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124 .\" ========================================================================
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125 .\"
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126 .IX Title "ESTATEINDICIESFINGERPRINTS 1"
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127 .TH ESTATEINDICIESFINGERPRINTS 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 EStateIndiciesFingerprints
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134 .SH "SYNOPSIS"
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135 .IX Header "SYNOPSIS"
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136 use Fingerprints::EStateIndiciesFingerprints;
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137 .PP
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138 use Fingerprints::EStateIndiciesFingerprints qw(:all);
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139 .SH "DESCRIPTION"
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140 .IX Header "DESCRIPTION"
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141 \&\fBEStateIndiciesFingerprints\fR [ Ref 75\-78 ] class provides the following methods:
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142 .PP
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143 new, GenerateFingerprints, GetDescription, SetEStateAtomTypesSetToUse,
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144 SetValuesPrecision, StringifyEStateIndiciesFingerprints
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145 .PP
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146 \&\fBEStateIndiciesFingerprints\fR is derived from \fBFingerprints\fR class which in turn
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147 is derived from \fBObjectProperty\fR base class that provides methods not explicitly defined
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148 in \fBAtomNeighborhoodsFingerprints\fR, \fBFingerprints\fR or \fBObjectProperty\fR classes using Perl's
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149 \&\s-1AUTOLOAD\s0 functionality. These methods are generated on-the-fly for a specified object property:
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150 .PP
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151 .Vb 3
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152 \& Set<PropertyName>(<PropertyValue>);
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153 \& $PropertyValue = Get<PropertyName>();
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154 \& Delete<PropertyName>();
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155 .Ve
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156 .PP
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157 E\-state atom types are assigned to all non-hydrogen atoms in a molecule using module
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158 AtomTypes::EStateAtomTypes.pm and E\-state values are calculated using module
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159 AtomicDescriptors::EStateValues.pm. Using E\-state atom types and E\-state values,
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160 \&\fBEStateIndiciesFingerprints\fR constituting sum of E\-state values for E\-sate atom types
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161 are generated.
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162 .PP
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163 Two types of E\-state atom types set size are allowed:
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164 .PP
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165 .Vb 4
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166 \& ArbitrarySize \- Corresponds to only E\-state atom types detected
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167 \& in molecule
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168 \& FixedSize \- Corresponds to fixed number of E\-state atom types previously
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169 \& defined
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170 .Ve
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171 .PP
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172 Module AtomTypes::EStateAtomTypes.pm, used to assign E\-state atom types to
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173 non-hydrogen atoms in the molecule, is able to assign atom types to any valid
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174 atom group. However, for \fIFixedSize\fR value of \fBEStateAtomTypesSetToUse\fR, only a
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175 fixed set of E\-state atom types corresponding to specific atom groups [ Appendix \s-1III\s0 in
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176 Ref 77 ] are used for fingerprints.
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177 .PP
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178 The fixed size E\-state atom type set size used during generation of fingerprints contains
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179 87 E\-state non-hydrogen atom types in EStateAtomTypes.csv data file distributed with
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180 MayaChemTools.
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181 .PP
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182 Combination of Type and EStateAtomTypesSetToUse allow generation of 2 different types of
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183 E\-state indicies fingerprints:
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184 .PP
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185 .Vb 1
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186 \& Type EStateAtomTypesSetToUse
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187 \&
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188 \& EStateIndicies ArbitrarySize [ default fingerprints ]
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189 \& EStateIndicies FixedSize
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190 .Ve
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191 .PP
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192 The current release of MayaChemTools generates the following types of E\-state
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193 fingerprints vector strings:
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194 .PP
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195 .Vb 4
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196 \& FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
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197 \& AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
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198 \& H SsssCH;24.778 4.387 1.993 25.023 \-1.435 3.975 14.006 29.759 \-0.073 3
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199 \& .024 \-2.270
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200 \&
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201 \& FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
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202 \& ValuesString;0 0 0 0 0 0 0 3.975 0 \-0.073 0 0 24.778 \-2.270 0 0 \-1.435
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203 \& 4.387 0 0 0 0 0 0 3.024 0 0 0 0 0 0 0 1.993 0 29.759 25.023 0 0 0 0 1
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204 \& 4.006 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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205 \& 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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206 \&
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207 \& FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
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208 \& IDsAndValuesString;SsLi SssBe SssssBem SsBH2 SssBH SsssB SssssBm SsCH3
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209 \& SdCH2 SssCH2 StCH SdsCH SaaCH SsssCH SddC StsC SdssC SaasC SaaaC Sssss
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210 \& C SsNH3p SsNH2 SssNH2p SdNH SssNH SaaNH StN SsssNHp SdsN SaaN SsssN Sd
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211 \& 0 0 0 0 0 0 0 3.975 0 \-0.073 0 0 24.778 \-2.270 0 0 \-1.435 4.387 0 0 0
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212 \& 0 0 0 3.024 0 0 0 0 0 0 0 1.993 0 29.759 25.023 0 0 0 0 14.006 0 0 0 0
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213 \& 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0...
