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124 .\" ========================================================================
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125 .\"
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126 .IX Title "PATHLENGTHFINGERPRINTS 1"
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127 .TH PATHLENGTHFINGERPRINTS 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 PathLengthFingerprints
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134 .SH "SYNOPSIS"
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135 .IX Header "SYNOPSIS"
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136 use Fingerprints::PathLengthFingerprints;
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137 .PP
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138 use Fingerprints::PathLengthFingerprints qw(:all);
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139 .SH "DESCRIPTION"
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140 .IX Header "DESCRIPTION"
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141 \&\fBPathLengthFingerprints\fR class provides the following methods:
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142 .PP
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143 new, GenerateFingerprints, , GetDescription, SetAtomIdentifierType,
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144 SetAtomicInvariantsToUse, SetFunctionalClassesToUse, SetMaxLength,
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145 SetMinLength, SetNumOfBitsToSetPerPath, SetType,
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146 StringifyPathLengthFingerprints
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147 .PP
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148 \&\fBPathLengthFingerprints\fR is derived from \fBFingerprints\fR class which in turn
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149 is derived from \fBObjectProperty\fR base class that provides methods not explicitly defined
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150 in \fBPathLengthFingerprints\fR, \fBFingerprints\fR or \fBObjectProperty\fR classes using Perl's
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151 \&\s-1AUTOLOAD\s0 functionality. These methods are generated on-the-fly for a specified object property:
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152 .PP
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153 .Vb 3
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154 \& Set<PropertyName>(<PropertyValue>);
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155 \& $PropertyValue = Get<PropertyName>();
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156 \& Delete<PropertyName>();
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157 .Ve
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158 .PP
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159 The current release of MayaChemTools supports generation of \fBAtomTypesFingerpritns\fR
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160 corresponding to following \fBAtomtomIdentifierTypes\fR:
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161 .PP
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162 .Vb 3
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163 \& AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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164 \& FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
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165 \& SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes
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166 .Ve
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167 .PP
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168 Based on the values specified for \fBType\fR, \fBAtomtomIdentifierTypes\fR, \fBMinPathLength\fR and
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169 \&\fBMaxPathLength\fR, all appropriate atom paths are generated for each atom in the molecule
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170 and collected in a list and the list is filtered to remove any structurally duplicate paths as
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171 indicated by the value of \fBUseUniquePaths\fR.
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172 .PP
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173 For molecules containing rings, atom paths starting from each atom can be traversed in four
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174 different ways:
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175 .PP
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176 .Vb 7
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177 \& o Atom paths without any rings and sharing of bonds in traversed paths.
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178 \& o Atom paths containing rings and without any sharing of bonds in
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179 \& traversed paths
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180 \& o All possible atom paths without any rings and sharing of bonds in
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181 \& traversed paths
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182 \& o All possible atom paths containing rings and with sharing of bonds in
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183 \& traversed paths.
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184 .Ve
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185 .PP
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186 Atom path traversal is terminated at the last ring atom. For molecules containing no rings,
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187 first two and last two types described above are equivalent.
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188 .PP
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189 \&\fBAllowSharedBonds\fR and \fBAllowRings\fR allow generation of different types of paths
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190 to be used for fingerprints generation.
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191 .PP
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192 The combination of \fBAllowSharedBonds\fR, \fBAllowRings\fR, and \fBUseBondSymbols\fR allows generation of
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193 8 different types of path length fingerprints:
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194 .PP
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195 .Vb 1
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196 \& AllowSharedBonds AllowRings UseBondSymbols
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197 \&
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198 \& 0 0 1 \- AtomPathsNoCyclesWithBondSymbols
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199 \& 0 1 1 \- AtomPathsWithCyclesWithBondSymbols
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200 \&
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201 \& 1 0 1 \- AllAtomPathsNoCyclesWithBondSymbols
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202 \& 1 1 1 \- AllAtomPathsWithCyclesWithBondSymbols
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203 \& [ DEFAULT ]
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204 \&
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205 \& 0 0 0 \- AtomPathsNoCyclesNoBondSymbols
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206 \& 0 1 0 \- AtomPathsWithCyclesNoBondSymbols
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207 \&
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208 \& 1 0 0 \- AllAtomPathsNoCyclesNoBondSymbols
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209 \& 1 1 0 \- AllAtomPathsWithCyclesNoWithBondSymbols
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210 .Ve
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211 .PP
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212 Additionally, possible values for option \fB\-\-AtomIdentifierType\fR in conjunction with corresponding
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213 specified values for \fBAtomicInvariantsToUse\fR and \fBFunctionalClassesToUse \fR changes the nature
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214 of atom path length strings and the fingerprints.
