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14 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./AtomTypesFingerprints.html" title="AtomTypesFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./DBSchemaTablesToTextFiles.html" title="DBSchemaTablesToTextFiles.html">Next</a></td><td width="34%" align="middle"><strong>CalculatePhysicochemicalProperties.pl</strong></td><td width="33%" align="right"><a href="././code/CalculatePhysicochemicalProperties.html" title="View source code">Code</a> | <a href="./../pdf/CalculatePhysicochemicalProperties.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/CalculatePhysicochemicalProperties.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/CalculatePhysicochemicalProperties.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/CalculatePhysicochemicalProperties.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
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16 </table>
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17 </div>
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18 <p>
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19 </p>
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20 <h2>NAME</h2>
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21 <p>CalculatePhysicochemicalProperties.pl - Calculate physicochemical properties for SD files</p>
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22 <p>
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23 </p>
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24 <h2>SYNOPSIS</h2>
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25 <p>CalculatePhysicochemicalProperties.pl SDFile(s)...</p>
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26 <p>PhysicochemicalProperties.pl [<strong>--AromaticityModel</strong> <em>AromaticityModelType</em>]
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27 [<strong>--CompoundID</strong> DataFieldName or LabelPrefixString]
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28 [<strong>--CompoundIDLabel</strong> text] [<strong>--CompoundIDMode</strong>] [<strong>--DataFields</strong> "FieldLabel1, FieldLabel2,..."]
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29 [<strong>-d, --DataFieldsMode</strong> All | Common | Specify | CompoundID] [<strong>-f, --Filter</strong> Yes | No] [<strong>-h, --help</strong>]
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30 [<strong>--HydrogenBonds</strong> HBondsType1 | HBondsType2] [<strong>-k, --KeepLargestComponent</strong> Yes | No]
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31 [<strong>-m, --mode</strong> All | RuleOf5 | RuleOf3 | "name1, [name2,...]"]
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32 [<strong>--MolecularComplexity</strong> <em>Name,Value, [Name,Value,...]</em>]
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33 [<strong>--OutDelim</strong> comma | tab | semicolon] [<strong>--output</strong> SD | text | both] [<strong>-o, --overwrite</strong>]
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34 [<strong>--Precision</strong> Name,Number,[Name,Number,..]] [<strong>--RotatableBonds</strong> Name,Value, [Name,Value,...]]
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35 [<strong>--RuleOf3Violations</strong> Yes | No] [<strong>--RuleOf5Violations</strong> Yes | No]
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36 [<strong>-q, --quote</strong> Yes | No] [<strong>-r, --root</strong> RootName]
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37 [<strong>-w, --WorkingDir</strong> dirname] SDFile(s)...</p>
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38 <p>
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39 </p>
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40 <h2>DESCRIPTION</h2>
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41 <p>Calculate physicochemical properties for <em>SDFile(s)</em> and create appropriate SD or CSV/TSV
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42 text file(s) containing calculated properties.</p>
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43 <p>The current release of MayaChemTools supports the calculation of these physicochemical
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44 properties:</p>
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45 <div class="OptionsBox">
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46 MolecularWeight, ExactMass, HeavyAtoms, Rings, AromaticRings,
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47 <br/> van der Waals MolecularVolume [ Ref 93 ], RotatableBonds,
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48 <br/> HydrogenBondDonors, HydrogenBondAcceptors, LogP and
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49 <br/> Molar Refractivity (SLogP and SMR) [ Ref 89 ], Topological Polar
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50 <br/> Surface Area (TPSA) [ Ref 90 ], Fraction of SP3 carbons (Fsp3Carbons)
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51 <br/> and SP3 carbons (Sp3Carbons) [ Ref 115-116, Ref 119 ],
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52 <br/> MolecularComplexity [ Ref 117-119 ]</div>
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53 <p>Multiple SDFile names are separated by spaces. The valid file extensions are <em>.sdf</em>
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54 and <em>.sd</em>. All other file names are ignored. All the SD files in a current directory
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55 can be specified either by <em>*.sdf</em> or the current directory name.</p>
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56 <p>The calculation of molecular complexity using <em>MolecularComplexityType</em> parameter
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57 corresponds to the number of bits-set or unique keys [ Ref 117-119 ] in molecular fingerprints.
