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1 NAME
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2 SDFileUtil
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3
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4 SYNOPSIS
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5 use SDFileUtil ;
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6
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7 use SDFileUtil qw(:all);
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8
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9 DESCRIPTION
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10 SDFileUtil module provides the following functions:
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11
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12 GenerateCmpdAtomAliasPropertyLines, GenerateCmpdAtomLine,
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13 GenerateCmpdBondLine, GenerateCmpdChargePropertyLines,
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14 GenerateCmpdCommentsLine, GenerateCmpdCountsLine,
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15 GenerateCmpdDataHeaderLabelsAndValuesLines,
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16 GenerateCmpdIsotopePropertyLines, GenerateCmpdMiscInfoLine,
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17 GenerateCmpdMolNameLine, GenerateCmpdRadicalPropertyLines,
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18 GenerateEmptyCtabBlockLines, GenerateMiscLineDateStamp,
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19 GetAllAndCommonCmpdDataHeaderLabels, GetCmpdDataHeaderLabels,
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20 GetCmpdDataHeaderLabelsAndValues, GetCmpdFragments, GetCtabLinesCount,
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21 GetInvalidAtomNumbers, GetUnknownAtoms, InternalBondOrderToMDLBondType,
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22 InternalBondStereochemistryToMDLBondStereo, InternalChargeToMDLCharge,
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23 InternalSpinMultiplicityToMDLRadical, IsCmpd2D, IsCmpd3D,
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24 MDLBondStereoToInternalBondStereochemistry,
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25 MDLBondTypeToInternalBondOrder, MDLChargeToInternalCharge,
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26 MDLRadicalToInternalSpinMultiplicity, ParseCmpdAtomAliasPropertyLine,
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27 ParseCmpdAtomLine, ParseCmpdBondLine, ParseCmpdChargePropertyLine,
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28 ParseCmpdCommentsLine, ParseCmpdCountsLine,
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29 ParseCmpdIsotopePropertyLine, ParseCmpdMiscInfoLine,
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30 ParseCmpdMolNameLine, ParseCmpdRadicalPropertyLine, ReadCmpdString,
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31 RemoveCmpdDataHeaderLabelAndValue, WashCmpd
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32
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33 METHODS
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34 GenerateCmpdAtomAliasPropertyLines
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35 @Lines = GenerateCmpdAtomAliasPropertyLines($AliasValuePairsRef);
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36
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37 Returns a formatted atom alias property lines corresponding to
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38 successive pairs of atom number and alias values specified by a
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39 refernce to an array. Two lines are generate for each atom number
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40 and alias value pairs: First line - A <AtomNum>; Second
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41 line:<AtomAlias>.
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42
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43 GenerateCmpdAtomLine
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44 $Line = GenerateCmpdAtomLine($AtomSymbol, $AtomX, $AtomY,
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45 $AtomZ, [$MassDifference, $Charge, $StereoParity]);
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46
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47 Returns a formatted atom data line containing all the input values.
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48
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49 GenerateCmpdBondLine
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50 $Line = GenerateCmpdBondLine($FirstAtomNum, $SecondAtomNum,
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51 $BondType, [$BondStereo]);
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52
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53 Returns a formatted bond data line containing all the input values.
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54
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55 GenerateCmpdChargePropertyLines
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56 @Lines = GenerateCmpdChargePropertyLines($ChargeValuePairsRef);
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57
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58 Returns a formatted M CHG property lines corresponding to successive
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59 pairs of atom number and charge values specified by a refernce to an
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60 array.
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61
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62 GenerateCmpdCommentsLine
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63 $Line = GenerateCmpdCommentsLine($Comments);
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64
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65 Returns a formatted comments data line.
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66
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67 GenerateCmpdCountsLine
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68 $Line = GenerateCmpdCountsLine($AtomCount, $BondCount,
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69 $ChiralFlag, [$PropertyCount, $Version]);
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70
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71 Returns a formatted line containing all the input values. The
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72 default values of 999 and V2000 are used for *PropertyCount* and
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73 *Version*.
