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124 .\" ========================================================================
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125 .\"
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126 .IX Title "EXTENDEDCONNECTIVITYFINGERPRINTS 1"
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127 .TH EXTENDEDCONNECTIVITYFINGERPRINTS 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 ExtendedConnectivityFingerprints
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134 .SH "SYNOPSIS"
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135 .IX Header "SYNOPSIS"
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136 use Fingerprints::ExtendedConnectivityFingerprints;
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137 .PP
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138 use Fingerprints::ExtendedConnectivityFingerprints qw(:all);
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139 .SH "DESCRIPTION"
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140 .IX Header "DESCRIPTION"
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141 ExtendedConnectivityFingerprints [ Ref 48, Ref 52 ] 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, SetNeighborhoodRadius,
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145 StringifyExtendedConnectivityFingerprints
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146 .PP
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147 \&\fBExtendedConnectivityFingerprints\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 \fBExtendedConnectivityFingerprints\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 \fBExtendedConnectivityFingerprints\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, \fBAtomicInvariantsToUse\fR
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168 and \fBFunctionalClassesToUse\fR, initial atom types are assigned to all non-hydrogen atoms in
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169 a molecule and these atom types strings are converted into initial atom identifier integers using
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170 \&\fBTextUtil::HashCode\fR function. The duplicate atom identifiers are removed.
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171 .PP
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172 For \fBNeighborhoodRadius\fR value of \fI0\fR, the initial set of unique atom identifiers comprises
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173 the molecule fingerprints. Otherwise, atom neighborhoods are generated for each non-hydrogen
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174 atom up-to specified \fBNeighborhoodRadius\fR value. For each non-hydrogen central atom
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175 at a specific radius, its neighbors at next radius level along with their bond orders and previously
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176 calculated atom identifiers are collected which in turn are used to generate a new integer
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177 atom identifier; the bond orders and atom identifier pairs list is first sorted by bond order
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178 followed by atom identifiers to make these values graph invariant.
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179 .PP
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180 After integer atom identifiers have been generated for all non-hydrogen atoms at all specified
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181 neighborhood radii, the duplicate integer atom identifiers corresponding to same hash code
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182 value generated using \fBTextUtil::HashCode\fR are tracked by keeping the atom identifiers at
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183 lower radius. Additionally, all structurally duplicate integer atom identifiers at each specified
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184 radius are also tracked by identifying equivalent atom and bonds corresponding to substructures
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185 used for generating atom identifier and keeping integer atom identifier with lowest value.
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186 .PP
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187 For \fIExtendedConnnectivity\fR value of fingerprints \fBType\fR, the duplicate identifiers are
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188 removed from the list and the unique atom identifiers constitute the extended connectivity
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189 fingerprints of a molecule.
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190 .PP
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191 For \fIExtendedConnnectivityCount\fR value of fingerprints \fBType\fR, the occurrence of each
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192 unique atom identifiers appears is counted and the unique atom identifiers along with their
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193 count constitute the extended connectivity fingerprints of a molecule.
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194 .PP
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195 For \fIExtendedConnectivityBits\fR value of fingerprints \fB\-m, \-\-mode\fR, the unique atom identifiers
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196 are used as a random number seed to generate a random integer value between 0 and \fB\-\-Size\fR which
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197 in turn is used to set corresponding bits in the fingerprint bit-vector string.
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198 .PP
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199 The current release of MayaChemTools generates the following types of extended connectivity
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200 fingerprints vector strings:
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201 .PP
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202 .Vb 6
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203 \& FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
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204 \& us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
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205 \& 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
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206 \& 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
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207 \& 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
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208 \& 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...
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209 \&
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210 \& FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
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211 \& :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
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212 \& 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
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213 \& 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
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214 \& 3 2 1 1 14 1 2 10 4 3 1 1 1 1 2 1 2 1 1 1 2 3 1 1 2 1 3 3 8 2 2 2 6 2
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215 \& 1 2 1 1 2 1 1 1 2 1 1 2 1 2 1 1 1 1 1 1 1 1 1 2 1 1
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216 \&
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217 \& FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
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218 \& es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
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219 \& 0000000001010000000110000011000000000000100000000000000000000000100001
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220 \& 1000000110000000000000000000000000010011000000000000000000000000010000
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221 \& 0000000000000000000000000010000000000000000001000000000000000000000000
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222 \& 0000000000010000100001000000000000101000000000000000100000000000000...
