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[Cdk-commits] SF.net SVN: cdk:[12750] paper-jchempaint/trunk
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From: <eg...@us...> - 2008-10-21 10:06:15
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Revision: 12750
http://cdk.svn.sourceforge.net/cdk/?rev=12750&view=rev
Author: egonw
Date: 2008-10-21 10:05:11 +0000 (Tue, 21 Oct 2008)
Log Message:
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Added some very tiny bits of initial content...
Modified Paths:
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paper-jchempaint/trunk/bibliography.bib
paper-jchempaint/trunk/paper.tex
Modified: paper-jchempaint/trunk/bibliography.bib
===================================================================
--- paper-jchempaint/trunk/bibliography.bib 2008-10-21 10:04:23 UTC (rev 12749)
+++ paper-jchempaint/trunk/bibliography.bib 2008-10-21 10:05:11 UTC (rev 12750)
@@ -0,0 +1,72 @@
+@ARTICLE{Trepalin2006,
+ author = {Trepalin, S. V. and Yarkov, A. V. and Pletnev, I. V. and Gakh, A.
+ A.},
+ title = {A Java chemical structure editor supporting the modular chemical
+ descriptor language (MCDL)},
+ journal = {MOLECULES},
+ year = {2006},
+ volume = {11},
+ pages = {219--231},
+ number = {4},
+ month = apr,
+ abstract = {A compact Modular Chemical Descriptor Language (MCDL) chemical structure
+ editor (Java applet) is described. The small size (approximately
+ 200 K-B) of the applet allows its use to display and edit chemical
+ structures in various Internet applications. The editor supports
+ the MCDL format, in which structures are presented in compact canonical
+ form and is capable of restoring bond orders as well as of managing
+ atom and bond drawing overlap. A small database of cage and large
+ cyclic fragment is used for optimal representation of difficult-to-draw
+ molecules. The improved algorithm of the structure diagram generation
+ can be used for other chemical notations that lack atomic coordinates
+ (SMILES, InChl).},
+ citedreferences = {ASH S, 1997, J CHEM INF COMP SCI, V37, P71 ; BABER JC, 1992, J CHEM
+ INF COMP SCI, V32, P401 ; BAJORATH J, 2001, J CHEM INF COMP SCI,
+ V41, P233 ; BREMSER W, 1978, ANAL CHIM ACTA, V103, P355 ; CIOSLOWSKI
+ J, 1991, J AM CHEM SOC, V113, P4142 ; CSIZMADIA F, 2000, J CHEM INF
+ COMP SCI, V40, P323 ; DALBY A, 1992, J CHEM INF COMP SCI, V32, P244
+ ; ERTL P, 1997, J MOL STRUC-THEOCHEM, V419, P113 ; FIGUERAS J, 1996,
+ J CHEM INF COMP SCI, V36, P986 ; FRICKER PC, 2004, J CHEM INF COMP
+ SCI, V44, P1065 ; GAKH AA, 2001, J CHEM INF COMP SCI, V41, P1494
+ ; HELSON HE, 1999, REV COMP CH, V13, P313 ; KRAUSE S, 2000, MOLECULES,
+ V5, P93 ; MAYER I, 1983, CHEM PHYS LETT, V97, P270 ; MAYER I, 1984,
+ CHEM PHYS LETT, V110, P440 ; PRASANNA MD, 2005, PROTEINS, V60, P1
+ ; RIGAUDY J, 1979, NOMENCLATURE ORGANIC ; ROVNER SL, 2005, CHEM ENG
+ NEWS, V83, P39 ; RZEPA HS, 1998, J CHEM INF COMP SCI, V38, P1048
+ ; RZEPA HS, 2005, NEW IN CHEM ED LIN S ; SCHNUR D, 1999, J CHEM INF
+ COMP SCI, V39, P36 ; SMITH EG, 1968, WISSWESSER LINE FORM ; STEIN
+ SE, 2003, P 2003 INT CHEM INF, P131 ; STEINBECK C, 2003, J CHEM INF
+ COMP SCI, V43, P493 ; TREPALIN SV, 1995, J CHEM INF COMP SCI, V35,
+ P405 ; WEININGER D, 1988, J CHEM INFORMATION C, V28, P31 ; WEININGER
+ D, 1989, J CHEM INF COMP SCI, V29, P97},
+ keywords = {DATABASE; CONNECTIVITY; GENERATION; MOLECULES; LIBRARIES; NOTATION;
+ INTERNET; VALENCE; DESIGN; SMILES},
+ owner = {egonw},
+ timestamp = {2006.11.07}
+}
+
+@ARTICLE{Steinbeck2003a,
+ author = {Steinbeck, C. and Kuhn, S. and Krause, S.},
+ title = {{NMRShiftDB} -- Constructing a Chemical Information System with Open
+ Source Components},
+ journal = {Journal of Chemical Information and Computer Sciences},
+ year = {2003},
+ volume = {43},
+ pages = {1733 - 1739},
+ number = {6},
+ owner = {egonw},
+ timestamp = {2008.01.07}
+}
+
+@ARTICLE{Krause2000,
+ author = {Krause, S. and Willighagen, E.L. and Steinbeck, C.},
+ title = {{JChemPaint} - Using the Collaborative Forces of the Internet to
+ Develop a Free Editor for 2D Chemical Structures},
+ journal = {Molecules},
+ year = {2000},
+ volume = {5},
+ pages = {93--98},
+ owner = {egonw},
+ review = {Now in CDK.},
+ timestamp = {2008.01.07}
+}
Modified: paper-jchempaint/trunk/paper.tex
===================================================================
--- paper-jchempaint/trunk/paper.tex 2008-10-21 10:04:23 UTC (rev 12749)
+++ paper-jchempaint/trunk/paper.tex 2008-10-21 10:05:11 UTC (rev 12750)
@@ -232,6 +232,25 @@
%%
\section*{Background}
+ The internet is becoming a primary communication tool for conducting
+ scientific research. \ldots On the one hand, increasingly tools are being
+ used to make the web more machine readble, but on the other hand, human
+ interaction is still a key component.
+
+ Drawing chemical structures is a key activity in querying web resources.
+ For examples, the NMRShiftDB is such a resource~\cite{Steinbeck2003a} where
+ NMR spectra of molecules can be looked up by drawing a molecular
+ substructure. This requires an chemical input editor. For the web, several
+ approaches are avaiable, including using Java
+ applets~\cite{Krause2000,Trepalin2006},
+ % FIXME: add Marvin, JME, Rich' editor
+ and JavaScript~\cite{PubChemEditor}.
+
+ Java applets have the advantage of being rather versatile, but can quickly
+ lead to large download sizes~\cite{Trepalin2006}.
+
+
+
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%% Results and Discussion %%
%%
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