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74
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75 GenerateCmpdDataHeaderLabelsAndValuesLines
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76 @Lines = GenerateCmpdDataHeaderLabelsAndValuesLines(
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77 $DataHeaderLabelsRef, $DataHeaderLabelsAndValuesRef,
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78 [$SortDataLabels]);
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79
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80 Returns formatted data lines containing header label and values
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81 lines corresponding to all data header labels in array reference
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82 *DataHeaderLabelsRef* with values in hash reference
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83 *DataHeaderLabelsAndValuesRef*. By default, data header labels are
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84 not sorted and correspond to the label order in array reference
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85 *DataHeaderLabelsRef*.
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86
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87 GenerateCmpdIsotopePropertyLines
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88 @Lines = GenerateCmpdIsotopePropertyLines($IsotopeValuePairsRef);
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89
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90 Returns a formatted M ISO property lines corresponding to successive
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91 pairs of atom number and isotope values specified by a refernce to
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92 an array.
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93
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94 GenerateCmpdMiscInfoLine
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95 $Line = GenerateCmpdMiscInfoLine([$ProgramName, $UserInitial,
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96 $Code]);
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97
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98 Returns a formatted line containing specified user initial, program
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99 name, date and code. Default values are: *ProgramName - MayaChem;
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100 UserInitial - NULL; Code - 2D*.
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101
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102 GenerateCmpdMolNameLine
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103 $Line = GenerateCmpdMolNameLine($MolName);
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104
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105 Returns a formatted molecule name data line.
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106
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107 GenerateCmpdRadicalPropertyLines
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108 @Lines = GenerateCmpdRadicalPropertyLines($RadicalValuePairsRef);
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109
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110 Returns a formatted M CHG property lines corresponding to successive
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111 pairs of atom number and multiplicity values specified by a refernce
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112 to an array.
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113
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114 GenerateEmptyCtabBlockLines
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115 $Lines = GenerateCmpdMiscInfoLine([$Date]);
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116
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117 Returns formatted lines representing empty CTAB block.
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118
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119 GenerateMiscLineDateStamp
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120 $Line = GenerateMiscLineDateStamp();
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121
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122 Returns date stamp for misc line.
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123
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124 GetAllAndCommonCmpdDataHeaderLabels
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125 ($CmpdCount, $DataFieldLabelsArrayRef,
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126 $CommonDataFieldLabelsArrayRef) =
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127 GetAllAndCommonCmpdDataHeaderLabels(\*SDFILE);
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128
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129 Returns number of comopunds, a reference to an array containing all
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130 unique data header label and a reference to an array containing
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131 common data field labels for all compounds in SD file.
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132
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133 GetCmpdDataHeaderLabels
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134 (@Labels) = GetCmpdDataHeaderLabels(\@CmpdLines);
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135
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136 Returns an array containg data header labels for a compound
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137
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138 GetCmpdDataHeaderLabelsAndValues
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139 (%DataValues) = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines);
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140
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141 Returns a hash conating data header labes and values for a compound.
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142
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143 GetCmpdFragments
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144 ($FragmentCount, $FragmentString) = GetCmpdFragments(\@CmpLines);
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145
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146 Figures out the number of disconnected fragments and return their
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147 values along with the atom numbers in a string delimited by new line
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148 character. Fragment data in FragmentString is sorted on based on its
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149 size.
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150
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151 GetCtabLinesCount
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152 $CtabLinesCount = GetCtabLinesCount(\@CmpdLines);
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153
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154 Returns number of lines present between the 4th line and the line
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155 containg "M END".
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156
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157 GetInvalidAtomNumbers
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158 ($InvalidAtomNumbersCount, $InvalidAtomNumbers, $InvalidAtomNumberLines) =
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159 GetInvalidAtomNumbers(\@CmpdLines);
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160
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161 Returns a list of values containing information about invalid atom
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162 numbers present in block or atom property lines.
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163
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164 GetUnknownAtoms
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165 ($UnknownAtomCount, $UnknownAtoms, $UnknownAtomLines) =
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166 GetUnknownAtoms(\@CmpdLines);
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167
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168 Returns a list of values containing information about atoms which
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169 contain special element symbols not present in the periodic table.
