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124 .\" ========================================================================
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125 .\"
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126 .IX Title "ATOMNEIGHBORHOODSFINGERPRINTS 1"
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127 .TH ATOMNEIGHBORHOODSFINGERPRINTS 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 AtomNeighborhoodsFingerprints
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134 .SH "SYNOPSIS"
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135 .IX Header "SYNOPSIS"
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136 use Fingerprints::AtomNeighborhoodsFingerprints;
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137 .PP
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138 use Fingerprints::AtomNeighborhoodsFingerprints qw(:all);
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139 .SH "DESCRIPTION"
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140 .IX Header "DESCRIPTION"
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141 \&\fBAtomNeighborhoodsFingerprints\fR [ Ref 53\-56, Ref 73 ] 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, SetMaxNeighborhoodRadius,
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145 SetMinNeighborhoodRadius, StringifyAtomNeighborhoodsFingerprints
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146 .PP
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147 \&\fBAtomNeighborhoodsFingerprints\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 \fBAtomNeighborhoodsFingerprints\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 \fBAtomNeighborhoodsFingerprints\fR
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159 corresponding to following \fBAtomIdentifierTypes\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 sucb as \fBAtomicInvariantsToUse\fR and \fBFunctionalClassesToUse\fR, initial atom types are
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169 assigned to all non-hydrogen atoms in a molecule. Using atom neighborhoods
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170 around each non-hydrogen central atom corresponding to radii between specified values
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171 \&\fBMinNeighborhoodRadius\fR and \fBMaxNeighborhoodRadius\fR, unique atom types at each radii
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172 level are counted and an atom neighborhood identifier is generated.
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173 .PP
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174 The format of an atom neighborhood identifier around a central non-hydrogen atom at a
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175 specific radius is:
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176 .PP
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177 .Vb 1
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178 \& NR<n>\-<AtomType>\-ATC<n>
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179 \&
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180 \& NR: Neighborhood radius
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181 \& AtomType: Assigned atom type
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182 \& ATC: Atom type count
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183 .Ve
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184 .PP
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185 The atom neighborhood identifier for non-hydrogen central atom corresponding to all specified radii
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186 is generated by concatenating neighborhood identifiers at each radii by colon as a delimiter:
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187 .PP
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188 .Vb 1
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189 \& NR<n>\-<AtomType>\-ATC<n>:NR<n>\-<AtomType>\-ATC<n>:...
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190 .Ve
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191 .PP
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192 The atom neighborhood identifiers for all non-hydrogen central atoms at all specified radii are
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193 concatenated using space as a delimiter and constitute atom neighborhood fingerprint of the molecule.
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194 .PP
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195 The current release of MayaChemTools generates the following types of atom neighborhoods
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196 fingerprints vector strings:
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197 .PP
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198 .Vb 6
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199 \& FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi
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200 \& us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0\-C.X1.BO1.H3\-AT
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201 \& C1:NR1\-C.X3.BO3.H1\-ATC1:NR2\-C.X1.BO1.H3\-ATC1:NR2\-C.X3.BO4\-ATC1 NR0\-C.X
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202 \& 1.BO1.H3\-ATC1:NR1\-C.X3.BO3.H1\-ATC1:NR2\-C.X1.BO1.H3\-ATC1:NR2\-C.X3.BO4\-A
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203 \& TC1 NR0\-C.X2.BO2.H2\-ATC1:NR1\-C.X2.BO2.H2\-ATC1:NR1\-C.X3.BO3.H1\-ATC1:NR2
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204 \& \-C.X2.BO2.H2\-ATC1:NR2\-N.X3.BO3\-ATC1:NR2\-O.X1.BO1.H1\-ATC1 NR0\-C.X2.B...
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205 \&
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206 \& FingerprintsVector;AtomNeighborhoods:DREIDINGAtomTypes:MinRadius0:MaxR
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207 \& adius2;41;AlphaNumericalValues;ValuesString;NR0\-C_2\-ATC1:NR1\-C_3\-ATC1:
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208 \& NR1\-O_2\-ATC1:NR1\-O_3\-ATC1:NR2\-C_3\-ATC1 NR0\-C_2\-ATC1:NR1\-C_R\-ATC1:NR1\-N
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209 \& _3\-ATC1:NR1\-O_2\-ATC1:NR2\-C_R\-ATC3 NR0\-C_3\-ATC1:NR1\-C_2\-ATC1:NR1\-C_3\-AT
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210 \& C1:NR2\-C_3\-ATC1:NR2\-O_2\-ATC1:NR2\-O_3\-ATC2 NR0\-C_3\-ATC1:NR1\-C_3\-ATC1:NR
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211 \& 1\-N_R\-ATC1:NR2\-C_3\-ATC1:NR2\-C_R\-ATC2 NR0\-C_3\-ATC1:NR1\-C_3\-ATC1:NR2\-...
