8 files changed, 1477 insertions, 0 deletions
diff --git a/java/docs/algo/APropertyBFS.html b/java/docs/algo/APropertyBFS.html
new file mode 100644
index 0000000..df26fb7
--- /dev/null
+++ b/java/docs/algo/APropertyBFS.html
@@ -0,0 +1,93 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTOR"
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.APROPERTYBFS"
+></A
+>Valence</H2
+><P
+>Breadth first search calculating the distance only between boolean atom properties (default: Atom in conjugated environment).</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+>
+\ No newline at end of file
diff --git a/java/docs/algo/BreadthFirstSearch.html b/java/docs/algo/BreadthFirstSearch.html
new file mode 100644
index 0000000..47c782c
--- /dev/null
+++ b/java/docs/algo/BreadthFirstSearch.html
@@ -0,0 +1,122 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.ALGORITHMS.BREADTHFIRSTSEARCH"
+></A
+>Breadth First Search (BFS)</H1
+><P
+>&#13;The BFS method performs a breadth-first search  [<A
+HREF="bibliography.html#CLR98"
+>clr98</A
+>] of a graph.
+A breadth-first search visits vertices that are closer to the
+source before visiting vertices that are further away. In this
+context `distance' is defined as the number of edges in the
+shortest path from the source vertex.
+<DIV
+CLASS="FIGURE"
+><A
+NAME="JOELIB.ALGORITHMS.BREADTHFIRSTSEARCH.PSEUDOCODE"
+></A
+><P
+><B
+>Figure 1. Pseudocode for the BFS algorithm</B
+></P
+><PRE
+CLASS="PROGRAMLISTING"
+>paint all vertices white;
+paint the source grey, set its distance to 0 and enqueue it;
+repeat
+  dequeue vertex v;
+  if v is the target, we're done - exit this algorithm;
+  paint v black;
+  for each white neighbor w of v
+	paint w grey;
+	set distance w to (distance v + 1);
+	set parent w to v;
+	enqueue w
+until the queue is empty
+if we haven't yet exited, we didn't find the target</PRE
+></DIV
+>
+The time complexity is <IMG
+SRC="formulas/o_e+v.gif"> [<A
+HREF="bibliography.html#CLR98"
+>clr98</A
+>].</P
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+>
+\ No newline at end of file
diff --git a/java/docs/algo/DepthFirstSearch.html b/java/docs/algo/DepthFirstSearch.html
new file mode 100644
index 0000000..a4afe64
--- /dev/null
+++ b/java/docs/algo/DepthFirstSearch.html
@@ -0,0 +1,137 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.ALGORITHMS.DEPTHFIRSTSEARCH"
+></A
+>Depth First Search (DFS)</H1
+><P
+>The DFS method performs a depth--first search  [<A
+HREF="bibliography.html#CLR98"
+>clr98</A
+>] of a graph.
+A depth--first search visits vertices that are further to the
+source before visiting vertices that are closer away. In this
+context `distance' is defined as the number of edges in the
+shortest path from the source vertex.
+<DIV
+CLASS="FIGURE"
+><A
+NAME="JOELIB.ALGORITHMS.DEPTHFIRSTSEARCH.PSEUDOCODE"
+></A
+><P
+><B
+>Figure 1. Pseudocode for the DFS algorithm</B
+></P
+><PRE
+CLASS="PROGRAMLISTING"
+>DFS(G)
+  {
+    For each v in V,
+    {
+      color[v]=white;
+      pred[u]=NULL
+    }
+
+    time=0;
+    For each u in V
+      If (color[u]=white) DFSVISIT(u)
+  }
+
+
+  DFSVISIT(u)
+  {
+    color[u]=gray;
+    d[u] = ++time;
+
+    For each v in Adj(u)  do
+      If (color[v] = white)
+      {
+        pred[v] = u;
+        DFSVISIT(v);
+      }
+
+    color[u] = black; f[u]=++time;
+  }</PRE
+></DIV
+>
+The time complexity is <IMG
+SRC="formulas/o_e+v.gif"> [<A
+HREF="bibliography.html#CLR98"
+>clr98</A
+>].</P
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+>
+\ No newline at end of file
diff --git a/java/docs/algo/DistanceMatrix.html b/java/docs/algo/DistanceMatrix.html
new file mode 100644
index 0000000..6a745e7
--- /dev/null
+++ b/java/docs/algo/DistanceMatrix.html
@@ -0,0 +1,102 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.ALGORITHMS.DISTANCEMATRIX"
+></A
+>Topological distance matrix</H1
+><P
+>Calculates the topological distances between all atom pairs.
