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124 .\" ========================================================================
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125 .\"
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126 .IX Title "TOPOLOGICALPHARMACOPHOREATOMPAIRSFINGERPRINTS 1"
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127 .TH TOPOLOGICALPHARMACOPHOREATOMPAIRSFINGERPRINTS 1 "2015-03-29" "perl v5.14.2" "MayaChemTools"
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128 .\" For nroff, turn off justification. Always turn off hyphenation; it makes
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129 .\" way too many mistakes in technical documents.
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130 .if n .ad l
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131 .nh
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132 .SH "NAME"
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133 TopologicalPharmacophoreAtomPairsFingerprints.pl \- Generate topological pharmacophore atom pairs fingerprints for SD files
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134 .SH "SYNOPSIS"
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135 .IX Header "SYNOPSIS"
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136 TopologicalPharmacophoreAtomPairsFingerprints.pl SDFile(s)...
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137 .PP
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138 TopologicalPharmacophoreAtomPairsFingerprints.pl [\fB\-\-AromaticityModel\fR \fIAromaticityModelType\fR]
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139 [\fB\-\-AtomPairsSetSizeToUse\fR \fIArbitrarySize | FixedSize\fR]
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140 [\fB\-a, \-\-AtomTypesToUse\fR \fI\*(L"AtomType1, AtomType2...\*(R"\fR]
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141 [\fB\-\-AtomTypesWeight\fR \fI\*(L"AtomType1, Weight1, AtomType2, Weight2...\*(R"\fR]
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142 [\fB\-\-CompoundID\fR \fIDataFieldName or LabelPrefixString\fR] [\fB\-\-CompoundIDLabel\fR \fItext\fR]
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143 [\fB\-\-CompoundIDMode\fR] [\fB\-\-DataFields\fR \fI\*(L"FieldLabel1, FieldLabel2,...\*(R"\fR]
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144 [\fB\-d, \-\-DataFieldsMode\fR \fIAll | Common | Specify | CompoundID\fR] [\fB\-f, \-\-Filter\fR \fIYes | No\fR]
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145 [\fB\-\-FingerprintsLabelMode\fR \fIFingerprintsLabelOnly | FingerprintsLabelWithIDs\fR] [\fB\-\-FingerprintsLabel\fR \fItext\fR]
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146 [\fB\-\-FuzzifyAtomPairsCount\fR \fIYes | No\fR] [\fB\-\-FuzzificationMode\fR \fIFuzzyBinning | FuzzyBinSmoothing\fR]
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147 [\fB\-\-FuzzificationMethodology\fR \fIFuzzyBinning | FuzzyBinSmoothing\fR] [\fB\-\-FuzzFactor\fR \fInumber\fR]
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148 [\fB\-h, \-\-help\fR] [\fB\-k, \-\-KeepLargestComponent\fR \fIYes | No\fR] [\fB\-\-MinDistance\fR \fInumber\fR]
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149 [\fB\-\-MaxDistance\fR \fInumber\fR] [\fB\-n, \-\-NormalizationMethodology\fR \fINone | ByHeavyAtomsCount | ByAtomTypesCount\fR]
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150 [\fB\-\-OutDelim\fR \fIcomma | tab | semicolon\fR] [\fB\-\-output\fR \fI\s-1SD\s0 | \s-1FP\s0 | text | all\fR] [\fB\-o, \-\-overwrite\fR]
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151 [\fB\-q, \-\-quote\fR \fIYes | No\fR] [\fB\-r, \-\-root\fR \fIRootName\fR] [\fB\-\-ValuesPrecision\fR \fInumber\fR]
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152 [\fB\-v, \-\-VectorStringFormat\fR \fIValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString\fR]
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153 [\fB\-w, \-\-WorkingDir\fR dirname] SDFile(s)...
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154 .SH "DESCRIPTION"
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155 .IX Header "DESCRIPTION"
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156 Generate topological pharmacophore atom pairs fingerprints [ Ref 60\-62, Ref 65, Ref 68 ] for
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157 \&\fISDFile(s)\fR and create appropriate \s-1SD\s0, \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) containing fingerprints vector
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158 strings corresponding to molecular fingerprints.
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159 .PP
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160 Multiple SDFile names are separated by spaces. The valid file extensions are \fI.sdf\fR
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161 and \fI.sd\fR. All other file names are ignored. All the \s-1SD\s0 files in a current directory
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162 can be specified either by \fI*.sdf\fR or the current directory name.
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163 .PP
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164 Based on the values specified for \fB\-\-AtomTypesToUse\fR, pharmacophore atom types are
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165 assigned to all non-hydrogen atoms in a molecule and a distance matrix is generated.
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166 A pharmacophore atom pairs basis set is initialized for all unique possible pairs within
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167 \&\fB\-\-MinDistance\fR and \fB\-\-MaxDistance\fR range.
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168 .PP
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169 .Vb 1
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170 \& Let:
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171 \&
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172 \& P = Valid pharmacophore atom type
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173 \&
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174 \& Px = Pharmacophore atom type x
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175 \& Py = Pharmacophore atom type y
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176 \&
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177 \& Dmin = Minimum distance corresponding to number of bonds between
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178 \& two atoms
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179 \& Dmax = Maximum distance corresponding to number of bonds between
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180 \& two atoms
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181 \& D = Distance corresponding to number of bonds between two atoms
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182 \&
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183 \& Px\-Dn\-Py = Pharmacophore atom pair ID for atom types Px and Py at
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184 \& distance Dn
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185 \&
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186 \& P = Number of pharmacophore atom types to consider
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187 \& PPDn = Number of possible unique pharmacophore atom pairs at a distance Dn
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188 \&
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189 \& PPT = Total number of possible pharmacophore atom pairs at all distances
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190 \& between Dmin and Dmax
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191 \&
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192 \& Then:
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193 \&
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194 \& PPD = (P * (P \- 1))/2 + P
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195 \&
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196 \& PPT = ((Dmax \- Dmin) + 1) * ((P * (P \- 1))/2 + P)
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197 \& = ((Dmax \- Dmin) + 1) * PPD
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198 \&
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199 \& So for default values of Dmin = 1, Dmax = 10 and P = 5,
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200 \&
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201 \& PPD = (5 * (5 \- 1))/2 + 5 = 15
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202 \& PPT = ((10 \- 1) + 1) * 15 = 150
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203 \&
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204 \& The pharmacophore atom pairs bais set includes 150 values.
