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1 NAME
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2 CalculatePhysicochemicalProperties.pl - Calculate physicochemical
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3 properties for SD files
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4
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5 SYNOPSIS
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6 CalculatePhysicochemicalProperties.pl SDFile(s)...
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7
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8 PhysicochemicalProperties.pl [--AromaticityModel *AromaticityModelType*]
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9 [--CompoundID DataFieldName or LabelPrefixString] [--CompoundIDLabel
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10 text] [--CompoundIDMode] [--DataFields "FieldLabel1, FieldLabel2,..."]
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11 [-d, --DataFieldsMode All | Common | Specify | CompoundID] [-f, --Filter
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12 Yes | No] [-h, --help] [--HydrogenBonds HBondsType1 | HBondsType2] [-k,
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13 --KeepLargestComponent Yes | No] [-m, --mode All | RuleOf5 | RuleOf3 |
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14 "name1, [name2,...]"] [--MolecularComplexity *Name,Value,
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15 [Name,Value,...]*] [--OutDelim comma | tab | semicolon] [--output SD |
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16 text | both] [-o, --overwrite] [--Precision
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17 Name,Number,[Name,Number,..]] [--RotatableBonds Name,Value,
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18 [Name,Value,...]] [--RuleOf3Violations Yes | No] [--RuleOf5Violations
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19 Yes | No] [-q, --quote Yes | No] [-r, --root RootName] [-w, --WorkingDir
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20 dirname] SDFile(s)...
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21
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22 DESCRIPTION
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23 Calculate physicochemical properties for *SDFile(s)* and create
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24 appropriate SD or CSV/TSV text file(s) containing calculated properties.
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25
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26 The current release of MayaChemTools supports the calculation of these
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27 physicochemical properties:
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28
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29 MolecularWeight, ExactMass, HeavyAtoms, Rings, AromaticRings,
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30 van der Waals MolecularVolume [ Ref 93 ], RotatableBonds,
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31 HydrogenBondDonors, HydrogenBondAcceptors, LogP and
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32 Molar Refractivity (SLogP and SMR) [ Ref 89 ], Topological Polar
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33 Surface Area (TPSA) [ Ref 90 ], Fraction of SP3 carbons (Fsp3Carbons)
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34 and SP3 carbons (Sp3Carbons) [ Ref 115-116, Ref 119 ],
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35 MolecularComplexity [ Ref 117-119 ]
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36
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37 Multiple SDFile names are separated by spaces. The valid file extensions
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38 are *.sdf* and *.sd*. All other file names are ignored. All the SD files
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39 in a current directory can be specified either by **.sdf* or the current
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40 directory name.
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41
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42 The calculation of molecular complexity using *MolecularComplexityType*
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43 parameter corresponds to the number of bits-set or unique keys [ Ref
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44 117-119 ] in molecular fingerprints. Default value for
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45 *MolecularComplexityType*: *MACCSKeys* of size 166. The calculation of
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46 MACCSKeys is relatively expensive and can take rather substantial amount
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47 of time.
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48
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49 OPTIONS
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50 --AromaticityModel *MDLAromaticityModel | TriposAromaticityModel |
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51 MMFFAromaticityModel | ChemAxonBasicAromaticityModel |
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52 ChemAxonGeneralAromaticityModel | DaylightAromaticityModel |
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53 MayaChemToolsAromaticityModel*
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54 Specify aromaticity model to use during detection of aromaticity.
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55 Possible values in the current release are: *MDLAromaticityModel,
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56 TriposAromaticityModel, MMFFAromaticityModel,
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57 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel,
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58 DaylightAromaticityModel or MayaChemToolsAromaticityModel*. Default
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59 value: *MayaChemToolsAromaticityModel*.
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60
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61 The supported aromaticity model names along with model specific
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62 control parameters are defined in AromaticityModelsData.csv, which
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63 is distributed with the current release and is available under
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64 lib/data directory. Molecule.pm module retrieves data from this file
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65 during class instantiation and makes it available to method
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66 DetectAromaticity for detecting aromaticity corresponding to a
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67 specific model.
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68
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69 --CompoundID *DataFieldName or LabelPrefixString*
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70 This value is --CompoundIDMode specific and indicates how compound
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71 ID is generated.
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72
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73 For *DataField* value of --CompoundIDMode option, it corresponds to
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74 datafield label name whose value is used as compound ID; otherwise,
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75 it's a prefix string used for generating compound IDs like
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76 LabelPrefixString<Number>. Default value, *Cmpd*, generates compound
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77 IDs which look like Cmpd<Number>.
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78
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79 Examples for *DataField* value of --CompoundIDMode:
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80
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81 MolID
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82 ExtReg
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83
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84 Examples for *LabelPrefix* or *MolNameOrLabelPrefix* value of
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85 --CompoundIDMode:
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86
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87 Compound
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88
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89 The value specified above generates compound IDs which correspond to
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90 Compound<Number> instead of default value of Cmpd<Number>.
