diff options
Diffstat (limited to 'java/docs')
170 files changed, 11084 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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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
+> 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"
+> </TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+> </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"
+> </TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+> </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"
+> </TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+> </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"
+> </TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+> </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"
+> </TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+> </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"
+> </TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+> </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"
+> </TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+> </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"
+> </TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+> </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"
+> </TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+> </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"
+> </TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+> </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"
+> </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] <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] <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] <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] <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] <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] <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] <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] <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] <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] <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] <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] <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] <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] <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] <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] <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] <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] <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] 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] 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] 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] <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] <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] <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] <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] <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] <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] <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"
+> </TD
+></TR
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+>Bibliography</TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+> </TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+> </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 Binary files differnew file mode 100644 index 0000000..c2ac4ac --- /dev/null +++ b/java/docs/algo/formulas/o_e+v.gif diff --git a/java/docs/feature/APropertyBFS.html b/java/docs/feature/APropertyBFS.html new file mode 100644 index 0000000..dd46d0b --- /dev/null +++ b/java/docs/feature/APropertyBFS.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.APROPERTYBFS" +></A +>Atom property breadth first search</H2 +><P +>Breadth first search calculating the distance only between boolean atom properties (default: Atom in conjugated environment).</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/APropertyDistanceMatrix.html b/java/docs/feature/APropertyDistanceMatrix.html new file mode 100644 index 0000000..056c875 --- /dev/null +++ b/java/docs/feature/APropertyDistanceMatrix.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.APROPERTYDISTANCEMATRIX" +></A +>Atom property distance matrix</H2 +><P +>Distance matrix calculating the distance only between boolean atom properties (default: Atom in conjugated environment).</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/AcidicGroups.html b/java/docs/feature/AcidicGroups.html new file mode 100644 index 0000000..1bb2d9e --- /dev/null +++ b/java/docs/feature/AcidicGroups.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.ACIDICGROUPS" +></A +>Number of acidic groups</H2 +><P +>Number of acidic groups.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/AliphaticOHGroups.html b/java/docs/feature/AliphaticOHGroups.html new file mode 100644 index 0000000..f0d8a24 --- /dev/null +++ b/java/docs/feature/AliphaticOHGroups.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.ALIPHATICOHGROUPS" +></A +>Number of aliphatic hydroxy groups</H2 +><P +>Number of aliphatic hydroxy groups.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/AromaticBonds.html b/java/docs/feature/AromaticBonds.html new file mode 100644 index 0000000..faa7fa2 --- /dev/null +++ b/java/docs/feature/AromaticBonds.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.AROMATICBONDS" +></A +>Number of aromatic bonds</H2 +><P +>Number of aromatic bonds.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/AromaticOHGroups.html b/java/docs/feature/AromaticOHGroups.html new file mode 100644 index 0000000..781c23b --- /dev/null +++ b/java/docs/feature/AromaticOHGroups.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.HBD1" +></A +>Number of Hydrogen Bond Donors (HBD)</H2 +><P +>Number of Hydrogen Bond Donors (HBD). The default SMARTS pattern is: [!#6;!H0].</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/AtomBondOrderSum.html b/java/docs/feature/AtomBondOrderSum.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomBondOrderSum.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomENAllredRochow.html b/java/docs/feature/AtomENAllredRochow.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomENAllredRochow.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomENPauling.html b/java/docs/feature/AtomENPauling.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomENPauling.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomENSanderson.html b/java/docs/feature/AtomENSanderson.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomENSanderson.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomElectronAffinity.html b/java/docs/feature/AtomElectronAffinity.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomElectronAffinity.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomExplicitHydrogenCount.html b/java/docs/feature/AtomExplicitHydrogenCount.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomExplicitHydrogenCount.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomFreeElectronsCount.html b/java/docs/feature/AtomFreeElectronsCount.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomFreeElectronsCount.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomFreeOxygenCount.html b/java/docs/feature/AtomFreeOxygenCount.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomFreeOxygenCount.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomHeavyValence.html b/java/docs/feature/AtomHeavyValence.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomHeavyValence.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomHeteroValence.html b/java/docs/feature/AtomHeteroValence.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomHeteroValence.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomHybridisation.html b/java/docs/feature/AtomHybridisation.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomHybridisation.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomImplicitHydrogenCount.html b/java/docs/feature/AtomImplicitHydrogenCount.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomImplicitHydrogenCount.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomImplicitValence.html b/java/docs/feature/AtomImplicitValence.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomImplicitValence.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomInAcceptor.html b/java/docs/feature/AtomInAcceptor.html new file mode 100644 index 0000000..5785a4f --- /dev/null +++ b/java/docs/feature/AtomInAcceptor.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.ATOMINACCEPTOR" +></A +>Atom in acceptor</H2 +><P +>Is this atom a hydrogen acceptor atom.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/AtomInAromaticSystem.html b/java/docs/feature/AtomInAromaticSystem.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomInAromaticSystem.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomInConjEnvironment.html b/java/docs/feature/AtomInConjEnvironment.html new file mode 100644 index 0000000..2a3289e --- /dev/null +++ b/java/docs/feature/AtomInConjEnvironment.html @@ -0,0 +1,184 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.ATOMINCONJENVIRONMENT" +></A +>Atom in conjugated environment</H2 +><P +>Atom in conjugated environment. +<DIV +CLASS="TABLE" +><A +NAME="AEN7" +></A +><P +><B +>Table 1. SMARTS definitions for assigning the conjugated atom property flag</B +></P +><TABLE +BORDER="1" +CLASS="CALSTABLE" +><THEAD +><TR +><TH +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>SMARTS</TH +><TH +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Description</TH +></TR +></THEAD +><TBODY +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>a</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Aromatic atoms</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>*=,#*-,=*=,#*</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>All butadien analogues</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>[N,P,O,S]=,#*-[*;!H0]</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>alpha, beta unsaturated (pi effect)</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>*=,#*-[F,Cl,Br,I]</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>alpha, beta unsaturated (sigma effect)</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>*=,#*-[N,P,O,S;!H0]</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>alpha, beta unsaturated (pi effect, tautomer)</TD +></TR +></TBODY +></TABLE +></DIV +></P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/AtomInDonAcc.html b/java/docs/feature/AtomInDonAcc.html new file mode 100644 index 0000000..61b8188 --- /dev/null +++ b/java/docs/feature/AtomInDonAcc.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.ATOMINDONACC" +></A +>Atom in donor or acceptor</H2 +><P +>Is this atom a hydrogen donor or acceptor atom.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/AtomInDonor.html b/java/docs/feature/AtomInDonor.html new file mode 100644 index 0000000..399b2f9 --- /dev/null +++ b/java/docs/feature/AtomInDonor.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.ATOMINDONOR" +></A +>Atom in donor</H2 +><P +>Is this atom a hydrogen donor atom.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/AtomInRing.html b/java/docs/feature/AtomInRing.html new file mode 100644 index 0000000..79b7741 --- /dev/null +++ b/java/docs/feature/AtomInRing.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.ATOMINRING" +></A +>Atom in ring</H2 +><P +>Is this atom a ring atom.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/AtomInRingsCount.html b/java/docs/feature/AtomInRingsCount.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomInRingsCount.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomInTerminalCarbon.html b/java/docs/feature/AtomInTerminalCarbon.html new file mode 100644 index 0000000..23c8b41 --- /dev/null +++ b/java/docs/feature/AtomInTerminalCarbon.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.ATOMINTERMINALCARBON" +></A +>Atom is terminal carbon</H2 +><P +>Is this atom a terminal carbon atom.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/AtomIsAlphaBetaUnsaturated.html b/java/docs/feature/AtomIsAlphaBetaUnsaturated.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomIsAlphaBetaUnsaturated.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomIsAmideNitrogen.html b/java/docs/feature/AtomIsAmideNitrogen.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomIsAmideNitrogen.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomIsAntiClockwise.html b/java/docs/feature/AtomIsAntiClockwise.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomIsAntiClockwise.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomIsAromaticNOxide.html b/java/docs/feature/AtomIsAromaticNOxide.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomIsAromaticNOxide.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomIsAxial.html b/java/docs/feature/AtomIsAxial.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomIsAxial.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomIsCarbon.html b/java/docs/feature/AtomIsCarbon.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomIsCarbon.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomIsCarboxylOxygen.html b/java/docs/feature/AtomIsCarboxylOxygen.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomIsCarboxylOxygen.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomIsChiral.html b/java/docs/feature/AtomIsChiral.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomIsChiral.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomIsClockwise.html b/java/docs/feature/AtomIsClockwise.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomIsClockwise.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomIsElectronegative.html b/java/docs/feature/AtomIsElectronegative.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomIsElectronegative.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomIsHalogen.html b/java/docs/feature/AtomIsHalogen.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomIsHalogen.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomIsHeteroatom.html b/java/docs/feature/AtomIsHeteroatom.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomIsHeteroatom.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomIsHydrogen.html b/java/docs/feature/AtomIsHydrogen.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomIsHydrogen.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomIsNegative.html b/java/docs/feature/AtomIsNegative.html new file mode 100644 index 0000000..2754ce0 --- /dev/null +++ b/java/docs/feature/AtomIsNegative.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.ATOMISNEGATIVE" +></A +>Atom is negative</H2 +><P +>Is this atom a negative charged atom.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/AtomIsNitroOxygen.html b/java/docs/feature/AtomIsNitroOxygen.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomIsNitroOxygen.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomIsNitrogen.html b/java/docs/feature/AtomIsNitrogen.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomIsNitrogen.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomIsNonPolarHydrogen.html b/java/docs/feature/AtomIsNonPolarHydrogen.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomIsNonPolarHydrogen.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomIsOxygen.html b/java/docs/feature/AtomIsOxygen.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomIsOxygen.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomIsPhosphateOxygen.html b/java/docs/feature/AtomIsPhosphateOxygen.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomIsPhosphateOxygen.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomIsPhosphorus.html b/java/docs/feature/AtomIsPhosphorus.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomIsPhosphorus.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomIsPolarHydrogen.html b/java/docs/feature/AtomIsPolarHydrogen.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomIsPolarHydrogen.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomIsPositive.html b/java/docs/feature/AtomIsPositive.html new file mode 100644 index 0000000..4f4204d --- /dev/null +++ b/java/docs/feature/AtomIsPositive.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.ATOMISPOSITIVE" +></A +>Atom is positive</H2 +><P +>Is this atom a positive charged atom.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/AtomIsSulfateOxygen.html b/java/docs/feature/AtomIsSulfateOxygen.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomIsSulfateOxygen.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomIsSulfur.html b/java/docs/feature/AtomIsSulfur.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomIsSulfur.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomIsUnsaturated.html b/java/docs/feature/AtomIsUnsaturated.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomIsUnsaturated.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomKekuleBondOrderSum.html b/java/docs/feature/AtomKekuleBondOrderSum.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomKekuleBondOrderSum.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomMass.html b/java/docs/feature/AtomMass.html new file mode 100644 index 0000000..f1a2cde --- /dev/null +++ b/java/docs/feature/AtomMass.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.ATOMMASS" +></A +>Atom masss</H2 +><P +>Atom mass.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/AtomPartialCharge.html b/java/docs/feature/AtomPartialCharge.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomPartialCharge.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomType.html b/java/docs/feature/AtomType.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomType.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomValence.html b/java/docs/feature/AtomValence.html new file mode 100644 index 0000000..dcd6db8 --- /dev/null +++ b/java/docs/feature/AtomValence.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.ATOMVALENCE" +></A +>Valence</H2 +><P +>Valence.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/AtomValenceSum.html b/java/docs/feature/AtomValenceSum.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/AtomValenceSum.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/AtomVanDerWaalsVolume.html b/java/docs/feature/AtomVanDerWaalsVolume.html new file mode 100644 index 0000000..bf76e72 --- /dev/null +++ b/java/docs/feature/AtomVanDerWaalsVolume.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.ATOMVANDERWAALSVOLUME" +></A +>Van der Waals volume</H2 +><P +>Van der Waals volume.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/Autocorrelation.html b/java/docs/feature/Autocorrelation.html new file mode 100644 index 0000000..53fe464 --- /dev/null +++ b/java/docs/feature/Autocorrelation.html @@ -0,0 +1,168 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.AUTOCORRELATION" +></A +>Moreau-Broto topological autocorrelation</H2 +><P +>Moreau-Broto topological autocorrelation [<A +HREF="bibliography.html#BMV84" +>bmv84</A +>]. +<DIV +CLASS="EQUATION" +><A +NAME="AEN8" +></A +><P +><B +>Equation 1. Moreau-Broto autocorrelation</B +></P +><DIV +CLASS="MEDIAOBJECT" +><P +><IMG +SRC="formulas/autocorrelation.gif" +ALIGN="CENTER"></P +></DIV +></DIV +> +where <SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>d<SUB +>ij</SUB +></B +></SPAN +> is the topological distance between the atoms +<SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>i</B +></SPAN +> and atom <SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>j</B +></SPAN +>, <SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>w<SUB +>i</SUB +></B +></SPAN +> +and <SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>w<SUB +>j</SUB +></B +></SPAN +> are the atom properties of the atoms <SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>i</B +></SPAN +> and +<SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>j</B +></SPAN +>.</P +><P +>It must be mentioned that the autocorrelation is only a special case of the radial distribution function ().</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/BCUT.html b/java/docs/feature/BCUT.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/BCUT.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/BasicGroups.html b/java/docs/feature/BasicGroups.html new file mode 100644 index 0000000..581d187 --- /dev/null +++ b/java/docs/feature/BasicGroups.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.BASICGROUPS" +></A +>Number of basic groups</H2 +><P +>Number of basic groups.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/BondInAromaticSystem.html b/java/docs/feature/BondInAromaticSystem.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/BondInAromaticSystem.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/BondInRing.html b/java/docs/feature/BondInRing.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/BondInRing.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/BondIsAmide.html b/java/docs/feature/BondIsAmide.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/BondIsAmide.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/BondIsCarbonyl.html b/java/docs/feature/BondIsCarbonyl.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/BondIsCarbonyl.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/BondIsClosure.html b/java/docs/feature/BondIsClosure.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/BondIsClosure.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/BondIsEster.html b/java/docs/feature/BondIsEster.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/BondIsEster.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/BondIsPrimaryAmide.html b/java/docs/feature/BondIsPrimaryAmide.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/BondIsPrimaryAmide.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/BondIsRotor.html b/java/docs/feature/BondIsRotor.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/BondIsRotor.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/BondKekuleType.html b/java/docs/feature/BondKekuleType.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/BondKekuleType.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/BurdenEigenvalues.html b/java/docs/feature/BurdenEigenvalues.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/BurdenEigenvalues.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/BurdenModifiedEigenvalues.html b/java/docs/feature/BurdenModifiedEigenvalues.html new file mode 100644 index 0000000..dc6a83b --- /dev/null +++ b/java/docs/feature/BurdenModifiedEigenvalues.html @@ -0,0 +1,96 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.BURDENMODIFIEDEIGENVALUES" +></A +>Burden modified eigenvalues</H2 +><P +>Burden modified eigenvalues [<A +HREF="bibliography.html#TC00" +>tc00</A +>].</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/CompressedFeatureMatrix.html b/java/docs/feature/CompressedFeatureMatrix.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/CompressedFeatureMatrix.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/ConjElectroTopolState.html b/java/docs/feature/ConjElectroTopolState.html new file mode 100644 index 0000000..bc0369e --- /dev/null +++ b/java/docs/feature/ConjElectroTopolState.html @@ -0,0 +1,173 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.CONJELECTROTOPOLSTATE" +></A +>Conjugated electrotopological state</H2 +><P +>Conjugated electrotopological state [<A +HREF="bibliography.html#WZ03" +>wz03</A +>,<A +HREF="bibliography.html#WFZ04B" +>wfz04b</A +>]. +<DIV +CLASS="EQUATION" +><A +NAME="AEN9" +></A +><P +><B +>Equation 1. Conjugated electrotopological state</B +></P +><DIV +CLASS="MEDIAOBJECT" +><P +><IMG +SRC="formulas/cets.gif" +ALIGN="CENTER"></P +></DIV +></DIV +> +<SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>I<SUB +>i</SUB +></B +></SPAN +> is the intrinsic state of atom <SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>i</B +></SPAN +> () +and <SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>k</B +></SPAN +> the distance influence. The distance influence is reduced by the conjugated topological distance +<DIV +CLASS="EQUATION" +><A +NAME="AEN19" +></A +><P +><B +>Equation 2. Conjugated topological distance</B +></P +><DIV +CLASS="MEDIAOBJECT" +><P +><IMG +SRC="formulas/ctd.gif" +ALIGN="CENTER"></P +></DIV +></DIV +> +where <SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>C<SUB +>i</SUB +></B +></SPAN +> is the conjugated atom <SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>i</B +></SPAN +> () +of the molecule.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/ConjugatedTopologicalDistance.html b/java/docs/feature/ConjugatedTopologicalDistance.html new file mode 100644 index 0000000..6deea0d --- /dev/null +++ b/java/docs/feature/ConjugatedTopologicalDistance.html @@ -0,0 +1,117 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.CONJUGATEDTOPOLOGICALDISTANCE" +></A +>Conjugated topological distance</H2 +><P +>Conjugated topological distance [<A +HREF="bibliography.html#WZ03" +>wz03</A +>,<A +HREF="bibliography.html#WFZ04B" +>wfz04b</A +>]. +<DIV +CLASS="EQUATION" +><A +NAME="AEN9" +></A +><P +><B +>Equation 1. Conjugated topological distance</B +></P +><DIV +CLASS="MEDIAOBJECT" +><P +><IMG +SRC="formulas/ctd.gif" +ALIGN="CENTER"></P +></DIV +></DIV +></P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/DistanceDistanceMatrix.html b/java/docs/feature/DistanceDistanceMatrix.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/DistanceDistanceMatrix.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/DistanceMatrix.html b/java/docs/feature/DistanceMatrix.html new file mode 100644 index 0000000..ecd0533 --- /dev/null +++ b/java/docs/feature/DistanceMatrix.html @@ -0,0 +1,111 @@ +<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTORS."
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.DISTANCEMATRIX"
+></A
+>Topological distance matrix</H2
+><P
+>Calculates the topological distances between all atom pairs.