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205 \&
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206 \& The atom pair IDs correspond to:
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207 \&
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208 \& Px\-Dn\-Py = Pharmacophore atom pair ID for atom types Px and Py at
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209 \& distance Dn
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210 \&
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211 \& For example: H\-D1\-H, H\-D2\-HBA, PI\-D5\-PI and so on
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212 .Ve
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213 .PP
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214 Using distance matrix and pharmacohore atom types, occurrence of unique pharmacohore atom
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215 pairs is counted. The contribution of each atom type to atom pair interaction is optionally
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216 weighted by specified \fB\-\-AtomTypesWeight\fR before assigning its count to appropriate distance
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217 bin. Based on \fB\-\-NormalizationMethodology\fR option, pharmacophore atom pairs count is optionally
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218 normalized. Additionally, pharmacohore atom pairs count is optionally fuzzified before or after
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219 the normalization controlled by values of \fB\-\-FuzzifyAtomPairsCount\fR, \fB\-\-FuzzificationMode\fR,
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220 \&\fB\-\-FuzzificationMethodology\fR and \fB\-\-FuzzFactor\fR options.
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221 .PP
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222 The final pharmacophore atom pairs count along with atom pair identifiers involving all non-hydrogen
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223 atoms, with optional normalization and fuzzification, constitute pharmacophore topological atom pairs
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224 fingerprints of the molecule.
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225 .PP
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226 For \fIArbitrarySize\fR value of \fB\-\-AtomPairsSetSizeToUse\fR option, the fingerprint vector correspond to
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227 only those topological pharmacophore atom pairs which are present and have non-zero count. However,
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228 for \fIFixedSize\fR value of \fB\-\-AtomPairsSetSizeToUse\fR option, the fingerprint vector contains all possible
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229 valid topological pharmacophore atom pairs with both zero and non-zero count values.
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230 .PP
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231 Example of \fI\s-1SD\s0\fR file containing topological pharmacophore atom pairs fingerprints string data:
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232 .PP
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233 .Vb 10
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234 \& ... ...
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235 \& ... ...
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236 \& $$$$
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237 \& ... ...
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238 \& ... ...
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239 \& ... ...
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240 \& 41 44 0 0 0 0 0 0 0 0999 V2000
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241 \& \-3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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242 \& ... ...
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243 \& 2 3 1 0 0 0 0
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244 \& ... ...
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245 \& M END
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246 \& > <CmpdID>
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247 \& Cmpd1
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248 \&
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249 \& > <TopologicalPharmacophoreAtomPairsFingerprints>
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250 \& FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
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251 \& Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H\-D1\-H H
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252 \& \-D1\-NI HBA\-D1\-NI HBD\-D1\-NI H\-D2\-H H\-D2\-HBA H\-D2\-HBD HBA\-D2\-HBA HBA\-D2\-
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253 \& HBD H\-D3\-H H\-D3\-HBA H\-D3\-HBD H\-D3\-NI HBA\-D3\-NI HBD\-D3\-NI H\-D4\-H H\-D...;
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254 \& 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10 3
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255 \& 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1
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256 \&
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257 \& $$$$
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258 \& ... ...
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259 \& ... ...
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260 .Ve
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261 .PP
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262 Example of \fI\s-1FP\s0\fR file containing topological pharmacophore atom pairs fingerprints string data:
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263 .PP
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264 .Vb 10
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265 \& #
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266 \& # Package = MayaChemTools 7.4
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267 \& # Release Date = Oct 21, 2010
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268 \& #
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269 \& # TimeStamp = Fri Mar 11 15:32:48 2011
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270 \& #
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271 \& # FingerprintsStringType = FingerprintsVector
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272 \& #
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273 \& # Description = TopologicalPharmacophoreAtomPairs:ArbitrarySize:MinDistance1:MaxDistance10
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274 \& # VectorStringFormat = IDsAndValuesString
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275 \& # VectorValuesType = NumericalValues
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276 \& #
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277 \& Cmpd1 54;H\-D1\-H H\-D1\-NI HBA\-D1\-NI HBD\-D1\-NI H\-D2\-H H\-D2\-HBA...;18 1 2...
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278 \& Cmpd2 61;H\-D1\-H H\-D1\-NI HBA\-D1\-NI HBD\-D1\-NI H\-D2\-H H\-D2\-HBA...;5 1 2 ...
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279 \& ... ...
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280 \& ... ..
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281 .Ve
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282 .PP
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283 Example of \s-1CSV\s0 \fIText\fR file containing topological pharmacophore atom pairs fingerprints string data:
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284 .PP
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285 .Vb 9
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286 \& "CompoundID","TopologicalPharmacophoreAtomPairsFingerprints"
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287 \& "Cmpd1","FingerprintsVector;TopologicalPharmacophoreAtomPairs:Arbitrary
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288 \& Size:MinDistance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H
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289 \& \-D1\-H H\-D1\-NI HBA\-D1\-NI HBD\-D1\-NI H\-D2\-H H\-D2\-HBA H\-D2\-HBD HBA\-D2\-HBA H
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290 \& BA\-D2\-HBD H\-D3\-H H\-D3\-HBA H\-D3\-HBD H\-D3\-NI HBA\-D3\-NI HBD\-D3\-NI H\-D4...;
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291 \& 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10 3
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292 \& 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1"
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293 \& ... ...
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294 \& ... ...
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295 .Ve
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296 .PP
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297 The current release of MayaChemTools generates the following types of topological pharmacophore
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298 atom pairs fingerprints vector strings:
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299 .PP
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300 .Vb 7
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301 \& FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
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302 \& Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H\-D1\-H H
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303 \& \-D1\-NI HBA\-D1\-NI HBD\-D1\-NI H\-D2\-H H\-D2\-HBA H\-D2\-HBD HBA\-D2\-HBA HBA\-D2\-
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304 \& HBD H\-D3\-H H\-D3\-HBA H\-D3\-HBD H\-D3\-NI HBA\-D3\-NI HBD\-D3\-NI H\-D4\-H H\-D4\-H
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305 \& BA H\-D4\-HBD HBA\-D4\-HBA HBA\-D4\-HBD HBD\-D4\-HBD H\-D5\-H H\-D5\-HBA H\-D5\-...;
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306 \& 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10
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307 \& 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1
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308 \&
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309 \& FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
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310 \& ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0
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311 \& 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3 1 0 0 0 1
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312 \& 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0 1 0 0 1 0
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313 \& 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0 0 37 10 8 0 0 0 0 1 0 0 0 0 0 0
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314 \& 0 35 10 9 0 0 3 3 0 0 1 0 0 0 0 0 28 7 7 4 0 0 0 0 0 0 0 0 0 0 0 18...
