annotate mayachemtools/bin/ModifyPDBFiles.pl @ 9:ab29fa5c8c1f draft default tip

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author deepakjadmin
date Thu, 15 Dec 2016 14:18:03 -0500
parents 73ae111cf86f
children
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1 #!/usr/bin/perl -w
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2 #
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3 # $RCSfile: ModifyPDBFiles.pl,v $
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4 # $Date: 2015/02/28 20:46:20 $
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5 # $Revision: 1.25 $
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6 #
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7 # Author: Manish Sud <msud@san.rr.com>
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8 #
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9 # Copyright (C) 2015 Manish Sud. All rights reserved.
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10 #
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11 # This file is part of MayaChemTools.
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12 #
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13 # MayaChemTools is free software; you can redistribute it and/or modify it under
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14 # the terms of the GNU Lesser General Public License as published by the Free
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15 # Software Foundation; either version 3 of the License, or (at your option) any
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16 # later version.
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17 #
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18 # MayaChemTools is distributed in the hope that it will be useful, but without
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19 # any warranty; without even the implied warranty of merchantability of fitness
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20 # for a particular purpose. See the GNU Lesser General Public License for more
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21 # details.
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22 #
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23 # You should have received a copy of the GNU Lesser General Public License
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24 # along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
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25 # write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
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26 # Boston, MA, 02111-1307, USA.
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27 #
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28
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29 use strict;
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30 use FindBin; use lib "$FindBin::Bin/../lib";
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31 use Getopt::Long;
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32 use File::Basename;
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33 use Text::ParseWords;
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34 use Benchmark;
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35 use FileUtil;
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36 use TextUtil;
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37 use PDBFileUtil;
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38
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39 my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime);
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40
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41 # Autoflush STDOUT
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42 $| = 1;
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43
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44 # Starting message...
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45 $ScriptName = basename($0);
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46 print "\n$ScriptName: Starting...\n\n";
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47 $StartTime = new Benchmark;
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48
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49 # Get the options and setup script...
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50 SetupScriptUsage();
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51 if ($Options{help} || @ARGV < 1) {
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52 die GetUsageFromPod("$FindBin::Bin/$ScriptName");
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53 }
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54
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55 my(@PDBFilesList);
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56 @PDBFilesList = ExpandFileNames(\@ARGV, "pdb");
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57
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58 # Process options...
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59 print "Processing options...\n";
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60 my(%OptionsInfo);
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61 ProcessOptions();
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62
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63 # Setup information about input files...
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64 print "Checking input PDB file(s)...\n";
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65 my(%PDBFilesInfo);
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66 RetrievePDBFilesInfo();
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67
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68 # Process input files..
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69 my($FileIndex);
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70 if (@PDBFilesList > 1) {
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71 print "\nProcessing PDB files...\n";
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72 }
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73 for $FileIndex (0 .. $#PDBFilesList) {
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74 if ($PDBFilesInfo{FileOkay}[$FileIndex]) {
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75 print "\nProcessing file $PDBFilesList[$FileIndex]...\n";
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76 ModifyPDBFiles($FileIndex);
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77 }
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78 }
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79 print "\n$ScriptName:Done...\n\n";
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80
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81 $EndTime = new Benchmark;
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82 $TotalTime = timediff ($EndTime, $StartTime);
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83 print "Total time: ", timestr($TotalTime), "\n";
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84
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85 ###############################################################################
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86
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87 # Modify appropriate information...
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88 sub ModifyPDBFiles {
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89 my($FileIndex) = @_;
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90 my($PDBFile, $PDBRecordLinesRef);
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91
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92 # Get PDB data...
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93 $PDBFile = $PDBFilesList[$FileIndex];
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94 $PDBRecordLinesRef = ReadPDBFile($PDBFile);
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95
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96 if ($OptionsInfo{Mode} =~ /^RenumberAtoms$/i) {
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97 RenumberAtoms($FileIndex, $PDBRecordLinesRef);
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98 }
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99 elsif ($OptionsInfo{Mode} =~ /^RenumberResidues$/i) {
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100 RenumberResidues($FileIndex, $PDBRecordLinesRef);
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101 }
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102 elsif ($OptionsInfo{Mode} =~ /^RenumberWaters$/i) {
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103 RenumberWaters($FileIndex, $PDBRecordLinesRef);
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104 }
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105 elsif ($OptionsInfo{Mode} =~ /^RenameChainIDs$/i) {
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106 RenameChainsIDs($FileIndex, $PDBRecordLinesRef);
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107 }
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108 }
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109
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110 # Renumber atom and hetro atom numbers...
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111 sub RenumberAtoms {
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112 my($FileIndex, $PDBRecordLinesRef) = @_;
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113 my($PDBFileName, $RecordLine, $ConectRecordLinesRef, $AtomNumber, $AtomName, $AlternateLocation, $ResidueName, $ChainID, $ResidueNumber, $InsertionCode, $X, $Y, $Z, $Occupancy, $TemperatureFactor, $SegmentID, $ElementSymbol, $AtomCharge, $NewAtomNumber, $RecordType, %OldToNewAtomNumbersMap);
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114
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115 $PDBFileName = $PDBFilesInfo{OutFileNames}[$FileIndex][0];
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116 print "Generating PDBFileName file $PDBFileName...\n";
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117 open OUTFILE, ">$PDBFileName" or die "Error: Can't open $PDBFileName: $! \n";
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118
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119 # Write out header and other older recors...
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120 WriteHeaderAndOlderRecords(\*OUTFILE, $PDBRecordLinesRef);
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121
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122 # Write out all ATOM records along with TER and model records to indicate
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123 # chains and multiple models..