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223 \&
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224 \& FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
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225 \& es:Radius2;1024;HexadecimalString;Ascending;000000010050c0600800000803
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226 \& 0300000091000004000000020000100000000124008200020000000040020000000000
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227 \& 2080000000820040010020000000008040000000000080001000000000400000000000
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228 \& 4040000090000061010000000800200000000000001400000000020080000000000020
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229 \& 00008020200000408000
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230 \&
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231 \& FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu
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232 \& s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8
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233 \& 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567
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234 \& 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012
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235 \& 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455
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236 \& 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404...
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237 \&
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238 \& FingerprintsVector;ExtendedConnectivityCount:FunctionalClassAtomTypes:
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239 \& Radius2;57;NumericalValues;IDsAndValuesString;24769214 508787397 85039
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240 \& 3286 862102353 981185303 1231636850 1649386610 1941540674 263599683 32
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241 \& 9205671 571109041 639579325 683993318 723853089 810600886 885767127...;
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242 \& 1 1 1 10 2 22 3 1 3 3 1 1 1 3 2 2 1 2 2 2 3 1 1 1 1 1 14 1 1 1 1 1 1 2
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243 \& 1 2 1 1 2 2 1 1 2 1 1 1 2 1 1 2 1 1 1 1 1 1 1
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244 \&
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245 \& FingerprintsBitVector;ExtendedConnectivityBits:FunctionalClassAtomType
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246 \& s:Radius2;1024;BinaryString;Ascending;00000000000000000000100000000000
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247 \& 0000000001000100000000001000000000000000000000000000000000101000000010
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248 \& 0000001000000000010000000000000000000000000000000000000000000000000100
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249 \& 0000000000001000000000000001000000000001001000000000000000000000000000
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250 \& 0000000000000000100000000000001000000000000000000000000000000000000...
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251 \&
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252 \& FingerprintsVector;ExtendedConnectivity:DREIDINGAtomTypes:Radius2;56;A
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253 \& lphaNumericalValues;ValuesString;280305427 357928343 721790579 1151822
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254 \& 898 1207111054 1380963747 1568213839 1603445250 4559268 55012922 18094
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255 \& 0813 335715751 534801009 684609658 829361048 972945982 999881534 10076
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256 \& 55741 1213692591 1222032501 1224517934 1235687794 1244268533 152812070
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257 \& 0 1629595024 1856308891 1978806036 2001865095 2096549435 172675415 ...
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258 \&
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259 \& FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp
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260 \& haNumericalValues;ValuesString;25189973 528584866 662581668 671034184
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261 \& 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450
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262 \& 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430
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263 \& 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134
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264 \& 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566...
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265 \&
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266 \& FingerprintsVector;ExtendedConnectivity:MMFF94AtomTypes:Radius2;64;Alp
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267 \& haNumericalValues;ValuesString;224051550 746527773 998750766 103704190
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268 \& 2 1239701709 1248384926 1259447756 1521678386 1631549126 1909437580 20
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269 \& 37095052 2104274756 2117729376 8770364 31445800 81450228 314289324 344
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270 \& 041929 581773587 638555787 692022098 811840536 929651561 936421792 988
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271 \& 636432 1048624296 1054288509 1369487579 1454058929 1519352190 17271...
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272 \&
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273 \& FingerprintsVector;ExtendedConnectivity:SLogPAtomTypes:Radius2;71;Alph
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274 \& aNumericalValues;ValuesString;78989290 116507218 489454042 888737940 1
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275 \& 162561799 1241797255 1251494264 1263717127 1471206899 1538061784 17654
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276 \& 07295 1795036542 1809833874 2020454493 2055310842 2117729376 11868981
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277 \& 56731842 149505242 184525155 196984339 288181334 481409282 556716568 6
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278 \& 41915747 679881756 721736571 794256218 908276640 992898760 10987549...
