annotate mayachemtools/docs/modules/man3/TopologicalAtomPairsFingerprints.3 @ 0:73ae111cf86f draft

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author deepakjadmin
date Wed, 20 Jan 2016 11:55:01 -0500
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96 .\}
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101 .ds d- \h'\*(#H'\(pd\h'-\w'~'u'\v'-.25m'\f2\(hy\fP\v'.25m'\h'-\*(#H'
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102 .ds D- D\\k:\h'-\w'D'u'\v'-.11m'\z\(hy\v'.11m'\h'|\\n:u'
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103 .ds th \*(#[\v'.3m'\s+1I\s-1\v'-.3m'\h'-(\w'I'u*2/3)'\s-1o\s+1\*(#]
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104 .ds Th \*(#[\s+2I\s-2\h'-\w'I'u*3/5'\v'-.3m'o\v'.3m'\*(#]
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108 .if v .ds ~ \\k:\h'-(\\n(.wu*9/10-\*(#H)'\s-2\u~\d\s+2\h'|\\n:u'
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109 .if v .ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'\v'-.4m'^\v'.4m'\h'|\\n:u'
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111 .if \n(.H>23 .if \n(.V>19 \
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112 \{\
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113 . ds : e
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114 . ds 8 ss
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118 . ds th \o'bp'
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122 .\}
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123 .rm #[ #] #H #V #F C
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124 .\" ========================================================================
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125 .\"
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126 .IX Title "TOPOLOGICALATOMPAIRSFINGERPRINTS 1"
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127 .TH TOPOLOGICALATOMPAIRSFINGERPRINTS 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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130 .if n .ad l
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131 .nh
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132 .SH "NAME"
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133 TopologicalAtomPairsFingerprints
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134 .SH "SYNOPSIS"
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135 .IX Header "SYNOPSIS"
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136 use Fingerprints::TopologicalAtomPairsFingerprints;
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137 .PP
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138 use Fingerprints::TopologicalAtomPairsFingerprints qw(:all);
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139 .SH "DESCRIPTION"
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140 .IX Header "DESCRIPTION"
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141 \&\fBTopologicalAtomPairsFingerprints\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, GetAtomPairIDs, GetDescription, SetAtomIdentifierType,
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144 SetAtomicInvariantsToUse, SetFunctionalClassesToUse, SetMaxDistance,
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145 SetMinDistance, StringifyTopologicalAtomPairsFingerprints
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146 .PP
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147 \&\fBTopologicalAtomPairsFingerprints\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 \fBTopologicalAtomPairsFingerprints\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 \fBAtomTypesFingerpritns\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 pairs within \fBMinDistance\fR and \fBMaxDistance\fR are identified and counted. An atom pair
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172 identifier is generated for each unique atom pair; the format of atom pair identifier is:
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173 .PP
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174 .Vb 1
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175 \& <AtomType1>\-D<n>\-<AtomType2>
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176 \&
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177 \& AtomType1, AtomType2: Atom types assigned to atom1 and atom2
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178 \& D: Distance between atom1 and atom2
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179 \&
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180 \& where AtomType1 <= AtomType2
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181 .Ve
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182 .PP
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183 The atom pair identifiers for all unique atom pairs corresponding to non-hydrogen atoms constitute
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184 topological atom pairs fingerprints of the molecule.
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185 .PP
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186 The current release of MayaChemTools generates the following types of topological atom pairs
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187 fingerprints vector strings:
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188 .PP
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189 .Vb 6
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190 \& FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
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191 \& istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
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192 \& .H3\-D1\-C.X3.BO3.H1 C.X2.BO2.H2\-D1\-C.X2.BO2.H2 C.X2.BO2.H2\-D1\-C.X3.BO3.
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193 \& H1 C.X2.BO2.H2\-D1\-C.X3.BO4 C.X2.BO2.H2\-D1\-N.X3.BO3 C.X2.BO3.H1\-D1\-...;
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194 \& 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1
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195 \& 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1...
