diff docs/modules/txt/SDFileUtil.txt @ 0:4816e4a8ae95 draft default tip

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+NAME
+    SDFileUtil
+
+SYNOPSIS
+    use SDFileUtil ;
+
+    use SDFileUtil qw(:all);
+
+DESCRIPTION
+    SDFileUtil module provides the following functions:
+
+    GenerateCmpdAtomAliasPropertyLines, GenerateCmpdAtomLine,
+    GenerateCmpdBondLine, GenerateCmpdChargePropertyLines,
+    GenerateCmpdCommentsLine, GenerateCmpdCountsLine,
+    GenerateCmpdDataHeaderLabelsAndValuesLines,
+    GenerateCmpdIsotopePropertyLines, GenerateCmpdMiscInfoLine,
+    GenerateCmpdMolNameLine, GenerateCmpdRadicalPropertyLines,
+    GenerateEmptyCtabBlockLines, GenerateMiscLineDateStamp,
+    GetAllAndCommonCmpdDataHeaderLabels, GetCmpdDataHeaderLabels,
+    GetCmpdDataHeaderLabelsAndValues, GetCmpdFragments, GetCtabLinesCount,
+    GetInvalidAtomNumbers, GetUnknownAtoms, InternalBondOrderToMDLBondType,
+    InternalBondStereochemistryToMDLBondStereo, InternalChargeToMDLCharge,
+    InternalSpinMultiplicityToMDLRadical, IsCmpd2D, IsCmpd3D,
+    MDLBondStereoToInternalBondStereochemistry,
+    MDLBondTypeToInternalBondOrder, MDLChargeToInternalCharge,
+    MDLRadicalToInternalSpinMultiplicity, ParseCmpdAtomAliasPropertyLine,
+    ParseCmpdAtomLine, ParseCmpdBondLine, ParseCmpdChargePropertyLine,
+    ParseCmpdCommentsLine, ParseCmpdCountsLine,
+    ParseCmpdIsotopePropertyLine, ParseCmpdMiscInfoLine,
+    ParseCmpdMolNameLine, ParseCmpdRadicalPropertyLine, ReadCmpdString,
+    RemoveCmpdDataHeaderLabelAndValue, WashCmpd
+
+METHODS
+    GenerateCmpdAtomAliasPropertyLines
+            @Lines = GenerateCmpdAtomAliasPropertyLines($AliasValuePairsRef);
+
+        Returns a formatted atom alias property lines corresponding to
+        successive pairs of atom number and alias values specified by a
+        refernce to an array. Two lines are generate for each atom number
+        and alias value pairs: First line - A <AtomNum>; Second
+        line:<AtomAlias>.
+
+    GenerateCmpdAtomLine
+            $Line = GenerateCmpdAtomLine($AtomSymbol, $AtomX, $AtomY,
+                    $AtomZ, [$MassDifference, $Charge, $StereoParity]);
+
+        Returns a formatted atom data line containing all the input values.
+
+    GenerateCmpdBondLine
+            $Line = GenerateCmpdBondLine($FirstAtomNum, $SecondAtomNum,
+                    $BondType, [$BondStereo]);
+
+        Returns a formatted bond data line containing all the input values.
+
+    GenerateCmpdChargePropertyLines
+            @Lines = GenerateCmpdChargePropertyLines($ChargeValuePairsRef);
+
+        Returns a formatted M CHG property lines corresponding to successive
+        pairs of atom number and charge values specified by a refernce to an
+        array.
+
+    GenerateCmpdCommentsLine
+            $Line = GenerateCmpdCommentsLine($Comments);
+
+        Returns a formatted comments data line.
+
+    GenerateCmpdCountsLine
+            $Line = GenerateCmpdCountsLine($AtomCount, $BondCount,
+                    $ChiralFlag, [$PropertyCount, $Version]);
+
+        Returns a formatted line containing all the input values. The
+        default values of 999 and V2000 are used for *PropertyCount* and
+        *Version*.
+
+    GenerateCmpdDataHeaderLabelsAndValuesLines
+            @Lines = GenerateCmpdDataHeaderLabelsAndValuesLines(
+                     $DataHeaderLabelsRef, $DataHeaderLabelsAndValuesRef,
+                     [$SortDataLabels]);
+
+        Returns formatted data lines containing header label and values
+        lines corresponding to all data header labels in array reference
+        *DataHeaderLabelsRef* with values in hash reference
+        *DataHeaderLabelsAndValuesRef*. By default, data header labels are
+        not sorted and correspond to the label order in array reference
+        *DataHeaderLabelsRef*.
+
+    GenerateCmpdIsotopePropertyLines
+            @Lines = GenerateCmpdIsotopePropertyLines($IsotopeValuePairsRef);
+
+        Returns a formatted M ISO property lines corresponding to successive
+        pairs of atom number and isotope values specified by a refernce to
+        an array.
+
+    GenerateCmpdMiscInfoLine
+            $Line = GenerateCmpdMiscInfoLine([$ProgramName, $UserInitial,
+                    $Code]);
+
+        Returns a formatted line containing specified user initial, program
+        name, date and code. Default values are: *ProgramName - MayaChem;
+        UserInitial - NULL; Code - 2D*.