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170
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171 InternalBondOrderToMDLBondType
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172 $MDLBondType = InternalBondOrderToMDLBondType($InternalBondOrder);
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173
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174 Returns value of *MDLBondType* corresponding to *InternalBondOrder*.
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175
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176 InternalBondOrder MDLBondType
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177
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178 1 1
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179 2 2
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180 3 3
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181 1.5 4
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182
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183 InternalBondStereochemistryToMDLBondStereo
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184 $MDLBondStereo = InternalBondStereochemistryToMDLBondStereo(
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185 $InternalBondStereo);
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186
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187 Returns value of *MDLBondStereo* corresponding to
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188 *InternalBondStereo* using following mapping:
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189
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190 InternalBondStereo MDLBondStereo
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191
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192 Up 1
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193 UpOrDown 4
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194 Down 6
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195 CisOrTrans 3
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196 Other 0
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197
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198 InternalChargeToMDLCharge
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199 $MDLCharge = InternalChargeToMDLCharge($InternalCharge);
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200
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201 Returns value of *MDLCharge* corresponding to *InternalCharge* using
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202 following mapping:
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203
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204 InternalCharge MDLCharge
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205
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206 3 1
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207 2 2
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208 1 3
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209 -1 5
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210 -2 6
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211 -3 7
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212
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213 InternalSpinMultiplicityToMDLRadical
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214 $MDLRadical = InternalSpinMultiplicityToMDLRadical(
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215 $InternalSpinMultiplicity);
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216
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217 Returns value of *MDLRadical* corresponding to
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218 *InternalSpinMultiplicity*. These value are equivalent.
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219
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220 MDLBondStereoToInternalBondType
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221 $InternalBondType = MDLBondStereoToInternalBondType($MDLBondStereo);
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222
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223 Returns value of *InternalBondType* corresponding to *MDLBondStereo*
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224 using mapping shown for InternalBondTypeToMDLBondStereo function.
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225
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226 IsCmpd2D
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227 $Status = IsCmpd2D();
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228
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229 Returns 1 or 0 based on whether z-coordinate of any atom is
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230 non-zero.
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231
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232 IsCmpd3D
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233 $Status = IsCmpd3D();
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234
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235 Returns 1 or 0 based on whether z-coordinate of any atom is
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236 non-zero.
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237
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238 MDLBondStereoToInternalBondStereochemistry
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239 $InternalBondStereo = MDLBondStereoToInternalBondStereochemistry(
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240 $MDLBondStereo);
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241
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242 Returns value of *InternalBondStereo* corresponding to
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243 *MDLBondStereo* using mapping shown for
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244 InternalBondStereochemistryToMDLBondStereo function.
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245
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246 MDLBondTypeToInternalBondOrder
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247 $InternalBondOrder = MDLBondTypeToInternalBondOrder($MDLBondType);
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248
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249 Returns value of *InternalBondOrder* corresponding to *MDLBondType*
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250 using mapping shown for InternalBondOrderToMDLBondType function.
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251
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252 MDLChargeToInternalCharge
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253 $InternalCharge = MDLChargeToInternalCharge($MDLCharge);
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254
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255 Returns value of *$InternalCharge* corresponding to *MDLCharge*
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256 using mapping shown for InternalChargeToMDLCharge function.
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257
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258 MDLRadicalToInternalSpinMultiplicity
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259 $InternalSpinMultiplicity = MDLRadicalToInternalSpinMultiplicity(
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260 $MDLRadical);
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261
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262 Returns value of *InternalSpinMultiplicity* corresponding to
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263 *MDLRadical*. These value are equivalent.
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264
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265 ParseCmpdAtomAliasPropertyLine
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266 @AtomNumAndValuePairs = ParseCmpdAtomAliasPropertyLine(
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267 $CurrentLine, $NexLine);
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268
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269 Parses atom alias propery lines in CTAB generic properties block and
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270 returns an array with successive pairs of values corresponding to
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271 atom number and its alias.