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196 \&
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197 \& FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
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198 \& istance1:MaxDistance10;223;NumericalValues;IDsAndValuesPairsString;C.X
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199 \& 1.BO1.H3\-D1\-C.X3.BO3.H1 2 C.X2.BO2.H2\-D1\-C.X2.BO2.H2 1 C.X2.BO2.H2\-D1\-
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200 \& C.X3.BO3.H1 4 C.X2.BO2.H2\-D1\-C.X3.BO4 1 C.X2.BO2.H2\-D1\-N.X3.BO3 1 C.X2
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201 \& .BO3.H1\-D1\-C.X2.BO3.H1 10 C.X2.BO3.H1\-D1\-C.X3.BO4 8 C.X3.BO3.H1\-D1\-C.X
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202 \& 3.BO4 1 C.X3.BO3.H1\-D1\-O.X1.BO1.H1 2 C.X3.BO4\-D1\-C.X3.BO4 6 C.X3.BO...
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203 \&
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204 \& FingerprintsVector;TopologicalAtomPairs:DREIDINGAtomTypes:MinDistance1
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205 \& :MaxDistance10;157;NumericalValues;IDsAndValuesString;C_2\-D1\-C_3 C_2\-D
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206 \& 1\-C_R C_2\-D1\-N_3 C_2\-D1\-O_2 C_2\-D1\-O_3 C_3\-D1\-C_3 C_3\-D1\-C_R C_3\-D1\-N_
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207 \& R C_3\-D1\-O_3 C_R\-D1\-C_R C_R\-D1\-F_ C_R\-D1\-N_3 C_R\-D1\-N_R C_2\-D2\-C_3 C_2
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208 \& 1 1 1 2 1 7 1 1 2 23 1 1 2 1 3 5 5 2 1 5 28 2 3 3 1 1 1 2 4 1 1 4 9 3
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209 \& 1 4 24 2 4 3 3 4 5 5 14 1 1 2 3 22 1 3 4 4 1 1 1 1 2 2 5 1 4 21 3 1...
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210 \&
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211 \& FingerprintsVector;TopologicalAtomPairs:EStateAtomTypes:MinDistance1:M
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212 \& axDistance10;251;NumericalValues;IDsAndValuesString;aaCH\-D1\-aaCH aaCH\-
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213 \& D1\-aasC aasC\-D1\-aasC aasC\-D1\-aasN aasC\-D1\-dssC aasC\-D1\-sF aasC\-D1\-ssNH
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214 \& aasC\-D1\-sssCH aasN\-D1\-ssCH2 dO\-D1\-dssC dssC\-D1\-sOH dssC\-D1\-ssCH2 d...;
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215 \& 10 8 5 2 1 1 1 1 1 2 1 1 1 2 2 1 4 10 12 2 2 6 3 1 3 2 2 1 1 1 1 1 1 1
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216 \& 1 1 5 2 1 1 6 12 2 2 2 2 6 1 3 2 2 5 2 2 1 2 1 1 1 1 1 1 3 1 3 19 2...
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217 \&
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218 \& FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi
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219 \& stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar\-D1\-Ar
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220 \& Ar\-D1\-Ar.HBA Ar\-D1\-HBD Ar\-D1\-Hal Ar\-D1\-None Ar.HBA\-D1\-None HBA\-D1\-NI H
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221 \& BA\-D1\-None HBA.HBD\-D1\-NI HBA.HBD\-D1\-None HBD\-D1\-None NI\-D1\-None No...;
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222 \& 23 2 1 1 2 1 1 1 1 2 1 1 7 28 3 1 3 2 8 2 1 1 1 5 1 5 24 3 3 4 2 13 4
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223 \& 1 1 4 1 5 22 4 4 3 1 19 1 1 1 1 1 2 2 3 1 1 8 25 4 5 2 3 1 26 1 4 1 ...
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224 \&
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225 \& FingerprintsVector;TopologicalAtomPairs:MMFF94AtomTypes:MinDistance1:M
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226 \& axDistance10;227;NumericalValues;IDsAndValuesPairsString;C5A\-D1\-C5B 2
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227 \& C5A\-D1\-CB 1 C5A\-D1\-CR 1 C5A\-D1\-N5 2 C5B\-D1\-C5B 1 C5B\-D1\-C=ON 1 C5B\-D1\-
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228 \& CB 1 C=ON\-D1\-NC=O 1 C=ON\-D1\-O=CN 1 CB\-D1\-CB 18 CB\-D1\-F 1 CB\-D1\-NC=O 1
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229 \& COO\-D1\-CR 1 COO\-D1\-O=CO 1 COO\-D1\-OC=O 1 CR\-D1\-CR 7 CR\-D1\-N5 1 CR\-D1\-OR
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230 \& 2 C5A\-D2\-C5A 1 C5A\-D2\-C5B 2 C5A\-D2\-C=ON 1 C5A\-D2\-CB 3 C5A\-D2\-CR 4 ...
