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Diffstat (limited to 'java/docs')
170 files changed, 0 insertions, 11084 deletions
diff --git a/java/docs/algo/APropertyBFS.html b/java/docs/algo/APropertyBFS.html deleted file mode 100644 index df26fb7..0000000 --- a/java/docs/algo/APropertyBFS.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.APROPERTYBFS" -></A ->Valence</H2 -><P ->Breadth first search calculating the distance only between boolean atom properties (default: Atom in conjugated environment).</P -></DIV -></DIV -></DIV -><DIV -CLASS="NAVFOOTER" -><HR -ALIGN="LEFT" -WIDTH="100%"><TABLE -SUMMARY="Footer navigation table" -WIDTH="100%" -BORDER="0" -CELLPADDING="0" -CELLSPACING="0" -><TR -><TD -WIDTH="33%" -ALIGN="left" -VALIGN="top" -> </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 deleted file mode 100644 index 47c782c..0000000 --- a/java/docs/algo/BreadthFirstSearch.html +++ /dev/null @@ -1,122 +0,0 @@ -<HTML
-><HEAD
-><TITLE
-></TITLE
-><META
-NAME="GENERATOR"
-CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
-REL="NEXT"
-TITLE="Bibliography"
-HREF="bibliography.html"></HEAD
-><BODY
-CLASS="ARTICLE"
-BGCOLOR="#FFFFFF"
-TEXT="#000000"
-LINK="#0000FF"
-VLINK="#840084"
-ALINK="#0000FF"
-><DIV
-CLASS="ARTICLE"
-><DIV
-CLASS="SECT1"
-><H1
-CLASS="SECT1"
-><A
-NAME="JOELIB.ALGORITHMS.BREADTHFIRSTSEARCH"
-></A
->Breadth First Search (BFS)</H1
-><P
-> 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 deleted file mode 100644 index a4afe64..0000000 --- a/java/docs/algo/DepthFirstSearch.html +++ /dev/null @@ -1,137 +0,0 @@ -<HTML
-><HEAD
-><TITLE
-></TITLE
-><META
-NAME="GENERATOR"
-CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
-REL="NEXT"
-TITLE="Bibliography"
-HREF="bibliography.html"></HEAD
-><BODY
-CLASS="ARTICLE"
-BGCOLOR="#FFFFFF"
-TEXT="#000000"
-LINK="#0000FF"
-VLINK="#840084"
-ALINK="#0000FF"
-><DIV
-CLASS="ARTICLE"
-><DIV
-CLASS="SECT1"
-><H1
-CLASS="SECT1"
-><A
-NAME="JOELIB.ALGORITHMS.DEPTHFIRSTSEARCH"
-></A
->Depth First Search (DFS)</H1
-><P
->The DFS method performs a depth--first search [<A
-HREF="bibliography.html#CLR98"
->clr98</A
->] of a graph.
-A depth--first search visits vertices that are further to the
-source before visiting vertices that are closer away. In this
-context `distance' is defined as the number of edges in the
-shortest path from the source vertex.
-<DIV
-CLASS="FIGURE"
-><A
-NAME="JOELIB.ALGORITHMS.DEPTHFIRSTSEARCH.PSEUDOCODE"
-></A
-><P
-><B
->Figure 1. Pseudocode for the DFS algorithm</B
-></P
-><PRE
-CLASS="PROGRAMLISTING"
->DFS(G)
- {
- For each v in V,
- {
- color[v]=white;
- pred[u]=NULL
- }
-
- time=0;
- For each u in V
- If (color[u]=white) DFSVISIT(u)
- }
-
-
- DFSVISIT(u)
- {
- color[u]=gray;
- d[u] = ++time;
-
- For each v in Adj(u) do
- If (color[v] = white)
- {
- pred[v] = u;
- DFSVISIT(v);
- }
-
- color[u] = black; f[u]=++time;
- }</PRE
-></DIV
->
-The time complexity is <IMG
-SRC="formulas/o_e+v.gif"> [<A
-HREF="bibliography.html#CLR98"
->clr98</A
->].</P
-></DIV
-></DIV
-><DIV
-CLASS="NAVFOOTER"
-><HR
-ALIGN="LEFT"
-WIDTH="100%"><TABLE
-SUMMARY="Footer navigation table"
-WIDTH="100%"
-BORDER="0"
-CELLPADDING="0"
-CELLSPACING="0"
-><TR
-><TD
-WIDTH="33%"
-ALIGN="left"
-VALIGN="top"
-> </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 deleted file mode 100644 index 6a745e7..0000000 --- a/java/docs/algo/DistanceMatrix.html +++ /dev/null @@ -1,102 +0,0 @@ -<HTML
-><HEAD
-><TITLE
-></TITLE
-><META
-NAME="GENERATOR"
-CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
-REL="NEXT"
-TITLE="Bibliography"
-HREF="bibliography.html"></HEAD
-><BODY
-CLASS="ARTICLE"
-BGCOLOR="#FFFFFF"
-TEXT="#000000"
-LINK="#0000FF"
-VLINK="#840084"
-ALINK="#0000FF"
-><DIV
-CLASS="ARTICLE"
-><DIV
-CLASS="SECT1"
-><H1
-CLASS="SECT1"
-><A
-NAME="JOELIB.ALGORITHMS.DISTANCEMATRIX"
-></A
->Topological distance matrix</H1
-><P
->Calculates the topological distances between all atom pairs.
