wildman & G. M. Crippen, Prediction of Physicochemical Parameters by Atomic Contributions , <em>J. Chem. Inf. Comput. Sci., </em> <b>1999</b> <i>, 39</i> , 868-873.
+<b><i>Article</i><a name=\"wei88\"> (wei88)</a></b>, D. Weininger, SMILES, a Chemical Language for Information Systems. 1. Introduction to Methodology and Encoding Rules. , <em>J. Chem. Inf. Comput. Sci., </em> <b>1988</b> <i>, 28</i> , 31-36.
+<b><i>Article</i><a name=\"wfz04a\"> (wfz04a)</a></b>, Wegner, J. K.; Fr&ouml;hlich, H. & Zell, A., Feature selection for Descriptor based Classification Models. 1. Theory and GA--SEC Algorithm , <em>J. Chem. Inf. Comput. Sci., </em> <b>2004</b> <i>, 44</i> . <a href=\"http://dx.doi.org/10.1021/ci0342324\">DOI: 10.1021/ci0342324</a>.
+<b><i>Article</i><a name=\"wfz04b\"> (wfz04b)</a></b>, J. K. Wegner; H. Fr&ouml;hlich & A. Zell, Feature selection for Descriptor based Classification Models. 2. Human Intestinal Absorption (HIA) , <em>J. Chem. Inf. Comput. Sci., </em> <b>2004</b> <i>, 44</i> . <a href=\"http://dx.doi.org/10.1021/ci034233w\">DOI: 10.1021/ci034233w</a>.
+<b><i>Article</i><a name=\"wil01\"> (wil01)</a></b>, E. L. Willighagen, Processing CML Conventions in Java , <em>Internet Journal of Chemistry, </em> <b>2001</b> <i>, 4</i> , 4.
+<b><i>Article</i><a name=\"www89\"> (www89)</a></b>, D. Weininger; A. Weininger & J. L. Weininger, Algorithm for generation of unique SMILES notation , <em>J. Chem. Inf. Comput. Sci., </em> <b>1989</b> <i>, 29</i> , 97-101.
+<b><i>Article</i><a name=\"wy96\"> (wy96)</a></b>, W. P. Walters & S. H. Yalkowsky, ESCHER--A Computer Program for the Determination of External Rotational Symmetry Numbers from Molecular Topology , <em>J. Chem. Inf. Comput. Sci., </em> <b>1996</b> <i>, 36</i> , 1015-1017.
+<b><i>Article</i><a name=\"wz03\"> (wz03)</a></b>, Wegner, J. K. & Zell, A., Prediction of Aqueous Solubility and Partition Coefficient Optimized by a Genetic Algorithm Based Descriptor Selection Method , <em>J. Chem. Inf. Comput. Sci., </em> <b>2003</b> <i>, 43</i> , 1077-1084 . <a href=\"http://dx.doi.org/10.1021/ci034006u\">DOI: 10.1021/ci034006u</a>.
+<b><i>Inbook</i><a name=\"zup89c\"> (zup89c)</a></b>, J. Zupan, Algorithms for Chemists , <em>Wiley, </em> <b>1989</b> , 102-142 . \ No newline at end of file
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+%
+% Filename: $RCSfile: literature.tex,v $
+% Authors: Joerg Wegner
+% Version: $Revision: 1.1.1.1 $
+% $Date: 2004/12/06 15:33:07 $
+% $Author: wegner $
+% Copyright (c) Joerg Wegner; CCC Computer Chemistry Center, Germany
+%
+% ------------------------------------------------------------------------
+% AMS-LaTeX Bibliography *************************************************
+% ------------------------------------------------------------------------
+\documentclass[11pt]{amsart}
+\usepackage[inactive]{srcltx}
+% **** -------------------------------------------------------------------
+\vfuzz1pc % Don't bother to report overfull boxes if over-edge is < 1pc
+\hfuzz1pc % Don't bother to report overfull boxes if over-edge is < 1pc
+
+%-------------------------------------------------------------------------------------------
+% JUST FOR TTH USERS !;-)
+%-------------------------------------------------------------------------------------------
+%%tth:\begin{html}<title>Literature JOELib, J.K. Wegner, 2003</title>\end{html}
+%%tth:\begin{html}<body bgcolor="#FFFFFF">\end{html}
+%-------------------------------------------------------------------------------------------
+
+%%% TITLE ----------------------------------------------------------------
+%%% ----------------------------------------------------------------------
+\begin{document}
+% ------------------------------------------------------------------------
+\nocite{*}
+% ------------------------------------------------------------------------
+\bibliographystyle{angewandte_chemie}
+\bibliography{literature}
+\end{document}
+% ------------------------------------------------------------------------
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diff --git a/java/jmat/data/matrixDecompositions/CholeskyDecomposition.class b/java/jmat/data/matrixDecompositions/CholeskyDecomposition.class
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diff --git a/java/jmat/data/matrixDecompositions/LUDecomposition.class b/java/jmat/data/matrixDecompositions/LUDecomposition.class
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diff --git a/java/jmat/function/DoubleFunctionInterpolation.class b/java/jmat/function/DoubleFunctionInterpolation.class