+Here a simple Breadth First Search  (BFS )
+is used to calculate these distances, which causes a running time of
+<SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>O(A<SUP
+>3</SUP
+>)</B
+></SPAN
+>, where
+<SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>A</B
+></SPAN
+> is the number of atoms.</P
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+>
+\ No newline at end of file
diff --git a/java/docs/algo/GeomDistanceMatrix.html b/java/docs/algo/GeomDistanceMatrix.html
new file mode 100644
index 0000000..76488d9
--- /dev/null
+++ b/java/docs/algo/GeomDistanceMatrix.html
@@ -0,0 +1,84 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.ALGORITHMS.GEOMDISTANCEMATRIX"
+></A
+>Geometrical distance matrix</H1
+><P
+>The geometrical distance matrix calculates the euklidian distance between the 3D coordinates of all atom pairs.</P
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+>
+\ No newline at end of file
diff --git a/java/docs/algo/Morgan.html b/java/docs/algo/Morgan.html
new file mode 100644
index 0000000..0a20be3
--- /dev/null
+++ b/java/docs/algo/Morgan.html
@@ -0,0 +1,157 @@
+<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.ALGORITHMS.MORGAN"
+></A
+>Morgan: Unique atom numbering</H1
+><P
+>Algorithm to get a unique numbering for molecules (graphs) [<A
+HREF="bibliography.html#MOR65"
+>mor65</A
+>].
+<DIV
+CLASS="FIGURE"
+><A
+NAME="JOELIB.ALGORITHMS.MORGAN.LABELING.PSEUDOCODE"
+></A
+><P
+><B
+>Figure 1. Pseudocode for the Morgan labeling algorithm</B
+></P
+><PRE
+CLASS="PROGRAMLISTING"
+>label each atom with its degree;
+labels=count the number of different labels;
+hasNTchanged=5;
+for all time
+  label each atom with sum of label+all neighbor labels;
+  actLabels=count the number of different labels;
+  if actLabels equal labels then
+    decrement hasNTchanged;
+    if hasNTchanged is zero break loop;
+  fi
+rof</PRE
+></DIV
+>
+The sloppy breaking criteria is necessary, because it's possible that the number of different labels can be
+constant for only two iterations. But that's not so interesting, let's continue with the
+renumbering part of the Morgan algorithm. As you can see, it's possible, that 'symmetric' atoms in the
+molecule will have same labels. Is there now a possibility to solve these 'labeling/renumbering' ties ?
+Yes, additional informations, like bond order and element number can be used for resolving renumbering ties
+or the suggested Jochum-Gasteiger canonical renumbering [<A
+HREF="bibliography.html#TC00"
+>tc00</A
+>] informations can be used.
+<DIV
+CLASS="FIGURE"
+><A
+NAME="JOELIB.ALGORITHMS.MORGAN.RENUMBERING.PSEUDOCODE"
+></A
+><P
+><B
+>Figure 2. Pseudocode for the Morgan renumbering algorithm</B
+></P
+><PRE
+CLASS="PROGRAMLISTING"
+>calculate the morgan atom labels;
+start breadth first search from this atom;
+choose node with the highest label and set new atom index to 1;
+repeat
+  build deque i of atoms with same BFS traversing number i;
+  if deque i contains no equal labels
+    renumber atoms in order of decreasing atom labels.
+  fi
+  else
+    try to resolve renumbering tie for the equal labels:
+      1. prefer atom with higher bond order for renumbering
+      2. prefer atom with higher element number for renumbering
+      3. ...
+    if tie solved
+      renumber atoms in order of decreasing atom labels.
