view strip-it/strip-it.xml @ 1:54edf22c93c0

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<tool id="stripit" name="Strip-it">
    <description> extracts predefined scaffolds from molecules</description>
    <requirements>
        <requirement type="package" version="1.0.0">silicos_it</requirement>
    </requirements>
    <command >
        strip-it --inputFormat ${infile.ext} --input $infile --output $outfile 2>&#38;1
    </command>
    <inputs>
        <param name="infile" type="data" format='sdf,mol,mol2,smi' label="Molecule file" />
    </inputs>
    <outputs>
        <data name="outfile" format="tabular" />
    </outputs>
    <tests>
        <test>
            <param name="infile" type='sdf' value="CID_3037.sdf"/>
            <data name="output" type="tabular" file="Strip-it_on_CID3037.tabular" />
        </test>
    </tests>
    <help>

**What it does**

Strip-it is a program that extracts predefined scaffolds from organic
molecules

The program comes with a number of predefined molecular scaffolds for
extraction. These scaffolds include, amongst others

	- Molecular frameworks as originally described by Bemis and
	  Murcko;1
	- Molecular frameworks and the reduced molecular frameworks as
	  described by Ansgar Schuffenhauer and coworkers;2
	- Scaffold topologies as described by Sara Pollock and coworkers.3

-----

**Example**

* input ::

	- input 
	 27 28  0     0  0  0  0  0  0999 V2000
	   -4.8550    1.3401    0.2120 Cl  0  0  0  0  0  0  0  0  0  0  0  0
	    4.8529   -1.3406    0.2121 Cl  0  0  0  0  0  0  0  0  0  0  0  0
	   -0.1809   -2.1668   -0.3789 O   0  0  0  0  0  0  0  0  0  0  0  0
	    0.1788    2.1664   -0.3787 O   0  0  0  0  0  0  0  0  0  0  0  0
	   -0.0011   -0.0002    1.4744 C   0  0  0  0  0  0  0  0  0  0  0  0
	   -1.2222   -0.2738    0.6597 C   0  0  0  0  0  0  0  0  0  0  0  0
	    1.2377    0.2772    0.6480 C   0  0  0  0  0  0  0  0  0  0  0  0
	   -1.2586   -1.3462   -0.2316 C   0  0  0  0  0  0  0  0  0  0  0  0
	    1.2565    1.3457   -0.2314 C   0  0  0  0  0  0  0  0  0  0  0  0
	   -2.3343    0.5568    0.7972 C   0  0  0  0  0  0  0  0  0  0  0  0
	    2.3322   -0.5574    0.7972 C   0  0  0  0  0  0  0  0  0  0  0  0
	   -2.4069   -1.5879   -0.9855 C   0  0  0  0  0  0  0  0  0  0  0  0
	    2.4048    1.5875   -0.9852 C   0  0  0  0  0  0  0  0  0  0  0  0
	   -3.4827    0.3152    0.0433 C   0  0  0  0  0  0  0  0  0  0  0  0
	    3.4807   -0.3156    0.0435 C   0  0  0  0  0  0  0  0  0  0  0  0
	   -3.5190   -0.7571   -0.8481 C   0  0  0  0  0  0  0  0  0  0  0  0
	    3.5170    0.7568   -0.8478 C   0  0  0  0  0  0  0  0  0  0  0  0
	   -0.1548    0.8649    2.1342 H   0  0  0  0  0  0  0  0  0  0  0  0
	    0.1601   -0.8435    2.1593 H   0  0  0  0  0  0  0  0  0  0  0  0
	   -2.3089    1.3938    1.4913 H   0  0  0  0  0  0  0  0  0  0  0  0
	    2.3053   -1.3909    1.4943 H   0  0  0  0  0  0  0  0  0  0  0  0
	   -2.4415   -2.4213   -1.6818 H   0  0  0  0  0  0  0  0  0  0  0  0
	    2.4469    2.4191   -1.6835 H   0  0  0  0  0  0  0  0  0  0  0  0
	   -4.4070   -0.9574   -1.4422 H   0  0  0  0  0  0  0  0  0  0  0  0
	    4.4050    0.9570   -1.4418 H   0  0  0  0  0  0  0  0  0  0  0  0
	    0.2961   -2.2262    0.4641 H   0  0  0  0  0  0  0  0  0  0  0  0
	    0.3872    2.8487   -1.0397 H   0  0  0  0  0  0  0  0  0  0  0  0
	  1 14  1  0  0  0  0
	  2 15  1  0  0  0  0
	  3  8  1  0  0  0  0
	  3 26  1  0  0  0  0
	  4  9  1  0  0  0  0
	  4 27  1  0  0  0  0
	  5  6  1  0  0  0  0



* output ::

	NAME	MOLECULE	RINGS_WITH_LINKERS_1	RINGS_WITH_LINKERS_2	MURCKO_1	MURCKO_2	OPREA_1	OPREA_2	OPREA_3	SCHUFFENHAUER_1	SCHUFFENHAUER_2	SCHUFFENHAUER_3	SCHUFFENHAUER_4	SCHUFFENHAUER_5
	3037	Oc1ccc(cc1Cc1cc(Cl)ccc1O)Cl	c1ccc(cc1)Cc1ccccc1	c1ccc(cc1)Cc1ccccc1	C1CCC(CC1)CC1CCCCC1	C1CCC(CC1)C1CCCCC1	C1CC1C1CC1	C1CC1C1CC1	C1CC1C1CC1	c1ccccc1

    </help>
</tool>