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diff --git a/java/jmat/function/TestDoubleFunctionExpression.class b/java/jmat/function/TestDoubleFunctionExpression.class
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diff --git a/java/jmat/function/expressionParser/Evaluator$Node.class b/java/jmat/function/expressionParser/Evaluator$Node.class
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diff --git a/java/jmat/function/expressionParser/Evaluator$Operator.class b/java/jmat/function/expressionParser/Evaluator$Operator.class
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diff --git a/java/jmat/function/expressionParser/Evaluator.class b/java/jmat/function/expressionParser/Evaluator.class
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diff --git a/java/jmat/io/data/MatrixFile.class b/java/jmat/io/data/MatrixFile.class
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diff --git a/java/jmat/io/gui/FrameView.class b/java/jmat/io/gui/FrameView.class
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diff --git a/java/jmat/io/gui/FunctionPlot2D.class b/java/jmat/io/gui/FunctionPlot2D.class
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diff --git a/java/jmat/io/gui/FunctionPlot3D.class b/java/jmat/io/gui/FunctionPlot3D.class
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diff --git a/java/jmat/io/gui/MatrixHist2D.class b/java/jmat/io/gui/MatrixHist2D.class
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diff --git a/java/jmat/io/gui/MatrixHist3D.class b/java/jmat/io/gui/MatrixHist3D.class
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diff --git a/java/jmat/io/gui/MatrixPlot2D.class b/java/jmat/io/gui/MatrixPlot2D.class
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diff --git a/java/jmat/io/gui/MatrixPlot3D.class b/java/jmat/io/gui/MatrixPlot3D.class
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diff --git a/java/jmat/io/gui/MatrixTable$DoubleModel.class b/java/jmat/io/gui/MatrixTable$DoubleModel.class
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diff --git a/java/jmat/io/gui/MatrixTable.class b/java/jmat/io/gui/MatrixTable.class
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diff --git a/java/jmat/io/gui/PanelParameters.class b/java/jmat/io/gui/PanelParameters.class
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diff --git a/java/jmat/io/gui/plotTools/Axe2D.class b/java/jmat/io/gui/plotTools/Axe2D.class
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diff --git a/java/jmat/io/gui/plotTools/Coordinates2D.class b/java/jmat/io/gui/plotTools/Coordinates2D.class
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diff --git a/java/jmat/io/gui/plotTools/DataPlot2D.class b/java/jmat/io/gui/plotTools/DataPlot2D.class
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diff --git a/java/jmat/io/gui/plotTools/Grid2D.class b/java/jmat/io/gui/plotTools/Grid2D.class
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diff --git a/java/jmat/test/Testjmat.class b/java/jmat/test/Testjmat.class
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diff --git a/java/joelib2.properties b/java/joelib2.properties
new file mode 100644
index 0000000..fdad7ff
--- /dev/null
+++ b/java/joelib2.properties
@@ -0,0 +1,502 @@
+##############################################################################
+##############################################################################
+##############################################################################
+#
+# JOELib2 properties
+#
+# \ slashes should be written as \\
+# spaces can be written as \ \, but white spaces are removed at the end of
+# lines !!!
+# Please use the Unicode expression \u0020 to encode white spaces !!!
+#
+##############################################################################
+#
+# Version: $Revision: 1.15 $
+# $Date: 2006/07/24 22:29:15 $
+# $Author: wegner $
+#
+##############################################################################
+# Copyright OELIB: OpenEye Scientific Software, Santa Fe,
+# U.S.A., 1999,2000,2001
+# Copyright JOELIB/JOELib2: Dept. Computer Architecture, University of
+# Tuebingen, Germany, 2001,2002,2003,2004,2005
+# Copyright JOELIB/JOELib2: ALTANA PHARMA AG, Konstanz, Germany,
+# 2003,2004,2005
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation version 2 of the License.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+##############################################################################
+##############################################################################
+
+##############################################################################