-Here a simple Breadth First Search (BFS )
-is used to calculate these distances, which causes a running time of
-<SPAN
-CLASS="bold"
-><B
-CLASS="EMPHASIS"
->O(A<SUP
->3</SUP
->)</B
-></SPAN
->, where
-<SPAN
-CLASS="bold"
-><B
-CLASS="EMPHASIS"
->A</B
-></SPAN
-> is the number of atoms.</P
-></DIV
-></DIV
-><DIV
-CLASS="NAVFOOTER"
-><HR
-ALIGN="LEFT"
-WIDTH="100%"><TABLE
-SUMMARY="Footer navigation table"
-WIDTH="100%"
-BORDER="0"
-CELLPADDING="0"
-CELLSPACING="0"
-><TR
-><TD
-WIDTH="33%"
-ALIGN="left"
-VALIGN="top"
-> </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 deleted file mode 100644 index 76488d9..0000000 --- a/java/docs/algo/GeomDistanceMatrix.html +++ /dev/null @@ -1,84 +0,0 @@ -<HTML
-><HEAD
-><TITLE
-></TITLE
-><META
-NAME="GENERATOR"
-CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
-REL="NEXT"
-TITLE="Bibliography"
-HREF="bibliography.html"></HEAD
-><BODY
-CLASS="ARTICLE"
-BGCOLOR="#FFFFFF"
-TEXT="#000000"
-LINK="#0000FF"
-VLINK="#840084"
-ALINK="#0000FF"
-><DIV
-CLASS="ARTICLE"
-><DIV
-CLASS="SECT1"
-><H1
-CLASS="SECT1"
-><A
-NAME="JOELIB.ALGORITHMS.GEOMDISTANCEMATRIX"
-></A
->Geometrical distance matrix</H1
-><P
->The geometrical distance matrix calculates the euklidian distance between the 3D coordinates of all atom pairs.</P
-></DIV
-></DIV
-><DIV
-CLASS="NAVFOOTER"
-><HR
-ALIGN="LEFT"
-WIDTH="100%"><TABLE
-SUMMARY="Footer navigation table"
-WIDTH="100%"
-BORDER="0"
-CELLPADDING="0"
-CELLSPACING="0"
-><TR
-><TD
-WIDTH="33%"
-ALIGN="left"
-VALIGN="top"
-> </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 deleted file mode 100644 index 0a20be3..0000000 --- a/java/docs/algo/Morgan.html +++ /dev/null @@ -1,157 +0,0 @@ -<HTML
-><HEAD
-><TITLE
-></TITLE
-><META
-NAME="GENERATOR"
-CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
-REL="NEXT"
-TITLE="Bibliography"
-HREF="bibliography.html"></HEAD
-><BODY
-CLASS="ARTICLE"
-BGCOLOR="#FFFFFF"
-TEXT="#000000"
-LINK="#0000FF"
-VLINK="#840084"
-ALINK="#0000FF"
-><DIV
-CLASS="ARTICLE"
-><DIV
-CLASS="SECT1"
-><H1
-CLASS="SECT1"
-><A
-NAME="JOELIB.ALGORITHMS.MORGAN"
-></A
->Morgan: Unique atom numbering</H1
-><P
->Algorithm to get a unique numbering for molecules (graphs) [<A
-HREF="bibliography.html#MOR65"
->mor65</A
->].
-<DIV
-CLASS="FIGURE"
-><A
-NAME="JOELIB.ALGORITHMS.MORGAN.LABELING.PSEUDOCODE"
-></A
-><P
-><B
->Figure 1. Pseudocode for the Morgan labeling algorithm</B
-></P
-><PRE
-CLASS="PROGRAMLISTING"
->label each atom with its degree;
-labels=count the number of different labels;
-hasNTchanged=5;
-for all time
- label each atom with sum of label+all neighbor labels;
- actLabels=count the number of different labels;
- if actLabels equal labels then
- decrement hasNTchanged;
- if hasNTchanged is zero break loop;
- fi
-rof</PRE
-></DIV
->
-The sloppy breaking criteria is necessary, because it's possible that the number of different labels can be
-constant for only two iterations. But that's not so interesting, let's continue with the
-renumbering part of the Morgan algorithm. As you can see, it's possible, that 'symmetric' atoms in the
-molecule will have same labels. Is there now a possibility to solve these 'labeling/renumbering' ties ?
-Yes, additional informations, like bond order and element number can be used for resolving renumbering ties
-or the suggested Jochum-Gasteiger canonical renumbering [<A
-HREF="bibliography.html#TC00"
->tc00</A
->] informations can be used.
-<DIV
-CLASS="FIGURE"
-><A
-NAME="JOELIB.ALGORITHMS.MORGAN.RENUMBERING.PSEUDOCODE"
-></A
-><P
-><B
->Figure 2. Pseudocode for the Morgan renumbering algorithm</B
-></P
-><PRE
-CLASS="PROGRAMLISTING"
->calculate the morgan atom labels;
-start breadth first search from this atom;
-choose node with the highest label and set new atom index to 1;
-repeat
- build deque i of atoms with same BFS traversing number i;
- if deque i contains no equal labels
- renumber atoms in order of decreasing atom labels.
- fi
- else
- try to resolve renumbering tie for the equal labels:
- 1. prefer atom with higher bond order for renumbering
- 2. prefer atom with higher element number for renumbering
- 3. ...
- if tie solved
- renumber atoms in order of decreasing atom labels.
- fi
- else
- show renumbering tie warning;
- esle
- esle
- increment i;
-until all atoms are numbered</PRE
-></DIV
->
-The uniquely renumbered molecule can be used to calculate molecule
-hashcodes and canonical/unique SMILES representations (see ).</P
-></DIV
-></DIV
-><DIV
-CLASS="NAVFOOTER"
-><HR
-ALIGN="LEFT"
-WIDTH="100%"><TABLE
-SUMMARY="Footer navigation table"
-WIDTH="100%"
-BORDER="0"
-CELLPADDING="0"
-CELLSPACING="0"
-><TR
-><TD
-WIDTH="33%"
-ALIGN="left"
-VALIGN="top"
-> </TD
-><TD
-WIDTH="34%"
-ALIGN="center"
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-> </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%"
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-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 deleted file mode 100644 index 5e0ebd1..0000000 --- a/java/docs/algo/bibliography.html +++ /dev/null @@ -1,782 +0,0 @@ -<HTML
-><HEAD
-><TITLE
->Bibliography</TITLE
-><META
-NAME="GENERATOR"
-CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
-REL="HOME"
-HREF="Morgan.html"><LINK
-REL="PREVIOUS"
-TITLE="Bibliography"
-HREF="bibliography.html"></HEAD
-><BODY
-CLASS="BIBLIOGRAPHY"
-BGCOLOR="#FFFFFF"
-TEXT="#000000"
-LINK="#0000FF"
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-CLASS="NAVHEADER"
-><TABLE
-SUMMARY="Header navigation table"
-WIDTH="100%"
-BORDER="0"
-CELLPADDING="0"
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-></TH
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-><TR
-><TD
-WIDTH="10%"
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-VALIGN="bottom"
-><A
-HREF="bibliography.html"
-ACCESSKEY="P"
->Prev</A
-></TD
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-WIDTH="80%"
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-> </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"