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215 .PP
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216 For each atom path in the filtered atom paths list, an atom path string is created using value of
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217 \&\fBAtomIdentifierType\fR and specified values to use for a particular atom identifier type.
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218 Value of \fBUseBondSymbols\fR controls whether bond order symbols are used during generation
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219 of atom path string. Atom symbol corresponds to element symbol and characters used to represent
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220 bond order are: \fI1 \- None; 2 \- '='; 3 \- '#'; 1.5 or aromatic \- ':'; others: bond order value\fR. By default,
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221 bond symbols are included in atom path strings. Exclusion of bond symbols in atom path strings
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222 results in fingerprints which correspond purely to atom paths without considering bonds.
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223 .PP
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224 \&\fBUseUniquePaths\fR controls the removal of structurally duplicate atom path strings are removed
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225 from the list.
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226 .PP
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227 For \fIPathLengthBits\fR value of \fBType\fR, each atom path is hashed to a 32 bit unsigned
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228 integer key using \fBTextUtil::HashCode\fR function. Using the hash key as a seed for a random number
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229 generator, a random integer value between 0 and \fBSize\fR is used to set corresponding bits
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230 in the fingerprint bit-vector string. Value of \fBNumOfBitsToSetPerPaths\fR option controls the number
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231 of time a random number is generated to set corresponding bits.
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232 .PP
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233 For \fI PathLengthCount\fR value of \fBType\fRn, the number of times an atom path appears
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234 is tracked and a fingerprints count-string corresponding to count of atom paths is generated.
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235 .PP
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236 The current release of MayaChemTools generates the following types of path length
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237 fingerprints bit-vector and vector strings:
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238 .PP
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239 .Vb 6
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240 \& FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
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241 \& th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110
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242 \& 0100010101011000101001011100110001000010001001101000001001001001001000
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243 \& 0010110100000111001001000001001010100100100000000011000000101001011100
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244 \& 0010000001000101010100000100111100110111011011011000000010110111001101
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245 \& 0101100011000000010001000011000010100011101100001000001000100000000...
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246 \&
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247 \& FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
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248 \& th1:MaxLength8;1024;HexadecimalString;Ascending;48caa1315d82d91122b029
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249 \& 42861c9409a4208182d12015509767bd0867653604481a8b1288000056090583603078
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250 \& 9cedae54e26596889ab121309800900490515224208421502120a0dd9200509723ae89
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251 \& 00024181b86c0122821d4e4880c38620dab280824b455404009f082003d52c212b4e6d
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252 \& 6ea05280140069c780290c43
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253 \&
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254 \& FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength
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255 \& 1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2
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256 \& C.X2.BO2.H2 4 C.X2.BO3.H1 14 C.X3.BO3.H1 3 C.X3.BO4 10 F.X1.BO1 1 N.X
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257 \& 2.BO2.H1 1 N.X3.BO3 1 O.X1.BO1.H1 3 O.X1.BO2 2 C.X1.BO1.H3C.X3.BO3.H1
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258 \& 2 C.X2.BO2.H2C.X2.BO2.H2 1 C.X2.BO2.H2C.X3.BO3.H1 4 C.X2.BO2.H2C.X3.BO
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259 \& 4 1 C.X2.BO2.H2N.X3.BO3 1 C.X2.BO3.H1:C.X2.BO3.H1 10 C.X2.BO3.H1:C....
