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comparison simsearch.xml @ 14:47d2bf691908

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ChemicalToolBoX update.
author Bjoern Gruening <bjoern.gruening@gmail.com>
date Sun, 02 Jun 2013 19:54:51 +0200
parents dbe9c82028d1
children b4eaf75cac77
comparison
equal deleted inserted replaced
13:dbe9c82028d1 14:47d2bf691908
4 <requirement type="package" version="1.1p1">chemfp</requirement> 4 <requirement type="package" version="1.1p1">chemfp</requirement>
5 <requirement type="package" version="2.3.2">openbabel</requirement> 5 <requirement type="package" version="2.3.2">openbabel</requirement>
6 </requirements> 6 </requirements>
7 <command> 7 <command>
8 #if $method_opts.method_opts_selector == "chemfp": 8 #if $method_opts.method_opts_selector == "chemfp":
9 ## TODO: remove all comment lines, in muti mode many comment lines will be appear, also in the middle of the result file, remove them
10 #if int($method_opts.knn) == 0:
11 #set $k = 'all'
12 #else:
13 #set $k = int($method_opts.knn)
14 #end if
15 simsearch 9 simsearch
10 #if int($method_opts.knn) == 0:
11 #set $k = 'all'
12 ## count is only available if k nearest neighbor search is disabled
13 $method_opts.counts
14 #else:
15 #set $k = int($method_opts.knn)
16 #end if
17
16 -k $k 18 -k $k
17 --threshold $method_opts.threshold 19
18 --query-format fps 20 --threshold $method_opts.threshold
19 $method_opts.counts 21 --query-format fps
20 --target-format fps 22 --target-format fps
21 -o "${outfile}" 23 -o "${outfile}"
22 24
23 ## build and search an in-memory data structure (faster for multiple queries) 25 ## build and search an in-memory data structure (faster for multiple queries)
24 --memory 26 --memory
65 </when> 67 </when>
66 </conditional> 68 </conditional>
67 <param name='knn' type='integer' value='0' label='select the k nearest neighbors' help='0 means all neighbors'> 69 <param name='knn' type='integer' value='0' label='select the k nearest neighbors' help='0 means all neighbors'>
68 <validator type="in_range" min="0" /> 70 <validator type="in_range" min="0" />
69 </param> 71 </param>
70 <param name='threshold' type='float' label='threshold' value='0.7'/> 72 <param name='threshold' type='float' value='0.7' label='threshold' />
71 <param name="counts" type="boolean" label="report counts (-c)" truevalue="-c" falsevalue="" checked="false" /> 73 <param name="counts" type="boolean" truevalue="-c" falsevalue="" checked="false" label="report counts (-c)" help="Is ignored if k nearest neighbor search is enabled" />
72 </when> 74 </when>
73 <when value="obabel"> 75 <when value="obabel">
74 <param name="query" type='data' format="smi,mol,sdf,inchi" label="query"/> 76 <param name="query" type='data' format="smi,mol,sdf,inchi" label="query"/>
75 <param name="fastsearch" type='data' format="obfs" label="OpenBabel Fastsearch Index"/> 77 <param name="fastsearch" type='data' format="obfs" label="OpenBabel Fastsearch Index"/>
76 <param name="threshold" type='float' label="threshold" value='0.7'/> 78 <param name="threshold" type='float' label="threshold" value='0.7'/>
93 <help> 95 <help>
94 96
95 97
96 **What it does** 98 **What it does**
97 99
98 similarity search of fingerprint data sets 100 Similarity search of compounds using fingerprint data sets. Depending on the input either chemfp_ of `Open Babel`_ is used.
99 101
100 -----
101 102
102 **Example** 103 **References**
103 104
104 * input:: 105 Please reference the `Open Babel`_ or the chemfp_ project.
105
106 - Target Database in FPS format
107 106
108 #FPS1 107 N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison. "Open Babel: An open chemical toolbox." J. Cheminf. (2011), 3, 33. `DOI:10.1186/1758-2946-3-33`_
109 #num_bits=881 108 The Open Babel Package http://openbabel.sourceforge.net/
110 #type=CACTVS-E_SCREEN/1.0 extended=2
111 #software=CACTVS/unknown
112 #source=Desktop/3579363516810334491.sdf
113 #date=2012-02-03T13:07:47
114 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701487e960
115 cc0bed3248000580644626004101b4844805901b041c2e19511e45039b8b2926101609401b13e408000000000001
116 00200000040080000010000002000000000000 55169009
117 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701087e960
118 cc0bed3248000580644626004101b4844805901b041c2e19111e45039b8b2926105609401313e408000000000001
119 00200000040080000010000002000000000000 55079807
120 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000b01087e960
121 cc0bed3248000580644626004101b4844805901b041c2e19511e45039b8b2924101609401b13e408000000000001
122 00200000040080000010000002000000000000 3153534
123 07ce0c000000000000000000000000000080060000000c000000000000001a800f0000780008100000103c87e960
124 cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2926101609401b13e408000000000001
125 00200000040080000010000002000000000000 55168823
126 07ce05000000000000000000000000000080060000000c000000000000001a800f0000780008100000101087e960
127 cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e408000000000001
128 00200000040080000010000002000000000000 55102353
129 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000b01487e9
130 60cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800003000
131 000100200000040080000010000002000000000000 55091849
132 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000103c87e9
133 60cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000
134 000100200000040080000010000002000000000000 55091752
135 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000b01487e9
136 60cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800001000
137 000100200000040080000010000002000000000000 55091467
138 07ce05000000000000000000000000000080060000000c000000000000001a800f0000780008100000101087e9
139 60cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000
140 000100200000040080000010000002000000000000 55091466
141 07ce05000000000000000000000000000080060000000c000000000000001a800f0000780008100000101087e9
142 60cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000
143 000100200000040080000010000002000000000000 55091416
144 03ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000101087e9
145 60cc0bed3248000580644626004101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000
146 000100200000040080000010000002000000000000 6499094
147 03ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000101087e9
148 60cc0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000
149 000100200000040080000010000002000000000000 6485578
150 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000b01087e9
151 60cc0bed3248000580644626004101b4844805901b041c2e19511e45039b8b2924101609401b13e40800001000
152 000100200000040080000010000002000000000000 6485577
153 109
154 - query :
155 #FPS1
156 #num_bits=881
157 #type=CACTVS-E_SCREEN/1.0 extended=2
158 #software=CACTVS/unknown
159 #source=CID_28434379.sdf
160 #date=2012-02-03T13:08:39
161 07ce04000000000000000000000000000080060000000c060000000000001a800f0000780008100000101487e9
162 608c0bed3248000580644626204101b4844805901b041c2e19511e45039b8b2924101609401b13e40800000000
163 000100200000040080000010000002000000000000 28434379
164 - k : 4
165 - threshold : 0.7
166 110
167 * output:: 111 .. _DOI:10.1186/1758-2946-3-33: http://www.jcheminf.com/content/3/1/33
168 112 .. _chemfp: http://chemfp.com/
169 #Simsearch/1 113 .. _`Open Babel`: http://openbabel.org/
170 #num_bits=881
171 #type=Tanimoto k=4 threshold=0.7
172 #software=chemfp/1.0
173 #queries=q.fps
174 #targets=target.fps
175 #query_sources=CID_28434379.sdf
176 #target_sources=Desktop/3579363516810334491.sdf
177 4 28434379 55091752 0.9684 55091466 0.9682 55091416 0.9682 55102353 0.9682
178
179 114
180 </help> 115 </help>
181 </tool> 116 </tool>