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\ 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 differdeleted file mode 100644 index c2ac4ac..0000000 --- a/java/docs/algo/formulas/o_e+v.gif +++ /dev/null diff --git a/java/docs/feature/APropertyBFS.html b/java/docs/feature/APropertyBFS.html deleted file mode 100644 index dd46d0b..0000000 --- a/java/docs/feature/APropertyBFS.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.APROPERTYBFS" -></A ->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 deleted file mode 100644 index 056c875..0000000 --- a/java/docs/feature/APropertyDistanceMatrix.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.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 deleted file mode 100644 index 1bb2d9e..0000000 --- a/java/docs/feature/AcidicGroups.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.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 deleted file mode 100644 index f0d8a24..0000000 --- a/java/docs/feature/AliphaticOHGroups.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.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 deleted file mode 100644 index faa7fa2..0000000 --- a/java/docs/feature/AromaticBonds.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.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 deleted file mode 100644 index 781c23b..0000000 --- a/java/docs/feature/AromaticOHGroups.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -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 ->
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\ No newline at end of file diff --git a/java/docs/feature/AtomInAcceptor.html b/java/docs/feature/AtomInAcceptor.html deleted file mode 100644 index 5785a4f..0000000 --- a/java/docs/feature/AtomInAcceptor.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.ATOMINACCEPTOR" -></A ->Atom in acceptor</H2 -><P ->Is this atom a hydrogen acceptor atom.</P -></DIV -></DIV -></DIV -><DIV -CLASS="NAVFOOTER" -><HR -ALIGN="LEFT" -WIDTH="100%"><TABLE -SUMMARY="Footer navigation table" -WIDTH="100%" -BORDER="0" -CELLPADDING="0" -CELLSPACING="0" -><TR -><TD -WIDTH="33%" -ALIGN="left" -VALIGN="top" -> </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 ->
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\ No newline at end of file diff --git a/java/docs/feature/AtomInConjEnvironment.html b/java/docs/feature/AtomInConjEnvironment.html deleted file mode 100644 index 2a3289e..0000000 --- a/java/docs/feature/AtomInConjEnvironment.html +++ /dev/null @@ -1,184 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -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 deleted file mode 100644 index 61b8188..0000000 --- a/java/docs/feature/AtomInDonAcc.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -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 deleted file mode 100644 index 399b2f9..0000000 --- a/java/docs/feature/AtomInDonor.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.ATOMINDONOR" -></A ->Atom in donor</H2 -><P ->Is this atom a hydrogen donor atom.</P -></DIV -></DIV -></DIV -><DIV -CLASS="NAVFOOTER" -><HR -ALIGN="LEFT" -WIDTH="100%"><TABLE -SUMMARY="Footer navigation table" -WIDTH="100%" -BORDER="0" -CELLPADDING="0" -CELLSPACING="0" -><TR -><TD -WIDTH="33%" -ALIGN="left" -VALIGN="top" -> </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 ->
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\ No newline at end of file diff --git a/java/docs/feature/AtomIsNegative.html b/java/docs/feature/AtomIsNegative.html deleted file mode 100644 index 2754ce0..0000000 --- a/java/docs/feature/AtomIsNegative.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.ATOMISNEGATIVE" -></A ->Atom is negative</H2 -><P ->Is this atom a negative charged atom.</P -></DIV -></DIV -></DIV -><DIV -CLASS="NAVFOOTER" -><HR -ALIGN="LEFT" -WIDTH="100%"><TABLE -SUMMARY="Footer navigation table" -WIDTH="100%" -BORDER="0" -CELLPADDING="0" -CELLSPACING="0" -><TR -><TD -WIDTH="33%" -ALIGN="left" -VALIGN="top" -> </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 ->
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\ No newline at end of file diff --git a/java/docs/feature/AtomIsPositive.html b/java/docs/feature/AtomIsPositive.html deleted file mode 100644 index 4f4204d..0000000 --- a/java/docs/feature/AtomIsPositive.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.ATOMISPOSITIVE" -></A ->Atom is positive</H2 -><P ->Is this atom a positive charged atom.</P -></DIV -></DIV -></DIV -><DIV -CLASS="NAVFOOTER" -><HR -ALIGN="LEFT" -WIDTH="100%"><TABLE -SUMMARY="Footer navigation table" -WIDTH="100%" -BORDER="0" -CELLPADDING="0" -CELLSPACING="0" -><TR -><TD -WIDTH="33%" -ALIGN="left" -VALIGN="top" -> </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 ->
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\ No newline at end of file diff --git a/java/docs/feature/AtomMass.html b/java/docs/feature/AtomMass.html deleted file mode 100644 index f1a2cde..0000000 --- a/java/docs/feature/AtomMass.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.ATOMMASS" -></A ->Atom masss</H2 -><P ->Atom mass.</P -></DIV -></DIV -></DIV -><DIV -CLASS="NAVFOOTER" -><HR -ALIGN="LEFT" -WIDTH="100%"><TABLE -SUMMARY="Footer navigation table" -WIDTH="100%" -BORDER="0" -CELLPADDING="0" -CELLSPACING="0" -><TR -><TD -WIDTH="33%" -ALIGN="left" -VALIGN="top" -> </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 ->
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\ No newline at end of file diff --git a/java/docs/feature/AtomValence.html b/java/docs/feature/AtomValence.html deleted file mode 100644 index dcd6db8..0000000 --- a/java/docs/feature/AtomValence.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.ATOMVALENCE" -></A ->Valence</H2 -><P ->Valence.</P -></DIV -></DIV -></DIV -><DIV -CLASS="NAVFOOTER" -><HR -ALIGN="LEFT" -WIDTH="100%"><TABLE -SUMMARY="Footer navigation table" -WIDTH="100%" -BORDER="0" -CELLPADDING="0" -CELLSPACING="0" -><TR -><TD -WIDTH="33%" -ALIGN="left" -VALIGN="top" -> </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 ->