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315 \&
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316 \& FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
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317 \& ance1:MaxDistance10;150;OrderedNumericalValues;IDsAndValuesString;H\-D1
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318 \& \-H H\-D1\-HBA H\-D1\-HBD H\-D1\-NI H\-D1\-PI HBA\-D1\-HBA HBA\-D1\-HBD HBA\-D1\-NI H
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319 \& BA\-D1\-PI HBD\-D1\-HBD HBD\-D1\-NI HBD\-D1\-PI NI\-D1\-NI NI\-D1\-PI PI\-D1\-PI H\-D
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320 \& 2\-H H\-D2\-HBA H\-D2\-HBD H\-D2\-NI H\-D2\-PI HBA\-D2\-HBA HBA\-D2\-HBD HBA\-D2...;
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321 \& 18 0 0 1 0 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3
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322 \& 1 0 0 0 1 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0
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323 \& 1 0 0 1 0 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0
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324 .Ve
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325 .SH "OPTIONS"
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326 .IX Header "OPTIONS"
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327 .IP "\fB\-\-AromaticityModel\fR \fIMDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel\fR" 4
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328 .IX Item "--AromaticityModel MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel"
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329 Specify aromaticity model to use during detection of aromaticity. Possible values in the current
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330 release are: \fIMDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
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331 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel
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332 or MayaChemToolsAromaticityModel\fR. Default value: \fIMayaChemToolsAromaticityModel\fR.
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333 .Sp
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334 The supported aromaticity model names along with model specific control parameters
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335 are defined in \fBAromaticityModelsData.csv\fR, which is distributed with the current release
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336 and is available under \fBlib/data\fR directory. \fBMolecule.pm\fR module retrieves data from
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337 this file during class instantiation and makes it available to method \fBDetectAromaticity\fR
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338 for detecting aromaticity corresponding to a specific model.
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339 .IP "\fB\-\-AtomPairsSetSizeToUse\fR \fIArbitrarySize | FixedSize\fR" 4
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340 .IX Item "--AtomPairsSetSizeToUse ArbitrarySize | FixedSize"
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341 Atom pairs set size to use during generation of topological pharmacophore atom pairs
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342 fingerprints.
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343 .Sp
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344 Possible values: \fIArbitrarySize | FixedSize\fR; Default value: \fIArbitrarySize\fR.
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345 .Sp
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346 For \fIArbitrarySize\fR value of \fB\-\-AtomPairsSetSizeToUse\fR option, the fingerprint vector
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347 correspond to only those topological pharmacophore atom pairs which are present and
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348 have non-zero count. However, for \fIFixedSize\fR value of \fB\-\-AtomPairsSetSizeToUse\fR
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349 option, the fingerprint vector contains all possible valid topological pharmacophore atom
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350 pairs with both zero and non-zero count values.
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351 .ie n .IP "\fB\-a, \-\-AtomTypesToUse\fR \fI""AtomType1,AtomType2,...""\fR" 4
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352 .el .IP "\fB\-a, \-\-AtomTypesToUse\fR \fI``AtomType1,AtomType2,...''\fR" 4
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353 .IX Item "-a, --AtomTypesToUse AtomType1,AtomType2,..."
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354 Pharmacophore atom types to use during generation of topological phramacophore
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355 atom pairs. It's a list of comma separated valid pharmacophore atom types.
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356 .Sp
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357 Possible values for pharmacophore atom types are: \fIAr, \s-1CA\s0, H, \s-1HBA\s0, \s-1HBD\s0, Hal, \s-1NI\s0, \s-1PI\s0, \s-1RA\s0\fR.
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358 Default value [ Ref 60\-62 ] : \fI\s-1HBD\s0,HBA,PI,NI,H\fR.
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359 .Sp
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360 The pharmacophore atom types abbreviations correspond to:
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361 .Sp
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362 .Vb 9
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363 \& HBD: HydrogenBondDonor
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364 \& HBA: HydrogenBondAcceptor
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365 \& PI : PositivelyIonizable
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366 \& NI : NegativelyIonizable
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367 \& Ar : Aromatic
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368 \& Hal : Halogen
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369 \& H : Hydrophobic
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370 \& RA : RingAtom
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371 \& CA : ChainAtom
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372 .Ve
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373 .Sp
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374 \&\fIAtomTypes::FunctionalClassAtomTypes\fR module is used to assign pharmacophore atom
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375 types. It uses following definitions [ Ref 60\-61, Ref 65\-66 ]:
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376 .Sp
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377 .Vb 4
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378 \& HydrogenBondDonor: NH, NH2, OH
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379 \& HydrogenBondAcceptor: N[!H], O
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380 \& PositivelyIonizable: +, NH2
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381 \& NegativelyIonizable: \-, C(=O)OH, S(=O)OH, P(=O)OH
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382 .Ve
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383 .ie n .IP "\fB\-\-AtomTypesWeight\fR \fI""AtomType1,Weight1,AtomType2,Weight2...""\fR" 4
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384 .el .IP "\fB\-\-AtomTypesWeight\fR \fI``AtomType1,Weight1,AtomType2,Weight2...''\fR" 4
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385 .IX Item "--AtomTypesWeight AtomType1,Weight1,AtomType2,Weight2..."
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386 Weights of specified pharmacophore atom types to use during calculation of their contribution
|
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387 to atom pair count. Default value: \fINone\fR. Valid values: real numbers greater than 0. In general
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388 it's comma delimited list of valid atom type and its weight.
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389 .Sp
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390 The weight values allow to increase the importance of specific pharmacophore atom type
|
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391 in the generated fingerprints. A weight value of 0 for an atom type eliminates its contribution to
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392 atom pair count where as weight value of 2 doubles its contribution.
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393 .IP "\fB\-\-CompoundID\fR \fIDataFieldName or LabelPrefixString\fR" 4
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394 .IX Item "--CompoundID DataFieldName or LabelPrefixString"
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395 This value is \fB\-\-CompoundIDMode\fR specific and indicates how compound \s-1ID\s0 is generated.
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396 .Sp
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397 For \fIDataField\fR value of \fB\-\-CompoundIDMode\fR option, it corresponds to datafield label name
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398 whose value is used as compound \s-1ID\s0; otherwise, it's a prefix string used for generating compound
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399 IDs like LabelPrefixString<Number>. Default value, \fICmpd\fR, generates compound IDs which
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400 look like Cmpd<Number>.
