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124 .\" ========================================================================
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125 .\"
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126 .IX Title "TOPOLOGICALATOMTRIPLETSFINGERPRINTS 1"
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127 .TH TOPOLOGICALATOMTRIPLETSFINGERPRINTS 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 TopologicalAtomTripletsFingerprints
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134 .SH "SYNOPSIS"
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135 .IX Header "SYNOPSIS"
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136 use Fingerprints::TopologicalAtomTripletsFingerprints;
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137 .PP
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138 use Fingerprints::TopologicalAtomTripletsFingerprints qw(:all);
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139 .SH "DESCRIPTION"
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140 .IX Header "DESCRIPTION"
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141 \&\fBTopologicalAtomTripletsFingerprints\fR [ Ref 57, Ref 59, Ref 72 ] class provides the following methods:
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142 .PP
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143 new, GenerateFingerprints, GetAtomTripletIDs, GetDescription,
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144 SetAtomIdentifierType, SetAtomicInvariantsToUse, SetFunctionalClassesToUse,
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145 SetMaxDistance, SetMinDistance, StringifyTopologicalAtomTripletsFingerprints
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146 .PP
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147 \&\fBTopologicalAtomTripletsFingerprints\fR is derived from \fBFingerprints\fR class which in turn
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148 is derived from \fBObjectProperty\fR base class that provides methods not explicitly defined
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149 in \fBTopologicalAtomTripletsFingerprints\fR, \fBFingerprints\fR or \fBObjectProperty\fR classes using Perl's
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150 \&\s-1AUTOLOAD\s0 functionality. These methods are generated on-the-fly for a specified object property:
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151 .PP
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152 .Vb 3
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153 \& Set<PropertyName>(<PropertyValue>);
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154 \& $PropertyValue = Get<PropertyName>();
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155 \& Delete<PropertyName>();
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156 .Ve
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157 .PP
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158 The current release of MayaChemTools supports generation of \fBTopologicalAtomTripletsFingerprints\fR
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159 corresponding to following \fBAtomtomIdentifierTypes\fR:
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160 .PP
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161 .Vb 3
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162 \& AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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163 \& FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
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164 \& SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes
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165 .Ve
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166 .PP
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167 Based on the values specified for \fBAtomIdentifierType\fR along with other specified
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168 parameters such as \fBAtomicInvariantsToUse\fR and \fBFunctionalClassesToUse\fR, initial
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169 atom types are assigned to all non-hydrogen atoms in a molecule. Using the distance
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170 matrix for the molecule and initial atom types assigned to non-hydrogen atoms, all unique atom
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171 triplets within \fBMinDistance\fR and \fBMaxDistance\fR are identified and counted. An atom triplet
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172 identifier is generated for each unique atom triplet; the format of atom triplet identifier is:
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173 .PP
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174 .Vb 1
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175 \& <ATx>\-Dyz\-<ATy>\-Dxz\-<ATz>\-Dxy
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176 \&
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177 \& ATx, ATy, ATz: Atom types assigned to atom x, atom y, and atom z
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178 \& Dxy: Distance between atom x and atom y
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179 \& Dxz: Distance between atom x and atom z
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180 \& Dyz: Distance between atom y and atom z
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181 \&
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182 \& where <AT1>\-D23 <= <AT2>\-D13 <= <AT3>\-D12
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183 .Ve
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184 .PP
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185 The atom triplet identifiers for all unique atom triplets corresponding to non-hydrogen atoms constitute
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186 topological atom triplets fingerprints of the molecule.
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187 .PP
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188 The current release of MayaChemTools generates the following types of topological atom triplets
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189 fingerprints vector strings:
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190 .PP
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191 .Vb 7
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192 \& FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
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193 \& inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
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194 \& .BO1.H3\-D1\-C.X1.BO1.H3\-D1\-C.X3.BO3.H1\-D2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D1
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195 \& 0\-C.X3.BO4\-D9 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D3\-N.X3.BO3\-D4 C.X1.BO1.H3\-D1
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196 \& \-C.X2.BO2.H2\-D4\-C.X2.BO2.H2\-D5 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D6\-C.X3....;
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197 \& 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2
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198 \& 2 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8...