+# resource locations of data files
+##############################################################################
+joelib2.data.BasicHybridisationTyper.resourceFile=joelib2/data/plain/hybridisation.txt
+joelib2.data.BasicAromaticityTyper.resourceFile=joelib2/data/plain/aromatic.txt
+joelib2.data.BasicAromaticityTyper.useAromaticityModel=true
+joelib2.data.BasicImplicitValenceTyper.resourceFile=joelib2/data/plain/implicitValence.txt
+joelib2.data.BasicAtomTyper.resourceFile=joelib2/data/plain/atomtype.txt
+joelib2.data.BasicElementHolder.resourceFile=joelib2/data/plain/element.txt
+joelib2.data.BasicIsotopeHolder.resourceFile=joelib2/data/plain/isotope.txt
+joelib2.data.BasicProtonationModel.resourceFile=joelib2/data/plain/phmodel.txt
+
+joelib2.data.BasicGroupContributionHolder.resourceDir=joelib2/data/plain
+joelib2.data.BasicGroupContributionHolder.contributionExtension=.contributions
+joelib2.data.BasicGroupContributionHolder.models=LogP MR PSA
+
+joelib2.feature.ResultFactory.resourceFile=joelib2/data/plain/knownResults.txt
+joelib2.process.types.DescriptorStatistic.descriptors2ignore=joelib2/data/plain/desc2ignore.txt
+joelib2.process.types.DescriptorBinning.descriptors2ignore=joelib2/data/plain/desc2ignore.txt
+
+##############################################################################
+# Database
+##############################################################################
+wsi.ra.database.DatabaseConnection.location=jdbc:mysql://localhost/test
+wsi.ra.database.DatabaseConnection.password=
+wsi.ra.database.DatabaseConnection.username=
+wsi.ra.database.DatabaseConnection.driver=org.gjt.mm.mysql.Driver
+
+##############################################################################
+# 2D rendering options
+##############################################################################
+joelib2.gui.render2D.Renderer2DModel.bond.length=30.0
+joelib2.gui.render2D.Renderer2DModel.bond.distance=6.0
+joelib2.gui.render2D.Renderer2DModel.bond.width=2.0
+joelib2.gui.render2D.Renderer2DModel.drawNumbers=true
+joelib2.gui.render2D.Renderer2DModel.useKekuleStructure=true
+joelib2.gui.render2D.Renderer2DModel.showEndCarbons=true
+joelib2.gui.render2D.Renderer2DModel.atomColoring=false
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+joelib2.gui.render2D.Renderer2DModel.orthoLineOffset=20
+joelib2.gui.render2D.Renderer2DModel.arrowOffset=10
+joelib2.gui.render2D.Renderer2DModel.arrowSize=5
+
+joelib2.gui.render2D.Renderer2DModel.background.color.r=255
+joelib2.gui.render2D.Renderer2DModel.background.color.g=255
+joelib2.gui.render2D.Renderer2DModel.background.color.b=255
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+joelib2.gui.render2D.Renderer2DModel.foreground.color.r=0
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+joelib2.gui.render2D.Renderer2DModel.foreground.color.b=0
+
+joelib2.gui.render2D.Renderer2DModel.highlight.color.r=255
+joelib2.gui.render2D.Renderer2DModel.highlight.color.g=0
+joelib2.gui.render2D.Renderer2DModel.highlight.color.b=0
+
+joelib2.gui.render2D.Renderer2DModel.number.color.r=0
+joelib2.gui.render2D.Renderer2DModel.number.color.g=0
+joelib2.gui.render2D.Renderer2DModel.number.color.b=255
+
+joelib2.gui.render2D.Renderer2DModel.conjugatedRing.color.r=0
+joelib2.gui.render2D.Renderer2DModel.conjugatedRing.color.g=0
+joelib2.gui.render2D.Renderer2DModel.conjugatedRing.color.b=0
+
+joelib2.gui.render2D.Renderer2DModel.arrow.color.r=0
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+joelib2.gui.render2D.Renderer2DModel.arrow.color.b=0
+
+joelib2.gui.render2D.Renderer2DModel.orthogonalLine.color.r=0
+joelib2.gui.render2D.Renderer2DModel.orthogonalLine.color.g=0
+joelib2.gui.render2D.Renderer2DModel.orthogonalLine.color.b=255
+
+##############################################################################
+# Smiles ARbitrary Target Specification (SMARTS) matcher parameters
+##############################################################################
+# '*' matches also explicite hydrogens when 'true'
+# '*' matches only non-hydrogen (heavy weight) atoms when 'false'
+joelib2.smarts.SMARTSParser.anyRecognizesExpliciteHydrogens=false
+
+##############################################################################
+# Supported file types
+##############################################################################
+joelib2.filetypes.1.name = SDF
+joelib2.filetypes.2.name = XYZ
+joelib2.filetypes.3.name = SMILES
+joelib2.filetypes.4.name = TINKER
+joelib2.filetypes.5.name = CTX
+joelib2.filetypes.6.name = CML
+joelib2.filetypes.7.name = POV
+joelib2.filetypes.8.name = MOL2