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58 Default value for <em>MolecularComplexityType</em>: <em>MACCSKeys</em> of size 166. The calculation
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59 of MACCSKeys is relatively expensive and can take rather substantial amount of time.</p>
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60 <p>
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61 </p>
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62 <h2>OPTIONS</h2>
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63 <dl>
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64 <dt><strong><strong>--AromaticityModel</strong> <em>MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel</em></strong></dt>
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65 <dd>
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66 <p>Specify aromaticity model to use during detection of aromaticity. Possible values in the current
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67 release are: <em>MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
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68 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel
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69 or MayaChemToolsAromaticityModel</em>. Default value: <em>MayaChemToolsAromaticityModel</em>.</p>
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70 <p>The supported aromaticity model names along with model specific control parameters
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71 are defined in <strong>AromaticityModelsData.csv</strong>, which is distributed with the current release
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72 and is available under <strong>lib/data</strong> directory. <strong>Molecule.pm</strong> module retrieves data from
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73 this file during class instantiation and makes it available to method <strong>DetectAromaticity</strong>
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74 for detecting aromaticity corresponding to a specific model.</p>
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75 </dd>
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76 <dt><strong><strong>--CompoundID</strong> <em>DataFieldName or LabelPrefixString</em></strong></dt>
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77 <dd>
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78 <p>This value is <strong>--CompoundIDMode</strong> specific and indicates how compound ID is generated.</p>
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79 <p>For <em>DataField</em> value of <strong>--CompoundIDMode</strong> option, it corresponds to datafield label name
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80 whose value is used as compound ID; otherwise, it's a prefix string used for generating compound
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81 IDs like LabelPrefixString<Number>. Default value, <em>Cmpd</em>, generates compound IDs which
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82 look like Cmpd<Number>.</p>
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83 <p>Examples for <em>DataField</em> value of <strong>--CompoundIDMode</strong>:</p>
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84 <div class="OptionsBox">
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85 MolID
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86 <br/> ExtReg</div>
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87 <p>Examples for <em>LabelPrefix</em> or <em>MolNameOrLabelPrefix</em> value of <strong>--CompoundIDMode</strong>:</p>
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88 <div class="OptionsBox">
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89 Compound</div>
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90 <p>The value specified above generates compound IDs which correspond to Compound<Number>
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91 instead of default value of Cmpd<Number>.</p>
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92 </dd>
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93 <dt><strong><strong>--CompoundIDLabel</strong> <em>text</em></strong></dt>
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94 <dd>
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95 <p>Specify compound ID column label for CSV/TSV text file(s) used during <em>CompoundID</em> value
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96 of <strong>--DataFieldsMode</strong> option. Default value: <em>CompoundID</em>.</p>
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97 </dd>
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98 <dt><strong><strong>--CompoundIDMode</strong> <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em></strong></dt>
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99 <dd>
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100 <p>Specify how to generate compound IDs and write to CSV/TSV text file(s) along with calculated
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101 physicochemical properties for <em>text | both</em> values of <strong>--output</strong> option: use a <em>SDFile(s)</em>
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102 datafield value; use molname line from <em>SDFile(s)</em>; generate a sequential ID with specific prefix;
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103 use combination of both MolName and LabelPrefix with usage of LabelPrefix values for empty
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104 molname lines.</p>
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105 <p>Possible values: <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em>.
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106 Default value: <em>LabelPrefix</em>.</p>
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107 <p>For <em>MolNameAndLabelPrefix</em> value of <strong>--CompoundIDMode</strong>, molname line in <em>SDFile(s)</em> takes
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108 precedence over sequential compound IDs generated using <em>LabelPrefix</em> and only empty molname
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109 values are replaced with sequential compound IDs.</p>
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110 <p>This is only used for <em>CompoundID</em> value of <strong>--DataFieldsMode</strong> option.</p>
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111 </dd>
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112 <dt><strong><strong>--DataFields</strong> <em>"FieldLabel1,FieldLabel2,..."</em></strong></dt>
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113 <dd>
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114 <p>Comma delimited list of <em>SDFiles(s)</em> data fields to extract and write to CSV/TSV text file(s) along
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115 with calculated physicochemical properties for <em>text | both</em> values of <strong>--output</strong> option.</p>
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116 <p>This is only used for <em>Specify</em> value of <strong>--DataFieldsMode</strong> option.</p>
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117 <p>Examples:</p>
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118 <div class="OptionsBox">
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119 Extreg
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120 <br/> MolID,CompoundName</div>
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121 </dd>
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122 <dt><strong><strong>-d, --DataFieldsMode</strong> <em>All | Common | Specify | CompoundID</em></strong></dt>
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123 <dd>
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124 <p>Specify how data fields in <em>SDFile(s)</em> are transferred to output CSV/TSV text file(s) along
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125 with calculated physicochemical properties for <em>text | both</em> values of <strong>--output</strong> option:
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126 transfer all SD data field; transfer SD data files common to all compounds; extract specified
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127 data fields; generate a compound ID using molname line, a compound prefix, or a combination
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128 of both. Possible values: <em>All | Common | specify | CompoundID</em>. Default value: <em>CompoundID</em>.</p>
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129 </dd>
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130 <dt><strong><strong>-f, --Filter</strong> <em>Yes | No</em></strong></dt>
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131 <dd>
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132 <p>Specify whether to check and filter compound data in SDFile(s). Possible values: <em>Yes or No</em>.
