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authorAndreas Maunz <andreas@maunz.de>2012-04-02 09:18:14 +0200
committerAndreas Maunz <andreas@maunz.de>2012-04-02 09:18:14 +0200
commit3cd136861c68b8c24cc653c903c620d55be4b294 (patch)
treeab50372c9ed9cab413e72b62f219d23ca481e935
parentcb67fe0e722a58b6fcf212ef045808dc9a13053a (diff)
Remove PC descriptor
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-rw-r--r--java/jtt/docbook/DocBookArticles.classbin3836 -> 0 bytes
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-rw-r--r--java/jtt/docbook/DocBookMolecules.classbin6460 -> 0 bytes
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-rw-r--r--java/jtt/latex/bibtex/Bibitem.classbin9802 -> 0 bytes
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-rw-r--r--java/jtt/util/Executable.classbin2620 -> 0 bytes
-rw-r--r--java/junit-3.8.1.jarbin121070 -> 0 bytes
-rw-r--r--java/linux/title2databin14514 -> 0 bytes
-rw-r--r--java/linux/title2data.cpp79
-rw-r--r--java/log4j.jarbin350525 -> 0 bytes
-rw-r--r--java/log4j.properties104
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-rw-r--r--java/optional.jarbin654735 -> 0 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
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-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
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-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
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-rw-r--r--java/resources/smartsEvaluation/alkali_elements.mol17
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-rw-r--r--java/resources/smartsEvaluation/butan.mol12
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-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
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-rw-r--r--java/windows/title2data.cpp82
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1211 files changed, 0 insertions, 76954 deletions
diff --git a/application.rb b/application.rb
index e75c96c..7c76b15 100644
--- a/application.rb
+++ b/application.rb
@@ -366,54 +366,6 @@ post '/:id' do
end
-# Create PC descriptors
-#
-# @param [String] pc_type
-# @return [text/uri-list] Task ID
-get '/:id/pcdesc' do
-algorithm = OpenTox::Algorithm::Generic.new(url_for('/dataset/id/pcdesc',:full))
- algorithm.metadata = {
- DC.title => 'Physico-chemical (PC) descriptor calculation',
- DC.creator => "andreas@maunz.de, vorgrimmlerdavid@gmx.de",
- RDF.type => [OT.Algorithm,OTA.PatternMiningSupervised],
- OT.parameters => [
- { DC.description => "Dataset URI", OT.paramScope => "mandatory", DC.title => "dataset_uri" },
- { DC.description => "PC type", OT.paramScope => "mandatory", DC.title => "pc_type" },
- ]
- }
- case request.env['HTTP_ACCEPT']
- when /text\/html/
- content_type "text/html"
- OpenTox.text_to_html algorithm.to_yaml
- when /application\/x-yaml/
- content_type "application/x-yaml"
- algorithm.to_yaml
- else
- response['Content-Type'] = 'application/rdf+xml'
- algorithm.to_rdfxml
- end
-end
-
-
-
-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 |task|
- 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, :task => task } )
- end
- raise OpenTox::ServiceUnavailableError.newtask.uri+"\n" if task.status == "Cancelled"
- halt 202,task.uri.to_s+"\n"
-end
-
-
-
# Deletes datasets that have been created by a crossvalidatoin that does not exist anymore
# (This can happen if a crossvalidation fails unexpectedly)
delete '/cleanup' do
diff --git a/java/Acme/IntHashtable.class b/java/Acme/IntHashtable.class
deleted file mode 100644
index d589d5e..0000000
--- a/java/Acme/IntHashtable.class
+++ /dev/null
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diff --git a/java/Acme/IntHashtableEntry.class b/java/Acme/IntHashtableEntry.class
deleted file mode 100644
index 68e61d2..0000000
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+++ /dev/null
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diff --git a/java/Acme/IntHashtableEnumerator.class b/java/Acme/IntHashtableEnumerator.class
deleted file mode 100644
index 094c480..0000000
--- a/java/Acme/IntHashtableEnumerator.class
+++ /dev/null
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diff --git a/java/Acme/JPM/Encoders/GifEncoder.class b/java/Acme/JPM/Encoders/GifEncoder.class
deleted file mode 100644
index 333716a..0000000
--- a/java/Acme/JPM/Encoders/GifEncoder.class
+++ /dev/null
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diff --git a/java/Acme/JPM/Encoders/GifEncoderHashitem.class b/java/Acme/JPM/Encoders/GifEncoderHashitem.class
deleted file mode 100644
index 98abe62..0000000
--- a/java/Acme/JPM/Encoders/GifEncoderHashitem.class
+++ /dev/null
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diff --git a/java/Acme/JPM/Encoders/GrayJPEG.class b/java/Acme/JPM/Encoders/GrayJPEG.class
deleted file mode 100644
index 218329b..0000000
--- a/java/Acme/JPM/Encoders/GrayJPEG.class
+++ /dev/null
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diff --git a/java/Acme/JPM/Encoders/ImageEncoder.class b/java/Acme/JPM/Encoders/ImageEncoder.class
deleted file mode 100644
index 6a987ea..0000000
--- a/java/Acme/JPM/Encoders/ImageEncoder.class
+++ /dev/null
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diff --git a/java/Acme/JPM/Encoders/PpmEncoder.class b/java/Acme/JPM/Encoders/PpmEncoder.class
deleted file mode 100644
index ec98b4d..0000000
--- a/java/Acme/JPM/Encoders/PpmEncoder.class
+++ /dev/null
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diff --git a/java/Jmol.jar b/java/Jmol.jar
deleted file mode 100644
index 2c7e5aa..0000000
--- a/java/Jmol.jar
+++ /dev/null
Binary files differ
diff --git a/java/JoelibFc.class b/java/JoelibFc.class
deleted file mode 100644
index 5e68988..0000000
--- a/java/JoelibFc.class
+++ /dev/null
Binary files differ
diff --git a/java/ant.jar b/java/ant.jar
deleted file mode 100644
index 3a67607..0000000
--- a/java/ant.jar
+++ /dev/null
Binary files differ
diff --git a/java/bin2hex.pl b/java/bin2hex.pl
deleted file mode 100644
index f419c3e..0000000
--- a/java/bin2hex.pl
+++ /dev/null
@@ -1,35 +0,0 @@
-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
deleted file mode 100644
index 1b80656..0000000
--- a/java/cformat/PrintfFormat$DecDouble.class
+++ /dev/null
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diff --git a/java/cformat/PrintfFormat$OutBuffer.class b/java/cformat/PrintfFormat$OutBuffer.class
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index 0f25b29..0000000
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+++ /dev/null
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diff --git a/java/cformat/PrintfFormat.class b/java/cformat/PrintfFormat.class
deleted file mode 100644
index 3b05ba1..0000000
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+++ /dev/null
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diff --git a/java/cformat/PrintfFormatTest$TestException.class b/java/cformat/PrintfFormatTest$TestException.class
deleted file mode 100644
index 93b3194..0000000
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+++ /dev/null
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deleted file mode 100644
index 6ea2158..0000000
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+++ /dev/null
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diff --git a/java/cformat/PrintfStream.class b/java/cformat/PrintfStream.class
deleted file mode 100644
index b2253a2..0000000
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+++ /dev/null
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diff --git a/java/cformat/PrintfWriter.class b/java/cformat/PrintfWriter.class
deleted file mode 100644
index 655110a..0000000
--- a/java/cformat/PrintfWriter.class
+++ /dev/null
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diff --git a/java/cformat/ScanfFormat$Cmatch.class b/java/cformat/ScanfFormat$Cmatch.class
deleted file mode 100644
index ec11d0d..0000000
--- a/java/cformat/ScanfFormat$Cmatch.class
+++ /dev/null
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deleted file mode 100644
index 2b15ef5..0000000
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+++ /dev/null
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diff --git a/java/cformat/ScanfFormatTest.class b/java/cformat/ScanfFormatTest.class
deleted file mode 100644
index bea49e6..0000000
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+++ /dev/null
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diff --git a/java/cformat/ScanfMatchException.class b/java/cformat/ScanfMatchException.class
deleted file mode 100644
index 4226d27..0000000
--- a/java/cformat/ScanfMatchException.class
+++ /dev/null
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diff --git a/java/cformat/ScanfReader.class b/java/cformat/ScanfReader.class
deleted file mode 100644
index f633f0e..0000000
--- a/java/cformat/ScanfReader.class
+++ /dev/null
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deleted file mode 100644
index 36fbaff..0000000
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diff --git a/java/com/obrador/DCT.class b/java/com/obrador/DCT.class
deleted file mode 100644
index 4113413..0000000
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+++ /dev/null
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diff --git a/java/com/obrador/Huffman.class b/java/com/obrador/Huffman.class
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index ce910f4..0000000
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index 95e93a5..0000000
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+++ /dev/null
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index 848ff71..0000000
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+++ /dev/null
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diff --git a/java/com/obrador/JpegInfo.class b/java/com/obrador/JpegInfo.class
deleted file mode 100644
index f84d191..0000000
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+++ /dev/null
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diff --git a/java/com/vladium/utils/ClassScope$1.class b/java/com/vladium/utils/ClassScope$1.class
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index 7449d2c..0000000
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index 0536ae1..0000000
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deleted file mode 100644
index df26fb7..0000000
--- a/java/docs/algo/APropertyBFS.html
+++ /dev/null
@@ -1,93 +0,0 @@
-<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
deleted file mode 100644
index 47c782c..0000000
--- a/java/docs/algo/BreadthFirstSearch.html
+++ /dev/null
@@ -1,122 +0,0 @@
-<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
deleted file mode 100644
index a4afe64..0000000
--- a/java/docs/algo/DepthFirstSearch.html
+++ /dev/null
@@ -1,137 +0,0 @@
-<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
deleted file mode 100644
index 6a745e7..0000000
--- a/java/docs/algo/DistanceMatrix.html
+++ /dev/null
@@ -1,102 +0,0 @@
-<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
deleted file mode 100644
index 76488d9..0000000
--- a/java/docs/algo/GeomDistanceMatrix.html
+++ /dev/null
@@ -1,84 +0,0 @@
-<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
deleted file mode 100644
index 0a20be3..0000000
--- a/java/docs/algo/Morgan.html
+++ /dev/null
@@ -1,157 +0,0 @@
-<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
deleted file mode 100644
index 5e0ebd1..0000000
--- a/java/docs/algo/bibliography.html
+++ /dev/null
@@ -1,782 +0,0 @@
-<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"
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-CLASS="BIBLIOENTRYBLOCK"
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+++ /dev/null
@@ -1,93 +0,0 @@
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-><DIV
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-><H1
-CLASS="SECT1"
-><A
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->Descriptor</H1
-><DIV
-CLASS="SECT2"
-><H2
-CLASS="SECT2"
-><A
-NAME="JOELIB.DESCRIPTORS.AROMATICBONDS"
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->Number of aromatic bonds</H2
-><P
->Number of aromatic bonds.</P
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->&nbsp;</TD
