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annotate rdkit_descriptors.xml @ 18:aa46f08461f9 default tip

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ChemicalToolBoX update.
author Bjoern Gruening <bjoern.gruening@gmail.com>
date Tue, 23 Jul 2013 14:54:29 +0200
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1 <tool id="ctb_rdkit_describtors" name="Descriptors" version="0.1">
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2 <description>calculated with RDKit</description>
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3 <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism>
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4 <requirements>
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5 <requirement type="package" version="2012_12_1">rdkit</requirement>
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6 </requirements>
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7 <command interpreter="python">rdkit_descriptors.py -i "${infile}" --iformat "${infile.ext}" -o "${outfile}" $header 2>&#38;1</command>
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8 <inputs>
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9 <param format="smi,sdf" name="infile" type="data" label="Molecule data in SD- or SMILES-format" help="Dataset missing? See TIP below"/>
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10 <param name="header" type="boolean" label="Include the descriptor name as header" truevalue="--header" falsevalue="" checked="false" />
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11 </inputs>
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12 <outputs>
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13 <data format="tabular" name="outfile" />
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14 </outputs>
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15 <tests>
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16 </tests>
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17 <help>
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18
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19 .. class:: infomark
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20
13
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21 **What this tool does**
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22
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23 | RDKit is an open source toolkit for cheminformatics and machine learning.
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24 | This implementation focuses on descriptor calculation, though, RDKit offers a vast number of other functions.
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25 |
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26 | The table below shows a brief overview of the descriptors.
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27 |
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28
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29 +-----------------------------------+------------+
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30 | Descriptor/Descriptor Family | Language |
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31 +===================================+============+
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32 | Gasteiger/Marsili Partial Charges | C++ |
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33 +-----------------------------------+------------+
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34 | BalabanJ | Python |
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35 +-----------------------------------+------------+
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36 | BertzCT | Python |
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37 +-----------------------------------+------------+
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38 | Ipc | Python |
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39 +-----------------------------------+------------+
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40 | HallKierAlpha | Python |
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41 +-----------------------------------+------------+
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42 | Kappa1 - Kappa3 | Python |
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43 +-----------------------------------+------------+
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44 | Chi0, Chi1 | Python |
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45 +-----------------------------------+------------+
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46 | Chi0n - Chi4n | Python |
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47 +-----------------------------------+------------+
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48 | Chi0v - Chi4v | Python |
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49 +-----------------------------------+------------+
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50 | MolLogP | C++ |
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51 +-----------------------------------+------------+
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52 | MolMR | C++ |
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53 +-----------------------------------+------------+
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54 | MolWt | C++ |
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55 +-----------------------------------+------------+
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56 | HeavyAtomCount | Python |
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57 +-----------------------------------+------------+
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58 | HeavyAtomMolWt | Python |
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59 +-----------------------------------+------------+
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60 | NHOHCount | C++ |
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61 +-----------------------------------+------------+
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62 | NOCount | C++ |
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63 +-----------------------------------+------------+
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64 | NumHAcceptors | C++ |
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65 +-----------------------------------+------------+
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66 | NumHDonors | C++ |
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67 +-----------------------------------+------------+
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68 | NumHeteroatoms | C++ |
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69 +-----------------------------------+------------+
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70 | NumRotatableBonds | C++ |
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71 +-----------------------------------+------------+
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72 | NumValenceElectrons | Python |
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73 +-----------------------------------+------------+
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74 | RingCount | C++ |
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75 +-----------------------------------+------------+
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76 | TPSA | C++ |
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77 +-----------------------------------+------------+
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78 | LabuteASA | C++ |
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79 +-----------------------------------+------------+
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80 | PEOE_VSA1 - PEOE_VSA14 | Python/C++ |
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81 +-----------------------------------+------------+
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82 | SMR_VSA1 - SMR_VSA10 | Python/C++ |
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83 +-----------------------------------+------------+
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84 | SlogP_VSA1 - SlogP_VSA12 | Python/C++ |
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85 +-----------------------------------+------------+
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86 | EState_VSA1 - EState_VSA11 | Python |
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87 +-----------------------------------+------------+
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88 | VSA_EState1 - VSA_EState10 | Python |
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89 +-----------------------------------+------------+
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90 | Topliss fragments | Python |
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91 +-----------------------------------+------------+
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92
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93 |
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94 | A full list of the descriptors can be obtained here_.
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95
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96 .. _here: https://code.google.com/p/rdkit/wiki/DescriptorsInTheRDKit
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97
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98 -----
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99
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100 .. class:: warningmark
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101
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102 **HINT**
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103
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104 Use the **cut columns from a table** tool to select just the desired descriptors.
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105
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106 -----
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107
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108 .. class:: infomark
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109
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110 **Input**
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111
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112 | - `SD-Format`_
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113 | - `SMILES Format`_
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114 | - TDT_
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115 | - SLN
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116 | - `Corina MOL2`_
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117
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118 .. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file
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119 .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
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120 .. _TDT: https://earray.chem.agilent.com/earray/helppages/index.htm#tdt_format_files.htm
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121 .. _Corina MOL2: http://www.molecular-networks.com/products/corina
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122
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123 -----
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124
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125 .. class:: infomark
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126
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127 **Output**
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128
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129 Tabularfile, where each descriptor (value) is shown in a seperate column.
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130
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131 -----
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132
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133 .. class:: informark
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134
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135 **Cite**
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136
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137 Greg Landrum - RDKit_: Open-source cheminformatics
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138
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139 .. _RDKit: http://www.rdkit.org
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140
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141
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142 </help>
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143 </tool>