annotate align-it/align-it.xml @ 1:fdc038522974 draft

Uploaded
author bgruening
date Sat, 24 Aug 2013 17:16:16 -0400
parents bb92d30b4f52
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
1 <tool id="ctb_alignit" name="Pharmacophore Alignment" version="0.1">
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
2 <description>and Optimization (Align-it)</description>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
3 <requirements>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
4 <requirement type="package" version="1.0.1">silicos_it</requirement>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
5 <requirement type="package" version="2.3.2">openbabel</requirement>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
6 </requirements>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
7 <command>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
8 align-it
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
9 #if str($database.ext).strip() == 'phar':
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
10 --dbType PHAR
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
11 #else:
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
12 --dbType ${database.ext}
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
13 #end if
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
14 --dbase $database
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
15
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
16 --reference $reference
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
17 #if str($reference.ext).strip() == 'phar':
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
18 --refType PHAR
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
19 #else:
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
20 --refType ${reference.ext}
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
21 #end if
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
22 #######################################
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
23 #### output options
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
24 #######################################
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
25 --pharmacophore $aligned_pharmacophores
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
26
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
27
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
28 ##--out $aligned_structures
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
29 ##--outType $oformat
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
30
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
31 #if float( str($cutoff) ) > 0:
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
32 --cutOff $cutoff
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
33 #end if
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
34 #if int( str($best) ) > 0:
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
35 --best $best
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
36 #end if
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
37 --rankBy $rankBy
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
38 --scores $score_result_file
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
39
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
40 #######################################
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
41 #### Options
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
42 #######################################
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
43
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
44 #set $fgroups_combined = str( $fgroups ).strip()
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
45 --funcGroup $fgroups_combined
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
46
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
47 --epsilon $epsilon
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
48 $merge
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
49 $noNormal
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
50 $noHybrid
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
51 $scoreOnly
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
52 $withExclusion
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
53
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
54 2>&#38;1
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
55 </command>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
56 <inputs>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
57 <param name="database" type="data" format='mol,mol2,sdf,smi,phar' label="Defines the database of molecules that will be used to screen"/>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
58 <param name="reference" type="data" format='mol,mol2,sdf,smi,phar' label="Reference Molecule"/>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
59
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
60 <param name="fgroups" type="select" multiple="True" display="checkboxes" label="Specify a subset of the available functional groups that are used in the alignment">
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
61 <option value='AROM' selected="true">aromatic rings</option>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
62 <option value='HDON' selected="true">hydrogen bond donors</option>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
63 <option value='HACC' selected="true">hydrogen bond acceptors</option>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
64 <option value='LIPO' selected="true">lipophilic spots</option>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
65 <option value='CHARGE' selected="true">charge centers</option>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
66 </param>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
67
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
68
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
69 <param name="epsilon" type="float" value="0.5" label='Change the tolerance for points to be matched in the alignment phase' help="The lower this value, the more strict the matching between two pharmacophores will have to be before they can be aligned.">
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
70 <validator type="in_range" min="0" max="1" />
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
71 </param>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
72 <param name='merge' type='boolean' truevalue='--merge' falsevalue='' label='Merge pharmacophore points' />
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
73 <param name='noNormal' type='boolean' truevalue='--noNormal' falsevalue='' label='No normal information is included during the alignment' help="Using this flag makes the pharmacophore models less specific but also less conformation-dependent."/>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
74 <param name='noHybrid' type='boolean' truevalue='--noHybrid' falsevalue='' label='Disable the use of hybrid pharmacophore points' help="Using this flag will increase the number of pharmacophore points."/>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
75 <param name='withExclusion' type='boolean' truevalue='--withExclusion' falsevalue='' label='Add exclusion spheres into the optimization process instead of processing them afterwards' help="When this flag is set, the exclusion spheres have also an impact on the optimization procedure." />
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
76 <param name='scoreOnly' type='boolean' truevalue='--scoreOnly' falsevalue='' label='No translational or rotational optimization will be performed' help=""/>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
77
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
