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1 <tool id="ctb_alignit_create_db" name="Pharmacophore" version="0.1">
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2 <description>generation (Align-it)</description>
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3 <requirements>
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1
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4 <requirement type="package" version="1.0.1">silicos_it</requirement>
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0
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5 <requirement type="package" version="2.3.2">openbabel</requirement>
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6 </requirements>
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7 <command>
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8 align-it
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9 --dbType ${database.ext}
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10 --dbase $database
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11 --pharmacophore $pharmacophores
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12 $merge
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13 $noHybrid
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14
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15 2>&1
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16 </command>
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17 <inputs>
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18 <param name="database" type="data" format='mol,mol2,sdf,smi' label="Defines the database of molecules that will be converted to pharmacophores" />
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19 <param name='merge' type='boolean' truevalue='--merge' falsevalue='' label='Merge pharmacophore points' />
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20 <param name='noHybrid' type='boolean' truevalue='--noHybrid' falsevalue='' label='Disable the use of hybrid pharmacophore points' help="Using this flag will increase the number of pharmacophore points."/>
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21 </inputs>
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22 <outputs>
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23 <data name="pharmacophores" format="phar" label="${tool.name} on ${on_string} (scores)"/>
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24 </outputs>
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25 <tests>
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26 <test>
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27 </test>
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28 </tests>
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29 <help>
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30
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31 .. class:: infomark
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32
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33 **What this tool does**
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34
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35 Align-it_ is a tool to align molecules according to their pharmacophores.
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36 A pharmacophore is an abstract concept based on the specific interactions
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37 observed in drug-receptor interactions: hydrogen bonding,
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38 charge transfer, electrostatic and hydrophobic interactions.
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39 Molecular modeling and/or screening based on pharmacophore similarities
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40 has been proven to be an important and useful method in drug discovery.
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41
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42 The functionality of Align-it_ consists mainly of two parts.
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43 The first functionality is the generation of pharmacophores from molecules
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44 (the function of this tool). Secondly, pairs of pharmacophores
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45 can be aligned (use the tool **Pharmacophore Alignment**). The resulting
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46 score is calculated from the volume overlap resulting of the alignments.
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47
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48 .. _Align-it: http://www.silicos-it.com/software/align-it/1.0.3/align-it.html
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49
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50 -----
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51
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52 .. class:: infomark
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53
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54 **Input**
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55
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56 * Example::
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57
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58 - database
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59
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60 30 31 0 0 0 0 0 0 0999 V2000
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61 1.9541 1.1500 -2.5078 Cl 0 0 0 0 0 0 0 0 0 0 0 0
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62 1.1377 -1.6392 2.1136 Cl 0 0 0 0 0 0 0 0 0 0 0 0
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63 -3.2620 -2.9284 -1.0647 O 0 0 0 0 0 0 0 0 0 0 0 0
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64 -2.7906 -1.9108 0.9092 O 0 0 0 0 0 0 0 0 0 0 0 0
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65 0.2679 -0.2051 -0.3990 N 0 0 0 0 0 0 0 0 0 0 0 0
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66 -2.0640 0.5139 -0.3769 C 0 0 0 0 0 0 0 0 0 0 0 0
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67 -0.7313 0.7178 -0.0192 C 0 0 0 0 0 0 0 0 0 0 0 0
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68 -2.4761 -0.6830 -1.1703 C 0 0 0 0 0 0 0 0 0 0 0 0
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69 1.6571 -0.2482 -0.1795 C 0 0 0 0 0 0 0 0 0 0 0 0
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70 -3.0382 1.4350 0.0081 C 0 0 0 0 0 0 0 0 0 0 0 0
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71 -0.3728 1.8429 0.7234 C 0 0 0 0 0 0 0 0 0 0 0 0
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72 -2.6797 2.5600 0.7506 C 0 0 0 0 0 0 0 0 0 0 0 0
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73 -1.3470 2.7640 1.1083 C 0 0 0 0 0 0 0 0 0 0 0 0
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74 2.5353 0.3477 -1.0918 C 0 0 0 0 0 0 0 0 0 0 0 0
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75 2.1740 -0.8865 0.9534 C 0 0 0 0 0 0 0 0 0 0 0 0
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76 -2.8480 -1.8749 -0.3123 C 0 0 0 0 0 0 0 0 0 0 0 0
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77 3.9124 0.3058 -0.8739 C 0 0 0 0 0 0 0 0 0 0 0 0
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78 3.5511 -0.9285 1.1713 C 0 0 0 0 0 0 0 0 0 0 0 0
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79 4.4203 -0.3324 0.2576 C 0 0 0 0 0 0 0 0 0 0 0 0
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80 -1.7086 -0.9792 -1.8930 H 0 0 0 0 0 0 0 0 0 0 0 0
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81 -3.3614 -0.4266 -1.7676 H 0 0 0 0 0 0 0 0 0 0 0 0
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82 -0.0861 -1.1146 -0.6780 H 0 0 0 0 0 0 0 0 0 0 0 0
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83 -4.0812 1.2885 -0.2604 H 0 0 0 0 0 0 0 0 0 0 0 0
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84 0.6569 2.0278 1.0167 H 0 0 0 0 0 0 0 0 0 0 0 0
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85 -3.4382 3.2769 1.0511 H 0 0 0 0 0 0 0 0 0 0 0 0
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86 -1.0683 3.6399 1.6868 H 0 0 0 0 0 0 0 0 0 0 0 0
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87 4.6037 0.7654 -1.5758 H 0 0 0 0 0 0 0 0 0 0 0 0
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88 3.9635 -1.4215 2.0480 H 0 0 0 0 0 0 0 0 0 0 0 0
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89 5.4925 -0.3651 0.4274 H 0 0 0 0 0 0 0 0 0 0 0 0
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90 -3.5025 -3.7011 -0.5102 H 0 0 0 0 0 0 0 0 0 0 0 0
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91
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92 - cutoff : 0.0
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93
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94 -----
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95
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96 .. class:: infomark
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97
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98 **Output**
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99
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100 * Example::
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101
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102 - aligned Pharmacophores
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103
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104 3033
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105 HYBL -1.98494 1.9958 0.532089 0.7 0 0 0 0
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106 HYBL 3.52122 -0.309347 0.122783 0.7 0 0 0 0
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107 HYBH -3.262 -2.9284 -1.0647 1 1 -3.5666 -3.7035 -1.61827
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108 HDON 0.2679 -0.2051 -0.399 1 1 -0.076102 -0.981133 -0.927616
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109 HACC -2.7906 -1.9108 0.9092 1 1 -2.74368 -1.94015 1.90767
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110 $$$$
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111
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112 -----
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113
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114 .. class:: infomark
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115
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116 **Cite**
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117
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118 `Silicos-it`_ - align-it
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119
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120 .. _Silicos-it: http://www.silicos-it.com/software/align-it/1.0.3/align-it.html
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121
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122 </help>
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123 </tool>
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