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279 \&
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280 \& FingerprintsVector;ExtendedConnectivity:SYBYLAtomTypes:Radius2;58;Alph
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281 \& aNumericalValues;ValuesString;199957044 313356892 455463968 465982819
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282 \& 1225318176 1678585943 1883366064 1963811677 2117729376 113784599 19153
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283 \& 8837 196629033 263865277 416380653 477036669 681527491 730724924 90906
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284 \& 5537 1021959189 1133014972 1174311016 1359441203 1573452838 1661585138
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285 \& 1668649038 1684198062 1812312554 1859266290 1891651106 2072549404 ...
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286 \&
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287 \& FingerprintsVector;ExtendedConnectivity:TPSAAtomTypes:Radius2;47;Alpha
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288 \& NumericalValues;ValuesString;20818206 259344053 862102353 1331904542 1
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289 \& 700688206 265614156 363161397 681332588 810600886 885767127 950172500
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290 \& 951454814 1059668746 1247054493 1382302230 1399502637 1805025917 19189
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291 \& 39561 2114677228 2126402271 8130483 17645742 32278373 149975755 160327
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292 \& 654 256360355 279492740 291251259 317592700 333763396 972105960 101...
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293 \&
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294 \& FingerprintsVector;ExtendedConnectivity:UFFAtomTypes:Radius2;56;AlphaN
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295 \& umericalValues;ValuesString;280305427 357928343 721790579 1151822898 1
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296 \& 207111054 1380963747 1568213839 1603445250 4559268 55012922 180940813
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297 \& 335715751 534801009 684609658 829361048 972945982 999881534 1007655741
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298 \& 1213692591 1222032501 1224517934 1235687794 1244268533 1528120700 162
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299 \& 9595024 1856308891 1978806036 2001865095 2096549435 172675415 18344...
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300 .Ve
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301 .SS "\s-1METHODS\s0"
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302 .IX Subsection "METHODS"
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303 .IP "\fBnew\fR" 4
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304 .IX Item "new"
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305 .Vb 2
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306 \& $NewExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
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307 \& %NamesAndValues);
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308 .Ve
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309 .Sp
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310 Using specified \fIExtendedConnectivityFingerprints\fR property names and values hash, \fBnew\fR
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311 method creates a new object and returns a reference to newly created \fBExtendedConnectivityFingerprints\fR
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312 object. By default, the following properties are initialized:
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313 .Sp
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314 .Vb 6
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315 \& Molecule = \*(Aq\*(Aq
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316 \& Type = \*(AqExtendedConnectivity\*(Aq
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317 \& NeighborhoodRadius = 2
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318 \& AtomIdentifierType = \*(Aq\*(Aq
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319 \& AtomicInvariantsToUse = [\*(AqAS\*(Aq, \*(AqX\*(Aq, \*(AqBO\*(Aq, \*(AqH\*(Aq, \*(AqFC\*(Aq, \*(AqMN\*(Aq]
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320 \& FunctionalClassesToUse = [\*(AqHBD\*(Aq, \*(AqHBA\*(Aq, \*(AqPI\*(Aq, \*(AqNI\*(Aq, \*(AqAr\*(Aq, \*(AqHal\*(Aq]
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321 .Ve
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322 .Sp
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323 Examples:
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324 .Sp
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325 .Vb 4
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326 \& $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
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327 \& \*(AqMolecule\*(Aq => $Molecule,
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328 \& \*(AqAtomIdentifierType\*(Aq =>
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329 \& \*(AqAtomicInvariantsAtomTypes\*(Aq);
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330 \&
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331 \& $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
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332 \& \*(AqType\*(Aq => \*(AqExtendedConnectivityCount\*(Aq,
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333 \& \*(AqMolecule\*(Aq => $Molecule,
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334 \& \*(AqAtomIdentifierType\*(Aq =>
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335 \& \*(AqAtomicInvariantsAtomTypes\*(Aq);
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336 \&
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337 \& $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