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260 \&
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261 \& FingerprintsVector;PathLengthCount:DREIDINGAtomTypes:MinLength1:MaxLen
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262 \& gth8;410;NumericalValues;IDsAndValuesPairsString;C_2 2 C_3 9 C_R 22 F_
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263 \& 1 N_3 1 N_R 1 O_2 2 O_3 3 C_2=O_2 2 C_2C_3 1 C_2C_R 1 C_2N_3 1 C_2O_3
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264 \& 1 C_3C_3 7 C_3C_R 1 C_3N_R 1 C_3O_3 2 C_R:C_R 21 C_R:N_R 2 C_RC_R 2 C
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265 \& _RF_ 1 C_RN_3 1 C_2C_3C_3 1 C_2C_R:C_R 2 C_2N_3C_R 1 C_3C_2=O_2 1 C_3C
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266 \& _2O_3 1 C_3C_3C_3 5 C_3C_3C_R 2 C_3C_3N_R 1 C_3C_3O_3 4 C_3C_R:C_R ...
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267 \&
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268 \& FingerprintsVector;PathLengthCount:EStateAtomTypes:MinLength1:MaxLengt
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269 \& h8;454;NumericalValues;IDsAndValuesPairsString;aaCH 14 aasC 8 aasN 1 d
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270 \& O 2 dssC 2 sCH3 2 sF 1 sOH 3 ssCH2 4 ssNH 1 sssCH 3 aaCH:aaCH 10 aaCH:
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271 \& aasC 8 aasC:aasC 3 aasC:aasN 2 aasCaasC 2 aasCdssC 1 aasCsF 1 aasCssNH
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272 \& 1 aasCsssCH 1 aasNssCH2 1 dO=dssC 2 dssCsOH 1 dssCssCH2 1 dssCssNH 1
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273 \& sCH3sssCH 2 sOHsssCH 2 ssCH2ssCH2 1 ssCH2sssCH 4 aaCH:aaCH:aaCH 6 a...
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274 \&
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275 \& FingerprintsVector;PathLengthCount:FunctionalClassAtomTypes:MinLength1
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276 \& :MaxLength8;404;NumericalValues;IDsAndValuesPairsString;Ar 22 Ar.HBA 1
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277 \& HBA 2 HBA.HBD 3 HBD 1 Hal 1 NI 1 None 10 Ar.HBA:Ar 2 Ar.HBANone 1 Ar:
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278 \& Ar 21 ArAr 2 ArHBD 1 ArHal 1 ArNone 2 HBA.HBDNI 1 HBA.HBDNone 2 HBA=NI
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279 \& 1 HBA=None 1 HBDNone 1 NINone 1 NoneNone 7 Ar.HBA:Ar:Ar 2 Ar.HBA:ArAr
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280 \& 1 Ar.HBA:ArNone 1 Ar.HBANoneNone 1 Ar:Ar.HBA:Ar 1 Ar:Ar.HBANone 2 ...
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281 \&
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282 \& FingerprintsVector;PathLengthCount:MMFF94AtomTypes:MinLength1:MaxLengt
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283 \& h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1
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284 \& 8 COO 1 CR 9 F 1 N5 1 NC=O 1 O=CN 1 O=CO 1 OC=O 1 OR 2 C5A:C5B 2 C5A:N
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285 \& 5 2 C5ACB 1 C5ACR 1 C5B:C5B 1 C5BC=ON 1 C5BCB 1 C=ON=O=CN 1 C=ONNC=O 1
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286 \& CB:CB 18 CBF 1 CBNC=O 1 COO=O=CO 1 COOCR 1 COOOC=O 1 CRCR 7 CRN5 1 CR
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287 \& OR 2 C5A:C5B:C5B 2 C5A:C5BC=ON 1 C5A:C5BCB 1 C5A:N5:C5A 1 C5A:N5CR ...
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288 \&
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289 \& FingerprintsVector;PathLengthCount:SLogPAtomTypes:MinLength1:MaxLength
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290 \& 8;518;NumericalValues;IDsAndValuesPairsString;C1 5 C10 1 C11 1 C14 1 C
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291 \& 18 14 C20 4 C21 2 C22 1 C5 2 CS 2 F 1 N11 1 N4 1 O10 1 O2 3 O9 1 C10C1
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292 \& 1 C10N11 1 C11C1 2 C11C21 1 C14:C18 2 C14F 1 C18:C18 10 C18:C20 4 C18
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293 \& :C22 2 C1C5 1 C1CS 4 C20:C20 1 C20:C21 1 C20:N11 1 C20C20 2 C21:C21 1
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294 \& C21:N11 1 C21C5 1 C22N4 1 C5=O10 1 C5=O9 1 C5N4 1 C5O2 1 CSO2 2 C10...