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401 .Sp
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402 Examples for \fIDataField\fR value of \fB\-\-CompoundIDMode\fR:
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403 .Sp
|
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|
404 .Vb 2
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405 \& MolID
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406 \& ExtReg
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407 .Ve
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408 .Sp
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409 Examples for \fILabelPrefix\fR or \fIMolNameOrLabelPrefix\fR value of \fB\-\-CompoundIDMode\fR:
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410 .Sp
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411 .Vb 1
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412 \& Compound
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413 .Ve
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414 .Sp
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415 The value specified above generates compound IDs which correspond to Compound<Number>
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416 instead of default value of Cmpd<Number>.
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417 .IP "\fB\-\-CompoundIDLabel\fR \fItext\fR" 4
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|
418 .IX Item "--CompoundIDLabel text"
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|
419 Specify compound \s-1ID\s0 column label for \s-1CSV/TSV\s0 text file(s) used during \fICompoundID\fR value
|
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420 of \fB\-\-DataFieldsMode\fR option. Default value: \fICompoundID\fR.
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421 .IP "\fB\-\-CompoundIDMode\fR \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR" 4
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422 .IX Item "--CompoundIDMode DataField | MolName | LabelPrefix | MolNameOrLabelPrefix"
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423 Specify how to generate compound IDs and write to \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) along with generated
|
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|
424 fingerprints for \fI\s-1FP\s0 | text | all\fR values of \fB\-\-output\fR option: use a \fISDFile(s)\fR datafield value;
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|
425 use molname line from \fISDFile(s)\fR; generate a sequential \s-1ID\s0 with specific prefix; use combination
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426 of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.
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427 .Sp
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428 Possible values: \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR.
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429 Default value: \fILabelPrefix\fR.
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430 .Sp
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431 For \fIMolNameAndLabelPrefix\fR value of \fB\-\-CompoundIDMode\fR, molname line in \fISDFile(s)\fR takes
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432 precedence over sequential compound IDs generated using \fILabelPrefix\fR and only empty molname
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433 values are replaced with sequential compound IDs.
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434 .Sp
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|
435 This is only used for \fICompoundID\fR value of \fB\-\-DataFieldsMode\fR option.
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436 .ie n .IP "\fB\-\-DataFields\fR \fI""FieldLabel1,FieldLabel2,...""\fR" 4
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437 .el .IP "\fB\-\-DataFields\fR \fI``FieldLabel1,FieldLabel2,...''\fR" 4
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438 .IX Item "--DataFields FieldLabel1,FieldLabel2,..."
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|
439 Comma delimited list of \fISDFiles(s)\fR data fields to extract and write to \s-1CSV/TSV\s0 text file(s) along
|
|
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440 with generated fingerprints for \fItext | all\fR values of \fB\-\-output\fR option.
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441 .Sp
|
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442 This is only used for \fISpecify\fR value of \fB\-\-DataFieldsMode\fR option.
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443 .Sp
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444 Examples:
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445 .Sp
|
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|
446 .Vb 2
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447 \& Extreg
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448 \& MolID,CompoundName
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449 .Ve
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|
450 .IP "\fB\-d, \-\-DataFieldsMode\fR \fIAll | Common | Specify | CompoundID\fR" 4
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451 .IX Item "-d, --DataFieldsMode All | Common | Specify | CompoundID"
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452 Specify how data fields in \fISDFile(s)\fR are transferred to output \s-1CSV/TSV\s0 text file(s) along
|
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|
453 with generated fingerprints for \fItext | all\fR values of \fB\-\-output\fR option: transfer all \s-1SD\s0
|
|
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454 data field; transfer \s-1SD\s0 data files common to all compounds; extract specified data fields;
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455 generate a compound \s-1ID\s0 using molname line, a compound prefix, or a combination of both.
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|
456 Possible values: \fIAll | Common | specify | CompoundID\fR. Default value: \fICompoundID\fR.
|
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|
457 .IP "\fB\-f, \-\-Filter\fR \fIYes | No\fR" 4
|
|
|
458 .IX Item "-f, --Filter Yes | No"
|
|
|
459 Specify whether to check and filter compound data in SDFile(s). Possible values: \fIYes or No\fR.
|
|
|
460 Default value: \fIYes\fR.
|
|
|
461 .Sp
|
|
|
462 By default, compound data is checked before calculating fingerprints and compounds containing
|
|
|
463 atom data corresponding to non-element symbols or no atom data are ignored.
|
|
|
464 .IP "\fB\-\-FingerprintsLabelMode\fR \fIFingerprintsLabelOnly | FingerprintsLabelWithIDs\fR" 4
|
|
|
465 .IX Item "--FingerprintsLabelMode FingerprintsLabelOnly | FingerprintsLabelWithIDs"
|
|
|
466 Specify how fingerprints label is generated in conjunction with \fB\-\-FingerprintsLabel\fR option value:
|
|
|
467 use fingerprints label generated only by \fB\-\-FingerprintsLabel\fR option value or append topological
|
|
|
468 atom pair count value IDs to \fB\-\-FingerprintsLabel\fR option value.
|
|
|
469 .Sp
|
|
|
470 Possible values: \fIFingerprintsLabelOnly | FingerprintsLabelWithIDs\fR. Default value:
|
|
|
471 \&\fIFingerprintsLabelOnly\fR.
|
|
|
472 .Sp
|
|
|
473 Topological atom pairs IDs appended to \fB\-\-FingerprintsLabel\fR value during \fIFingerprintsLabelWithIDs\fR
|
|
|
474 values of \fB\-\-FingerprintsLabelMode\fR correspond to atom pair count values in fingerprint vector string.
|
|
|
475 .Sp
|
|
|
476 \&\fIFingerprintsLabelWithIDs\fR value of \fB\-\-FingerprintsLabelMode\fR is ignored during \fIArbitrarySize\fR value
|
|
|
477 of \fB\-\-AtomPairsSetSizeToUse\fR option and topological atom pairs IDs not appended to the label.
|
|
|
478 .IP "\fB\-\-FingerprintsLabel\fR \fItext\fR" 4
|
|
|
479 .IX Item "--FingerprintsLabel text"
|
|
|
480 \&\s-1SD\s0 data label or text file column label to use for fingerprints string in output \s-1SD\s0 or
|
|
|
481 \&\s-1CSV/TSV\s0 text file(s) specified by \fB\-\-output\fR. Default value: \fITopologicalPharmacophoreAtomPairsFingerprints\fR.