+Here a simple BFS (see also )
+is used to calculate these distances, which causes a running time of
+<SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>O(A<SUP
+>3</SUP
+>)</B
+></SPAN
+>, where
+<SPAN
+CLASS="bold"
+><B
+CLASS="EMPHASIS"
+>A</B
+></SPAN
+> is the number of atoms.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+> </TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+> </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"
+> </TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+> </TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+>
\ No newline at end of file diff --git a/java/docs/feature/Dummy.html b/java/docs/feature/Dummy.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/Dummy.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/ElectrogeometricalState.html b/java/docs/feature/ElectrogeometricalState.html new file mode 100644 index 0000000..d25b39a --- /dev/null +++ b/java/docs/feature/ElectrogeometricalState.html @@ -0,0 +1,139 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.ELECTROGEOMETRICALSTATE" +></A +>Electrogeometrical state</H2 +><P +>Electrogeometrical state [<A +HREF="bibliography.html#WZ03" +>wz03</A +>,<A +HREF="bibliography.html#WFZ04B" +>wfz04b</A +>]. +<DIV +CLASS="EQUATION" +><A +NAME="AEN9" +></A +><P +><B +>Equation 1. Electrogeometrical state</B +></P +><DIV +CLASS="MEDIAOBJECT" +><P +><IMG +SRC="formulas/egs.gif" +ALIGN="CENTER"></P +></DIV +></DIV +> +<SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>I<SUB +>i</SUB +></B +></SPAN +> is the intrinsic state of atom <SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>i</B +></SPAN +> () +and <SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>k</B +></SPAN +> the distance influence.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/ElectrotopologicalState.html b/java/docs/feature/ElectrotopologicalState.html new file mode 100644 index 0000000..6de0bf2 --- /dev/null +++ b/java/docs/feature/ElectrotopologicalState.html @@ -0,0 +1,139 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.ELECTROTOPOLOGICALSTATE" +></A +>Electrotopological state</H2 +><P +>Electrotopological state [<A +HREF="bibliography.html#TC00" +>tc00</A +>,<A +HREF="bibliography.html#WFZ04B" +>wfz04b</A +>]. +<DIV +CLASS="EQUATION" +><A +NAME="AEN9" +></A +><P +><B +>Equation 1. Electrotopological state</B +></P +><DIV +CLASS="MEDIAOBJECT" +><P +><IMG +SRC="formulas/ets.gif" +ALIGN="CENTER"></P +></DIV +></DIV +> +<SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>I<SUB +>i</SUB +></B +></SPAN +> is the intrinsic state of atom <SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>i</B +></SPAN +> () +and <SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>k</B +></SPAN +> the distance influence.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/FractionRotatableBonds.html b/java/docs/feature/FractionRotatableBonds.html new file mode 100644 index 0000000..a34080c --- /dev/null +++ b/java/docs/feature/FractionRotatableBonds.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.FRACTIONROTATABLEBONDS" +></A +>Fraction of rotatable bonds</H2 +><P +>Fraction of rotatable bonds.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/GeomDistanceMatrix.html b/java/docs/feature/GeomDistanceMatrix.html new file mode 100644 index 0000000..ff8cc05 --- /dev/null +++ b/java/docs/feature/GeomDistanceMatrix.html @@ -0,0 +1,93 @@ +<HTML
+><HEAD
+><TITLE
+></TITLE
+><META
+NAME="GENERATOR"
+CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
+REL="NEXT"
+TITLE="Bibliography"
+HREF="bibliography.html"></HEAD
+><BODY
+CLASS="ARTICLE"
+BGCOLOR="#FFFFFF"
+TEXT="#000000"
+LINK="#0000FF"
+VLINK="#840084"
+ALINK="#0000FF"
+><DIV
+CLASS="ARTICLE"
+><DIV
+CLASS="SECT1"
+><H1
+CLASS="SECT1"
+><A
+NAME="JOELIB.DESCRIPTORS."
+></A
+>Descriptor</H1
+><DIV
+CLASS="SECT2"
+><H2
+CLASS="SECT2"
+><A
+NAME="JOELIB.DESCRIPTORS.GEOMDISTANCEMATRIX"
+></A
+>Geometrical distance matrix</H2
+><P
+>The geometrical distance matrix calculates the euklidian distance between the 3D coordinates of all atom pairs.</P
+></DIV
+></DIV
+></DIV
+><DIV
+CLASS="NAVFOOTER"
+><HR
+ALIGN="LEFT"
+WIDTH="100%"><TABLE
+SUMMARY="Footer navigation table"
+WIDTH="100%"
+BORDER="0"
+CELLPADDING="0"
+CELLSPACING="0"
+><TR
+><TD
+WIDTH="33%"
+ALIGN="left"
+VALIGN="top"
+> </TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+> </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"
+> </TD
+><TD
+WIDTH="34%"
+ALIGN="center"
+VALIGN="top"
+> </TD
+><TD
+WIDTH="33%"
+ALIGN="right"
+VALIGN="top"
+>Bibliography</TD
+></TR
+></TABLE
+></DIV
+></BODY
+></HTML
+>
\ No newline at end of file diff --git a/java/docs/feature/GeometricalDiameter.html b/java/docs/feature/GeometricalDiameter.html new file mode 100644 index 0000000..242edc6 --- /dev/null +++ b/java/docs/feature/GeometricalDiameter.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.GEOMETRICALDIAMETER" +></A +>Geometrical diameter</H2 +><P +>Geometrical diameter.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/GeometricalRadius.html b/java/docs/feature/GeometricalRadius.html new file mode 100644 index 0000000..76a2596 --- /dev/null +++ b/java/docs/feature/GeometricalRadius.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.GEOMETRICALRADIUS" +></A +>Geometrical radius</H2 +><P +>Geometrical radius.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/GeometricalShapeCoefficient.html b/java/docs/feature/GeometricalShapeCoefficient.html new file mode 100644 index 0000000..e1401be --- /dev/null +++ b/java/docs/feature/GeometricalShapeCoefficient.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.GEOMETRICALSHAPECOEFFICIENT" +></A +>Geometrical shape coefficient</H2 +><P +>Geometrical shape coefficient.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/GlobalTopologicalChargeIndex.html b/java/docs/feature/GlobalTopologicalChargeIndex.html new file mode 100644 index 0000000..63e2715 --- /dev/null +++ b/java/docs/feature/GlobalTopologicalChargeIndex.html @@ -0,0 +1,96 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.GLOBALTOPOLOGICALCHARGEINDEX" +></A +>Global topological charge</H2 +><P +>Global topological charge [<A +HREF="bibliography.html#TC00" +>tc00</A +>].</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/GraphPotentials.html b/java/docs/feature/GraphPotentials.html new file mode 100644 index 0000000..a192e96 --- /dev/null +++ b/java/docs/feature/GraphPotentials.html @@ -0,0 +1,131 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.GRAPHPOTENTIALS" +></A +>Graph potentials</H2 +><P +>Graph potentials [<A +HREF="bibliography.html#WY96" +>wy96</A +>] or rotational symmetry descriptor. Only the connection table +is needed to calculate the external rotational symmetry, or topological equivalent atoms. +<DIV +CLASS="EQUATION" +><A +NAME="AEN8" +></A +><P +><B +>Equation 1. Graph potentials</B +></P +><DIV +CLASS="MEDIAOBJECT" +><P +><IMG +SRC="formulas/graphpotentials_1.gif" +ALIGN="CENTER"></P +></DIV +></DIV +> +where <SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>v<SUB +>i</SUB +></B +></SPAN +> is the valence (vertex degree) of the atom +<SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>i</B +></SPAN +>.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/GraphShapeCoefficient.html b/java/docs/feature/GraphShapeCoefficient.html new file mode 100644 index 0000000..735e913 --- /dev/null +++ b/java/docs/feature/GraphShapeCoefficient.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.GRAPHSHAPECOEFFICIENT" +></A +>Graph shape coefficient</H2 +><P +>Graph shape coefficient.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/HBA1.html b/java/docs/feature/HBA1.html new file mode 100644 index 0000000..6dcb012 --- /dev/null +++ b/java/docs/feature/HBA1.html @@ -0,0 +1,94 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.HBA1" +></A +>Number of Hydrogen Bond Acceptors (HBA) 1</H2 +><P +>Number of Hydrogen Bond Acceptors (HBA) 1. +The default SMARTS pattern is: [$([!#6;+0]);!$([F,Cl,Br,I]);!$([o,s,nX3]);!$([Nv5,Pv5,Sv4,Sv6])].</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/HBA2.html b/java/docs/feature/HBA2.html new file mode 100644 index 0000000..4ad7747 --- /dev/null +++ b/java/docs/feature/HBA2.html @@ -0,0 +1,94 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.HBA2" +></A +>Number of Hydrogen Bond Acceptors (HBA) 2</H2 +><P +>Number of Hydrogen Bond Acceptors (HBA) 2. +The default SMARTS pattern is: [$([$([#8,#16]);!$(*=N~O);!$(*~N=O);X1,X2]),$([#7;v3;!$([nH]);!$(*(-a)-a)])].</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/HBD1.html b/java/docs/feature/HBD1.html new file mode 100644 index 0000000..58922cf --- /dev/null +++ b/java/docs/feature/HBD1.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.HBD1" +></A +>Number of Hydrogen Bond Donors (HBD) 1</H2 +><P +>Number of Hydrogen Bond Donors (HBD) 1. The default SMARTS pattern is: [!#6;!H0].</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/HBD2.html b/java/docs/feature/HBD2.html new file mode 100644 index 0000000..a66a20f --- /dev/null +++ b/java/docs/feature/HBD2.html @@ -0,0 +1,94 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.HBD2" +></A +>Number of Hydrogen Bond Donors (HBD) 2</H2 +><P +>Number of Hydrogen Bond Donors (HBD) 2. +The default SMARTS pattern is: [$([O;H1,-&!$(*-N=O)]),$([S;H1&X2,-&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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/HeavyBonds.html b/java/docs/feature/HeavyBonds.html new file mode 100644 index 0000000..c460fba --- /dev/null +++ b/java/docs/feature/HeavyBonds.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.HEAVYBONDS" +></A +>Number of heavy bonds</H2 +><P +>Number of heavy bonds.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/HeteroCycles.html b/java/docs/feature/HeteroCycles.html new file mode 100644 index 0000000..d1e124f --- /dev/null +++ b/java/docs/feature/HeteroCycles.