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199 \&
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200 \& FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
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201 \& inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesPairsString
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202 \& ;C.X1.BO1.H3\-D1\-C.X1.BO1.H3\-D1\-C.X3.BO3.H1\-D2 1 C.X1.BO1.H3\-D1\-C.X2.BO
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203 \& 2.H2\-D10\-C.X3.BO4\-D9 2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D3\-N.X3.BO3\-D4 2 C.X
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204 \& 1.BO1.H3\-D1\-C.X2.BO2.H2\-D4\-C.X2.BO2.H2\-D5 2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2
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205 \& \-D6\-C.X3.BO3.H1\-D5 2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D6\-C.X3.BO3.H1\-D7 2...
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206 \&
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207 \& FingerprintsVector;TopologicalAtomTriplets:DREIDINGAtomTypes:MinDistan
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208 \& ce1:MaxDistance10;2377;NumericalValues;IDsAndValuesString;C_2\-D1\-C_2\-D
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209 \& 9\-C_3\-D10 C_2\-D1\-C_2\-D9\-C_R\-D10 C_2\-D1\-C_3\-D1\-C_3\-D2 C_2\-D1\-C_3\-D10\-C_
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210 \& 3\-D9 C_2\-D1\-C_3\-D2\-C_3\-D3 C_2\-D1\-C_3\-D2\-C_R\-D3 C_2\-D1\-C_3\-D3\-C_3\-D4 C_
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211 \& 2\-D1\-C_3\-D3\-N_R\-D4 C_2\-D1\-C_3\-D3\-O_3\-D2 C_2\-D1\-C_3\-D4\-C_3\-D5 C_2\-D...;
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212 \& 1 1 1 2 1 1 3 1 1 2 2 1 1 1 1 1 1 1 1 2 1 3 4 5 1 1 6 4 2 2 3 1 1 1 2
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213 \& 2 1 2 1 1 2 2 2 1 2 1 2 1 1 3 3 2 6 4 2 1 1 1 2 2 1 1 1 1 1 1 1 1 1...
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214 \&
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215 \& FingerprintsVector;TopologicalAtomTriplets:EStateAtomTypes:MinDistance
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216 \& 1:MaxDistance10;3298;NumericalValues;IDsAndValuesString;aaCH\-D1\-aaCH\-D
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217 \& 1\-aaCH\-D2 aaCH\-D1\-aaCH\-D1\-aasC\-D2 aaCH\-D1\-aaCH\-D10\-aaCH\-D9 aaCH\-D1\-aaC
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218 \& H\-D10\-aasC\-D9 aaCH\-D1\-aaCH\-D2\-aaCH\-D3 aaCH\-D1\-aaCH\-D2\-aasC\-D1 aaCH\-D1\-
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219 \& aaCH\-D2\-aasC\-D3 aaCH\-D1\-aaCH\-D3\-aasC\-D2 aaCH\-D1\-aaCH\-D4\-aasC\-D5 aa...;
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220 \& 6 4 24 4 16 8 8 4 8 8 8 12 10 14 4 16 24 4 12 2 2 4 1 10 2 2 15 2 2 2
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221 \& 2 2 2 14 4 2 2 2 2 1 2 10 2 2 4 1 2 4 8 3 3 3 4 6 4 2 2 3 3 1 1 1 2 1
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222 \& 2 2 4 2 3 2 1 2 4 5 3 2 2 1 2 4 3 2 8 12 6 2 2 4 4 7 1 4 2 4 2 2 2 ...