|
|
|
482 .IP "\fB\-\-FuzzifyAtomPairsCount\fR \fIYes | No\fR" 4
|
|
|
483 .IX Item "--FuzzifyAtomPairsCount Yes | No"
|
|
|
484 To fuzzify or not to fuzzify atom pairs count. Possible values: \fIYes or No\fR. Default value:
|
|
|
485 \&\fINo\fR.
|
|
|
486 .IP "\fB\-\-FuzzificationMode\fR \fIBeforeNormalization | AfterNormalization\fR" 4
|
|
|
487 .IX Item "--FuzzificationMode BeforeNormalization | AfterNormalization"
|
|
|
488 When to fuzzify atom pairs count. Possible values: \fIBeforeNormalization | AfterNormalizationYes\fR.
|
|
|
489 Default value: \fIAfterNormalization\fR.
|
|
|
490 .IP "\fB\-\-FuzzificationMethodology\fR \fIFuzzyBinning | FuzzyBinSmoothing\fR" 4
|
|
|
491 .IX Item "--FuzzificationMethodology FuzzyBinning | FuzzyBinSmoothing"
|
|
|
492 How to fuzzify atom pairs count. Possible values: \fIFuzzyBinning | FuzzyBinSmoothing\fR.
|
|
|
493 Default value: \fIFuzzyBinning\fR.
|
|
|
494 .Sp
|
|
|
495 In conjunction with values for options \fB\-\-FuzzifyAtomPairsCount\fR, \fB\-\-FuzzificationMode\fR and
|
|
|
496 \&\fB\-\-FuzzFactor\fR, \fB\-\-FuzzificationMethodology\fR option is used to fuzzify pharmacophore atom
|
|
|
497 pairs count.
|
|
|
498 .Sp
|
|
|
499 Let:
|
|
|
500 .Sp
|
|
|
501 .Vb 3
|
|
|
502 \& Px = Pharmacophore atom type x
|
|
|
503 \& Py = Pharmacophore atom type y
|
|
|
504 \& PPxy = Pharmacophore atom pair between atom type Px and Py
|
|
|
505 \&
|
|
|
506 \& PPxyDn = Pharmacophore atom pairs count between atom type Px and Py
|
|
|
507 \& at distance Dn
|
|
|
508 \& PPxyDn\-1 = Pharmacophore atom pairs count between atom type Px and Py
|
|
|
509 \& at distance Dn \- 1
|
|
|
510 \& PPxyDn+1 = Pharmacophore atom pairs count between atom type Px and Py
|
|
|
511 \& at distance Dn + 1
|
|
|
512 \&
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|
|
513 \& FF = FuzzFactor for FuzzyBinning and FuzzyBinSmoothing
|
|
|
514 .Ve
|
|
|
515 .Sp
|
|
|
516 Then:
|
|
|
517 .Sp
|
|
|
518 For \fIFuzzyBinning\fR:
|
|
|
519 .Sp
|
|
|
520 .Vb 1
|
|
|
521 \& PPxyDn = PPxyDn (Unchanged)
|
|
|
522 \&
|
|
|
523 \& PPxyDn\-1 = PPxyDn\-1 + PPxyDn * FF
|
|
|
524 \& PPxyDn+1 = PPxyDn+1 + PPxyDn * FF
|
|
|
525 .Ve
|
|
|
526 .Sp
|
|
|
527 For \fIFuzzyBinSmoothing\fR:
|
|
|
528 .Sp
|
|
|
529 .Vb 2
|
|
|
530 \& PPxyDn = PPxyDn \- PPxyDn * 2FF for Dmin < Dn < Dmax
|
|
|
531 \& PPxyDn = PPxyDn \- PPxyDn * FF for Dn = Dmin or Dmax
|
|
|
532 \&
|
|
|
533 \& PPxyDn\-1 = PPxyDn\-1 + PPxyDn * FF
|
|
|
534 \& PPxyDn+1 = PPxyDn+1 + PPxyDn * FF
|
|
|
535 .Ve
|
|
|
536 .Sp
|
|
|
537 In both fuzzification schemes, a value of 0 for \s-1FF\s0 implies no fuzzification of occurrence counts.
|
|
|
538 A value of 1 during \fIFuzzyBinning\fR corresponds to maximum fuzzification of occurrence counts;
|
|
|
539 however, a value of 1 during \fIFuzzyBinSmoothing\fR ends up completely distributing the value over
|
|
|
540 the previous and next distance bins.
|
|
|
541 .Sp
|
|
|
542 So for default value of \fB\-\-FuzzFactor\fR (\s-1FF\s0) 0.15, the occurrence count of pharmacohore atom pairs
|
|
|
543 at distance Dn during FuzzyBinning is left unchanged and the counts at distances Dn \-1 and Dn + 1
|
|
|
544 are incremented by PPxyDn * 0.15.
|
|
|
545 .Sp
|
|
|
546 And during \fIFuzzyBinSmoothing\fR the occurrence counts at Distance Dn is scaled back using multiplicative
|
|
|
547 factor of (1 \- 2*0.15) and the occurrence counts at distances Dn \-1 and Dn + 1 are incremented by
|
|
|
548 PPxyDn * 0.15. In otherwords, occurrence bin count is smoothed out by distributing it over the
|
|
|
549 previous and next distance value.
|
|
|
550 .IP "\fB\-\-FuzzFactor\fR \fInumber\fR" 4
|
|
|
551 .IX Item "--FuzzFactor number"
|
|
|
552 Specify by how much to fuzzify atom pairs count. Default value: \fI0.15\fR. Valid values: For
|
|
|
553 \&\fIFuzzyBinning\fR value of \fB\-\-FuzzificationMethodology\fR option: \fIbetween 0 and 1.0\fR; For
|
|
|
554 \&\fIFuzzyBinSmoothing\fR value of \fB\-\-FuzzificationMethodology\fR option: \fIbetween 0 and 0.5\fR.
|
|
|
555 .IP "\fB\-h, \-\-help\fR" 4
|
|
|
556 .IX Item "-h, --help"
|
|
|
557 Print this help message.
|
|
|
558 .IP "\fB\-k, \-\-KeepLargestComponent\fR \fIYes | No\fR" 4
|
|
|
559 .IX Item "-k, --KeepLargestComponent Yes | No"
|
|
|
560 Generate fingerprints for only the largest component in molecule. Possible values:
|
|
|
561 \&\fIYes or No\fR. Default value: \fIYes\fR.