+    fi
+    else
+      show renumbering tie warning;
+    esle
+  esle
+  increment i;
+until all atoms are numbered</PRE
+></DIV
+>
+The uniquely renumbered molecule can be used to calculate molecule
+hashcodes and canonical/unique SMILES representations (see ).</P
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="N"
+>Next</A
+></TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+>
+\ No newline at end of file
diff --git a/java/docs/algo/bibliography.html b/java/docs/algo/bibliography.html
new file mode 100644
index 0000000..5e0ebd1
--- /dev/null
+++ b/java/docs/algo/bibliography.html
@@ -0,0 +1,782 @@
+<HTML
+><HEAD
+><TITLE
+>Bibliography</TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="HOME"
+HREF="Morgan.html"><LINK
+REL="PREVIOUS"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="BIBLIOGRAPHY"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="NAVHEADER"
+><TABLE
+SUMMARY="Header navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TH
+COLSPAN="3"
+ALIGN="center"
+></TH
+></TR
+><TR
+><TD
+WIDTH="10%"
+ALIGN="left"
+VALIGN="bottom"
+><A
+HREF="bibliography.html"
+ACCESSKEY="P"
+>Prev</A
+></TD
+><TD
+WIDTH="80%"
+ALIGN="center"
+VALIGN="bottom"
+></TD
+><TD
+WIDTH="10%"
+ALIGN="right"
+VALIGN="bottom"
+>&nbsp;</TD
+></TR
+></TABLE
+><HR
+ALIGN="LEFT"
+WIDTH="100%"></DIV
+><A
+NAME="AEN14"
+></A
+><H1
+><A
+NAME="AEN14"
+></A
+>Bibliography</H1
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="BMV84"
+></A
+><P
+>[bmv84]&nbsp;<SPAN
+CLASS="AUTHOR"
+>P. Broto, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>G. Moreau, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and C. Vandycke</SPAN
+>, <I
+CLASS="CITETITLE"
+>Molecular Structures: Perception, Autocorrelation Descriptor and SAR Studies</I
+>, <I
+CLASS="CITETITLE"
+>Eur. J. Med. Chem.</I
+>, 19, 66-70, 1984.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="BS93"
+></A
+><P
+>[bs93]&nbsp;<SPAN
+CLASS="AUTHOR"
+>B. L. Bush </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and R. P. Sheridan</SPAN
+>, <I
+CLASS="CITETITLE"
+>PATTY: A Programmable Atom Typer and Language for Automatic Classification of Atoms in Molecular Databases</I
+>, <I
+CLASS="CITETITLE"
+>J. Chem. Inf. Comput. Sci.</I
+>, 33, 756-762, 1993.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="CLR98"
+></A
+><P
+>[clr98]&nbsp;<SPAN
+CLASS="AUTHOR"
+>T. Cormen, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>C. Leiserson, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and R. L. Rivest</SPAN
+>, 0-262-03141-8, MIT-Press, <I
+>Introduction to Algorithms</I
+>, 1998.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="DL93"
+></A
+><P
+>[dl93]&nbsp;<SPAN
+CLASS="AUTHOR"
+>A. N. Davies </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and P. Lampen</SPAN
+>, <I
+CLASS="CITETITLE"
+>JCAMP-DX for NMR</I
+>, <I
+CLASS="CITETITLE"
+>Appl. Spec.</I
+>, 47, 1093-1099, 1993.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="DW88"
+></A
+><P
+>[dw88]&nbsp;<SPAN
+CLASS="AUTHOR"
+>R. S. Mc Donald </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and P. A. Wilks</SPAN
+>, <I
+CLASS="CITETITLE"
+>JCAMP-DX: A Standard Form for Exchange of Infrared Spectra in Computer Readable Form</I
+>, <I
+CLASS="CITETITLE"
+>Appl. Spec.</I
+>, 42, 151-162, 1988.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="ERS00"
+></A
+><P
+>[ers00]&nbsp;<SPAN
+CLASS="AUTHOR"
+>P. Ertl, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>B. Rohde, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and P. Selzer</SPAN
+>, <I
+CLASS="CITETITLE"
+>Fast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of drug transport properties</I
+>, <I
+CLASS="CITETITLE"
+>J. Med. Chem.</I
+>, 43, 3714-3717, 2000.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="FIG96"
+></A
+><P
+>[fig96]&nbsp;<SPAN
+CLASS="AUTHOR"
+>J. Figueras</SPAN
+>, <I
+CLASS="CITETITLE"
+>Ring Perception Using Breadth-First Search</I
+>, <I
+CLASS="CITETITLE"
+>J. Chem. Inf. Comput. Sci.</I
+>, 36, 986-991, 1996.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="GAS95"
+></A
+><P
+>[gas95]&nbsp;<SPAN
+CLASS="AUTHOR"
+>J. Gasteiger</SPAN
+>, <I
+>Keyword Reference Manual for Gasteiger Clear Text Files</I