+
+    GenerateCmpdMolNameLine
+            $Line = GenerateCmpdMolNameLine($MolName);
+
+        Returns a formatted molecule name data line.
+
+    GenerateCmpdRadicalPropertyLines
+            @Lines = GenerateCmpdRadicalPropertyLines($RadicalValuePairsRef);
+
+        Returns a formatted M CHG property lines corresponding to successive
+        pairs of atom number and multiplicity values specified by a refernce
+        to an array.
+
+    GenerateEmptyCtabBlockLines
+            $Lines = GenerateCmpdMiscInfoLine([$Date]);
+
+        Returns formatted lines representing empty CTAB block.
+
+    GenerateMiscLineDateStamp
+            $Line = GenerateMiscLineDateStamp();
+
+        Returns date stamp for misc line.
+
+    GetAllAndCommonCmpdDataHeaderLabels
+            ($CmpdCount, $DataFieldLabelsArrayRef,
+               $CommonDataFieldLabelsArrayRef) =
+                  GetAllAndCommonCmpdDataHeaderLabels(\*SDFILE);
+
+        Returns number of comopunds, a reference to an array containing all
+        unique data header label and a reference to an array containing
+        common data field labels for all compounds in SD file.
+
+    GetCmpdDataHeaderLabels
+            (@Labels) = GetCmpdDataHeaderLabels(\@CmpdLines);
+
+        Returns an array containg data header labels for a compound
+
+    GetCmpdDataHeaderLabelsAndValues
+            (%DataValues) = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines);
+
+        Returns a hash conating data header labes and values for a compound.
+
+    GetCmpdFragments
+            ($FragmentCount, $FragmentString) = GetCmpdFragments(\@CmpLines);
+
+        Figures out the number of disconnected fragments and return their
+        values along with the atom numbers in a string delimited by new line
+        character. Fragment data in FragmentString is sorted on based on its
+        size.
+
+    GetCtabLinesCount
+            $CtabLinesCount = GetCtabLinesCount(\@CmpdLines);
+
+        Returns number of lines present between the 4th line and the line
+        containg "M END".
+
+    GetInvalidAtomNumbers
+            ($InvalidAtomNumbersCount, $InvalidAtomNumbers, $InvalidAtomNumberLines) =
+               GetInvalidAtomNumbers(\@CmpdLines);
+
+        Returns a list of values containing information about invalid atom
+        numbers present in block or atom property lines.
+
+    GetUnknownAtoms
+            ($UnknownAtomCount, $UnknownAtoms, $UnknownAtomLines) =
+               GetUnknownAtoms(\@CmpdLines);
+
+        Returns a list of values containing information about atoms which
+        contain special element symbols not present in the periodic table.
+
+    InternalBondOrderToMDLBondType
+            $MDLBondType = InternalBondOrderToMDLBondType($InternalBondOrder);
+
+        Returns value of *MDLBondType* corresponding to *InternalBondOrder*.
+
+            InternalBondOrder  MDLBondType
+
+             1                  1
+             2                  2
+             3                  3
+             1.5                4
+
+    InternalBondStereochemistryToMDLBondStereo
+            $MDLBondStereo = InternalBondStereochemistryToMDLBondStereo(
+                             $InternalBondStereo);
+
+        Returns value of *MDLBondStereo* corresponding to
+        *InternalBondStereo* using following mapping:
+
+            InternalBondStereo  MDLBondStereo
+
+             Up          1
+             UpOrDown    4
+             Down        6
+             CisOrTrans  3
+             Other       0
+
+    InternalChargeToMDLCharge
+            $MDLCharge = InternalChargeToMDLCharge($InternalCharge);
+
+        Returns value of *MDLCharge* corresponding to *InternalCharge* using
+        following mapping:
+
+            InternalCharge  MDLCharge
+
+             3               1
+             2               2
+             1               3
+            -1              5
+            -2              6
+            -3              7
+
+    InternalSpinMultiplicityToMDLRadical
+            $MDLRadical = InternalSpinMultiplicityToMDLRadical(
+                          $InternalSpinMultiplicity);
+
+        Returns value of *MDLRadical* corresponding to
+        *InternalSpinMultiplicity*. These value are equivalent.
+
+    MDLBondStereoToInternalBondType
+            $InternalBondType = MDLBondStereoToInternalBondType($MDLBondStereo);
+
+        Returns value of *InternalBondType* corresponding to *MDLBondStereo*
+        using mapping shown for InternalBondTypeToMDLBondStereo function.
+
+    IsCmpd2D
+            $Status = IsCmpd2D();
+
+        Returns 1 or 0 based on whether z-coordinate of any atom is
+        non-zero.
+
+    IsCmpd3D
+            $Status = IsCmpd3D();
+
+        Returns 1 or 0 based on whether z-coordinate of any atom is
+        non-zero.
+
+    MDLBondStereoToInternalBondStereochemistry
+            $InternalBondStereo = MDLBondStereoToInternalBondStereochemistry(
+                                  $MDLBondStereo);
+
+        Returns value of *InternalBondStereo* corresponding to
+        *MDLBondStereo* using mapping shown for
+        InternalBondStereochemistryToMDLBondStereo function.