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338 \& \*(AqType\*(Aq => \*(AqExtendedConnectivityBits\*(Aq,
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339 \& \*(AqMolecule\*(Aq => $Molecule,
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340 \& \*(AqSize\*(Aq => 1024,
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341 \& \*(AqAtomIdentifierType\*(Aq =>
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342 \& \*(AqAtomicInvariantsAtomTypes\*(Aq);
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343 \&
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344 \& $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
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345 \& \*(AqType\*(Aq => \*(AqExtendedConnectivity\*(Aq,
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346 \& \*(AqMolecule\*(Aq => $Molecule,
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347 \& \*(AqNeighborhoodRadius\*(Aq => 2,
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348 \& \*(AqAtomIdentifierType\*(Aq =>
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349 \& \*(AqAtomicInvariantsAtomTypes\*(Aq,
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350 \& \*(AqAtomicInvariantsToUse\*(Aq =>
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351 \& [\*(AqAS\*(Aq, \*(AqX\*(Aq, \*(AqBO\*(Aq, \*(AqH\*(Aq, \*(AqFC\*(Aq, \*(AqMN\*(Aq] );
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352 \&
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353 \& $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
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354 \& \*(AqType\*(Aq => \*(AqExtendedConnectivity\*(Aq,
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355 \& \*(AqMolecule\*(Aq => $Molecule,
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356 \& \*(AqNeighborhoodRadius\*(Aq => 2,
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357 \& \*(AqAtomIdentifierType\*(Aq =>
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358 \& \*(AqFunctionalClassAtomTypes\*(Aq,
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359 \& \*(AqFunctionalClassesToUse\*(Aq =>
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360 \& [\*(AqHBD\*(Aq, \*(AqHBA\*(Aq, \*(AqPI\*(Aq, \*(AqNI\*(Aq, \*(AqAr\*(Aq, \*(AqHal\*(Aq] );
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361 \&
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362 \& $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
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363 \& \*(AqType\*(Aq => \*(AqExtendedConnectivity\*(Aq,
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364 \& \*(AqMolecule\*(Aq => $Molecule,;
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365 \& \*(AqAtomIdentifierType\*(Aq =>
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366 \& \*(AqMMFF94AtomTypes\*(Aq);
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367 \&
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368 \& $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
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369 \& \*(AqType\*(Aq => \*(AqExtendedConnectivityCount\*(Aq,
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370 \& \*(AqMolecule\*(Aq => $Molecule,;
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371 \& \*(AqAtomIdentifierType\*(Aq =>
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372 \& \*(AqMMFF94AtomTypes\*(Aq);
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373 \&
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374 \& $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
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375 \& \*(AqType\*(Aq => \*(AqExtendedConnectivityCount\*(Aq,
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376 \& \*(AqMolecule\*(Aq => $Molecule,;
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377 \& \*(AqAtomIdentifierType\*(Aq =>
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378 \& \*(AqSLogPAtomTypes\*(Aq);
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379 \&
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380 \& $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
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381 \& \*(AqType\*(Aq => \*(AqExtendedConnectivity\*(Aq,
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382 \& \*(AqMolecule\*(Aq => $Molecule,;
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383 \& \*(AqAtomIdentifierType\*(Aq =>
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384 \& \*(AqSLogPAtomTypes\*(Aq);
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385 \&
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386 \& $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
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387 \& \*(AqType\*(Aq => \*(AqExtendedConnectivity\*(Aq,
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388 \& \*(AqMolecule\*(Aq => $Molecule,;
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389 \& \*(AqAtomIdentifierType\*(Aq =>
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390 \& \*(AqSYBYLAtomTypes\*(Aq);
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391 \&
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392 \& $ExtendedConnectivityFingerprints\->GenerateFingerprints();
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393 \& print "$ExtendedConnectivityFingerprints\en";
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394 .Ve
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395 .IP "\fBGenerateFingerprints\fR" 4
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396 .IX Item "GenerateFingerprints"
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397 .Vb 1
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398 \& $ExtendedConnectivityFingerprints\->GenerateFingerprints();
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399 .Ve
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400 .Sp
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401 Generates extended connectivity fingerprints and returns \fIExtendedConnectivityFingerprints\fR.