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91
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92 --CompoundIDLabel *text*
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93 Specify compound ID column label for CSV/TSV text file(s) used
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94 during *CompoundID* value of --DataFieldsMode option. Default value:
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95 *CompoundID*.
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96
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97 --CompoundIDMode *DataField | MolName | LabelPrefix |
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98 MolNameOrLabelPrefix*
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99 Specify how to generate compound IDs and write to CSV/TSV text
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100 file(s) along with calculated physicochemical properties for *text |
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101 both* values of --output option: use a *SDFile(s)* datafield value;
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102 use molname line from *SDFile(s)*; generate a sequential ID with
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103 specific prefix; use combination of both MolName and LabelPrefix
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104 with usage of LabelPrefix values for empty molname lines.
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105
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106 Possible values: *DataField | MolName | LabelPrefix |
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107 MolNameOrLabelPrefix*. Default value: *LabelPrefix*.
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108
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109 For *MolNameAndLabelPrefix* value of --CompoundIDMode, molname line
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110 in *SDFile(s)* takes precedence over sequential compound IDs
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111 generated using *LabelPrefix* and only empty molname values are
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112 replaced with sequential compound IDs.
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113
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114 This is only used for *CompoundID* value of --DataFieldsMode option.
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115
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116 --DataFields *"FieldLabel1,FieldLabel2,..."*
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117 Comma delimited list of *SDFiles(s)* data fields to extract and
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118 write to CSV/TSV text file(s) along with calculated physicochemical
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119 properties for *text | both* values of --output option.
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120
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121 This is only used for *Specify* value of --DataFieldsMode option.
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122
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123 Examples:
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124
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125 Extreg
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126 MolID,CompoundName
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127
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128 -d, --DataFieldsMode *All | Common | Specify | CompoundID*
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129 Specify how data fields in *SDFile(s)* are transferred to output
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130 CSV/TSV text file(s) along with calculated physicochemical
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131 properties for *text | both* values of --output option: transfer all
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132 SD data field; transfer SD data files common to all compounds;
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133 extract specified data fields; generate a compound ID using molname
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134 line, a compound prefix, or a combination of both. Possible values:
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135 *All | Common | specify | CompoundID*. Default value: *CompoundID*.
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136
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137 -f, --Filter *Yes | No*
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138 Specify whether to check and filter compound data in SDFile(s).
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139 Possible values: *Yes or No*. Default value: *Yes*.
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140
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141 By default, compound data is checked before calculating
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142 physiochemical properties and compounds containing atom data
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143 corresponding to non-element symbols or no atom data are ignored.
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144
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145 -h, --help
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146 Print this help message.
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147
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148 --HydrogenBonds *HBondsType1 | HBondsType2*
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149 Parameters to control calculation of hydrogen bond donors and
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150 acceptors. Possible values: *HBondsType1, HydrogenBondsType1,
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151 HBondsType2, HydrogenBondsType2*. Default value: *HBondsType2* which
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152 corresponds to RuleOf5 definition for number of hydrogen bond donors
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153 and acceptors.
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154
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155 The current release of MayaChemTools supports identification of two
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156 types of hydrogen bond donor and acceptor atoms with these names:
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157
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158 HBondsType1 or HydrogenBondsType1
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159 HBondsType2 or HydrogenBondsType2
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160
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161 The names of these hydrogen bond types are rather arbitrary.
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162 However, their definitions have specific meaning and are as follows:
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163
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164 HydrogenBondsType1 [ Ref 60-61, Ref 65-66 ]:
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165
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166 Donor: NH, NH2, OH - Any N and O with available H
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167 Acceptor: N[!H], O - Any N without available H and any O
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168
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169 HydrogenBondsType2 [ Ref 91 ]:
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170
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171 Donor: NH, NH2, OH - N and O with available H
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172 Acceptor: N, O - And N and O
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173
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174 -k, --KeepLargestComponent *Yes | No*
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175 Calculate physicochemical properties for only the largest component
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176 in molecule. Possible values: *Yes or No*. Default value: *Yes*.
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177
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178 For molecules containing multiple connected components,
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179 physicochemical properties can be calculated in two different ways:
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180 use all connected components or just the largest connected
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181 component. By default, all atoms except for the largest connected
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182 component are deleted before calculation of physicochemical
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183 properties.
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184
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185 -m, --mode *All | RuleOf5 | RuleOf3 | "name1, [name2,...]"*
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186 Specify physicochemical properties to calculate for SDFile(s):
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187 calculate all available physical chemical properties; calculate
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188 properties corresponding to Rule of 5; or use a comma delimited list
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189 of supported physicochemical properties. Possible values: *All |
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190 RuleOf5 | RuleOf3 | "name1, [name2,...]"*.
