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[Cdk-commits] SF.net SVN: cdk:[15051] cdk-taverna-paper/trunk/cdk-taverna
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From: <eg...@us...> - 2009-11-07 22:25:26
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Revision: 15051
http://cdk.svn.sourceforge.net/cdk/?rev=15051&view=rev
Author: egonw
Date: 2009-11-07 22:24:39 +0000 (Sat, 07 Nov 2009)
Log Message:
-----------
Enabled figures again. Disabling should be done by uncommenting the lines 81-82
Modified Paths:
--------------
cdk-taverna-paper/trunk/cdk-taverna/bmc_article.tex
Added Paths:
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cdk-taverna-paper/trunk/cdk-taverna/pics/IterativeQSARWorkflow.pdf
cdk-taverna-paper/trunk/cdk-taverna/pics/QSARWorkerUIsmall.pdf
cdk-taverna-paper/trunk/cdk-taverna/pics/QSARWorkflow.pdf
cdk-taverna-paper/trunk/cdk-taverna/pics/databaseSubstructureSearch.pdf
cdk-taverna-paper/trunk/cdk-taverna/pics/reactionEnumerationWF2.pdf
Removed Paths:
-------------
cdk-taverna-paper/trunk/cdk-taverna/pics/Iterative_QSAR_Workflow.pdf
cdk-taverna-paper/trunk/cdk-taverna/pics/QSAR_Worker_UI_small.pdf
cdk-taverna-paper/trunk/cdk-taverna/pics/QSAR_Workflow.pdf
cdk-taverna-paper/trunk/cdk-taverna/pics/database_substructure_search.pdf
cdk-taverna-paper/trunk/cdk-taverna/pics/reactionEnumerationWF_2.pdf
Modified: cdk-taverna-paper/trunk/cdk-taverna/bmc_article.tex
===================================================================
--- cdk-taverna-paper/trunk/cdk-taverna/bmc_article.tex 2009-11-07 21:26:38 UTC (rev 15050)
+++ cdk-taverna-paper/trunk/cdk-taverna/bmc_article.tex 2009-11-07 22:24:39 UTC (rev 15051)
@@ -78,8 +78,8 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\def\includegraphic{}
-\def\includegraphics{}
+% \def\includegraphic{}
+% \def\includegraphics{}
@@ -658,8 +658,8 @@
\section*{Figures}
\begin{figure*}[h!]
- %\centering
- %\includegraphics[angle=0,clip=false,scale=.4]{pics/substructureworkflow.pdf}\\
+ \centering
+ \includegraphics[angle=0,clip=false,scale=.4]{pics/substructureworkflow.pdf}
\caption{Workflow performing a topological substructure search (Scenario~1) on
molecules from a MDL SD file~\cite{MyExperiementWFSubstructure}.
The input of this workflow is a SMILES string
@@ -668,8 +668,8 @@
\end{figure*}
\begin{figure*}[h!]
- %\centering
- %\includegraphics[angle=90,clip=false,scale=.4]{pics/database_substructure_search.pdf}\\
+ \centering
+ \includegraphics[angle=90,clip=false,scale=.4]{pics/databaseSubstructureSearch.pdf}
\caption{Workflow performing a substructure search (Scenario~1)
in a database~\cite{MyExperiementWFSubstructureDB}.
The substructure is loaded from a MDL SD file. The output is a PDF
@@ -680,8 +680,8 @@
\begin{figure*}[h!]
- %\centering
- %\includegraphics[angle=0,clip=false,scale=.5]{pics/QSAR_Workflow.pdf}\\
+ \centering
+ \includegraphics[angle=0,clip=false,scale=.5]{pics/QSARWorkflow.pdf}
\caption{Workflow calculating various QSAR descriptors (Scenario~2) for molecules
from a PostgreSQL database. The results of the calculation are stored in a CSV file.}
\label{fig:QSARWorkflow}
@@ -689,8 +689,8 @@
\begin{figure*}[h!]
- %\centering
- %\includegraphics[angle=-90,clip=true,scale=.5]{pics/QSAR_Worker_UI_small.pdf}\\
+ \centering
+ \includegraphics[angle=-90,clip=true,scale=.5]{pics/QSARWorkerUIsmall.pdf}
\caption{User interface to select QSAR descriptors to be calculated for each molecule during
the execution of the descriptor calculation workflow shown in Figure~\ref{fig:QSARWorkflow}.}
\label{fig:QSARWorkerUI}
@@ -700,8 +700,8 @@
\begin{figure*}[h!]
- %\centering
- %\includegraphics[angle=0,clip=false,scale=.3]{pics/timeneededtocalculatemoleculardescriptors.pdf}\\
+ \centering
+ \includegraphics[angle=0,clip=false,scale=.3]{pics/timeneededtocalculatemoleculardescriptors.pdf}
\caption{Overview of the time needed to calculate different molecular descriptors for 1000
molecules~\cite{CDKTavernaBlogWeb}.}
\label{fig:TimeCalculateDescriptors}
@@ -710,8 +710,8 @@
\begin{figure*}[h!]