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.HETEROCYCLES" +></A +>Number of heterocycles</H2 +><P +>Number of heterocycles.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/HydrophobicGroups.html b/java/docs/feature/HydrophobicGroups.html new file mode 100644 index 0000000..020d78c --- /dev/null +++ b/java/docs/feature/HydrophobicGroups.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.HYDROPHOBICGROUPS" +></A +>Number of hydrophobic groups</H2 +><P +>Number of hydrophobic groups.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/IntrinsicState.html b/java/docs/feature/IntrinsicState.html new file mode 100644 index 0000000..82c8c76 --- /dev/null +++ b/java/docs/feature/IntrinsicState.html @@ -0,0 +1,145 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.INTRINSICSTATE" +></A +>Intrinsic topological state</H2 +><P +>Intrinsic topological state [<A +HREF="bibliography.html#TC00" +>tc00</A +>,<A +HREF="bibliography.html#WFZ04B" +>wfz04b</A +>]. +<DIV +CLASS="EQUATION" +><A +NAME="AEN9" +></A +><P +><B +>Equation 1. Intrinsic topological state</B +></P +><DIV +CLASS="MEDIAOBJECT" +><P +><IMG +SRC="formulas/istate.gif" +ALIGN="CENTER"></P +></DIV +></DIV +> +where <SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>L<SUB +>i</SUB +></B +></SPAN +> is the principal quantum number, +<IMG +SRC="formulas/delta_i_nu.gif"> is the number of valence electrons, and +<IMG +SRC="formulas/delta_i.gif"> is the number of sigma electrons of the +<SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>i</B +></SPAN +>th atom <SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>a<SUB +>i</SUB +></B +></SPAN +>.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/KierShape1.html b/java/docs/feature/KierShape1.html new file mode 100644 index 0000000..9690413 --- /dev/null +++ b/java/docs/feature/KierShape1.html @@ -0,0 +1,176 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.KIERSHAPE1" +></A +>Kier Shape 1</H2 +><P +>The Kier shape +<IMG +SRC="formulas/kier1.gif"> descriptor [<A +HREF="bibliography.html#TC00" +>tc00</A +>] +can be defined as :</P +><DIV +CLASS="EQUATION" +><A +NAME="AEN10" +></A +><P +><B +>Equation 1. Kier shape 1</B +></P +><DIV +CLASS="MEDIAOBJECT" +><P +><IMG +SRC="formulas/kier1_1.gif" +ALIGN="CENTER"></P +></DIV +></DIV +><P +><SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>P<SUB +>max</SUB +></B +></SPAN +> is the maximum number of paths of length 1. +<SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>P<SUB +>min</SUB +></B +></SPAN +> is the minimum number of paths of length 1 in a molecule graph of same +atom number. +<SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>P1</B +></SPAN +> is the number of paths in the given molecule of length 1. +or:</P +><DIV +CLASS="EQUATION" +><A +NAME="AEN21" +></A +><P +><B +>Equation 2. Kier shape 1 (alternative formulation)</B +></P +><DIV +CLASS="MEDIAOBJECT" +><P +><IMG +SRC="formulas/kier1_2.gif" +ALIGN="CENTER"></P +></DIV +></DIV +><P +><SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>A</B +></SPAN +> means the number of nodes in the molecules graph. +<SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>P1</B +></SPAN +> is the number of paths of length 1 in the given molecule.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/KierShape2.html b/java/docs/feature/KierShape2.html new file mode 100644 index 0000000..d3117b2 --- /dev/null +++ b/java/docs/feature/KierShape2.html @@ -0,0 +1,131 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.KIERSHAPE2" +></A +>Kier shape 2</H2 +><P +>The Kier shape +<IMG +SRC="formulas/kier2.gif"> descriptor [<A +HREF="bibliography.html#TC00" +>tc00</A +>] +can be defined as :</P +><DIV +CLASS="EQUATION" +><A +NAME="AEN10" +></A +><P +><B +>Equation 1. Kier shape 2</B +></P +><DIV +CLASS="MEDIAOBJECT" +><P +><IMG +SRC="formulas/kier2_1.gif" +ALIGN="CENTER"></P +></DIV +></DIV +><P +><SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>A</B +></SPAN +> means the number of nodes in the molecules graph. +<SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>P2</B +></SPAN +> is the number of paths of length 2 in the given molecule.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/KierShape3.html b/java/docs/feature/KierShape3.html new file mode 100644 index 0000000..7b760b5 --- /dev/null +++ b/java/docs/feature/KierShape3.html @@ -0,0 +1,131 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.KIERSHAPE3" +></A +>Kier shape 3</H2 +><P +>The Kier shape +<IMG +SRC="formulas/kier3.gif"> descriptor [<A +HREF="bibliography.html#TC00" +>tc00</A +>] +can be defined as :</P +><DIV +CLASS="EQUATION" +><A +NAME="AEN10" +></A +><P +><B +>Equation 1. Kier shape 3</B +></P +><DIV +CLASS="MEDIAOBJECT" +><P +><IMG +SRC="formulas/kier3_1.gif" +ALIGN="CENTER"></P +></DIV +></DIV +><P +><SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>A</B +></SPAN +> means the number of nodes in the molecules graph. +<SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>P3</B +></SPAN +> is the number of paths of length 3 in the given molecule.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/LogP.html b/java/docs/feature/LogP.html new file mode 100644 index 0000000..914533b --- /dev/null +++ b/java/docs/feature/LogP.html @@ -0,0 +1,96 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.LOGP" +></A +>Octanol/Water partition coefficient (logP)</H2 +><P +>Octanol/Water partition coefficient (logP) or hydrophobicity [<A +HREF="bibliography.html#WC99" +>wc99</A +>].</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/MolarRefractivity.html b/java/docs/feature/MolarRefractivity.html new file mode 100644 index 0000000..88757de --- /dev/null +++ b/java/docs/feature/MolarRefractivity.html @@ -0,0 +1,96 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.MOLARREFRACTIVITY" +></A +>Molar refractivity (MR)</H2 +><P +>Molar refractivity (MR) [<A +HREF="bibliography.html#WC99" +>wc99</A +>].</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/MolecularWeight.html b/java/docs/feature/MolecularWeight.html new file mode 100644 index 0000000..e463e1c --- /dev/null +++ b/java/docs/feature/MolecularWeight.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.MOLECULARWEIGHT" +></A +>Molecular weight (MW)</H2 +><P +>Molecular weight (MW).</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/MoleculeHashcode.html b/java/docs/feature/MoleculeHashcode.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/MoleculeHashcode.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/NO2Groups.html b/java/docs/feature/NO2Groups.html new file mode 100644 index 0000000..6fa91d4 --- /dev/null +++ b/java/docs/feature/NO2Groups.html @@ -0,0 +1,97 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.NO2GROUPS" +></A +>Number of -NO<SUB +>2</SUB +> groups</H2 +><P +>Number of -NO<SUB +>2</SUB +> groups.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/NumberOfAtoms.html b/java/docs/feature/NumberOfAtoms.html new file mode 100644 index 0000000..f79063f --- /dev/null +++ b/java/docs/feature/NumberOfAtoms.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.NUMBEROFATOMS" +></A +>Number of atoms</H2 +><P +>Number of atoms.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/NumberOfB.html b/java/docs/feature/NumberOfB.html new file mode 100644 index 0000000..fd7e2e4 --- /dev/null +++ b/java/docs/feature/NumberOfB.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.NUMBEROFB" +></A +>Number of boron atoms</H2 +><P +>Number of boron atoms.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/NumberOfBonds.html b/java/docs/feature/NumberOfBonds.html new file mode 100644 index 0000000..22dfb7e --- /dev/null +++ b/java/docs/feature/NumberOfBonds.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.NUMBEROFBONDS" +></A +>Number of bonds</H2 +><P +>Number of bonds.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/NumberOfBr.html b/java/docs/feature/NumberOfBr.html new file mode 100644 index 0000000..5807bb9 --- /dev/null +++ b/java/docs/feature/NumberOfBr.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.NUMBEROFBR" +></A +>Number of bromine atoms</H2 +><P +>Number of bromine atoms.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/NumberOfC.html b/java/docs/feature/NumberOfC.html new file mode 100644 index 0000000..a1b224e --- /dev/null +++ b/java/docs/feature/NumberOfC.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.NUMBEROFC" +></A +>Number of carbon atoms</H2 +><P +>Number of carbon atoms.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/NumberOfCl.html b/java/docs/feature/NumberOfCl.html new file mode 100644 index 0000000..04892d5 --- /dev/null +++ b/java/docs/feature/NumberOfCl.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.NUMBEROFCL" +></A +>Number of chlorine atoms</H2 +><P +>Number of chlorine atoms.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/NumberOfF.html b/java/docs/feature/NumberOfF.html new file mode 100644 index 0000000..c12b2f5 --- /dev/null +++ b/java/docs/feature/NumberOfF.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.NUMBEROFF" +></A +>Number of fluorine atoms</H2 +><P +>Number of fluorine atoms.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/NumberOfHal.html b/java/docs/feature/NumberOfHal.html new file mode 100644 index 0000000..11df356 --- /dev/null +++ b/java/docs/feature/NumberOfHal.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.NUMBEROFHAL" +></A +>Number of halogen atoms</H2 +><P +>Number of halogen atoms.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/NumberOfI.html b/java/docs/feature/NumberOfI.html new file mode 100644 index 0000000..0580e12 --- /dev/null +++ b/java/docs/feature/NumberOfI.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.NUMBEROFI" +></A +>Number of iodine atoms</H2 +><P +>Number of iodine atoms.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/NumberOfN.html b/java/docs/feature/NumberOfN.html new file mode 100644 index 0000000..bd65ada --- /dev/null +++ b/java/docs/feature/NumberOfN.