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124 %OldToNewAtomNumbersMap = ();
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125 $NewAtomNumber = $OptionsInfo{StartingAtomNumber};
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126 for $RecordLine (@{$PDBRecordLinesRef}) {
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127 if (IsAtomRecordType($RecordLine) || IsHetatmRecordType($RecordLine)) {
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128 $RecordType = GetPDBRecordType($RecordLine);
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129
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130 ($AtomNumber, $AtomName, $AlternateLocation, $ResidueName, $ChainID, $ResidueNumber, $InsertionCode, $X, $Y, $Z, $Occupancy, $TemperatureFactor, $SegmentID, $ElementSymbol, $AtomCharge) = ParseAtomOrHetatmRecordLine($RecordLine);
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131
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132 print OUTFILE GenerateAtomOrHetatmRecordLine($RecordType, $NewAtomNumber, $AtomName, $AlternateLocation, $ResidueName, $ChainID, $ResidueNumber, $InsertionCode, $X, $Y, $Z, $Occupancy, $TemperatureFactor, $SegmentID, $ElementSymbol, $AtomCharge), "\n";
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133
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134 $OldToNewAtomNumbersMap{$AtomNumber} = $NewAtomNumber;
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135 $NewAtomNumber++;
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136 }
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137 elsif (IsTerRecordType($RecordLine)) {
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138 $NewAtomNumber++;
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139 print OUTFILE GenerateTerRecordLine($NewAtomNumber, $ResidueName, $ChainID, $ResidueNumber, $InsertionCode), "\n";
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140 }
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141 elsif (IsModelRecordType($RecordLine)) {
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142 print OUTFILE "$RecordLine\n";
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143 }
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144 elsif (IsEndmdlRecordType($RecordLine)) {
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145 print OUTFILE "$RecordLine\n";
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146 # Restart numbering...
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147 $NewAtomNumber = $OptionsInfo{StartingAtomNumber};
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148 }
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149 }
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150
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151 # Write out modified CONECT records...
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152 my($ModifiedConectAtomNum, $ConectAtomNum, @ConectAtomNums, @ModifiedConectAtomNums);
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153 LINE: for $RecordLine (@{$PDBRecordLinesRef}) {
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154 if (!IsConectRecordType($RecordLine)) {
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155 next LINE;
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156 }
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157 @ConectAtomNums = ();
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158 @ModifiedConectAtomNums = ();
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159 push @ConectAtomNums, ParseConectRecordLine($RecordLine);
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160 ATOMNUMBER: for $ConectAtomNum (@ConectAtomNums) {
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161 $ModifiedConectAtomNum = $ConectAtomNum;
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162 if (defined($ConectAtomNum)) {
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163 $AtomNumber = $ConectAtomNum;
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164 if ($AtomNumber) {
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165 if (exists $OldToNewAtomNumbersMap{$AtomNumber}) {
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166 $ModifiedConectAtomNum = $OldToNewAtomNumbersMap{$AtomNumber};
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167 }
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168 }
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169 }
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170 push @ModifiedConectAtomNums, $ModifiedConectAtomNum;
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171 }
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172 # Write out the record...
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173 print OUTFILE GenerateConectRecordLine(@ModifiedConectAtomNums), "\n";
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174 }
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175
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176 # Write out END record...
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177 print OUTFILE GenerateEndRecordLine(), "\n";
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178
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179 close OUTFILE;
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180 }
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181
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182 # Renumber residues...
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183 sub RenumberResidues {
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184 my($FileIndex, $PDBRecordLinesRef) = @_;
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185 my($PDBFileName, $RecordLine, $ConectRecordLinesRef, $AtomNumber, $AtomName, $AlternateLocation, $ResidueName, $ChainID, $ResidueNumber, $InsertionCode, $X, $Y, $Z, $Occupancy, $TemperatureFactor, $SegmentID, $ElementSymbol, $AtomCharge, $NewResidueNumber, $NewHetatmResidueNumber, $TERCount, $TotalTERCount, $PreviousResidueNumber, $PreviousHetatmResidueNumber, $RecordType);
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186
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187 $PDBFileName = $PDBFilesInfo{OutFileNames}[$FileIndex][0];
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188 print "Generating PDBFileName file $PDBFileName...\n";
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189 open OUTFILE, ">$PDBFileName" or die "Error: Can't open $PDBFileName: $! \n";
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190
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191 # Write out header and other older recors...
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192 WriteHeaderAndOlderRecords(\*OUTFILE, $PDBRecordLinesRef);
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193
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194 # Do a quick count of all TER records...
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195 $TotalTERCount = 0;
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196 for $RecordLine (@{$PDBRecordLinesRef}) {
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197 if (IsTerRecordType($RecordLine)) {
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198 $TotalTERCount++;
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199 }
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200 }
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201
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202 # Write out all ATOM records along with TER and model records to indicate
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203 # chains and multiple models..
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diff changeset
204 $NewResidueNumber = $OptionsInfo{StartingResidueNumber};
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
205 $NewHetatmResidueNumber = $OptionsInfo{StartingHetatmResidueNumber};
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
206
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
207 $TERCount = 0;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
208 $PreviousResidueNumber = 0;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
209 $PreviousHetatmResidueNumber = 0;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
210
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
211 for $RecordLine (@{$PDBRecordLinesRef}) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
212 if (IsAtomRecordType($RecordLine) || (IsHetatmRecordType($RecordLine) && ($TERCount < $TotalTERCount || $OptionsInfo{HetatmResidueNumberMode} =~ /^Automatic$/i))) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
213 $RecordType = GetPDBRecordType($RecordLine);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
214 ($AtomNumber, $AtomName, $AlternateLocation, $ResidueName, $ChainID, $ResidueNumber, $InsertionCode, $X, $Y, $Z, $Occupancy, $TemperatureFactor, $SegmentID, $ElementSymbol, $AtomCharge) = ParseAtomOrHetatmRecordLine($RecordLine);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
215
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
216 if ($PreviousResidueNumber && $PreviousResidueNumber != $ResidueNumber) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
217 $PreviousResidueNumber = $ResidueNumber;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
218 $NewResidueNumber++;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
219 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
220 else {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
221 # First residue in a chain...