78 <!--
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
79 <param name='oformat' type='select' format='text' label="The aligned database structures are written to an output file of the following format">
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
80 <option value='smi'>SMILES</option>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
81 <option value='inchi'>InChI</option>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
82 <option value='sdf'>SD file</option>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
83 </param>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
84 -->
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
85
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
86 <param name="cutoff" type="float" value="0" label="Only structures with a score larger than this cutoff will be written to the files" help="This value should be between 0 and 1.">
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
87 <validator type="in_range" min="0" max="1" />
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
88 </param>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
89 <param name="best" type="integer" value="0" label="With this option only a limited number of best scoring structures are written to the files" help="0 means this option is deactivated">
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
90 <validator type="in_range" min="0"/>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
91 </param>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
92
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
93 <param name='rankBy' type='select' format='text' label="This option defines the used scoring scheme">
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
94 <option value='TANIMOTO'>Tanimoto</option>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
95 <option value='TVERSKY_REF'>TVERSKY_REF</option>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
96 <option value='TVERSKY_DB'>TVERSKY_DB</option>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
97 </param>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
98
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
99 </inputs>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
100 <outputs>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
101 <data name="aligned_pharmacophores" format="phar" label="${tool.name} on ${on_string} (aligned pharmacophores)"/>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
102 <!--<data name="aligned_structures" format="smi" label="${tool.name} on ${on_string} (aligned structures)">
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
103 <change_format>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
104 <when input="oformat" value="inchi" format="inchi"/>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
105 <when input="oformat" value="sdf" format="sdf"/>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
106 </change_format>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
107 </data>-->
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
108 <data name="score_result_file" format="tabular" label="${tool.name} on ${on_string} (scores)"/>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
109 </outputs>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
110 <tests>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
111 <test>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
112 </test>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
113 </tests>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
114 <help>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
115
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
116 .. class:: infomark
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
117
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
118 **What this tool does**
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
119
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
120 Align-it_ is a tool to align molecules according to their pharmacophores.
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
121 A pharmacophore is an abstract concept based on the specific interactions
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
122 observed in drug-receptor interactions: hydrogen bonding,
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
123 charge transfer, electrostatic and hydrophobic interactions.
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
124 Molecular modeling and/or screening based on pharmacophore similarities
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
125 has been proven to be an important and useful method in drug discovery.
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
126
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
127 The functionality of Align-it_ consists mainly of two parts.
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
128 The first functionality is the generation of pharmacophores from molecules
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
129 (use the tool **Pharmacophore generation** if you want to store these for further use).
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
130 Secondly, pairs of pharmacophores can be aligned (the function of this tool). The resulting
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
131 score is calculated from the volume overlap resulting of the alignments.
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
132
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
133 .. _Align-it: http://www.silicos-it.com/software/align-it/1.0.3/align-it.html
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
134
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
135 -----
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
136
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
137 .. class:: infomark
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
138
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
139 **Input**
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
140
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
141 * Example::
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
142
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
143 - database
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
144
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
145 30 31 0 0 0 0 0 0 0999 V2000
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
146 1.9541 1.1500 -2.5078 Cl 0 0 0 0 0 0 0 0 0 0 0 0
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
147 1.1377 -1.6392 2.1136 Cl 0 0 0 0 0 0 0 0 0 0 0 0
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
148 -3.2620 -2.9284 -1.0647 O 0 0 0 0 0 0 0 0 0 0 0 0
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
149 -2.7906 -1.9108 0.9092 O 0 0 0 0 0 0 0 0 0 0 0 0
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
150 0.2679 -0.2051 -0.3990 N 0 0 0 0 0 0 0 0 0 0 0 0
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
151 -2.0640 0.5139 -0.3769 C 0 0 0 0 0 0 0 0 0 0 0 0
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
152 -0.7313 0.7178 -0.0192 C 0 0 0 0 0 0 0 0 0 0 0 0
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
153 -2.4761 -0.6830 -1.1703 C 0 0 0 0 0 0 0 0 0 0 0 0
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
154 1.6571 -0.2482 -0.1795 C 0 0 0 0 0 0 0 0 0 0 0 0
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
155 -3.0382 1.4350 0.0081 C 0 0 0 0 0 0 0 0 0 0 0 0
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
156 -0.3728 1.8429 0.7234 C 0 0 0 0 0 0 0 0 0 0 0 0
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
157 -2.6797 2.5600 0.7506 C 0 0 0 0 0 0 0 0 0 0 0 0
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
