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124 .\" ========================================================================
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125 .\"
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126 .IX Title "SDFILEUTIL 1"
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127 .TH SDFILEUTIL 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 SDFileUtil
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134 .SH "SYNOPSIS"
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135 .IX Header "SYNOPSIS"
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136 use SDFileUtil ;
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137 .PP
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138 use SDFileUtil qw(:all);
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139 .SH "DESCRIPTION"
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140 .IX Header "DESCRIPTION"
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141 \&\fBSDFileUtil\fR module provides the following functions:
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142 .PP
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143 GenerateCmpdAtomAliasPropertyLines, GenerateCmpdAtomLine, GenerateCmpdBondLine,
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144 GenerateCmpdChargePropertyLines, GenerateCmpdCommentsLine, GenerateCmpdCountsLine,
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145 GenerateCmpdDataHeaderLabelsAndValuesLines, GenerateCmpdIsotopePropertyLines,
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146 GenerateCmpdMiscInfoLine, GenerateCmpdMolNameLine,
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147 GenerateCmpdRadicalPropertyLines, GenerateEmptyCtabBlockLines,
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148 GenerateMiscLineDateStamp, GetAllAndCommonCmpdDataHeaderLabels,
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149 GetCmpdDataHeaderLabels, GetCmpdDataHeaderLabelsAndValues, GetCmpdFragments,
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150 GetCtabLinesCount, GetInvalidAtomNumbers, GetUnknownAtoms,
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151 InternalBondOrderToMDLBondType, InternalBondStereochemistryToMDLBondStereo,
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152 InternalChargeToMDLCharge, InternalSpinMultiplicityToMDLRadical, IsCmpd2D,
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153 IsCmpd3D, MDLBondStereoToInternalBondStereochemistry,
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154 MDLBondTypeToInternalBondOrder, MDLChargeToInternalCharge,
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155 MDLRadicalToInternalSpinMultiplicity, ParseCmpdAtomAliasPropertyLine,
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156 ParseCmpdAtomLine, ParseCmpdBondLine, ParseCmpdChargePropertyLine,
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157 ParseCmpdCommentsLine, ParseCmpdCountsLine, ParseCmpdIsotopePropertyLine,
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158 ParseCmpdMiscInfoLine, ParseCmpdMolNameLine, ParseCmpdRadicalPropertyLine,
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159 ReadCmpdString, RemoveCmpdDataHeaderLabelAndValue, WashCmpd
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160 .SH "METHODS"
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161 .IX Header "METHODS"
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162 .IP "\fBGenerateCmpdAtomAliasPropertyLines\fR" 4
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163 .IX Item "GenerateCmpdAtomAliasPropertyLines"
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164 .Vb 1
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165 \& @Lines = GenerateCmpdAtomAliasPropertyLines($AliasValuePairsRef);
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166 .Ve
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167 .Sp
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168 Returns a formatted atom alias property lines corresponding to successive pairs
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169 of atom number and alias values specified by a refernce to an array. Two lines
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170 are generate for each atom number and alias value pairs: First line \- A <AtomNum>;
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171 Second line:<AtomAlias>.
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172 .IP "\fBGenerateCmpdAtomLine\fR" 4
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173 .IX Item "GenerateCmpdAtomLine"
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174 .Vb 2
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175 \& $Line = GenerateCmpdAtomLine($AtomSymbol, $AtomX, $AtomY,
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176 \& $AtomZ, [$MassDifference, $Charge, $StereoParity]);
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177 .Ve
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178 .Sp
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179 Returns a formatted atom data line containing all the input values.
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180 .IP "\fBGenerateCmpdBondLine\fR" 4
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181 .IX Item "GenerateCmpdBondLine"
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182 .Vb 2
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183 \& $Line = GenerateCmpdBondLine($FirstAtomNum, $SecondAtomNum,
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184 \& $BondType, [$BondStereo]);
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185 .Ve
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186 .Sp
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187 Returns a formatted bond data line containing all the input values.
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188 .IP "\fBGenerateCmpdChargePropertyLines\fR" 4
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189 .IX Item "GenerateCmpdChargePropertyLines"
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190 .Vb 1
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191 \& @Lines = GenerateCmpdChargePropertyLines($ChargeValuePairsRef);
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192 .Ve
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193 .Sp
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194 Returns a formatted M \s-1CHG\s0 property lines corresponding to successive pairs of
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195 atom number and charge values specified by a refernce to an array.