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133 Default value: <em>Yes</em>.</p>
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134 <p>By default, compound data is checked before calculating physiochemical properties and compounds
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135 containing atom data corresponding to non-element symbols or no atom data are ignored.</p>
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136 </dd>
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137 <dt><strong><strong>-h, --help</strong></strong></dt>
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138 <dd>
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139 <p>Print this help message.</p>
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140 </dd>
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141 <dt><strong><strong>--HydrogenBonds</strong> <em>HBondsType1 | HBondsType2</em></strong></dt>
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142 <dd>
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143 <p>Parameters to control calculation of hydrogen bond donors and acceptors. Possible values:
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144 <em>HBondsType1, HydrogenBondsType1, HBondsType2, HydrogenBondsType2</em>. Default value:
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145 <em>HBondsType2</em> which corresponds to <strong>RuleOf5</strong> definition for number of hydrogen bond
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146 donors and acceptors.</p>
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147 <p>The current release of MayaChemTools supports identification of two types of hydrogen bond
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148 donor and acceptor atoms with these names:</p>
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149 <div class="OptionsBox">
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150 HBondsType1 or HydrogenBondsType1
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151 <br/> HBondsType2 or HydrogenBondsType2</div>
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152 <p>The names of these hydrogen bond types are rather arbitrary. However, their definitions have
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153 specific meaning and are as follows:</p>
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154 <div class="OptionsBox">
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155 HydrogenBondsType1 [ Ref 60-61, Ref 65-66 ]:</div>
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156 <div class="OptionsBox">
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157 Donor: NH, NH2, OH - Any N and O with available H
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158 Acceptor: N[!H], O - Any N without available H and any O</div>
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159 <div class="OptionsBox">
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160 HydrogenBondsType2 [ Ref 91 ]:</div>
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161 <div class="OptionsBox">
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162 Donor: NH, NH2, OH - N and O with available H
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163 Acceptor: N, O - And N and O</div>
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164 </dd>
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165 <dt><strong><strong>-k, --KeepLargestComponent</strong> <em>Yes | No</em></strong></dt>
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166 <dd>
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167 <p>Calculate physicochemical properties for only the largest component in molecule. Possible values:
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168 <em>Yes or No</em>. Default value: <em>Yes</em>.</p>
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169 <p>For molecules containing multiple connected components, physicochemical properties can be
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170 calculated in two different ways: use all connected components or just the largest connected
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171 component. By default, all atoms except for the largest connected component are
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172 deleted before calculation of physicochemical properties.</p>
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173 </dd>
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174 <dt><strong><strong>-m, --mode</strong> <em>All | RuleOf5 | RuleOf3 | "name1, [name2,...]"</em></strong></dt>
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175 <dd>
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176 <p>Specify physicochemical properties to calculate for SDFile(s): calculate all available physical
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177 chemical properties; calculate properties corresponding to Rule of 5; or use a comma delimited
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178 list of supported physicochemical properties. Possible values: <em>All | RuleOf5 | RuleOf3 |
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179 "name1, [name2,...]"</em>.</p>
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180 <p>Default value: <em>MolecularWeight, HeavyAtoms, MolecularVolume, RotatableBonds, HydrogenBondDonors,
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181 HydrogenBondAcceptors, SLogP, TPSA</em>. These properties are calculated by default.</p>
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182 <p><em>RuleOf5</em> [ Ref 91 ] includes these properties: <em>MolecularWeight, HydrogenBondDonors, HydrogenBondAcceptors,
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183 SLogP</em>. <em>RuleOf5</em> states: MolecularWeight <= 500, HydrogenBondDonors <= 5, HydrogenBondAcceptors <= 10, and
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184 logP <= 5.</p>
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185 <p><em>RuleOf3</em> [ Ref 92 ] includes these properties: <em>MolecularWeight, RotatableBonds, HydrogenBondDonors,
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186 HydrogenBondAcceptors, SLogP, TPSA</em>. <em>RuleOf3</em> states: MolecularWeight <= 300, RotatableBonds <= 3,
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187 HydrogenBondDonors <= 3, HydrogenBondAcceptors <= 3, logP <= 3, and TPSA <= 60.</p>
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188 <p><em>All</em> calculates all supported physicochemical properties: <em>MolecularWeight, ExactMass,
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189 HeavyAtoms, Rings, AromaticRings, MolecularVolume, RotatableBonds, HydrogenBondDonors,
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190 HydrogenBondAcceptors, SLogP, SMR, TPSA, Fsp3Carbons, Sp3Carbons, MolecularComplexity</em>.</p>
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191 </dd>
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192 <dt><strong><strong>--MolecularComplexity</strong> <em>Name,Value, [Name,Value,...]</em></strong></dt>
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193 <dd>
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194 <p>Parameters to control calculation of molecular complexity: it's a comma delimited list of parameter
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195 name and value pairs.</p>
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196 <p>Possible parameter names: <em>MolecularComplexityType, AtomIdentifierType,
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197 AtomicInvariantsToUse, FunctionalClassesToUse, MACCSKeysSize, NeighborhoodRadius,
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198 MinPathLength, MaxPathLength, UseBondSymbols, MinDistance, MaxDistance,
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199 UseTriangleInequality, DistanceBinSize, NormalizationMethodology</em>.</p>
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200 <p>The valid paramater valuse for each parameter name are described in the following sections.</p>
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201 <p>The current release of MayaChemTools supports calculation of molecular complexity using
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202 <em>MolecularComplexityType</em> parameter corresponding to the number of bits-set or unique
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203 keys [ Ref 117-119 ] in molecular fingerprints. The valid values for <em>MolecularComplexityType</em>
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204 are:</p>
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205 <div class="OptionsBox">
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206 AtomTypesFingerprints
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207 <br/> ExtendedConnectivityFingerprints
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208 <br/> MACCSKeys
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209 <br/> PathLengthFingerprints
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210 <br/> TopologicalAtomPairsFingerprints
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211 <br/> TopologicalAtomTripletsFingerprints
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212 <br/> TopologicalAtomTorsionsFingerprints
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213 <br/> TopologicalPharmacophoreAtomPairsFingerprints
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214 <br/> TopologicalPharmacophoreAtomTripletsFingerprints</div>
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215 <p>Default value for <em>MolecularComplexityType</em>: <em>MACCSKeys</em>.</p>
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216 <p><em>AtomIdentifierType</em> parameter name correspods to atom types used during generation of
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217 fingerprints. The valid values for <em>AtomIdentifierType</em> are: <em>AtomicInvariantsAtomTypes,
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218 DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes,
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219 SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</em>. <em>AtomicInvariantsAtomTypes</em>
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220 is not supported for during the following values of <em>MolecularComplexityType</em>: <em>MACCSKeys,
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221 TopologicalPharmacophoreAtomPairsFingerprints, TopologicalPharmacophoreAtomTripletsFingerprints</em>.