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191
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192 Default value: *MolecularWeight, HeavyAtoms, MolecularVolume,
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193 RotatableBonds, HydrogenBondDonors, HydrogenBondAcceptors, SLogP,
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194 TPSA*. These properties are calculated by default.
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195
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196 *RuleOf5* [ Ref 91 ] includes these properties: *MolecularWeight,
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197 HydrogenBondDonors, HydrogenBondAcceptors, SLogP*. *RuleOf5* states:
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198 MolecularWeight <= 500, HydrogenBondDonors <= 5,
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199 HydrogenBondAcceptors <= 10, and logP <= 5.
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200
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201 *RuleOf3* [ Ref 92 ] includes these properties: *MolecularWeight,
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202 RotatableBonds, HydrogenBondDonors, HydrogenBondAcceptors, SLogP,
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203 TPSA*. *RuleOf3* states: MolecularWeight <= 300, RotatableBonds <=
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204 3, HydrogenBondDonors <= 3, HydrogenBondAcceptors <= 3, logP <= 3,
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205 and TPSA <= 60.
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206
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207 *All* calculates all supported physicochemical properties:
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208 *MolecularWeight, ExactMass, HeavyAtoms, Rings, AromaticRings,
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209 MolecularVolume, RotatableBonds, HydrogenBondDonors,
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210 HydrogenBondAcceptors, SLogP, SMR, TPSA, Fsp3Carbons, Sp3Carbons,
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211 MolecularComplexity*.
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212
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213 --MolecularComplexity *Name,Value, [Name,Value,...]*
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214 Parameters to control calculation of molecular complexity: it's a
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215 comma delimited list of parameter name and value pairs.
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216
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217 Possible parameter names: *MolecularComplexityType,
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218 AtomIdentifierType, AtomicInvariantsToUse, FunctionalClassesToUse,
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219 MACCSKeysSize, NeighborhoodRadius, MinPathLength, MaxPathLength,
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220 UseBondSymbols, MinDistance, MaxDistance, UseTriangleInequality,
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221 DistanceBinSize, NormalizationMethodology*.
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222
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223 The valid paramater valuse for each parameter name are described in
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224 the following sections.
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225
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226 The current release of MayaChemTools supports calculation of
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227 molecular complexity using *MolecularComplexityType* parameter
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228 corresponding to the number of bits-set or unique keys [ Ref 117-119
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229 ] in molecular fingerprints. The valid values for
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230 *MolecularComplexityType* are:
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231
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232 AtomTypesFingerprints
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233 ExtendedConnectivityFingerprints
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234 MACCSKeys
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235 PathLengthFingerprints
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236 TopologicalAtomPairsFingerprints
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237 TopologicalAtomTripletsFingerprints
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238 TopologicalAtomTorsionsFingerprints
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239 TopologicalPharmacophoreAtomPairsFingerprints
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240 TopologicalPharmacophoreAtomTripletsFingerprints
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241
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242 Default value for *MolecularComplexityType*: *MACCSKeys*.
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243
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244 *AtomIdentifierType* parameter name correspods to atom types used
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245 during generation of fingerprints. The valid values for
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246 *AtomIdentifierType* are: *AtomicInvariantsAtomTypes,
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247 DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes,
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248 MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes,
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249 UFFAtomTypes*. *AtomicInvariantsAtomTypes* is not supported for
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250 during the following values of *MolecularComplexityType*:
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251 *MACCSKeys, TopologicalPharmacophoreAtomPairsFingerprints,
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252 TopologicalPharmacophoreAtomTripletsFingerprints*.
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253 *FunctionalClassAtomTypes* is the only valid value for
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254 *AtomIdentifierType* for topological pharmacophore fingerprints.
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255
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256 Default value for *AtomIdentifierType*: *AtomicInvariantsAtomTypes*
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257 for all except topological pharmacophore fingerprints where it is
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258 *FunctionalClassAtomTypes*.
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259
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260 *AtomicInvariantsToUse* parameter name and values are used during
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261 *AtomicInvariantsAtomTypes* value of parameter *AtomIdentifierType*.
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262 It's a list of space separated valid atomic invariant atom types.