-><TD
-WIDTH="33%"
-ALIGN="right"
-VALIGN="top"
-><A
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->Next</A
-></TD
-></TR
-><TR
-><TD
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->&nbsp;</TD
-><TD
-WIDTH="34%"
-ALIGN="center"
-VALIGN="top"
->&nbsp;</TD
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-WIDTH="33%"
-ALIGN="right"
-VALIGN="top"
->Bibliography</TD
-></TR
-></TABLE
-></DIV
-></BODY
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-> \ No newline at end of file
diff --git a/java/docs/feature/AromaticOHGroups.html b/java/docs/feature/AromaticOHGroups.html
deleted file mode 100644
index 781c23b..0000000
--- a/java/docs/feature/AromaticOHGroups.html
+++ /dev/null
@@ -1,93 +0,0 @@
-<HTML
-><HEAD
-><TITLE
-></TITLE
-><META
-NAME="GENERATOR"
-CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
-REL="NEXT"
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-HREF="bibliography.html"></HEAD
-><BODY
-CLASS="ARTICLE"
-BGCOLOR="#FFFFFF"
-TEXT="#000000"
-LINK="#0000FF"
-VLINK="#840084"
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-><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
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-CELLSPACING="0"
-><TR
-><TD
-WIDTH="33%"
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-VALIGN="top"
->&nbsp;</TD
-><TD
-WIDTH="34%"
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-VALIGN="top"
->&nbsp;</TD
-><TD
-WIDTH="33%"
-ALIGN="right"
-VALIGN="top"
-><A
-HREF="bibliography.html"
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->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"
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->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
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomBondOrderSum.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomENAllredRochow.html b/java/docs/feature/AtomENAllredRochow.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomENAllredRochow.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomENPauling.html b/java/docs/feature/AtomENPauling.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomENPauling.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomENSanderson.html b/java/docs/feature/AtomENSanderson.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomENSanderson.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomElectronAffinity.html b/java/docs/feature/AtomElectronAffinity.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomElectronAffinity.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomExplicitHydrogenCount.html b/java/docs/feature/AtomExplicitHydrogenCount.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomExplicitHydrogenCount.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomFreeElectronsCount.html b/java/docs/feature/AtomFreeElectronsCount.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomFreeElectronsCount.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomFreeOxygenCount.html b/java/docs/feature/AtomFreeOxygenCount.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomFreeOxygenCount.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomHeavyValence.html b/java/docs/feature/AtomHeavyValence.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomHeavyValence.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomHeteroValence.html b/java/docs/feature/AtomHeteroValence.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomHeteroValence.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomHybridisation.html b/java/docs/feature/AtomHybridisation.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomHybridisation.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomImplicitHydrogenCount.html b/java/docs/feature/AtomImplicitHydrogenCount.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomImplicitHydrogenCount.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomImplicitValence.html b/java/docs/feature/AtomImplicitValence.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomImplicitValence.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomInAcceptor.html b/java/docs/feature/AtomInAcceptor.html
deleted file mode 100644
index 5785a4f..0000000
--- a/java/docs/feature/AtomInAcceptor.html
+++ /dev/null
@@ -1,93 +0,0 @@
-<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
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomInAromaticSystem.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomInConjEnvironment.html b/java/docs/feature/AtomInConjEnvironment.html
deleted file mode 100644
index 2a3289e..0000000
--- a/java/docs/feature/AtomInConjEnvironment.html
+++ /dev/null
@@ -1,184 +0,0 @@
-<HTML
-><HEAD
-><TITLE
-></TITLE
-><META
-NAME="GENERATOR"
-CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
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-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"
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->Atom in conjugated environment</H2
-><P
->Atom in conjugated environment.
-<DIV
-CLASS="TABLE"
-><A
-NAME="AEN7"
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-><P
-><B
->Table 1. SMARTS definitions for assigning the conjugated atom property flag</B
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-BORDER="1"
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-><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
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-></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
deleted file mode 100644
index 61b8188..0000000
--- a/java/docs/feature/AtomInDonAcc.html
+++ /dev/null
@@ -1,93 +0,0 @@
-<HTML
-><HEAD
-><TITLE
-></TITLE
-><META
-NAME="GENERATOR"
-CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
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-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
deleted file mode 100644
index 399b2f9..0000000
--- a/java/docs/feature/AtomInDonor.html
+++ /dev/null
@@ -1,93 +0,0 @@
-<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
deleted file mode 100644
index 79b7741..0000000
--- a/java/docs/feature/AtomInRing.html
+++ /dev/null
@@ -1,93 +0,0 @@
-<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
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomInRingsCount.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomInTerminalCarbon.html b/java/docs/feature/AtomInTerminalCarbon.html
deleted file mode 100644
index 23c8b41..0000000
--- a/java/docs/feature/AtomInTerminalCarbon.html
+++ /dev/null
@@ -1,93 +0,0 @@
-<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
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomIsAlphaBetaUnsaturated.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsAmideNitrogen.html b/java/docs/feature/AtomIsAmideNitrogen.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomIsAmideNitrogen.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsAntiClockwise.html b/java/docs/feature/AtomIsAntiClockwise.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomIsAntiClockwise.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsAromaticNOxide.html b/java/docs/feature/AtomIsAromaticNOxide.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomIsAromaticNOxide.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsAxial.html b/java/docs/feature/AtomIsAxial.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomIsAxial.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsCarbon.html b/java/docs/feature/AtomIsCarbon.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomIsCarbon.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsCarboxylOxygen.html b/java/docs/feature/AtomIsCarboxylOxygen.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomIsCarboxylOxygen.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsChiral.html b/java/docs/feature/AtomIsChiral.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomIsChiral.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsClockwise.html b/java/docs/feature/AtomIsClockwise.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomIsClockwise.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsElectronegative.html b/java/docs/feature/AtomIsElectronegative.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomIsElectronegative.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsHalogen.html b/java/docs/feature/AtomIsHalogen.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomIsHalogen.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsHeteroatom.html b/java/docs/feature/AtomIsHeteroatom.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomIsHeteroatom.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsHydrogen.html b/java/docs/feature/AtomIsHydrogen.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomIsHydrogen.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsNegative.html b/java/docs/feature/AtomIsNegative.html
deleted file mode 100644
index 2754ce0..0000000
--- a/java/docs/feature/AtomIsNegative.html
+++ /dev/null
@@ -1,93 +0,0 @@
-<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
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomIsNitroOxygen.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsNitrogen.html b/java/docs/feature/AtomIsNitrogen.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomIsNitrogen.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsNonPolarHydrogen.html b/java/docs/feature/AtomIsNonPolarHydrogen.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomIsNonPolarHydrogen.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsOxygen.html b/java/docs/feature/AtomIsOxygen.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomIsOxygen.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsPhosphateOxygen.html b/java/docs/feature/AtomIsPhosphateOxygen.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomIsPhosphateOxygen.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsPhosphorus.html b/java/docs/feature/AtomIsPhosphorus.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomIsPhosphorus.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsPolarHydrogen.html b/java/docs/feature/AtomIsPolarHydrogen.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomIsPolarHydrogen.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsPositive.html b/java/docs/feature/AtomIsPositive.html
deleted file mode 100644
index 4f4204d..0000000
--- a/java/docs/feature/AtomIsPositive.html
+++ /dev/null
@@ -1,93 +0,0 @@
-<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
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomIsSulfateOxygen.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsSulfur.html b/java/docs/feature/AtomIsSulfur.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomIsSulfur.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomIsUnsaturated.html b/java/docs/feature/AtomIsUnsaturated.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomIsUnsaturated.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomKekuleBondOrderSum.html b/java/docs/feature/AtomKekuleBondOrderSum.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomKekuleBondOrderSum.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomMass.html b/java/docs/feature/AtomMass.html
deleted file mode 100644
index f1a2cde..0000000
--- a/java/docs/feature/AtomMass.html
+++ /dev/null
@@ -1,93 +0,0 @@
-<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
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomPartialCharge.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomType.html b/java/docs/feature/AtomType.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomType.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomValence.html b/java/docs/feature/AtomValence.html
deleted file mode 100644
index dcd6db8..0000000
--- a/java/docs/feature/AtomValence.html
+++ /dev/null
@@ -1,93 +0,0 @@
-<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
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/AtomValenceSum.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/AtomVanDerWaalsVolume.html b/java/docs/feature/AtomVanDerWaalsVolume.html
deleted file mode 100644
index bf76e72..0000000
--- a/java/docs/feature/AtomVanDerWaalsVolume.html
+++ /dev/null
@@ -1,93 +0,0 @@
-<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