+
+    MDLBondTypeToInternalBondOrder
+            $InternalBondOrder = MDLBondTypeToInternalBondOrder($MDLBondType);
+
+        Returns value of *InternalBondOrder* corresponding to *MDLBondType*
+        using mapping shown for InternalBondOrderToMDLBondType function.
+
+    MDLChargeToInternalCharge
+            $InternalCharge = MDLChargeToInternalCharge($MDLCharge);
+
+        Returns value of *$InternalCharge* corresponding to *MDLCharge*
+        using mapping shown for InternalChargeToMDLCharge function.
+
+    MDLRadicalToInternalSpinMultiplicity
+            $InternalSpinMultiplicity = MDLRadicalToInternalSpinMultiplicity(
+                                        $MDLRadical);
+
+        Returns value of *InternalSpinMultiplicity* corresponding to
+        *MDLRadical*. These value are equivalent.
+
+    ParseCmpdAtomAliasPropertyLine
+            @AtomNumAndValuePairs = ParseCmpdAtomAliasPropertyLine(
+                                    $CurrentLine, $NexLine);
+
+        Parses atom alias propery lines in CTAB generic properties block and
+        returns an array with successive pairs of values corresponding to
+        atom number and its alias.
+
+    ParseCmpdAtomLine
+            ($AtomSymbol, $AtomX, $AtomY, $AtomZ, $MassDifference, $Charge,
+               $StereoParity) = ParseCmpdAtomLine($AtomDataLine);
+
+        Parses compound data line containing atom information and returns a
+        list of values.
+
+    ParseCmpdBondLine
+            ($FirstAtomNum, $SecondAtomNum, $BondType) =
+               ParseCmpdBondLine($BondDataLine);
+
+        Parses compound data line containing bond information and returns a
+        list of values.
+
+    ParseCmpdCommentsLine
+            $Comments = ParseCmpdCommentsLine($CommentsDataLine);
+
+        Returns the comment string.
+
+    ParseCmpdChargePropertyLine
+            @AtomNumAndValuePairs = ParseCmpdChargePropertyLine(
+                                    $ChargeDataLine);
+
+        Parses charge propery line in CTAB generic properties block and
+        returns an array with successive pairs of values corresponding to
+        atom number and its charge.
+
+    ParseCmpdCountsLine
+            ($AtomCount, $BondCount, $ChiralFlag, $PropertyCount, $Version) =
+               ParseCmpdCountsLine(\@CountDataLines);
+
+        Returns a list of values containing count information.
+
+    ParseCmpdMiscInfoLine
+            ($UserInitial, $ProgramName, $Date, $Code, $ScalingFactor1, $ScalingFactor2,
+               $Energy, $RegistryNum) =  ParseCmpdMiscInfoLine($Line);
+
+        Returns a list of values containing miscellaneous information.
+
+    ParseCmpdIsotopePropertyLine
+            @AtomNumAndValuePairs = ParseCmpdIsotopePropertyLine(
+                                    $IsotopeDataLine);
+
+        Parses isotopic propery line in CTAB generic properties block and
+        returns an array with successive pairs of values corresponding to
+        atom number and absolute mass of atom isotope.
+
+    ParseCmpdMolNameLine
+            $MolName = ParseCmpdMolNameLine($Line);
+
+        Returns a string containing molecule name.
+
+    ParseCmpdRadicalPropertyLine
+            @AtomNumAndValuePairs = ParseCmpdRadicalPropertyLine(
+                                    $RadicalDataLine);
+
+        Parses radical propery line in CTAB generic properties block and
+        returns an array with successive pairs of values corresponding to
+        atom number and radical number value.
+
+    RemoveCmpdDataHeaderLabelAndValue
+            $NewCmpdString = RemoveCmpdDataHeaderLabelAndValue($CmpdString,
+                                                               $DataHeaderLabel);
+
+        Returns a NewCmpdString after removing *DataHeaderLabel* along with
+        its value from *CmpdString*.
+
+    ReadCmpdString
+            $CmpdString = ReadCmpdString(\*SDFILEHANDLE);
+
+        Returns a string containing all the data lines for the next
+        available compound in an already open file indicated by
+        SDFILEHANDLE. A NULL string is returned on EOF.
+
+    WashCmpd
+            ($FragmentCount, $Fragments, $WashedCmpdString) = 
+               WashCmpd(\@CmpdLines);
+
+        Figures out the number of disconnected fragments and return their
+        values along with the atom numbers in a string delimited by new line
+        character. Fragment data in FragmentString is sorted on based on its
+        size.
+
+AUTHOR
+    Manish Sud <[e-mail]>
+
+SEE ALSO
+    TextUtil.pm
+
+COPYRIGHT
+    Copyright (C) 2015 Manish Sud. All rights reserved.
+
+    This file is part of MayaChemTools.
+
+    MayaChemTools is free software; you can redistribute it and/or modify it
+    under the terms of the GNU Lesser General Public License as published by
+    the Free Software Foundation; either version 3 of the License, or (at
+    your option) any later version.
+