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231 \&
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232 \& FingerprintsVector;TopologicalAtomPairs:SLogPAtomTypes:MinDistance1:Ma
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233 \& xDistance10;329;NumericalValues;IDsAndValuesPairsString;C1\-D1\-C10 1 C1
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234 \& \-D1\-C11 2 C1\-D1\-C5 1 C1\-D1\-CS 4 C10\-D1\-N11 1 C11\-D1\-C21 1 C14\-D1\-C18 2
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235 \& C14\-D1\-F 1 C18\-D1\-C18 10 C18\-D1\-C20 4 C18\-D1\-C22 2 C20\-D1\-C20 3 C20\-D
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236 \& 1\-C21 1 C20\-D1\-N11 1 C21\-D1\-C21 1 C21\-D1\-C5 1 C21\-D1\-N11 1 C22\-D1\-N4 1
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237 \& C5\-D1\-N4 1 C5\-D1\-O10 1 C5\-D1\-O2 1 C5\-D1\-O9 1 CS\-D1\-O2 2 C1\-D2\-C1 3...
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238 \&
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239 \& FingerprintsVector;TopologicalAtomPairs:SYBYLAtomTypes:MinDistance1:Ma
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240 \& xDistance10;159;NumericalValues;IDsAndValuesPairsString;C.2\-D1\-C.3 1 C
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241 \& .2\-D1\-C.ar 1 C.2\-D1\-N.am 1 C.2\-D1\-O.2 1 C.2\-D1\-O.co2 2 C.3\-D1\-C.3 7 C.
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242 \& 3\-D1\-C.ar 1 C.3\-D1\-N.ar 1 C.3\-D1\-O.3 2 C.ar\-D1\-C.ar 23 C.ar\-D1\-F 1 C.a
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243 \& r\-D1\-N.am 1 C.ar\-D1\-N.ar 2 C.2\-D2\-C.3 1 C.2\-D2\-C.ar 3 C.3\-D2\-C.3 5 C.3
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244 \& \-D2\-C.ar 5 C.3\-D2\-N.ar 2 C.3\-D2\-O.3 4 C.3\-D2\-O.co2 2 C.ar\-D2\-C.ar 2...
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245 \&
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246 \& FingerprintsVector;TopologicalAtomPairs:TPSAAtomTypes:MinDistance1:Max
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247 \& Distance10;64;NumericalValues;IDsAndValuesPairsString;N21\-D1\-None 3 N7
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248 \& \-D1\-None 2 None\-D1\-None 34 None\-D1\-O3 2 None\-D1\-O4 3 N21\-D2\-None 5 N7\-
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249 \& D2\-None 3 N7\-D2\-O3 1 None\-D2\-None 44 None\-D2\-O3 2 None\-D2\-O4 5 O3\-D2\-O
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250 \& 4 1 N21\-D3\-None 7 N7\-D3\-None 4 None\-D3\-None 45 None\-D3\-O3 4 None\-D3\-O4
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251 \& 5 N21\-D4\-N7 1 N21\-D4\-None 5 N21\-D4\-O3 1 N21\-D4\-O4 1 N7\-D4\-None 4 N...
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252 \&
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253 \& FingerprintsVector;TopologicalAtomPairs:UFFAtomTypes:MinDistance1:MaxD
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254 \& istance10;157;NumericalValues;IDsAndValuesPairsString;C_2\-D1\-C_3 1 C_2
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255 \& \-D1\-C_R 1 C_2\-D1\-N_3 1 C_2\-D1\-O_2 2 C_2\-D1\-O_3 1 C_3\-D1\-C_3 7 C_3\-D1\-C
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256 \& _R 1 C_3\-D1\-N_R 1 C_3\-D1\-O_3 2 C_R\-D1\-C_R 23 C_R\-D1\-F_ 1 C_R\-D1\-N_3 1
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257 \& C_R\-D1\-N_R 2 C_2\-D2\-C_3 1 C_2\-D2\-C_R 3 C_3\-D2\-C_3 5 C_3\-D2\-C_R 5 C_3\-D
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258 \& 2\-N_R 2 C_3\-D2\-O_2 1 C_3\-D2\-O_3 5 C_R\-D2\-C_R 28 C_R\-D2\-F_ 2 C_R\-D2\-...