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263
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264 Possible values for atomic invariants are: *AS, X, BO, LBO, SB, DB,
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265 TB, H, Ar, RA, FC, MN, SM*. Default value for
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266 *AtomicInvariantsToUse* parameter are set differently for different
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267 fingerprints using *MolecularComplexityType* parameter as shown
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268 below:
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269
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270 MolecularComplexityType AtomicInvariantsToUse
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271
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272 AtomTypesFingerprints AS X BO H FC
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273 TopologicalAtomPairsFingerprints AS X BO H FC
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274 TopologicalAtomTripletsFingerprints AS X BO H FC
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275 TopologicalAtomTorsionsFingerprints AS X BO H FC
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276
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277 ExtendedConnectivityFingerprints AS X BO H FC MN
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278 PathLengthFingerprints AS
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279
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280 The atomic invariants abbreviations correspond to:
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281
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282 AS = Atom symbol corresponding to element symbol
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283
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284 X<n> = Number of non-hydrogen atom neighbors or heavy atoms
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285 BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
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286 LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
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287 SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
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288 DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
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289 TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
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290 H<n> = Number of implicit and explicit hydrogens for atom
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291 Ar = Aromatic annotation indicating whether atom is aromatic
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292 RA = Ring atom annotation indicating whether atom is a ring
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293 FC<+n/-n> = Formal charge assigned to atom
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294 MN<n> = Mass number indicating isotope other than most abundant isotope
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295 SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
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296 3 (triplet)
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297
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298 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class
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299 corresponds to:
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300
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301 AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n>
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302
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303 Except for AS which is a required atomic invariant in atom types,
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304 all other atomic invariants are optional. Atom type specification
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305 doesn't include atomic invariants with zero or undefined values.
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306
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307 In addition to usage of abbreviations for specifying atomic
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308 invariants, the following descriptive words are also allowed:
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309
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310 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
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311 BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
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312 LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
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313 SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
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314 DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
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315 TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
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316 H : NumOfImplicitAndExplicitHydrogens
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317 Ar : Aromatic
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318 RA : RingAtom
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319 FC : FormalCharge
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320 MN : MassNumber
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321 SM : SpinMultiplicity
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322
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323 *AtomTypes::AtomicInvariantsAtomTypes* module is used to assign
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324 atomic invariant atom types.
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325
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326 *FunctionalClassesToUse* parameter name and values are used during
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327 *FunctionalClassAtomTypes* value of parameter *AtomIdentifierType*.
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328 It's a list of space separated valid atomic invariant atom types.
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329
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330 Possible values for atom functional classes are: *Ar, CA, H, HBA,
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331 HBD, Hal, NI, PI, RA*.
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332
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333 Default value for *FunctionalClassesToUse* parameter is set to:
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334
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335 HBD HBA PI NI Ar Hal
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336
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337 for all fingerprints except for the following two
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338 *MolecularComplexityType* fingerints:
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339
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340 MolecularComplexityType FunctionalClassesToUse
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341
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342 TopologicalPharmacophoreAtomPairsFingerprints HBD HBA P, NI H
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343 TopologicalPharmacophoreAtomTripletsFingerprints HBD HBA PI NI H Ar
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344
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345 The functional class abbreviations correspond to:
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346
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347 HBD: HydrogenBondDonor
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348 HBA: HydrogenBondAcceptor
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349 PI : PositivelyIonizable
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350 NI : NegativelyIonizable
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351 Ar : Aromatic
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352 Hal : Halogen
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353 H : Hydrophobic
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354 RA : RingAtom
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355 CA : ChainAtom
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356
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357 Functional class atom type specification for an atom corresponds to:
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358
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359 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA
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360
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361 *AtomTypes::FunctionalClassAtomTypes* module is used to assign
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362 functional class atom types. It uses following definitions [ Ref
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363 60-61, Ref 65-66 ]:
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364
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365 HydrogenBondDonor: NH, NH2, OH
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366 HydrogenBondAcceptor: N[!H], O
|
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|
367 PositivelyIonizable: +, NH2
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|
368 NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH
|
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369
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370 *MACCSKeysSize* parameter name is only used during *MACCSKeys* value
|
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|
371 of *MolecularComplexityType* and corresponds to the size of MACCS
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|
372 key set. Possible values: *166 or 322*. Default value: *166*.
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373
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374 *NeighborhoodRadius* parameter name is only used during
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|
375 *ExtendedConnectivityFingerprints* value of
|
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|
376 *MolecularComplexityType* and corresponds to atomic neighborhoods
|
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|
377 radius for generating extended connectivity fingerprints. Possible
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378 values: positive integer. Default value: *2*.
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379
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380 *MinPathLength* and *MaxPathLength* parameters are only used during
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|
381 *PathLengthFingerprints* value of *MolecularComplexityType* and
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|
382 correspond to minimum and maximum path lengths to use for generating
|
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|
383 path length fingerprints. Possible values: positive integers.
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384 Default value: *MinPathLength - 1*; *MaxPathLength - 8*.