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212 \&
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213 \& FingerprintsVector;AtomNeighborhoods:EStateAtomTypes:MinRadius0:MaxRad
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214 \& ius2;41;AlphaNumericalValues;ValuesString;NR0\-aaCH\-ATC1:NR1\-aaCH\-ATC1:
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215 \& NR1\-aasC\-ATC1:NR2\-aaCH\-ATC1:NR2\-aasC\-ATC1:NR2\-sF\-ATC1 NR0\-aaCH\-ATC1:NR
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216 \& 1\-aaCH\-ATC1:NR1\-aasC\-ATC1:NR2\-aaCH\-ATC1:NR2\-aasC\-ATC1:NR2\-sF\-ATC1 NR0\-
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217 \& aaCH\-ATC1:NR1\-aaCH\-ATC1:NR1\-aasC\-ATC1:NR2\-aaCH\-ATC1:NR2\-aasC\-ATC2 NR0\-
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218 \& aaCH\-ATC1:NR1\-aaCH\-ATC1:NR1\-aasC\-ATC1:NR2\-aaCH\-ATC1:NR2\-aasC\-ATC2 N...
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219 \&
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220 \& FingerprintsVector;AtomNeighborhoods:FunctionalClassAtomTypes:MinRadiu
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221 \& s0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0\-Ar\-ATC1:NR1\-Ar\-
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222 \& ATC1:NR1\-Ar.HBA\-ATC1:NR1\-None\-ATC1:NR2\-Ar\-ATC2:NR2\-None\-ATC4 NR0\-Ar\-AT
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223 \& C1:NR1\-Ar\-ATC2:NR1\-Ar.HBA\-ATC1:NR2\-Ar\-ATC5:NR2\-None\-ATC1 NR0\-Ar\-ATC1:N
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224 \& R1\-Ar\-ATC2:NR1\-HBD\-ATC1:NR2\-Ar\-ATC2:NR2\-None\-ATC1 NR0\-Ar\-ATC1:NR1\-Ar\-A
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225 \& TC2:NR1\-Hal\-ATC1:NR2\-Ar\-ATC2 NR0\-Ar\-ATC1:NR1\-Ar\-ATC2:NR1\-None\-ATC1:...
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226 \&
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227 \& FingerprintsVector;AtomNeighborhoods:MMFF94AtomTypes:MinRadius0:MaxRad
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228 \& ius2;41;AlphaNumericalValues;ValuesString;NR0\-C5A\-ATC1:NR1\-C5B\-ATC1:NR
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229 \& 1\-CB\-ATC1:NR1\-N5\-ATC1:NR2\-C5A\-ATC1:NR2\-C5B\-ATC1:NR2\-CB\-ATC3:NR2\-CR\-ATC
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230 \& 1 NR0\-C5A\-ATC1:NR1\-C5B\-ATC1:NR1\-CR\-ATC1:NR1\-N5\-ATC1:NR2\-C5A\-ATC1:NR2\-C
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231 \& 5B\-ATC1:NR2\-C=ON\-ATC1:NR2\-CR\-ATC3 NR0\-C5B\-ATC1:NR1\-C5A\-ATC1:NR1\-C5B\-AT
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232 \& C1:NR1\-C=ON\-ATC1:NR2\-C5A\-ATC1:NR2\-CB\-ATC1:NR2\-CR\-ATC1:NR2\-N5\-ATC1:N...