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223 \&
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224 \& FingerprintsVector;TopologicalAtomTriplets:FunctionalClassAtomTypes:Mi
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225 \& nDistance1:MaxDistance10;2182;NumericalValues;IDsAndValuesString;Ar\-D1
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226 \& \-Ar\-D1\-Ar\-D2 Ar\-D1\-Ar\-D1\-Ar.HBA\-D2 Ar\-D1\-Ar\-D10\-Ar\-D9 Ar\-D1\-Ar\-D10\-Hal
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227 \& \-D9 Ar\-D1\-Ar\-D2\-Ar\-D2 Ar\-D1\-Ar\-D2\-Ar\-D3 Ar\-D1\-Ar\-D2\-Ar.HBA\-D1 Ar\-D1\-Ar
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228 \& \-D2\-Ar.HBA\-D2 Ar\-D1\-Ar\-D2\-Ar.HBA\-D3 Ar\-D1\-Ar\-D2\-HBD\-D1 Ar\-D1\-Ar\-D2...;
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229 \& 27 1 32 2 2 63 3 2 1 2 1 2 3 1 1 40 3 1 2 2 2 2 4 2 2 47 4 2 2 1 2 1 5
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230 \& 2 2 51 4 3 1 3 1 9 1 1 50 3 3 4 1 9 50 2 2 3 3 5 45 1 1 1 2 1 2 2 3 3
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231 \& 4 4 3 2 1 1 3 4 5 5 3 1 2 3 2 3 5 7 2 7 3 7 1 1 2 2 2 2 3 1 4 3 1 2...
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232 \&
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233 \& FingerprintsVector;TopologicalAtomTriplets:MMFF94AtomTypes:MinDistance
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234 \& 1:MaxDistance10;2966;NumericalValues;IDsAndValuesString;C5A\-D1\-C5A\-D1\-
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235 \& N5\-D2 C5A\-D1\-C5A\-D2\-C5B\-D2 C5A\-D1\-C5A\-D3\-CB\-D2 C5A\-D1\-C5A\-D3\-CR\-D2 C5A
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236 \& \-D1\-C5B\-D1\-C5B\-D2 C5A\-D1\-C5B\-D2\-C=ON\-D1 C5A\-D1\-C5B\-D2\-CB\-D1 C5A\-D1\-C5B
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237 \& \-D3\-C=ON\-D2 C5A\-D1\-C5B\-D3\-CB\-D2 C5A\-D1\-C=ON\-D3\-NC=O\-D2 C5A\-D1\-C=ON\-D3\-
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238 \& O=CN\-D2 C5A\-D1\-C=ON\-D4\-NC=O\-D3 C5A\-D1\-C=ON\-D4\-O=CN\-D3 C5A\-D1\-CB\-D1\-...
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239 \&
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240 \& FingerprintsVector;TopologicalAtomTriplets:SLogPAtomTypes:MinDistance1
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241 \& :MaxDistance10;3710;NumericalValues;IDsAndValuesString;C1\-D1\-C1\-D1\-C11
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242 \& \-D2 C1\-D1\-C1\-D1\-CS\-D2 C1\-D1\-C1\-D10\-C5\-D9 C1\-D1\-C1\-D3\-C10\-D2 C1\-D1\-C1\-D
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243 \& 3\-C5\-D2 C1\-D1\-C1\-D3\-CS\-D2 C1\-D1\-C1\-D3\-CS\-D4 C1\-D1\-C1\-D4\-C10\-D5 C1\-D1\-C
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244 \& 1\-D4\-C11\-D5 C1\-D1\-C1\-D5\-C10\-D4 C1\-D1\-C1\-D5\-C5\-D4 C1\-D1\-C1\-D6\-C11\-D7 C1
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245 \& \-D1\-C1\-D6\-CS\-D5 C1\-D1\-C1\-D6\-CS\-D7 C1\-D1\-C1\-D8\-C11\-D9 C1\-D1\-C1\-D8\-CS...
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246 \&
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247 \& FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1
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248 \& :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2\-D1\-C.2\-D9\-C
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249 \& .3\-D10 C.2\-D1\-C.2\-D9\-C.ar\-D10 C.2\-D1\-C.3\-D1\-C.3\-D2 C.2\-D1\-C.3\-D10\-C.3\-
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250 \& D9 C.2\-D1\-C.3\-D2\-C.3\-D3 C.2\-D1\-C.3\-D2\-C.ar\-D3 C.2\-D1\-C.3\-D3\-C.3\-D4 C.2
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251 \& \-D1\-C.3\-D3\-N.ar\-D4 C.2\-D1\-C.3\-D3\-O.3\-D2 C.2\-D1\-C.3\-D4\-C.3\-D5 C.2\-D1\-C.