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222 <em>FunctionalClassAtomTypes</em> is the only valid value for <em>AtomIdentifierType</em> for topological
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223 pharmacophore fingerprints.</p>
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224 <p>Default value for <em>AtomIdentifierType</em>: <em>AtomicInvariantsAtomTypes</em>
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225 for all except topological pharmacophore fingerprints where it is <em>FunctionalClassAtomTypes</em>.</p>
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226 <p><em>AtomicInvariantsToUse</em> parameter name and values are used during <em>AtomicInvariantsAtomTypes</em>
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227 value of parameter <em>AtomIdentifierType</em>. It's a list of space separated valid atomic invariant atom types.</p>
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228 <p>Possible values for atomic invariants are: <em>AS, X, BO, LBO, SB, DB, TB, H, Ar, RA, FC, MN, SM</em>.
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229 Default value for <em>AtomicInvariantsToUse</em> parameter are set differently for different fingerprints
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230 using <em>MolecularComplexityType</em> parameter as shown below:</p>
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231 <div class="OptionsBox">
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232 MolecularComplexityType AtomicInvariantsToUse</div>
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233 <div class="OptionsBox">
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234 AtomTypesFingerprints AS X BO H FC
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235 <br/> TopologicalAtomPairsFingerprints AS X BO H FC
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236 <br/> TopologicalAtomTripletsFingerprints AS X BO H FC
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237 <br/> TopologicalAtomTorsionsFingerprints AS X BO H FC</div>
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238 <div class="OptionsBox">
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239 ExtendedConnectivityFingerprints AS X BO H FC MN
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240 <br/> PathLengthFingerprints AS</div>
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241 <p>The atomic invariants abbreviations correspond to:</p>
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242 <div class="OptionsBox">
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243 AS = Atom symbol corresponding to element symbol</div>
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244 <div class="OptionsBox">
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245 X<n> = Number of non-hydrogen atom neighbors or heavy atoms
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246 <br/> BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
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247 <br/> LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
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248 <br/> SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
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249 <br/> DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
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250 <br/> TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
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251 <br/> H<n> = Number of implicit and explicit hydrogens for atom
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252 <br/> Ar = Aromatic annotation indicating whether atom is aromatic
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253 <br/> RA = Ring atom annotation indicating whether atom is a ring
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254 <br/> FC<+n/-n> = Formal charge assigned to atom
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255 <br/> MN<n> = Mass number indicating isotope other than most abundant isotope
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256 <br/> SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
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257 3 (triplet)</div>
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258 <p>Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</p>
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259 <div class="OptionsBox">
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260 AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n></div>
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261 <p>Except for AS which is a required atomic invariant in atom types, all other atomic invariants are
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262 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.</p>
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263 <p>In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
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264 are also allowed:</p>
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265 <div class="OptionsBox">
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266 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
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267 <br/> BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
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268 <br/> LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
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269 <br/> SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
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270 <br/> DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
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271 <br/> TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
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272 <br/> H : NumOfImplicitAndExplicitHydrogens
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273 <br/> Ar : Aromatic
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274 <br/> RA : RingAtom
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275 <br/> FC : FormalCharge
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276 <br/> MN : MassNumber
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277 <br/> SM : SpinMultiplicity</div>
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278 <p><em>AtomTypes::AtomicInvariantsAtomTypes</em> module is used to assign atomic invariant
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279 atom types.</p>
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280 <p><em>FunctionalClassesToUse</em> parameter name and values are used during <em>FunctionalClassAtomTypes</em>
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281 value of parameter <em>AtomIdentifierType</em>. It's a list of space separated valid atomic invariant atom types.</p>
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282 <p>Possible values for atom functional classes are: <em>Ar, CA, H, HBA, HBD, Hal, NI, PI, RA</em>.</p>
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283 <p>Default value for <em>FunctionalClassesToUse</em> parameter is set to:</p>
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284 <div class="OptionsBox">
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285 HBD HBA PI NI Ar Hal</div>
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286 <p>for all fingerprints except for the following two <em>MolecularComplexityType</em> fingerints:</p>
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287 <div class="OptionsBox">
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288 MolecularComplexityType FunctionalClassesToUse</div>
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289 <div class="OptionsBox">
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290 TopologicalPharmacophoreAtomPairsFingerprints HBD HBA P, NI H
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291 <br/> TopologicalPharmacophoreAtomTripletsFingerprints HBD HBA PI NI H Ar</div>
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292 <p>The functional class abbreviations correspond to:</p>
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293 <div class="OptionsBox">
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294 HBD: HydrogenBondDonor