- %\centering
- %\includegraphics[angle=0,clip=false,scale=.5]{pics/Iterative_QSAR_Workflow.pdf}
+ \centering
+ \includegraphics[angle=0,clip=false,scale=.5]{pics/IterativeQSARWorkflow.pdf}
\caption{Workflow iteratively calculating different QSAR descriptors (Scenario~3)
for molecules loaded from a PostgreSQL
database~\cite{MyExperiementWFQSAR}. The results are stored in a CSV file.}
@@ -721,8 +721,8 @@
\begin{figure*}[h!]
- %\centering
- %\includegraphics[angle=0,clip=false,scale=.5]{pics/AtomTypingWF.pdf}\\
+ \centering
+ \includegraphics[angle=0,clip=false,scale=.5]{pics/AtomTypingWF.pdf}
\caption{Workflow for iterative loading of molecules from a database and searches for molecules
with atom types unknown to the Chemistry Development Kit (Scenario~4).}
\label{fig:AtomTypingWF}
@@ -731,16 +731,16 @@
\begin{figure*}[h!]
- %\centering
- %\includegraphics[angle=0,clip=false,scale=.5]{pics/AtomTypingResults.pdf}\\
+ \centering
+ \includegraphics[angle=0,clip=false,scale=.5]{pics/AtomTypingResults.pdf}
\caption{Allocation of the unknown atom types detected during the analysis of the ChEBI database.}
\label{fig:AtomTypingResults}
\end{figure*}
\begin{figure*}[h!]
- %\centering
- %\includegraphics[angle=0,clip=flase,scale=.4]{pics/reactionEnumerationWF_2.pdf}\\
+ \centering
+ \includegraphics[angle=0,clip=flase,scale=.4]{pics/reactionEnumerationWF2.pdf}
\caption{Reaction enumeration (Scenario~5) loading a generic reaction from a MDL RXN file and two reactant lists
from MDL SD files. The products from the enumeration are stored as MDL molfiles. Besides these files
a PDF document showing the 2D structure of the products is created. At the end Bioclipse will start up
@@ -752,8 +752,8 @@
\begin{figure*}[h!]
- %\centering
- %\includegraphics[angle=0,clip=false,scale=.5]{pics/reactionenumeration.pdf}\\
+ \centering
+ \includegraphics[angle=0,clip=false,scale=.5]{pics/reactionenumeration.pdf}
\caption{Reaction enumeration example with two building blocks. For each building block, a list of three reactants is defined. This enumeration results in nine different products.}
\label{fig:ReactionEnumerationSchema}
\end{figure*}
@@ -761,8 +761,8 @@
\begin{figure*}[h!]
- %\centering
- %\includegraphics[angle=0,clip=false,scale=.5]{pics/ATR2AClassificationWF.pdf}\\
+ \centering
+ \includegraphics[angle=0,clip=false,scale=.5]{pics/ATR2AClassificationWF.pdf}
\caption{Workflow loading a data vector from a database and performs an ART2A classification (Scenario~6).}
\label{fig:ART2AClassification}
\end{figure*}
@@ -770,8 +770,8 @@
\begin{figure*}[h!]
- %\centering
- %\includegraphics[angle=0,clip=false,scale=.5]{pics/ART2ACluster.pdf}\\
+ \centering
+ \includegraphics[angle=0,clip=false,scale=.5]{pics/ART2ACluster.pdf}
\caption{Occupancies of different detected clusters for three databases with the
goal to compare two proprietary Natural Product databases with the ChEBI database.}
\label{fig:ART2AClassificationResult}
Copied: cdk-taverna-paper/trunk/cdk-taverna/pics/IterativeQSARWorkflow.pdf (from rev 15045, cdk-taverna-paper/trunk/cdk-taverna/pics/Iterative_QSAR_Workflow.pdf)
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Deleted: cdk-taverna-paper/trunk/cdk-taverna/pics/Iterative_QSAR_Workflow.pdf
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Copied: cdk-taverna-paper/trunk/cdk-taverna/pics/QSARWorkerUIsmall.pdf (from rev 15045, cdk-taverna-paper/trunk/cdk-taverna/pics/QSAR_Worker_UI_small.pdf)
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Copied: cdk-taverna-paper/trunk/cdk-taverna/pics/QSARWorkflow.pdf (from rev 15045, cdk-taverna-paper/trunk/cdk-taverna/pics/QSAR_Workflow.pdf)
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Deleted: cdk-taverna-paper/trunk/cdk-taverna/pics/QSAR_Worker_UI_small.pdf
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Deleted: cdk-taverna-paper/trunk/cdk-taverna/pics/QSAR_Workflow.pdf
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Copied: cdk-taverna-paper/trunk/cdk-taverna/pics/databaseSubstructureSearch.pdf (from rev 15045, cdk-taverna-paper/trunk/cdk-taverna/pics/database_substructure_search.pdf)
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Deleted: cdk-taverna-paper/trunk/cdk-taverna/pics/database_substructure_search.pdf
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Copied: cdk-taverna-paper/trunk/cdk-taverna/pics/reactionEnumerationWF2.pdf (from rev 15045, cdk-taverna-paper/trunk/cdk-taverna/pics/reactionEnumerationWF_2.pdf)
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Deleted: cdk-taverna-paper/trunk/cdk-taverna/pics/reactionEnumerationWF_2.pdf
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