deleted file mode 100644
index 53fe464..0000000
--- a/java/docs/feature/Autocorrelation.html
+++ /dev/null
@@ -1,168 +0,0 @@
-<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"
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-CELLPADDING="0"
-CELLSPACING="0"
-><TR
-><TD
-WIDTH="33%"
-ALIGN="left"
-VALIGN="top"
->&nbsp;</TD
-><TD
-WIDTH="34%"
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-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
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/BCUT.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/BasicGroups.html b/java/docs/feature/BasicGroups.html
deleted file mode 100644
index 581d187..0000000
--- a/java/docs/feature/BasicGroups.html
+++ /dev/null
@@ -1,93 +0,0 @@
-<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"
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-><DIV
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-><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
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/BondInAromaticSystem.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/BondInRing.html b/java/docs/feature/BondInRing.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/BondInRing.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/BondIsAmide.html b/java/docs/feature/BondIsAmide.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/BondIsAmide.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/BondIsCarbonyl.html b/java/docs/feature/BondIsCarbonyl.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/BondIsCarbonyl.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/BondIsClosure.html b/java/docs/feature/BondIsClosure.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/BondIsClosure.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/BondIsEster.html b/java/docs/feature/BondIsEster.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/BondIsEster.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/BondIsPrimaryAmide.html b/java/docs/feature/BondIsPrimaryAmide.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/BondIsPrimaryAmide.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/BondIsRotor.html b/java/docs/feature/BondIsRotor.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/BondIsRotor.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/BondKekuleType.html b/java/docs/feature/BondKekuleType.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/BondKekuleType.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/BurdenEigenvalues.html b/java/docs/feature/BurdenEigenvalues.html
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/BurdenEigenvalues.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/BurdenModifiedEigenvalues.html b/java/docs/feature/BurdenModifiedEigenvalues.html
deleted file mode 100644
index dc6a83b..0000000
--- a/java/docs/feature/BurdenModifiedEigenvalues.html
+++ /dev/null
@@ -1,96 +0,0 @@
-<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
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/CompressedFeatureMatrix.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/ConjElectroTopolState.html b/java/docs/feature/ConjElectroTopolState.html
deleted file mode 100644
index bc0369e..0000000
--- a/java/docs/feature/ConjElectroTopolState.html
+++ /dev/null
@@ -1,173 +0,0 @@
-<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
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->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
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-><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
-> ()
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-></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%"
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-VALIGN="top"
->&nbsp;</TD
-><TD
-WIDTH="33%"
-ALIGN="right"
-VALIGN="top"
-><A
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-ACCESSKEY="N"
->Next</A
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-></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
deleted file mode 100644
index 6deea0d..0000000
--- a/java/docs/feature/ConjugatedTopologicalDistance.html
+++ /dev/null
@@ -1,117 +0,0 @@
-<HTML
-><HEAD
-><TITLE
-></TITLE
-><META
-NAME="GENERATOR"
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-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
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/DistanceDistanceMatrix.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/DistanceMatrix.html b/java/docs/feature/DistanceMatrix.html
deleted file mode 100644
index ecd0533..0000000
--- a/java/docs/feature/DistanceMatrix.html
+++ /dev/null
@@ -1,111 +0,0 @@
-<HTML
-><HEAD
-><TITLE
-></TITLE
-><META
-NAME="GENERATOR"
-CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
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-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 )
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-<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
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/Dummy.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/ElectrogeometricalState.html b/java/docs/feature/ElectrogeometricalState.html
deleted file mode 100644
index d25b39a..0000000
--- a/java/docs/feature/ElectrogeometricalState.html
+++ /dev/null
@@ -1,139 +0,0 @@
-<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
deleted file mode 100644
index 6de0bf2..0000000
--- a/java/docs/feature/ElectrotopologicalState.html
+++ /dev/null
@@ -1,139 +0,0 @@
-<HTML
-><HEAD
-><TITLE
-></TITLE
-><META
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-REL="NEXT"
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-HREF="bibliography.html"></HEAD
-><BODY
-CLASS="ARTICLE"
-BGCOLOR="#FFFFFF"
-TEXT="#000000"
-LINK="#0000FF"
-VLINK="#840084"
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-><DIV
-CLASS="SECT1"
-><H1
-CLASS="SECT1"
-><A
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->Descriptor</H1
-><DIV
-CLASS="SECT2"
-><H2
-CLASS="SECT2"
-><A
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-></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
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-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
deleted file mode 100644
index a34080c..0000000
--- a/java/docs/feature/FractionRotatableBonds.html
+++ /dev/null
@@ -1,93 +0,0 @@
-<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"
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-><DIV
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-><H1
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-><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%"
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-CELLPADDING="0"
-CELLSPACING="0"
-><TR
-><TD
-WIDTH="33%"
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->&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"
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->&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
deleted file mode 100644
index ff8cc05..0000000
--- a/java/docs/feature/GeomDistanceMatrix.html
+++ /dev/null
@@ -1,93 +0,0 @@
-<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
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-></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"
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-CELLSPACING="0"
-><TR
-><TD
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->&nbsp;</TD
-><TD
-WIDTH="34%"
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-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
deleted file mode 100644
index 242edc6..0000000
--- a/java/docs/feature/GeometricalDiameter.html
+++ /dev/null
@@ -1,93 +0,0 @@
-<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"
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-><DIV
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-><DIV
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-><H1
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-><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
deleted file mode 100644
index 76a2596..0000000
--- a/java/docs/feature/GeometricalRadius.html
+++ /dev/null
@@ -1,93 +0,0 @@
-<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
deleted file mode 100644
index e1401be..0000000
--- a/java/docs/feature/GeometricalShapeCoefficient.html
+++ /dev/null
@@ -1,93 +0,0 @@
-<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"
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->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
deleted file mode 100644
index 63e2715..0000000
--- a/java/docs/feature/GlobalTopologicalChargeIndex.html
+++ /dev/null
@@ -1,96 +0,0 @@
-<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"
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-><H1
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-><A
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-></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"
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-><TR
-><TD
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-VALIGN="top"
->&nbsp;</TD
-><TD
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->&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
deleted file mode 100644
index a192e96..0000000
--- a/java/docs/feature/GraphPotentials.html
+++ /dev/null
@@ -1,131 +0,0 @@
-<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"
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-><DIV
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-><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
deleted file mode 100644
index 735e913..0000000
--- a/java/docs/feature/GraphShapeCoefficient.html
+++ /dev/null
@@ -1,93 +0,0 @@
-<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"
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-><DIV
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-><H1
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->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"
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-><TR
-><TD
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-VALIGN="top"
->&nbsp;</TD
-><TD
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->&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
deleted file mode 100644
index 6dcb012..0000000
--- a/java/docs/feature/HBA1.html
+++ /dev/null
@@ -1,94 +0,0 @@
-<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"
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-><DIV
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-><H1
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->Descriptor</H1
-><DIV
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-><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]);!$([Nv5,Pv5,Sv4,Sv6])].</P
-></DIV
-></DIV
-></DIV
-><DIV
-CLASS="NAVFOOTER"
-><HR
-ALIGN="LEFT"
-WIDTH="100%"><TABLE
-SUMMARY="Footer navigation table"
-WIDTH="100%"
-BORDER="0"
-CELLPADDING="0"
-CELLSPACING="0"
-><TR
-><TD
-WIDTH="33%"
-ALIGN="left"
-VALIGN="top"
->&nbsp;</TD
-><TD
-WIDTH="34%"
-ALIGN="center"
-VALIGN="top"
->&nbsp;</TD
-><TD
-WIDTH="33%"
-ALIGN="right"
-VALIGN="top"
-><A
-HREF="bibliography.html"
-ACCESSKEY="N"
->Next</A
-></TD
-></TR
-><TR
-><TD
-WIDTH="33%"
-ALIGN="left"
-VALIGN="top"
->&nbsp;</TD
-><TD
-WIDTH="34%"
-ALIGN="center"
-VALIGN="top"
->&nbsp;</TD
-><TD
-WIDTH="33%"
-ALIGN="right"
-VALIGN="top"
->Bibliography</TD
-></TR
-></TABLE
-></DIV
-></BODY
-></HTML
-> \ No newline at end of file
diff --git a/java/docs/feature/HBA2.html b/java/docs/feature/HBA2.html
deleted file mode 100644
index 4ad7747..0000000
--- a/java/docs/feature/HBA2.html
+++ /dev/null
@@ -1,94 +0,0 @@
-<HTML
-><HEAD
-><TITLE
-></TITLE
-><META
-NAME="GENERATOR"
-CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
-REL="NEXT"
-TITLE="Bibliography"
-HREF="bibliography.html"></HEAD
-><BODY
-CLASS="ARTICLE"
-BGCOLOR="#FFFFFF"
-TEXT="#000000"
-LINK="#0000FF"
-VLINK="#840084"
-ALINK="#0000FF"
-><DIV
-CLASS="ARTICLE"
-><DIV
-CLASS="SECT1"
-><H1
-CLASS="SECT1"
-><A
-NAME="JOELIB.DESCRIPTOR"
-></A
->Descriptor</H1
-><DIV
-CLASS="SECT2"
-><H2
-CLASS="SECT2"
-><A
-NAME="JOELIB.DESCRIPTORS.HBA2"
-></A
->Number of Hydrogen Bond Acceptors (HBA) 2</H2
-><P
->Number of Hydrogen Bond Acceptors (HBA) 2.