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272
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273 ParseCmpdAtomLine
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274 ($AtomSymbol, $AtomX, $AtomY, $AtomZ, $MassDifference, $Charge,
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275 $StereoParity) = ParseCmpdAtomLine($AtomDataLine);
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276
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277 Parses compound data line containing atom information and returns a
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278 list of values.
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279
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280 ParseCmpdBondLine
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281 ($FirstAtomNum, $SecondAtomNum, $BondType) =
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282 ParseCmpdBondLine($BondDataLine);
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283
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284 Parses compound data line containing bond information and returns a
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285 list of values.
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286
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287 ParseCmpdCommentsLine
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288 $Comments = ParseCmpdCommentsLine($CommentsDataLine);
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289
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290 Returns the comment string.
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291
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292 ParseCmpdChargePropertyLine
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293 @AtomNumAndValuePairs = ParseCmpdChargePropertyLine(
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294 $ChargeDataLine);
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295
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296 Parses charge propery line in CTAB generic properties block and
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297 returns an array with successive pairs of values corresponding to
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298 atom number and its charge.
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299
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300 ParseCmpdCountsLine
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301 ($AtomCount, $BondCount, $ChiralFlag, $PropertyCount, $Version) =
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302 ParseCmpdCountsLine(\@CountDataLines);
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303
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304 Returns a list of values containing count information.
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305
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306 ParseCmpdMiscInfoLine
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307 ($UserInitial, $ProgramName, $Date, $Code, $ScalingFactor1, $ScalingFactor2,
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308 $Energy, $RegistryNum) = ParseCmpdMiscInfoLine($Line);
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309
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310 Returns a list of values containing miscellaneous information.
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311
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312 ParseCmpdIsotopePropertyLine
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313 @AtomNumAndValuePairs = ParseCmpdIsotopePropertyLine(
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314 $IsotopeDataLine);
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315
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316 Parses isotopic propery line in CTAB generic properties block and
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317 returns an array with successive pairs of values corresponding to
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318 atom number and absolute mass of atom isotope.
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319
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320 ParseCmpdMolNameLine
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321 $MolName = ParseCmpdMolNameLine($Line);
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322
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323 Returns a string containing molecule name.
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324
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325 ParseCmpdRadicalPropertyLine
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326 @AtomNumAndValuePairs = ParseCmpdRadicalPropertyLine(
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327 $RadicalDataLine);
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328
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329 Parses radical propery line in CTAB generic properties block and
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330 returns an array with successive pairs of values corresponding to
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331 atom number and radical number value.
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332
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333 RemoveCmpdDataHeaderLabelAndValue
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334 $NewCmpdString = RemoveCmpdDataHeaderLabelAndValue($CmpdString,
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335 $DataHeaderLabel);
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336
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337 Returns a NewCmpdString after removing *DataHeaderLabel* along with
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338 its value from *CmpdString*.
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339
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340 ReadCmpdString
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341 $CmpdString = ReadCmpdString(\*SDFILEHANDLE);
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342
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343 Returns a string containing all the data lines for the next
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344 available compound in an already open file indicated by
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345 SDFILEHANDLE. A NULL string is returned on EOF.
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346
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347 WashCmpd
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348 ($FragmentCount, $Fragments, $WashedCmpdString) =
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349 WashCmpd(\@CmpdLines);
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350
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351 Figures out the number of disconnected fragments and return their
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352 values along with the atom numbers in a string delimited by new line
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353 character. Fragment data in FragmentString is sorted on based on its
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354 size.
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355
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356 AUTHOR
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357 Manish Sud <msud@san.rr.com>
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358
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359 SEE ALSO
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360 TextUtil.pm
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361
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362 COPYRIGHT
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363 Copyright (C) 2015 Manish Sud. All rights reserved.
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364
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365 This file is part of MayaChemTools.
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366
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367 MayaChemTools is free software; you can redistribute it and/or modify it
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368 under the terms of the GNU Lesser General Public License as published by
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369 the Free Software Foundation; either version 3 of the License, or (at
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370 your option) any later version.
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371
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