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385
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386 *UseBondSymbols* parameter is only used during
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|
387 *PathLengthFingerprints* value of *MolecularComplexityType* and
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388 indicates whether bond symbols are included in atom path strings
|
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|
389 used to generate path length fingerprints. Possible value: *Yes or
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|
390 No*. Default value: *Yes*.
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|
391
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392 *MinDistance* and *MaxDistance* parameters are only used during
|
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|
393 *TopologicalAtomPairsFingerprints* and
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|
394 *TopologicalAtomTripletsFingerprints* values of
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|
395 *MolecularComplexityType* and correspond to minimum and maximum bond
|
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|
396 distance between atom pairs during topological pharmacophore
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397 fingerprints. Possible values: positive integers. Default value:
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398 *MinDistance - 1*; *MaxDistance - 10*.
|
|
|
399
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|
400 *UseTriangleInequality* parameter is used during these values for
|
|
|
401 *MolecularComplexityType*: *TopologicalAtomTripletsFingerprints* and
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|
402 *TopologicalPharmacophoreAtomTripletsFingerprints*. Possible values:
|
|
|
403 *Yes or No*. It determines wheter to apply triangle inequality to
|
|
|
404 distance triplets. Default value:
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|
405 *TopologicalAtomTripletsFingerprints - No*;
|
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|
406 *TopologicalPharmacophoreAtomTripletsFingerprints - Yes*.
|
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|
407
|
|
|
408 *DistanceBinSize* parameter is used during
|
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|
409 *TopologicalPharmacophoreAtomTripletsFingerprints* value of
|
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|
410 *MolecularComplexityType* and correspons to distance bin size used
|
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|
411 for binning distances during generation of topological pharmacophore
|
|
|
412 atom triplets fingerprints. Possible value: positive integer.
|
|
|
413 Default value: *2*.
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|
414
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|
|
415 *NormalizationMethodology* is only used for these values for
|
|
|
416 *MolecularComplexityType*: *ExtendedConnectivityFingerprints*,
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|
417 *TopologicalPharmacophoreAtomPairsFingerprints* and
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|
|
418 *TopologicalPharmacophoreAtomTripletsFingerprints*. It corresponds
|
|
|
419 to normalization methodology to use for scaling the number of
|
|
|
420 bits-set or unique keys during generation of fingerprints. Possible
|
|
|
421 values during *ExtendedConnectivityFingerprints*: *None or
|
|
|
422 ByHeavyAtomsCount*; Default value: *None*. Possible values during
|
|
|
423 topological pharmacophore atom pairs and tripletes fingerprints:
|
|
|
424 *None or ByPossibleKeysCount*; Default value: *None*.
|
|
|
425 *ByPossibleKeysCount* corresponds to total number of possible
|
|
|
426 topological pharmacophore atom pairs or triplets in a molecule.
|
|
|
427
|
|
|
428 Examples of *MolecularComplexity* name and value parameters:
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|
|
429
|
|
|
430 MolecularComplexityType,AtomTypesFingerprints,AtomIdentifierType,
|
|
|
431 AtomicInvariantsAtomTypes,AtomicInvariantsToUse,AS X BO H FC
|
|
|
432
|
|
|
433 MolecularComplexityType,ExtendedConnectivityFingerprints,
|
|
|
434 AtomIdentifierType,AtomicInvariantsAtomTypes,
|
|
|
435 AtomicInvariantsToUse,AS X BO H FC MN,NeighborhoodRadius,2,
|
|
|
436 NormalizationMethodology,None
|
|
|
437
|
|
|
438 MolecularComplexityType,MACCSKeys,MACCSKeysSize,166
|
|
|
439
|
|
|
440 MolecularComplexityType,PathLengthFingerprints,AtomIdentifierType,
|
|
|
441 AtomicInvariantsAtomTypes,AtomicInvariantsToUse,AS,MinPathLength,
|
|
|
442 1,MaxPathLength,8,UseBondSymbols,Yes
|
|
|
443
|
|
|
444 MolecularComplexityType,TopologicalAtomPairsFingerprints,
|
|
|
445 AtomIdentifierType,AtomicInvariantsAtomTypes,AtomicInvariantsToUse,
|
|
|
446 AS X BO H FC,MinDistance,1,MaxDistance,10
|
|
|
447
|
|
|
448 MolecularComplexityType,TopologicalAtomTripletsFingerprints,
|
|
|
449 AtomIdentifierType,AtomicInvariantsAtomTypes,AtomicInvariantsToUse,
|
|
|
450 AS X BO H FC,MinDistance,1,MaxDistance,10,UseTriangleInequality,No
|
|
|
451
|
|
|
452 MolecularComplexityType,TopologicalAtomTorsionsFingerprints,
|
|
|
453 AtomIdentifierType,AtomicInvariantsAtomTypes,AtomicInvariantsToUse,
|
|
|
454 AS X BO H FC
|
|
|
455
|
|
|
456 MolecularComplexityType,TopologicalPharmacophoreAtomPairsFingerprints,
|
|
|
457 AtomIdentifierType,FunctionalClassAtomTypes,FunctionalClassesToUse,
|
|
|
458 HBD HBA PI NI H,MinDistance,1,MaxDistance,10,NormalizationMethodology,
|
|
|
459 None
|
|
|
460
|
|
|
461 MolecularComplexityType,TopologicalPharmacophoreAtomTripletsFingerprints,
|
|
|
462 AtomIdentifierType,FunctionalClassAtomTypes,FunctionalClassesToUse,
|
|
|
463 HBD HBA PI NI H Ar,MinDistance,1,MaxDistance,10,NormalizationMethodology,
|
|
|
464 None,UseTriangleInequality,Yes,NormalizationMethodology,None,
|
|
|
465 DistanceBinSize,2
|
|
|
466
|
|
|
467 --OutDelim *comma | tab | semicolon*
|
|
|
468 Delimiter for output CSV/TSV text file(s). Possible values: *comma,
|
|
|
469 tab, or semicolon* Default value: *comma*.
