|
0
|
1 <tool id="shapeit" name="Shape-it">
|
|
|
2 <description> alignment of a reference molecule against a database of molecules using the shape of the molecules</description>
|
|
|
3 <requirements>
|
|
|
4 <requirement type="package" version="1.0.0">silicos_it</requirement>
|
|
|
5 </requirements>
|
|
|
6 <command >
|
|
|
7 shape-it --Format ${database.ext} --dbase $database --reference $reference --addIterations $addIterations --best $best --out $output 2>&1
|
|
|
8 </command>
|
|
|
9 <inputs>
|
|
|
10 <param name="database" type="data" format='sdf,mol,mol2,smi' label="database" />
|
|
|
11 <param name="reference" type="data" format='sdf,mol,mol2,smi' label="refrence" />
|
|
|
12 <param name="cutoff" type="float" value="0.0" />
|
|
|
13 <param name='addIterations' type='integer' value='0' label='Perform N additional optimization steps with the simulated annealing procedure' />
|
|
|
14 <param name='best' type='integer' value='0' label='the N best scoring molecules are reported' />
|
|
|
15 </inputs>
|
|
|
16 <outputs>
|
|
|
17 <data name="output" format_source='database' />
|
|
|
18 </outputs>
|
|
|
19 <tests>
|
|
|
20 <test>
|
|
|
21 <param name="database" ftype='sdf' value="CID_3033.sdf" />
|
|
|
22 <param name="reference" type="sdf" value='CID_3037.sdf' />
|
|
|
23 <param name="cutoff" value="0.0" />
|
|
|
24 <param name='addIterations' value='0' />
|
|
|
25 <param name='best' value='0' />
|
|
|
26 <output name="output" ftype='sdf' file="shapeit_on_CID3033_and_CID3037.sdf" />
|
|
|
27 </test>
|
|
|
28 </tests>
|
|
|
29 <help>
|
|
|
30
|
|
|
31 **What it does**
|
|
|
32
|
|
|
33 Shape-it is a program for the alignment of a reference molecule against a
|
|
|
34 database of molecules using the shape of the molecules. It is based on
|
|
|
35 the use of Gaussian volumes as descriptor for molecular shape as it was
|
|
|
36 introduced by Grant and Pickup1 .
|
|
|
37
|
|
|
38 The program expects one reference molecule with
|
|
|
39 its three-dimensional coordinates and one database files containing one
|
|
|
40 or more molecules in three dimensions. The results are either the alignment
|
|
|
41 of all database molecules and their respective scores or the N best
|
|
|
42 scoring molecules from the complete database.
|
|
|
43
|
|
|
44 -----
|
|
|
45
|
|
|
46 **Example**
|
|
|
47
|
|
|
48 * input::
|
|
|
49
|
|
|
50 - database
|
|
|
51 27 28 0 0 0 0 0 0 0999 V2000
|
|
|
52 -4.8550 1.3401 0.2120 Cl 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
53 4.8529 -1.3406 0.2121 Cl 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
54 -0.1809 -2.1668 -0.3789 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
55 0.1788 2.1664 -0.3787 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
56 -0.0011 -0.0002 1.4744 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
57 -1.2222 -0.2738 0.6597 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
58 1.2377 0.2772 0.6480 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
59 -1.2586 -1.3462 -0.2316 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
60 1.2565 1.3457 -0.2314 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
61 -2.3343 0.5568 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
62 2.3322 -0.5574 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
63 -2.4069 -1.5879 -0.9855 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
64 2.4048 1.5875 -0.9852 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
65 -3.4827 0.3152 0.0433 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
66 3.4807 -0.3156 0.0435 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
67 -3.5190 -0.7571 -0.8481 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
68 3.5170 0.7568 -0.8478 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
69 -0.1548 0.8649 2.1342 H 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
70 0.1601 -0.8435 2.1593 H 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
71 -2.3089 1.3938 1.4913 H 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
72 2.3053 -1.3909 1.4943 H 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
73 -2.4415 -2.4213 -1.6818 H 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
74 2.4469 2.4191 -1.6835 H 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
75 -4.4070 -0.9574 -1.4422 H 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
76 4.4050 0.9570 -1.4418 H 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
77 0.2961 -2.2262 0.4641 H 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
78 0.3872 2.8487 -1.0397 H 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
79 1 14 1 0 0 0 0
|
|
|
80 2 15 1 0 0 0 0
|
|
|
81 3 8 1 0 0 0 0
|
|
|
82 3 26 1 0 0 0 0
|
|
|
83 4 9 1 0 0 0 0
|
|
|
84 4 27 1 0 0 0 0
|
|
|
85 5 6 1 0 0 0 0
|
|
|
86 5 7 1 0 0 0 0
|
|
|
87 .....