+joelib2.filetypes.9.name = PDB
+joelib2.filetypes.10.name = MATLAB
+joelib2.filetypes.11.name = FLAT
+joelib2.filetypes.11.representation = joelib2.io.types.Flat
+joelib2.filetypes.12.name = MOLCONNZ
+joelib2.filetypes.12.representation = joelib2.io.types.MolconnZ
+joelib2.filetypes.13.name = HIN
+joelib2.filetypes.14.name = GAUSSIANCART
+joelib2.filetypes.15.name = JPEG
+joelib2.filetypes.16.name = GIF
+joelib2.filetypes.17.name = PPM
+# PNG requires another implementation or Marvin
+#joelib2.filetypes.18.name = PNG
+joelib2.filetypes.18.name = BMP
+joelib2.filetypes.19.name = PDF
+joelib2.filetypes.20.name = ZIP
+joelib2.filetypes.21.name = PREP
+joelib2.filetypes.22.name = MOPACOUT
+
+#joelib2.filetypes.16.name = GHEMICAL
+
+# if you want another loader/writer define one
+#joelib2.filetypes.1.representation = joelib2.io.types.MDLSD
+#joelib2.filetypes.2.representation = joelib2.io.types.XYZ
+#joelib2.filetypes.3.representation = joelib2.io.types.Smiles
+
+##############################################################################
+# filters
+##############################################################################
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+joelib2.filter.1.representation =joelib2.process.filter.NOTFilter
+joelib2.filter.1.descriptionFile =docs/process/notFilter
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+joelib2.filter.5.descriptionFile =docs/process/descriptorFilter
+joelib2.filter.6.name =NativeValueFilter
+joelib2.filter.6.representation =joelib2.process.filter.NativeValueFilter
+joelib2.filter.6.descriptionFile =docs/process/nativeValueFilter
+
+##############################################################################
+# processes
+##############################################################################
+joelib2.process.1.name =ProcessPipe
+joelib2.process.1.representation =joelib2.process.ProcessPipe
+joelib2.process.1.descriptionFile =docs/process/processPipe
+joelib2.process.2.name =FeatureSelectionWriter
+joelib2.process.2.representation =joelib2.process.types.FeatureSelectionWriter
+joelib2.process.2.descriptionFile =docs/process/featureSelectionWriter
+joelib2.process.3.name =DescriptorStatistic
+joelib2.process.3.representation =joelib2.process.types.DescStatistic
+joelib2.process.3.descriptionFile =docs/process/descriptorStatistic
+################
+joelib2.process.4.name =DescriptorBinning
+joelib2.process.4.representation =joelib2.process.types.DescBinning
+joelib2.process.4.descriptionFile =docs/process/descriptorBinning
+joelib2.process.types.DescBinning.numberOfBins=20
+################
+joelib2.process.5.name =DistanceCalculation
+joelib2.process.5.representation =joelib2.process.types.DistanceCalculation
+joelib2.process.5.descriptionFile =docs/process/distanceCalculation
+
+##############################################################################
+# miscellaneous
+##############################################################################
+
+#SD Files
+# if set to false aromatic bonds are stored, so this structure can be used
+# as QUERY structure. That's only an export feature, internally you can have
+# both types by using the kekule bonds or the 'normal/aromatic' bonds.
+joelib2.io.types.MDLSD.writeAromaticityAsKekuleSystem=true
+
+#SMILES
+joelib2.smiles.SMILESGenerator.assignCisTransInformations=true
+joelib2.smiles.SMILESGenerator.assignChiralityInformations=true
+joelib2.io.types.Smiles.canonical=false
+joelib2.io.types.Smiles.lineStructure=SMILES|TITLE
+joelib2.io.types.Smiles.lineStructure.delimiter=|
+joelib2.io.types.Smiles.lineStructure.input.delimiter=\u0020\t\n\r
+joelib2.io.types.Smiles.lineStructure.output.delimiter=\u0020
+
+# MolconnZ
+joelib2.io.types.MolconnZ.parserDefinition=joelib2/data/plain/molconnz350.txt
+
+# Flat
+joelib2.io.types.Flat.lineStructure.input.delimiter=\u0020\t\n\r
+joelib2.io.types.Flat.lineStructure.output.delimiter=\t
+joelib2.io.types.Flat.lineStructure.delimiter=\u0020\t
+joelib2.io.types.Flat.lineStructure=TITLE
+
+###########
+# CML
+# version: 1.0 and 2.0
+# ouput: attributearray, array, large, huge
+# delimiter: if you comment this line, standard white space will be used
+# force.formalCharge: formal charges will be always written, even when they are zero
+# partialCharge: write partial atom charge
+# hydrogen=joelib2.feature.types.count: write number of implicite+explicite hydrogens
+###########
+## use slower memory saving preparser for avoiding to load the complete data set into memory
+## This flag will be automatically switched 'ON' for CML files in compressed ZIP files !