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295 \&
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296 \& FingerprintsVector;PathLengthCount:SYBYLAtomTypes:MinLength1:MaxLength
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297 \& 8;412;NumericalValues;IDsAndValuesPairsString;C.2 2 C.3 9 C.ar 22 F 1
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298 \& N.am 1 N.ar 1 O.2 1 O.3 2 O.co2 2 C.2=O.2 1 C.2=O.co2 1 C.2C.3 1 C.2C.
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299 \& ar 1 C.2N.am 1 C.2O.co2 1 C.3C.3 7 C.3C.ar 1 C.3N.ar 1 C.3O.3 2 C.ar:C
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300 \& .ar 21 C.ar:N.ar 2 C.arC.ar 2 C.arF 1 C.arN.am 1 C.2C.3C.3 1 C.2C.ar:C
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301 \& .ar 2 C.2N.amC.ar 1 C.3C.2=O.co2 1 C.3C.2O.co2 1 C.3C.3C.3 5 C.3C.3...
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302 \&
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303 \& FingerprintsVector;PathLengthCount:TPSAAtomTypes:MinLength1:MaxLength8
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304 \& ;331;NumericalValues;IDsAndValuesPairsString;N21 1 N7 1 None 34 O3 2 O
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305 \& 4 3 N21:None 2 N21None 1 N7None 2 None:None 21 None=O3 2 NoneNone 13 N
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306 \& oneO4 3 N21:None:None 2 N21:NoneNone 2 N21NoneNone 1 N7None:None 2 N7N
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307 \& one=O3 1 N7NoneNone 1 None:N21:None 1 None:N21None 2 None:None:None 20
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308 \& None:NoneNone 12 NoneN7None 1 NoneNone=O3 2 NoneNoneNone 8 NoneNon...
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309 \&
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310 \& FingerprintsVector;PathLengthCount:UFFAtomTypes:MinLength1:MaxLength8;
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311 \& 410;NumericalValues;IDsAndValuesPairsString;C_2 2 C_3 9 C_R 22 F_ 1 N_
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312 \& 3 1 N_R 1 O_2 2 O_3 3 C_2=O_2 2 C_2C_3 1 C_2C_R 1 C_2N_3 1 C_2O_3 1 C_
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313 \& 3C_3 7 C_3C_R 1 C_3N_R 1 C_3O_3 2 C_R:C_R 21 C_R:N_R 2 C_RC_R 2 C_RF_
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314 \& 1 C_RN_3 1 C_2C_3C_3 1 C_2C_R:C_R 2 C_2N_3C_R 1 C_3C_2=O_2 1 C_3C_2O_3
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315 \& 1 C_3C_3C_3 5 C_3C_3C_R 2 C_3C_3N_R 1 C_3C_3O_3 4 C_3C_R:C_R 1 C_3...