158 -1.3470 2.7640 1.1083 C 0 0 0 0 0 0 0 0 0 0 0 0
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
159 2.5353 0.3477 -1.0918 C 0 0 0 0 0 0 0 0 0 0 0 0
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
160 2.1740 -0.8865 0.9534 C 0 0 0 0 0 0 0 0 0 0 0 0
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
161 -2.8480 -1.8749 -0.3123 C 0 0 0 0 0 0 0 0 0 0 0 0
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
162 3.9124 0.3058 -0.8739 C 0 0 0 0 0 0 0 0 0 0 0 0
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
163 3.5511 -0.9285 1.1713 C 0 0 0 0 0 0 0 0 0 0 0 0
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
164 4.4203 -0.3324 0.2576 C 0 0 0 0 0 0 0 0 0 0 0 0
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
165 -1.7086 -0.9792 -1.8930 H 0 0 0 0 0 0 0 0 0 0 0 0
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
166 -3.3614 -0.4266 -1.7676 H 0 0 0 0 0 0 0 0 0 0 0 0
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
167 -0.0861 -1.1146 -0.6780 H 0 0 0 0 0 0 0 0 0 0 0 0
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
168 -4.0812 1.2885 -0.2604 H 0 0 0 0 0 0 0 0 0 0 0 0
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
169 0.6569 2.0278 1.0167 H 0 0 0 0 0 0 0 0 0 0 0 0
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
170 -3.4382 3.2769 1.0511 H 0 0 0 0 0 0 0 0 0 0 0 0
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
171 -1.0683 3.6399 1.6868 H 0 0 0 0 0 0 0 0 0 0 0 0
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
172 4.6037 0.7654 -1.5758 H 0 0 0 0 0 0 0 0 0 0 0 0
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
173 3.9635 -1.4215 2.0480 H 0 0 0 0 0 0 0 0 0 0 0 0
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
174 5.4925 -0.3651 0.4274 H 0 0 0 0 0 0 0 0 0 0 0 0
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
175 -3.5025 -3.7011 -0.5102 H 0 0 0 0 0 0 0 0 0 0 0 0
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
176
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
177 - cutoff : 0.0
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
178
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
179 -----
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
180
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
181 .. class:: infomark
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
182
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
183 **Output**
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
184
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
185 The format of the output file is shown in the table below:
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
186
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
187 +--------+-----------------------------------------------------------------------+
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
188 | Column | Content |
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
189 +========+=======================================================================+
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
190 | 1 | Id of the reference structure |
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
191 +--------+-----------------------------------------------------------------------+
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
192 | 2 | Maximum volume of the reference structure |
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
193 +--------+-----------------------------------------------------------------------+
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
194 | 3 | Id of the database structure |
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
195 +--------+-----------------------------------------------------------------------+
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
196 | 4 | Maximum volume of the database structure |
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
197 +--------+-----------------------------------------------------------------------+
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
198 | 5 | Maximum volume overlap of the two structures |
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
199 +--------+-----------------------------------------------------------------------+
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
200 | 6 | Overlap between pharmacophore and exclusion spheres in the reference |
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
201 +--------+-----------------------------------------------------------------------+
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
202 | 7 | Corrected volume overlap between database pharmacophore and reference |
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
203 +--------+-----------------------------------------------------------------------+
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
204 | 8 | Number of pharmacophore points in the processed pharmacophore |
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
205 +--------+-----------------------------------------------------------------------+
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
206 | 9 | TANIMOTO score |
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
207 +--------+-----------------------------------------------------------------------+
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
208 | 10 | TVERSKY_REF score |
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
209 +--------+-----------------------------------------------------------------------+
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
210 | 11 | TVERSKY_DB score |
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
211 +--------+-----------------------------------------------------------------------+
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
212
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
213
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
214 * Example::
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
215
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
216 - aligned Pharmacophores
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
217
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
218 3033
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
219 HYBL -1.98494 1.9958 0.532089 0.7 0 0 0 0
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
220 HYBL 3.52122 -0.309347 0.122783 0.7 0 0 0 0
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
221 HYBH -3.262 -2.9284 -1.0647 1 1 -3.5666 -3.7035 -1.61827
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
222 HDON 0.2679 -0.2051 -0.399 1 1 -0.076102 -0.981133 -0.927616
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
223 HACC -2.7906 -1.9108 0.9092 1 1 -2.74368 -1.94015 1.90767
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
224 $$$$
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
225
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
226 -----
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
227
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
228 .. class:: infomark
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
229
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
230 **Cite**
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
231
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
232 `Silicos-it`_ - align-it
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
233
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
234 .. _Silicos-it: http://www.silicos-it.com/software/align-it/1.0.3/align-it.html
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
235
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
236
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
237 </help>
bb92d30b4f52 Uploaded
bgruening
parents:
diff changeset
238 </tool>