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\ No newline at end of file diff --git a/java/docs/feature/AtomVanDerWaalsVolume.html b/java/docs/feature/AtomVanDerWaalsVolume.html deleted file mode 100644 index bf76e72..0000000 --- a/java/docs/feature/AtomVanDerWaalsVolume.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.ATOMVANDERWAALSVOLUME" -></A ->Van der Waals volume</H2 -><P ->Van der Waals volume.</P -></DIV -></DIV -></DIV -><DIV -CLASS="NAVFOOTER" -><HR -ALIGN="LEFT" -WIDTH="100%"><TABLE -SUMMARY="Footer navigation table" -WIDTH="100%" -BORDER="0" -CELLPADDING="0" -CELLSPACING="0" -><TR -><TD -WIDTH="33%" -ALIGN="left" -VALIGN="top" -> </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 deleted file mode 100644 index 53fe464..0000000 --- a/java/docs/feature/Autocorrelation.html +++ /dev/null @@ -1,168 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.AUTOCORRELATION" -></A ->Moreau-Broto topological autocorrelation</H2 -><P ->Moreau-Broto topological autocorrelation [<A -HREF="bibliography.html#BMV84" ->bmv84</A ->]. -<DIV -CLASS="EQUATION" -><A -NAME="AEN8" -></A -><P -><B ->Equation 1. Moreau-Broto autocorrelation</B -></P -><DIV -CLASS="MEDIAOBJECT" -><P -><IMG -SRC="formulas/autocorrelation.gif" -ALIGN="CENTER"></P -></DIV -></DIV -> -where <SPAN -CLASS="bold" -><B -CLASS="EMPHASIS" ->d<SUB ->ij</SUB -></B -></SPAN -> is the topological distance between the atoms -<SPAN -CLASS="bold" -><B -CLASS="EMPHASIS" ->i</B -></SPAN -> and atom <SPAN -CLASS="bold" -><B -CLASS="EMPHASIS" ->j</B -></SPAN ->, <SPAN -CLASS="bold" -><B -CLASS="EMPHASIS" ->w<SUB ->i</SUB -></B -></SPAN -> -and <SPAN -CLASS="bold" -><B -CLASS="EMPHASIS" ->w<SUB ->j</SUB -></B -></SPAN -> are the atom properties of the atoms <SPAN -CLASS="bold" -><B -CLASS="EMPHASIS" ->i</B -></SPAN -> and -<SPAN -CLASS="bold" -><B -CLASS="EMPHASIS" ->j</B -></SPAN ->.</P -><P ->It must be mentioned that the autocorrelation is only a special case of the radial distribution function ().</P -></DIV -></DIV -></DIV -><DIV -CLASS="NAVFOOTER" -><HR -ALIGN="LEFT" -WIDTH="100%"><TABLE -SUMMARY="Footer navigation table" -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 ->
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\ No newline at end of file diff --git a/java/docs/feature/BurdenModifiedEigenvalues.html b/java/docs/feature/BurdenModifiedEigenvalues.html deleted file mode 100644 index dc6a83b..0000000 --- a/java/docs/feature/BurdenModifiedEigenvalues.html +++ /dev/null @@ -1,96 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.BURDENMODIFIEDEIGENVALUES" -></A ->Burden modified eigenvalues</H2 -><P ->Burden modified eigenvalues [<A -HREF="bibliography.html#TC00" ->tc00</A ->].</P -></DIV -></DIV -></DIV -><DIV -CLASS="NAVFOOTER" -><HR -ALIGN="LEFT" -WIDTH="100%"><TABLE -SUMMARY="Footer navigation table" -WIDTH="100%" -BORDER="0" -CELLPADDING="0" -CELLSPACING="0" -><TR -><TD -WIDTH="33%" -ALIGN="left" -VALIGN="top" -> </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 ->
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\ No newline at end of file diff --git a/java/docs/feature/ConjElectroTopolState.html b/java/docs/feature/ConjElectroTopolState.html deleted file mode 100644 index bc0369e..0000000 --- a/java/docs/feature/ConjElectroTopolState.html +++ /dev/null @@ -1,173 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.CONJELECTROTOPOLSTATE" -></A ->Conjugated electrotopological state</H2 -><P ->Conjugated electrotopological state [<A -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 deleted file mode 100644 index 6deea0d..0000000 --- a/java/docs/feature/ConjugatedTopologicalDistance.html +++ /dev/null @@ -1,117 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -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 deleted file mode 100644 index 0d10a46..0000000 --- a/java/docs/feature/DistanceDistanceMatrix.html +++ /dev/null @@ -1,3 +0,0 @@ -<HTML> -Dummy -</HTML>
\ No newline at end of file diff --git a/java/docs/feature/DistanceMatrix.html b/java/docs/feature/DistanceMatrix.html deleted file mode 100644 index ecd0533..0000000 --- a/java/docs/feature/DistanceMatrix.html +++ /dev/null @@ -1,111 +0,0 @@ -<HTML
-><HEAD
-><TITLE
-></TITLE
-><META
-NAME="GENERATOR"
-CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
-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
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-> </TD
-><TD
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->Bibliography</TD
-></TR
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->
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\ No newline at end of file diff --git a/java/docs/feature/ElectrogeometricalState.html b/java/docs/feature/ElectrogeometricalState.html deleted file mode 100644 index d25b39a..0000000 --- a/java/docs/feature/ElectrogeometricalState.html +++ /dev/null @@ -1,139 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.ELECTROGEOMETRICALSTATE" -></A ->Electrogeometrical state</H2 -><P ->Electrogeometrical state [<A -HREF="bibliography.html#WZ03" ->wz03</A ->,<A -HREF="bibliography.html#WFZ04B" ->wfz04b</A ->]. -<DIV -CLASS="EQUATION" -><A -NAME="AEN9" -></A -><P -><B ->Equation 1. Electrogeometrical state</B -></P -><DIV -CLASS="MEDIAOBJECT" -><P -><IMG -SRC="formulas/egs.gif" -ALIGN="CENTER"></P -></DIV -></DIV -> -<SPAN -CLASS="bold" -><B -CLASS="EMPHASIS" ->I<SUB ->i</SUB -></B -></SPAN -> is the intrinsic state of atom <SPAN -CLASS="bold" -><B -CLASS="EMPHASIS" ->i</B -></SPAN -> () -and <SPAN -CLASS="bold" -><B -CLASS="EMPHASIS" ->k</B -></SPAN -> the distance influence.</P -></DIV -></DIV -></DIV -><DIV -CLASS="NAVFOOTER" -><HR -ALIGN="LEFT" -WIDTH="100%"><TABLE -SUMMARY="Footer navigation table" -WIDTH="100%" -BORDER="0" -CELLPADDING="0" -CELLSPACING="0" -><TR -><TD -WIDTH="33%" -ALIGN="left" -VALIGN="top" -> </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 deleted file mode 100644 index 6de0bf2..0000000 --- a/java/docs/feature/ElectrotopologicalState.html +++ /dev/null @@ -1,139 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.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 deleted file mode 100644 index a34080c..0000000 --- a/java/docs/feature/FractionRotatableBonds.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -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 deleted file mode 100644 index ff8cc05..0000000 --- a/java/docs/feature/GeomDistanceMatrix.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML
-><HEAD
-><TITLE
-></TITLE
-><META
-NAME="GENERATOR"
-CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK
-REL="NEXT"
-TITLE="Bibliography"
-HREF="bibliography.html"></HEAD
-><BODY
-CLASS="ARTICLE"
-BGCOLOR="#FFFFFF"
-TEXT="#000000"
-LINK="#0000FF"
-VLINK="#840084"
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-><DIV
-CLASS="ARTICLE"
-><DIV
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-><H1
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-NAME="JOELIB.DESCRIPTORS."