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316 .Ve
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317 .SS "\s-1METHODS\s0"
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318 .IX Subsection "METHODS"
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319 .IP "\fBnew\fR" 4
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320 .IX Item "new"
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321 .Vb 2
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322 \& $NewPathLengthFingerprints = new PathLengthFingerprints(
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323 \& %NamesAndValues);
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324 .Ve
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325 .Sp
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326 Using specified \fIPathLengthFingerprints\fR property names and values hash, \fBnew\fR method creates a new object
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327 and returns a reference to newly created \fBPathLengthFingerprints\fR object. By default, the following properties are
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328 initialized:
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329 .Sp
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330 .Vb 10
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331 \& Molecule = \*(Aq\*(Aq;
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332 \& Type = \*(Aq\*(Aq
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333 \& Size = 1024
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334 \& MinSize = 32
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335 \& MaxSize = 2**32
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336 \& NumOfBitsToSetPerPath = 1
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337 \& MinLength = 1
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338 \& MaxLength = 8
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339 \& AllowSharedBonds = 1
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340 \& AllowRings = 1
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341 \& UseBondSymbols = 1
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342 \& UseUniquePaths = \*(Aq\*(Aq
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343 \& AtomIdentifierType = \*(Aq\*(Aq
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344 \& SetAtomicInvariantsToUse = [\*(AqAS\*(Aq]
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345 \& FunctionalClassesToUse = [\*(AqHBD\*(Aq, \*(AqHBA\*(Aq, \*(AqPI\*(Aq, \*(AqNI\*(Aq, \*(AqAr\*(Aq, \*(AqHal\*(Aq]
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346 .Ve
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347 .Sp
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348 Examples:
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349 .Sp
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350 .Vb 5
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351 \& $PathLengthFingerprints = new PathLengthFingerprints(
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352 \& \*(AqMolecule\*(Aq => $Molecule,
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353 \& \*(AqType\*(Aq => \*(AqPathLengthBits\*(Aq,
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354 \& \*(AqAtomIdentifierType\*(Aq =
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355 \& \*(AqAtomicInvariantsAtomTypes\*(Aq);
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356 \&
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357 \& $PathLengthFingerprints = new PathLengthFingerprints(
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358 \& \*(AqMolecule\*(Aq => $Molecule,
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359 \& \*(AqType\*(Aq => \*(AqPathLengthBits\*(Aq,
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360 \& \*(AqSize\*(Aq => 1024,
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361 \& \*(AqMinLength\*(Aq => 1,
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362 \& \*(AqMaxLength\*(Aq => 8,
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363 \& \*(AqAllowRings\*(Aq => 1,
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364 \& \*(AqAllowSharedBonds\*(Aq => 1,
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365 \& \*(AqUseBondSymbols\*(Aq => 1,
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366 \& \*(AqUseUniquePaths\*(Aq => 1,
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367 \& \*(AqAtomIdentifierType\*(Aq =
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368 \& \*(AqAtomicInvariantsAtomTypes\*(Aq,
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369 \& \*(AqAtomicInvariantsToUse\*(Aq => [\*(AqAS\*(Aq]);
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370 \&
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371 \& $PathLengthFingerprints = new PathLengthFingerprints(
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372 \& \*(AqMolecule\*(Aq => $Molecule,
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373 \& \*(AqType\*(Aq => \*(AqPathLengthCount\*(Aq,
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374 \& \*(AqMinLength\*(Aq => 1,
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375 \& \*(AqMaxLength\*(Aq => 8,
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376 \& \*(AqAllowRings\*(Aq => 1,
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377 \& \*(AqAllowSharedBonds\*(Aq => 1,
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378 \& \*(AqUseBondSymbols\*(Aq => 1,
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379 \& \*(AqUseUniquePaths\*(Aq => 1,
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380 \& \*(AqAtomIdentifierType\*(Aq =>
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381 \& \*(AqAtomicInvariantsAtomTypes\*(Aq,
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382 \& \*(AqAtomicInvariantsToUse\*(Aq => [\*(AqAS\*(Aq]);
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383 \&
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384 \& $PathLengthFingerprints = new PathLengthFingerprints(
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385 \& \*(AqMolecule\*(Aq => $Molecule,
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386 \& \*(AqType\*(Aq => \*(AqPathLengthBits\*(Aq,
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387 \& \*(AqAtomIdentifierType\*(Aq =
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388 \& \*(AqSLogPAtomTypes\*(Aq);
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389 \&
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390 \& $PathLengthFingerprints = new PathLengthFingerprints(
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391 \& \*(AqMolecule\*(Aq => $Molecule,
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392 \& \*(AqType\*(Aq => \*(AqPathLengthCount\*(Aq,
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393 \& \*(AqAtomIdentifierType\*(Aq =
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394 \& \*(AqSYBYLAtomTypes\*(Aq);
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395 \&
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396 \& $PathLengthFingerprints = new PathLengthFingerprints(
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397 \& \*(AqMolecule\*(Aq => $Molecule,
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398 \& \*(AqType\*(Aq => \*(AqPathLengthBits\*(Aq,
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399 \& \*(AqAtomIdentifierType\*(Aq =
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400 \& \*(AqFunctionalClassAtomTypes\*(Aq,
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401 \& \*(AqFunctionalClassesToUse\*(Aq => [\*(AqHBD\*(Aq, \*(AqHBA\*(Aq, \*(AqAr\*(Aq]);
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402 \&
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403 \& $PathLengthFingerprints\->GenerateFingerprints();
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404 \& print "$PathLengthFingerprints\en";
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405 .Ve
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406 .IP "\fBGetDescription\fR" 4
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407 .IX Item "GetDescription"
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408 .Vb 1
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409 \& $Description = $PathLengthFingerprints\->GetDescription();
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410 .Ve
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411 .Sp
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412 Returns a string containing description of path length fingerprints.