|
|
|
470
|
|
|
471 --output *SD | text | both*
|
|
|
472 Type of output files to generate. Possible values: *SD, text, or
|
|
|
473 both*. Default value: *text*.
|
|
|
474
|
|
|
475 -o, --overwrite
|
|
|
476 Overwrite existing files.
|
|
|
477
|
|
|
478 --Precision *Name,Number,[Name,Number,..]*
|
|
|
479 Precision of calculated property values in the output file: it's a
|
|
|
480 comma delimited list of property name and precision value pairs.
|
|
|
481 Possible property names: *MolecularWeight, ExactMass*. Possible
|
|
|
482 values: positive intergers. Default value: *MolecularWeight,2,
|
|
|
483 ExactMass,4*.
|
|
|
484
|
|
|
485 Examples:
|
|
|
486
|
|
|
487 ExactMass,3
|
|
|
488 MolecularWeight,1,ExactMass,2
|
|
|
489
|
|
|
490 -q, --quote *Yes | No*
|
|
|
491 Put quote around column values in output CSV/TSV text file(s).
|
|
|
492 Possible values: *Yes or No*. Default value: *Yes*.
|
|
|
493
|
|
|
494 -r, --root *RootName*
|
|
|
495 New file name is generated using the root: <Root>.<Ext>. Default for
|
|
|
496 new file names: <SDFileName><PhysicochemicalProperties>.<Ext>. The
|
|
|
497 file type determines <Ext> value. The sdf, csv, and tsv <Ext> values
|
|
|
498 are used for SD, comma/semicolon, and tab delimited text files,
|
|
|
499 respectively.This option is ignored for multiple input files.
|
|
|
500
|
|
|
501 --RotatableBonds *Name,Value, [Name,Value,...]*
|
|
|
502 Parameters to control calculation of rotatable bonds [ Ref 92 ]:
|
|
|
503 it's a comma delimited list of parameter name and value pairs.
|
|
|
504 Possible parameter names: *IgnoreTerminalBonds,
|
|
|
505 IgnoreBondsToTripleBonds, IgnoreAmideBonds, IgnoreThioamideBonds,
|
|
|
506 IgnoreSulfonamideBonds*. Possible parameter values: *Yes or No*. By
|
|
|
507 default, value of all parameters is set to *Yes*.
|
|
|
508
|
|
|
509 --RuleOf3Violations *Yes | No*
|
|
|
510 Specify whether to calculate RuleOf3Violations for SDFile(s).
|
|
|
511 Possible values: *Yes or No*. Default value: *No*.
|
|
|
512
|
|
|
513 For *Yes* value of RuleOf3Violations, in addition to calculating
|
|
|
514 total number of RuleOf3 violations, individual violations for
|
|
|
515 compounds are also written to output files.
|
|
|
516
|
|
|
517 RuleOf3 [ Ref 92 ] states: MolecularWeight <= 300, RotatableBonds <=
|
|
|
518 3, HydrogenBondDonors <= 3, HydrogenBondAcceptors <= 3, logP <= 3,
|
|
|
519 and TPSA <= 60.
|
|
|
520
|
|
|
521 --RuleOf5Violations *Yes | No*
|
|
|
522 Specify whether to calculate RuleOf5Violations for SDFile(s).
|
|
|
523 Possible values: *Yes or No*. Default value: *No*.
|
|
|
524
|
|
|
525 For *Yes* value of RuleOf5Violations, in addition to calculating
|
|
|
526 total number of RuleOf5 violations, individual violations for
|
|
|
527 compounds are also written to output files.