-></A
->Descriptor</H1
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-CLASS="SECT2"
-><H2
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-><A
-NAME="JOELIB.DESCRIPTORS.GEOMDISTANCEMATRIX"
-></A
->Geometrical distance matrix</H2
-><P
->The geometrical distance matrix calculates the euklidian distance between the 3D coordinates of all atom pairs.</P
-></DIV
-></DIV
-></DIV
-><DIV
-CLASS="NAVFOOTER"
-><HR
-ALIGN="LEFT"
-WIDTH="100%"><TABLE
-SUMMARY="Footer navigation table"
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-><TR
-><TD
-WIDTH="33%"
-ALIGN="left"
-VALIGN="top"
-> </TD
-><TD
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-ALIGN="center"
-VALIGN="top"
-> </TD
-><TD
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-ALIGN="right"
-VALIGN="top"
-><A
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-ACCESSKEY="N"
->Next</A
-></TD
-></TR
-><TR
-><TD
-WIDTH="33%"
-ALIGN="left"
-VALIGN="top"
-> </TD
-><TD
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-VALIGN="top"
-> </TD
-><TD
-WIDTH="33%"
-ALIGN="right"
-VALIGN="top"
->Bibliography</TD
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-></DIV
-></BODY
-></HTML
->
\ No newline at end of file diff --git a/java/docs/feature/GeometricalDiameter.html b/java/docs/feature/GeometricalDiameter.html deleted file mode 100644 index 242edc6..0000000 --- a/java/docs/feature/GeometricalDiameter.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -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 deleted file mode 100644 index 76a2596..0000000 --- a/java/docs/feature/GeometricalRadius.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.GEOMETRICALRADIUS" -></A ->Geometrical radius</H2 -><P ->Geometrical radius.</P -></DIV -></DIV -></DIV -><DIV -CLASS="NAVFOOTER" -><HR -ALIGN="LEFT" -WIDTH="100%"><TABLE -SUMMARY="Footer navigation table" -WIDTH="100%" -BORDER="0" -CELLPADDING="0" -CELLSPACING="0" -><TR -><TD -WIDTH="33%" -ALIGN="left" -VALIGN="top" -> </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 deleted file mode 100644 index e1401be..0000000 --- a/java/docs/feature/GeometricalShapeCoefficient.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -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 deleted file mode 100644 index 63e2715..0000000 --- a/java/docs/feature/GlobalTopologicalChargeIndex.html +++ /dev/null @@ -1,96 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -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 deleted file mode 100644 index a192e96..0000000 --- a/java/docs/feature/GraphPotentials.html +++ /dev/null @@ -1,131 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -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 deleted file mode 100644 index 735e913..0000000 --- a/java/docs/feature/GraphShapeCoefficient.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -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 deleted file mode 100644 index 6dcb012..0000000 --- a/java/docs/feature/HBA1.html +++ /dev/null @@ -1,94 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -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 deleted file mode 100644 index 4ad7747..0000000 --- a/java/docs/feature/HBA2.html +++ /dev/null @@ -1,94 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.HBA2" -></A ->Number of Hydrogen Bond Acceptors (HBA) 2</H2 -><P ->Number of Hydrogen Bond Acceptors (HBA) 2. -The default SMARTS pattern is: [$([$([#8,#16]);!$(*=N~O);!$(*~N=O);X1,X2]),$([#7;v3;!$([nH]);!$(*(-a)-a)])].</P -></DIV -></DIV -></DIV -><DIV -CLASS="NAVFOOTER" -><HR -ALIGN="LEFT" -WIDTH="100%"><TABLE -SUMMARY="Footer navigation table" -WIDTH="100%" -BORDER="0" -CELLPADDING="0" -CELLSPACING="0" -><TR -><TD -WIDTH="33%" -ALIGN="left" -VALIGN="top" -> </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 deleted file mode 100644 index 58922cf..0000000 --- a/java/docs/feature/HBD1.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.HBD1" -></A ->Number of Hydrogen Bond Donors (HBD) 1</H2 -><P ->Number of Hydrogen Bond Donors (HBD) 1. The default SMARTS pattern is: [!#6;!H0].</P -></DIV -></DIV -></DIV -><DIV -CLASS="NAVFOOTER" -><HR -ALIGN="LEFT" -WIDTH="100%"><TABLE -SUMMARY="Footer navigation table" -WIDTH="100%" -BORDER="0" -CELLPADDING="0" -CELLSPACING="0" -><TR -><TD -WIDTH="33%" -ALIGN="left" -VALIGN="top" -> </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 deleted file mode 100644 index a66a20f..0000000 --- a/java/docs/feature/HBD2.html +++ /dev/null @@ -1,94 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.HBD2" -></A ->Number of Hydrogen Bond Donors (HBD) 2</H2 -><P ->Number of Hydrogen Bond Donors (HBD) 2. -The default SMARTS pattern is: [$([O;H1,-&!$(*-N=O)]),$([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 deleted file mode 100644 index c460fba..0000000 --- a/java/docs/feature/HeavyBonds.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.HEAVYBONDS" -></A ->Number of heavy bonds</H2 -><P ->Number of heavy bonds.</P -></DIV -></DIV -></DIV -><DIV -CLASS="NAVFOOTER" -><HR -ALIGN="LEFT" -WIDTH="100%"><TABLE -SUMMARY="Footer navigation table" -WIDTH="100%" -BORDER="0" -CELLPADDING="0" -CELLSPACING="0" -><TR -><TD -WIDTH="33%" -ALIGN="left" -VALIGN="top" -> </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 deleted file mode 100644 index d1e124f..0000000 --- a/java/docs/feature/HeteroCycles.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.HETEROCYCLES" -></A ->Number of heterocycles</H2 -><P ->Number of heterocycles.</P -></DIV -></DIV -></DIV -><DIV -CLASS="NAVFOOTER" -><HR -ALIGN="LEFT" -WIDTH="100%"><TABLE -SUMMARY="Footer navigation table" -WIDTH="100%" -BORDER="0" -CELLPADDING="0" -CELLSPACING="0" -><TR -><TD -WIDTH="33%" -ALIGN="left" -VALIGN="top" -> </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 deleted file mode 100644 index 020d78c..0000000 --- a/java/docs/feature/HydrophobicGroups.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.HYDROPHOBICGROUPS" -></A ->Number of hydrophobic groups</H2 -><P ->Number of hydrophobic groups.