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deepakjadmin
parents:
diff changeset
222 $PreviousResidueNumber = $ResidueNumber;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
223 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
224 print OUTFILE GenerateAtomOrHetatmRecordLine($RecordType, $AtomNumber, $AtomName, $AlternateLocation, $ResidueName, $ChainID, $NewResidueNumber, $InsertionCode, $X, $Y, $Z, $Occupancy, $TemperatureFactor, $SegmentID, $ElementSymbol, $AtomCharge), "\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
225
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
226 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
227 elsif (IsHetatmRecordType($RecordLine)) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
228 ($AtomNumber, $AtomName, $AlternateLocation, $ResidueName, $ChainID, $ResidueNumber, $InsertionCode, $X, $Y, $Z, $Occupancy, $TemperatureFactor, $SegmentID, $ElementSymbol, $AtomCharge) = ParseHetatmRecordLine($RecordLine);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
229
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
230 # User HETATM residue numbers...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
231 if ($PreviousHetatmResidueNumber && $PreviousHetatmResidueNumber != $ResidueNumber) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
232 $PreviousHetatmResidueNumber = $ResidueNumber;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
233 $NewHetatmResidueNumber++;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
234 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
235 else {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
236 # First HETATM residue outside a chain...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
237 $PreviousHetatmResidueNumber = $ResidueNumber;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
238 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
239
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deepakjadmin
parents:
diff changeset
240 print OUTFILE GenerateHetatmRecordLine($AtomNumber, $AtomName, $AlternateLocation, $ResidueName, $ChainID, $NewHetatmResidueNumber, $InsertionCode, $X, $Y, $Z, $Occupancy, $TemperatureFactor, $SegmentID, $ElementSymbol, $AtomCharge), "\n";
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deepakjadmin
parents:
diff changeset
241 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
242 elsif (IsTerRecordType($RecordLine)) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
243 $TERCount++;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
244 $AtomNumber++;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
245 print OUTFILE GenerateTerRecordLine($AtomNumber, $ResidueName, $ChainID, $NewResidueNumber, $InsertionCode), "\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
246 # For per chain numbering, start over again...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
247 if ($OptionsInfo{ResidueNumberMode} =~ /^PerChain$/i) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
248 if ($TERCount < $TotalTERCount ) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
249 $NewResidueNumber = $OptionsInfo{StartingResidueNumber};
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
250 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
251 $PreviousResidueNumber = 0;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
252 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
253 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
254 elsif (IsModelRecordType($RecordLine)) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
255 print OUTFILE "$RecordLine\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
256 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
257 elsif (IsEndmdlRecordType($RecordLine)) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
258 print OUTFILE "$RecordLine\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
259 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
260 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
261
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
262 # Write out CONECT records...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
263 for $RecordLine (@{$PDBRecordLinesRef}) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
264 if (IsConectRecordType($RecordLine)) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
265 print OUTFILE "$RecordLine\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
266 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
267 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
268
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
269 # Write out END record...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
270 print OUTFILE GenerateEndRecordLine(), "\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
271
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
272 close OUTFILE;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
273 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
274
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
275 # Renumber water residues...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
276 sub RenumberWaters {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
277 my($FileIndex, $PDBRecordLinesRef) = @_;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
278 my($PDBFileName, $RecordLine, $ConectRecordLinesRef, $AtomNumber, $AtomName, $AlternateLocation, $ResidueName, $ChainID, $ResidueNumber, $InsertionCode, $X, $Y, $Z, $Occupancy, $TemperatureFactor, $SegmentID, $ElementSymbol, $AtomCharge, $NewResidueNumber, $RecordType);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
279
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
280 $PDBFileName = $PDBFilesInfo{OutFileNames}[$FileIndex][0];
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
281 print "Generating PDBFileName file $PDBFileName...\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
282 open OUTFILE, ">$PDBFileName" or die "Error: Can't open $PDBFileName: $! \n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
283
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
284 # Write out header and other older recors...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
285 WriteHeaderAndOlderRecords(\*OUTFILE, $PDBRecordLinesRef);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
286
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
287 # Write out all ATOM records along with TER and model records to indicate
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
288 # chains and multiple models..