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214 .Ve
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215 .SS "\s-1METHODS\s0"
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216 .IX Subsection "METHODS"
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217 .IP "\fBnew\fR" 4
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218 .IX Item "new"
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219 .Vb 1
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220 \& $EStateIndiciesFingerprints = new EStateIndiciesFingerprints(%NamesAndValues);
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221 .Ve
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222 .Sp
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223 Using specified \fIEStateIndiciesFingerprints\fR property names and values hash, \fBnew\fR method creates a new object
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224 and returns a reference to newly created \fBPathLengthFingerprints\fR object. By default, the
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225 following properties are initialized:
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226 .Sp
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227 .Vb 4
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228 \& Molecule = \*(Aq\*(Aq;
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229 \& Type = \*(AqEStateIndicies\*(Aq
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230 \& EStateAtomTypesSetToUse = \*(AqArbitrarySize\*(Aq
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231 \& ValuesPrecision = 3
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232 .Ve
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233 .Sp
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234 Examples:
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235 .Sp
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236 .Vb 4
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237 \& $EStateIndiciesFingerprints = new AtomTypesFingerprints(
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238 \& \*(AqMolecule\*(Aq => $Molecule,
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239 \& \*(AqEStateAtomTypesSetToUse\*(Aq =>
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240 \& \*(AqArbitrarySize\*(Aq);
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241 \&
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242 \& $EStateIndiciesFingerprints = new AtomTypesFingerprints(
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243 \& \*(AqMolecule\*(Aq => $Molecule,
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244 \& \*(AqEStateAtomTypesSetToUse\*(Aq =>
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245 \& \*(AqFixedSize\*(Aq);
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246 \&
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247 \& $EStateIndiciesFingerprints\->GenerateFingerprints();
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248 \& print "$EStateIndiciesFingerprints\en";
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249 .Ve
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250 .IP "\fBGenerateFingerprints\fR" 4
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251 .IX Item "GenerateFingerprints"
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252 .Vb 2
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253 \& $EStateIndiciesFingerprints = $EStateIndiciesFingerprints\->
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254 \& GenerateEStateIndiciesFingerprints();
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255 .Ve
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256 .Sp
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257 Generates EState keys fingerprints and returns \fIEStateIndiciesFingerprints\fR.
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258 .IP "\fBGetDescription\fR" 4
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259 .IX Item "GetDescription"
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260 .Vb 1
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261 \& $Description = $EStateIndiciesFingerprints\->GetDescription();
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262 .Ve
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263 .Sp
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264 Returns a string containing description of EState keys fingerprints.
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265 .IP "\fBSetEStateAtomTypesSetToUse\fR" 4
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266 .IX Item "SetEStateAtomTypesSetToUse"
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267 .Vb 1
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268 \& $EStateIndiciesFingerprints\->SetEStateAtomTypesSetToUse($Value);
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269 .Ve
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270 .Sp
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271 Sets \fIValue\fR of \fIEStateAtomTypesSetToUse\fR and returns \fIEStateIndiciesFingerprints\fR.
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272 Possible values: \fIArbitrarySize or FixedSize\fR. Default value: \fIArbitrarySize\fR.
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273 .IP "\fBSetValuesPrecision\fR" 4
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274 .IX Item "SetValuesPrecision"
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275 .Vb 1
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276 \& $EStateIndiciesFingerprints\->SetValuesPrecision($Precision);
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277 .Ve
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278 .Sp
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279 Sets precesion of E\-state values to use during generation of E\-state indices fingerprints
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280 and returns \fIEStateIndiciesFingerprints\fR. Possible values: \fIPositive integers\fR.
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281 Default value: \fI3\fR.
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282 .IP "\fBStringifyEStateIndiciesFingerprints\fR" 4
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283 .IX Item "StringifyEStateIndiciesFingerprints"
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284 .Vb 1
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285 \& $String = $EStateIndiciesFingerprints\->StringifyEStateIndiciesFingerprints();
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286 .Ve
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287 .Sp
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288 Returns a string containing information about \fIEStateIndiciesFingerprints\fR object.
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289 .SH "AUTHOR"
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290 .IX Header "AUTHOR"
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291 Manish Sud <msud@san.rr.com>
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292 .SH "SEE ALSO"
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293 .IX Header "SEE ALSO"
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294 Fingerprints.pm, FingerprintsStringUtil.pm, AtomNeighborhoodsFingerprints.pm, AtomTypesFingerprints.pm,
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295 ExtendedConnectivityFingerprints.pm, MACCSKeys.pm, PathLengthFingerprints.pm,
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296 TopologicalAtomPairsFingerprints.pm, TopologicalAtomTripletsFingerprints.pm,
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297 TopologicalAtomTorsionsFingerprints.pm, TopologicalPharmacophoreAtomPairsFingerprints.pm,
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298 TopologicalPharmacophoreAtomTripletsFingerprints.pm
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299 .SH "COPYRIGHT"
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300 .IX Header "COPYRIGHT"
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301 Copyright (C) 2015 Manish Sud. All rights reserved.
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302 .PP
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303 This file is part of MayaChemTools.
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304 .PP
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305 MayaChemTools is free software; you can redistribute it and/or modify it under
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306 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
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307 Software Foundation; either version 3 of the License, or (at your option)
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308 any later version.
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