diff confab.xml @ 0:4a73b5059c22 draft

Uploaded
author bgruening
date Thu, 15 Aug 2013 03:31:39 -0400
parents
children 731ad135ddb4
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/confab.xml	Thu Aug 15 03:31:39 2013 -0400
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+<tool id="ctb_confab" name="Conformer calculation" version="0.1">
+    <description>for molecules (confab)</description>
+    <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="100" shared_inputs="" merge_outputs="outfile"></parallelism>
+    <requirements>
+        <requirement type="package" version="1.0.1">confab</requirement>
+    </requirements>
+    <command> confab 
+        -i ${infile.ext}
+        -o sdf
+        -r $RMSD 
+        -e $energy 
+        -c $conformers 
+        $first_conformer 
+        $infile
+        $outfile 2>&#38;1
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="sdf,mol2" label="Input molecule with 3D coordinates" help="Dataset missing? See TIP below"/>
+        <param name='RMSD' type='float' value='0.5' label='RMSD cutoff (in Angstrom)' />
+        <param name='energy' type='float' value='50.0' label='Energy cutoff (in kcal/mol)' />
+        <param name='conformers' type='integer' value='100' label='Max number of conformers to test' />
+        <param name='first_conformer' type='boolean' truevalue='-a' falsevalue='' label='Include the input conformation as the first conformer' />
+    </inputs>
+    <outputs>
+        <data format="sdf" name="outfile" label="${tool.name} on ${on_string}"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" value='CID_3033.sdf' ftype='sdf' />
+            <param name='RMSD'  value='0.5' />
+            <param name='energy' value='50.0' />
+            <param name='conformers' value='100000' />
+            <param name='first_conformer' value='-a' />
+            <output name="outfile" file='confab_on_CID_3033.sdf' ftype='sdf' />
+        </test>	
+    </tests>
+<help>
+
+.. class:: infomark
+
+**What this tool does**
+
+Confab_ is a conformation generator. The algorithm starts with an input 3D structure which, after some initialisation steps, is used to generate multiple conformers which are filtered on-the-fly to identify diverse low energy conformers.
+
+.. _Confab: https://code.google.com/p/confab/
+
+-----
+
+.. class:: infomark
+
+**Input**
+
+* Example::
+	
+	21.2060    9.9350   63.0810 C   0  0  0  0  0  0  0  0  0  0  0  0
+	21.2410    9.4460   64.5510 C   0  0  0  0  0  0  0  0  0  0  0  0
+	22.0000    8.1250   64.6300 C   0  0  0  0  0  0  0  0  0  0  0  0
+	21.7010    7.3010   65.5120 O   0  0  0  0  0  0  0  0  0  0  0  0
+	23.1180    7.8720   63.7340 C   0  0  0  0  0  0  0  0  0  0  0  0
+	23.4530    8.7270   62.7850 C   0  0  0  0  0  0  0  0  0  0  0  0
+	24.6970    8.4430   61.9510 C   0  0  0  0  0  0  0  0  0  0  0  0
+
+	.......
+
+	1  2  1  0  0  0  0
+	1 11  1  0  0  0  0
+	2  3  1  0  0  0  0
+	3  4  2  0  0  0  0
+	3  5  1  0  0  0  0
+	5  6  2  0  0  0  0
+	6  7  1  0  0  0  0
+
+	RMSD cutoff (in Angstrom)	0.5
+	Energy cutoff (in kcal/mol)	50.0
+	Max number of conformers to test	100000
+	Include the input conformation as the first conformer	False
+
+-----
+
+.. class:: infomark
+
+**Output**
+
+* Example::
+
+     23 26  0  0  0  0  0  0  0  0999 V2000
+   21.2060    9.9350   63.0810 C   0  0  0  0  0  0  0  0  0  0  0  0
+   21.2410    9.4460   64.5510 C   0  0  0  0  0  0  0  0  0  0  0  0
+   22.0000    8.1250   64.6300 C   0  0  0  0  0  0  0  0  0  0  0  0
+   21.7010    7.3010   65.5120 O   0  0  0  0  0  0  0  0  0  0  0  0
+   23.1180    7.8720   63.7340 C   0  0  0  0  0  0  0  0  0  0  0  0
+   23.4530    8.7270   62.7850 C   0  0  0  0  0  0  0  0  0  0  0  0
+   24.6970    8.4430   61.9510 C   0  0  0  0  0  0  0  0  0  0  0  0
+   24.4490    8.6370   60.4430 C   0  0  0  0  0  0  0  0  0  0  0  0
+   23.7890    9.9970   60.0980 C   0  0  2  0  0  0  0  0  0  0  0  0
+   22.4340   10.0950   60.8720 C   0  0  1  0  0  0  0  0  0  0  0  0
+   22.6140   10.0230   62.4340 C   0  0  1  0  0  0  0  0  0  0  0  0
+   21.6330   11.3540   60.4500 C   0  0  0  0  0  0  0  0  0  0  0  0
+   21.4320   11.4340   58.9110 C   0  0  0  0  0  0  0  0  0  0  0  0
+   22.7860   11.4040   58.1690 C   0  0  1  0  0  0  0  0  0  0  0  0
+   23.4830   10.0600   58.5980 C   0  0  1  0  0  0  0  0  0  0  0  0
+   24.6740    9.9180   57.6180 C   0  0  0  0  0  0  0  0  0  0  0  0
+   24.0720   10.4500   56.2670 C   0  0  0  0  0  0  0  0  0  0  0  0
+   22.7140   11.1490   56.6270 C   0  0  2  0  0  0  0  0  0  0  0  0
+   23.6590   12.6770   58.4540 C   0  0  0  0  0  0  0  0  0  0  0  0
+   23.4270   11.2460   63.0070 C   0  0  0  0  0  0  0  0  0  0  0  0
+   22.3750   12.3880   55.7810 C   0  0  0  0  0  0  0  0  0  0  0  0
+   23.2120   12.8760   55.0520 O   0  0  0  0  0  0  0  0  0  0  0  0
+   21.0090   12.9760   55.8570 C   0  0  0  0  0  0  0  0  0  0  0  0
+
+::
+
+  1  2  1  0  0  0  0
+  1 11  1  0  0  0  0
+  2  3  1  0  0  0  0
+  3  4  2  0  0  0  0
+  3  5  1  0  0  0  0
+  5  6  2  0  0  0  0
+  6  7  1  0  0  0  0
+  6 11  1  0  0  0  0
+  7  8  1  0  0  0  0
+  9  8  1  6  0  0  0
+ 10  9  1  1  0  0  0
+
+-----
+
+.. class:: infomark
+
+**Cite**
+
+Confab_
+
+.. _Confab: https://code.google.com/p/confab/
+
+
+ </help>
+
+</tool>