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
289 $NewResidueNumber = $OptionsInfo{StartingWaterResidueNumber};
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
290 for $RecordLine (@{$PDBRecordLinesRef}) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
291 if (IsAtomRecordType($RecordLine) || IsHetatmRecordType($RecordLine)) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
292 $RecordType = GetPDBRecordType($RecordLine);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
293
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
294 ($AtomNumber, $AtomName, $AlternateLocation, $ResidueName, $ChainID, $ResidueNumber, $InsertionCode, $X, $Y, $Z, $Occupancy, $TemperatureFactor, $SegmentID, $ElementSymbol, $AtomCharge) = ParseAtomOrHetatmRecordLine($RecordLine);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
295
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
296 if (exists $OptionsInfo{SpecifiedWaterResiduesMap}{$ResidueName}) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
297 $ResidueNumber = $NewResidueNumber;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
298 print OUTFILE GenerateAtomOrHetatmRecordLine($RecordType, $AtomNumber, $AtomName, $AlternateLocation, $ResidueName, $ChainID, $ResidueNumber, $InsertionCode, $X, $Y, $Z, $Occupancy, $TemperatureFactor, $SegmentID, $ElementSymbol, $AtomCharge), "\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
299 $NewResidueNumber++;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
300 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
301 else {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
302 print OUTFILE "$RecordLine\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
303 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
304 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
305 elsif (IsTerRecordType($RecordLine)) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
306 print OUTFILE "$RecordLine\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
307 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
308 elsif (IsModelRecordType($RecordLine)) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
309 print OUTFILE "$RecordLine\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
310 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
311 elsif (IsEndmdlRecordType($RecordLine)) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
312 print OUTFILE "$RecordLine\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
313 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
314 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
315
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
316 # Write out CONECT records...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
317 for $RecordLine (@{$PDBRecordLinesRef}) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
318 if (IsConectRecordType($RecordLine)) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
319 print OUTFILE "$RecordLine\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
320 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
321 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
322
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
323 # Write out END record...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
324 print OUTFILE GenerateEndRecordLine(), "\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
325
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
326 close OUTFILE;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
327 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
328
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
329 # Rename chain IDs...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
330 sub RenameChainsIDs {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
331 my($FileIndex, $PDBRecordLinesRef) = @_;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
332 my($PDBFileName, $RecordLine, $ConectRecordLinesRef, $AtomNumber, $AtomName, $AlternateLocation, $ResidueName, $ChainID, $ResidueNumber, $InsertionCode, $X, $Y, $Z, $Occupancy, $TemperatureFactor, $SegmentID, $ElementSymbol, $AtomCharge, $RecordType, $PreviousChainID, $FirstChainID, $NewChainID, $NewChainIDCounter, %OldToNewChainIDsMap);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
333
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
334 $PDBFileName = $PDBFilesInfo{OutFileNames}[$FileIndex][0];
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
335 print "Generating PDBFileName file $PDBFileName...\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
336 open OUTFILE, ">$PDBFileName" or die "Error: Can't open $PDBFileName: $! \n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
337
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
338 # Write out header and other older recors...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
339 WriteHeaderAndOlderRecords(\*OUTFILE, $PDBRecordLinesRef);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
340
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
341 # Write out all ATOM records along with TER and model records to indicate
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
342 # chains and multiple models..
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
343 %OldToNewChainIDsMap = ();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
344 $NewChainIDCounter = $OptionsInfo{StartingChainID};
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
345 $FirstChainID = 1;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
346 $PreviousChainID = '';
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
347 LINE: for $RecordLine (@{$PDBRecordLinesRef}) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
348 if (IsAtomRecordType($RecordLine) || IsHetatmRecordType($RecordLine)) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
349 $RecordType = GetPDBRecordType($RecordLine);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
350
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
351 ($AtomNumber, $AtomName, $AlternateLocation, $ResidueName, $ChainID, $ResidueNumber, $InsertionCode, $X, $Y, $Z, $Occupancy, $TemperatureFactor, $SegmentID, $ElementSymbol, $AtomCharge) = ParseAtomOrHetatmRecordLine($RecordLine);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
352
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
353 if (exists $OptionsInfo{SpecifiedWaterResiduesMap}{$ResidueName}) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
354 # Chain IDs are not assigned to water residues...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
355 print OUTFILE "$RecordLine\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
356 next LINE;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
357 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
358
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
359 if ($FirstChainID) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
360 $FirstChainID = 0;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
361 $PreviousChainID = $ChainID;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
362 if ($ChainID || (!$ChainID && $OptionsInfo{RenameEmptyChainIDs})) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
363 $NewChainID = $NewChainIDCounter;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
364 $OldToNewChainIDsMap{$ChainID} = $NewChainID;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
365 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
366 else {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
367 $NewChainID = '';
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
368 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
369 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
370 elsif ($PreviousChainID ne $ChainID) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
371 if ($ChainID || (!$ChainID && $OptionsInfo{RenameEmptyChainIDs})) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
372 $PreviousChainID = $ChainID;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
373 if (exists $OldToNewChainIDsMap{$ChainID}) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
374 $NewChainID = $OldToNewChainIDsMap{$ChainID};
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
375 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
376 else {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
377 $NewChainIDCounter++;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
378 $NewChainID = $NewChainIDCounter;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
379 $OldToNewChainIDsMap{$ChainID} = $NewChainID;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
380 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
381 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
382 else {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
383 $NewChainID = '';
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
384 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
385 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
386
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
387 print OUTFILE GenerateAtomOrHetatmRecordLine($RecordType, $AtomNumber, $AtomName, $AlternateLocation, $ResidueName, $NewChainID, $ResidueNumber, $InsertionCode, $X, $Y, $Z, $Occupancy, $TemperatureFactor, $SegmentID, $ElementSymbol, $AtomCharge), "\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
388 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
389 elsif (IsTerRecordType($RecordLine)) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
390 $AtomNumber++;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
391 print OUTFILE GenerateTerRecordLine($AtomNumber, $ResidueName, $NewChainID, $ResidueNumber, $InsertionCode), "\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
392 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
393 elsif (IsModelRecordType($RecordLine)) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
394 print OUTFILE "$RecordLine\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
395 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
396 elsif (IsEndmdlRecordType($RecordLine)) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
397 print OUTFILE "$RecordLine\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
398 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
399 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
400