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413 .IP "\fBGenerateFingerprints\fR" 4
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414 .IX Item "GenerateFingerprints"
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415 .Vb 1
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416 \& $PathLengthFingerprints\->GenerateFingerprints();
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417 .Ve
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418 .Sp
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419 Generates path length fingerprints and returns \fIPathLengthFingerprints\fR.
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420 .IP "\fBSetMaxLength\fR" 4
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421 .IX Item "SetMaxLength"
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422 .Vb 1
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423 \& $PathLengthFingerprints\->SetMaxLength($Length);
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424 .Ve
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425 .Sp
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426 Sets maximum value of atom path length to be used during atom path length fingerprints
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427 generation and returns \fIPathLengthFingerprints\fR
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428 .IP "\fBSetAtomIdentifierType\fR" 4
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429 .IX Item "SetAtomIdentifierType"
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430 .Vb 1
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431 \& $PathLengthFingerprints\->SetAtomIdentifierType();
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432 .Ve
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433 .Sp
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434 Sets atom \fIIdentifierType\fR to use during path length fingerprints generation and
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435 returns \fIPathLengthFingerprints\fR.
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436 .Sp
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437 Possible values: \fIAtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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438 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
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439 TPSAAtomTypes, UFFAtomTypes\fR.
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|
440 .IP "\fBSetAtomicInvariantsToUse\fR" 4
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441 .IX Item "SetAtomicInvariantsToUse"
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442 .Vb 2
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443 \& $PathLengthFingerprints\->SetAtomicInvariantsToUse($ValuesRef);
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444 \& $PathLengthFingerprints\->SetAtomicInvariantsToUse(@Values);
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445 .Ve
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446 .Sp
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447 Sets atomic invariants to use during \fIAtomicInvariantsAtomTypes\fR value of \fIAtomIdentifierType\fR
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448 for path length fingerprints generation and returns \fIPathLengthFingerprints\fR.
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449 .Sp
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450 Possible values for atomic invariants are: \fI\s-1AS\s0, X, \s-1BO\s0, \s-1LBO\s0, \s-1SB\s0, \s-1DB\s0, \s-1TB\s0,
|
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|
451 H, Ar, \s-1RA\s0, \s-1FC\s0, \s-1MN\s0, \s-1SM\s0\fR. Default value: \fI\s-1AS\s0\fR.
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452 .Sp
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|
|
453 The atomic invariants abbreviations correspond to:
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454 .Sp
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455 .Vb 1
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|
456 \& AS = Atom symbol corresponding to element symbol
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457 \&
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|
458 \& X<n> = Number of non\-hydrogen atom neighbors or heavy atoms
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|
459 \& BO<n> = Sum of bond orders to non\-hydrogen atom neighbors or heavy atoms
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|
|
460 \& LBO<n> = Largest bond order of non\-hydrogen atom neighbors or heavy atoms
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|
461 \& SB<n> = Number of single bonds to non\-hydrogen atom neighbors or heavy atoms
|
|
|
462 \& DB<n> = Number of double bonds to non\-hydrogen atom neighbors or heavy atoms
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|
|
463 \& TB<n> = Number of triple bonds to non\-hydrogen atom neighbors or heavy atoms
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|
|
464 \& H<n> = Number of implicit and explicit hydrogens for atom
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|
|
465 \& Ar = Aromatic annotation indicating whether atom is aromatic
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|
|
466 \& RA = Ring atom annotation indicating whether atom is a ring
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|
|
467 \& FC<+n/\-n> = Formal charge assigned to atom
|
|
|
468 \& MN<n> = Mass number indicating isotope other than most abundant isotope
|
|
|
469 \& SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
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|
470 \& 3 (triplet)
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|
471 .Ve
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472 .Sp
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|
473 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:
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474 .Sp
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|
475 .Vb 1
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476 \& 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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|
|
477 .Ve
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|
|
478 .Sp
|
|
|
479 Except for \s-1AS\s0 which is a required atomic invariant in atom types, all other atomic invariants are
|
|
|
480 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.