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196 .IP "\fBGenerateCmpdCommentsLine\fR" 4
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197 .IX Item "GenerateCmpdCommentsLine"
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198 .Vb 1
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199 \& $Line = GenerateCmpdCommentsLine($Comments);
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200 .Ve
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201 .Sp
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202 Returns a formatted comments data line.
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203 .IP "\fBGenerateCmpdCountsLine\fR" 4
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204 .IX Item "GenerateCmpdCountsLine"
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205 .Vb 2
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206 \& $Line = GenerateCmpdCountsLine($AtomCount, $BondCount,
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207 \& $ChiralFlag, [$PropertyCount, $Version]);
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208 .Ve
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209 .Sp
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210 Returns a formatted line containing all the input values. The default values of 999
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211 and V2000 are used for \fIPropertyCount\fR and \fIVersion\fR.
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212 .IP "\fBGenerateCmpdDataHeaderLabelsAndValuesLines\fR" 4
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213 .IX Item "GenerateCmpdDataHeaderLabelsAndValuesLines"
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214 .Vb 3
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215 \& @Lines = GenerateCmpdDataHeaderLabelsAndValuesLines(
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216 \& $DataHeaderLabelsRef, $DataHeaderLabelsAndValuesRef,
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217 \& [$SortDataLabels]);
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218 .Ve
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219 .Sp
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220 Returns formatted data lines containing header label and values lines corresponding to
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221 all data header labels in array reference \fIDataHeaderLabelsRef\fR with values in hash
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222 reference \fIDataHeaderLabelsAndValuesRef\fR. By default, data header labels are
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223 not sorted and correspond to the label order in array reference \fIDataHeaderLabelsRef\fR.
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224 .IP "\fBGenerateCmpdIsotopePropertyLines\fR" 4
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225 .IX Item "GenerateCmpdIsotopePropertyLines"
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226 .Vb 1
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227 \& @Lines = GenerateCmpdIsotopePropertyLines($IsotopeValuePairsRef);
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228 .Ve
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229 .Sp
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230 Returns a formatted M \s-1ISO\s0 property lines corresponding to successive pairs of
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231 atom number and isotope values specified by a refernce to an array.
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232 .IP "\fBGenerateCmpdMiscInfoLine\fR" 4
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233 .IX Item "GenerateCmpdMiscInfoLine"
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234 .Vb 2
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235 \& $Line = GenerateCmpdMiscInfoLine([$ProgramName, $UserInitial,
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236 \& $Code]);
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237 .Ve
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238 .Sp
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239 Returns a formatted line containing specified user initial, program name, date and code.
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240 Default values are: \fIProgramName \- MayaChem; UserInitial \- \s-1NULL\s0; Code \- 2D\fR.
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241 .IP "\fBGenerateCmpdMolNameLine\fR" 4
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242 .IX Item "GenerateCmpdMolNameLine"
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243 .Vb 1
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244 \& $Line = GenerateCmpdMolNameLine($MolName);
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245 .Ve
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246 .Sp
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247 Returns a formatted molecule name data line.
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248 .IP "\fBGenerateCmpdRadicalPropertyLines\fR" 4
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249 .IX Item "GenerateCmpdRadicalPropertyLines"
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250 .Vb 1
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251 \& @Lines = GenerateCmpdRadicalPropertyLines($RadicalValuePairsRef);
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252 .Ve
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253 .Sp
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254 Returns a formatted M \s-1CHG\s0 property lines corresponding to successive pairs of
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255 atom number and multiplicity values specified by a refernce to an array.
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256 .IP "\fBGenerateEmptyCtabBlockLines\fR" 4
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257 .IX Item "GenerateEmptyCtabBlockLines"
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258 .Vb 1
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259 \& $Lines = GenerateCmpdMiscInfoLine([$Date]);
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260 .Ve
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261 .Sp
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262 Returns formatted lines representing empty \s-1CTAB\s0 block.
