Mercurial > repos > bgruening > chemfp

diff chemfp_sdf2fps/sdf2fps.xml @ 0:a8ac5250d59c

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author bgruening
date Tue, 26 Mar 2013 13:05:41 -0400
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children 21d29a7f13d8
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chemfp_sdf2fps/sdf2fps.xml	Tue Mar 26 13:05:41 2013 -0400
@@ -0,0 +1,93 @@
+<tool id="sdf2fps" name="SDF to Fingerprint" version="0.1.1">
+    <description>extract fingerprints from sdf files metadata</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>
+        sdf2fps --pubchem "${infile}" > "${outfile}"
+    </command>
+    <inputs>
+        <param name="infile" type='data' format="sdf" label="SDF file with fingerprints as metadata"/>
+    </inputs>
+    <outputs>
+        <data name="outfile" format="fps"/>
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+
+
+**What it does**
+
+Read a SDF file and extract the fingerprints, to stores them in a fps-file.
+TODO: currently it only works for PubChem
+
+-----
+
+**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;
+
+* output::
+
+	#FPS1
+	#num_bits=881
+	#type=CACTVS-E_SCREEN/1.0 extended=2
+	#software=CACTVS/unknown
+	#source=/home/mohammed/galaxy-central/database/files/000/dataset_409.dat
+	#date=2012-02-03T10:44:12
+	07ce04000000000000000000000000000080060000000c0600
+	00000000001a800f0000780008100000101487e9608c0bed32
+	48000580644626204101b4844805901b041c2e19511e45039b
+	8b2924101609401b13e4080000000000010020000004008000
+	0010000002000000000000	28434379
+
+
+    </help>
+</tool>