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.NUMBEROFN" +></A +>Number of nitrogen atoms</H2 +><P +>Number of nitrogen atoms.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/NumberOfO.html b/java/docs/feature/NumberOfO.html new file mode 100644 index 0000000..7ecbe0a --- /dev/null +++ b/java/docs/feature/NumberOfO.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.NUMBEROFO" +></A +>Number of oxygen atoms</H2 +><P +>Number of oxygen atoms.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/NumberOfP.html b/java/docs/feature/NumberOfP.html new file mode 100644 index 0000000..3669e91 --- /dev/null +++ b/java/docs/feature/NumberOfP.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.NUMBEROFP" +></A +>Number of phosphorus atoms</H2 +><P +>Number of phosphorus atoms.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/NumberOfS.html b/java/docs/feature/NumberOfS.html new file mode 100644 index 0000000..b735ee5 --- /dev/null +++ b/java/docs/feature/NumberOfS.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.NUMBEROFS" +></A +>Number of sulfur atoms</H2 +><P +>Number of sulfur atoms.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/OSOGroups.html b/java/docs/feature/OSOGroups.html new file mode 100644 index 0000000..ca49ebf --- /dev/null +++ b/java/docs/feature/OSOGroups.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.OSOGROUPS" +></A +>Number of -OSO atoms</H2 +><P +>Number of -OSO atoms.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/PolarSurfaceArea.html b/java/docs/feature/PolarSurfaceArea.html new file mode 100644 index 0000000..357056f --- /dev/null +++ b/java/docs/feature/PolarSurfaceArea.html @@ -0,0 +1,96 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.POLARSURFACEAREA" +></A +>Polar surface area (PSA)</H2 +><P +>Polar surface area (PSA) [<A +HREF="bibliography.html#ERS00" +>ers00</A +>].</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/RadialDistributionFunction.html b/java/docs/feature/RadialDistributionFunction.html new file mode 100644 index 0000000..09d9600 --- /dev/null +++ b/java/docs/feature/RadialDistributionFunction.html @@ -0,0 +1,230 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.RADIALDISTRIBUTIONFUNCTION" +></A +>Radial distribution function (RDF)</H2 +><P +>The radial distribution function (RDF) [<A +HREF="bibliography.html#MSG99" +>msg99</A +>,<A +HREF="bibliography.html#WFZ04B" +>wfz04b</A +>] can be interpreted as the probability distribution of finding an atom in a spherical volume of +radius <SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>r</B +></SPAN +>. +<DIV +CLASS="EQUATION" +><A +NAME="AEN14" +></A +><P +><B +>Equation 1. Radial distribution function</B +></P +><DIV +CLASS="MEDIAOBJECT" +><P +><IMG +SRC="formulas/rdf.gif" +ALIGN="CENTER"></P +></DIV +></DIV +> +where <SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>r<SUB +>ij</SUB +></B +></SPAN +> is the geometrical distance between the atoms +<SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>i</B +></SPAN +> and atom <SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>j</B +></SPAN +>, <SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>w<SUB +>i</SUB +></B +></SPAN +> +and <SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>w<SUB +>j</SUB +></B +></SPAN +> are the atom properties of the atoms <SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>i</B +></SPAN +> and +<SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>j</B +></SPAN +>. <SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>B</B +></SPAN +> is the smoothing parameter +(fuzziness of the distance <SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>r<SUB +>ij</SUB +></B +></SPAN +>) for the interatomic distance and +<SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>f</B +></SPAN +> the scaling factor.</P +><P +>If <SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>B</B +></SPAN +> aims to infinity the RDF code approximates to the autocorrelation function () and the fuzziness +of the distance <SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>r<SUB +>ij</SUB +></B +></SPAN +> vanishes. So the RDF code can be treated as a generalized +autocorrelation function.</P +><P +>The RDF user parameters can be defined in the <TT +CLASS="FILENAME" +>joelib.properties</TT +>-file, otherwise the default parameters will be used:</P +><PRE +CLASS="PROGRAMLISTING" +>jcompchem.joelib.desc.types.RadialDistributionFunction.minSphericalVolume = 0.2 +joelib.desc.types.RadialDistributionFunction.maxSphericalVolume = 10.0 +joelib.desc.types.RadialDistributionFunction.sphericalVolumeResolution = 0.2 +joelib.desc.types.RadialDistributionFunction.smoothingFactor = 25</PRE +><P +>Optional the RDF can be calculated with protonated molecules, but you must be sure that all available atom +properties are calculated with hydrogens also. Because this is not the standard, this option should be only used by developers.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/RotatableBonds.html b/java/docs/feature/RotatableBonds.html new file mode 100644 index 0000000..42ef0d9 --- /dev/null +++ b/java/docs/feature/RotatableBonds.html @@ -0,0 +1,94 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.ROTATABLEBONDS" +></A +>Number of rotatable bonds</H2 +><P +>Number of rotatable bonds, where the atoms are heavy atoms with bond order one and a hybridization which is not one (no sp). +Additionally the bond is a non-ring-bond.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/SMILESMolecule.html b/java/docs/feature/SMILESMolecule.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/SMILESMolecule.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/SO2Groups.html b/java/docs/feature/SO2Groups.html new file mode 100644 index 0000000..e4cd9a7 --- /dev/null +++ b/java/docs/feature/SO2Groups.html @@ -0,0 +1,97 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.SO2GROUPS" +></A +>Number of -SO<SUB +>2</SUB +> atoms</H2 +><P +>Number of -SO<SUB +>2</SUB +> atoms.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/SOGroups.html b/java/docs/feature/SOGroups.html new file mode 100644 index 0000000..fd3e45a --- /dev/null +++ b/java/docs/feature/SOGroups.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.SOGROUPS" +></A +>Number of -SO groups</H2 +><P +>Number of -SO groups.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/SSKey3DS.html b/java/docs/feature/SSKey3DS.html new file mode 100644 index 0000000..fad741d --- /dev/null +++ b/java/docs/feature/SSKey3DS.html @@ -0,0 +1,779 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.SSKEY3DS" +></A +>Pharmacophore fingerprint</H2 +><P +>Pharmacophore fingerprint [<A +HREF="bibliography.html#GXSB00" +>gxsb00</A +>]. +<DIV +CLASS="TABLE" +><A +NAME="AEN8" +></A +><P +><B +>Table 1. Pharmacophore fingerprint definition</B +></P +><TABLE +BORDER="1" +CLASS="CALSTABLE" +><THEAD +><TR +><TH +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Bit position</TH +><TH +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Set when</TH +></TR +></THEAD +><TBODY +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>1</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Fraction of rotatable bonds > 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 > 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 > 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 > 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 > 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 > 2</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>7</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Aromatic bonds in molecule > 8</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>8</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Aromatic bonds in molecule > 16</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>9</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Aromatic bonds in molecule > 20</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>10</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Aromatic bonds in molecule > 26</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>11</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Aromatic bonds in molecule > 32</TD +></TR +><TR +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>12</TD +><TD +WIDTH="50%" +ALIGN="LEFT" +VALIGN="TOP" +>Aromatic bonds in molecule > 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 >= 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 >= 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 >= 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 >= 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 >= 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 >= 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 >= 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 >= 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 >= 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 >= 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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/TopologicalAtomPair.html b/java/docs/feature/TopologicalAtomPair.html new file mode 100644 index 0000000..32731b0 --- /dev/null +++ b/java/docs/feature/TopologicalAtomPair.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.TOPOLOGICALATOMPAIR" +></A +>Valence</H2 +><P +>Atom pair descriptor using topological distances.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/TopologicalDiameter.html b/java/docs/feature/TopologicalDiameter.html new file mode 100644 index 0000000..660bbb6 --- /dev/null +++ b/java/docs/feature/TopologicalDiameter.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.TOPOLOGICALDIAMETER" +></A +>Topological diameter</H2 +><P +>Topological diameter.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/TopologicalRadius.html b/java/docs/feature/TopologicalRadius.html new file mode 100644 index 0000000..07299fa --- /dev/null +++ b/java/docs/feature/TopologicalRadius.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.TOPOLOGICALRADIUS" +></A +>Topological radius</H2 +><P +>Topological radius.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/WeightedBurdenEigenvalues.html b/java/docs/feature/WeightedBurdenEigenvalues.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/WeightedBurdenEigenvalues.html @@ -0,0 +1,3 @@ +<HTML> +Dummy +</HTML>