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263 .IP "\fBGenerateMiscLineDateStamp\fR" 4
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264 .IX Item "GenerateMiscLineDateStamp"
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265 .Vb 1
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266 \& $Line = GenerateMiscLineDateStamp();
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267 .Ve
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268 .Sp
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269 Returns date stamp for misc line.
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270 .IP "\fBGetAllAndCommonCmpdDataHeaderLabels\fR" 4
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271 .IX Item "GetAllAndCommonCmpdDataHeaderLabels"
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272 .Vb 3
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273 \& ($CmpdCount, $DataFieldLabelsArrayRef,
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274 \& $CommonDataFieldLabelsArrayRef) =
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275 \& GetAllAndCommonCmpdDataHeaderLabels(\e*SDFILE);
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276 .Ve
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277 .Sp
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278 Returns number of comopunds, a reference to an array containing all unique data header
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279 label and a reference to an array containing common data field labels for all compounds
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280 in \s-1SD\s0 file.
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281 .IP "\fBGetCmpdDataHeaderLabels\fR" 4
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282 .IX Item "GetCmpdDataHeaderLabels"
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283 .Vb 1
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284 \& (@Labels) = GetCmpdDataHeaderLabels(\e@CmpdLines);
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285 .Ve
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286 .Sp
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287 Returns an array containg data header labels for a compound
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288 .IP "\fBGetCmpdDataHeaderLabelsAndValues\fR" 4
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289 .IX Item "GetCmpdDataHeaderLabelsAndValues"
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290 .Vb 1
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291 \& (%DataValues) = GetCmpdDataHeaderLabelsAndValues(\e@CmpdLines);
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292 .Ve
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293 .Sp
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294 Returns a hash conating data header labes and values for a compound.
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295 .IP "\fBGetCmpdFragments\fR" 4
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296 .IX Item "GetCmpdFragments"
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297 .Vb 1
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298 \& ($FragmentCount, $FragmentString) = GetCmpdFragments(\e@CmpLines);
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299 .Ve
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300 .Sp
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301 Figures out the number of disconnected fragments and return their values along
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302 with the atom numbers in a string delimited by new line character. Fragment data
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303 in \fBFragmentString\fR is sorted on based on its size.
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304 .IP "\fBGetCtabLinesCount\fR" 4
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305 .IX Item "GetCtabLinesCount"
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306 .Vb 1
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307 \& $CtabLinesCount = GetCtabLinesCount(\e@CmpdLines);
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308 .Ve
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309 .Sp
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310 Returns number of lines present between the 4th line and the line containg \*(L"M \s-1END\s0\*(R".
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311 .IP "\fBGetInvalidAtomNumbers\fR" 4
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312 .IX Item "GetInvalidAtomNumbers"
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313 .Vb 2
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314 \& ($InvalidAtomNumbersCount, $InvalidAtomNumbers, $InvalidAtomNumberLines) =
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315 \& GetInvalidAtomNumbers(\e@CmpdLines);
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316 .Ve
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317 .Sp
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318 Returns a list of values containing information about invalid atom numbers present
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319 in block or atom property lines.
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320 .IP "\fBGetUnknownAtoms\fR" 4
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321 .IX Item "GetUnknownAtoms"
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322 .Vb 2
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323 \& ($UnknownAtomCount, $UnknownAtoms, $UnknownAtomLines) =
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324 \& GetUnknownAtoms(\e@CmpdLines);
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325 .Ve
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326 .Sp
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327 Returns a list of values containing information about atoms which contain special element
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328 symbols not present in the periodic table.
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329 .IP "\fBInternalBondOrderToMDLBondType\fR" 4
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330 .IX Item "InternalBondOrderToMDLBondType"
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331 .Vb 1
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332 \& $MDLBondType = InternalBondOrderToMDLBondType($InternalBondOrder);
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333 .Ve
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334 .Sp
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335 Returns value of \fIMDLBondType\fR corresponding to \fIInternalBondOrder\fR.
