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124 .\" ========================================================================
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125 .\"
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126 .IX Title "MOLECULEFILEIO 1"
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127 .TH MOLECULEFILEIO 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 MoleculeFileIO
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134 .SH "SYNOPSIS"
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135 .IX Header "SYNOPSIS"
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136 use MoleculeFileIO;
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137 .PP
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138 use MoleculeFileIO qw(:all);
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139 .SH "DESCRIPTION"
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140 .IX Header "DESCRIPTION"
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141 \&\fBMoleculeFileIO\fR class provides the following methods:
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142 .PP
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143 new, Close, IsSupportedMoleculeFileFormat, Open, ReadMolecule,
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144 ReadMoleculeString, WriteMolecule
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145 .PP
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146 The following methods can also be used as functions:
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147 .PP
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148 IsSupportedMoleculeFileFormat
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149 .SS "\s-1METHODS\s0"
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150 .IX Subsection "METHODS"
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151 .IP "\fBnew\fR" 4
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152 .IX Item "new"
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153 .Vb 1
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154 \& $NewMoleculeFileIO = new MoleculeFileIO([%PropertyNameAndValues]);
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155 .Ve
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156 .Sp
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157 Using specified \fIMoleculeFileIO\fR property names and values hash, \fBnew\fR method
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158 creates a new object and returns a reference to newly created \fBMoleculeFileIO\fR object.
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159 By default, following properties are initialized:
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160 .Sp
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161 .Vb 3
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162 \& Name = ""
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163 \& Mode = ""
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164 \& FileIORef = ""
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165 .Ve
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166 .Sp
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167 Based on extension of specified file \fIName\fR, an input class is automatically associated to
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168 provide molecule read and write methods.
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169 .Sp
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170 Examples:
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171 .Sp
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172 .Vb 9
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173 \& $Name = "Water.mol";
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174 \& $Mode = "Read";
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175 \& $MoleculeFileIO = new MoleculeFileIO(\*(AqName\*(Aq => $Name,
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176 \& \*(AqMode\*(Aq => $Mode);
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177 \& $MoleculeFileIO\->Open();
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178 \& $Molecule = $MoleculeFileIO\->ReadMolecule();
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179 \& $Molecule\->DetectRings();
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180 \& print "$Molecule\en";
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181 \& $MoleculeFileIO\->Close();
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182 \&
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183 \& $MoleculeFileIO = new MoleculeFileIO(\*(AqName\*(Aq => \*(AqSample1.sdf\*(Aq,
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184 \& \*(AqMode\*(Aq => \*(AqRead\*(Aq);
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185 \& $MoleculeFileIO\->Open();
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186 \& while ($Molecule = $MoleculeFileIO1\->ReadMolecule()) {
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187 \& $Molecule\->DetectRings();
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188 \& print "$Molecule\en";
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189 \&
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190 \& $DataLabelsAndValuesRef =
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191 \& $Molecule\->GetDataFieldLabelAndValues();
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192 \& for $DataLabel (sort keys %{$DataLabelsAndValuesRef} ) {
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193 \& $DataValue = $DataLabelsAndValuesRef\->{$DataLabel};
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194 \& print "<DataLabel: $DataLabel; DataValue: $DataValue>; ";
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195 \& }
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196 \& print "\en";
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197 \& }
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198 \& $MoleculeFileIO\->Close();
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199 .Ve
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200 .IP "\fBClose\fR" 4
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201 .IX Item "Close"
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202 .Vb 1
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203 \& $MoleculeFileIO\->Close();
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204 .Ve
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205 .Sp
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206 Closes an open file
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207 .IP "\fBIsSupportedMoleculeFileFormat\fR" 4
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208 .IX Item "IsSupportedMoleculeFileFormat"
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209 .Vb 4
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210 \& $Status = $MoleculeFileIO\->IsSupportedMoleculeFileFormat($Name);
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211 \& $Status = MoleculeFileIO::IsSupportedMoleculeFileFormat($Name);
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212 \& ($Status, $FormatType, $IOClassName) =
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213 \& $MoleculeFileIO::IsSupportedMoleculeFileFormat($Name);
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214 .Ve
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215 .Sp
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216 Returns 1 or 0 based on whether input file \fIName\fR format is supported. In list context,
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217 value of supported format type and name of associated \s-1IO\s0 class is also returned.
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218 .Sp
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219 File extension is used to determine file format. Currently, following file extensions are
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220 supported:
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221 .Sp
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222 .Vb 1
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223 \& FileExts \- FormatType \- AssociatedIOClassName
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224 \&
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225 \& .mol \- MDLMOL \- MDLMolFileIO
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226 \& .sdf, .sd \- SDF \- SDFileIO
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227 .Ve
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228 .IP "\fBOpen\fR" 4
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229 .IX Item "Open"
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230 .Vb 1
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231 \& $MoleculeFileIO\->Open([$Mode]);
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232 .Ve
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233 .Sp
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234 Opens a file in a specified \fIMode\fR. Default mode value: \fIRead\fR. Supported mode
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235 values:
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236 .Sp
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237 .Vb 1
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238 \& Read, Write, Append, <, >, >>, r, w, or a
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239 .Ve
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240 .IP "\fBReadMolecule\fR" 4
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241 .IX Item "ReadMolecule"
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242 .Vb 1
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243 \& $Molecule = $MoleculeFileIO\->ReadMolecule();
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244 .Ve
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245 .Sp
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246 Reads molecule data from the file and returns a \fIMolecule\fR object.
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247 .IP "\fBReadMoleculeString\fR" 4
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248 .IX Item "ReadMoleculeString"
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249 .Vb 1
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250 \& $MoleculeString = $MoleculeFileIO\->ReadMoleculeString();
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251 .Ve
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252 .Sp
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253 Reads molecule data from a file and returns a \fIMolecule\fR string.
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254 .IP "\fBWriteMolecule\fR" 4
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255 .IX Item "WriteMolecule"
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256 .Vb 1
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257 \& $MoleculeFileIO\->WriteMolecule();
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258 .Ve
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259 .Sp
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260 Write molecule data to a file for a \fIMolecule\fR.
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261 .SH "AUTHOR"
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262 .IX Header "AUTHOR"
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263 Manish Sud <msud@san.rr.com>
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264 .SH "SEE ALSO"
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265 .IX Header "SEE ALSO"
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266 FileIO.pm, MDLMolFileIO.pm, SDFileIO.pm
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267 .SH "COPYRIGHT"
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268 .IX Header "COPYRIGHT"
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269 Copyright (C) 2015 Manish Sud. All rights reserved.
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270 .PP
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271 This file is part of MayaChemTools.
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272 .PP
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273 MayaChemTools is free software; you can redistribute it and/or modify it under
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274 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
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275 Software Foundation; either version 3 of the License, or (at your option)
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276 any later version.
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