|
|
|
481 .Sp
|
|
|
482 In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
|
|
|
483 are also allowed:
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|
484 .Sp
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|
|
485 .Vb 12
|
|
|
486 \& X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
|
|
|
487 \& BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
|
|
|
488 \& LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
|
|
|
489 \& SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
|
|
|
490 \& DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
|
|
|
491 \& TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
|
|
|
492 \& H : NumOfImplicitAndExplicitHydrogens
|
|
|
493 \& Ar : Aromatic
|
|
|
494 \& RA : RingAtom
|
|
|
495 \& FC : FormalCharge
|
|
|
496 \& MN : MassNumber
|
|
|
497 \& SM : SpinMultiplicity
|
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|
498 .Ve
|
|
|
499 .Sp
|
|
|
500 \&\fIAtomTypes::AtomicInvariantsAtomTypes\fR module is used to assign atomic invariant
|
|
|
501 atom types.
|
|
|
502 .IP "\fBSetFunctionalClassesToUse\fR" 4
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|
|
503 .IX Item "SetFunctionalClassesToUse"
|
|
|
504 .Vb 2
|
|
|
505 \& $PathLengthFingerprints\->SetFunctionalClassesToUse($ValuesRef);
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|
|
506 \& $PathLengthFingerprints\->SetFunctionalClassesToUse(@Values);
|
|
|
507 .Ve
|
|
|
508 .Sp
|
|
|
509 Sets functional classes invariants to use during \fIFunctionalClassAtomTypes\fR value of \fIAtomIdentifierType\fR
|
|
|
510 for path length fingerprints generation and returns \fIPathLengthFingerprints\fR.
|
|
|
511 .Sp
|
|
|
512 Possible values for atom functional classes are: \fIAr, \s-1CA\s0, H, \s-1HBA\s0, \s-1HBD\s0, Hal, \s-1NI\s0, \s-1PI\s0, \s-1RA\s0\fR.
|
|
|
513 Default value [ Ref 24 ]: \fI\s-1HBD\s0,HBA,PI,NI,Ar,Hal\fR.
|
|
|
514 .Sp
|
|
|
515 The functional class abbreviations correspond to:
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|
|
516 .Sp
|
|
|
517 .Vb 9
|
|
|
518 \& HBD: HydrogenBondDonor
|
|
|
519 \& HBA: HydrogenBondAcceptor
|
|
|
520 \& PI : PositivelyIonizable
|
|
|
521 \& NI : NegativelyIonizable
|
|
|
522 \& Ar : Aromatic
|
|
|
523 \& Hal : Halogen
|
|
|
524 \& H : Hydrophobic
|
|
|
525 \& RA : RingAtom
|
|
|
526 \& CA : ChainAtom
|
|
|
527 \&
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|
|
528 \& Functional class atom type specification for an atom corresponds to:
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|
|
529 \&
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|
|
530 \& Ar.CA.H.HBA.HBD.Hal.NI.PI.RA or None
|
|
|
531 .Ve
|
|
|
532 .Sp
|
|
|
533 \&\fIAtomTypes::FunctionalClassAtomTypes\fR module is used to assign functional class atom
|
|
|
534 types. It uses following definitions [ Ref 60\-61, Ref 65\-66 ]:
|
|
|
535 .Sp
|
|
|
536 .Vb 4
|
|
|
537 \& HydrogenBondDonor: NH, NH2, OH
|
|
|
538 \& HydrogenBondAcceptor: N[!H], O
|
|
|
539 \& PositivelyIonizable: +, NH2
|
|
|
540 \& NegativelyIonizable: \-, C(=O)OH, S(=O)OH, P(=O)OH
|
|
|
541 .Ve
|
|
|
542 .IP "\fBSetMinLength\fR" 4
|
|
|
543 .IX Item "SetMinLength"
|
|
|
544 .Vb 1
|
|
|
545 \& $PathLengthFingerprints\->SetMinLength($Length);
|
|
|
546 .Ve
|
|
|
547 .Sp
|
|
|
548 Sets minimum value of atom path length to be used during atom path length fingerprints
|
|
|
549 generation and returns \fIPathLengthFingerprints\fR.