+## The basic convert does not need it, because it uses already another sequential
+## SAX reader (forced by a callback)
+joelib2.io.types.ChemicalMarkupLanguage.useSlowerMemorySavingPreparser=false
+###########
+joelib2.io.types.ChemicalMarkupLanguage.output.defaultVersion=2.0
+joelib2.io.types.ChemicalMarkupLanguage.defaultDelimiter=\u0020
+#joelib2.io.types.ChemicalMarkupLanguage.defaultDelimiter=|
+joelib2.io.types.ChemicalMarkupLanguage.output=huge
+joelib2.io.types.ChemicalMarkupLanguage.output.force.formalCharge=false
+joelib2.io.types.ChemicalMarkupLanguage.output.partialCharge=true
+joelib2.io.types.ChemicalMarkupLanguage.output.hydrogenCount=true
+joelib2.io.types.ChemicalMarkupLanguage.output.useNamespace=true
+joelib2.io.types.ChemicalMarkupLanguage.output.namespace=cml
+joelib2.io.types.ChemicalMarkupLanguage.output.xmlDeclaration=http://www.xml-cml.org/schema/cml2/core
+joelib2.io.types.ChemicalMarkupLanguage.DTD.resourceDir=joelib2/io/types/cml/data/
+###########
+## a first step to 'reproducable' descriptor calculation algorithms
+joelib2.io.types.ChemicalMarkupLanguage.output.storeChemistryKernelInfo=true
+## these informations are not really a CML standard
+###########
+joelib2.io.types.ChemicalMarkupLanguage.output.symmetryInformations=false
+###########
+
+# PovRay
+# ouput type can be: stick, sphere, ball_and_stick
+joelib2.io.types.POVRay.output=ball_and_stick
+joelib2.io.types.POVRay.atomPropertyColoring=false
+joelib2.io.types.POVRay.atomProperty=Gasteiger_Marsili
+
+# Image writer
+joelib2.gui.render2D.Mol2Image.defaultWidth=500
+joelib2.gui.render2D.Mol2Image.defaultHeight=400
+
+# PDF writer
+joelib2.io.types.PDF.fontSize=10
+joelib2.io.types.PDF.fontOffset=2
+joelib2.io.types.PDF.pageBorder=20
+
+joelib2.temporary.directory.windows=C:\\temp
+joelib2.temporary.directory.linux=/tmp
+
+joelib2.process.types.DescBinning.descriptors2ignore=joelib2/data/plain/desc2ignore.txt
+joelib2.process.types.DescStatistic.descriptors2ignore=joelib2/data/plain/desc2ignore.txt
+joelib2.process.types.DescVarianceNorm.descriptors2ignore=joelib2/data/plain/desc2ignore.txt
+joelib2.feature.data.MolDesc=joelib2.feature.types.counter.descriptors2ignore=joelib2/data/plain/desc2ignore.txt
+joelib2.feature.data.MoleculesDescriptorMatrix.descriptors2ignore=joelib2/data/plain/desc2ignore.txt
+
+joelib2.feature.data.MoleculesDescriptorMatrix.normalizeOnLoad=true
+#joelib2.feature.data.MoleculesDescriptorMatrix.normalizeStatFile=../../datasets/test.sdf
+
+##############################################################################
+# number output (!!!) format
+# import not implemented for locale!=en and/or groupingUsed!=false
+##############################################################################
+
+# initialize the number ouput format !
+# number of '0' means the minimum number of digits to use
+# number of '#' means the maximum number of digits to use
+# in the property file you must use \# to quote the #'s
+# If not used all digits will be used.
+# deviant to the Java standard the exponential terms with E0 are removed.
+
+#wsi.ra.text.DecimalFormatHelper.double.format=0.\#\#\#\#\#E0
+
+# the both following parameters should be used carefully, because
+# the import is not implemented correctly !!!
+# e.g.: en, de
+
+#wsi.ra.text.DecimalFormatHelper.double.locale=en
+#wsi.ra.text.DecimalFormatHelper.double.groupingUsed=false
+
+##############################################################################
+# external processes
+##############################################################################
+joelib2.external.1.name =Title2Data
+joelib2.external.1.representation =joelib2.ext.Title2Data
+joelib2.external.1.descriptionFile =docs/ext/title2Data
+joelib2.external.1.linux =../lib/linux/title2data
+joelib2.external.1.windows =..\lib\windows\title2data.exe
+joelib2.external.1.argument.1 =MOL_TITLE
+
+##############################################################################
+# Features and feature properties
+##############################################################################
+joelib2.feature.addIfNotExist=true
+##############################################
+joelib2.feature.0.representation =joelib2.ring.RingFinderSSSR
+joelib2.feature.1.representation =joelib2.algo.BFS
+joelib2.feature.2.representation =joelib2.algo.DFS
+joelib2.feature.3.representation =joelib2.algo.APropertyBFS
+joelib2.feature.4.representation =joelib2.feature.types.atomlabel.AtomBondOrderSum
+joelib2.feature.5.representation =joelib2.feature.types.atomlabel.AtomElectronAffinity
+joelib2.feature.6.representation =joelib2.feature.types.atomlabel.AtomENAllredRochow
+joelib2.feature.7.representation =joelib2.feature.types.atomlabel.AtomENPauling
+joelib2.feature.8.representation =joelib2.feature.types.atomlabel.AtomENSanderson