|
|
|
562 .Sp
|
|
|
563 For molecules containing multiple connected components, fingerprints can be generated
|
|
|
564 in two different ways: use all connected components or just the largest connected
|
|
|
565 component. By default, all atoms except for the largest connected component are
|
|
|
566 deleted before generation of fingerprints.
|
|
|
567 .IP "\fB\-\-MinDistance\fR \fInumber\fR" 4
|
|
|
568 .IX Item "--MinDistance number"
|
|
|
569 Minimum bond distance between atom pairs for generating topological pharmacophore atom
|
|
|
570 pairs. Default value: \fI1\fR. Valid values: positive integers including 0 and less than \fB\-\-MaxDistance\fR.
|
|
|
571 .IP "\fB\-\-MaxDistance\fR \fInumber\fR" 4
|
|
|
572 .IX Item "--MaxDistance number"
|
|
|
573 Maximum bond distance between atom pairs for generating topological pharmacophore atom
|
|
|
574 pairs. Default value: \fI10\fR. Valid values: positive integers and greater than \fB\-\-MinDistance\fR.
|
|
|
575 .IP "\fB\-n, \-\-NormalizationMethodology\fR \fINone | ByHeavyAtomsCount | ByAtomTypesCount\fR" 4
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|
|
576 .IX Item "-n, --NormalizationMethodology None | ByHeavyAtomsCount | ByAtomTypesCount"
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|
|
577 Normalization methodology to use for scaling the occurrence count of pharmacophore atom
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|
|
578 pairs within specified distance range. Possible values: \fINone, ByHeavyAtomsCount or
|
|
|
579 ByAtomTypesCount\fR. Default value: \fINone\fR.
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|
|
580 .IP "\fB\-\-OutDelim\fR \fIcomma | tab | semicolon\fR" 4
|
|
|
581 .IX Item "--OutDelim comma | tab | semicolon"
|
|
|
582 Delimiter for output \s-1CSV/TSV\s0 text file(s). Possible values: \fIcomma, tab, or semicolon\fR
|
|
|
583 Default value: \fIcomma\fR.
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|
|
584 .IP "\fB\-\-output\fR \fI\s-1SD\s0 | \s-1FP\s0 | text | all\fR" 4
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|
|
585 .IX Item "--output SD | FP | text | all"
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|
|
586 Type of output files to generate. Possible values: \fI\s-1SD\s0, \s-1FP\s0, text, or all\fR. Default value: \fItext\fR.
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|
|
587 .IP "\fB\-o, \-\-overwrite\fR" 4
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|
|
588 .IX Item "-o, --overwrite"
|
|
|
589 Overwrite existing files.
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|
|
590 .IP "\fB\-q, \-\-quote\fR \fIYes | No\fR" 4
|
|
|
591 .IX Item "-q, --quote Yes | No"
|
|
|
592 Put quote around column values in output \s-1CSV/TSV\s0 text file(s). Possible values:
|
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|
593 \&\fIYes or No\fR. Default value: \fIYes\fR
|
|
|
594 .IP "\fB\-r, \-\-root\fR \fIRootName\fR" 4
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|
595 .IX Item "-r, --root RootName"
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|
|
596 New file name is generated using the root: <Root>.<Ext>. Default for new file names:
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|
597 <SDFileName><TopologicalPharmacophoreAtomPairsFP>.<Ext>. The file type determines <Ext> value.
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|
|
598 The sdf, fpf, csv, and tsv <Ext> values are used for \s-1SD\s0, \s-1FP\s0, comma/semicolon, and tab
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|
|
599 delimited text files, respectively.This option is ignored for multiple input files.
|
|
|
600 .IP "\fB\-\-ValuesPrecision\fR \fInumber\fR" 4
|
|
|
601 .IX Item "--ValuesPrecision number"
|
|
|
602 Precision of atom pairs count real values which might be generated after normalization
|
|
|
603 or fuzzification. Default value: up to \fI2\fR decimal places. Valid values: positive integers.
|
|
|
604 .IP "\fB\-v, \-\-VectorStringFormat\fR \fIValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString\fR" 4
|
|
|
605 .IX Item "-v, --VectorStringFormat ValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString"
|
|
|
606 Format of fingerprints vector string data in output \s-1SD\s0, \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) specified by
|
|
|
607 \&\fB\-\-output\fR option. Possible values: \fIValuesString, IDsAndValuesString | IDsAndValuesPairsString
|
|
|
608 | ValuesAndIDsString | ValuesAndIDsPairsString\fR.
|
|
|
609 .Sp
|
|
|
610 Default value during \fIFixedSize\fR value of \fB\-\-AtomPairsSetSizeToUse\fR option: \fIValuesString\fR. Default
|
|
|
611 value during \fIArbitrarySize\fR value of \fB\-\-AtomPairsSetSizeToUse\fR option: \fIIDsAndValuesString\fR.
|
|
|
612 .Sp
|
|
|
613 \&\fIValuesString\fR option value is not allowed for \fIArbitrarySize\fR value of \fB\-\-AtomPairsSetSizeToUse\fR
|
|
|
614 option.
|
|
|
615 .Sp
|
|
|
616 Examples:
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|
617 .Sp
|
|
|
618 .Vb 7
|
|
|
619 \& FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
|
|
|
620 \& Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H\-D1\-H H
|
|
|
621 \& \-D1\-NI HBA\-D1\-NI HBD\-D1\-NI H\-D2\-H H\-D2\-HBA H\-D2\-HBD HBA\-D2\-HBA HBA\-D2\-
|
|
|
622 \& HBD H\-D3\-H H\-D3\-HBA H\-D3\-HBD H\-D3\-NI HBA\-D3\-NI HBD\-D3\-NI H\-D4\-H H\-D4\-H
|
|
|
623 \& BA H\-D4\-HBD HBA\-D4\-HBA HBA\-D4\-HBD HBD\-D4\-HBD H\-D5\-H H\-D5\-HBA H\-D5\-...;
|
|
|
624 \& 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10
|
|
|
625 \& 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1
|
|
|
626 \&
|
|
|
627 \& FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
|
|
|
628 \& ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0
|
|
|
629 \& 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3 1 0 0 0 1
|
|
|
630 \& 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0 1 0 0 1 0
|
|
|
631 \& 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0 0 37 10 8 0 0 0 0 1 0 0 0 0 0 0
|
|
|
632 \& 0 35 10 9 0 0 3 3 0 0 1 0 0 0 0 0 28 7 7 4 0 0 0 0 0 0 0 0 0 0 0 18...