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
401 # Write out CONECT records...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
402 for $RecordLine (@{$PDBRecordLinesRef}) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
403 if (IsConectRecordType($RecordLine)) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
404 print OUTFILE "$RecordLine\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
405 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
406 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
407
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
408 # Write out END record...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
409 print OUTFILE GenerateEndRecordLine(), "\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
410
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
411 close OUTFILE;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
412 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
413
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
414
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
415 # Write out modifed header and other older records...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
416 sub WriteHeaderAndOlderRecords {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
417 my($OutFileRef, $PDBRecordLinesRef) = @_;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
418
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
419 if ($OptionsInfo{ModifyHeaderRecord}) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
420 # Write out modified HEADER record...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
421 my($Classification, $DepositionDate, $IDCode) = GetHeaderRecordInformation($PDBRecordLinesRef);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
422 $Classification = 'Data modified using MayaChemTools';
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
423 print $OutFileRef GenerateHeaderRecordLine($IDCode, $Classification), "\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
424 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
425 else {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
426 print $OutFileRef $PDBRecordLinesRef->[0], "\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
427 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
428
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
429 # Write out any old records...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
430 if ($OptionsInfo{KeepOldRecords}) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
431 my($RecordLineIndex, $RecordLine);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
432 # Skip HEADER record and write out older records all the way upto first MODEL/ATOM/HETATM records from input file...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
433 RECORDLINE: for $RecordLineIndex (1 .. $#{$PDBRecordLinesRef}) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
434 $RecordLine = $PDBRecordLinesRef->[$RecordLineIndex];
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
435 if (IsModelRecordType($RecordLine) || IsAtomRecordType($RecordLine) || IsHetatmRecordType($RecordLine)) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
436 last RECORDLINE;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
437 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
438 print $OutFileRef "$RecordLine\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
439 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
440 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
441 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
442
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
443 # Get header record information assuming it's the first record...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
444 sub GetHeaderRecordInformation {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
445 my($PDBRecordLinesRef) = @_;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
446 my($Classification, $DepositionDate, $IDCode, $HeaderRecordLine);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
447
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
448 ($Classification, $DepositionDate, $IDCode) = ('') x 3;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
449 $HeaderRecordLine = $PDBRecordLinesRef->[0];
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
450 if (IsHeaderRecordType($HeaderRecordLine)) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
451 ($Classification, $DepositionDate, $IDCode) = ParseHeaderRecordLine($HeaderRecordLine);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
452 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
453 return ($Classification, $DepositionDate, $IDCode);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
454 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
455
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
456
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
457 # Process option values...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
458 sub ProcessOptions {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
459 %OptionsInfo = ();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
460 $OptionsInfo{Mode} = $Options{mode};
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
461
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
462 $OptionsInfo{StartingAtomNumber} = $Options{atomnumberstart};
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
463 $OptionsInfo{StartingChainID} = $Options{chainidstart};
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
464 $OptionsInfo{RenameEmptyChainIDs} = ($Options{chainidrenameempty} =~ /^Yes$/i) ? 1 : 0;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
465
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
466 $OptionsInfo{KeepOldRecords} = ($Options{keepoldrecords} =~ /^Yes$/i) ? 1 : 0;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
467 $OptionsInfo{ModifyHeaderRecord} = ($Options{modifyheader} =~ /^Yes$/i) ? 1 : 0;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
468
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
469 $OptionsInfo{ResidueNumberMode} = $Options{residuenumbermode};
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
470 $OptionsInfo{StartingResidueNumber} = $Options{residuenumberstart};
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
471
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
472 $OptionsInfo{HetatmResidueNumberMode} = $Options{residuenumberhetatmmode};
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
473 $OptionsInfo{StartingHetatmResidueNumber} = $Options{residuenumberstarthetatm};
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
474
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
475 $OptionsInfo{OverwriteFiles} = $Options{overwrite} ? 1 : 0;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
476 $OptionsInfo{OutFileRoot} = $Options{root} ? $Options{root} : 0;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
477
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
478 $OptionsInfo{WaterResidueNames} = $Options{waterresiduenames};
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
479 $OptionsInfo{StartingWaterResidueNumber} = $Options{waterresiduestart};
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
480 @{$OptionsInfo{SpecifiedWaterResiduesList}} = ();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
481 %{$OptionsInfo{SpecifiedWaterResiduesMap}} = ();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
482
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
483 my(@SpecifiedWaterResiduesList);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
484 @SpecifiedWaterResiduesList = ();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
485 my($WaterResidueName);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
486 if ($OptionsInfo{WaterResidueNames} =~ /Automatic/i) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
487 push @SpecifiedWaterResiduesList, ('HOH', 'WAT', 'H2O');
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
488 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
489 else {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
490 @SpecifiedWaterResiduesList = split /\,/, $Options{waterresiduenames};
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
491 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
492 for $WaterResidueName (@SpecifiedWaterResiduesList) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
493 $OptionsInfo{SpecifiedWaterResiduesMap}{$WaterResidueName} = $WaterResidueName;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
494 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
495 push @{$OptionsInfo{SpecifiedWaterResiduesList}}, @SpecifiedWaterResiduesList;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
496 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
497
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
498 # Retrieve information about PDB files...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
499 sub RetrievePDBFilesInfo {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
500 my($Index, $PDBFile, $PDBRecordLinesRef, $ChainsAndResiduesInfoRef, $FileDir, $FileName, $FileExt, $OutFileName, $OutFileRoot, $Mode, $OutFileMode, @OutFileNames);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
501
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
502 %PDBFilesInfo = ();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
503 @{$PDBFilesInfo{FileOkay}} = ();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
504 @{$PDBFilesInfo{OutFileRoot}} = ();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
505 @{$PDBFilesInfo{OutFileNames}} = ();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
506
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
507 FILELIST: for $Index (0 .. $#PDBFilesList) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
508 $PDBFilesInfo{FileOkay}[$Index] = 0;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
509
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
510 $PDBFilesInfo{OutFileRoot}[$Index] = '';
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
511 @{$PDBFilesInfo{OutFileNames}[$Index]} = ();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
512 @{$PDBFilesInfo{OutFileNames}[$Index]} = ();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
513