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259 .Ve
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260 .SS "\s-1METHODS\s0"
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261 .IX Subsection "METHODS"
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262 .IP "\fBnew\fR" 4
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263 .IX Item "new"
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264 .Vb 2
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265 \& $NewTopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints(
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266 \& %NamesAndValues);
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267 .Ve
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268 .Sp
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269 Using specified \fITopologicalAtomPairsFingerprints\fR property names and values hash, \fBnew\fR
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270 method creates a new object and returns a reference to newly created \fBTopologicalAtomPairsFingerprints\fR
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271 object. By default, the following properties are initialized:
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272 .Sp
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273 .Vb 7
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274 \& Molecule = \*(Aq\*(Aq
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275 \& Type = \*(AqTopologicalAtomPairs\*(Aq
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276 \& MinDistance = 1
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277 \& MaxDistance = 10
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278 \& AtomIdentifierType = \*(Aq\*(Aq
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279 \& AtomicInvariantsToUse = [\*(AqAS\*(Aq, \*(AqX\*(Aq, \*(AqBO\*(Aq, \*(AqH\*(Aq, \*(AqFC\*(Aq]
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280 \& FunctionalClassesToUse = [\*(AqHBD\*(Aq, \*(AqHBA\*(Aq, \*(AqPI\*(Aq, \*(AqNI\*(Aq, \*(AqAr\*(Aq, \*(AqHal\*(Aq]
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281 .Ve
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282 .Sp
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283 Examples:
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284 .Sp
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285 .Vb 4
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286 \& $TopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints(
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287 \& \*(AqMolecule\*(Aq => $Molecule,
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288 \& \*(AqAtomIdentifierType\*(Aq =>
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289 \& \*(AqAtomicInvariantsAtomTypes\*(Aq);
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290 \&
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291 \& $TopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints(
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292 \& \*(AqMolecule\*(Aq => $Molecule,
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293 \& \*(AqMinDistance\*(Aq => 1,
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294 \& \*(AqMaxDistance\*(Aq => 10,
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295 \& \*(AqAtomIdentifierType\*(Aq =>
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296 \& \*(AqAtomicInvariantsAtomTypes\*(Aq,
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297 \& \*(AqAtomicInvariantsToUse\*(Aq =>
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298 \& [\*(AqAS\*(Aq, \*(AqX\*(Aq, \*(AqBO\*(Aq, \*(AqH\*(Aq, \*(AqFC\*(Aq] );
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299 \&
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300 \& $TopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints(
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301 \& \*(AqMolecule\*(Aq => $Molecule,
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302 \& \*(AqAtomIdentifierType\*(Aq =>
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303 \& \*(AqEStateAtomTypes\*(Aq);
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304 \&
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305 \& $TopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints(
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306 \& \*(AqMolecule\*(Aq => $Molecule,
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307 \& \*(AqAtomIdentifierType\*(Aq =>
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308 \& \*(AqSLogPAtomTypes\*(Aq);
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309 \&
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310 \& $TopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints(
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311 \& \*(AqMolecule\*(Aq => $Molecule,
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312 \& \*(AqMinDistance\*(Aq => 1,
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313 \& \*(AqMaxDistance\*(Aq => 10,
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314 \& \*(AqAtomIdentifierType\*(Aq =>
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315 \& \*(AqFunctionalClassAtomTypes\*(Aq,
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316 \& \*(AqFunctionalClassesToUse\*(Aq =>
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317 \& [\*(AqHBD\*(Aq, \*(AqHBA\*(Aq, \*(AqPI\*(Aq, \*(AqNI\*(Aq, \*(AqAr\*(Aq, \*(AqHal\*(Aq]);
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318 \&
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319 \&
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320 \& $TopologicalAtomPairsFingerprints\->GenerateFingerprints();
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321 \& print "$TopologicalAtomPairsFingerprints\en";
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322 .Ve
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323 .IP "\fBGetDescription\fR" 4
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324 .IX Item "GetDescription"
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325 .Vb 1
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326 \& $Description = $TopologicalAtomPairsFingerprints\->GetDescription();
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327 .Ve
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328 .Sp
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329 Returns a string containing description of topological atom pairs fingerprints fingerprints.
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330 .IP "\fBGenerateFingerprints\fR" 4
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331 .IX Item "GenerateFingerprints"
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332 .Vb 1
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333 \& $TopologicalAtomPairsFingerprints\->GenerateFingerprints();
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334 .Ve
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335 .Sp
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336 Generates topological atom pairs fingerprints and returns \fITopologicalAtomPairsFingerprints\fR.