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402 .IP "\fBGetDescription\fR" 4
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403 .IX Item "GetDescription"
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404 .Vb 1
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405 \& $Description = $ExtendedConnectivityFingerprints\->GetDescription();
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406 .Ve
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407 .Sp
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408 Returns a string containing description of extended connectivity fingerprints
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409 fingerprints.
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410 .IP "\fBSetAtomIdentifierType\fR" 4
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411 .IX Item "SetAtomIdentifierType"
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412 .Vb 1
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413 \& $ExtendedConnectivityFingerprints\->SetAtomIdentifierType($IdentifierType);
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414 .Ve
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415 .Sp
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416 Sets atom \fIIdentifierType\fR to use during extended connectivity fingerprints generation and
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417 returns \fIExtendedConnectivityFingerprints\fR.
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418 .Sp
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419 Possible values: \fIAtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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420 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
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421 TPSAAtomTypes, UFFAtomTypes\fR.
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422 .IP "\fBSetAtomicInvariantsToUse\fR" 4
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423 .IX Item "SetAtomicInvariantsToUse"
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424 .Vb 2
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425 \& $ExtendedConnectivityFingerprints\->SetAtomicInvariantsToUse($ValuesRef);
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426 \& $ExtendedConnectivityFingerprints\->SetAtomicInvariantsToUse(@Values);
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427 .Ve
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428 .Sp
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429 Sets atomic invariants to use during \fIAtomicInvariantsAtomTypes\fR value of \fIAtomIdentifierType\fR
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430 for extended connectivity fingerprints generation and returns \fIExtendedConnectivityFingerprints\fR.
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431 .Sp
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432 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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433 H, Ar, \s-1RA\s0, \s-1FC\s0, \s-1MN\s0, \s-1SM\s0\fR. Default value [ Ref 24 ]: \fI\s-1AS\s0,X,BO,H,FC,MN\fR.
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434 .Sp
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435 The atomic invariants abbreviations correspond to:
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436 .Sp
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437 .Vb 1
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438 \& AS = Atom symbol corresponding to element symbol
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439 \&
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440 \& X<n> = Number of non\-hydrogen atom neighbors or heavy atoms
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441 \& BO<n> = Sum of bond orders to non\-hydrogen atom neighbors or heavy atoms
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442 \& LBO<n> = Largest bond order of non\-hydrogen atom neighbors or heavy atoms
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443 \& SB<n> = Number of single bonds to non\-hydrogen atom neighbors or heavy atoms
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444 \& DB<n> = Number of double bonds to non\-hydrogen atom neighbors or heavy atoms
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445 \& TB<n> = Number of triple bonds to non\-hydrogen atom neighbors or heavy atoms
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446 \& H<n> = Number of implicit and explicit hydrogens for atom
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447 \& Ar = Aromatic annotation indicating whether atom is aromatic
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448 \& RA = Ring atom annotation indicating whether atom is a ring
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449 \& FC<+n/\-n> = Formal charge assigned to atom
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450 \& MN<n> = Mass number indicating isotope other than most abundant isotope
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451 \& SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
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452 \& 3 (triplet)
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453 .Ve
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454 .Sp
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455 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:
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456 .Sp
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457 .Vb 1
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458 \& 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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459 .Ve
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460 .Sp
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461 Except for \s-1AS\s0 which is a required atomic invariant in atom types, all other atomic invariants are
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462 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.
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463 .Sp
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464 In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
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465 are also allowed:
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466 .Sp
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467 .Vb 12
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468 \& X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
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469 \& BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
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470 \& LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
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471 \& SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
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472 \& DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
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473 \& TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
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474 \& H : NumOfImplicitAndExplicitHydrogens
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475 \& Ar : Aromatic
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476 \& RA : RingAtom
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477 \& FC : FormalCharge
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478 \& MN : MassNumber
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479 \& SM : SpinMultiplicity
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480 .Ve
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481 .Sp
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482 \&\fIAtomTypes::AtomicInvariantsAtomTypes\fR module is used to assign atomic invariant
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483 atom types.