</P -></DIV -></DIV -></DIV -><DIV -CLASS="NAVFOOTER" -><HR -ALIGN="LEFT" -WIDTH="100%"><TABLE -SUMMARY="Footer navigation table" -WIDTH="100%" -BORDER="0" -CELLPADDING="0" -CELLSPACING="0" -><TR -><TD -WIDTH="33%" -ALIGN="left" -VALIGN="top" -> </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 deleted file mode 100644 index 82c8c76..0000000 --- a/java/docs/feature/IntrinsicState.html +++ /dev/null @@ -1,145 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.INTRINSICSTATE" -></A ->Intrinsic topological state</H2 -><P ->Intrinsic topological state [<A -HREF="bibliography.html#TC00" ->tc00</A ->,<A -HREF="bibliography.html#WFZ04B" ->wfz04b</A ->]. -<DIV -CLASS="EQUATION" -><A -NAME="AEN9" -></A -><P -><B ->Equation 1. Intrinsic topological state</B -></P -><DIV -CLASS="MEDIAOBJECT" -><P -><IMG -SRC="formulas/istate.gif" -ALIGN="CENTER"></P -></DIV -></DIV -> -where <SPAN -CLASS="bold" -><B -CLASS="EMPHASIS" ->L<SUB ->i</SUB -></B -></SPAN -> is the principal quantum number, -<IMG -SRC="formulas/delta_i_nu.gif"> is the number of valence electrons, and -<IMG -SRC="formulas/delta_i.gif"> is the number of sigma electrons of the -<SPAN -CLASS="bold" -><B -CLASS="EMPHASIS" ->i</B -></SPAN ->th atom <SPAN -CLASS="bold" -><B -CLASS="EMPHASIS" ->a<SUB ->i</SUB -></B -></SPAN ->.</P -></DIV -></DIV -></DIV -><DIV -CLASS="NAVFOOTER" -><HR -ALIGN="LEFT" -WIDTH="100%"><TABLE -SUMMARY="Footer navigation table" -WIDTH="100%" -BORDER="0" -CELLPADDING="0" -CELLSPACING="0" -><TR -><TD -WIDTH="33%" -ALIGN="left" -VALIGN="top" -> </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 deleted file mode 100644 index 9690413..0000000 --- a/java/docs/feature/KierShape1.html +++ /dev/null @@ -1,176 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.KIERSHAPE1" -></A ->Kier Shape 1</H2 -><P ->The Kier shape -<IMG -SRC="formulas/kier1.gif"> descriptor [<A -HREF="bibliography.html#TC00" ->tc00</A ->] -can be defined as :</P -><DIV -CLASS="EQUATION" -><A -NAME="AEN10" -></A -><P -><B ->Equation 1. Kier shape 1</B -></P -><DIV -CLASS="MEDIAOBJECT" -><P -><IMG -SRC="formulas/kier1_1.gif" -ALIGN="CENTER"></P -></DIV -></DIV -><P -><SPAN -CLASS="bold" -><B -CLASS="EMPHASIS" ->P<SUB ->max</SUB -></B -></SPAN -> is the maximum number of paths of length 1. -<SPAN -CLASS="bold" -><B -CLASS="EMPHASIS" ->P<SUB ->min</SUB -></B -></SPAN -> is the minimum number of paths of length 1 in a molecule graph of same -atom number. -<SPAN -CLASS="bold" -><B -CLASS="EMPHASIS" ->P1</B -></SPAN -> is the number of paths in the given molecule of length 1. -or:</P -><DIV -CLASS="EQUATION" -><A -NAME="AEN21" -></A -><P -><B ->Equation 2. Kier shape 1 (alternative formulation)</B -></P -><DIV -CLASS="MEDIAOBJECT" -><P -><IMG -SRC="formulas/kier1_2.gif" -ALIGN="CENTER"></P -></DIV -></DIV -><P -><SPAN -CLASS="bold" -><B -CLASS="EMPHASIS" ->A</B -></SPAN -> means the number of nodes in the molecules graph. -<SPAN -CLASS="bold" -><B -CLASS="EMPHASIS" ->P1</B -></SPAN -> is the number of paths of length 1 in the given molecule.</P -></DIV -></DIV -></DIV -><DIV -CLASS="NAVFOOTER" -><HR -ALIGN="LEFT" -WIDTH="100%"><TABLE -SUMMARY="Footer navigation table" -WIDTH="100%" -BORDER="0" -CELLPADDING="0" -CELLSPACING="0" -><TR -><TD -WIDTH="33%" -ALIGN="left" -VALIGN="top" -> </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 deleted file mode 100644 index d3117b2..0000000 --- a/java/docs/feature/KierShape2.html +++ /dev/null @@ -1,131 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.KIERSHAPE2" -></A ->Kier shape 2</H2 -><P ->The Kier shape -<IMG -SRC="formulas/kier2.gif"> descriptor [<A -HREF="bibliography.html#TC00" ->tc00</A ->] -can be defined as :</P -><DIV -CLASS="EQUATION" -><A -NAME="AEN10" -></A -><P -><B ->Equation 1. Kier shape 2</B -></P -><DIV -CLASS="MEDIAOBJECT" -><P -><IMG -SRC="formulas/kier2_1.gif" -ALIGN="CENTER"></P -></DIV -></DIV -><P -><SPAN -CLASS="bold" -><B -CLASS="EMPHASIS" ->A</B -></SPAN -> means the number of nodes in the molecules graph. -<SPAN -CLASS="bold" -><B -CLASS="EMPHASIS" ->P2</B -></SPAN -> is the number of paths of length 2 in the given molecule.</P -></DIV -></DIV -></DIV -><DIV -CLASS="NAVFOOTER" -><HR -ALIGN="LEFT" -WIDTH="100%"><TABLE -SUMMARY="Footer navigation table" -WIDTH="100%" -BORDER="0" -CELLPADDING="0" -CELLSPACING="0" -><TR -><TD -WIDTH="33%" -ALIGN="left" -VALIGN="top" -> </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 deleted file mode 100644 index 7b760b5..0000000 --- a/java/docs/feature/KierShape3.html +++ /dev/null @@ -1,131 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.KIERSHAPE3" -></A ->Kier shape 3</H2 -><P ->The Kier shape -<IMG -SRC="formulas/kier3.gif"> descriptor [<A -HREF="bibliography.html#TC00" ->tc00</A ->] -can be defined as :</P -><DIV -CLASS="EQUATION" -><A -NAME="AEN10" -></A -><P -><B ->Equation 1. Kier shape 3</B -></P -><DIV -CLASS="MEDIAOBJECT" -><P -><IMG -SRC="formulas/kier3_1.gif" -ALIGN="CENTER"></P -></DIV -></DIV -><P -><SPAN -CLASS="bold" -><B -CLASS="EMPHASIS" ->A</B -></SPAN -> means the number of nodes in the molecules graph. -<SPAN -CLASS="bold" -><B -CLASS="EMPHASIS" ->P3</B -></SPAN -> is the number of paths of length 3 in the given molecule.</P -></DIV -></DIV -></DIV -><DIV -CLASS="NAVFOOTER" -><HR -ALIGN="LEFT" -WIDTH="100%"><TABLE -SUMMARY="Footer navigation table" -WIDTH="100%" -BORDER="0" -CELLPADDING="0" -CELLSPACING="0" -><TR -><TD -WIDTH="33%" -ALIGN="left" -VALIGN="top" -> </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 deleted file mode 100644 index 914533b..0000000 --- a/java/docs/feature/LogP.html +++ /dev/null @@ -1,96 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.LOGP" -></A ->Octanol/Water partition coefficient (logP)</H2 -><P ->Octanol/Water partition coefficient (logP) or hydrophobicity [<A -HREF="bibliography.html#WC99" ->wc99</A ->].</P -></DIV -></DIV -></DIV -><DIV -CLASS="NAVFOOTER" -><HR -ALIGN="LEFT" -WIDTH="100%"><TABLE -SUMMARY="Footer navigation table" -WIDTH="100%" -BORDER="0" -CELLPADDING="0" -CELLSPACING="0" -><TR -><TD -WIDTH="33%" -ALIGN="left" -VALIGN="top" -> </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 deleted file mode 100644 index 88757de..0000000 --- a/java/docs/feature/MolarRefractivity.html +++ /dev/null @@ -1,96 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.MOLARREFRACTIVITY" -></A ->Molar refractivity (MR)</H2 -><P ->Molar refractivity (MR) [<A -HREF="bibliography.html#WC99" ->wc99</A ->].</P -></DIV -></DIV -></DIV -><DIV -CLASS="NAVFOOTER" -><HR -ALIGN="LEFT" -WIDTH="100%"><TABLE -SUMMARY="Footer navigation table" -WIDTH="100%" -BORDER="0" -CELLPADDING="0" -CELLSPACING="0" -><TR -><TD -WIDTH="33%" -ALIGN="left" -VALIGN="top" -> </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 deleted file mode 100644 index e463e1c..0000000 --- a/java/docs/feature/MolecularWeight.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.MOLECULARWEIGHT" -></A ->Molecular weight (MW)</H2 -><P ->Molecular weight (MW).</P -></DIV -></DIV -></DIV -><DIV -CLASS="NAVFOOTER" -><HR -ALIGN="LEFT" -WIDTH="100%"><TABLE -SUMMARY="Footer navigation table" -WIDTH="100%" -BORDER="0" -CELLPADDING="0" -CELLSPACING="0" -><TR -><TD -WIDTH="33%" -ALIGN="left" -VALIGN="top" -> </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 deleted file mode 100644 index 0d10a46..0000000 --- a/java/docs/feature/MoleculeHashcode.html +++ /dev/null @@ -1,3 +0,0 @@ -<HTML> -Dummy -</HTML>