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336 .Sp
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337 .Vb 1
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338 \& InternalBondOrder MDLBondType
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339 \&
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340 \& 1 1
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341 \& 2 2
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342 \& 3 3
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343 \& 1.5 4
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344 .Ve
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345 .IP "\fBInternalBondStereochemistryToMDLBondStereo\fR" 4
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346 .IX Item "InternalBondStereochemistryToMDLBondStereo"
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347 .Vb 2
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348 \& $MDLBondStereo = InternalBondStereochemistryToMDLBondStereo(
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349 \& $InternalBondStereo);
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350 .Ve
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351 .Sp
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352 Returns value of \fIMDLBondStereo\fR corresponding to \fIInternalBondStereo\fR using following
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353 mapping:
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354 .Sp
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355 .Vb 1
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356 \& InternalBondStereo MDLBondStereo
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357 \&
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358 \& Up 1
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359 \& UpOrDown 4
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360 \& Down 6
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361 \& CisOrTrans 3
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362 \& Other 0
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363 .Ve
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364 .IP "\fBInternalChargeToMDLCharge\fR" 4
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365 .IX Item "InternalChargeToMDLCharge"
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366 .Vb 1
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367 \& $MDLCharge = InternalChargeToMDLCharge($InternalCharge);
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368 .Ve
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369 .Sp
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370 Returns value of \fIMDLCharge\fR corresponding to \fIInternalCharge\fR using following
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371 mapping:
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372 .Sp
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373 .Vb 1
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374 \& InternalCharge MDLCharge
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375 \&
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376 \& 3 1
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377 \& 2 2
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378 \& 1 3
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379 \& \-1 5
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380 \& \-2 6
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381 \& \-3 7
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382 .Ve
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383 .IP "\fBInternalSpinMultiplicityToMDLRadical\fR" 4
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384 .IX Item "InternalSpinMultiplicityToMDLRadical"
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385 .Vb 2
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386 \& $MDLRadical = InternalSpinMultiplicityToMDLRadical(
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387 \& $InternalSpinMultiplicity);
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388 .Ve
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389 .Sp
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390 Returns value of \fIMDLRadical\fR corresponding to \fIInternalSpinMultiplicity\fR. These
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391 value are equivalent.
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392 .IP "\fBMDLBondStereoToInternalBondType\fR" 4
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393 .IX Item "MDLBondStereoToInternalBondType"
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394 .Vb 1
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395 \& $InternalBondType = MDLBondStereoToInternalBondType($MDLBondStereo);
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396 .Ve
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397 .Sp
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398 Returns value of \fIInternalBondType\fR corresponding to \fIMDLBondStereo\fR using
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399 mapping shown for \fBInternalBondTypeToMDLBondStereo\fR function.
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400 .IP "\fBIsCmpd2D\fR" 4
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401 .IX Item "IsCmpd2D"
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402 .Vb 1
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403 \& $Status = IsCmpd2D();
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404 .Ve
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405 .Sp
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406 Returns 1 or 0 based on whether z\-coordinate of any atom is non-zero.
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407 .IP "\fBIsCmpd3D\fR" 4
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408 .IX Item "IsCmpd3D"
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409 .Vb 1
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410 \& $Status = IsCmpd3D();
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411 .Ve
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412 .Sp
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413 Returns 1 or 0 based on whether z\-coordinate of any atom is non-zero.
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414 .IP "\fBMDLBondStereoToInternalBondStereochemistry\fR" 4
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415 .IX Item "MDLBondStereoToInternalBondStereochemistry"
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416 .Vb 2
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417 \& $InternalBondStereo = MDLBondStereoToInternalBondStereochemistry(
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418 \& $MDLBondStereo);
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419 .Ve
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420 .Sp
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421 Returns value of \fIInternalBondStereo\fR corresponding to \fIMDLBondStereo\fR using
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422 mapping shown for \fBInternalBondStereochemistryToMDLBondStereo\fR function.
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423 .IP "\fBMDLBondTypeToInternalBondOrder\fR" 4
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424 .IX Item "MDLBondTypeToInternalBondOrder"
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425 .Vb 1
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426 \& $InternalBondOrder = MDLBondTypeToInternalBondOrder($MDLBondType);
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427 .Ve
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428 .Sp
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429 Returns value of \fIInternalBondOrder\fR corresponding to \fIMDLBondType\fR using
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430 mapping shown for \fBInternalBondOrderToMDLBondType\fR function.