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337 .IP "\fBGetAtomPairIDs\fR" 4
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338 .IX Item "GetAtomPairIDs"
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339 .Vb 2
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340 \& $AtomPairIDsRef = $TopologicalAtomPairsFingerprints\->GetAtomPairIDs();
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341 \& @AtomPairIDs = $TopologicalAtomPairsFingerprints\->GetAtomPairIDs();
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342 .Ve
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343 .Sp
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344 Returns atom pair IDs corresponding to atom pairs count values in topological atom pairs
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345 fingerprints vector as an array or reference to an array.
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346 .IP "\fBSetAtomIdentifierType\fR" 4
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347 .IX Item "SetAtomIdentifierType"
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348 .Vb 1
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349 \& $TopologicalAtomPairsFingerprints\->SetAtomIdentifierType($IdentifierType);
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350 .Ve
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351 .Sp
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352 Sets atom \fIIdentifierType\fR to use during atom pairs fingerprints generation and
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353 returns \fITopologicalAtomPairsFingerprints\fR.
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354 .Sp
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355 Possible values: \fIAtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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356 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
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357 TPSAAtomTypes, UFFAtomTypes\fR.
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358 .IP "\fBSetAtomicInvariantsToUse\fR" 4
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359 .IX Item "SetAtomicInvariantsToUse"
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360 .Vb 2
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361 \& $TopologicalAtomPairsFingerprints\->SetAtomicInvariantsToUse($ValuesRef);
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362 \& $TopologicalAtomPairsFingerprints\->SetAtomicInvariantsToUse(@Values);
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363 .Ve
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364 .Sp
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365 Sets atomic invariants to use during \fIAtomicInvariantsAtomTypes\fR value of \fIAtomIdentifierType\fR
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366 for topological atom pairs fingerprints generation and returns \fITopologicalAtomPairsFingerprints\fR.
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367 .Sp
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368 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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369 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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370 .Sp
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371 The atomic invariants abbreviations correspond to:
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372 .Sp
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373 .Vb 1
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374 \& AS = Atom symbol corresponding to element symbol
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375 \&
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376 \& X<n> = Number of non\-hydrogen atom neighbors or heavy atoms
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377 \& BO<n> = Sum of bond orders to non\-hydrogen atom neighbors or heavy atoms
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378 \& LBO<n> = Largest bond order of non\-hydrogen atom neighbors or heavy atoms
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379 \& SB<n> = Number of single bonds to non\-hydrogen atom neighbors or heavy atoms
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380 \& DB<n> = Number of double bonds to non\-hydrogen atom neighbors or heavy atoms
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381 \& TB<n> = Number of triple bonds to non\-hydrogen atom neighbors or heavy atoms
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382 \& H<n> = Number of implicit and explicit hydrogens for atom
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383 \& Ar = Aromatic annotation indicating whether atom is aromatic
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384 \& RA = Ring atom annotation indicating whether atom is a ring
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385 \& FC<+n/\-n> = Formal charge assigned to atom
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386 \& MN<n> = Mass number indicating isotope other than most abundant isotope
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387 \& SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
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388 \& 3 (triplet)
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389 .Ve
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390 .Sp
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391 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:
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392 .Sp
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393 .Vb 1
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394 \& 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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395 .Ve
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396 .Sp
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397 Except for \s-1AS\s0 which is a required atomic invariant in atom types, all other atomic invariants are
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398 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.
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399 .Sp
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400 In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
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401 are also allowed:
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402 .Sp
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403 .Vb 12
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404 \& X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
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405 \& BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
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406 \& LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
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407 \& SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
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408 \& DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
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409 \& TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
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410 \& H : NumOfImplicitAndExplicitHydrogens
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411 \& Ar : Aromatic
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412 \& RA : RingAtom
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413 \& FC : FormalCharge
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414 \& MN : MassNumber
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415 \& SM : SpinMultiplicity
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416 .Ve
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417 .Sp
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418 \&\fIAtomTypes::AtomicInvariantsAtomTypes\fR module is used to assign atomic invariant
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419 atom types.