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233 \&
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234 \& FingerprintsVector;AtomNeighborhoods:SLogPAtomTypes:MinRadius0:MaxRadi
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235 \& us2;41;AlphaNumericalValues;ValuesString;NR0\-C1\-ATC1:NR1\-C10\-ATC1:NR1\-
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236 \& CS\-ATC1:NR2\-C1\-ATC1:NR2\-N11\-ATC1:NR2\-O2\-ATC1 NR0\-C1\-ATC1:NR1\-C11\-ATC1:
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237 \& NR2\-C1\-ATC1:NR2\-C21\-ATC1 NR0\-C1\-ATC1:NR1\-C11\-ATC1:NR2\-C1\-ATC1:NR2\-C21\-
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238 \& ATC1 NR0\-C1\-ATC1:NR1\-C5\-ATC1:NR1\-CS\-ATC1:NR2\-C1\-ATC1:NR2\-O2\-ATC2:NR2\-O
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239 \& 9\-ATC1 NR0\-C1\-ATC1:NR1\-CS\-ATC2:NR2\-C1\-ATC2:NR2\-O2\-ATC2 NR0\-C10\-ATC1...
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240 \&
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241 \& FingerprintsVector;AtomNeighborhoods:SYBYLAtomTypes:MinRadius0:MaxRadi
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242 \& us2;41;AlphaNumericalValues;ValuesString;NR0\-C.2\-ATC1:NR1\-C.3\-ATC1:NR1
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243 \& \-O.co2\-ATC2:NR2\-C.3\-ATC1 NR0\-C.2\-ATC1:NR1\-C.ar\-ATC1:NR1\-N.am\-ATC1:NR1\-
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244 \& O.2\-ATC1:NR2\-C.ar\-ATC3 NR0\-C.3\-ATC1:NR1\-C.2\-ATC1:NR1\-C.3\-ATC1:NR2\-C.3\-
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245 \& ATC1:NR2\-O.3\-ATC1:NR2\-O.co2\-ATC2 NR0\-C.3\-ATC1:NR1\-C.3\-ATC1:NR1\-N.ar\-AT
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246 \& C1:NR2\-C.3\-ATC1:NR2\-C.ar\-ATC2 NR0\-C.3\-ATC1:NR1\-C.3\-ATC1:NR2\-C.3\-ATC...
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247 \&
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248 \& FingerprintsVector;AtomNeighborhoods:TPSAAtomTypes:MinRadius0:MaxRadiu
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249 \& s2;41;AlphaNumericalValues;ValuesString;NR0\-N21\-ATC1:NR1\-None\-ATC3:NR2
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250 \& \-None\-ATC5 NR0\-N7\-ATC1:NR1\-None\-ATC2:NR2\-None\-ATC3:NR2\-O3\-ATC1 NR0\-Non
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251 \& e\-ATC1:NR1\-N21\-ATC1:NR1\-None\-ATC1:NR2\-None\-ATC3 NR0\-None\-ATC1:NR1\-N21\-
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252 \& ATC1:NR1\-None\-ATC2:NR2\-None\-ATC6 NR0\-None\-ATC1:NR1\-N21\-ATC1:NR1\-None\-A
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253 \& TC2:NR2\-None\-ATC6 NR0\-None\-ATC1:NR1\-N7\-ATC1:NR1\-None\-ATC1:NR1\-O3\-AT...
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254 \&
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255 \& FingerprintsVector;AtomNeighborhoods:UFFAtomTypes:MinRadius0:MaxRadius
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256 \& 2;41;AlphaNumericalValues;ValuesString;NR0\-C_2\-ATC1:NR1\-C_3\-ATC1:NR1\-O
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257 \& _2\-ATC1:NR1\-O_3\-ATC1:NR2\-C_3\-ATC1 NR0\-C_2\-ATC1:NR1\-C_R\-ATC1:NR1\-N_3\-AT
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258 \& C1:NR1\-O_2\-ATC1:NR2\-C_R\-ATC3 NR0\-C_3\-ATC1:NR1\-C_2\-ATC1:NR1\-C_3\-ATC1:NR
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259 \& 2\-C_3\-ATC1:NR2\-O_2\-ATC1:NR2\-O_3\-ATC2 NR0\-C_3\-ATC1:NR1\-C_3\-ATC1:NR1\-N_R
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260 \& \-ATC1:NR2\-C_3\-ATC1:NR2\-C_R\-ATC2 NR0\-C_3\-ATC1:NR1\-C_3\-ATC1:NR2\-C_3\-A...