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431 .IP "\fBMDLChargeToInternalCharge\fR" 4
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432 .IX Item "MDLChargeToInternalCharge"
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433 .Vb 1
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434 \& $InternalCharge = MDLChargeToInternalCharge($MDLCharge);
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435 .Ve
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436 .Sp
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437 Returns value of \fI\f(CI$InternalCharge\fI\fR corresponding to \fIMDLCharge\fR using
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438 mapping shown for \fBInternalChargeToMDLCharge\fR function.
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439 .IP "\fBMDLRadicalToInternalSpinMultiplicity\fR" 4
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440 .IX Item "MDLRadicalToInternalSpinMultiplicity"
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441 .Vb 2
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442 \& $InternalSpinMultiplicity = MDLRadicalToInternalSpinMultiplicity(
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443 \& $MDLRadical);
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444 .Ve
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445 .Sp
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446 Returns value of \fIInternalSpinMultiplicity\fR corresponding to \fIMDLRadical\fR. These
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447 value are equivalent.
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448 .IP "\fBParseCmpdAtomAliasPropertyLine\fR" 4
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449 .IX Item "ParseCmpdAtomAliasPropertyLine"
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450 .Vb 2
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451 \& @AtomNumAndValuePairs = ParseCmpdAtomAliasPropertyLine(
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452 \& $CurrentLine, $NexLine);
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453 .Ve
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454 .Sp
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455 Parses atom alias propery lines in \s-1CTAB\s0 generic properties block and returns an array
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456 with successive pairs of values corresponding to atom number and its alias.
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457 .IP "\fBParseCmpdAtomLine\fR" 4
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458 .IX Item "ParseCmpdAtomLine"
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459 .Vb 2
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460 \& ($AtomSymbol, $AtomX, $AtomY, $AtomZ, $MassDifference, $Charge,
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461 \& $StereoParity) = ParseCmpdAtomLine($AtomDataLine);
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462 .Ve
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463 .Sp
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464 Parses compound data line containing atom information and returns a list
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465 of values.
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466 .IP "\fBParseCmpdBondLine\fR" 4
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467 .IX Item "ParseCmpdBondLine"
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468 .Vb 2
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469 \& ($FirstAtomNum, $SecondAtomNum, $BondType) =
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470 \& ParseCmpdBondLine($BondDataLine);
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471 .Ve
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472 .Sp
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473 Parses compound data line containing bond information and returns a list of
|
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474 values.
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475 .IP "\fBParseCmpdCommentsLine\fR" 4
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476 .IX Item "ParseCmpdCommentsLine"
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477 .Vb 1
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478 \& $Comments = ParseCmpdCommentsLine($CommentsDataLine);
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479 .Ve
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480 .Sp
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481 Returns the comment string.
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482 .IP "\fBParseCmpdChargePropertyLine\fR" 4
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483 .IX Item "ParseCmpdChargePropertyLine"
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484 .Vb 2
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485 \& @AtomNumAndValuePairs = ParseCmpdChargePropertyLine(
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486 \& $ChargeDataLine);
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487 .Ve
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488 .Sp
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489 Parses charge propery line in \s-1CTAB\s0 generic properties block and returns an array
|
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|
490 with successive pairs of values corresponding to atom number and its charge.
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|
491 .IP "\fBParseCmpdCountsLine\fR" 4
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492 .IX Item "ParseCmpdCountsLine"
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|
493 .Vb 2
|
|
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494 \& ($AtomCount, $BondCount, $ChiralFlag, $PropertyCount, $Version) =
|
|
|
495 \& ParseCmpdCountsLine(\e@CountDataLines);
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|
496 .Ve
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|
|
497 .Sp
|
|
|
498 Returns a list of values containing count information.
|
|
|
499 .IP "\fBParseCmpdMiscInfoLine\fR" 4
|
|
|
500 .IX Item "ParseCmpdMiscInfoLine"
|
|
|
501 .Vb 2
|
|
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502 \& ($UserInitial, $ProgramName, $Date, $Code, $ScalingFactor1, $ScalingFactor2,
|
|
|
503 \& $Energy, $RegistryNum) = ParseCmpdMiscInfoLine($Line);
|
|
|
504 .Ve
|
|
|
505 .Sp
|
|
|
506 Returns a list of values containing miscellaneous information.
|
|
|
507 .IP "\fBParseCmpdIsotopePropertyLine\fR" 4
|
|
|
508 .IX Item "ParseCmpdIsotopePropertyLine"
|
|
|
509 .Vb 2
|
|
|
510 \& @AtomNumAndValuePairs = ParseCmpdIsotopePropertyLine(
|
|
|
511 \& $IsotopeDataLine);
|
|
|
512 .Ve
|
|
|
513 .Sp
|
|
|
514 Parses isotopic propery line in \s-1CTAB\s0 generic properties block and returns an array
|
|
|
515 with successive pairs of values corresponding to atom number and absolute mass of
|
|
|
516 atom isotope.