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252 \& 3\-D5\-C.3\-D6 C.2\-D1\-C.3\-D5\-O.3\-D4 C.2\-D1\-C.3\-D6\-C.3\-D7 C.2\-D1\-C.3\-D7...
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253 \&
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254 \& FingerprintsVector;TopologicalAtomTriplets:TPSAAtomTypes:MinDistance1:
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255 \& MaxDistance10;1007;NumericalValues;IDsAndValuesString;N21\-D1\-N7\-D3\-Non
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256 \& e\-D4 N21\-D1\-N7\-D5\-None\-D4 N21\-D1\-None\-D1\-None\-D2 N21\-D1\-None\-D2\-None\-D
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257 \& 2 N21\-D1\-None\-D2\-None\-D3 N21\-D1\-None\-D3\-None\-D4 N21\-D1\-None\-D4\-None\-D5
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258 \& N21\-D1\-None\-D4\-O3\-D3 N21\-D1\-None\-D4\-O4\-D3 N21\-D1\-None\-D5\-None\-D6 N21\-
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259 \& D1\-None\-D6\-None\-D7 N21\-D1\-None\-D6\-O4\-D5 N21\-D1\-None\-D7\-None\-D8 N21\-...
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260 \&
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261 \& FingerprintsVector;TopologicalAtomTriplets:UFFAtomTypes:MinDistance1:M
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262 \& axDistance10;2377;NumericalValues;IDsAndValuesString;C_2\-D1\-C_2\-D9\-C_3
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263 \& \-D10 C_2\-D1\-C_2\-D9\-C_R\-D10 C_2\-D1\-C_3\-D1\-C_3\-D2 C_2\-D1\-C_3\-D10\-C_3\-D9
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264 \& C_2\-D1\-C_3\-D2\-C_3\-D3 C_2\-D1\-C_3\-D2\-C_R\-D3 C_2\-D1\-C_3\-D3\-C_3\-D4 C_2\-D1\-
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265 \& C_3\-D3\-N_R\-D4 C_2\-D1\-C_3\-D3\-O_3\-D2 C_2\-D1\-C_3\-D4\-C_3\-D5 C_2\-D1\-C_3\-D5\-
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266 \& C_3\-D6 C_2\-D1\-C_3\-D5\-O_3\-D4 C_2\-D1\-C_3\-D6\-C_3\-D7 C_2\-D1\-C_3\-D7\-C_3\-...
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267 .Ve
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268 .SS "\s-1METHODS\s0"
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269 .IX Subsection "METHODS"
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270 .IP "\fBnew\fR" 4
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271 .IX Item "new"
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272 .Vb 2
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273 \& $NewTopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints(
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274 \& %NamesAndValues);
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275 .Ve
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276 .Sp
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277 Using specified \fITopologicalAtomTripletsFingerprints\fR property names and values hash, \fBnew\fR
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278 method creates a new object and returns a reference to newly created \fBTopologicalAtomTripletsFingerprints\fR
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279 object. By default, the following properties are initialized:
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280 .Sp
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281 .Vb 8
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282 \& Molecule = \*(Aq\*(Aq
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283 \& Type = \*(AqTopologicalAtomTriplets\*(Aq
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284 \& MinDistance = 1
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285 \& MaxDistance = 10
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286 \& UseTriangleInequality = 1
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287 \& AtomIdentifierType = \*(Aq\*(Aq
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288 \& AtomicInvariantsToUse = [\*(AqAS\*(Aq, \*(AqX\*(Aq, \*(AqBO\*(Aq, \*(AqH\*(Aq, \*(AqFC\*(Aq]
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289 \& FunctionalClassesToUse = [\*(AqHBD\*(Aq, \*(AqHBA\*(Aq, \*(AqPI\*(Aq, \*(AqNI\*(Aq, \*(AqAr\*(Aq, \*(AqHal\*(Aq]
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290 .Ve
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291 .Sp
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292 Examples:
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293 .Sp
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294 .Vb 4
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295 \& $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints(
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296 \& \*(AqMolecule\*(Aq => $Molecule,
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297 \& \*(AqAtomIdentifierType\*(Aq =>
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298 \& \*(AqAtomicInvariantsAtomTypes\*(Aq);
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299 \&
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300 \& $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints(
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301 \& \*(AqMolecule\*(Aq => $Molecule,
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302 \& \*(AqMinDistance\*(Aq => 1,