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295 <br/> HBA: HydrogenBondAcceptor
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296 <br/> PI : PositivelyIonizable
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297 <br/> NI : NegativelyIonizable
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298 <br/> Ar : Aromatic
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299 <br/> Hal : Halogen
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300 <br/> H : Hydrophobic
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301 <br/> RA : RingAtom
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302 <br/> CA : ChainAtom</div>
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303 <div class="OptionsBox">
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304 Functional class atom type specification for an atom corresponds to:</div>
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305 <div class="OptionsBox">
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306 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA</div>
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307 <p><em>AtomTypes::FunctionalClassAtomTypes</em> module is used to assign functional class atom
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308 types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:</p>
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309 <div class="OptionsBox">
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310 HydrogenBondDonor: NH, NH2, OH
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311 <br/> HydrogenBondAcceptor: N[!H], O
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312 <br/> PositivelyIonizable: +, NH2
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313 <br/> NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</div>
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314 <p><em>MACCSKeysSize</em> parameter name is only used during <em>MACCSKeys</em> value of
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315 <em>MolecularComplexityType</em> and corresponds to the size of MACCS key set. Possible
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316 values: <em>166 or 322</em>. Default value: <em>166</em>.</p>
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317 <p><em>NeighborhoodRadius</em> parameter name is only used during <em>ExtendedConnectivityFingerprints</em>
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318 value of <em>MolecularComplexityType</em> and corresponds to atomic neighborhoods radius for
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319 generating extended connectivity fingerprints. Possible values: positive integer. Default value:
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320 <em>2</em>.</p>
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321 <p><em>MinPathLength</em> and <em>MaxPathLength</em> parameters are only used during <em>PathLengthFingerprints</em>
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322 value of <em>MolecularComplexityType</em> and correspond to minimum and maximum path lengths to use
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323 for generating path length fingerprints. Possible values: positive integers. Default value: <em>MinPathLength - 1</em>;
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324 <em>MaxPathLength - 8</em>.</p>
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325 <p><em>UseBondSymbols</em> parameter is only used during <em>PathLengthFingerprints</em> value of
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326 <em>MolecularComplexityType</em> and indicates whether bond symbols are included in atom path
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327 strings used to generate path length fingerprints. Possible value: <em>Yes or No</em>. Default value:
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328 <em>Yes</em>.</p>
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329 <p><em>MinDistance</em> and <em>MaxDistance</em> parameters are only used during <em>TopologicalAtomPairsFingerprints</em>
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330 and <em>TopologicalAtomTripletsFingerprints</em> values of <em>MolecularComplexityType</em> and correspond to
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331 minimum and maximum bond distance between atom pairs during topological pharmacophore fingerprints.
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332 Possible values: positive integers. Default value: <em>MinDistance - 1</em>; <em>MaxDistance - 10</em>.</p>
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333 <p><em>UseTriangleInequality</em> parameter is used during these values for <em>MolecularComplexityType</em>:
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334 <em>TopologicalAtomTripletsFingerprints</em> and <em>TopologicalPharmacophoreAtomTripletsFingerprints</em>.
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335 Possible values: <em>Yes or No</em>. It determines wheter to apply triangle inequality to distance triplets.
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336 Default value: <em>TopologicalAtomTripletsFingerprints - No</em>;
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337 <em>TopologicalPharmacophoreAtomTripletsFingerprints - Yes</em>.</p>
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338 <p><em>DistanceBinSize</em> parameter is used during <em>TopologicalPharmacophoreAtomTripletsFingerprints</em>
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339 value of <em>MolecularComplexityType</em> and correspons to distance bin size used for binning
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340 distances during generation of topological pharmacophore atom triplets fingerprints. Possible
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341 value: positive integer. Default value: <em>2</em>.</p>
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342 <p><em>NormalizationMethodology</em> is only used for these values for <em>MolecularComplexityType</em>:
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343 <em>ExtendedConnectivityFingerprints</em>, <em>TopologicalPharmacophoreAtomPairsFingerprints</em>
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344 and <em>TopologicalPharmacophoreAtomTripletsFingerprints</em>. It corresponds to normalization
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345 methodology to use for scaling the number of bits-set or unique keys during generation of
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346 fingerprints. Possible values during <em>ExtendedConnectivityFingerprints</em>: <em>None or
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347 ByHeavyAtomsCount</em>; Default value: <em>None</em>. Possible values during topological
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348 pharmacophore atom pairs and tripletes fingerprints: <em>None or ByPossibleKeysCount</em>;
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349 Default value: <em>None</em>. <em>ByPossibleKeysCount</em> corresponds to total number of
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350 possible topological pharmacophore atom pairs or triplets in a molecule.</p>
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351 <p>Examples of <em>MolecularComplexity</em> name and value parameters:</p>
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352 <div class="OptionsBox">
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353 MolecularComplexityType,AtomTypesFingerprints,AtomIdentifierType,
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354 <br/> AtomicInvariantsAtomTypes,AtomicInvariantsToUse,AS X BO H FC</div>
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355 <div class="OptionsBox">
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356 MolecularComplexityType,ExtendedConnectivityFingerprints,
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357 <br/> AtomIdentifierType,AtomicInvariantsAtomTypes,
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358 <br/> AtomicInvariantsToUse,AS X BO H FC MN,NeighborhoodRadius,2,
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359 <br/> NormalizationMethodology,None</div>
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360 <div class="OptionsBox">