+>.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="GBT02"
+></A
+><P
+>[gbt02]&nbsp;<SPAN
+CLASS="AUTHOR"
+>A. Golbraikh, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>D. Bonchev, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and A. Tropsha</SPAN
+>, <I
+CLASS="CITETITLE"
+>Novel Z/E-Isomerism Descriptors Derived from Molecular Topology and Their Application to QSAR Analysis</I
+>, <I
+CLASS="CITETITLE"
+>J. Chem. Inf. Comput. Sci.</I
+>, 42, 769-787, 2002.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="GHHJS91"
+></A
+><P
+>[ghhjs91]&nbsp;<SPAN
+CLASS="AUTHOR"
+>J. Gasteiger, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>B. M. Hendriks, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>P. Hoever, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>C. Jochum, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and H. Somberg</SPAN
+>, <I
+CLASS="CITETITLE"
+>JCAMP-CS: A Standard Format for Chemical Structure Information in Computer Readable Form</I
+>, <I
+CLASS="CITETITLE"
+>Appl. Spec.</I
+>, 45, 4-11, 1991.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="GM78"
+></A
+><P
+>[gm78]&nbsp;<SPAN
+CLASS="AUTHOR"
+>J. Gasteiger </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and M. Marsili</SPAN
+>, <I
+CLASS="CITETITLE"
+>A New Model for Calculating Atomic Charges in Molecules</I
+>, <I
+CLASS="CITETITLE"
+>Tetrahedron Lett.</I
+>, ?, 3181-3184, 1978.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="GT03"
+></A
+><P
+>[gt03]&nbsp;<SPAN
+CLASS="AUTHOR"
+>A. Golbraikh </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and A. Tropsha</SPAN
+>, <I
+CLASS="CITETITLE"
+>QSAR Modeling Using Chirality Descriptors Derived from Molecular Topology</I
+>, <I
+CLASS="CITETITLE"
+>J. Chem. Inf. Comput. Sci.</I
+>, 42, 144-154, 2003.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="GXSB00"
+></A
+><P
+>[gxsb00]&nbsp;<SPAN
+CLASS="AUTHOR"
+>L. Xue, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>F. L. Stahura, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>J. W. Godden, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and J. Bajorath</SPAN
+>, <I
+CLASS="CITETITLE"
+>Searching for molecules with similar biological activity: analysis by fingerprint profiling</I
+>, <I
+CLASS="CITETITLE"
+>Pac. Symp. Biocomput.</I
+>, 8, 566-575, 2000.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="LHDL94"
+></A
+><P
+>[lhdl94]&nbsp;<SPAN
+CLASS="AUTHOR"
+>P. Lampen, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>H. Hillig, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>A. N. Davies, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and M. Linscheid</SPAN
+>, <I
+CLASS="CITETITLE"
+>JCAMP-DX for Mass Spectrometry</I
+>, <I
+CLASS="CITETITLE"
+>Appl. Spec.</I
+>, 48, 1545-1552, 1994.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="MOR65"
+></A
+><P
+>[mor65]&nbsp;<SPAN
+CLASS="AUTHOR"
+>H. L. Morgan</SPAN
+>, <I
+CLASS="CITETITLE"
+>The Generation of a Unique Machine Description for Chemical Structures - A Technique Developed at Chemical Abstracts Service</I
+>, <I
+CLASS="CITETITLE"
+>J. Chem. Doc.</I
+>, 5, 107-113, 1965.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="MR99"
+></A
+><P
+>[mr99]&nbsp;<SPAN
+CLASS="AUTHOR"
+>P. Murray-Rust </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and H. S. Rzepa</SPAN
+>, <I
+CLASS="CITETITLE"
+>Chemical Markup, XML, and the Worldwide Web. 1. Basic Principles</I
+>, <I
+CLASS="CITETITLE"
+>J. Chem. Inf. Comput. Sci.</I
+>, 39, 928-942, 1999.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="MR01A"
+></A
+><P
+>[mr01a]&nbsp;<SPAN
+CLASS="AUTHOR"
+>P. Murray-Rust </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and H. S. Rzepa</SPAN
+>, <I
+CLASS="CITETITLE"
+>Chemical Markup, XML and the World-Wide Web. 2. Information Objects and the CMLDOM</I
+>, <I
+CLASS="CITETITLE"
+>J. Chem. Inf. Comput. Sci.</I
+>, 41, ?-?, 2001.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="MR01B"
+></A
+><P
+>[mr01b]&nbsp;<SPAN
+CLASS="AUTHOR"
+>G. V. Gkoutos, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>P. Murray-Rust, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>H. S. Rzepa, </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and M. Wright</SPAN