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
514 $PDBFile = $PDBFilesList[$Index];
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
515 if (!(-e $PDBFile)) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
516 warn "Warning: Ignoring file $PDBFile: It doesn't exist\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
517 next FILELIST;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
518 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
519 if (!CheckFileType($PDBFile, "pdb")) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
520 warn "Warning: Ignoring file $PDBFile: It's not a PDB file\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
521 next FILELIST;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
522 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
523 if (! open PDBFILE, "$PDBFile") {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
524 warn "Warning: Ignoring file $PDBFile: Couldn't open it: $! \n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
525 next FILELIST;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
526 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
527 close PDBFILE;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
528
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
529 # Get PDB data...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
530 $PDBRecordLinesRef = ReadPDBFile($PDBFile);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
531 $ChainsAndResiduesInfoRef = GetChainsAndResidues($PDBRecordLinesRef);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
532 if (!scalar @{$ChainsAndResiduesInfoRef->{ChainIDs}}) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
533 warn "Warning: Ignoring file $PDBFile: No chains found \n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
534 next FILELIST;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
535 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
536
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
537 # Setup output file names...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
538 @OutFileNames = ();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
539 $FileDir = ""; $FileName = ""; $FileExt = "";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
540 ($FileDir, $FileName, $FileExt) = ParseFileName($PDBFile);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
541 if ($OptionsInfo{OutFileRoot} && (@PDBFilesList == 1)) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
542 my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($OptionsInfo{OutFileRoot});
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
543 if ($RootFileName && $RootFileExt) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
544 $FileName = $RootFileName;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
545 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
546 else {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
547 $FileName = $OptionsInfo{OutFileRoot};
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
548 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
549 $OutFileRoot = $FileName;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
550 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
551 else {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
552 $OutFileRoot = $FileName;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
553 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
554 $Mode = $OptionsInfo{Mode};
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
555 MODE: {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
556 if ($Mode =~ /^RenumberAtoms$/i) { $OutFileMode = 'RenumberAtoms'; last MODE;}
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
557 if ($Mode =~ /^RenumberResidues$/i) { $OutFileMode = 'RenumberResidues'; last MODE;}
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
558 if ($Mode =~ /^RenumberWaters$/i) { $OutFileMode = 'RenumberWaters'; last MODE;}
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
559 if ($Mode =~ /^RenameChainIDs$/i) { $OutFileMode = 'RenameChainIDs'; last MODE;}
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
560 $OutFileMode = '';
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
561 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
562 $OutFileName = "${OutFileRoot}${OutFileMode}.pdb";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
563 push @OutFileNames, $OutFileName;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
564
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
565 $PDBFilesInfo{FileOkay}[$Index] = 1;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
566 $PDBFilesInfo{OutFileRoot}[$Index] = $OutFileRoot;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
567
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
568 push @{$PDBFilesInfo{OutFileNames}[$Index]}, @OutFileNames;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
569 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
570 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
571
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
572 # Setup script usage and retrieve command line arguments specified using various options...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
573 sub SetupScriptUsage {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
574
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
575 # Retrieve all the options...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
576 %Options = ();
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
577 $Options{atomnumberstart} = 1;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
578 $Options{chainidstart} = 'A';
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
579 $Options{chainidrenameempty} = 'No';
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
580 $Options{keepoldrecords} = 'no';
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
581 $Options{mode} = 'RenumberResidues';
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
582 $Options{modifyheader} = 'yes';
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
583 $Options{residuenumbermode} = 'PerChain';
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
584 $Options{residuenumberstart} = 1;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
585 $Options{residuenumberhetatmmode} = 'Automatic';
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
586 $Options{residuenumberstarthetatm} = 6000;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
587 $Options{waterresiduenames} = 'Automatic';
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
588 $Options{waterresiduestart} = 8000;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
589
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
590 if (!GetOptions(\%Options, "help|h", "atomnumberstart|a=i", "chainidstart|c=s", "chainidrenameempty=s", "keepoldrecords|k=s", "mode|m=s", "modifyheader=s", "overwrite|o", "residuenumbermode=s", "residuenumberstart=i", "residuenumberhetatmmode=s", "residuenumberstarthetatm=i", "root|r=s", "sequencelength=i", "waterresiduenames=s", "waterresiduestart=i", "workingdir|w=s")) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
591 die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
592 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
593 if ($Options{workingdir}) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
594 if (! -d $Options{workingdir}) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
595 die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
596 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
597 chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
598 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
599 if (!IsPositiveInteger($Options{atomnumberstart})) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
600 die "Error: The value specified, $Options{atomnumberstart}, for option \"-a, --AtomNumberStart\" is not valid. Allowed values: >0\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
601 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
602 if ((length($Options{chainidstart}) > 1) || ($Options{chainidstart} !~ /[A-Z]/i)) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
603 die "Error: The value specified, $Options{chainidstart}, for option \"-c, --ChainIDStart\" is not valid. Allowed values: a single character from A to Z\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
604 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
605 if ($Options{chainidrenameempty} !~ /^(yes|no)$/i) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
606 die "Error: The value specified, $Options{chainidrenameempty}, for option \"--chainidrenameempty\" is not valid. Allowed values: yes or no\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
607 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
608 if ($Options{keepoldrecords} !~ /^(yes|no)$/i) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
609 die "Error: The value specified, $Options{keepoldrecords}, for option \"--KeepOldRecords\" is not valid. Allowed values: yes or no\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
610 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
611 if ($Options{mode} !~ /^(RenumberAtoms|RenumberResidues|RenumberWaters|RenameChainIDs)$/i) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
612 die "Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: RenumberAtoms, RenumberResidues, RenumberWaters or RenameChainIDs\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
613 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
614 if ($Options{modifyheader} !~ /^(yes|no)$/i) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
615 die "Error: The value specified, $Options{modifyheader}, for option \"--ModifyHeader\" is not valid. Allowed values: yes or no\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
616 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
617 if ($Options{residuenumbermode} !~ /^(Sequential|PerChain)$/i) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
618 die "Error: The value specified, $Options{residuenumbermode}, for option \"--ResidueNumberMode\" is not valid. Allowed values: Sequential or PerChain\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
619 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
620 if (!IsPositiveInteger($Options{residuenumberstart})) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