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361 MolecularComplexityType,MACCSKeys,MACCSKeysSize,166</div>
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362 <div class="OptionsBox">
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363 MolecularComplexityType,PathLengthFingerprints,AtomIdentifierType,
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364 <br/> AtomicInvariantsAtomTypes,AtomicInvariantsToUse,AS,MinPathLength,
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365 <br/> 1,MaxPathLength,8,UseBondSymbols,Yes</div>
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366 <div class="OptionsBox">
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367 MolecularComplexityType,TopologicalAtomPairsFingerprints,
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368 <br/> AtomIdentifierType,AtomicInvariantsAtomTypes,AtomicInvariantsToUse,
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369 <br/> AS X BO H FC,MinDistance,1,MaxDistance,10</div>
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370 <div class="OptionsBox">
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371 MolecularComplexityType,TopologicalAtomTripletsFingerprints,
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372 <br/> AtomIdentifierType,AtomicInvariantsAtomTypes,AtomicInvariantsToUse,
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373 <br/> AS X BO H FC,MinDistance,1,MaxDistance,10,UseTriangleInequality,No</div>
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374 <div class="OptionsBox">
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375 MolecularComplexityType,TopologicalAtomTorsionsFingerprints,
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376 <br/> AtomIdentifierType,AtomicInvariantsAtomTypes,AtomicInvariantsToUse,
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377 <br/> AS X BO H FC</div>
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378 <div class="OptionsBox">
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379 MolecularComplexityType,TopologicalPharmacophoreAtomPairsFingerprints,
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380 <br/> AtomIdentifierType,FunctionalClassAtomTypes,FunctionalClassesToUse,
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381 <br/> HBD HBA PI NI H,MinDistance,1,MaxDistance,10,NormalizationMethodology,
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382 <br/> None</div>
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383 <div class="OptionsBox">
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384 MolecularComplexityType,TopologicalPharmacophoreAtomTripletsFingerprints,
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385 <br/> AtomIdentifierType,FunctionalClassAtomTypes,FunctionalClassesToUse,
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386 <br/> HBD HBA PI NI H Ar,MinDistance,1,MaxDistance,10,NormalizationMethodology,
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387 <br/> None,UseTriangleInequality,Yes,NormalizationMethodology,None,
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388 <br/> DistanceBinSize,2</div>
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389 </dd>
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390 <dt><strong><strong>--OutDelim</strong> <em>comma | tab | semicolon</em></strong></dt>
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391 <dd>
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392 <p>Delimiter for output CSV/TSV text file(s). Possible values: <em>comma, tab, or semicolon</em>
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393 Default value: <em>comma</em>.</p>
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394 </dd>
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395 <dt><strong><strong>--output</strong> <em>SD | text | both</em></strong></dt>
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396 <dd>
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397 <p>Type of output files to generate. Possible values: <em>SD, text, or both</em>. Default value: <em>text</em>.</p>
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398 </dd>
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399 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
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400 <dd>
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401 <p>Overwrite existing files.</p>
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402 </dd>
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403 <dt><strong><strong>--Precision</strong> <em>Name,Number,[Name,Number,..]</em></strong></dt>
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404 <dd>
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405 <p>Precision of calculated property values in the output file: it's a comma delimited list of
|
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406 property name and precision value pairs. Possible property names: <em>MolecularWeight,
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407 ExactMass</em>. Possible values: positive intergers. Default value: <em>MolecularWeight,2,
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408 ExactMass,4</em>.</p>
|
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|
409 <p>Examples:</p>
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410 <div class="OptionsBox">
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411 ExactMass,3
|
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412 <br/> MolecularWeight,1,ExactMass,2</div>
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413 </dd>
|
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414 <dt><strong><strong>-q, --quote</strong> <em>Yes | No</em></strong></dt>
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415 <dd>
|
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416 <p>Put quote around column values in output CSV/TSV text file(s). Possible values:
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417 <em>Yes or No</em>. Default value: <em>Yes</em>.</p>
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418 </dd>
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419 <dt><strong><strong>-r, --root</strong> <em>RootName</em></strong></dt>
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420 <dd>
|
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421 <p>New file name is generated using the root: <Root>.<Ext>. Default for new file names:
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422 <SDFileName><PhysicochemicalProperties>.<Ext>. The file type determines <Ext> value.
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|
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423 The sdf, csv, and tsv <Ext> values are used for SD, comma/semicolon, and tab
|
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424 delimited text files, respectively.This option is ignored for multiple input files.</p>
|
|
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425 </dd>
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|
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426 <dt><strong><strong>--RotatableBonds</strong> <em>Name,Value, [Name,Value,...]</em></strong></dt>
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427 <dd>
|
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428 <p>Parameters to control calculation of rotatable bonds [ Ref 92 ]: it's a comma delimited list of parameter
|
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429 name and value pairs. Possible parameter names: <em>IgnoreTerminalBonds, IgnoreBondsToTripleBonds,
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430 IgnoreAmideBonds, IgnoreThioamideBonds, IgnoreSulfonamideBonds</em>. Possible parameter values:
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431 <em>Yes or No</em>. By default, value of all parameters is set to <em>Yes</em>.</p>
|
|
|
432 </dd>
|
|
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433 <dt><strong><strong>--RuleOf3Violations</strong> <em>Yes | No</em></strong></dt>
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434 <dd>
|
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|
435 <p>Specify whether to calculate <strong>RuleOf3Violations</strong> for SDFile(s). Possible values: <em>Yes or No</em>.