-The default SMARTS pattern is: [$([$([#8,#16]);!$(*=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
deleted file mode 100644
index 58922cf..0000000
--- a/java/docs/feature/HBD1.html
+++ /dev/null
@@ -1,93 +0,0 @@
-<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
deleted file mode 100644
index a66a20f..0000000
--- a/java/docs/feature/HBD2.html
+++ /dev/null
@@ -1,94 +0,0 @@
-<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
deleted file mode 100644
index c460fba..0000000
--- a/java/docs/feature/HeavyBonds.html
+++ /dev/null
@@ -1,93 +0,0 @@
-<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
deleted file mode 100644
index d1e124f..0000000
--- a/java/docs/feature/HeteroCycles.html
+++ /dev/null
@@ -1,93 +0,0 @@
-<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
deleted file mode 100644
index 020d78c..0000000
--- a/java/docs/feature/HydrophobicGroups.html
+++ /dev/null
@@ -1,93 +0,0 @@
-<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
deleted file mode 100644
index 82c8c76..0000000
--- a/java/docs/feature/IntrinsicState.html
+++ /dev/null
@@ -1,145 +0,0 @@
-<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
deleted file mode 100644
index 9690413..0000000
--- a/java/docs/feature/KierShape1.html
+++ /dev/null
@@ -1,176 +0,0 @@
-<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
deleted file mode 100644
index d3117b2..0000000
--- a/java/docs/feature/KierShape2.html
+++ /dev/null
@@ -1,131 +0,0 @@
-<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
deleted file mode 100644
index 7b760b5..0000000
--- a/java/docs/feature/KierShape3.html
+++ /dev/null
@@ -1,131 +0,0 @@
-<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
deleted file mode 100644
index 914533b..0000000
--- a/java/docs/feature/LogP.html
+++ /dev/null
@@ -1,96 +0,0 @@
-<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
deleted file mode 100644
index 88757de..0000000
--- a/java/docs/feature/MolarRefractivity.html
+++ /dev/null
@@ -1,96 +0,0 @@
-<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
deleted file mode 100644
index e463e1c..0000000
--- a/java/docs/feature/MolecularWeight.html
+++ /dev/null
@@ -1,93 +0,0 @@
-<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
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/MoleculeHashcode.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/NO2Groups.html b/java/docs/feature/NO2Groups.html
deleted file mode 100644
index 6fa91d4..0000000
--- a/java/docs/feature/NO2Groups.html
+++ /dev/null
@@ -1,97 +0,0 @@
-<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
deleted file mode 100644
index f79063f..0000000
--- a/java/docs/feature/NumberOfAtoms.html
+++ /dev/null
@@ -1,93 +0,0 @@
-<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
deleted file mode 100644
index fd7e2e4..0000000
--- a/java/docs/feature/NumberOfB.html
+++ /dev/null
@@ -1,93 +0,0 @@
-<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
deleted file mode 100644
index 22dfb7e..0000000
--- a/java/docs/feature/NumberOfBonds.html
+++ /dev/null
@@ -1,93 +0,0 @@
-<HTML
-><HEAD
-><TITLE
-></TITLE
-><META
-NAME="GENERATOR"
-CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
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-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
deleted file mode 100644
index 5807bb9..0000000
--- a/java/docs/feature/NumberOfBr.html
+++ /dev/null
@@ -1,93 +0,0 @@
-<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
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-></DIV
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-> \ No newline at end of file
diff --git a/java/docs/feature/NumberOfC.html b/java/docs/feature/NumberOfC.html
deleted file mode 100644
index a1b224e..0000000
--- a/java/docs/feature/NumberOfC.html
+++ /dev/null
@@ -1,93 +0,0 @@
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-> \ No newline at end of file
diff --git a/java/docs/feature/NumberOfCl.html b/java/docs/feature/NumberOfCl.html
deleted file mode 100644
index 04892d5..0000000
--- a/java/docs/feature/NumberOfCl.html
+++ /dev/null
@@ -1,93 +0,0 @@
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->Number of chlorine atoms.</P
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-></BODY
-></HTML
-> \ No newline at end of file
diff --git a/java/docs/feature/NumberOfF.html b/java/docs/feature/NumberOfF.html
deleted file mode 100644
index c12b2f5..0000000
--- a/java/docs/feature/NumberOfF.html
+++ /dev/null
@@ -1,93 +0,0 @@
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->Number of fluorine atoms</H2
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->Number of fluorine atoms.</P
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->Bibliography</TD
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-></BODY
-></HTML
-> \ No newline at end of file
diff --git a/java/docs/feature/NumberOfHal.html b/java/docs/feature/NumberOfHal.html
deleted file mode 100644
index 11df356..0000000
--- a/java/docs/feature/NumberOfHal.html
+++ /dev/null
@@ -1,93 +0,0 @@
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-HREF="bibliography.html"></HEAD
-><BODY
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->Number of halogen atoms</H2
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->Number of halogen atoms.</P
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->Bibliography</TD
-></TR
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-></DIV
-></BODY
-></HTML
-> \ No newline at end of file
diff --git a/java/docs/feature/NumberOfI.html b/java/docs/feature/NumberOfI.html
deleted file mode 100644
index 0580e12..0000000
--- a/java/docs/feature/NumberOfI.html
+++ /dev/null
@@ -1,93 +0,0 @@
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-HREF="bibliography.html"></HEAD
-><BODY
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->Number of iodine atoms</H2
-><P
->Number of iodine atoms.</P
-></DIV
-></DIV
-></DIV
-><DIV
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-><HR
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-><A
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->Next</A
-></TD
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-><TR
-><TD
-WIDTH="33%"
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->&nbsp;</TD
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->&nbsp;</TD
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->Bibliography</TD
-></TR
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-></DIV
-></BODY
-></HTML
-> \ No newline at end of file
diff --git a/java/docs/feature/NumberOfN.html b/java/docs/feature/NumberOfN.html
deleted file mode 100644
index bd65ada..0000000
--- a/java/docs/feature/NumberOfN.html
+++ /dev/null
@@ -1,93 +0,0 @@
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-><HEAD
-><TITLE
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-><META
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-HREF="bibliography.html"></HEAD
-><BODY
-CLASS="ARTICLE"
-BGCOLOR="#FFFFFF"
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-><DIV
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->Number of nitrogen atoms</H2
-><P
->Number of nitrogen atoms.</P
-></DIV
-></DIV
-></DIV
-><DIV
-CLASS="NAVFOOTER"
-><HR
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-><TR
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-><TR
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->Bibliography</TD
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-></BODY
-></HTML
-> \ No newline at end of file
diff --git a/java/docs/feature/NumberOfO.html b/java/docs/feature/NumberOfO.html
deleted file mode 100644
index 7ecbe0a..0000000
--- a/java/docs/feature/NumberOfO.html
+++ /dev/null
@@ -1,93 +0,0 @@
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-HREF="bibliography.html"></HEAD
-><BODY
-CLASS="ARTICLE"
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->Number of oxygen atoms</H2
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->Number of oxygen atoms.</P
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-><TR
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->Bibliography</TD
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-></BODY
-></HTML
-> \ No newline at end of file
diff --git a/java/docs/feature/NumberOfP.html b/java/docs/feature/NumberOfP.html
deleted file mode 100644
index 3669e91..0000000
--- a/java/docs/feature/NumberOfP.html
+++ /dev/null
@@ -1,93 +0,0 @@
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-><BODY
-CLASS="ARTICLE"
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->Number of phosphorus atoms</H2
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->Number of phosphorus atoms.</P
-></DIV
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-></DIV
-><DIV
-CLASS="NAVFOOTER"
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-><TR
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-></HTML
-> \ No newline at end of file
diff --git a/java/docs/feature/NumberOfS.html b/java/docs/feature/NumberOfS.html
deleted file mode 100644
index b735ee5..0000000
--- a/java/docs/feature/NumberOfS.html
+++ /dev/null
@@ -1,93 +0,0 @@
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-><BODY
-CLASS="ARTICLE"
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->Number of sulfur atoms</H2
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->Number of sulfur atoms.</P
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-><DIV
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-></HTML
-> \ No newline at end of file
diff --git a/java/docs/feature/OSOGroups.html b/java/docs/feature/OSOGroups.html
deleted file mode 100644
index ca49ebf..0000000
--- a/java/docs/feature/OSOGroups.html
+++ /dev/null
@@ -1,93 +0,0 @@
-<HTML
-><HEAD
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-><META
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-><BODY
-CLASS="ARTICLE"
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->Number of -OSO atoms</H2
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->Number of -OSO atoms.</P
-></DIV
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->Bibliography</TD
-></TR
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-></HTML
-> \ No newline at end of file
diff --git a/java/docs/feature/PolarSurfaceArea.html b/java/docs/feature/PolarSurfaceArea.html
deleted file mode 100644
index 357056f..0000000
--- a/java/docs/feature/PolarSurfaceArea.html
+++ /dev/null
@@ -1,96 +0,0 @@
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-><BODY
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->Polar surface area (PSA)</H2
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->Polar surface area (PSA) [<A
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->ers00</A
->].</P
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-><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
deleted file mode 100644
index 09d9600..0000000
--- a/java/docs/feature/RadialDistributionFunction.html
+++ /dev/null
@@ -1,230 +0,0 @@
-<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"
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->&nbsp;</TD
-><TD
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-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
deleted file mode 100644
index 42ef0d9..0000000
--- a/java/docs/feature/RotatableBonds.html
+++ /dev/null
@@ -1,94 +0,0 @@
-<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
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/SMILESMolecule.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/SO2Groups.html b/java/docs/feature/SO2Groups.html
deleted file mode 100644
index e4cd9a7..0000000
--- a/java/docs/feature/SO2Groups.html
+++ /dev/null
@@ -1,97 +0,0 @@
-<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
deleted file mode 100644
index fd3e45a..0000000
--- a/java/docs/feature/SOGroups.html
+++ /dev/null
@@ -1,93 +0,0 @@
-<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"
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->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
deleted file mode 100644
index fad741d..0000000
--- a/java/docs/feature/SSKey3DS.html
+++ /dev/null
@@ -1,779 +0,0 @@