|
|
|
633 \&
|
|
|
634 \& FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
|
|
|
635 \& ance1:MaxDistance10;150;OrderedNumericalValues;IDsAndValuesString;H\-D1
|
|
|
636 \& \-H H\-D1\-HBA H\-D1\-HBD H\-D1\-NI H\-D1\-PI HBA\-D1\-HBA HBA\-D1\-HBD HBA\-D1\-NI H
|
|
|
637 \& BA\-D1\-PI HBD\-D1\-HBD HBD\-D1\-NI HBD\-D1\-PI NI\-D1\-NI NI\-D1\-PI PI\-D1\-PI H\-D
|
|
|
638 \& 2\-H H\-D2\-HBA H\-D2\-HBD H\-D2\-NI H\-D2\-PI HBA\-D2\-HBA HBA\-D2\-HBD HBA\-D2...;
|
|
|
639 \& 18 0 0 1 0 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3
|
|
|
640 \& 1 0 0 0 1 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0
|
|
|
641 \& 1 0 0 1 0 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0
|
|
|
642 .Ve
|
|
|
643 .IP "\fB\-w, \-\-WorkingDir\fR \fIDirName\fR" 4
|
|
|
644 .IX Item "-w, --WorkingDir DirName"
|
|
|
645 Location of working directory. Default value: current directory.
|
|
|
646 .SH "EXAMPLES"
|
|
|
647 .IX Header "EXAMPLES"
|
|
|
648 To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding to distances
|
|
|
649 from 1 through 10 using default atom types with no weighting, normalization, and fuzzification
|
|
|
650 of atom pairs count and create a SampleTPAPFP.csv file containing sequential compound IDs along
|
|
|
651 with fingerprints vector strings data in ValuesString format, type:
|
|
|
652 .PP
|
|
|
653 .Vb 2
|
|
|
654 \& % TopologicalPharmacophoreAtomPairsFingerprints.pl \-r SampleTPAPFP
|
|
|
655 \& \-o Sample.sdf
|
|
|
656 .Ve
|
|
|
657 .PP
|
|
|
658 To generate topological pharmacophore atom pairs fingerprints of fixed size corresponding to distances
|
|
|
659 from 1 through 10 using default atom types with no weighting, normalization, and fuzzification
|
|
|
660 of atom pairs count and create a SampleTPAPFP.csv file containing sequential compound IDs along
|
|
|
661 with fingerprints vector strings data in ValuesString format, type:
|
|
|
662 .PP
|
|
|
663 .Vb 2
|
|
|
664 \& % TopologicalPharmacophoreAtomPairsFingerprints.pl
|
|
|
665 \& \-\-AtomPairsSetSizeToUse FixedSize \-r SampleTPAPFP\-o Sample.sdf
|
|
|
666 .Ve
|
|
|
667 .PP
|
|
|
668 To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding to distances
|
|
|
669 from 1 through 10 using default atom types with no weighting, normalization, and fuzzification
|
|
|
670 of atom pairs count and create SampleTPAPFP.sdf, SampleTPAPFP.fpf and SampleTPAPFP.csv files containing
|
|
|
671 sequential compound IDs in \s-1CSV\s0 file along with fingerprints vector strings data in ValuesString
|
|
|
672 format, type:
|
|
|
673 .PP
|
|
|
674 .Vb 2
|
|
|
675 \& % TopologicalPharmacophoreAtomPairsFingerprints.pl \-\-output all
|
|
|
676 \& \-r SampleTPAPFP \-o Sample.sdf
|
|
|
677 .Ve
|
|
|
678 .PP
|
|
|
679 To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding to distances
|
|
|
680 from 1 through 10 using default atom types with no weighting, normalization, and fuzzification
|
|
|
681 of atom pairs count and create a SampleTPAPFP.csv file containing sequential compound IDs along
|
|
|
682 with fingerprints vector strings data in IDsAndValuesPairsString format, type:
|
|
|
683 .PP
|
|
|
684 .Vb 2
|
|
|
685 \& % TopologicalPharmacophoreAtomPairsFingerprints.pl \-\-VectorStringFormat
|
|
|
686 \& IDsAndValuesPairsString \-r SampleTPAPFP \-o Sample.sdf
|
|
|
687 .Ve
|
|
|
688 .PP
|
|
|
689 To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding to distances
|
|
|
690 from 1 through 6 using default atom types with no weighting, normalization, and fuzzification
|
|
|
691 of atom pairs count and create a SampleTPAPFP.csv file containing sequential compound IDs along
|
|
|
692 with fingerprints vector strings data in ValuesString format, type:
|
|
|
693 .PP
|
|
|
694 .Vb 2
|
|
|
695 \& % TopologicalPharmacophoreAtomPairsFingerprints.pl \-\-MinDistance 1
|
|
|
696 \& \-MaxDistance 6 \-r SampleTPAPFP \-o Sample.sdf
|
|
|
697 .Ve
|
|
|
698 .PP
|
|
|
699 To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding to distances
|
|
|
700 from 1 through 10 using \*(L"\s-1HBD\s0,HBA,PI,NI\*(R" atom types with double the weighting for \*(L"\s-1HBD\s0,HBA\*(R" and
|
|
|
701 normalization by HeavyAtomCount but no fuzzification of atom pairs count and create a
|
|
|
702 SampleTPAPFP.csv file containing sequential compound IDs along with fingerprints vector strings
|
|
|
703 data in ValuesString format, type:
|
|
|
704 .PP
|
|
|
705 .Vb 4
|
|
|
706 \& % TopologicalPharmacophoreAtomPairsFingerprints.pl \-\-MinDistance 1
|
|
|
707 \& \-MaxDistance 10 \-\-AtomTypesToUse "HBD,HBA,PI, NI" \-\-AtomTypesWeight
|
|
|
708 \& "HBD,2,HBA,2,PI,1,NI,1" \-\-NormalizationMethodology ByHeavyAtomsCount
|
|
|
709 \& \-\-FuzzifyAtomPairsCount No \-r SampleTPAPFP \-o Sample.sdf
|
|
|
710 .Ve
|
|
|
711 .PP
|
|
|
712 To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding to
|
|
|
713 distances from 1 through 10 using \*(L"\s-1HBD\s0,HBA,PI,NI,H\*(R" atom types with no weighting of atom types and
|
|
|
714 normalization but with fuzzification of atom pairs count using FuzzyBinning methodology
|
|
|
715 with FuzzFactor value 0.15 and create a SampleTPAPFP.csv file containing sequential compound
|
|
|