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261 .Ve
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262 .SS "\s-1METHODS\s0"
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263 .IX Subsection "METHODS"
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264 .IP "\fBnew\fR" 4
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265 .IX Item "new"
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266 .Vb 2
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267 \& $NewAtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
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268 \& %NamesAndValues);
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269 .Ve
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270 .Sp
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271 Using specified \fIAtomNeighborhoodsFingerprints\fR property names and values hash, \fBnew\fR
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272 method creates a new object and returns a reference to newly created \fBAtomNeighborhoodsFingerprints\fR
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273 object. By default, the following properties are initialized:
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274 .Sp
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275 .Vb 7
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276 \& Molecule = \*(Aq\*(Aq
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277 \& Type = \*(AqAtomNeighborhoods\*(Aq
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278 \& MinNeighborhoodRadius = 0
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279 \& MaxNeighborhoodRadius = 2
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280 \& AtomIdentifierType = \*(Aq\*(Aq
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281 \& AtomicInvariantsToUse = [\*(AqAS\*(Aq, \*(AqX\*(Aq, \*(AqBO\*(Aq, \*(AqH\*(Aq, \*(AqFC\*(Aq, \*(AqMN\*(Aq]
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282 \& FunctionalClassesToUse = [\*(AqHBD\*(Aq, \*(AqHBA\*(Aq, \*(AqPI\*(Aq, \*(AqNI\*(Aq, \*(AqAr\*(Aq, \*(AqHal\*(Aq]
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283 .Ve
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284 .Sp
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285 Examples:
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286 .Sp
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287 .Vb 4
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288 \& $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
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289 \& \*(AqMolecule\*(Aq => $Molecule,
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290 \& \*(AqAtomIdentifierType\*(Aq =>
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291 \& "AtomicInvariantsAtomTypes");
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292 \&
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293 \& $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
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294 \& \*(AqMolecule\*(Aq => $Molecule,
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295 \& \*(AqMinNeighborhoodRadius\*(Aq => 0,
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296 \& \*(AqMaxNeighborhoodRadius\*(Aq => 2,
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297 \& \*(AqAtomIdentifierType\*(Aq =>
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298 \& \*(AqAtomicInvariantsAtomTypes\*(Aq,
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299 \& \*(AqAtomicInvariantsToUse\*(Aq =>
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300 \& [\*(AqAS\*(Aq, \*(AqX\*(Aq, \*(AqBO\*(Aq, \*(AqH\*(Aq, \*(AqFC\*(Aq] );
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301 \&
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302 \& $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
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303 \& \*(AqMolecule\*(Aq => $Molecule,
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304 \& \*(AqAtomIdentifierType\*(Aq =>
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305 \& \*(AqSYBYLAtomTypes\*(Aq);
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306 \&
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307 \& $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
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308 \& \*(AqMolecule\*(Aq => $Molecule,
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309 \& \*(AqAtomIdentifierType\*(Aq =>
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310 \& \*(AqMMFF94AtomTypes\*(Aq);
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311 \&
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312 \& $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
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313 \& \*(AqMolecule\*(Aq => $Molecule,
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314 \& \*(AqAtomIdentifierType\*(Aq =>
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315 \& \*(AqAtomicInvariantsAtomTypes\*(Aq);
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316 \&
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317 \& $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
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318 \& \*(AqMolecule\*(Aq => $Molecule,
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319 \& \*(AqMinNeighborhoodRadius\*(Aq => 0,
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320 \& \*(AqMaxNeighborhoodRadius\*(Aq => 2,
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321 \& \*(AqAtomIdentifierType\*(Aq =>
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322 \& \*(AqFunctionalClassAtomTypes\*(Aq,
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323 \& \*(AqFunctionalClassesToUse\*(Aq =>
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324 \& [\*(AqHBD\*(Aq, \*(AqHBA\*(Aq, \*(AqPI\*(Aq, \*(AqNI\*(Aq, \*(AqAr\*(Aq, \*(AqHal\*(Aq] );
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325 \&
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326 \& $AtomNeighborhoodsFingerprints\->GenerateFingerprints();
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327 \& print "$AtomNeighborhoodsFingerprints\en";
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328 .Ve
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329 .IP "\fBGenerateFingerprints\fR" 4
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330 .IX Item "GenerateFingerprints"
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331 .Vb 1
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332 \& $AtomNeighborhoodsFingerprints\->GenerateFingerprints();
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333 .Ve
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334 .Sp
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335 Generates atom neighborhood fingerprints and returns \fIAtomNeighborhoodsFingerprints\fR.