\ No newline at end of file diff --git a/java/docs/feature/WeightedBurdenModifiedEigenvalues.html b/java/docs/feature/WeightedBurdenModifiedEigenvalues.html new file mode 100644 index 0000000..0e93938 --- /dev/null +++ b/java/docs/feature/WeightedBurdenModifiedEigenvalues.html @@ -0,0 +1,93 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.WEIGHTEDBURDENMODIFIEDEIGENVALUES" +></A +>Weighted burden modified eigenvalues</H2 +><P +>Accepts six different weighted atom properties to calculate BCUT values.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/ZagrebIndex1.html b/java/docs/feature/ZagrebIndex1.html new file mode 100644 index 0000000..130990f --- /dev/null +++ b/java/docs/feature/ZagrebIndex1.html @@ -0,0 +1,123 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.ZAGREBINDEX1" +></A +>Zagreb index 1</H2 +><P +>Zagreb index 1 [<A +HREF="bibliography.html#TC00" +>tc00</A +>].</P +><DIV +CLASS="EQUATION" +><A +NAME="AEN8" +></A +><P +><B +>Equation 1. Zagreb index 1</B +></P +><DIV +CLASS="MEDIAOBJECT" +><P +><IMG +SRC="formulas/zagreb1.gif" +ALIGN="CENTER"></P +></DIV +></DIV +><P +>where <SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>a</B +></SPAN +> are all atoms of the hydrogen depleted graph and +<IMG +SRC="formulas/delta.gif"> is the vertex degree.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +>Bibliography</TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/ZagrebIndex2.html b/java/docs/feature/ZagrebIndex2.html new file mode 100644 index 0000000..735a797 --- /dev/null +++ b/java/docs/feature/ZagrebIndex2.html @@ -0,0 +1,143 @@ +<HTML +><HEAD +><TITLE +></TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="NEXT" +TITLE="Bibliography" +HREF="bibliography.html"></HEAD +><BODY +CLASS="ARTICLE" +BGCOLOR="#FFFFFF" +TEXT="#000000" +LINK="#0000FF" +VLINK="#840084" +ALINK="#0000FF" +><DIV +CLASS="ARTICLE" +><DIV +CLASS="SECT1" +><H1 +CLASS="SECT1" +><A +NAME="JOELIB.DESCRIPTOR" +></A +>Descriptor</H1 +><DIV +CLASS="SECT2" +><H2 +CLASS="SECT2" +><A +NAME="JOELIB.DESCRIPTORS.ZAGREBINDEX2" +></A +>Zagreb index 2</H2 +><P +>Zagreb index 2 [<A +HREF="bibliography.html#TC00" +>tc00</A +>].</P +><DIV +CLASS="EQUATION" +><A +NAME="AEN8" +></A +><P +><B +>Equation 1. Zagreb index 2</B +></P +><DIV +CLASS="MEDIAOBJECT" +><P +><IMG +SRC="formulas/zagreb2.gif" +ALIGN="CENTER"></P +></DIV +></DIV +><P +>where <SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>b</B +></SPAN +> are all bonds of the hydrogen depleted graph and +<IMG +SRC="formulas/delta.gif"> is the vertex degree. +<SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>i</B +></SPAN +> and <SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>j</B +></SPAN +> are the atom indices +of the atoms connected to the bond <SPAN +CLASS="bold" +><B +CLASS="EMPHASIS" +>b</B +></SPAN +>.</P +></DIV +></DIV +></DIV +><DIV +CLASS="NAVFOOTER" +><HR +ALIGN="LEFT" +WIDTH="100%"><TABLE +SUMMARY="Footer navigation table" +WIDTH="100%" +BORDER="0" +CELLPADDING="0" +CELLSPACING="0" +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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" +> </TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </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/bibliography.html b/java/docs/feature/bibliography.html new file mode 100644 index 0000000..0770682 --- /dev/null +++ b/java/docs/feature/bibliography.html @@ -0,0 +1,911 @@ +<HTML +><HEAD +><TITLE +>Bibliography</TITLE +><META +NAME="GENERATOR" +CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK +REL="HOME" +HREF="ZagrebIndex2.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" +> </TD +></TR +></TABLE +><HR +ALIGN="LEFT" +WIDTH="100%"></DIV +><A +NAME="AEN20" +></A +><H1 +><A +NAME="AEN20" +></A +>Bibliography</H1 +><DIV +CLASS="BIBLIOENTRY" +><A +NAME="BMV84" +></A +><P +>[bmv84] <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] <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] <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] <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] <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] <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] <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] <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] <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] <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] <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] <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] <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] <SPAN +CLASS="AUTHOR" +>P. Lampen, </SPAN +><SPAN +CLASS="AUTHOR" +>H. Hillig, </SPAN +><SPAN +CLASS="AUTHOR" +>A. N. Davies, </SPAN +><SPAN +CLASS="AUTHOR" +>and M. Linscheid</SPAN +>, <I +CLASS="CITETITLE" +>JCAMP-DX for Mass Spectrometry</I +>, <I +CLASS="CITETITLE" +>Appl. Spec.</I +>, 48, 1545-1552, 1994.</P +><DIV +CLASS="BIBLIOENTRYBLOCK" +STYLE="margin-left: 0.5in" +></DIV +></DIV +><DIV +CLASS="BIBLIOENTRY" +><A +NAME="ML91" +></A +><P +>[ml91] <SPAN +CLASS="AUTHOR" +>E. C. Meng </SPAN +><SPAN +CLASS="AUTHOR" +>and R. A. Lewis</SPAN +>, <I +CLASS="CITETITLE" +>{D}etermination of {M}olecular {T}opology and {A}tomic {H}ybridisation {S}tates from {H}eavy {A}tom {C}oordinates</I +>, <I +CLASS="CITETITLE" +>J. Comp. Chem.</I +>, 12, 891-898, 1991.</P +><DIV +CLASS="BIBLIOENTRYBLOCK" +STYLE="margin-left: 0.5in" +></DIV +></DIV +><DIV +CLASS="BIBLIOENTRY" +><A +NAME="MOR65" +></A +><P +>[mor65] <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] <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] <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] <SPAN +CLASS="AUTHOR" +>G. V. Gkoutos, </SPAN +><SPAN +CLASS="AUTHOR" +>P. Murray-Rust, </SPAN +><SPAN +CLASS="AUTHOR" +>H. S. Rzepa, </SPAN +><SPAN +CLASS="AUTHOR" +>and M. Wright</SPAN +>, <I +CLASS="CITETITLE" +>Chemical markup, XML, and the world-wide web. 3. toward a signed semantic chemical web of trust</I +>, <I +CLASS="CITETITLE" +>J. Chem. Inf. Comput. Sci.</I +>, 41, 1295-1300, 2001.</P +><DIV +CLASS="BIBLIOENTRYBLOCK" +STYLE="margin-left: 0.5in" +></DIV +></DIV +><DIV +CLASS="BIBLIOENTRY" +><A +NAME="MSG99" +></A +><P +>[msg99] <SPAN +CLASS="AUTHOR" +>M. C. Hemmer, </SPAN +><SPAN +CLASS="AUTHOR" +>V. Steinhauer, </SPAN +><SPAN +CLASS="AUTHOR" +>and J. Gasteiger</SPAN +>, <I +CLASS="CITETITLE" +>Deriving the 3D Structure of Organic Molecules from their Infrared Spectra</I +>, <I +CLASS="CITETITLE" +>Vibrat. Spect.</I +>, 19, 63-67, 1999.</P +><DIV +CLASS="BIBLIOENTRYBLOCK" +STYLE="margin-left: 0.5in" +></DIV +></DIV +><DIV +CLASS="BIBLIOENTRY" +><A +NAME="SDF" +></A +><P +>[sdf] 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] 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] 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] <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] <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] <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] <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] <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] <SPAN +CLASS="AUTHOR" +>W. P. Walters </SPAN +><SPAN +CLASS="AUTHOR" +>and S. H. Yalkowsky</SPAN +>, <I +CLASS="CITETITLE" +>ESCHER-A Computer Program for the Determination of External Rotational Symmetry Numbers from Molecular Topology</I +>, <I +CLASS="CITETITLE" +>J. Chem. Inf. Comput. Sci.</I +>, 36, 1015-1017, 1996.</P +><DIV +CLASS="BIBLIOENTRYBLOCK" +STYLE="margin-left: 0.5in" +></DIV +></DIV +><DIV +CLASS="BIBLIOENTRY" +><A +NAME="WZ03" +></A +><P +>[wz03] <SPAN +CLASS="AUTHOR" +>J. K. Wegner </SPAN +><SPAN +CLASS="AUTHOR" +>and A. Zell</SPAN +>, <I +CLASS="CITETITLE" +>Prediction of Aqueous Solubility and Partition Coefficient Optimized by a Genetic Algorithm Based Descriptor Selection Method</I +>, <I +CLASS="CITETITLE" +>J. Chem. Inf. Comput. Sci.</I +>, 43, 1077-1084, 2003.</P +><DIV +CLASS="BIBLIOENTRYBLOCK" +STYLE="margin-left: 0.5in" +></DIV +></DIV +><DIV +CLASS="BIBLIOENTRY" +><A +NAME="WFZ04A" +></A +><P +>[wfz04a] <SPAN +CLASS="AUTHOR" +>J. K. Wegner, </SPAN +><SPAN +CLASS="AUTHOR" +>H. Froehlich, </SPAN +><SPAN +CLASS="AUTHOR" +>and A. Zell</SPAN +>, <I +CLASS="CITETITLE" +>Feature Selection for Descriptor based Classification Models. 1. Theory and GA-SEC Algorithm</I +>, <I +CLASS="CITETITLE" +>J. Chem. Inf. Comput. Sci.</I +>, 44, ASAP alert, 2004.</P +><DIV +CLASS="BIBLIOENTRYBLOCK" +STYLE="margin-left: 0.5in" +></DIV +></DIV +><DIV +CLASS="BIBLIOENTRY" +><A +NAME="WFZ04B" +></A +><P +>[wfz04b] <SPAN +CLASS="AUTHOR" +>J. K. Wegner, </SPAN +><SPAN +CLASS="AUTHOR" +>H. Froehlich, </SPAN +><SPAN +CLASS="AUTHOR" +>and A. Zell</SPAN +>, <I +CLASS="CITETITLE" +>Feature Selection for Descriptor based Classification Models. 2. Human Intestinal Absorption</I +>, <I +CLASS="CITETITLE" +>J. Chem. Inf. Comput. Sci.</I +>, 44, ASAP alert, 2004.</P +><DIV +CLASS="BIBLIOENTRYBLOCK" +STYLE="margin-left: 0.5in" +></DIV +></DIV +><DIV +CLASS="BIBLIOENTRY" +><A +NAME="ZUP89" +></A +><P +>[zup89] <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="ZagrebIndex2.html" +ACCESSKEY="H" +>Home</A +></TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +> </TD +></TR +><TR +><TD +WIDTH="33%" +ALIGN="left" +VALIGN="top" +>Bibliography</TD +><TD +WIDTH="34%" +ALIGN="center" +VALIGN="top" +> </TD +><TD +WIDTH="33%" +ALIGN="right" +VALIGN="top" +> </TD +></TR +></TABLE +></DIV +></BODY +></HTML +>
