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