view chemfp_sdf2fps/sdf2fps.xml @ 20:21d29a7f13d8

ChemicalToolBoX update.

<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>
        <requirement type="package" version="2.3.2">openbabel</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>