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303 \& \*(AqMaxDistance\*(Aq => 10,
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304 \& \*(AqAtomIdentifierType\*(Aq =>
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305 \& \*(AqAtomicInvariantsAtomTypes\*(Aq,
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306 \& \*(AqAtomicInvariantsToUse\*(Aq =>
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307 \& [\*(AqAS\*(Aq, \*(AqX\*(Aq, \*(AqBO\*(Aq, \*(AqH\*(Aq, \*(AqFC\*(Aq] );
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308 \&
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309 \& $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints(
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310 \& \*(AqMolecule\*(Aq => $Molecule,
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311 \& \*(AqAtomIdentifierType\*(Aq =>
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312 \& \*(AqDREIDINGAtomTypes\*(Aq);
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313 \&
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314 \& $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints(
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315 \& \*(AqMolecule\*(Aq => $Molecule,
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316 \& \*(AqAtomIdentifierType\*(Aq =>
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317 \& \*(AqMMFF94AtomTypes\*(Aq);
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318 \&
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319 \& $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints(
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320 \& \*(AqMolecule\*(Aq => $Molecule,
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321 \& \*(AqAtomIdentifierType\*(Aq =>
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322 \& \*(AqTPSAAtomTypes\*(Aq);
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323 \&
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324 \& $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints(
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325 \& \*(AqMolecule\*(Aq => $Molecule,
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326 \& \*(AqMinDistance\*(Aq => 1,
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327 \& \*(AqMaxDistance\*(Aq => 10,
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328 \& \*(AqAtomIdentifierType\*(Aq =>
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329 \& \*(AqFunctionalClassAtomTypes\*(Aq,
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330 \& \*(AqFunctionalClassesToUse\*(Aq =>
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331 \& [\*(AqHBD\*(Aq, \*(AqHBA\*(Aq, \*(AqPI\*(Aq, \*(AqNI\*(Aq, \*(AqAr\*(Aq, \*(AqHal\*(Aq]);
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332 \&
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333 \& $TopologicalAtomTripletsFingerprints\->GenerateFingerprints();
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334 \& print "$TopologicalAtomTripletsFingerprints\en";
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335 .Ve
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336 .IP "\fBGetDescription\fR" 4
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337 .IX Item "GetDescription"
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338 .Vb 1
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339 \& $Return = $TopologicalAtomTripletsFingerprints\->GetDescription();
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340 .Ve
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341 .Sp
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342 Returns a string containing description of topological atom triplets fingerprints.
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343 .IP "\fBGenerateFingerprints\fR" 4
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344 .IX Item "GenerateFingerprints"
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345 .Vb 1
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346 \& $TopologicalAtomTripletsFingerprints\->GenerateFingerprints();
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347 .Ve
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348 .Sp
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349 Generates topological atom triplets fingerprints and returns \fITopologicalAtomTripletsFingerprints\fR.
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350 .IP "\fBGetAtomTripletIDs\fR" 4
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351 .IX Item "GetAtomTripletIDs"
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352 .Vb 2
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353 \& $AtomTripletIDsRef = $TopologicalAtomTripletsFingerprints\->GetAtomTripletIDs();
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354 \& @AtomTripletIDs = $TopologicalAtomTripletsFingerprints\->GetAtomTripletIDs();
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355 .Ve
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356 .Sp
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357 Returns atom triplet IDs corresponding to atom triplets count values in topological atom triplets
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358 fingerprints vector as an array or reference to an array.
