Mercurial > repos > bgruening > chemfp
comparison chemfp_ob2fps/ob2fps.xml @ 0:a8ac5250d59c
Uploaded
author | bgruening |
---|---|
date | Tue, 26 Mar 2013 13:05:41 -0400 |
parents | |
children | 438bc12d591b |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:a8ac5250d59c |
---|---|
1 <tool id="chemfp_ob2fps" name="Molecules to Fingerprints" version="0.1.2"> | |
2 <description>with different fingerprint types</description> | |
3 <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism> | |
4 <requirements> | |
5 <requirement type="package" version="1.1p1">chemfp</requirement> | |
6 </requirements> | |
7 <command> | |
8 ob2fps $fptype --in "${infile.ext}" "${infile}" -o "${outfile}" --errors report 2>&1 | |
9 </command> | |
10 <inputs> | |
11 <param name="infile" type='data' format="sdf,smi,mol,mol2,cml,inchi" label="molecule file"/> | |
12 <param name='fptype' type='select' format='text'> | |
13 <option value='--FP2'>FP2</option> | |
14 <option value='--FP3'>FP3</option> | |
15 <option value='--FP4'>FP4</option> | |
16 <option value='--MACCS'>MACCS</option> | |
17 </param> | |
18 </inputs> | |
19 <outputs> | |
20 <data name="outfile" format="fps" /> | |
21 </outputs> | |
22 <tests> | |
23 <!-- FP2 --> | |
24 <test> | |
25 <param name="infile" value="CID_2244.sdf" ftype="sdf" /> | |
26 <param name="fptype" value="--FP2" /> | |
27 <output name="outfile" file="CID_2244_FP2.fps" ftype="fps" /> | |
28 </test> | |
29 <test> | |
30 <param name="infile" value="CID_2244.smi" ftype="smi" /> | |
31 <param name="fptype" value="--FP2" /> | |
32 <output name="outfile" file="CID_2244_FP2.fps" ftype="fps" /> | |
33 </test> | |
34 <!-- FP3 --> | |
35 <test> | |
36 <param name="infile" value="CID_2244.sdf" ftype="sdf" /> | |
37 <param name="fptype" value="--FP3" /> | |
38 <output name="outfile" file="CID_2244_FP3.fps" ftype="fps" /> | |
39 </test> | |
40 <test> | |
41 <param name="infile" value="CID_2244.smi" ftype="smi" /> | |
42 <param name="fptype" value="--FP3" /> | |
43 <output name="outfile" file="CID_2244_FP3.fps" ftype="fps" /> | |
44 </test> | |
45 <!-- FP4 --> | |
46 <test> | |
47 <param name="infile" value="CID_2244.sdf" ftype="sdf" /> | |
48 <param name="fptype" value="--FP4" /> | |
49 <output name="outfile" file="CID_2244_FP4.fps" ftype="fps" /> | |
50 </test> | |
51 <test> | |
52 <param name="infile" value="CID_2244.smi" ftype="smi" /> | |
53 <param name="fptype" value="--FP4" /> | |
54 <output name="outfile" file="CID_2244_FP4.fps" ftype="fps" /> | |
55 </test> | |
56 <!-- MACCS --> | |
57 <test> | |
58 <param name="infile" value="CID_2244.sdf" ftype="sdf" /> | |
59 <param name="fptype" value="--MACCS" /> | |
60 <output name="outfile" file="CID_2244_MACCS.fps" ftype="fps" /> | |
61 </test> | |
62 <test> | |
63 <param name="infile" value="CID_2244.smi" ftype="smi" /> | |
64 <param name="fptype" value="--MACCS" /> | |
65 <output name="outfile" file="CID_2244_MACCS.fps" ftype="fps" /> | |
66 </test> | |
67 </tests> | |
68 <help> | |
69 | |
70 | |
71 **What it does** | |
72 | |
73 Generate fingerprints using OpenBabel | |
74 | |
75 ----- | |
76 | |
77 **Example** | |
78 | |
79 * input:: | |
80 | |
81 - SDF File | |
82 | |
83 28434379 | |
84 -OEChem-02031205132D | |
85 | |
86 37 39 0 0 0 0 0 0 0999 V2000 | |
87 8.1648 -1.8842 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 | |
88 6.0812 -0.2134 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 | |
89 6.0812 -1.8229 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 | |
90 2.5369 -2.0182 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 | |
91 6.3919 0.7371 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
92 7.3704 0.9433 0.0000 C 0 0 0 0 | |
93 ...... | |
94 1 15 1 0 0 0 0 | |
95 1 35 1 0 0 0 0 | |
96 2 5 1 0 0 0 0 | |
97 2 11 1 0 0 0 0 | |
98 2 12 1 0 0 0 0 | |
99 3 12 2 0 0 0 0 | |
100 3 13 1 0 0 0 0 | |
101 4 18 1 0 0 0 0 | |
102 ...... | |
103 | |
104 >PUBCHEM_COMPOUND_CID< | |
105 28434379 | |
106 | |
107 > <PUBCHEM_COMPOUND_CANONICALIZED> | |
108 1 | |
109 | |
110 > <PUBCHEM_CACTVS_COMPLEXITY> | |
111 280 | |
112 | |
113 > <PUBCHEM_CACTVS_HBOND_ACCEPTOR> | |
114 2 | |
115 | |
116 > <PUBCHEM_CACTVS_HBOND_DONOR> | |
117 2 | |
118 | |
119 > <PUBCHEM_CACTVS_ROTATABLE_BOND> | |
120 2 | |
121 | |
122 > <PUBCHEM_CACTVS_SUBSKEYS> | |
123 AAADceBzIAAAAAAAAAAAAAAAAAAAAWAAAAAwYAAAAAAAAFgB8AAAHgAQCAAACCjhlwYx0LdMEgCgASZiZASCgC0hEqAJ2CA4dJiKeKLA2dGUJAhokALYyCcQAAAAAACAAAQAACAAAQAACAAAQAAAAAAAAA== | |
124 | |
125 > | |
126 | |
127 - type : FP2 | |
128 | |
129 * output:: | |
130 | |
131 #FPS1 | |
132 #num_bits=1021 | |
133 #type=OpenBabel-FP2/1 | |
134 #software=OpenBabel/2.3.0 | |
135 #source=/tmp/dataset_409.dat.sdf | |
136 #date=2012-02-03T11:13:39 | |
137 c0000000000008c0000846000400000000000010800000000000004000000000100010000700802170000018000000c | |
138 0010000000020600208008000008000000c000c02c00002000000c00000100000008001400c800001c0180000000300 | |
139 10000000000080000000c0000060000c0000060810000010000000800102000000 28434379 | |
140 | |
141 | |
142 </help> | |
143 </tool> |