621 die "Error: The value specified, $Options{residuenumberstart}, for option \"--ResidueNumberStart\" is not valid. Allowed values: >0\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
622 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
623 if ($Options{residuenumberhetatmmode} !~ /^(automatic|specify)$/i) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
624 die "Error: The value specified, $Options{residuenumberhetatmmode}, for option \"--residuenumbermode\" is not valid. Allowed values: automatic or specify\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
625 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
626 if (!IsPositiveInteger($Options{residuenumberstarthetatm})) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
627 die "Error: The value specified, $Options{residuenumberstarthetatm}, for option \"--residuenumberstartHetatm\" is not valid. Allowed values: >0\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
628 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
629 if (!IsPositiveInteger $Options{waterresiduestart}) {
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
630 die "Error: The value specified, $Options{waterresiduestart}, for option \"--waterresiduestart\" is not valid. Allowed values: >0\n";
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
631 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
632 }
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
633
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
634 __END__
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
635
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
636 =head1 NAME
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
637
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
638 ModifyPDBFiles.pl - Modify data in PDBFile(s)
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
639
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
640 =head1 SYNOPSIS
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
641
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
642 ModifyPDBFiles.pl PDBFile(s)...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
643
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
644 ModifyPDBFiles.pl [B<-a, --AtomNumberStart> number] [B<-c, --ChainIDStart> character]
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
645 [B<--ChainIDRenameEmpty> yes | no] [B<-h, --help>] [B<-k, --KeepOldRecords> yes | no]
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
646 [B<-m, --mode > RenumberAtoms | RenumberResidues | RenumberWaters | RenameChainIDs]
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
647 [B<--ModifyHeader> yes | no] [B<-o, --overwrite>] [B<--ResidueNumberMode> Sequential | PerChain]
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
648 [B<--ResidueNumberStart> number] [B<--ResidueNumberHetatmMode> automatic | specify]
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
649 [B<--ResidueNumberStarHetatm> number] [B<-r, --root> rootname]
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
650 [B<--WaterResidueNames> Automatic | "ResidueName, [ResidueName,...]"] [B<--WaterResidueStart> number]
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
651 [B<-w, --WorkingDir> dirname] PDBFile(s)...
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
652
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
653 =head1 DESCRIPTION
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
654
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
655 Modify data in I<PDBFile(s)>: renumber atoms, residues, and water residues or assign new
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
656 chain IDs. Multiple PDBFile names are separated by spaces. The valid file extension is I<.pdb>.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
657 All other file name extensions are ignored during the wild card expansion. All the PDB files
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
658 in a current directory can be specified either by I<*.pdb> or the current directory name.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
659
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
660 =head1 OPTIONS
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
661
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
662 =over 4
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
663
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
664 =item B<-a, --AtomNumberStart> I<number>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
665
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
666 Starting atom number to use during I<RenumberAtoms> value of B<-m, --mode> option. Default: I<1>.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
667 Valid values: positive integers.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
668
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
669 =item B<-c, --ChainIDStart> I<character>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
670
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
671 A single character to use for starting IDs for chains during I<RenameChainIDs> value of B<-m, --mode> option.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
672 Default: I<A>. Valid values: I<A to Z>.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
673
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
674 =item B<--ChainIDRenameEmpty> I<Yes | No>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
675
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
676 Specify whether to rename empty chain IDs during I<RenameChainIDs> B<-m, --mode> value. By
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
677 default, ATOM and HETATM records with no chain IDs are left unchanged. Possible values:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
678 I<yes | no>. Default: I<No>.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
679
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
680 =item B<-h, --help>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
681
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
682 Print this help message.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
683
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
684 =item B<-k, --KeepOldRecords> I<yes | no>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
685
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
686 Specify whether to transfer old non ATOM and HETATM records from input PDBFile(s) to new
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
687 PDBFile(s). By default, except for the HEADER record, all records other than ATOM/HETATM
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
688 are dropped during the generation of new PDB files. Possible values: I<yes | no>.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
689 Default: I<no>.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
690
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
691 =item B<-m, --mode > I<RenumberAtoms | RenumberResidues | RenumberWaters | RenameChainIDs>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
692
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
693 Specify how to modify I<PDBFile(s)>. Possible values: I<RenumberAtoms | RenumberResidues
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
694 | RenumberWaters | RenameChainIDs>. Default: I<RenumberResidues>.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
695
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
696 For I<RenumberAtoms> mode, residue number in ATOM and HETATM records are reassigned
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
697 sequentially starting using value of B<-a, --AtomNumberStart> option.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
698
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
699 For I<RenumberResidues> mode, serial number in ATOM and HETATM records are reassigned
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
700 either sequentially or statring from specified values for ATOM and HETATM records in each
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
701 chain.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
702
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
703 For I<RenumberWaters> mode, residue number for waters are reassigned starting from a specific
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
704 value.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
705
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
706 For I<RenameChainIDs> mode, all the chain IDs are reassigned starting from a specific chain ID.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
707
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
708 During the generation of new PDB files, unnecessary CONECT records are dropped.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
709
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
710 =item B<--ModifyHeader> I<yes | no>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
711
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
712 Specify whether to modify HEADER record during the generation of new PDB files
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
713 Possible values: I<yes | no>. Default: I<yes>. By defailt, Classification data is replaced
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
714 by I<Data modified using MayaChemTools> before writing out HEADER record.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
715
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
716 =item B<-o, --overwrite>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
717
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
718 Overwrite existing files
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
719
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
720 =item B<--ResidueNumberMode> I<Sequential | PerChain>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
721
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
722 Specify how to renumber residues: renumber residues sequentially across all the chains
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
723 or start from the begining for each chain. Possible values: I<Sequential | PerChain>. Default:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
724 I<PerChain>.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