-<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%"
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->&nbsp;</TD
-><TD
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-ALIGN="right"
-VALIGN="top"
->Bibliography</TD
-></TR
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-></DIV
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-> \ No newline at end of file
diff --git a/java/docs/feature/TopologicalAtomPair.html b/java/docs/feature/TopologicalAtomPair.html
deleted file mode 100644
index 32731b0..0000000
--- a/java/docs/feature/TopologicalAtomPair.html
+++ /dev/null
@@ -1,93 +0,0 @@
-<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"
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-LINK="#0000FF"
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-><H1
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-><A
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->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"
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-BORDER="0"
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-><TR
-><TD
-WIDTH="33%"
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->&nbsp;</TD
-><TD
-WIDTH="34%"
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->&nbsp;</TD
-><TD
-WIDTH="33%"
-ALIGN="right"
-VALIGN="top"
-><A
-HREF="bibliography.html"
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->Next</A
-></TD
-></TR
-><TR
-><TD
-WIDTH="33%"
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-VALIGN="top"
->&nbsp;</TD
-><TD
-WIDTH="34%"
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->&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
deleted file mode 100644
index 660bbb6..0000000
--- a/java/docs/feature/TopologicalDiameter.html
+++ /dev/null
@@ -1,93 +0,0 @@
-<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"
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-><DIV
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-><DIV
-CLASS="SECT1"
-><H1
-CLASS="SECT1"
-><A
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-></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"
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->&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
deleted file mode 100644
index 07299fa..0000000
--- a/java/docs/feature/TopologicalRadius.html
+++ /dev/null
@@ -1,93 +0,0 @@
-<HTML
-><HEAD
-><TITLE
-></TITLE
-><META
-NAME="GENERATOR"
-CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
-REL="NEXT"
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-HREF="bibliography.html"></HEAD
-><BODY
-CLASS="ARTICLE"
-BGCOLOR="#FFFFFF"
-TEXT="#000000"
-LINK="#0000FF"
-VLINK="#840084"
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-><DIV
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-><H1
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->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
deleted file mode 100644
index 0d10a46..0000000
--- a/java/docs/feature/WeightedBurdenEigenvalues.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML>
-Dummy
-</HTML> \ No newline at end of file
diff --git a/java/docs/feature/WeightedBurdenModifiedEigenvalues.html b/java/docs/feature/WeightedBurdenModifiedEigenvalues.html
deleted file mode 100644
index 0e93938..0000000
--- a/java/docs/feature/WeightedBurdenModifiedEigenvalues.html
+++ /dev/null
@@ -1,93 +0,0 @@
-<HTML
-><HEAD
-><TITLE
-></TITLE
-><META
-NAME="GENERATOR"
-CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
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-HREF="bibliography.html"></HEAD
-><BODY
-CLASS="ARTICLE"
-BGCOLOR="#FFFFFF"
-TEXT="#000000"
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-><H1
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-><A
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-></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
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-><TR
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->&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%"
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->&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
deleted file mode 100644
index 130990f..0000000
--- a/java/docs/feature/ZagrebIndex1.html
+++ /dev/null
@@ -1,123 +0,0 @@
-<HTML
-><HEAD
-><TITLE
-></TITLE
-><META
-NAME="GENERATOR"
-CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
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-HREF="bibliography.html"></HEAD
-><BODY
-CLASS="ARTICLE"
-BGCOLOR="#FFFFFF"
-TEXT="#000000"
-LINK="#0000FF"
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-><DIV
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-><H1
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-><A
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-><DIV
-CLASS="SECT2"
-><H2
-CLASS="SECT2"
-><A
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-></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
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-WIDTH="100%"><TABLE
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-BORDER="0"
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->&nbsp;</TD
-><TD
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->Next</A
-></TD
-></TR
-><TR
-><TD
-WIDTH="33%"
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->&nbsp;</TD
-><TD
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->Bibliography</TD
-></TR
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-></HTML
-> \ No newline at end of file
diff --git a/java/docs/feature/ZagrebIndex2.html b/java/docs/feature/ZagrebIndex2.html
deleted file mode 100644
index 735a797..0000000
--- a/java/docs/feature/ZagrebIndex2.html
+++ /dev/null
@@ -1,143 +0,0 @@
-<HTML
-><HEAD
-><TITLE
-></TITLE
-><META
-NAME="GENERATOR"
-CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
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-HREF="bibliography.html"></HEAD
-><BODY
-CLASS="ARTICLE"
-BGCOLOR="#FFFFFF"
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->Zagreb index 2</H2
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->Zagreb index 2 [<A
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->tc00</A
->].</P
-><DIV
-CLASS="EQUATION"
-><A
-NAME="AEN8"
-></A
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-><B
->Equation 1. Zagreb index 2</B
-></P
-><DIV
-CLASS="MEDIAOBJECT"
-><P
-><IMG
-SRC="formulas/zagreb2.gif"
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-></DIV
-></DIV
-><P
->where <SPAN
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-><B
-CLASS="EMPHASIS"
->b</B
-></SPAN
-> are all bonds of the hydrogen depleted graph and
-<IMG
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-<SPAN
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-><B
-CLASS="EMPHASIS"
->i</B
-></SPAN
-> and <SPAN
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-></SPAN
-> are the atom indices
-of the atoms connected to the bond <SPAN
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-><B
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->b</B
-></SPAN
->.</P
-></DIV
-></DIV
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->&nbsp;</TD
-><TD
-WIDTH="34%"
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->&nbsp;</TD
-><TD
-WIDTH="33%"
-ALIGN="right"
-VALIGN="top"
-><A
-HREF="bibliography.html"
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->Next</A
-></TD
-></TR
-><TR
-><TD
-WIDTH="33%"
-ALIGN="left"
-VALIGN="top"
->&nbsp;</TD
-><TD
-WIDTH="34%"
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->&nbsp;</TD
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-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/bibliography.html b/java/docs/feature/bibliography.html
deleted file mode 100644
index 0770682..0000000
--- a/java/docs/feature/bibliography.html
+++ /dev/null
@@ -1,911 +0,0 @@
-<HTML
-><HEAD
-><TITLE
->Bibliography</TITLE
-><META
-NAME="GENERATOR"
-CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
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-HREF="bibliography.html"></HEAD
-><BODY
-CLASS="BIBLIOGRAPHY"
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-></TR
-><TR
-><TD
-WIDTH="10%"
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-><A
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->Prev</A
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-></TD
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-WIDTH="10%"
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-></TABLE
-><HR
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diff --git a/java/jmat/function/DoubleFunctionExpression.class b/java/jmat/function/DoubleFunctionExpression.class
deleted file mode 100644
index 121e787..0000000
--- a/java/jmat/function/DoubleFunctionExpression.class
+++ /dev/null
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diff --git a/java/jmat/function/DoubleFunctionInterpolation.class b/java/jmat/function/DoubleFunctionInterpolation.class
deleted file mode 100644
index bc9e36d..0000000
--- a/java/jmat/function/DoubleFunctionInterpolation.class
+++ /dev/null
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diff --git a/java/jmat/function/InvokeDoubleFunction.class b/java/jmat/function/InvokeDoubleFunction.class
deleted file mode 100644
index 9b3a797..0000000
--- a/java/jmat/function/InvokeDoubleFunction.class
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diff --git a/java/jmat/function/InvokeMatrixFunction.class b/java/jmat/function/InvokeMatrixFunction.class
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diff --git a/java/jmat/function/MatrixFunction.class b/java/jmat/function/MatrixFunction.class
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+++ /dev/null
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diff --git a/java/jmat/function/MatrixFunctionExpression.class b/java/jmat/function/MatrixFunctionExpression.class
deleted file mode 100644
index 06a637c..0000000
--- a/java/jmat/function/MatrixFunctionExpression.class
+++ /dev/null
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diff --git a/java/jmat/function/TestDoubleFunction.class b/java/jmat/function/TestDoubleFunction.class
deleted file mode 100644
index ea4532a..0000000
--- a/java/jmat/function/TestDoubleFunction.class
+++ /dev/null
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diff --git a/java/jmat/function/TestDoubleFunctionExpression.class b/java/jmat/function/TestDoubleFunctionExpression.class
deleted file mode 100644
index ef9321f..0000000
--- a/java/jmat/function/TestDoubleFunctionExpression.class
+++ /dev/null
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diff --git a/java/jmat/function/expressionParser/Evaluator$Node.class b/java/jmat/function/expressionParser/Evaluator$Node.class
deleted file mode 100644
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--- a/java/jmat/function/expressionParser/Evaluator$Node.class
+++ /dev/null
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diff --git a/java/jmat/function/expressionParser/Evaluator$Operator.class b/java/jmat/function/expressionParser/Evaluator$Operator.class
deleted file mode 100644
index 5d0fe8b..0000000
--- a/java/jmat/function/expressionParser/Evaluator$Operator.class
+++ /dev/null
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diff --git a/java/jmat/function/expressionParser/Evaluator.class b/java/jmat/function/expressionParser/Evaluator.class
deleted file mode 100644
index bb9264d..0000000
--- a/java/jmat/function/expressionParser/Evaluator.class
+++ /dev/null
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diff --git a/java/jmat/io/data/MatrixFile.class b/java/jmat/io/data/MatrixFile.class
deleted file mode 100644
index a0f6161..0000000
--- a/java/jmat/io/data/MatrixFile.class
+++ /dev/null
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diff --git a/java/jmat/io/data/MatrixMMLFile.class b/java/jmat/io/data/MatrixMMLFile.class
deleted file mode 100644
index 1e1fb42..0000000
--- a/java/jmat/io/data/MatrixMMLFile.class
+++ /dev/null
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diff --git a/java/jmat/io/data/TextFile.class b/java/jmat/io/data/TextFile.class
deleted file mode 100644
