Mercurial > repos > bgruening > chemfp

diff chemfp_ob2fps/ob2fps.xml @ 0:a8ac5250d59c

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author bgruening
date Tue, 26 Mar 2013 13:05:41 -0400
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children 438bc12d591b
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_ob2fps/ob2fps.xml	Tue Mar 26 13:05:41 2013 -0400
@@ -0,0 +1,143 @@
+<tool id="chemfp_ob2fps" name="Molecules to Fingerprints" version="0.1.2">
+    <description>with different fingerprint types</description>
+    <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism>
+    <requirements>
+        <requirement type="package" version="1.1p1">chemfp</requirement>
+    </requirements>
+    <command>
+        ob2fps $fptype --in "${infile.ext}" "${infile}" -o "${outfile}" --errors report 2>&#38;1
+    </command>
+    <inputs>
+        <param name="infile" type='data' format="sdf,smi,mol,mol2,cml,inchi" label="molecule file"/>
+        <param name='fptype' type='select' format='text'>
+            <option value='--FP2'>FP2</option>
+            <option value='--FP3'>FP3</option>
+            <option value='--FP4'>FP4</option>
+            <option value='--MACCS'>MACCS</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="outfile" format="fps" />
+    </outputs>
+    <tests>
+        <!-- FP2 -->
+        <test>
+            <param name="infile" value="CID_2244.sdf" ftype="sdf" />
+            <param name="fptype" value="--FP2" />
+            <output name="outfile" file="CID_2244_FP2.fps" ftype="fps" />
+        </test>
+        <test>
+            <param name="infile" value="CID_2244.smi" ftype="smi" />
+            <param name="fptype" value="--FP2" />
+            <output name="outfile" file="CID_2244_FP2.fps" ftype="fps" />
+        </test>
+        <!-- FP3 -->
+        <test>
+            <param name="infile" value="CID_2244.sdf" ftype="sdf" />
+            <param name="fptype" value="--FP3" />
+            <output name="outfile" file="CID_2244_FP3.fps" ftype="fps" />
+        </test>
+        <test>
+            <param name="infile" value="CID_2244.smi" ftype="smi" />
+            <param name="fptype" value="--FP3" />
+            <output name="outfile" file="CID_2244_FP3.fps" ftype="fps" />
+        </test>
+        <!-- FP4 -->
+        <test>
+            <param name="infile" value="CID_2244.sdf" ftype="sdf" />
+            <param name="fptype" value="--FP4" />
+            <output name="outfile" file="CID_2244_FP4.fps" ftype="fps" />
+        </test>
+        <test>
+            <param name="infile" value="CID_2244.smi" ftype="smi" />
+            <param name="fptype" value="--FP4" />
+            <output name="outfile" file="CID_2244_FP4.fps" ftype="fps" />
+        </test>
+        <!-- MACCS -->
+        <test>
+            <param name="infile" value="CID_2244.sdf" ftype="sdf" />
+            <param name="fptype" value="--MACCS" />
+            <output name="outfile" file="CID_2244_MACCS.fps" ftype="fps" />
+        </test>
+        <test>
+            <param name="infile" value="CID_2244.smi" ftype="smi" />
+            <param name="fptype" value="--MACCS" />
+            <output name="outfile" file="CID_2244_MACCS.fps" ftype="fps" />
+        </test>
+    </tests>
+    <help>
+
+
+**What it does**
+
+Generate fingerprints using OpenBabel
+
+-----
+
+**Example**
+
+* input::
+	
+	      - SDF File
+
+		28434379
+		  -OEChem-02031205132D
+
+		 37 39  0     0  0  0  0  0  0999 V2000
+		    8.1648   -1.8842    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+		    6.0812   -0.2134    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+		    6.0812   -1.8229    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+		    2.5369   -2.0182    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+		    6.3919    0.7371    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+		    7.3704    0.9433    0.0000 C   0  0  0  0 
+		    ......
+		  1 15  1  0  0  0  0
+		  1 35  1  0  0  0  0
+		  2  5  1  0  0  0  0
+		  2 11  1  0  0  0  0
+		  2 12  1  0  0  0  0
+		  3 12  2  0  0  0  0
+		  3 13  1  0  0  0  0
+		  4 18  1  0  0  0  0
+		  ......
+
+			&gt;PUBCHEM_COMPOUND_CID&lt;
+			28434379
+
+			&gt; &lt;PUBCHEM_COMPOUND_CANONICALIZED&gt;
+			1
+
+			&gt; &lt;PUBCHEM_CACTVS_COMPLEXITY&gt;
+			280
+
+			&gt; &lt;PUBCHEM_CACTVS_HBOND_ACCEPTOR&gt;
+			2
+
+			&gt; &lt;PUBCHEM_CACTVS_HBOND_DONOR&gt;
+			2
+
+			&gt; &lt;PUBCHEM_CACTVS_ROTATABLE_BOND&gt;
+			2
+
+			&gt; &lt;PUBCHEM_CACTVS_SUBSKEYS&gt;
+			AAADceBzIAAAAAAAAAAAAAAAAAAAAWAAAAAwYAAAAAAAAFgB8AAAHgAQCAAACCjhlwYx0LdMEgCgASZiZASCgC0hEqAJ2CA4dJiKeKLA2dGUJAhokALYyCcQAAAAAACAAAQAACAAAQAACAAAQAAAAAAAAA==
+
+			&gt;
+
+		- type : FP2
+
+* output::
+
+	#FPS1
+	#num_bits=1021
+	#type=OpenBabel-FP2/1
+	#software=OpenBabel/2.3.0
+	#source=/tmp/dataset_409.dat.sdf
+	#date=2012-02-03T11:13:39
+	c0000000000008c0000846000400000000000010800000000000004000000000100010000700802170000018000000c
+	0010000000020600208008000008000000c000c02c00002000000c00000100000008001400c800001c0180000000300
+	10000000000080000000c0000060000c0000060810000010000000800102000000	28434379
+
+
+    </help>
+</tool>