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436 Default value: <em>No</em>.</p>
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437 <p>For <em>Yes</em> value of <strong>RuleOf3Violations</strong>, in addition to calculating total number of <strong>RuleOf3</strong> violations,
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438 individual violations for compounds are also written to output files.</p>
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|
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439 <p><strong>RuleOf3</strong> [ Ref 92 ] states: MolecularWeight <= 300, RotatableBonds <= 3, HydrogenBondDonors <= 3,
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440 HydrogenBondAcceptors <= 3, logP <= 3, and TPSA <= 60.</p>
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441 </dd>
|
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442 <dt><strong><strong>--RuleOf5Violations</strong> <em>Yes | No</em></strong></dt>
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443 <dd>
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444 <p>Specify whether to calculate <strong>RuleOf5Violations</strong> for SDFile(s). Possible values: <em>Yes or No</em>.
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445 Default value: <em>No</em>.</p>
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446 <p>For <em>Yes</em> value of <strong>RuleOf5Violations</strong>, in addition to calculating total number of <strong>RuleOf5</strong> violations,
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447 individual violations for compounds are also written to output files.</p>
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|
|
448 <p><strong>RuleOf5</strong> [ Ref 91 ] states: MolecularWeight <= 500, HydrogenBondDonors <= 5, HydrogenBondAcceptors <= 10,
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449 and logP <= 5.</p>
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450 </dd>
|
|
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451 <dt><strong><strong>--TPSA</strong> <em>Name,Value, [Name,Value,...]</em></strong></dt>
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452 <dd>
|
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453 <p>Parameters to control calculation of TPSA: it's a comma delimited list of parameter name and value
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454 pairs. Possible parameter names: <em>IgnorePhosphorus, IgnoreSulfur</em>. Possible parameter values:
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455 <em>Yes or No</em>. By default, value of all parameters is set to <em>Yes</em>.</p>
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456 <p>By default, TPSA atom contributions from Phosphorus and Sulfur atoms are not included during
|
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457 TPSA calculations. [ Ref 91 ]</p>
|
|
|
458 </dd>
|
|
|
459 <dt><strong><strong>-w, --WorkingDir</strong> <em>DirName</em></strong></dt>
|
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460 <dd>
|
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461 <p>Location of working directory. Default value: current directory.</p>
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462 </dd>
|
|
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463 </dl>
|
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464 <p>
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465 </p>
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466 <h2>EXAMPLES</h2>
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467 <p>To calculate default set of physicochemical properties - MolecularWeight, HeavyAtoms,
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468 MolecularVolume, RotatableBonds, HydrogenBondDonor, HydrogenBondAcceptors, SLogP,
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469 TPSA - and generate a SamplePhysicochemicalProperties.csv file containing sequential
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470 compound IDs along with properties data, type:</p>
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471 <div class="ExampleBox">
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472 % CalculatePhysicochemicalProperties.pl -o Sample.sdf</div>
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473 <p>To calculate all available physicochemical properties and generate both SampleAllProperties.csv
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474 and SampleAllProperties.sdf files containing sequential compound IDs in CSV file along with
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475 properties data, type:</p>
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476 <div class="ExampleBox">
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477 % CalculatePhysicochemicalProperties.pl -m All --output both
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478 -r SampleAllProperties -o Sample.sdf</div>
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479 <p>To calculate RuleOf5 physicochemical properties and generate a SampleRuleOf5Properties.csv file
|
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480 containing sequential compound IDs along with properties data, type:</p>
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481 <div class="ExampleBox">
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482 % CalculatePhysicochemicalProperties.pl -m RuleOf5
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483 -r SampleRuleOf5Properties -o Sample.sdf</div>
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484 <p>To calculate RuleOf5 physicochemical properties along with counting RuleOf5 violations and generate
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485 a SampleRuleOf5Properties.csv file containing sequential compound IDs along with properties data, type:</p>
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486 <div class="ExampleBox">
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487 % CalculatePhysicochemicalProperties.pl -m RuleOf5 --RuleOf5Violations Yes
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488 -r SampleRuleOf5Properties -o Sample.sdf</div>
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489 <p>To calculate RuleOf3 physicochemical properties and generate a SampleRuleOf3Properties.csv file
|
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490 containing sequential compound IDs along with properties data, type:</p>
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491 <div class="ExampleBox">
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492 % CalculatePhysicochemicalProperties.pl -m RuleOf3
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493 -r SampleRuleOf3Properties -o Sample.sdf</div>
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494 <p>To calculate RuleOf3 physicochemical properties along with counting RuleOf3 violations and generate
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495 a SampleRuleOf3Properties.csv file containing sequential compound IDs along with properties data, type:</p>
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496 <div class="ExampleBox">
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497 % CalculatePhysicochemicalProperties.pl -m RuleOf3 --RuleOf3Violations Yes
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498 -r SampleRuleOf3Properties -o Sample.sdf</div>
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499 <p>To calculate a specific set of physicochemical properties and generate a SampleProperties.csv file
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500 containing sequential compound IDs along with properties data, type:</p>
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501 <div class="ExampleBox">
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502 % CalculatePhysicochemicalProperties.pl -m "Rings,AromaticRings"
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503 -r SampleProperties -o Sample.sdf</div>
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504 <p>To calculate HydrogenBondDonors and HydrogenBondAcceptors using HydrogenBondsType1 definition
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505 and generate a SampleProperties.csv file containing sequential compound IDs along with properties
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506 data, type:</p>
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507 <div class="ExampleBox">
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508 % CalculatePhysicochemicalProperties.pl -m "HydrogenBondDonors,HydrogenBondAcceptors"
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509 --HydrogenBonds HBondsType1 -r SampleProperties -o Sample.sdf</div>
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510 <p>To calculate TPSA using sulfur and phosphorus atoms along with nitrogen and oxygen atoms and
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511 generate a SampleProperties.csv file containing sequential compound IDs along with properties
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512 data, type:</p>