index 634ed7f..0000000
--- a/java/jmat/io/data/TextFile.class
+++ /dev/null
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diff --git a/java/jmat/io/data/fileTools/CharFile.class b/java/jmat/io/data/fileTools/CharFile.class
deleted file mode 100644
index 9f12755..0000000
--- a/java/jmat/io/data/fileTools/CharFile.class
+++ /dev/null
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diff --git a/java/jmat/io/data/fileTools/MatrixMML.class b/java/jmat/io/data/fileTools/MatrixMML.class
deleted file mode 100644
index 061439d..0000000
--- a/java/jmat/io/data/fileTools/MatrixMML.class
+++ /dev/null
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diff --git a/java/jmat/io/data/fileTools/MatrixString.class b/java/jmat/io/data/fileTools/MatrixString.class
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diff --git a/java/jmat/io/data/fileTools/TextString.class b/java/jmat/io/data/fileTools/TextString.class
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--- a/java/jmat/io/data/fileTools/TextString.class
+++ /dev/null
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diff --git a/java/jmat/io/data/fileTools/XMLFile.class b/java/jmat/io/data/fileTools/XMLFile.class
deleted file mode 100644
index 9a44203..0000000
--- a/java/jmat/io/data/fileTools/XMLFile.class
+++ /dev/null
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diff --git a/java/jmat/io/gui/FrameView.class b/java/jmat/io/gui/FrameView.class
deleted file mode 100644
index ab5196e..0000000
--- a/java/jmat/io/gui/FrameView.class
+++ /dev/null
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diff --git a/java/jmat/io/gui/FunctionPlot2D.class b/java/jmat/io/gui/FunctionPlot2D.class
deleted file mode 100644
index 6cd4805..0000000
--- a/java/jmat/io/gui/FunctionPlot2D.class
+++ /dev/null
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diff --git a/java/jmat/io/gui/FunctionPlot3D.class b/java/jmat/io/gui/FunctionPlot3D.class
deleted file mode 100644
index b5e77bd..0000000
--- a/java/jmat/io/gui/FunctionPlot3D.class
+++ /dev/null
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diff --git a/java/jmat/io/gui/MatrixHist2D.class b/java/jmat/io/gui/MatrixHist2D.class
deleted file mode 100644
index de5a68b..0000000
--- a/java/jmat/io/gui/MatrixHist2D.class
+++ /dev/null
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diff --git a/java/jmat/io/gui/MatrixHist3D.class b/java/jmat/io/gui/MatrixHist3D.class
deleted file mode 100644
index 287a081..0000000
--- a/java/jmat/io/gui/MatrixHist3D.class
+++ /dev/null
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diff --git a/java/jmat/io/gui/MatrixPlot2D.class b/java/jmat/io/gui/MatrixPlot2D.class
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--- a/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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--- a/java/jmat/io/gui/MatrixPlot3D.class
+++ /dev/null
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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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--- a/java/jmat/io/gui/MatrixTable$DoubleModel.class
+++ /dev/null
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diff --git a/java/jmat/io/gui/MatrixTable.class b/java/jmat/io/gui/MatrixTable.class
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--- a/java/jmat/io/gui/MatrixTable.class
+++ /dev/null
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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/Plot2D.class b/java/jmat/io/gui/Plot2D.class
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diff --git a/java/jmat/io/gui/Plot3D.class b/java/jmat/io/gui/Plot3D.class
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diff --git a/java/jmat/io/gui/Progress.class b/java/jmat/io/gui/Progress.class
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diff --git a/java/jmat/io/gui/TextWindow.class b/java/jmat/io/gui/TextWindow.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/Coordinates3D.class b/java/jmat/io/gui/plotTools/Coordinates3D.class
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--- a/java/jmat/io/gui/plotTools/Coordinates3D.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/DataPlot3D.class b/java/jmat/io/gui/plotTools/DataPlot3D.class
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diff --git a/java/jmat/io/gui/plotTools/Eye3D.class b/java/jmat/io/gui/plotTools/Eye3D.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/io/gui/plotTools/Grid3D.class b/java/jmat/io/gui/plotTools/Grid3D.class
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diff --git a/java/jmat/io/gui/plotTools/NotedPoint2D.class b/java/jmat/io/gui/plotTools/NotedPoint2D.class
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diff --git a/java/jmat/io/gui/plotTools/NotedPoint3D.class b/java/jmat/io/gui/plotTools/NotedPoint3D.class
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diff --git a/java/jmat/io/gui/plotTools/PlotAttributes.class b/java/jmat/io/gui/plotTools/PlotAttributes.class
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--- a/java/jmat/io/gui/plotTools/PlotAttributes.class
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diff --git a/java/jmat/test/Testjmat.class b/java/jmat/test/Testjmat.class
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--- a/java/jmat/test/Testjmat.class
+++ /dev/null
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diff --git a/java/joelib2.properties b/java/joelib2.properties
deleted file mode 100644
index fdad7ff..0000000
--- a/java/joelib2.properties
+++ /dev/null
@@ -1,502 +0,0 @@
-##############################################################################
-##############################################################################
-##############################################################################
-#
-# 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
-joelib2.gui.render2D.Renderer2DModel.drawCarbonAtoms=false
-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
-
-joelib2.gui.render2D.Renderer2DModel.foreground.color.r=0
-joelib2.gui.render2D.Renderer2DModel.foreground.color.g=0
-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
-joelib2.gui.render2D.Renderer2DModel.arrow.color.g=255
-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
-##############################################################################
-joelib2.filter.1.name =NOTFilter
-joelib2.filter.1.representation =joelib2.process.filter.NOTFilter
-joelib2.filter.1.descriptionFile =docs/process/notFilter
-joelib2.filter.2.name =ORFilter
-joelib2.filter.2.representation =joelib2.process.filter.ORFilter
-joelib2.filter.2.descriptionFile =docs/process/orFilter
-joelib2.filter.3.name =ANDFilter
-joelib2.filter.3.representation =joelib2.process.filter.ANDFilter
-joelib2.filter.3.descriptionFile =docs/process/andFilter
-joelib2.filter.4.name =HasDataFilter
-joelib2.filter.4.representation =joelib2.process.filter.HasDataFilter
-joelib2.filter.4.descriptionFile =docs/process/hasDataFilter
-joelib2.filter.5.name =DescriptorFilter
-joelib2.filter.5.representation =joelib2.process.filter.DescriptorFilter
-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
deleted file mode 100644
index c579574..0000000
--- a/java/joelib2/algo/APropertyBFS.class
+++ /dev/null
Binary files differ
diff --git a/java/joelib2/algo/BFS.class b/java/joelib2/algo/BFS.class
deleted file mode 100644
index ba1faf0..0000000
--- a/java/joelib2/algo/BFS.class
+++ /dev/null
Binary files differ
diff --git a/java/joelib2/algo/BFSResult.class b/java/joelib2/algo/BFSResult.class
deleted file mode 100644
index 5b0ae2f..0000000
--- a/java/joelib2/algo/BFSResult.class
+++ /dev/null
Binary files differ
diff --git a/java/joelib2/algo/DFS.class b/java/joelib2/algo/DFS.class
deleted file mode 100644
index 2eb3ef6..0000000
--- a/java/joelib2/algo/DFS.class
+++ /dev/null
Binary files differ
diff --git a/java/joelib2/algo/DFSResult.class b/java/joelib2/algo/DFSResult.class
deleted file mode 100644
index a70c41a..0000000
--- a/java/joelib2/algo/DFSResult.class
+++ /dev/null
Binary files differ
diff --git a/java/joelib2/algo/clique/BronKerbosch.class b/java/joelib2/algo/clique/BronKerbosch.class
deleted file mode 100644
index 94ca8ec..0000000
--- a/java/joelib2/algo/clique/BronKerbosch.class
+++ /dev/null
Binary files differ
diff --git a/java/joelib2/algo/clique/CliqueFinder.class b/java/joelib2/algo/clique/CliqueFinder.class
deleted file mode 100644
index afae197..0000000
--- a/java/joelib2/algo/clique/CliqueFinder.class
+++ /dev/null
Binary files differ
diff --git a/java/joelib2/algo/clique/DFMax.class b/java/joelib2/algo/clique/DFMax.class
deleted file mode 100644
index a17b5f0..0000000
--- a/java/joelib2/algo/clique/DFMax.class
+++ /dev/null
Binary files differ
diff --git a/java/joelib2/algo/clique/SHIAComparator.class b/java/joelib2/algo/clique/SHIAComparator.class
deleted file mode 100644
index 94b03c8..0000000
--- a/java/joelib2/algo/clique/SHIAComparator.class
+++ /dev/null
Binary files differ
diff --git a/java/joelib2/algo/clique/Set.class b/java/joelib2/algo/clique/Set.class
deleted file mode 100644
index f8234f9..0000000
--- a/java/joelib2/algo/clique/Set.class
+++ /dev/null
Binary files differ
diff --git a/java/joelib2/algo/contribution/BasicGroupContributions.class b/java/joelib2/algo/contribution/BasicGroupContributions.class
deleted file mode 100644
index fe247f4..0000000
--- a/java/joelib2/algo/contribution/BasicGroupContributions.class
+++ /dev/null
Binary files differ
diff --git a/java/joelib2/algo/contribution/GroupContributionPredictor.class b/java/joelib2/algo/contribution/GroupContributionPredictor.class
deleted file mode 100644
index 0a67402..0000000
--- a/java/joelib2/algo/contribution/GroupContributionPredictor.class
+++ /dev/null
Binary files differ
diff --git a/java/joelib2/algo/contribution/GroupContributions.class b/java/joelib2/algo/contribution/GroupContributions.class
deleted file mode 100644
index 49f32af..0000000
--- a/java/joelib2/algo/contribution/GroupContributions.class
+++ /dev/null
Binary files differ
diff --git a/java/joelib2/algo/datamining/weka/APWekaHelper.class b/java/joelib2/algo/datamining/weka/APWekaHelper.class
deleted file mode 100644
index 55c4f4d..0000000
--- a/java/joelib2/algo/datamining/weka/APWekaHelper.class
+++ /dev/null
Binary files differ
diff --git a/java/joelib2/algo/datamining/weka/InstancesHelper.class b/java/joelib2/algo/datamining/weka/InstancesHelper.class
deleted file mode 100644
index 8eed4d0..0000000
--- a/java/joelib2/algo/datamining/weka/InstancesHelper.class
+++ /dev/null
Binary files differ
diff --git a/java/joelib2/algo/datamining/weka/MolInstance.class b/java/joelib2/algo/datamining/weka/MolInstance.class
deleted file mode 100644
index 3f3ef28..0000000
--- a/java/joelib2/algo/datamining/weka/MolInstance.class
+++ /dev/null
Binary files differ
diff --git a/java/joelib2/algo/datamining/weka/MolInstances.class b/java/joelib2/algo/datamining/weka/MolInstances.class
deleted file mode 100644
index b56a0dd..0000000
--- a/java/joelib2/algo/datamining/weka/MolInstances.class
+++ /dev/null
Binary files differ
diff --git a/java/joelib2/algo/datamining/weka/MolInstancesCache.class b/java/joelib2/algo/datamining/weka/MolInstancesCache.class
deleted file mode 100644
index 1ef0d25..0000000
--- a/java/joelib2/algo/datamining/weka/MolInstancesCache.class
+++ /dev/null
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diff --git a/java/joelib2/algo/datamining/weka/MolSparseInstance.class b/java/joelib2/algo/datamining/weka/MolSparseInstance.class
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diff --git a/java/joelib2/data/plain/LogP.contributions b/java/joelib2/data/plain/LogP.contributions
deleted file mode 100644
index 4f4ac68..0000000
--- a/java/joelib2/data/plain/LogP.contributions
+++ /dev/null
@@ -1,169 +0,0 @@
-VENDOR: http://joelib.sf.net
-RELEASE_VERSION: $Revision: 1.2 $
-RELEASE_DATE: $Date: 2005/01/07 07:18:15 $
-
-########################################################################
-# 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.