+>, <I
+CLASS="CITETITLE"
+>Chemical markup, XML, and the world-wide web. 3. toward a signed semantic chemical web of trust</I
+>, <I
+CLASS="CITETITLE"
+>J. Chem. Inf. Comput. Sci.</I
+>, 41, 1295-1300, 2001.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="SDF"
+></A
+><P
+>[sdf]&nbsp;Inc. MDL Information Systems, <I
+><A
+HREF="http://www.mdli.com/downloads/literature/ctfile.pdf"
+TARGET="_top"
+>Structured Data File format</A
+></I
+>.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="SMARTS"
+></A
+><P
+>[smarts]&nbsp;Inc. Daylight Chemical Information Systems, <I
+><A
+HREF="http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html"
+TARGET="_top"
+>Smiles ARbitrary Target Specification (SMARTS)</A
+></I
+>.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="SMILES"
+></A
+><P
+>[smiles]&nbsp;Inc. Daylight Chemical Information Systems, <I
+><A
+HREF="http://www.daylight.com/dayhtml/smiles/smiles-intro.html"
+TARGET="_top"
+>Simplified Molecular Input Line Entry System (SMILES)</A
+></I
+>.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="TC00"
+></A
+><P
+>[tc00]&nbsp;<SPAN
+CLASS="AUTHOR"
+>R. Todeschini </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and V. Consonni</SPAN
+>, 3-52-29913-0, Wiley-VCH, <I
+>Handbook of Molecular Descriptors</I
+>.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="WC99"
+></A
+><P
+>[wc99]&nbsp;<SPAN
+CLASS="AUTHOR"
+>S. A. Wildman </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and G. M. Crippen</SPAN
+>, <I
+CLASS="CITETITLE"
+>Prediction of Physicochemical Parameters by Atomic Contributions</I
+>, <I
+CLASS="CITETITLE"
+>J. Chem. Inf. Comput. Sci.</I
+>, 39, 868-873, 1999.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="WEI88"
+></A
+><P
+>[wei88]&nbsp;<SPAN
+CLASS="AUTHOR"
+>D. Weinenger</SPAN
+>, <I
+CLASS="CITETITLE"
+>SMILES: a Chemical Language for Information Systems. 1. Introduction to Methodology and Encoding Rules</I
+>, <I
+CLASS="CITETITLE"
+>J. Chem. Inf. Comput. Sci.</I
+>, 28, 31-36, 1988.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="WEI89"
+></A
+><P
+>[wei89]&nbsp;<SPAN
+CLASS="AUTHOR"
+>D. Weinenger</SPAN
+>, <I
+CLASS="CITETITLE"
+>SMILES 2: Algorithm for Generation of Unique SMILES Notation</I
+>, <I
+CLASS="CITETITLE"
+>J. Chem. Inf. Comput. Sci.</I
+>, 29, 97-101, 1989.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="WIL01"
+></A
+><P
+>[wil01]&nbsp;<SPAN
+CLASS="AUTHOR"
+>E. L. Willighagen</SPAN
+>, <I
+><A
+HREF="http://www.ijc.com/abstracts/abstract4n4.html"
+TARGET="_top"
+>Processing CML Conventions in Java</A
+></I
+>, <I
+CLASS="CITETITLE"
+>Internet Journal of Chemistry</I
+>, 4, 4, 2001.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="WY96"
+></A
+><P
+>[wy96]&nbsp;<SPAN
+CLASS="AUTHOR"
+>W. P. Walters </SPAN
+><SPAN
+CLASS="AUTHOR"
+>and S. H. Yalkowsky</SPAN
+>, <I
+CLASS="CITETITLE"
+>ESCHER-A Computer Program for the Determination of External Rotational Symmetry Numbers from Molecular Topology</I
+>, <I
+CLASS="CITETITLE"
+>J. Chem. Inf. Comput. Sci.</I
+>, 36, 1015-1017, 1996.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="BIBLIOENTRY"
+><A
+NAME="ZUP89"
+></A
+><P
+>[zup89]&nbsp;<SPAN
+CLASS="AUTHOR"
+>J. Zupan</SPAN
+>, 0-471-92173-4, Wiley-VCH, <I
+>Algorithms for Chemists</I
+>.</P
+><DIV
+CLASS="BIBLIOENTRYBLOCK"
+STYLE="margin-left: 0.5in"
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+><A
+HREF="bibliography.html"
+ACCESSKEY="P"
+>Prev</A
+></TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+><A
+HREF="Morgan.html"
+ACCESSKEY="H"
+>Home</A
+></TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>&nbsp;</TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>Bibliography</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+>&nbsp;</TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>&nbsp;</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+>
+\ No newline at end of file
diff --git a/java/docs/algo/formulas/o_e+v.gif b/java/docs/algo/formulas/o_e+v.gif
new file mode 100644
index 0000000..c2ac4ac
--- /dev/null
+++ b/java/docs/algo/formulas/o_e+v.gif