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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 \& $Description = $AtomNeighborhoodsFingerprints\->GetDescription();
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340 .Ve
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341 .Sp
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342 Returns a string containing description of atom neighborhood fingerprints.
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343 .IP "\fBSetAtomIdentifierType\fR" 4
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344 .IX Item "SetAtomIdentifierType"
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345 .Vb 1
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346 \& $AtomNeighborhoodsFingerprints\->SetAtomIdentifierType($IdentifierType);
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347 .Ve
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348 .Sp
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349 Sets atom \fIIdentifierType\fR to use during atom neighborhood fingerprints generation and
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350 returns \fIAtomNeighborhoodsFingerprints\fR.
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351 .Sp
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352 Possible values: \fIAtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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353 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
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354 TPSAAtomTypes, UFFAtomTypes\fR.
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355 .IP "\fBSetAtomicInvariantsToUse\fR" 4
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356 .IX Item "SetAtomicInvariantsToUse"
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357 .Vb 2
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358 \& $AtomNeighborhoodsFingerprints\->SetAtomicInvariantsToUse($ValuesRef);
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359 \& $AtomNeighborhoodsFingerprints\->SetAtomicInvariantsToUse(@Values);
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360 .Ve
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361 .Sp
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362 Sets atomic invariants to use during \fIAtomicInvariantsAtomTypes\fR value of \fIAtomIdentifierType\fR
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363 for atom neighborhood fingerprints generation and returns \fIAtomNeighborhoodsFingerprints\fR.
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364 .Sp
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365 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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366 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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367 .Sp
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368 The atomic invariants abbreviations correspond to:
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369 .Sp
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370 .Vb 1
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371 \& AS = Atom symbol corresponding to element symbol
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372 \&
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373 \& X<n> = Number of non\-hydrogen atom neighbors or heavy atoms
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374 \& BO<n> = Sum of bond orders to non\-hydrogen atom neighbors or heavy atoms
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375 \& LBO<n> = Largest bond order of non\-hydrogen atom neighbors or heavy atoms
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376 \& SB<n> = Number of single bonds to non\-hydrogen atom neighbors or heavy atoms
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377 \& DB<n> = Number of double bonds to non\-hydrogen atom neighbors or heavy atoms
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378 \& TB<n> = Number of triple bonds to non\-hydrogen atom neighbors or heavy atoms
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379 \& H<n> = Number of implicit and explicit hydrogens for atom
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380 \& Ar = Aromatic annotation indicating whether atom is aromatic
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381 \& RA = Ring atom annotation indicating whether atom is a ring
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382 \& FC<+n/\-n> = Formal charge assigned to atom
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383 \& MN<n> = Mass number indicating isotope other than most abundant isotope
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384 \& SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
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385 \& 3 (triplet)
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386 .Ve
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387 .Sp
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388 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:
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389 .Sp
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390 .Vb 1
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391 \& 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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392 .Ve
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393 .Sp
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394 Except for \s-1AS\s0 which is a required atomic invariant in atom types, all other atomic invariants are
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395 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.
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396 .Sp
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397 In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
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398 are also allowed:
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399 .Sp
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400 .Vb 12
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401 \& X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
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402 \& BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
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403 \& LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
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404 \& SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
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405 \& DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
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406 \& TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
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407 \& H : NumOfImplicitAndExplicitHydrogens
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408 \& Ar : Aromatic
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409 \& RA : RingAtom
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410 \& FC : FormalCharge
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411 \& MN : MassNumber
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412 \& SM : SpinMultiplicity
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413 .Ve
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414 .Sp
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415 \&\fIAtomTypes::AtomicInvariantsAtomTypes\fR module is used to assign atomic invariant
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416 atom types.
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417 .IP "\fBSetFunctionalClassesToUse\fR" 4
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418 .IX Item "SetFunctionalClassesToUse"
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419 .Vb 2
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420 \& $AtomNeighborhoodsFingerprints\->SetFunctionalClassesToUse($ValuesRef);
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421 \& $AtomNeighborhoodsFingerprints\->SetFunctionalClassesToUse(@Values);
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422 .Ve
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423 .Sp
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424 Sets functional classes invariants to use during \fIFunctionalClassAtomTypes\fR value of \fIAtomIdentifierType\fR
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425 for atom neighborhoods fingerprints generation and returns \fIAtomNeighborhoodsFingerprints\fR.