-########################################################################
-# LopP Atomic Contributions
-# ref. Wildman, S.A. and Crippen, G.M., J. Chem. Inf. Comput. Sci., 1999, 39, 868-873.
-# Table below is adapted from above ref. uncommon p- and d-block elements have not been included.
-########################################################################
-;hydrogen
-[*] 0.1125
-[#6] 0.123
-[#1] 0.123
-[O][CX4] -0.2677
-[O]c -0.2677
-[O][#5] -0.2677
-[O][#14] -0.2677
-[O][#15] -0.2677
-[O][#33] -0.2677
-[O][#50] -0.2677
-[#5] -0.2677
-[#14] -0.2677
-[#15] -0.2677
-[#16] -0.2677
-[#50] -0.2677
-[#7] 0.2142
-[O][#7] 0.2142
-[O]C=[#6] 0.298
-[O]C=[#7] 0.298
-[O]C=O 0.298
-[O]C=S 0.298
-[O]O 0.298
-[O]S 0.298
-;heavy
-[*] 0
-[#6] 0.0813
-[CH4] 0.1441
-[CH3]C 0.1441
-[CH2](C)C 0.1441
-[CH](C)(C)C 0
-[C](C)(C)(C)C 0
-[CH3][O,N,F,Cl,Br,#15,#16,#53;!a] -0.2035
-[CH2X4][O,N,F,Cl,Br,#15,#16,#53;!a] -0.2035
-[CHX4][O,N,F,Cl,Br,#15,#16,#53;!a] -0.2051
-[CH0X4][O,N,F,Cl,Br,#15,#16,#53;!a] -0.2051
-[C]=[A!#6] -0.2783
-[CH2]=C 0.1551
-[CH1](=C)A 0.1551
-[CH0](=C)(A)A 0.1551
-[C](=C)=C 0.1551
-[CX2]#A 0.0017
-[CH3]c 0.0845
-[CH3][a!#6] -0.1444
-[CH2X4]a -0.0516
-[CHX4]a 0.1193
-[CH0X4]a -0.0967
-[c][#5,#14,#15,#33,#34,#50,#80] -0.5443
-[c][#9] 0
-[c][#17] 0.245
-[c][#35] 0.198
-[c][#53] 0
-[cH] 0.1581
-[c](:a)(:a):a 0.2955
-[c](:a)(:a)-a 0.2713
-[c](:a)(:a)-C 0.136
-[c](:a)(:a)-N 0.4619
-[c](:a)(:a)-O 0.5437
-[c](:a)(:a)-S 0.1893
-[c](:a)(:a)=C -0.8186
-[c](:a)(:a)=N -0.8186
-[c](:a)(:a)=O -0.8186
-[C](=C)(a)A 0.264
-[C](=C)(c)a 0.264
-[CH](=C)a 0.264
-[C]=c 0.264
-[CX4][!#6;!#7;!#8;!#9;!#15;!#16;!#17;!#35;!#53] 0.2148
-[#7] -0.4806
-[NH2+0]A -1.019
-[NH+0](A)A -0.7096
-[NH2+0]a -1.027
-[NH+0](A)a -0.5188
-[NH+0](a)a -0.5188
-[NH+0]=A 0.0839
-[NH+0]=a 0.0839
-[N+0](=A)A 0.1836
-[N+0](=A)a 0.1836
-[N+0](=a)A 0.1836
-[N+0](=a)a 0.1836
-[N+0](A)(A)A -0.3187
-[N+0](a)(A)A -0.4458
-[N+0](a)(a)A -0.4458
-[N+0](a)(a)a -0.4458
-[N+0]#A 0.01508
-[NH3+*] -1.95
-[NH2+*] -1.95
-[NH+*] -1.95
-[n+0] -0.3239
-[n+*] -1.119
-[NH0+*](A)(A)(A)A -0.3396
-[NH0+*](=A)(A)A -0.3396
-[NH0+*](=A)(A)a -0.3396
-[NH0+*](=[#6])=[#7] -0.3396
-[N+*]#A 0.2887
-[N-*] 0.2887
-[N+*](=[N-*])=N 0.2887
-[#8] -0.1188
-[o] 0.1552
-[OH] -0.2893
-[OH2] -0.2893
-[O](C)C -0.0684
-[OH0](C)[A!#6] -0.0684
-[OH0]([A!#6])[A!#6] -0.0684
-[O](A)a -0.4195
-[O](a)a -0.4195
-[O]=[#8] 0.0335
-[O]=[#7] 0.0335
-[OX1-*][#7] 0.0335
-[OX1-*][#16] -0.3339
-[OX1-*][#15;#33;#43;#53] -1.189
-[O]=c 0.1788
-[O]=[CH]C -0.1526
-[O]=C(C)C -0.1526
-[O]=[CH0](C)[A;!6] -0.1526
-[O]=[CH]N -0.1526
-[O]=[CH]O -0.1526
-[O]=[CH2] -0.1526
-[O]=[CX2]=O -0.1526
-[O]=[CH]c 0.1129
-[O]=C(C)c 0.1129
-[O]=C(c)c 0.1129
-[O]=[CH0](c)[a!#6] 0.1129
-[O]=[CH0](c)[A!#6] 0.1129
-[O]=[CH0](C)[a!#6] 0.1129
-[O]=C([A!#6])[A!#6] 0.4833
-[O]=C([A!#6])[a!#6] 0.4833
-[O]=C([a!#6])[a!#6] 0.4833
-[O-1]C(=O) -1.326
-[#9-0] 0.4202
-[#17-0] 0.6895
-[#35-0] 0.8456
-[#53-0] 0.8857
-[#9-*] -2.996
-[#17-*] -2.996
-[#35-*] -2.996
-[#53-*] -2.996
-[#53+*] -2.996
-[#15] 0.8612
-[S-0] 0.6482
-[S-*] -0.0024
-[S+*] -0.0024
-[s] 0.6237
-[B,Si,Ga,Ge,As,Se,Sn,Te,Pb,Nc,Nr,Kr,Xe,Rn] -0.3808
-[Fe,Cu,Zn,Tc,Cd,Pt,Au,Hg] -0.0025 \ No newline at end of file
diff --git a/java/joelib2/data/plain/MR.contributions b/java/joelib2/data/plain/MR.contributions
deleted file mode 100644
index 45a47ff..0000000
--- a/java/joelib2/data/plain/MR.contributions
+++ /dev/null
@@ -1,168 +0,0 @@
-VENDOR: http://joelib.sf.net
-RELEASE_VERSION: $Revision: 1.2 $
-RELEASE_DATE: $Date: 2005/01/07 07:18:15 $
-
-#########################################################################
-# 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.
-########################################################################
-# MR Atomic Contributions
-# ref. Wildman, S.A. and Crippen, G.M., J. Chem. Inf. Comput. Sci., 1999, 39, 868-873.
-# Table below is adapted from above ref. uncommon p- and d-block elements have not been included.