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420 .IP "\fBSetFunctionalClassesToUse\fR" 4
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421 .IX Item "SetFunctionalClassesToUse"
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422 .Vb 2
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423 \& $TopologicalAtomPairsFingerprints\->SetFunctionalClassesToUse($ValuesRef);
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424 \& $TopologicalAtomPairsFingerprints\->SetFunctionalClassesToUse(@Values);
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425 .Ve
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426 .Sp
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427 Sets functional classes invariants to use during \fIFunctionalClassAtomTypes\fR value of \fIAtomIdentifierType\fR
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428 for topological atom pairs fingerprints generation and returns \fITopologicalAtomPairsFingerprints\fR.
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429 .Sp
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430 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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431 Default value [ Ref 24 ]: \fI\s-1HBD\s0,HBA,PI,NI,Ar,Hal\fR.
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432 .Sp
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433 The functional class abbreviations correspond to:
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434 .Sp
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435 .Vb 9
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436 \& HBD: HydrogenBondDonor
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437 \& HBA: HydrogenBondAcceptor
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438 \& PI : PositivelyIonizable
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439 \& NI : NegativelyIonizable
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440 \& Ar : Aromatic
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441 \& Hal : Halogen
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442 \& H : Hydrophobic
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443 \& RA : RingAtom
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444 \& CA : ChainAtom
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445 \&
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446 \& Functional class atom type specification for an atom corresponds to:
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447 \&
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448 \& Ar.CA.H.HBA.HBD.Hal.NI.PI.RA or None
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449 .Ve
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450 .Sp
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451 \&\fIAtomTypes::FunctionalClassAtomTypes\fR module is used to assign functional class atom
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452 types. It uses following definitions [ Ref 60\-61, Ref 65\-66 ]:
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453 .Sp
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454 .Vb 4
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455 \& HydrogenBondDonor: NH, NH2, OH
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456 \& HydrogenBondAcceptor: N[!H], O
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457 \& PositivelyIonizable: +, NH2
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458 \& NegativelyIonizable: \-, C(=O)OH, S(=O)OH, P(=O)OH
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459 .Ve
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460 .IP "\fBSetMaxDistance\fR" 4
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461 .IX Item "SetMaxDistance"
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462 .Vb 1
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463 \& $TopologicalAtomPairsFingerprints\->SetMaxDistance($Distance);
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464 .Ve
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465 .Sp
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466 Sets maximum distance to use during topological atom pairs fingerprints generation and
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467 returns \fITopologicalAtomPairsFingerprints\fR.
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468 .IP "\fBSetMinDistance\fR" 4
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469 .IX Item "SetMinDistance"
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470 .Vb 1
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471 \& $TopologicalAtomPairsFingerprints\->SetMinDistance($Distance);
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472 .Ve
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473 .Sp
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474 Sets minimum distance to use during topological atom pairs fingerprints generation and
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475 returns \fITopologicalAtomPairsFingerprints\fR.
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476 .IP "\fBStringifyTopologicalAtomPairsFingerprints\fR" 4
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477 .IX Item "StringifyTopologicalAtomPairsFingerprints"
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478 .Vb 2
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479 \& $String = $TopologicalAtomPairsFingerprints\->
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480 \& StringifyTopologicalAtomPairsFingerprints();
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481 .Ve
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482 .Sp
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483 Returns a string containing information about \fITopologicalAtomPairsFingerprints\fR object.
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484 .SH "AUTHOR"
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485 .IX Header "AUTHOR"
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486 Manish Sud <msud@san.rr.com>
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487 .SH "SEE ALSO"
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488 .IX Header "SEE ALSO"
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489 Fingerprints.pm, FingerprintsStringUtil.pm, AtomNeighborhoodsFingerprints.pm,
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490 AtomTypesFingerprints.pm, EStateIndiciesFingerprints.pm, ExtendedConnectivityFingerprints.pm,
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491 MACCSKeys.pm, PathLengthFingerprints.pm, TopologicalAtomTripletsFingerprints.pm,
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492 TopologicalAtomTorsionsFingerprints.pm, TopologicalPharmacophoreAtomPairsFingerprints.pm,
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493 TopologicalPharmacophoreAtomTripletsFingerprints.pm
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494 .SH "COPYRIGHT"
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495 .IX Header "COPYRIGHT"
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496 Copyright (C) 2015 Manish Sud. All rights reserved.
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497 .PP
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498 This file is part of MayaChemTools.
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499 .PP
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500 MayaChemTools is free software; you can redistribute it and/or modify it under
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501 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
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502 Software Foundation; either version 3 of the License, or (at your option)
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503 any later version.