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|
|
550 .IP "\fBSetMaxLength\fR" 4
|
|
|
551 .IX Item "SetMaxLength"
|
|
|
552 .Vb 1
|
|
|
553 \& $PathLengthFingerprints\->SetMaxLength($Length);
|
|
|
554 .Ve
|
|
|
555 .Sp
|
|
|
556 Sets maximum value of atom path length to be used during atom path length fingerprints
|
|
|
557 generation and returns \fIPathLengthFingerprints\fR.
|
|
|
558 .IP "\fBSetNumOfBitsToSetPerPath\fR" 4
|
|
|
559 .IX Item "SetNumOfBitsToSetPerPath"
|
|
|
560 .Vb 1
|
|
|
561 \& $PathLengthFingerprints\->SetNumOfBitsToSetPerPath($NumOfBits);
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|
|
562 .Ve
|
|
|
563 .Sp
|
|
|
564 Sets number of bits to set for each path during \fIPathLengthBits\fR \fBType \fR during path length fingerprints
|
|
|
565 generation and returns \fIPathLengthFingerprints\fR.
|
|
|
566 .IP "\fBSetType\fR" 4
|
|
|
567 .IX Item "SetType"
|
|
|
568 .Vb 1
|
|
|
569 \& $PathLengthFingerprints\->SetType($Type);
|
|
|
570 .Ve
|
|
|
571 .Sp
|
|
|
572 Sets type of path length fingerprints and returns \fIPathLengthFingerprints\fR. Possible values:
|
|
|
573 \&\fIPathLengthBits or PathLengthCount\fR.
|
|
|
574 .IP "\fBStringifyPathLengthFingerprints\fR" 4
|
|
|
575 .IX Item "StringifyPathLengthFingerprints"
|
|
|
576 .Vb 1
|
|
|
577 \& $String = $PathLengthFingerprints\->StringifyPathLengthFingerprints();
|
|
|
578 .Ve
|
|
|
579 .Sp
|
|
|
580 Returns a string containing information about \fIPathLengthFingerprints\fR object.
|
|
|
581 .SH "AUTHOR"
|
|
|
582 .IX Header "AUTHOR"
|
|
|
583 Manish Sud <msud@san.rr.com>
|
|
|
584 .SH "SEE ALSO"
|
|
|
585 .IX Header "SEE ALSO"
|
|
|
586 Fingerprints.pm, FingerprintsStringUtil.pm, AtomNeighborhoodsFingerprints.pm,
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|
|
587 AtomTypesFingerprints.pm, EStateIndiciesFingerprints.pm, ExtendedConnectivityFingerprints.pm,
|
|
|
588 MACCSKeys.pm, TopologicalAtomPairsFingerprints.pm, TopologicalAtomTripletsFingerprints.pm,
|
|
|
589 TopologicalAtomTorsionsFingerprints.pm, TopologicalPharmacophoreAtomPairsFingerprints.pm,
|
|
|
590 TopologicalPharmacophoreAtomTripletsFingerprints.pm
|
|
|
591 .SH "COPYRIGHT"
|
|
|
592 .IX Header "COPYRIGHT"
|
|
|
593 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
594 .PP
|
|
|
595 This file is part of MayaChemTools.
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|
596 .PP
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|
|
597 MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
|
598 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
|
|
|
599 Software Foundation; either version 3 of the License, or (at your option)
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|
600 any later version.
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