\ No newline at end of file diff --git a/java/docs/feature/formulas/alpha.gif b/java/docs/feature/formulas/alpha.gif Binary files differnew file mode 100644 index 0000000..ce58924 --- /dev/null +++ b/java/docs/feature/formulas/alpha.gif diff --git a/java/docs/feature/formulas/autocorrelation.gif b/java/docs/feature/formulas/autocorrelation.gif Binary files differnew file mode 100644 index 0000000..d22ffd1 --- /dev/null +++ b/java/docs/feature/formulas/autocorrelation.gif diff --git a/java/docs/feature/formulas/cets.gif b/java/docs/feature/formulas/cets.gif Binary files differnew file mode 100644 index 0000000..9663110 --- /dev/null +++ b/java/docs/feature/formulas/cets.gif diff --git a/java/docs/feature/formulas/chi_iA.gif b/java/docs/feature/formulas/chi_iA.gif Binary files differnew file mode 100644 index 0000000..91cf9eb --- /dev/null +++ b/java/docs/feature/formulas/chi_iA.gif diff --git a/java/docs/feature/formulas/ctd.gif b/java/docs/feature/formulas/ctd.gif Binary files differnew file mode 100644 index 0000000..f65f86e --- /dev/null +++ b/java/docs/feature/formulas/ctd.gif diff --git a/java/docs/feature/formulas/delta.gif b/java/docs/feature/formulas/delta.gif Binary files differnew file mode 100644 index 0000000..ccf925c --- /dev/null +++ b/java/docs/feature/formulas/delta.gif diff --git a/java/docs/feature/formulas/delta_i.gif b/java/docs/feature/formulas/delta_i.gif Binary files differnew file mode 100644 index 0000000..92fd91e --- /dev/null +++ b/java/docs/feature/formulas/delta_i.gif diff --git a/java/docs/feature/formulas/delta_i_nu.gif b/java/docs/feature/formulas/delta_i_nu.gif Binary files differnew file mode 100644 index 0000000..a8db468 --- /dev/null +++ b/java/docs/feature/formulas/delta_i_nu.gif diff --git a/java/docs/feature/formulas/egs.gif b/java/docs/feature/formulas/egs.gif Binary files differnew file mode 100644 index 0000000..9eb1c8e --- /dev/null +++ b/java/docs/feature/formulas/egs.gif diff --git a/java/docs/feature/formulas/elctronegativity_charge.gif b/java/docs/feature/formulas/elctronegativity_charge.gif Binary files differnew file mode 100644 index 0000000..8e8f313 --- /dev/null +++ b/java/docs/feature/formulas/elctronegativity_charge.gif diff --git a/java/docs/feature/formulas/electronegativity_charge.gif b/java/docs/feature/formulas/electronegativity_charge.gif Binary files differnew file mode 100644 index 0000000..09a4ae0 --- /dev/null +++ b/java/docs/feature/formulas/electronegativity_charge.gif diff --git a/java/docs/feature/formulas/ets.gif b/java/docs/feature/formulas/ets.gif Binary files differnew file mode 100644 index 0000000..dbba541 --- /dev/null +++ b/java/docs/feature/formulas/ets.gif diff --git a/java/docs/feature/formulas/graphpotentials_1.gif b/java/docs/feature/formulas/graphpotentials_1.gif Binary files differnew file mode 100644 index 0000000..6214a62 --- /dev/null +++ b/java/docs/feature/formulas/graphpotentials_1.gif diff --git a/java/docs/feature/formulas/istate.gif b/java/docs/feature/formulas/istate.gif Binary files differnew file mode 100644 index 0000000..878cc08 --- /dev/null +++ b/java/docs/feature/formulas/istate.gif diff --git a/java/docs/feature/formulas/kier1.gif b/java/docs/feature/formulas/kier1.gif Binary files differnew file mode 100644 index 0000000..bf5580c --- /dev/null +++ b/java/docs/feature/formulas/kier1.gif diff --git a/java/docs/feature/formulas/kier1_1.gif b/java/docs/feature/formulas/kier1_1.gif Binary files differnew file mode 100644 index 0000000..50dff33 --- /dev/null +++ b/java/docs/feature/formulas/kier1_1.gif diff --git a/java/docs/feature/formulas/kier1_2.gif b/java/docs/feature/formulas/kier1_2.gif Binary files differnew file mode 100644 index 0000000..38628bb --- /dev/null +++ b/java/docs/feature/formulas/kier1_2.gif diff --git a/java/docs/feature/formulas/kier2.gif b/java/docs/feature/formulas/kier2.gif Binary files differnew file mode 100644 index 0000000..196b247 --- /dev/null +++ b/java/docs/feature/formulas/kier2.gif diff --git a/java/docs/feature/formulas/kier2_1.gif b/java/docs/feature/formulas/kier2_1.gif Binary files differnew file mode 100644 index 0000000..7261e18 --- /dev/null +++ b/java/docs/feature/formulas/kier2_1.gif diff --git a/java/docs/feature/formulas/kier3.gif b/java/docs/feature/formulas/kier3.gif Binary files differnew file mode 100644 index 0000000..4fd0c28 --- /dev/null +++ b/java/docs/feature/formulas/kier3.gif diff --git a/java/docs/feature/formulas/kier3_1.gif b/java/docs/feature/formulas/kier3_1.gif Binary files differnew file mode 100644 index 0000000..249e02d --- /dev/null +++ b/java/docs/feature/formulas/kier3_1.gif diff --git a/java/docs/feature/formulas/nu_i.gif b/java/docs/feature/formulas/nu_i.gif Binary files differnew file mode 100644 index 0000000..f528742 --- /dev/null +++ b/java/docs/feature/formulas/nu_i.gif diff --git a/java/docs/feature/formulas/rdf.gif b/java/docs/feature/formulas/rdf.gif Binary files differnew file mode 100644 index 0000000..4e70121 --- /dev/null +++ b/java/docs/feature/formulas/rdf.gif diff --git a/java/docs/feature/formulas/rdf2.gif b/java/docs/feature/formulas/rdf2.gif Binary files differnew file mode 100644 index 0000000..29e9b1d --- /dev/null +++ b/java/docs/feature/formulas/rdf2.gif diff --git a/java/docs/feature/formulas/zagreb1.gif b/java/docs/feature/formulas/zagreb1.gif Binary files differnew file mode 100644 index 0000000..1db393b --- /dev/null +++ b/java/docs/feature/formulas/zagreb1.gif diff --git a/java/docs/feature/formulas/zagreb2.gif b/java/docs/feature/formulas/zagreb2.gif Binary files differnew file mode 100644 index 0000000..2b313eb --- /dev/null +++ b/java/docs/feature/formulas/zagreb2.gif diff --git a/java/docs/literature.html b/java/docs/literature.html new file mode 100644 index 0000000..c414bd9 --- /dev/null +++ b/java/docs/literature.html @@ -0,0 +1,44 @@ +<b><i>Article</i><a name=\"bk02\"> (bk02)</a></b>, M. Böhm & G. Klebe, Development of New Hydrogen--Bond Descriptors and Their Application to Comparative Molecular Field Analyses , <em>J. Med. Chem., </em> <b>2002</b> <i>, 45</i> , 1585-1597.
+<b><i>Article</i><a name=\"bmv84\"> (bmv84)</a></b>, P. Broto; G. Moreau & C. Vandycke, Molecular Structures: Perception, Autocorrelation Descriptor and SAR Studies , <em>Eur. J. Med. Chem., </em> <b>1984</b> <i>, 19</i> , 66-70.
+<b><i>Book</i><a name=\"br90\"> (br90)</a></b>, D. Bonchev & D. H. Rouvray, D. Bonchev & D. H. Rouvray <i>(ed.)</i>, Chemical Graph Theory: Introduction and Fundamentals , <em>Gordon and Breach Science Publishers, </em> <b>1990</b> <i>, 1</i>.
+<b><i>Article</i><a name=\"bs93\"> (bs93)</a></b>, B.L.Bush & R.P.Sheridan, PATTY: A Programmable Atom Typer and Language for Automatic Classification of Atoms in Molecular Databases. , <em>J. Chem. Inf. Comput. Sci., </em> <b>1993</b> <i>, 33</i> , 756-762.
+<b><i>Inbook</i><a name=\"clr98bfs\"> (clr98bfs)</a></b>, T. H. Cormen; C. E. Leiserson & R. L. Rivest, Introduction to Algorithms , 23.2, <em>MIT--Press, </em> <b>1998</b> , 469-477.
+<b><i>Inbook</i><a name=\"clr98complexity\"> (clr98complexity)</a></b>, T. H. Cormen; C. E. Leiserson & R. L. Rivest, Introduction to Algorithms , 2, <em>MIT--Press, </em> <b>1998</b> , 23-41.
+<b><i>Inbook</i><a name=\"clr98dfs\"> (clr98dfs)</a></b>, T. H. Cormen; C. E. Leiserson & R. L. Rivest, Introduction to Algorithms , 23.3, <em>MIT--Press, </em> <b>1998</b> , 477-483.
+<b><i>Incollection</i><a name=\"dhl90\"> (dhl90)</a></b>, A.N. Davies; H. Hilling & M. Linscheid, J. Gasteiger <i>(ed.)</i>, JCAMP--DX, a standard ? , <em>Springer--Verlag, </em> <b>1990</b> , 147-156.
+<b><i>Article</i><a name=\"dl93\"> (dl93)</a></b>, A. N. Davies & P. Lampen, JCAMP--DX for NMR , <em>Appl. Spec., </em> <b>1993</b> <i>, 47</i> , 1093-1099.
+<b><i>Article</i><a name=\"dw88\"> (dw88)</a></b>, R. S. Mc Donald & Paul A. Wilks, JCAMP--DX: A Standard Form for Exchange of Infrared Spectra in Computer Readable Form , <em>Appl. Spec., </em> <b>1988</b> <i>, 42</i> , 151-162 . <b><i>Article</i><a name=\"ers00\"> (ers00)</a></b>, P. Ertl; B. Rohde & P. Selzer, Fast Calculation of Molecular Polar Surface Area as a Sum of Fragment-Based Contributions and Its Application to the Prediction of Drug Transport Properties , <em>J. Med. Chem. 2000, 43, 3714-3717, </em> <b>2000</b> <i>, 43</i> , 3714-3717.
+<b><i>Article</i><a name=\"fig96\"> (fig96)</a></b>, J. Figueras, Ring Perception Using Breadth--First Search , <em>J. Chem. Inf. Comput. Sci., </em> <b>1996</b> <i>, 36</i> , 986-991.
+<b><i>Article</i><a name=\"ghhjs91\"> (ghhjs91)</a></b>, J. Gasteiger; B. M. P. Hendriks; P. Hoever; C. Jochum & H. Somberg, JCAMP--CS: A Standard Format for Chemical Structure Information in Computer Readable Form , <em>Appl. Spec., </em> <b>1991</b> <i>, 45</i> , 4-11.
+<b><i>Article</i><a name=\"gm78\"> (gm78)</a></b>, J. Gasteiger & M. Marsili, A New Model for Calculating Atomic Charges in Molecules , <em>Tetrahedron Lett., </em> <b>1978</b> , 3181-3184.
+<b><i>Article</i><a name=\"gmrw01\"> (gmrw01)</a></b>, G. V. Gkoutos; P. Murray--Rust; S. Rzepa & M. Wright, Chemical Markup, XML, and the World--Wide Web. 3. Toward a Signed Semantic Chemical Web of Trust , <em>J. Chem. Inf. Comput. Sci., </em> <b>2001</b> <i>, 41</i> , 1295-1300 . <a href=\"http://dx.doi.org/10.1021/ci000406v\">DOI: 10.1021/ci000406v</a>.
+<b><i>Article</i><a name=\"gwb98\"> (gwb98)</a></b>, J. Gillet; P. Willett & J. Bradshaw, Identification of Biological Activity Profiles Using Substructural Analysis and Genetic Algorithms , <em>J. Chem. Inf. Comput. Sci., </em> <b>1998</b> <i>, 38</i> , 165-179.
+<b><i>Article</i><a name=\"gxsb00\"> (gxsb00)</a></b>, L. Xue; F. L. Stahura; J. W. Godden & J. Bajorath, Searching for molecules with similar biological activity: analysis by fingerprint profiling , <em>Pac. Symp. Biocomput., </em> <b>2000</b> <i>, 8</i> , 566-575.
+<b><i>Misc</i><a name=\"jwd00\"> (jwd00)</a></b>, C. A. James; D. Weininger & J. Delany, Daylight Theory Manual.