\ No newline at end of file diff --git a/java/docs/feature/NO2Groups.html b/java/docs/feature/NO2Groups.html deleted file mode 100644 index 6fa91d4..0000000 --- a/java/docs/feature/NO2Groups.html +++ /dev/null @@ -1,97 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.NO2GROUPS" -></A ->Number of -NO<SUB ->2</SUB -> groups</H2 -><P ->Number of -NO<SUB ->2</SUB -> groups.</P -></DIV -></DIV -></DIV -><DIV -CLASS="NAVFOOTER" -><HR -ALIGN="LEFT" -WIDTH="100%"><TABLE -SUMMARY="Footer navigation table" -WIDTH="100%" -BORDER="0" -CELLPADDING="0" -CELLSPACING="0" -><TR -><TD -WIDTH="33%" -ALIGN="left" -VALIGN="top" -> </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 deleted file mode 100644 index f79063f..0000000 --- a/java/docs/feature/NumberOfAtoms.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.NUMBEROFATOMS" -></A ->Number of atoms</H2 -><P ->Number of atoms.</P -></DIV -></DIV -></DIV -><DIV -CLASS="NAVFOOTER" -><HR -ALIGN="LEFT" -WIDTH="100%"><TABLE -SUMMARY="Footer navigation table" -WIDTH="100%" -BORDER="0" -CELLPADDING="0" -CELLSPACING="0" -><TR -><TD -WIDTH="33%" -ALIGN="left" -VALIGN="top" -> </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 deleted file mode 100644 index fd7e2e4..0000000 --- a/java/docs/feature/NumberOfB.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.NUMBEROFB" -></A ->Number of boron atoms</H2 -><P ->Number of boron atoms.</P -></DIV -></DIV -></DIV -><DIV -CLASS="NAVFOOTER" -><HR -ALIGN="LEFT" -WIDTH="100%"><TABLE -SUMMARY="Footer navigation table" -WIDTH="100%" -BORDER="0" -CELLPADDING="0" -CELLSPACING="0" -><TR -><TD -WIDTH="33%" -ALIGN="left" -VALIGN="top" -> </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 deleted file mode 100644 index 22dfb7e..0000000 --- a/java/docs/feature/NumberOfBonds.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -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 deleted file mode 100644 index 5807bb9..0000000 --- a/java/docs/feature/NumberOfBr.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.NUMBEROFBR" -></A ->Number of bromine atoms</H2 -><P ->Number of bromine atoms.</P -></DIV -></DIV -></DIV -><DIV -CLASS="NAVFOOTER" -><HR -ALIGN="LEFT" -WIDTH="100%"><TABLE -SUMMARY="Footer navigation table" -WIDTH="100%" -BORDER="0" -CELLPADDING="0" -CELLSPACING="0" -><TR -><TD -WIDTH="33%" -ALIGN="left" -VALIGN="top" -> </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 deleted file mode 100644 index a1b224e..0000000 --- a/java/docs/feature/NumberOfC.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.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 deleted file mode 100644 index 04892d5..0000000 --- a/java/docs/feature/NumberOfCl.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.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 deleted file mode 100644 index c12b2f5..0000000 --- a/java/docs/feature/NumberOfF.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.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 deleted file mode 100644 index 11df356..0000000 --- a/java/docs/feature/NumberOfHal.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.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 deleted file mode 100644 index 0580e12..0000000 --- a/java/docs/feature/NumberOfI.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.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 deleted file mode 100644 index bd65ada..0000000 --- a/java/docs/feature/NumberOfN.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.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 deleted file mode 100644 index 7ecbe0a..0000000 --- a/java/docs/feature/NumberOfO.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.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 deleted file mode 100644 index 3669e91..0000000 --- a/java/docs/feature/NumberOfP.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.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 deleted file mode 100644 index b735ee5..0000000 --- a/java/docs/feature/NumberOfS.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.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 deleted file mode 100644 index ca49ebf..0000000 --- a/java/docs/feature/OSOGroups.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.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 deleted file mode 100644 index 357056f..0000000 --- a/java/docs/feature/PolarSurfaceArea.html +++ /dev/null @@ -1,96 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.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 deleted file mode 100644 index 09d9600..0000000 --- a/java/docs/feature/RadialDistributionFunction.html +++ /dev/null @@ -1,230 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.RADIALDISTRIBUTIONFUNCTION" -></A ->Radial distribution function (RDF)</H2 -><P ->The radial distribution function (RDF) [<A -HREF="bibliography.html#MSG99" ->msg99</A ->,<A -HREF="bibliography.html#WFZ04B" ->wfz04b</A ->] can be interpreted as the probability distribution of finding an atom in a spherical volume of -radius <SPAN -CLASS="bold" -><B -CLASS="EMPHASIS" ->r</B -></SPAN ->. -<DIV -CLASS="EQUATION" -><A -NAME="AEN14" -></A -><P -><B ->Equation 1. Radial distribution function</B -></P -><DIV -CLASS="MEDIAOBJECT" -><P -><IMG -SRC="formulas/rdf.gif" -ALIGN="CENTER"></P -></DIV -></DIV -> -where <SPAN -CLASS="bold" -><B -CLASS="EMPHASIS" ->r<SUB ->ij</SUB -></B -></SPAN -> is the geometrical distance between the atoms -<SPAN -CLASS="bold" -><B -CLASS="EMPHASIS" ->i</B -></SPAN -> and atom <SPAN -CLASS="bold" -><B -CLASS="EMPHASIS" ->j</B -></SPAN ->, <SPAN -CLASS="bold" -><B -CLASS="EMPHASIS" ->w<SUB ->i</SUB -></B -></SPAN -> -and <SPAN -CLASS="bold" -><B -CLASS="EMPHASIS" ->w<SUB ->j</SUB -></B -></SPAN -> are the atom properties of the atoms <SPAN -CLASS="bold" -><B -CLASS="EMPHASIS" ->i</B -></SPAN -> and -<SPAN -CLASS="bold" -><B -CLASS="EMPHASIS" ->j</B -></SPAN ->. <SPAN -CLASS="bold" -><B -CLASS="EMPHASIS" ->B</B -></SPAN -> is the smoothing parameter -(fuzziness of the distance <SPAN -CLASS="bold" -><B -CLASS="EMPHASIS" ->r<SUB ->ij</SUB -></B -></SPAN ->) for the interatomic distance and -<SPAN -CLASS="bold" -><B -CLASS="EMPHASIS" ->f</B -></SPAN -> the scaling factor.