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484 .IP "\fBSetFunctionalClassesToUse\fR" 4
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485 .IX Item "SetFunctionalClassesToUse"
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486 .Vb 2
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487 \& $ExtendedConnectivityFingerprints\->SetFunctionalClassesToUse($ValuesRef);
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488 \& $ExtendedConnectivityFingerprints\->SetFunctionalClassesToUse(@Values);
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489 .Ve
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490 .Sp
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491 Sets functional classes invariants to use during \fIFunctionalClassAtomTypes\fR value of \fIAtomIdentifierType\fR
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492 for extended connectivity fingerprints generation and returns \fIExtendedConnectivityFingerprints\fR.
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493 .Sp
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494 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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495 Default value [ Ref 24 ]: \fI\s-1HBD\s0,HBA,PI,NI,Ar,Hal\fR.
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496 .Sp
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497 The functional class abbreviations correspond to:
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498 .Sp
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499 .Vb 9
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500 \& HBD: HydrogenBondDonor
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501 \& HBA: HydrogenBondAcceptor
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502 \& PI : PositivelyIonizable
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503 \& NI : NegativelyIonizable
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504 \& Ar : Aromatic
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505 \& Hal : Halogen
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506 \& H : Hydrophobic
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507 \& RA : RingAtom
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508 \& CA : ChainAtom
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509 \&
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510 \& Functional class atom type specification for an atom corresponds to:
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511 \&
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512 \& Ar.CA.H.HBA.HBD.Hal.NI.PI.RA or None
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513 .Ve
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514 .Sp
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515 \&\fIAtomTypes::FunctionalClassAtomTypes\fR module is used to assign functional class atom
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516 types. It uses following definitions [ Ref 60\-61, Ref 65\-66 ]:
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517 .Sp
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518 .Vb 4
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519 \& HydrogenBondDonor: NH, NH2, OH
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520 \& HydrogenBondAcceptor: N[!H], O
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521 \& PositivelyIonizable: +, NH2
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522 \& NegativelyIonizable: \-, C(=O)OH, S(=O)OH, P(=O)OH
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523 .Ve
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524 .IP "\fBSetNeighborhoodRadius\fR" 4
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525 .IX Item "SetNeighborhoodRadius"
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526 .Vb 1
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527 \& $ExtendedConnectivityFingerprints\->SetNeighborhoodRadius($Radius);
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528 .Ve
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529 .Sp
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530 Sets neighborhood radius to use during extended connectivity fingerprints generation and
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531 returns \fIExtendedConnectivityFingerprints\fR.
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532 .IP "\fBStringifyExtendedConnectivityFingerprints\fR" 4
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533 .IX Item "StringifyExtendedConnectivityFingerprints"
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534 .Vb 1
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535 \& $String = $Fingerprints\->StringifyExtendedConnectivityFingerprints();
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536 .Ve
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537 .Sp
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538 Returns a string containing information about \fIExtendedConnectivityFingerprints\fR object.
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539 .SH "AUTHOR"
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540 .IX Header "AUTHOR"
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|
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541 Manish Sud <msud@san.rr.com>
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542 .SH "SEE ALSO"
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543 .IX Header "SEE ALSO"
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544 Fingerprints.pm, FingerprintsStringUtil.pm, AtomNeighborhoodsFingerprints.pm,
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545 AtomTypesFingerprints.pm, EStateIndiciesFingerprints.pm, MACCSKeys.pm,
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546 PathLengthFingerprints.pm, TopologicalAtomPairsFingerprints.pm,
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547 TopologicalAtomTripletsFingerprints.pm, TopologicalAtomTorsionsFingerprints.pm,
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548 TopologicalPharmacophoreAtomPairsFingerprints.pm,
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549 TopologicalPharmacophoreAtomTripletsFingerprints.pm
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550 .SH "COPYRIGHT"
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551 .IX Header "COPYRIGHT"
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552 Copyright (C) 2015 Manish Sud. All rights reserved.
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553 .PP
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554 This file is part of MayaChemTools.
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555 .PP
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556 MayaChemTools is free software; you can redistribute it and/or modify it under
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557 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
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558 Software Foundation; either version 3 of the License, or (at your option)
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559 any later version.
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