|
|
|
517 .IP "\fBParseCmpdMolNameLine\fR" 4
|
|
|
518 .IX Item "ParseCmpdMolNameLine"
|
|
|
519 .Vb 1
|
|
|
520 \& $MolName = ParseCmpdMolNameLine($Line);
|
|
|
521 .Ve
|
|
|
522 .Sp
|
|
|
523 Returns a string containing molecule name.
|
|
|
524 .IP "\fBParseCmpdRadicalPropertyLine\fR" 4
|
|
|
525 .IX Item "ParseCmpdRadicalPropertyLine"
|
|
|
526 .Vb 2
|
|
|
527 \& @AtomNumAndValuePairs = ParseCmpdRadicalPropertyLine(
|
|
|
528 \& $RadicalDataLine);
|
|
|
529 .Ve
|
|
|
530 .Sp
|
|
|
531 Parses radical propery line in \s-1CTAB\s0 generic properties block and returns an array
|
|
|
532 with successive pairs of values corresponding to atom number and radical number
|
|
|
533 value.
|
|
|
534 .IP "\fBRemoveCmpdDataHeaderLabelAndValue\fR" 4
|
|
|
535 .IX Item "RemoveCmpdDataHeaderLabelAndValue"
|
|
|
536 .Vb 2
|
|
|
537 \& $NewCmpdString = RemoveCmpdDataHeaderLabelAndValue($CmpdString,
|
|
|
538 \& $DataHeaderLabel);
|
|
|
539 .Ve
|
|
|
540 .Sp
|
|
|
541 Returns a \fBNewCmpdString\fR after removing \fIDataHeaderLabel\fR along with its
|
|
|
542 value from \fICmpdString\fR.
|
|
|
543 .IP "\fBReadCmpdString\fR" 4
|
|
|
544 .IX Item "ReadCmpdString"
|
|
|
545 .Vb 1
|
|
|
546 \& $CmpdString = ReadCmpdString(\e*SDFILEHANDLE);
|
|
|
547 .Ve
|
|
|
548 .Sp
|
|
|
549 Returns a string containing all the data lines for the next available compound
|
|
|
550 in an already open file indicated by \s-1SDFILEHANDLE\s0. A \s-1NULL\s0 string is returned
|
|
|
551 on \s-1EOF\s0.
|
|
|
552 .IP "\fBWashCmpd\fR" 4
|
|
|
553 .IX Item "WashCmpd"
|
|
|
554 .Vb 2
|
|
|
555 \& ($FragmentCount, $Fragments, $WashedCmpdString) =
|
|
|
556 \& WashCmpd(\e@CmpdLines);
|
|
|
557 .Ve
|
|
|
558 .Sp
|
|
|
559 Figures out the number of disconnected fragments and return their values along
|
|
|
560 with the atom numbers in a string delimited by new line character. Fragment data
|
|
|
561 in \fBFragmentString\fR is sorted on based on its size.
|
|
|
562 .SH "AUTHOR"
|
|
|
563 .IX Header "AUTHOR"
|
|
|
564 Manish Sud <msud@san.rr.com>
|
|
|
565 .SH "SEE ALSO"
|
|
|
566 .IX Header "SEE ALSO"
|
|
|
567 TextUtil.pm
|
|
|
568 .SH "COPYRIGHT"
|
|
|
569 .IX Header "COPYRIGHT"
|
|
|
570 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
571 .PP
|
|
|
572 This file is part of MayaChemTools.
|
|
|
573 .PP
|
|
|
574 MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
|
575 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
|
|
|
576 Software Foundation; either version 3 of the License, or (at your option)
|
|
|
577 any later version.
|
