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124 .\" ========================================================================
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125 .\"
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126 .IX Title "TPSADESCRIPTORS 1"
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127 .TH TPSADESCRIPTORS 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 TPSADescriptors
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134 .SH "SYNOPSIS"
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135 .IX Header "SYNOPSIS"
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136 use MolecularDescriptors::TPSADescriptors;
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137 .PP
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138 use MolecularDescriptors::TPSADescriptors qw(:all);
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139 .SH "DESCRIPTION"
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140 .IX Header "DESCRIPTION"
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141 \&\fBTPSADescriptors\fR class provides the following methods:
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142 .PP
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143 new, GenerateDescriptors, GetDescriptorNames, StringifyTPSADescriptors
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144 .PP
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145 \&\fBTPSADescriptors\fR is derived from \fBMolecularDescriptors\fR class which in turn
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146 is derived from \fBObjectProperty\fR base class that provides methods not explicitly defined
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147 in \fBTPSADescriptors\fR, \fBMolecularDescriptors\fR or \fBObjectProperty\fR classes using Perl's
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148 \&\s-1AUTOLOAD\s0 functionality. These methods are generated on-the-fly for a specified object property:
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149 .PP
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150 .Vb 3
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151 \& Set<PropertyName>(<PropertyValue>);
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152 \& $PropertyValue = Get<PropertyName>();
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153 \& Delete<PropertyName>();
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154 .Ve
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155 .PP
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156 After Topological Polar Surface Area (\s-1TPSA\s0) atom types [ Ref 90\-91 ] has been assigned
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157 to appropriate atoms in a molecule using AtomTypes::TPSAAtomTypes.pm module, \s-1TPSA\s0 value
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158 is calculated by adding up contributions of each appropriate atom type.
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159 .PP
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160 By default, MayaChemTools only uses nitrogen and oxygen atoms during calculation
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161 of \s-1TPSA\s0 and ignores phosphorous and sulfur atoms. [ Ref 90 \- 91 ]
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162 .SS "\s-1METHODS\s0"
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163 .IX Subsection "METHODS"
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164 .IP "\fBnew\fR" 4
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165 .IX Item "new"
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166 .Vb 2
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167 \& $NewTPSADescriptors = new MolecularDescriptors::TPSADescriptors(
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168 \& %NamesAndValues);
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169 .Ve
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170 .Sp
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171 Using specified \fITPSADescriptors\fR property names and values hash, \fBnew\fR
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172 method creates a new object and returns a reference to newly created \fBTPSADescriptors\fR
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173 object. By default, the following properties are initialized:
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174 .Sp
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175 .Vb 6
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176 \& Molecule = \*(Aq\*(Aq
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177 \& Type = \*(AqTPSA\*(Aq
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178 \& IgnorePhosphorus = 1
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179 \& IgnoreSulfur = 1
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180 \& @DescriptorNames = (\*(AqTPSA\*(Aq)
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181 \& @DescriptorValues = (\*(AqNone\*(Aq)
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182 .Ve
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183 .Sp
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184 Examples:
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185 .Sp
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186 .Vb 2
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187 \& $TPSADescriptors = new MolecularDescriptors::TPSADescriptors(
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188 \& \*(AqMolecule\*(Aq => $Molecule);
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189 \&
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190 \& $TPSADescriptors = new MolecularDescriptors::TPSADescriptors();
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191 \&
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192 \& $TPSADescriptors = new MolecularDescriptors::TPSADescriptors(
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193 \& \*(AqIgnorePhosphorus\*(Aq => 0,
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194 \& \*(AqIgnoreSulfur\*(Aq => 0);
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195 \&
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196 \& $TPSADescriptors\->SetMolecule($Molecule);
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197 \& $TPSADescriptors\->GenerateDescriptors();
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198 \& print "TPSADescriptors: $TPSADescriptors\en";
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199 .Ve
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200 .IP "\fBGenerateDescriptors\fR" 4
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201 .IX Item "GenerateDescriptors"
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202 .Vb 1
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203 \& $TPSADescriptors\->GenerateDescriptors();
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204 .Ve
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205 .Sp
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206 Calculate \s-1TPSA\s0 value for a molecule and returns \fITPSADescriptors\fR.
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207 .IP "\fBGetDescriptorNames\fR" 4
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208 .IX Item "GetDescriptorNames"
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209 .Vb 3
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210 \& @DescriptorNames = $TPSADescriptors\->GetDescriptorNames();
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211 \& @DescriptorNames = MolecularDescriptors::TPSADescriptors::
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212 \& GetDescriptorNames();
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213 .Ve
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214 .Sp
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215 Returns all available descriptor names as an array.
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216 .IP "\fBStringifyTPSADescriptors\fR" 4
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217 .IX Item "StringifyTPSADescriptors"
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218 .Vb 1
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219 \& $String = $TPSADescriptors\->StringifyTPSADescriptors();
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220 .Ve
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221 .Sp
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222 Returns a string containing information about \fITPSADescriptors\fR object.
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223 .SH "AUTHOR"
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224 .IX Header "AUTHOR"
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225 Manish Sud <msud@san.rr.com>
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226 .SH "SEE ALSO"
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227 .IX Header "SEE ALSO"
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228 MolecularDescriptors.pm, MolecularDescriptorsGenerator.pm
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229 .SH "COPYRIGHT"
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230 .IX Header "COPYRIGHT"
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231 Copyright (C) 2015 Manish Sud. All rights reserved.
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232 .PP
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233 This file is part of MayaChemTools.
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234 .PP
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235 MayaChemTools is free software; you can redistribute it and/or modify it under
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236 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
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237 Software Foundation; either version 3 of the License, or (at your option)
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238 any later version.
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