|
|
|
528
|
|
|
529 RuleOf5 [ Ref 91 ] states: MolecularWeight <= 500,
|
|
|
530 HydrogenBondDonors <= 5, HydrogenBondAcceptors <= 10, and logP <= 5.
|
|
|
531
|
|
|
532 --TPSA *Name,Value, [Name,Value,...]*
|
|
|
533 Parameters to control calculation of TPSA: it's a comma delimited
|
|
|
534 list of parameter name and value pairs. Possible parameter names:
|
|
|
535 *IgnorePhosphorus, IgnoreSulfur*. Possible parameter values: *Yes or
|
|
|
536 No*. By default, value of all parameters is set to *Yes*.
|
|
|
537
|
|
|
538 By default, TPSA atom contributions from Phosphorus and Sulfur atoms
|
|
|
539 are not included during TPSA calculations. [ Ref 91 ]
|
|
|
540
|
|
|
541 -w, --WorkingDir *DirName*
|
|
|
542 Location of working directory. Default value: current directory.
|
|
|
543
|
|
|
544 EXAMPLES
|
|
|
545 To calculate default set of physicochemical properties -
|
|
|
546 MolecularWeight, HeavyAtoms, MolecularVolume, RotatableBonds,
|
|
|
547 HydrogenBondDonor, HydrogenBondAcceptors, SLogP, TPSA - and generate a
|
|
|
548 SamplePhysicochemicalProperties.csv file containing sequential compound
|
|
|
549 IDs along with properties data, type:
|
|
|
550
|
|
|
551 % CalculatePhysicochemicalProperties.pl -o Sample.sdf
|
|
|
552
|
|
|
553 To calculate all available physicochemical properties and generate both
|
|
|
554 SampleAllProperties.csv and SampleAllProperties.sdf files containing
|
|
|
555 sequential compound IDs in CSV file along with properties data, type:
|
|
|
556
|
|
|
557 % CalculatePhysicochemicalProperties.pl -m All --output both
|
|
|
558 -r SampleAllProperties -o Sample.sdf
|
|
|
559
|
|
|
560 To calculate RuleOf5 physicochemical properties and generate a
|
|
|
561 SampleRuleOf5Properties.csv file containing sequential compound IDs
|
|
|
562 along with properties data, type:
|
|
|
563
|
|
|
564 % CalculatePhysicochemicalProperties.pl -m RuleOf5
|
|
|
565 -r SampleRuleOf5Properties -o Sample.sdf
|
|
|
566
|
|
|
567 To calculate RuleOf5 physicochemical properties along with counting
|
|
|
568 RuleOf5 violations and generate a SampleRuleOf5Properties.csv file
|
|
|
569 containing sequential compound IDs along with properties data, type:
|
|
|
570
|
|
|
571 % CalculatePhysicochemicalProperties.pl -m RuleOf5 --RuleOf5Violations Yes
|
|
|
572 -r SampleRuleOf5Properties -o Sample.sdf
|
|
|
573
|
|
|
574 To calculate RuleOf3 physicochemical properties and generate a
|
|
|
575 SampleRuleOf3Properties.csv file containing sequential compound IDs
|
|
|
576 along with properties data, type:
|
|
|
577
|
|
|
578 % CalculatePhysicochemicalProperties.pl -m RuleOf3
|
|
|
579 -r SampleRuleOf3Properties -o Sample.sdf
|
|
|
580
|
|
|
581 To calculate RuleOf3 physicochemical properties along with counting
|
|
|
582 RuleOf3 violations and generate a SampleRuleOf3Properties.csv file
|
|
|
583 containing sequential compound IDs along with properties data, type:
|
|
|
584
|
|
|
585 % CalculatePhysicochemicalProperties.pl -m RuleOf3 --RuleOf3Violations Yes
|
|
|
586 -r SampleRuleOf3Properties -o Sample.sdf
|
|
|
587
|
|
|
588 To calculate a specific set of physicochemical properties and generate a
|
|
|
589 SampleProperties.csv file containing sequential compound IDs along with
|
|
|
590 properties data, type:
|
|
|
591
|
|
|
592 % CalculatePhysicochemicalProperties.pl -m "Rings,AromaticRings"
|
|
|
593 -r SampleProperties -o Sample.sdf
|
|
|
594
|
|
|
595 To calculate HydrogenBondDonors and HydrogenBondAcceptors using
|
|
|
596 HydrogenBondsType1 definition and generate a SampleProperties.csv file
|
|
|
597 containing sequential compound IDs along with properties data, type:
|
|
|
598
|
|
|
599 % CalculatePhysicochemicalProperties.pl -m "HydrogenBondDonors,HydrogenBondAcceptors"
|
|
|
600 --HydrogenBonds HBondsType1 -r SampleProperties -o Sample.sdf
|
|
|
601
|
|
|
602 To calculate TPSA using sulfur and phosphorus atoms along with nitrogen
|
|
|
603 and oxygen atoms and generate a SampleProperties.csv file containing
|
|
|
604 sequential compound IDs along with properties data, type:
|
|
|
605
|
|
|