+joelib2.feature.9.representation =joelib2.feature.types.atomlabel.AtomExplicitHydrogenCount
+joelib2.feature.10.representation =joelib2.feature.types.atomlabel.AtomFreeElectronsCount
+joelib2.feature.11.representation =joelib2.feature.types.atomlabel.AtomFreeOxygenCount
+joelib2.feature.12.representation =joelib2.feature.types.atomlabel.AtomHeavyValence
+joelib2.feature.13.representation =joelib2.feature.types.atomlabel.AtomHeteroValence
+joelib2.feature.14.representation =joelib2.feature.types.atomlabel.AtomHybridisation
+joelib2.feature.15.representation =joelib2.feature.types.atomlabel.AtomImplicitHydrogenCount
+joelib2.feature.16.representation =joelib2.feature.types.atomlabel.AtomImplicitValence
+joelib2.feature.17.representation =joelib2.feature.types.atomlabel.AtomInAcceptor
+joelib2.feature.18.representation =joelib2.feature.types.atomlabel.AtomInAromaticSystem
+joelib2.feature.19.representation =joelib2.feature.types.atomlabel.AtomInConjEnvironment
+joelib2.feature.20.representation =joelib2.feature.types.atomlabel.AtomInDonAcc
+joelib2.feature.21.representation =joelib2.feature.types.atomlabel.AtomInDonor
+joelib2.feature.22.representation =joelib2.feature.types.atomlabel.AtomInRing
+joelib2.feature.23.representation =joelib2.feature.types.atomlabel.AtomInRingsCount
+joelib2.feature.24.representation =joelib2.feature.types.atomlabel.AtomInTerminalCarbon
+joelib2.feature.25.representation =joelib2.feature.types.atomlabel.AtomIsAlphaBetaUnsaturated
+joelib2.feature.26.representation =joelib2.feature.types.atomlabel.AtomIsAmideNitrogen
+joelib2.feature.27.representation =joelib2.feature.types.atomlabel.AtomIsAntiClockwise
+joelib2.feature.28.representation =joelib2.feature.types.atomlabel.AtomIsAromaticNOxide
+joelib2.feature.29.representation =joelib2.feature.types.atomlabel.AtomIsAxial
+joelib2.feature.30.representation =joelib2.feature.types.atomlabel.AtomIsCarbon
+joelib2.feature.31.representation =joelib2.feature.types.atomlabel.AtomIsCarboxylOxygen
+joelib2.feature.32.representation =joelib2.feature.types.atomlabel.AtomIsChiral
+joelib2.feature.33.representation =joelib2.feature.types.atomlabel.AtomIsClockwise
+joelib2.feature.34.representation =joelib2.feature.types.atomlabel.AtomIsElectronegative
+joelib2.feature.35.representation =joelib2.feature.types.atomlabel.AtomIsHalogen
+joelib2.feature.36.representation =joelib2.feature.types.atomlabel.AtomIsHeteroatom
+joelib2.feature.37.representation =joelib2.feature.types.atomlabel.AtomIsHydrogen
+joelib2.feature.38.representation =joelib2.feature.types.atomlabel.AtomIsNegative
+joelib2.feature.39.representation =joelib2.feature.types.atomlabel.AtomIsNitrogen
+joelib2.feature.40.representation =joelib2.feature.types.atomlabel.AtomIsNitroOxygen
+joelib2.feature.41.representation =joelib2.feature.types.atomlabel.AtomIsNonPolarHydrogen
+joelib2.feature.42.representation =joelib2.feature.types.atomlabel.AtomIsOxygen
+joelib2.feature.43.representation =joelib2.feature.types.atomlabel.AtomIsPhosphateOxygen
+joelib2.feature.44.representation =joelib2.feature.types.atomlabel.AtomIsPhosphorus
+joelib2.feature.45.representation =joelib2.feature.types.atomlabel.AtomIsPolarHydrogen
+joelib2.feature.46.representation =joelib2.feature.types.atomlabel.AtomIsPositive
+joelib2.feature.47.representation =joelib2.feature.types.atomlabel.AtomIsSulfateOxygen
+joelib2.feature.48.representation =joelib2.feature.types.atomlabel.AtomIsSulfur
+joelib2.feature.49.representation =joelib2.feature.types.atomlabel.AtomIsUnsaturated
+joelib2.feature.50.representation =joelib2.feature.types.atomlabel.AtomKekuleBondOrderSum
+joelib2.feature.51.representation =joelib2.feature.types.atomlabel.AtomMass
+joelib2.feature.52.representation =joelib2.feature.types.atomlabel.AtomPartialCharge
+joelib2.feature.53.representation =joelib2.feature.types.atomlabel.AtomType
+joelib2.feature.54.representation =joelib2.feature.types.atomlabel.AtomValence
+joelib2.feature.55.representation =joelib2.feature.types.atomlabel.AtomValenceSum
+joelib2.feature.56.representation =joelib2.feature.types.atomlabel.AtomVanDerWaalsVolume
+joelib2.feature.57.representation =joelib2.feature.types.atompair.TopologicalAtomPair
+joelib2.feature.58.representation =joelib2.feature.types.bondlabel.BondInAromaticSystem
+joelib2.feature.59.representation =joelib2.feature.types.bondlabel.BondInRing
+joelib2.feature.60.representation =joelib2.feature.types.bondlabel.BondIsAmide
+joelib2.feature.61.representation =joelib2.feature.types.bondlabel.BondIsCarbonyl
+joelib2.feature.62.representation =joelib2.feature.types.bondlabel.BondIsClosure
+joelib2.feature.63.representation =joelib2.feature.types.bondlabel.BondIsEster
+joelib2.feature.64.representation =joelib2.feature.types.bondlabel.BondIsPrimaryAmide