|
|
|
88
|
|
|
89 - reference
|
|
|
90
|
|
|
91 30 31 0 0 0 0 0 0 0999 V2000
|
|
|
92 1.9541 1.1500 -2.5078 Cl 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
93 1.1377 -1.6392 2.1136 Cl 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
94 -3.2620 -2.9284 -1.0647 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
95 -2.7906 -1.9108 0.9092 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
96 0.2679 -0.2051 -0.3990 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
97 -2.0640 0.5139 -0.3769 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
98 -0.7313 0.7178 -0.0192 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
99 -2.4761 -0.6830 -1.1703 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
100 1.6571 -0.2482 -0.1795 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
101 -3.0382 1.4350 0.0081 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
102 -0.3728 1.8429 0.7234 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
103 -2.6797 2.5600 0.7506 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
104 -1.3470 2.7640 1.1083 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
105 2.5353 0.3477 -1.0918 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
106 2.1740 -0.8865 0.9534 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
107 -2.8480 -1.8749 -0.3123 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
108 3.9124 0.3058 -0.8739 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
109 3.5511 -0.9285 1.1713 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
110 4.4203 -0.3324 0.2576 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
111 -1.7086 -0.9792 -1.8930 H 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
112 -3.3614 -0.4266 -1.7676 H 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
113 -0.0861 -1.1146 -0.6780 H 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
114 -4.0812 1.2885 -0.2604 H 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
115 0.6569 2.0278 1.0167 H 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
116 -3.4382 3.2769 1.0511 H 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
117 -1.0683 3.6399 1.6868 H 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
118 4.6037 0.7654 -1.5758 H 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
119 3.9635 -1.4215 2.0480 H 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
120 5.4925 -0.3651 0.4274 H 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
121 -3.5025 -3.7011 -0.5102 H 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
122 1 14 1 0 0 0 0
|
|
|
123 2 15 1 0 0 0 0
|
|
|
124 3 16 1 0 0 0 0
|
|
|
125 3 30 1 0 0 0 0
|
|
|
126 4 16 2 0 0 0 0
|
|
|
127 5 7 1 0 0 0 0
|
|
|
128 5 9 1 0 0 0 0
|
|
|
129 5 22 1 0 0 0 0
|
|
|
130 6 7 1 0 0 0 0
|
|
|
131 6 8 1 0 0 0 0
|
|
|
132 ......
|
|
|
133
|
|
|
134 - cutoff : 0.0
|
|
|
135
|
|
|
136 * output::
|
|
|
137
|
|
|
138 27 28 0 0 0 0 0 0 0 0999 V2000
|
|
|
139 -4.8550 1.3401 0.2120 Cl 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
140 4.8529 -1.3406 0.2121 Cl 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
141 -0.1809 -2.1668 -0.3789 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
142 0.1788 2.1664 -0.3787 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
143 -0.0011 -0.0002 1.4744 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
144 -1.2222 -0.2738 0.6597 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
145 1.2377 0.2772 0.6480 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
146 -1.2586 -1.3462 -0.2316 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
147 1.2565 1.3457 -0.2314 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
148 -2.3343 0.5568 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
149 2.3322 -0.5574 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
150 -2.4069 -1.5879 -0.9855 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
151 2.4048 1.5875 -0.9852 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
152 -3.4827 0.3152 0.0433 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
153 3.4807 -0.3156 0.0435 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
154 -3.5190 -0.7571 -0.8481 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
155 3.5170 0.7568 -0.8478 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
156 -0.1548 0.8649 2.1342 H 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
157 0.1601 -0.8435 2.1593 H 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
158 -2.3089 1.3938 1.4913 H 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
159 2.3053 -1.3909 1.4943 H 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
160 -2.4415 -2.4213 -1.6818 H 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
161 2.4469 2.4191 -1.6835 H 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
162 -4.4070 -0.9574 -1.4422 H 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
163 4.4050 0.9570 -1.4418 H 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
164 0.2961 -2.2262 0.4641 H 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
165 0.3872 2.8487 -1.0397 H 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
166 1 14 1 0 0 0 0
|
|
|
167 2 15 1 0 0 0 0
|
|
|
168 3 8 1 0 0 0 0
|
|
|
169 3 26 1 0 0 0 0
|
|
|
170 4 9 1 0 0 0 0
|
|
|
171 4 27 1 0 0 0 0
|
|
|
172 5 6 1 0 0 0 0
|
|
|
173 5 7 1 0 0 0 0
|
|
|
174 5 18 1 0 0 0 0
|
|
|
175 5 19 1 0 0 0 0
|
|
|
176 6 8 2 0 0 0 0
|
|
|
177 ......
|
|
|
178
|
|
|
179 </help>
|
|
|
180 </tool>
|