+<b><i>Article</i><a name=\"lhdl94\"> (lhdl94)</a></b>, P. Lampen; H. Hillig; A. N. Davies & Michael Linscheid, JCAMP--DX for Mass Spectrometry , <em>Appl. Spec., </em> <b>1994</b> <i>, 48</i> , 1545-1552.
+<b><i>Article</i><a name=\"lldf01\"> (lldf01)</a></b>, C. A. Lipinski; F. Lombardo; B. W. Dominy & P. J. Feeney, Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings , <em>Adv. Drug Delivery Reviews, </em> <b>2001</b> <i>, 46</i> , 3-26.
+<b><i>Misc</i><a name=\"mdlMolFormat\"> (mdlMolFormat)</a></b>, MDL Information Systems, Inc., MDL CTfile Formats.
+<b><i>Article</i><a name=\"ml91\"> (ml91)</a></b>, E. C. Meng & R. A. Lewis, Determination of Molecular Topology and Atomic Hybridisation States from Heavy Atom Coordinates , <em>J. Comp. Chem., </em> <b>1991</b> <i>, 12</i> , 891-898.
+<b><i>Article</i><a name=\"mor65\"> (mor65)</a></b>, H. L. Morgan, The Generation of a Unique Machine Description for Chemical Structures -- A Technique Developed at Chemical Abstracts Service. , <em>J. Chem. Doc., </em> <b>1965</b> <i>, 5</i> , 107-113.
+<b><i>Article</i><a name=\"mr01\"> (mr01)</a></b>, P. Murray--Rust & H. S. Rzepa, Chemical Markup, XML and the World--Wide Web. 2. Information Objects and the CMLDOM , <em>J. Chem. Inf. Comput. Sci., </em> <b>2001</b> <i>, 41</i> , 1113-1123 . <a href=\"http://dx.doi.org/10.1021/ci000404a\">DOI: 10.1021/ci000404a</a>.
+<b><i>Article</i><a name=\"mr03\"> (mr03)</a></b>, P. Murray--Rust & H. S. Rzepa, Chemical Markup, XML and the World--Wide Web. 4. CML Schema , <em>J. Chem. Inf. Comput. Sci., </em> <b>2003</b> <i>, 43</i> , 757-772 . <a href=\"http://dx.doi.org/10.1021/ci0256541\">DOI: 10.1021/ci0256541</a>.
+<b><i>Article</i><a name=\"mrww04\"> (mrww04)</a></b>, P. Murray--Rust; H. S. Rzepa; J. Williamson & E. L. Willighagen, Chemical Markup, XML and the World--Wide Web. 5. Applications of Chemical Metadata in RSS Aggregators , <em>J. Chem. Inf. Comput. Sci., </em> <b>2004</b> <i>, 44</i> , 462-469 . <a href=\"http://dx.doi.org/10.1021/ci034244p\">DOI: 10.1021/ci034244p</a>.
+<b><i>Article</i><a name=\"odtl01\"> (odtl01)</a></b>, T. I. Oprea; A. M. Davis; S. J. Teague & P. D. Leeson, Is There a Difference between Leads and Drugs? A Historical Perspective , <em>J. Chem. Inf. Comput. Sci., </em> <b>2001</b> <i>, 41</i> , 1308-1315 . <a href=\"http://dx.doi.org/10.1021/ci010366a\">DOI: 10.1021/ci010366a</a>.
+<b><i>Misc</i><a name=\"pdbFormat\"> (pdbFormat)</a></b>, Protein Data Bank (PDB) File Format , <b>2002</b>.
+<b><i>Misc</i><a name=\"povray\"> (povray)</a></b>, POV--Team, Persistence of Vision Raytracer (POVRay).
+<b><i>Article</i><a name=\"rr99b\"> (rr99b)</a></b>, P. Murray--Rust & H. S. Rzepa, Chemical Markup, XML, and the Worldwide Web. 1. Basic Principles , <em>J. Chem. Inf. Comput. Sci., </em> <b>1999</b> <i>, 39</i> , 928-942 . <a href=\"http://dx.doi.org/10.1021/ci990052b\">DOI: 10.1021/ci990052b</a>.
+<b><i>Manual</i><a name=\"smarts\"> (smarts)</a></b>, Daylight Chemical Information Systems, Inc., Smiles ARbitrary Target Specification (SMARTS).
+<b><i>Manual</i><a name=\"smilesFormat\"> (smilesFormat)</a></b>, Daylight Chemical Information Systems, Inc., Simplified Molecular Input Line Entry System (SMILES).
+<b><i>Manual</i><a name=\"sybylmol2\"> (sybylmol2)</a></b>, Tripos, Tripos Mol2 File Format.
+<b><i>Inbook</i><a name=\"tc00kiershape\"> (tc00kiershape)</a></b>, R. Todeschini & V. Consonni, Handbook of Molecular Descriptors , K, <em>Wiley--VCH, </em> <b>2000</b> , 248-250.
+<b><i>Inbook</i><a name=\"tc00zagrebgroup\"> (tc00zagrebgroup)</a></b>, R. Todeschini & V. Consonni, Handbook of Molecular Descriptors , Z, <em>Wiley--VCH, </em> <b>2000</b> , 509.
+<b><i>Book</i><a name=\"tri92\"> (tri92)</a></b>, N. Trinajsti, Chemical Graph Theory , <em>CRC Press, Florida, U.S.A., </em> <b>1992</b>.
+<b><i>Article</i><a name=\"wc99\"> (wc99)</a></b>, S. A. Wildman & G. M. Crippen, Prediction of Physicochemical Parameters by Atomic Contributions , <em>J. Chem. Inf. Comput. Sci., </em> <b>1999</b> <i>, 39</i> , 868-873.
+<b><i>Article</i><a name=\"wei88\"> (wei88)</a></b>, D. Weininger, SMILES, a Chemical Language for Information Systems. 1. Introduction to Methodology and Encoding Rules. , <em>J. Chem. Inf. Comput. Sci., </em> <b>1988</b> <i>, 28</i> , 31-36.
+<b><i>Article</i><a name=\"wfz04a\"> (wfz04a)</a></b>, Wegner, J. K.; Fröhlich, H. & Zell, A., Feature selection for Descriptor based Classification Models. 1. Theory and GA--SEC Algorithm , <em>J. Chem. Inf. Comput. Sci., </em> <b>2004</b> <i>, 44</i> . <a href=\"http://dx.doi.org/10.1021/ci0342324\">DOI: 10.1021/ci0342324</a>.
+<b><i>Article</i><a name=\"wfz04b\"> (wfz04b)</a></b>, J. K. Wegner; H. Fröhlich & A. Zell, Feature selection for Descriptor based Classification Models. 2. Human Intestinal Absorption (HIA) , <em>J. Chem. Inf. Comput. Sci., </em> <b>2004</b> <i>, 44</i> . <a href=\"http://dx.doi.org/10.1021/ci034233w\">DOI: 10.1021/ci034233w</a>.
+<b><i>Article</i><a name=\"wil01\"> (wil01)</a></b>, E. L. Willighagen, Processing CML Conventions in Java , <em>Internet Journal of Chemistry, </em> <b>2001</b> <i>, 4</i> , 4.
+<b><i>Article</i><a name=\"www89\"> (www89)</a></b>, D. Weininger; A. Weininger & J. L. Weininger, Algorithm for generation of unique SMILES notation , <em>J. Chem. Inf. Comput. Sci., </em> <b>1989</b> <i>, 29</i> , 97-101.
+<b><i>Article</i><a name=\"wy96\"> (wy96)</a></b>, W. P. Walters & S. H. Yalkowsky, ESCHER--A Computer Program for the Determination of External Rotational Symmetry Numbers from Molecular Topology , <em>J. Chem. Inf. Comput. Sci., </em> <b>1996</b> <i>, 36</i> , 1015-1017.
+<b><i>Article</i><a name=\"wz03\"> (wz03)</a></b>, Wegner, J. K. & Zell, A., Prediction of Aqueous Solubility and Partition Coefficient Optimized by a Genetic Algorithm Based Descriptor Selection Method , <em>J. Chem. Inf. Comput. Sci., </em> <b>2003</b> <i>, 43</i> , 1077-1084 . <a href=\"http://dx.doi.org/10.1021/ci034006u\">DOI: 10.1021/ci034006u</a>.
+<b><i>Inbook</i><a name=\"zup89c\"> (zup89c)</a></b>, J. Zupan, Algorithms for Chemists , <em>Wiley, </em> <b>1989</b> , 102-142 .
\ No newline at end of file diff --git a/java/docs/literature.tex b/java/docs/literature.tex new file mode 100644 index 0000000..1befd3f --- /dev/null +++ b/java/docs/literature.tex @@ -0,0 +1,34 @@ +%
+% Filename: $RCSfile: literature.tex,v $
+% Authors: Joerg Wegner
+% Version: $Revision: 1.1.1.1 $
+% $Date: 2004/12/06 15:33:07 $
+% $Author: wegner $
+% Copyright (c) Joerg Wegner; CCC Computer Chemistry Center, Germany
+%
+% ------------------------------------------------------------------------
+% AMS-LaTeX Bibliography *************************************************
+% ------------------------------------------------------------------------
+\documentclass[11pt]{amsart}
+\usepackage[inactive]{srcltx}
+% **** -------------------------------------------------------------------
+\vfuzz1pc % Don't bother to report overfull boxes if over-edge is < 1pc
+\hfuzz1pc % Don't bother to report overfull boxes if over-edge is < 1pc
+
+%-------------------------------------------------------------------------------------------
+% JUST FOR TTH USERS !;-)
+%-------------------------------------------------------------------------------------------
+%%tth:\begin{html}<title>Literature JOELib, J.K. Wegner, 2003</title>\end{html}
+%%tth:\begin{html}<body bgcolor="#FFFFFF">\end{html}
+%-------------------------------------------------------------------------------------------
+
+%%% TITLE ----------------------------------------------------------------
+%%% ----------------------------------------------------------------------
+\begin{document}
+% ------------------------------------------------------------------------
+\nocite{*}
+% ------------------------------------------------------------------------
+\bibliographystyle{angewandte_chemie}
+\bibliography{literature}
+\end{document}
+% ------------------------------------------------------------------------
|