606 % CalculatePhysicochemicalProperties.pl -m "TPSA" --TPSA "IgnorePhosphorus,No,
|
|
|
607 IgnoreSulfur,No" -r SampleProperties -o Sample.sdf
|
|
|
608
|
|
|
609 To calculate MolecularComplexity using extendend connectivity
|
|
|
610 fingerprints corresponding to atom neighborhood radius of 2 with atomic
|
|
|
611 invariant atom types without any scaling and generate a
|
|
|
612 SampleProperties.csv file containing sequential compound IDs along with
|
|
|
613 properties data, type:
|
|
|
614
|
|
|
615 % CalculatePhysicochemicalProperties.pl -m MolecularComplexity --MolecularComplexity
|
|
|
616 "MolecularComplexityType,ExtendedConnectivityFingerprints,NeighborhoodRadius,2,
|
|
|
617 AtomIdentifierType, AtomicInvariantsAtomTypes,
|
|
|
618 AtomicInvariantsToUse,AS X BO H FC MN,NormalizationMethodology,None"
|
|
|
619 -r SampleProperties -o Sample.sdf
|
|
|
620
|
|
|
621 To calculate RuleOf5 physicochemical properties along with counting
|
|
|
622 RuleOf5 violations and generate a SampleRuleOf5Properties.csv file
|
|
|
623 containing compound IDs from molecule name line along with properties
|
|
|
624 data, type:
|
|
|
625
|
|
|
626 % CalculatePhysicochemicalProperties.pl -m RuleOf5 --RuleOf5Violations Yes
|
|
|
627 --DataFieldsMode CompoundID --CompoundIDMode MolName
|
|
|
628 -r SampleRuleOf5Properties -o Sample.sdf
|
|
|
629
|
|
|
630 To calculate all available physicochemical properties and generate a
|
|
|
631 SampleAllProperties.csv file containing compound ID using specified data
|
|
|
632 field along with along with properties data, type:
|
|
|
633
|
|
|
634 % CalculatePhysicochemicalProperties.pl -m All
|
|
|
635 --DataFieldsMode CompoundID --CompoundIDMode DataField --CompoundID Mol_ID
|
|
|
636 -r SampleAllProperties -o Sample.sdf
|
|
|
637
|
|
|
638 To calculate all available physicochemical properties and generate a
|
|
|
639 SampleAllProperties.csv file containing compound ID using combination of
|
|
|
640 molecule name line and an explicit compound prefix along with properties
|
|
|
641 data, type:
|
|
|
642
|
|
|
643 % CalculatePhysicochemicalProperties.pl -m All
|
|
|
644 --DataFieldsMode CompoundID --CompoundIDMode MolnameOrLabelPrefix
|
|
|
645 --CompoundID Cmpd --CompoundIDLabel MolID -r SampleAllProperties
|
|
|
646 -o Sample.sdf
|
|
|
647
|
|
|
648 To calculate all available physicochemical properties and generate a
|
|
|
649 SampleAllProperties.csv file containing specific data fields columns
|
|
|
650 along with with properties data, type:
|
|
|
651
|
|
|
652 % CalculatePhysicochemicalProperties.pl -m All
|
|
|
653 --DataFieldsMode Specify --DataFields Mol_ID -r SampleAllProperties
|
|
|
654 -o Sample.sdf
|
|
|
655
|
|
|
656 To calculate all available physicochemical properties and generate a
|
|
|
657 SampleAllProperties.csv file containing common data fields columns along
|
|
|
658 with with properties data, type:
|
|
|
659
|
|
|
660 % CalculatePhysicochemicalProperties.pl -m All
|
|
|
661 --DataFieldsMode Common -r SampleAllProperties -o Sample.sdf
|
|
|
662
|
|
|
663 To calculate all available physicochemical properties and generate both
|
|
|
664 SampleAllProperties.csv and CSV files containing all data fields columns
|
|
|
665 in CSV files along with with properties data, type:
|
|
|
666
|
|
|
667 % CalculatePhysicochemicalProperties.pl -m All
|
|
|
668 --DataFieldsMode All --output both -r SampleAllProperties
|
|
|
669 -o Sample.sdf
|
|
|
670
|
|
|
671 AUTHOR
|
|
|
672 Manish Sud <msud@san.rr.com>
|
|
|
673
|
|
|
674 SEE ALSO
|
|
|
675 ExtractFromSDtFiles.pl, ExtractFromTextFiles.pl, InfoSDFiles.pl,
|
|
|
676 InfoTextFiles.pl
|
|
|
677
|
|
|
678 COPYRIGHT
|
|
|
679 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
680
|
|
|
681 This file is part of MayaChemTools.
|
|
|
682
|
|
|
683 MayaChemTools is free software; you can redistribute it and/or modify it
|
|
|
684 under the terms of the GNU Lesser General Public License as published by
|
|
|
685 the Free Software Foundation; either version 3 of the License, or (at
|
|
|
686 your option) any later version.
|
|
|
687
|