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359 .IP "\fBSetAtomIdentifierType\fR" 4
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360 .IX Item "SetAtomIdentifierType"
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361 .Vb 1
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362 \& $TopologicalAtomTripletsFingerprints\->SetAtomIdentifierType($IdentifierType);
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363 .Ve
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364 .Sp
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365 Sets atom \fIIdentifierType\fR to use during atom triplets fingerprints generation and
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366 returns \fITopologicalAtomTripletsFingerprints\fR.
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367 .Sp
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368 Possible values: \fIAtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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369 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
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370 TPSAAtomTypes, UFFAtomTypes\fR.
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371 .IP "\fBSetAtomicInvariantsToUse\fR" 4
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372 .IX Item "SetAtomicInvariantsToUse"
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373 .Vb 2
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374 \& $TopologicalAtomTripletsFingerprints\->SetAtomicInvariantsToUse($ValuesRef);
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375 \& $TopologicalAtomTripletsFingerprints\->SetAtomicInvariantsToUse(@Values);
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376 .Ve
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377 .Sp
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378 Sets atomic invariants to use during \fIAtomicInvariantsAtomTypes\fR value of \fIAtomIdentifierType\fR
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379 for topological atom triplets fingerprints generation and returns \fITopologicalAtomTripletsFingerprints\fR.
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380 .Sp
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381 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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382 H, Ar, \s-1RA\s0, \s-1FC\s0, \s-1MN\s0, \s-1SM\s0\fR. Default value: \fI\s-1AS\s0,X,BO,H,FC\fR.
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383 .Sp
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384 The atomic invariants abbreviations correspond to:
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385 .Sp
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386 .Vb 1
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387 \& AS = Atom symbol corresponding to element symbol
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388 \&
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389 \& X<n> = Number of non\-hydrogen atom neighbors or heavy atoms
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390 \& BO<n> = Sum of bond orders to non\-hydrogen atom neighbors or heavy atoms
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391 \& LBO<n> = Largest bond order of non\-hydrogen atom neighbors or heavy atoms
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392 \& SB<n> = Number of single bonds to non\-hydrogen atom neighbors or heavy atoms
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393 \& DB<n> = Number of double bonds to non\-hydrogen atom neighbors or heavy atoms
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394 \& TB<n> = Number of triple bonds to non\-hydrogen atom neighbors or heavy atoms
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395 \& H<n> = Number of implicit and explicit hydrogens for atom
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396 \& Ar = Aromatic annotation indicating whether atom is aromatic
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397 \& RA = Ring atom annotation indicating whether atom is a ring
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398 \& FC<+n/\-n> = Formal charge assigned to atom
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399 \& MN<n> = Mass number indicating isotope other than most abundant isotope
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400 \& SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
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401 \& 3 (triplet)
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402 .Ve
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403 .Sp
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404 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:
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405 .Sp
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406 .Vb 1
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407 \& 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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408 .Ve
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409 .Sp
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410 Except for \s-1AS\s0 which is a required atomic invariant in atom types, all other atomic invariants are
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411 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.
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412 .Sp
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413 In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
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414 are also allowed:
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415 .Sp
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416 .Vb 12
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417 \& X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
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418 \& BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
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419 \& LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
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420 \& SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
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421 \& DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
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422 \& TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
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423 \& H : NumOfImplicitAndExplicitHydrogens
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424 \& Ar : Aromatic
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425 \& RA : RingAtom
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426 \& FC : FormalCharge
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427 \& MN : MassNumber
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428 \& SM : SpinMultiplicity
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429 .Ve
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430 .Sp
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431 \&\fIAtomTypes::AtomicInvariantsAtomTypes\fR module is used to assign atomic invariant
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432 atom types.
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433 .IP "\fBSetFunctionalClassesToUse\fR" 4
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434 .IX Item "SetFunctionalClassesToUse"
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435 .Vb 2
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436 \& $TopologicalTripletsFingerprints\->SetFunctionalClassesToUse($ValuesRef);
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437 \& $TopologicalTripletsFingerprints\->SetFunctionalClassesToUse(@Values);
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438 .Ve
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439 .Sp
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440 Sets functional classes invariants to use during \fIFunctionalClassAtomTypes\fR value of \fIAtomIdentifierType\fR
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441 for topological atom triplets fingerprints generation and returns \fITopologicalAtomTripletsFingerprints\fR.