</P -><P ->If <SPAN -CLASS="bold" -><B -CLASS="EMPHASIS" ->B</B -></SPAN -> aims to infinity the RDF code approximates to the autocorrelation function () and the fuzziness -of the distance <SPAN -CLASS="bold" -><B -CLASS="EMPHASIS" ->r<SUB ->ij</SUB -></B -></SPAN -> vanishes. So the RDF code can be treated as a generalized -autocorrelation function.</P -><P ->The RDF user parameters can be defined in the <TT -CLASS="FILENAME" ->joelib.properties</TT ->-file, otherwise the default parameters will be used:</P -><PRE -CLASS="PROGRAMLISTING" ->jcompchem.joelib.desc.types.RadialDistributionFunction.minSphericalVolume = 0.2 -joelib.desc.types.RadialDistributionFunction.maxSphericalVolume = 10.0 -joelib.desc.types.RadialDistributionFunction.sphericalVolumeResolution = 0.2 -joelib.desc.types.RadialDistributionFunction.smoothingFactor = 25</PRE -><P ->Optional the RDF can be calculated with protonated molecules, but you must be sure that all available atom -properties are calculated with hydrogens also. Because this is not the standard, this option should be only used by developers.</P -></DIV -></DIV -></DIV -><DIV -CLASS="NAVFOOTER" -><HR -ALIGN="LEFT" -WIDTH="100%"><TABLE -SUMMARY="Footer navigation table" -WIDTH="100%" -BORDER="0" -CELLPADDING="0" -CELLSPACING="0" -><TR -><TD -WIDTH="33%" -ALIGN="left" -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 deleted file mode 100644 index 42ef0d9..0000000 --- a/java/docs/feature/RotatableBonds.html +++ /dev/null @@ -1,94 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.ROTATABLEBONDS" -></A ->Number of rotatable bonds</H2 -><P ->Number of rotatable bonds, where the atoms are heavy atoms with bond order one and a hybridization which is not one (no sp). -Additionally the bond is a non-ring-bond.</P -></DIV -></DIV -></DIV -><DIV -CLASS="NAVFOOTER" -><HR -ALIGN="LEFT" -WIDTH="100%"><TABLE -SUMMARY="Footer navigation table" -WIDTH="100%" -BORDER="0" -CELLPADDING="0" -CELLSPACING="0" -><TR -><TD -WIDTH="33%" -ALIGN="left" -VALIGN="top" -> </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 deleted file mode 100644 index 0d10a46..0000000 --- a/java/docs/feature/SMILESMolecule.html +++ /dev/null @@ -1,3 +0,0 @@ -<HTML> -Dummy -</HTML>
\ No newline at end of file diff --git a/java/docs/feature/SO2Groups.html b/java/docs/feature/SO2Groups.html deleted file mode 100644 index e4cd9a7..0000000 --- a/java/docs/feature/SO2Groups.html +++ /dev/null @@ -1,97 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.SO2GROUPS" -></A ->Number of -SO<SUB ->2</SUB -> atoms</H2 -><P ->Number of -SO<SUB ->2</SUB -> atoms.</P -></DIV -></DIV -></DIV -><DIV -CLASS="NAVFOOTER" -><HR -ALIGN="LEFT" -WIDTH="100%"><TABLE -SUMMARY="Footer navigation table" -WIDTH="100%" -BORDER="0" -CELLPADDING="0" -CELLSPACING="0" -><TR -><TD -WIDTH="33%" -ALIGN="left" -VALIGN="top" -> </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 deleted file mode 100644 index fd3e45a..0000000 --- a/java/docs/feature/SOGroups.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></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 deleted file mode 100644 index fad741d..0000000 --- a/java/docs/feature/SSKey3DS.html +++ /dev/null @@ -1,779 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -ALINK="#0000FF" -><DIV -CLASS="ARTICLE" -><DIV -CLASS="SECT1" -><H1 -CLASS="SECT1" -><A -NAME="JOELIB.DESCRIPTOR" -></A ->Descriptor</H1 -><DIV -CLASS="SECT2" -><H2 -CLASS="SECT2" -><A -NAME="JOELIB.DESCRIPTORS.SSKEY3DS" -></A ->Pharmacophore fingerprint</H2 -><P ->Pharmacophore fingerprint [<A -HREF="bibliography.html#GXSB00" ->gxsb00</A ->]. -<DIV -CLASS="TABLE" -><A -NAME="AEN8" -></A -><P -><B ->Table 1. Pharmacophore fingerprint definition</B -></P -><TABLE -BORDER="1" -CLASS="CALSTABLE" -><THEAD -><TR -><TH -WIDTH="50%" -ALIGN="LEFT" -VALIGN="TOP" ->Bit position</TH -><TH -WIDTH="50%" -ALIGN="LEFT" -VALIGN="TOP" ->Set when</TH -></TR -></THEAD -><TBODY -><TR -><TD -WIDTH="50%" -ALIGN="LEFT" -VALIGN="TOP" ->1</TD -><TD -WIDTH="50%" -ALIGN="LEFT" -VALIGN="TOP" ->Fraction of rotatable bonds > 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 deleted file mode 100644 index 32731b0..0000000 --- a/java/docs/feature/TopologicalAtomPair.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -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 deleted file mode 100644 index 660bbb6..0000000 --- a/java/docs/feature/TopologicalDiameter.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -TITLE="Bibliography" -HREF="bibliography.html"></HEAD -><BODY -CLASS="ARTICLE" -BGCOLOR="#FFFFFF" -TEXT="#000000" -LINK="#0000FF" -VLINK="#840084" -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 deleted file mode 100644 index 07299fa..0000000 --- a/java/docs/feature/TopologicalRadius.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -REL="NEXT" -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 deleted file mode 100644 index 0d10a46..0000000 --- a/java/docs/feature/WeightedBurdenEigenvalues.html +++ /dev/null @@ -1,3 +0,0 @@ -<HTML> -Dummy -</HTML>
\ No newline at end of file diff --git a/java/docs/feature/WeightedBurdenModifiedEigenvalues.html b/java/docs/feature/WeightedBurdenModifiedEigenvalues.html deleted file mode 100644 index 0e93938..0000000 --- a/java/docs/feature/WeightedBurdenModifiedEigenvalues.html +++ /dev/null @@ -1,93 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -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 deleted file mode 100644 index 130990f..0000000 --- a/java/docs/feature/ZagrebIndex1.html +++ /dev/null @@ -1,123 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -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 deleted file mode 100644 index 735a797..0000000 --- a/java/docs/feature/ZagrebIndex2.html +++ /dev/null @@ -1,143 +0,0 @@ -<HTML -><HEAD -><TITLE -></TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -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 deleted file mode 100644 index 0770682..0000000 --- a/java/docs/feature/bibliography.html +++ /dev/null @@ -1,911 +0,0 @@ -<HTML -><HEAD -><TITLE ->Bibliography</TITLE -><META -NAME="GENERATOR" -CONTENT="Modular DocBook HTML Stylesheet Version 1.7"><LINK -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 ->
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-<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 .
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