716 IDs along with fingerprints vector strings data in ValuesString format, type:
|
|
|
717 .PP
|
|
|
718 .Vb 5
|
|
|
719 \& % TopologicalPharmacophoreAtomPairsFingerprints.pl \-\-MinDistance 1
|
|
|
720 \& \-\-MaxDistance 10 \-\-AtomTypesToUse "HBD,HBA,PI, NI,H" \-\-AtomTypesWeight
|
|
|
721 \& "HBD,1,HBA,1,PI,1,NI,1,H,1" \-\-NormalizationMethodology None
|
|
|
722 \& \-\-FuzzifyAtomPairsCount Yes \-\-FuzzificationMethodology FuzzyBinning
|
|
|
723 \& \-\-FuzzFactor 0.5 \-r SampleTPAPFP \-o Sample.sdf
|
|
|
724 .Ve
|
|
|
725 .PP
|
|
|
726 To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding to distances
|
|
|
727 distances from 1 through 10 using default atom types with no weighting,
|
|
|
728 normalization, and fuzzification of atom pairs count and create a SampleTPAPFP.csv
|
|
|
729 file containing compound \s-1ID\s0 from molecule name line along with fingerprints vector strings
|
|
|
730 data, type:
|
|
|
731 .PP
|
|
|
732 .Vb 2
|
|
|
733 \& % TopologicalPharmacophoreAtomPairsFingerprints.pl \-\-DataFieldsMode
|
|
|
734 \& CompoundID \-CompoundIDMode MolName \-r SampleTPAPFP \-o Sample.sdf
|
|
|
735 .Ve
|
|
|
736 .PP
|
|
|
737 To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding
|
|
|
738 to distances from 1 through 10 using default atom types with no weighting,
|
|
|
739 normalization, and fuzzification of atom pairs count and create a SampleTPAPFP.csv
|
|
|
740 file containing compound IDs using specified data field along with fingerprints vector strings
|
|
|
741 data, type:
|
|
|
742 .PP
|
|
|
743 .Vb 3
|
|
|
744 \& % TopologicalPharmacophoreAtomPairsFingerprints.pl \-\-DataFieldsMode
|
|
|
745 \& CompoundID \-CompoundIDMode DataField \-\-CompoundID Mol_ID
|
|
|
746 \& \-r SampleTPAPFP \-o Sample.sdf
|
|
|
747 .Ve
|
|
|
748 .PP
|
|
|
749 To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding
|
|
|
750 to distances from 1 through 10 using default atom types with no weighting,
|
|
|
751 normalization, and fuzzification of atom pairs count and create a SampleTPAPFP.csv
|
|
|
752 file containing compound \s-1ID\s0 using combination of molecule name line and an explicit compound
|
|
|
753 prefix along with fingerprints vector strings data, type:
|
|
|
754 .PP
|
|
|
755 .Vb 3
|
|
|
756 \& % TopologicalPharmacophoreAtomPairsFingerprints.pl \-\-DataFieldsMode
|
|
|
757 \& CompoundID \-CompoundIDMode MolnameOrLabelPrefix
|
|
|
758 \& \-\-CompoundID Cmpd \-\-CompoundIDLabel MolID \-r SampleTPAPFP \-o Sample.sdf
|
|
|
759 .Ve
|
|
|
760 .PP
|
|
|
761 To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding
|
|
|
762 to distances from 1 through 10 using default atom types with no weighting,
|
|
|
763 normalization, and fuzzification of atom pairs count and create a SampleTPAPFP.csv
|
|
|
764 file containing specific data fields columns along with fingerprints vector strings
|
|
|
765 data, type:
|
|
|
766 .PP
|
|
|
767 .Vb 2
|
|
|
768 \& % TopologicalPharmacophoreAtomPairsFingerprints.pl \-\-DataFieldsMode
|
|
|
769 \& Specify \-\-DataFields Mol_ID \-r SampleTPAPFP \-o Sample.sdf
|
|
|
770 .Ve
|
|
|
771 .PP
|
|
|
772 To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding
|
|
|
773 to distances from 1 through 10 using default atom types with no weighting,
|
|
|
774 normalization, and fuzzification of atom pairs count and create a SampleTPAPFP.csv
|
|
|
775 file containing common data fields columns along with fingerprints vector strings
|
|
|
776 data, type:
|
|
|
777 .PP
|
|
|
778 .Vb 2
|
|
|
779 \& % TopologicalPharmacophoreAtomPairsFingerprints.pl \-\-DataFieldsMode
|
|
|
780 \& Common \-r SampleTPAPFP \-o Sample.sdf
|
|
|
781 .Ve
|
|
|
782 .PP
|
|
|
783 To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding
|
|
|
784 to distances from 1 through 10 using default atom types with no weighting,
|
|
|
785 normalization, and fuzzification of atom pairs count and create SampleTPAPFP.sdf, SampleTPAPFP.fpf,
|
|
|
786 and SampleTPAPFP.csv files containing all data fields columns in \s-1CSV\s0 file along with fingerprints
|
|
|
787 data, type:
|
|
|
788 .PP
|
|
|
789 .Vb 2
|
|
|
790 \& % TopologicalPharmacophoreAtomPairsFingerprints.pl \-\-DataFieldsMode
|
|
|
791 \& All \-\-output all \-r SampleTPAPFP \-o Sample.sdf
|
|
|
792 .Ve
|
|
|
793 .SH "AUTHOR"
|
|
|
794 .IX Header "AUTHOR"
|
|
|
795 Manish Sud <msud@san.rr.com>
|
|
|
796 .SH "SEE ALSO"
|
|
|
797 .IX Header "SEE ALSO"
|
|
|
798 InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, AtomNeighborhoodsFingerprints.pl,
|
|
|
799 ExtendedConnectivityFingerprints.pl, MACCSKeysFingerprints.pl, PathLengthFingerprints.pl,
|
|
|
800 TopologicalAtomPairsFingerprints.pl, TopologicalAtomTorsionsFingerprints.pl,
|
|
|
801 TopologicalPharmacophoreAtomTripletsFingerprints.pl
|
|
|
802 .SH "COPYRIGHT"
|
|
|
803 .IX Header "COPYRIGHT"
|
|
|
804 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
805 .PP
|
|
|
806 This file is part of MayaChemTools.
|
|
|
807 .PP
|
|
|
808 MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
|
809 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
|
|
|
810 Software Foundation; either version 3 of the License, or (at your option)
|
|
|
811 any later version.
|