+joelib2.feature.65.representation =joelib2.feature.types.bondlabel.BondIsRotor
+joelib2.feature.66.representation =joelib2.feature.types.bondlabel.BondKekuleType
+joelib2.feature.67.representation =joelib2.feature.types.count.AcidicGroups
+joelib2.feature.68.representation =joelib2.feature.types.count.AliphaticOHGroups
+joelib2.feature.69.representation =joelib2.feature.types.count.AromaticBonds
+joelib2.feature.70.representation =joelib2.feature.types.count.AromaticOHGroups
+joelib2.feature.71.representation =joelib2.feature.types.count.BasicGroups
+joelib2.feature.72.representation =joelib2.feature.types.count.HBA1
+joelib2.feature.73.representation =joelib2.feature.types.count.HBA2
+joelib2.feature.74.representation =joelib2.feature.types.count.HBD1
+joelib2.feature.75.representation =joelib2.feature.types.count.HBD2
+joelib2.feature.76.representation =joelib2.feature.types.count.HeavyBonds
+joelib2.feature.77.representation =joelib2.feature.types.count.HeteroCycles
+joelib2.feature.78.representation =joelib2.feature.types.count.HydrophobicGroups
+joelib2.feature.79.representation =joelib2.feature.types.count.NO2Groups
+joelib2.feature.80.representation =joelib2.feature.types.count.NumberOfAtoms
+joelib2.feature.81.representation =joelib2.feature.types.count.NumberOfB
+joelib2.feature.82.representation =joelib2.feature.types.count.NumberOfBonds
+joelib2.feature.83.representation =joelib2.feature.types.count.NumberOfBr
+joelib2.feature.84.representation =joelib2.feature.types.count.NumberOfC
+joelib2.feature.85.representation =joelib2.feature.types.count.NumberOfCl
+joelib2.feature.86.representation =joelib2.feature.types.count.NumberOfF
+joelib2.feature.87.representation =joelib2.feature.types.count.NumberOfHal
+joelib2.feature.88.representation =joelib2.feature.types.count.NumberOfI
+joelib2.feature.89.representation =joelib2.feature.types.count.NumberOfN
+joelib2.feature.90.representation =joelib2.feature.types.count.NumberOfO
+joelib2.feature.91.representation =joelib2.feature.types.count.NumberOfP
+joelib2.feature.92.representation =joelib2.feature.types.count.NumberOfS
+joelib2.feature.93.representation =joelib2.feature.types.count.OSOGroups
+joelib2.feature.94.representation =joelib2.feature.types.count.SO2Groups
+joelib2.feature.95.representation =joelib2.feature.types.count.SOGroups
+joelib2.feature.96.representation =joelib2.feature.types.APropertyDistanceMatrix
+joelib2.feature.97.representation =joelib2.feature.types.Autocorrelation
+joelib2.feature.98.representation =joelib2.feature.types.BCUT
+joelib2.feature.99.representation =joelib2.feature.types.BurdenEigenvalues
+joelib2.feature.100.representation =joelib2.feature.types.BurdenModifiedEigenvalues
+joelib2.feature.101.representation =joelib2.feature.types.ConjElectroTopolState
+joelib2.feature.102.representation =joelib2.feature.types.ConjugatedTopologicalDistance
+joelib2.feature.103.representation =joelib2.feature.types.DistanceDistanceMatrix
+joelib2.feature.104.representation =joelib2.feature.types.DistanceMatrix
+joelib2.feature.105.representation =joelib2.feature.types.ElectrogeometricalState
+joelib2.feature.106.representation =joelib2.feature.types.ElectrotopologicalState
+joelib2.feature.107.representation =joelib2.feature.types.FractionRotatableBonds
+joelib2.feature.108.representation =joelib2.feature.types.GeomDistanceMatrix
+joelib2.feature.109.representation =joelib2.feature.types.GeometricalDiameter
+joelib2.feature.110.representation =joelib2.feature.types.GeometricalRadius
+joelib2.feature.111.representation =joelib2.feature.types.GeometricalShapeCoefficient
+joelib2.feature.112.representation =joelib2.feature.types.GlobalTopologicalChargeIndex
+joelib2.feature.113.representation =joelib2.feature.types.GraphPotentials
+joelib2.feature.114.representation =joelib2.feature.types.GraphShapeCoefficient
+joelib2.feature.115.representation =joelib2.feature.types.IntrinsicState
+joelib2.feature.116.representation =joelib2.feature.types.KierShape1
+joelib2.feature.117.representation =joelib2.feature.types.KierShape2
+joelib2.feature.118.representation =joelib2.feature.types.KierShape3
+joelib2.feature.119.representation =joelib2.feature.types.LogP
+joelib2.feature.120.representation =joelib2.feature.types.MolarRefractivity
+joelib2.feature.121.representation =joelib2.feature.types.MolecularWeight
+joelib2.feature.122.representation =joelib2.feature.types.PolarSurfaceArea
+j##############################################
+joelib2.feature.123.representation =joelib2.feature.types.RadialDistributionFunction
+joelib2.feature.types.RadialDistributionFunction.minSphericalVolume = 0.2
+joelib2.feature.types.RadialDistributionFunction.maxSphericalVolume = 10.0
+joelib2.feature.types.RadialDistributionFunction.sphericalVolumeResolution = 0.05