-########################################################################
-;hydrogen
-[*] 1.112
-[#6] 1.057
-[#1] 1.057
-[O][CX4] 1.395
-[O]c 1.395
-[O][#5] 1.395
-[O][#14] 1.395
-[O][#15] 1.395
-[O][#33] 1.395
-[O][#50] 1.395
-[#5] 1.395
-[#14] 1.395
-[#15] 1.395
-[#16] 1.395
-[#50] 1.395
-[#7] 0.9627
-[O][#7] 0.9627
-[O]C=[#6] 1.805
-[O]C=[#7] 1.805
-[O]C=O 1.805
-[O]C=S 1.805
-[O]O 1.805
-[O]S 1.805
-;heavy
-[*] 0
-[#6] 3.243
-[CH4] 2.503
-[CH3]C 2.503
-[CH2](C)C 2.503
-[CH](C)(C)C 2.433
-[C](C)(C)(C)C 2.433
-[CH3][O,N,F,Cl,Br,#15,#16,#53;!a] 2.753
-[CH2X4][O,N,F,Cl,Br,#15,#16,#53;!a] 2.753
-[CHX4][O,N,F,Cl,Br,#15,#16,#53;!a] 2.731
-[CH0X4][O,N,F,Cl,Br,#15,#16,#53;!a] 2.731
-[C]=[A!#6] 5.007
-[CH2]=C 3.513
-[CH1](=C)A 3.513
-[CH0](=C)(A)A 3.513
-[C](=C)=C 3.513
-[CX2]#A 3.888
-[CH3]c 2.464
-[CH3][a!#6] 2.412
-[CH2X4]a 2.488
-[CHX4]a 2.582
-[CH0X4]a 2.576
-[c][#5,#14,#15,#33,#34,#50,#80] 4.041
-[c][#9] 3.257
-[c][#17] 3.564
-[c][#35] 3.18
-[c][#53] 3.104
-[cH] 3.35
-[c](:a)(:a):a 4.346
-[c](:a)(:a)-a 3.904
-[c](:a)(:a)-C 3.509
-[c](:a)(:a)-N 4.067
-[c](:a)(:a)-O 3.853
-[c](:a)(:a)-S 2.673
-[c](:a)(:a)=C 3.135
-[c](:a)(:a)=N 3.135
-[c](:a)(:a)=O 3.135
-[C](=C)(a)A 4.305
-[C](=C)(c)a 4.305
-[CH](=C)a 4.305
-[C]=c 4.305
-[CX4][!#6;!#7;!#8;!#9;!#15;!#16;!#17;!#35;!#53] 2.693
-[#7] 2.134
-[NH2+0]A 2.262
-[NH+0](A)A 2.173
-[NH2+0]a 2.827
-[NH+0](A)a 3
-[NH+0](a)a 3
-[NH+0]=A 1.757
-[NH+0]=a 1.757
-[N+0](=A)A 2.428
-[N+0](=A)a 2.428
-[N+0](=a)A 2.428
-[N+0](=a)a 2.428
-[N+0](A)(A)A 1.839
-[N+0](a)(A)A 2.819
-[N+0](a)(a)A 2.819
-[N+0](a)(a)a 2.819
-[N+0]#A 1.725
-[NH3+*] 2.134
-[NH2+*] 2.134
-[NH+*] 2.134
-[n+0] 2.202
-[n+*] 2.134
-[NH0+*](A)(A)(A)A 0.2604
-[NH0+*](=A)(A)A 0.2604
-[NH0+*](=A)(A)a 0.2604
-[NH0+*](=[#6])=[#7] 0.2604
-[N+*]#A 3.359
-[N-*] 3.359
-[N+*](=[N-*])=N 3.359
-[#8] 0.6865
-[o] 1.08
-[OH] 0.8238
-[OH2] 0.8238
-[O](C)C 1.085
-[OH0](C)[A!#6] 1.085
-[OH0]([A!#6])[A!#6] 1.085
-[O](A)a 1.182
-[O](a)a 1.182
-[O]=[#8] 3.367
-[O]=[#7] 3.367
-[OX1-*][#7] 3.367
-[OX1-*][#16] 0.7774
-[OX1-*][#15;#33;#43;#53] 0
-[O]=c 3.135
-[O]=[CH]C 0
-[O]=C(C)C 0
-[O]=[CH0](C)[A;!6] 0
-[O]=[CH]N 0
-[O]=[CH]O 0
-[O]=[CH2] 0
-[O]=[CX2]=O 0
-[O]=[CH]c 0.2215
-[O]=C(C)c 0.2215
-[O]=C(c)c 0.2215
-[O]=[CH0](c)[a!#6] 0.2215
-[O]=[CH0](c)[A!#6] 0.2215
-[O]=[CH0](C)[a!#6] 0.2215
-[O]=C([A!#6])[A!#6] 0.389
-[O]=C([A!#6])[a!#6] 0.389
-[O]=C([a!#6])[a!#6] 0.389
-[O-1]C(=O) 0.6865
-[#9-0] 1.108
-[#17-0] 5.853
-[#35-0] 8.927
-[#53-0] 14.02
-[#9-*] 1.108
-[#17-*] 5.853
-[#35-*] 8.927
-[#53-*] 14.02
-[#53+*] 14.02
-[#15] 6.92
-[S-0] 7.591
-[S-*] 7.365
-[S+*] 7.365
-[s] 6.691
-[B,Si,Ga,Ge,As,Se,Sn,Te,Pb,Nc,Nr,Kr,Xe,Rn] -0.3808 \ No newline at end of file
diff --git a/java/joelib2/data/plain/PSA.contributions b/java/joelib2/data/plain/PSA.contributions
deleted file mode 100644
index 56f1597..0000000
--- a/java/joelib2/data/plain/PSA.contributions
+++ /dev/null
@@ -1,68 +0,0 @@
-VENDOR: http://joelib.sf.net
-RELEASE_VERSION: $Revision: 1.2 $
-RELEASE_DATE: $Date: 2005/01/07 07:18:15 $
-
-#########################################################################
-# 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.
-########################################################################
-# Atomic Contributions to Polar Surface Area PSA
-# ref. Ertl P., Rohde R., Selzer P., J. Med. Chem. 2000, 43, 3714-3717
-########################################################################
-[*] 0.00
-[N](-*)(-*)-* 3.24
-[N](-*)=* 12.36
-[N]#* 23.79
-[N](-*)(=*)=* 11.68
-[N](=*)#* 13.60
-[N]1(-*)-*-*-1 3.01
-[NH](-*)-* 12.03
-[NH]1-*-*-1 21.94
-[NH]=* 23.85
-[NH2]-* 26.02
-[N+](-*)(-*)(-*)-* 0.00
-[N+](-*)(-*)=* 3.01
-[N+](-*)#* 4.36
-[NH+](-*)(-*)-* 4.44
-[NH+](-*)=* 13.97
-[NH2+](-*)-* 16.61
-[NH2+]=* 25.59
-[NH3+]-* 27.64
-[n](:*):* 12.89
-[n](:*)(:*):* 4.41
-[n](-*)(:*):* 4.93
-[n](=*)(:*):* 8.39
-[nH](:*):* 15.79
-[n+](:*)(:*):* 4.10
-[n+](-*)(:*):* 3.88
-[nH+](:*):* 14.14
-[O](-*)-* 9.23
-[O]1-*-*-1 12.53
-[O]=* 17.07
-[OH]-* 20.23
-[O-]-* 23.06
-[o](:*):* 13.14
-[S](-*)-* 25.30
-[S]=* 32.09
-[S](-*)(-*)=* 19.21
-[S](-*)(-*)(=*)=* 8.38
-[SH]-* 38.80
-[s](:*):* 28.24
-[s](=*)(:*):* 21.70
-[P](-*)(-*)-* 13.59
-[P](-*)=* 34.14
-[P](-*)(-*)(-*)=* 9.81
-[PH](-*)(-*)=* 23.47
diff --git a/java/joelib2/data/plain/aromatic.txt b/java/joelib2/data/plain/aromatic.txt
deleted file mode 100644
index 0d7c9c5..0000000
--- a/java/joelib2/data/plain/aromatic.txt
+++ /dev/null
@@ -1,54 +0,0 @@
-VENDOR: http://joelib.sf.net
-RELEASE_VERSION: $Revision: 1.4 $
-RELEASE_DATE: $Date: 2005/02/08 20:25:34 $
-
-########################################################################
-# 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.
-########################################################################
-
-#PATTERN MIN MAX
-#carbon patterns
-[#6Q2r+,#6Q3r+] 1 1
-[#6r]=@* 1 1
-[#6rQ3]=!@* 1 1
-# external double bonds to hetero atoms contribute no electrons to the
-# aromatic system. This makes sense, because chinoid systems are non-
-# aromatic, e.g. 1,4-Benzochinon
-[#6rQ3]=!@[!#6] 0 0
-[#6rQ3-] 2 2
-
-#nitrogen patterns
-[#7r](-@*)-@* 2 2
-[#7rQ2]=@* 1 1
-[#7Q3+] 1 1
-[#7rQ3]=O 1 1
-[#7Q2-] 2 2
-
-#oxygen patterns
-[#8r] 2 2
-[#8r+] 1 1
-
-#sulfur patterns
-[#16rQ2] 2 2
-[#16rQ2+] 1 1
-[#16rQ3]=!@O 2 2
-
-#other misc patterns
-[#15rQ3] 2 2
-#[#34rQ2] 2 2
-#[#52rQ2] 2 2
-
diff --git a/java/joelib2/data/plain/atomtype.txt b/java/joelib2/data/plain/atomtype.txt
deleted file mode 100644
index 4fd7605..0000000
--- a/java/joelib2/data/plain/atomtype.txt
+++ /dev/null
@@ -1,88 +0,0 @@
-VENDOR: http://joelib.sf.net
-RELEASE_VERSION: $Revision: 1.3 $
-RELEASE_DATE: $Date: 2005/01/07 07:18:15 $
-
-################################################################################
-# #
-# Used to assign the internal atom type to an atom. #
-# It is allowed to use assigned hybridisation patterns here, e.g. [#6^3] #
-# The LAST PATTERN MATCHED is used to assign values. Additions to this file #
-# should be placed in the EXTRA DEFINITIONS section #
-# #
-################################################################################
-# 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