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442 .Sp
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443 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.
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444 Default value [ Ref 24 ]: \fI\s-1HBD\s0,HBA,PI,NI,Ar,Hal\fR.
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445 .Sp
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446 The functional class abbreviations correspond to:
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447 .Sp
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448 .Vb 9
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449 \& HBD: HydrogenBondDonor
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450 \& HBA: HydrogenBondAcceptor
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451 \& PI : PositivelyIonizable
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452 \& NI : NegativelyIonizable
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453 \& Ar : Aromatic
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454 \& Hal : Halogen
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455 \& H : Hydrophobic
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456 \& RA : RingAtom
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457 \& CA : ChainAtom
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458 \&
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459 \& Functional class atom type specification for an atom corresponds to:
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460 \&
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461 \& Ar.CA.H.HBA.HBD.Hal.NI.PI.RA or None
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462 .Ve
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463 .Sp
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464 \&\fIAtomTypes::FunctionalClassAtomTypes\fR module is used to assign functional class atom
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465 types. It uses following definitions [ Ref 60\-61, Ref 65\-66 ]:
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466 .Sp
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467 .Vb 4
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468 \& HydrogenBondDonor: NH, NH2, OH
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469 \& HydrogenBondAcceptor: N[!H], O
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470 \& PositivelyIonizable: +, NH2
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471 \& NegativelyIonizable: \-, C(=O)OH, S(=O)OH, P(=O)OH
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472 .Ve
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473 .IP "\fBSetMaxDistance\fR" 4
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474 .IX Item "SetMaxDistance"
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475 .Vb 1
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476 \& $TopologicalAtomTripletsFingerprints\->SetMaxDistance($Distance);
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477 .Ve
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478 .Sp
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479 Sets maximum distance to use during topological atom triplets fingerprints generation and
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480 returns \fITopologicalAtomTripletsFingerprints\fR.
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481 .IP "\fBSetMinDistance\fR" 4
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482 .IX Item "SetMinDistance"
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483 .Vb 1
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484 \& $TopologicalAtomTripletsFingerprints\->SetMinDistance($Distance);
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485 .Ve
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486 .Sp
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487 Sets minimum distance to use during topological atom triplets fingerprints generation and
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488 returns \fITopologicalAtomTripletsFingerprints\fR.
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489 .IP "\fBStringifyTopologicalAtomTripletsFingerprints\fR" 4
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490 .IX Item "StringifyTopologicalAtomTripletsFingerprints"
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491 .Vb 2
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492 \& $String = $TopologicalAtomTripletsFingerprints\->
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493 \& StringifyTopologicalAtomTripletsFingerprints();
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494 .Ve
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495 .Sp
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496 Returns a string containing information about \fITopologicalAtomTripletsFingerprints\fR object.
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497 .SH "AUTHOR"
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498 .IX Header "AUTHOR"
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499 Manish Sud <msud@san.rr.com>
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500 .SH "SEE ALSO"
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501 .IX Header "SEE ALSO"
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502 Fingerprints.pm, FingerprintsStringUtil.pm, AtomNeighborhoodsFingerprints.pm,
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503 AtomTypesFingerprints.pm, EStateIndiciesFingerprints.pm, ExtendedConnectivityFingerprints.pm,
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504 MACCSKeys.pm, PathLengthFingerprints.pm, TopologicalAtomPairsFingerprints.pm,
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505 TopologicalAtomTorsionsFingerprints.pm, TopologicalPharmacophoreAtomPairsFingerprints.pm,
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506 TopologicalPharmacophoreAtomTripletsFingerprints.pm
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507 .SH "COPYRIGHT"
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508 .IX Header "COPYRIGHT"
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509 Copyright (C) 2015 Manish Sud. All rights reserved.
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510 .PP
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511 This file is part of MayaChemTools.
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512 .PP
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513 MayaChemTools is free software; you can redistribute it and/or modify it under
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514 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
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515 Software Foundation; either version 3 of the License, or (at your option)
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516 any later version.
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