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426 .Sp
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427 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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428 Default value [ Ref 24 ]: \fI\s-1HBD\s0,HBA,PI,NI,Ar,Hal\fR.
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429 .Sp
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430 The functional class abbreviations correspond to:
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431 .Sp
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432 .Vb 9
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433 \& HBD: HydrogenBondDonor
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434 \& HBA: HydrogenBondAcceptor
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435 \& PI : PositivelyIonizable
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436 \& NI : NegativelyIonizable
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437 \& Ar : Aromatic
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438 \& Hal : Halogen
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439 \& H : Hydrophobic
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440 \& RA : RingAtom
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441 \& CA : ChainAtom
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442 \&
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443 \& Functional class atom type specification for an atom corresponds to:
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444 \&
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445 \& Ar.CA.H.HBA.HBD.Hal.NI.PI.RA or None
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446 .Ve
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447 .Sp
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448 \&\fIAtomTypes::FunctionalClassAtomTypes\fR module is used to assign functional class atom
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449 types. It uses following definitions [ Ref 60\-61, Ref 65\-66 ]:
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450 .Sp
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451 .Vb 4
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452 \& HydrogenBondDonor: NH, NH2, OH
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453 \& HydrogenBondAcceptor: N[!H], O
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454 \& PositivelyIonizable: +, NH2
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455 \& NegativelyIonizable: \-, C(=O)OH, S(=O)OH, P(=O)OH
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456 .Ve
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457 .IP "\fBSetMaxNeighborhoodRadius\fR" 4
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458 .IX Item "SetMaxNeighborhoodRadius"
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459 .Vb 1
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460 \& $AtomNeighborhoodsFingerprints\->SetMaxNeighborhoodRadius($Radius);
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461 .Ve
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462 .Sp
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463 Sets maximum neighborhood radius to use during atom neighborhood fingerprints generation and
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464 returns \fIAtomNeighborhoodsFingerprints\fR.
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465 .IP "\fBSetMinNeighborhoodRadius\fR" 4
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466 .IX Item "SetMinNeighborhoodRadius"
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467 .Vb 1
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468 \& $AtomNeighborhoodsFingerprints\->SetMinNeighborhoodRadius($Radius);
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469 .Ve
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470 .Sp
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471 Sets minimum neighborhood radius to use during atom neighborhood fingerprints generation and
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472 returns \fIAtomNeighborhoodsFingerprints\fR.
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473 .IP "\fBStringifyAtomNeighborhoodsFingerprints\fR" 4
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474 .IX Item "StringifyAtomNeighborhoodsFingerprints"
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475 .Vb 1
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476 \& $String = $Fingerprints\->StringifyAtomNeighborhoodsFingerprints();
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477 .Ve
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478 .Sp
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479 Returns a string containing information about \fIAtomNeighborhoodsFingerprints\fR object.
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480 .SH "AUTHOR"
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481 .IX Header "AUTHOR"
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482 Manish Sud <msud@san.rr.com>
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483 .SH "SEE ALSO"
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484 .IX Header "SEE ALSO"
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485 Fingerprints.pm, FingerprintsStringUtil.pm, AtomTypesFingerprints.pm, EStateIndiciesFingerprints.pm,
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486 ExtendedConnectivityFingerprints.pm, MACCSKeys.pm, PathLengthFingerprints.pm,
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487 TopologicalAtomPairsFingerprints.pm, TopologicalAtomTripletsFingerprints.pm,
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488 TopologicalAtomTorsionsFingerprints.pm, TopologicalPharmacophoreAtomPairsFingerprints.pm,
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489 TopologicalPharmacophoreAtomTripletsFingerprints.pm
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490 .SH "COPYRIGHT"
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491 .IX Header "COPYRIGHT"
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492 Copyright (C) 2015 Manish Sud. All rights reserved.
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493 .PP
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494 This file is part of MayaChemTools.
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495 .PP
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496 MayaChemTools is free software; you can redistribute it and/or modify it under
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497 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
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498 Software Foundation; either version 3 of the License, or (at your option)
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499 any later version.
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