+joelib2.feature.types.RadialDistributionFunction.smoothingFactor = 25
+##############################################
+joelib2.feature.124.representation =joelib2.feature.types.RotatableBonds
+joelib2.feature.125.representation =joelib2.feature.types.SMILESMolecule
+joelib2.feature.126.representation =joelib2.feature.types.SSKey3DS
+joelib2.feature.127.representation =joelib2.feature.types.TopologicalDiameter
+joelib2.feature.128.representation =joelib2.feature.types.TopologicalRadius
+joelib2.feature.129.representation =joelib2.feature.types.WeightedBurdenEigenvalues
+joelib2.feature.130.representation =joelib2.feature.types.WeightedBurdenModifiedEigenvalues
+joelib2.feature.131.representation =joelib2.feature.types.ZagrebIndex1
+joelib2.feature.132.representation =joelib2.feature.types.MoleculeHashcode
+joelib2.feature.133.representation =joelib2.feature.types.CharacteristicPolynomialCoefficients
+joelib2.feature.134.representation =joelib2.feature.types.CharacteristicPolynomial
+#joelib2.feature.135.representation =joelib2.feature.types.cfm.CompressedFeatureMatrix
+#joelib2.feature.136.representation =
+#joelib2.feature.137.representation =
+#joelib2.feature.138.representation =
+#joelib2.feature.139.representation =
+#joelib2.feature.140.representation =
+#joelib2.feature.141.representation =
+
+##############################################################################
+# End of JOELib2 properties definitions
+##############################################################################
+
+##############################################################################
+# Start of JTextTools definitions
+##############################################################################
+jtt.docbook.DocBookEquations.latex=/usr/bin/latex
+jtt.docbook.DocBookEquations.dvips=/usr/bin/dvips
+jtt.docbook.DocBookEquations.convert=/usr/bin/convert
+#jtt.docbook.DocBookEquations.latex=C:/Programme/latex/texmf/miktex/bin/latex.exe
+#jtt.docbook.DocBookEquations.dvips=C:/Programme/latex/texmf/miktex/bin/dvips.exe
+#jtt.docbook.DocBookEquations.convert=C:/Programme/ImageMagick/convert.exe
+jtt.docbook.DocBookEquations.fontSize=12
+jtt.docbook.DocBookEquations.bold=true
+jtt.docbook.DocBookEquations.large=true
+jtt.docbook.DocBookEquations.fileExtension=sgml
+
+jtt.docbook.DocBookMolecules.fileExtension=sgml
+
+jtt.docbook.Jade.jade=/usr/bin/jade
+#jtt.docbook.Jade.jade=C:/cygwin/usr/share/sgml/docbook/jade121/jade
+jtt.docbook.Jade.DSSSL.rtf=/usr/share/sgml/docbook/dsssl-stylesheets-1.77/print/docbook.dsl
+jtt.docbook.Jade.DSSSL.html=/usr/share/sgml/docbook/dsssl-stylesheets-1.77/html/docbook.dsl
+jtt.docbook.Jade.SGML.catalg.files=/usr/share/sgml/docbook_4.2/docbook.cat:/usr/share/sgml/jade_dsl/catalog
+jtt.docbook.Jade.index=true
+
+jtt.docbook.DocBookArticles.version=XML V4.2
+jtt.docbook.DocBookArticles.fileExtension=sgml
+jtt.docbook.DocBookArticles.DTD=/usr/share/sgml/docbook_4.2/docbook.dtd
+##############################################################################
+# End of JTextTools definitions
+##############################################################################
diff --git a/java/joelib2/algo/APropertyBFS.class b/java/joelib2/algo/APropertyBFS.class
new file mode 100644
index 0000000..c579574
--- /dev/null
+++ b/java/joelib2/algo/APropertyBFS.class
Binary files differ
diff --git a/java/joelib2/algo/BFS.class b/java/joelib2/algo/BFS.class
new file mode 100644
index 0000000..ba1faf0
--- /dev/null
+++ b/java/joelib2/algo/BFS.class
Binary files differ
diff --git a/java/joelib2/algo/BFSResult.class b/java/joelib2/algo/BFSResult.class
new file mode 100644
index 0000000..5b0ae2f
--- /dev/null
+++ b/java/joelib2/algo/BFSResult.class
Binary files differ
diff --git a/java/joelib2/algo/DFS.class b/java/joelib2/algo/DFS.class
new file mode 100644
index 0000000..2eb3ef6
--- /dev/null
+++ b/java/joelib2/algo/DFS.class
Binary files differ
diff --git a/java/joelib2/algo/DFSResult.class b/java/joelib2/algo/DFSResult.class
new file mode 100644
index 0000000..a70c41a
--- /dev/null
+++ b/java/joelib2/algo/DFSResult.class
Binary files differ
diff --git a/java/joelib2/algo/clique/BronKerbosch.class b/java/joelib2/algo/clique/BronKerbosch.class
new file mode 100644
index 0000000..94ca8ec
--- /dev/null
+++ b/java/joelib2/algo/clique/BronKerbosch.class
Binary files differ
diff --git a/java/joelib2/algo/clique/CliqueFinder.class b/java/joelib2/algo/clique/CliqueFinder.class
new file mode 100644
index 0000000..afae197
--- /dev/null
+++ b/java/joelib2/algo/clique/CliqueFinder.class
Binary files differ
diff --git a/java/joelib2/algo/clique/DFMax.class b/java/joelib2/algo/clique/DFMax.class
new file mode 100644
index 0000000..a17b5f0
--- /dev/null
+++ b/java/joelib2/algo/clique/DFMax.class
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