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513 <div class="ExampleBox">
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514 % CalculatePhysicochemicalProperties.pl -m "TPSA" --TPSA "IgnorePhosphorus,No,
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515 IgnoreSulfur,No" -r SampleProperties -o Sample.sdf</div>
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|
516 <p>To calculate MolecularComplexity using extendend connectivity fingerprints corresponding
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|
517 to atom neighborhood radius of 2 with atomic invariant atom types without any scaling and
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518 generate a SampleProperties.csv file containing sequential compound IDs along with properties
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519 data, type:</p>
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520 <div class="ExampleBox">
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521 % CalculatePhysicochemicalProperties.pl -m MolecularComplexity --MolecularComplexity
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522 "MolecularComplexityType,ExtendedConnectivityFingerprints,NeighborhoodRadius,2,
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523 AtomIdentifierType, AtomicInvariantsAtomTypes,
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524 AtomicInvariantsToUse,AS X BO H FC MN,NormalizationMethodology,None"
|
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|
525 -r SampleProperties -o Sample.sdf</div>
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526 <p>To calculate RuleOf5 physicochemical properties along with counting RuleOf5 violations and generate
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527 a SampleRuleOf5Properties.csv file containing compound IDs from molecule name line along with
|
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528 properties data, type:</p>
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529 <div class="ExampleBox">
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530 % CalculatePhysicochemicalProperties.pl -m RuleOf5 --RuleOf5Violations Yes
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531 --DataFieldsMode CompoundID --CompoundIDMode MolName
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|
532 -r SampleRuleOf5Properties -o Sample.sdf</div>
|
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533 <p>To calculate all available physicochemical properties and generate a SampleAllProperties.csv
|
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534 file containing compound ID using specified data field along with along with properties data,
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535 type:</p>
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536 <div class="ExampleBox">
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537 % CalculatePhysicochemicalProperties.pl -m All
|
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538 --DataFieldsMode CompoundID --CompoundIDMode DataField --CompoundID Mol_ID
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539 -r SampleAllProperties -o Sample.sdf</div>
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540 <p>To calculate all available physicochemical properties and generate a SampleAllProperties.csv
|
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541 file containing compound ID using combination of molecule name line and an explicit compound
|
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542 prefix along with properties data, type:</p>
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543 <div class="ExampleBox">
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544 % CalculatePhysicochemicalProperties.pl -m All
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545 --DataFieldsMode CompoundID --CompoundIDMode MolnameOrLabelPrefix
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546 --CompoundID Cmpd --CompoundIDLabel MolID -r SampleAllProperties
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547 -o Sample.sdf</div>
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548 <p>To calculate all available physicochemical properties and generate a SampleAllProperties.csv
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549 file containing specific data fields columns along with with properties data, type:</p>
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550 <div class="ExampleBox">
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551 % CalculatePhysicochemicalProperties.pl -m All
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552 --DataFieldsMode Specify --DataFields Mol_ID -r SampleAllProperties
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553 -o Sample.sdf</div>
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554 <p>To calculate all available physicochemical properties and generate a SampleAllProperties.csv
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555 file containing common data fields columns along with with properties data, type:</p>
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556 <div class="ExampleBox">
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557 % CalculatePhysicochemicalProperties.pl -m All
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558 --DataFieldsMode Common -r SampleAllProperties -o Sample.sdf</div>
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559 <p>To calculate all available physicochemical properties and generate both SampleAllProperties.csv
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560 and CSV files containing all data fields columns in CSV files along with with properties data, type:</p>
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561 <div class="ExampleBox">
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562 % CalculatePhysicochemicalProperties.pl -m All
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563 --DataFieldsMode All --output both -r SampleAllProperties
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564 -o Sample.sdf</div>
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565 <p>
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566 </p>
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567 <h2>AUTHOR</h2>
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568 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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569 <p>
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570 </p>
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571 <h2>SEE ALSO</h2>
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572 <p><a href="./ExtractFromSDtFiles.html">ExtractFromSDtFiles.pl</a>, <a href="./ExtractFromTextFiles.html">ExtractFromTextFiles.pl</a>, <a href="./InfoSDFiles.html">InfoSDFiles.pl</a>, <a href="./InfoTextFiles.html">InfoTextFiles.pl</a>
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573 </p>
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574 <p>
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575 </p>
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576 <h2>COPYRIGHT</h2>
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577 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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578 <p>This file is part of MayaChemTools.</p>
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579 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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580 the terms of the GNU Lesser General Public License as published by the Free
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581 Software Foundation; either version 3 of the License, or (at your option)
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582 any later version.</p>
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583 <p> </p><p> </p><div class="DocNav">
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584 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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585 <tr align="left" valign="top"><td width="33%" align="left"><a href="./AtomTypesFingerprints.html" title="AtomTypesFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./DBSchemaTablesToTextFiles.html" title="DBSchemaTablesToTextFiles.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>CalculatePhysicochemicalProperties.pl</strong></td></tr>
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586 </table>
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587 </div>
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588 <br />
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589 <center>
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590 <img src="../../images/h2o2.png">
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591 </center>
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592 </body>
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593 </html>
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