725
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
726 =item B<--ResidueNumberStart> I<number>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
727
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
728 Starting residue number to use for ATOM records in chains. Default: I<1>. Valid values
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
729 positive integers.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
730
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
731 For I<Sequential> value of B<--ResidueNumberMode> option, residue numbers are
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
732 assigned sequentially across all the chains starting from the specified value.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
733
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
734 For I<PerChain> value of B<--ResidueNumberMode> option, residue numbers are
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
735 starting again from the specified value for each chain.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
736
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
737 HETATM residues with in the chains are numbered using this value as well
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
738
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
739 =item B<--ResidueNumberHetatmMode> I<automatic | specify>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
740
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
741 Specify how to start residue number for HETATM records: use the next sequential
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
742 residue number after the last residue number from ATOM records or start from a
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
743 specific residue number. Possible values: I<automatic | specify>. Default:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
744 I<automatic>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
745
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
746 For I<automatic> , residue number after highest residue number of ATOM
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
747 records is used as the starting residue number for HETATM records.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
748
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
749 For I<specify>, value of option B<--ResidueNumberStarHetatm> is used as the
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
750 starting residue number for HETATM records.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
751
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
752 This option along with B<--ResidueNumberStartHetatm> only applies to HETATM records
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
753 outside the chains.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
754
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
755 =item B<--ResidueNumberStartHetatm> I<number>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
756
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
757 Starting residue number to use for HETATM records. Default: I<6000>. Valid values
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
758 positive integers.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
759
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
760 =item B<-r, --root> I<rootname>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
761
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
762 New PDB and sequence file name is generated using the root: <Root><Mode>.<Ext>.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
763 Default new file name: <PDBFileName><Mode>.pdb. This option is ignored for multiple
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
764 input files.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
765
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
766 =item B<--WaterResidueNames> I<Automatic | "ResidueName,[ResidueName,...]">
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
767
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
768 Identification of water residues during I<RenumberWaters> value of B<-m, --mode> option. Possible
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
769 values: I<Automatic | "ResidueName,[ResidueName,...]">. Default: I<Automatic> which corresponds
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
770 to "HOH,WAT,H20". You can also specify a different comma delimited list of residue names
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
771 to use for water.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
772
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
773 =item B<--WaterResidueStart> I<number>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
774
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
775 Starting water residue number to use during I<RenumberWaters> B<-m, --mode> value.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
776 Default: I<8000>. Valid values: positive integers.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
777
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
778 =item B<-w, --WorkingDir> I<dirname>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
779
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
780 Location of working directory. Default: current directory.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
781
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
782 =back
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
783
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
784 =head1 EXAMPLES
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
785
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
786 To renumber ATOM and HETATM residues starting from 1 for each chain with continuation to
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
787 HETATM residues outside TER records in Sample2.pdb and generate
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
788 Sample2RenumberResidues.pdb file, type:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
789
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
790 % ModifyPDBFiles.pl Sample1.pdb
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
791
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
792 To renumber ATOM and HETATM residues sequentially across all chains starting from 1 with
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
793 continuation to HETATM residues outside TER records in Sample2.pdb and generate
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
794 Sample2RenumberResidues.pdb file, type:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
795
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
796 % ModifyPDBFiles.pl --ResidueNumberMode Sequential -o Sample1.pdb
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
797
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
798 To renumber ATOM and HETATM residues sequentially across all chains starting from 1 and
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
799 HETATM residues outside TER records starting from 6000 in Sample2.pdb and generate
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
800 Sample2RenumberResidues.pdb file, type:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
801
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
802 % ModifyPDBFiles.pl --ResidueNumberMode Sequential
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
803 --ResidueNumberHetatmMode Specify -o Sample1.pdb
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
804
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
805
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
806 To renumber ATOM and HETATM residues sequentially across all chains starting from 100 for
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
807 ATOM/HETATM residues with in TER records and starting from 999 for HETATM residues
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
808 outside TER records in Sample2.pdb and generate Sample2RenumberResidues.pdb file, type:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
809
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
810 % ModifyPDBFiles.pl --ResidueNumberMode Sequential
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
811 --ResidueNumberHetatmMode Specify --ResidueNumberStart 100
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
812 --ResidueNumberStartHetatm 999 -o Sample2.pdb
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
813
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
814 To renumber ATOM and HETATM residues from 100 for each chain and starting from 999 for
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
815 HETATM residues outside TER records in Sample2.pdb and generate Sample2RenumberResidues.pdb
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
816 file, type:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
817
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
818 % ModifyPDBFiles.pl --ResidueNumberMode PerChain
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
819 --ResidueNumberHetatmMode Specify --ResidueNumberStart 100
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
820 --ResidueNumberStartHetatm 999 -o Sample2.pdb
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
821
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
822 To renumber ATOM serial numbers sequentially starting from 100 in Sample1.pdb file and generate
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
823 Sample1RenumberAtoms.pdb file, type:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
824
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
825 % ModifyPDBFiles.pl -m RenumberAtoms --AtomNumberStart 100
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
826 -o Sample1.pdb
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
827
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
828 To renumber water residues identified by "HOH,WAT" starting from residue number 1000
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
829 in Sample2.pdb file and generate Sample2RenumberWaters.pdb file, type:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
830
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
831 % ModifyPDBFiles.pl -m RenumberWaters --WaterResidueNames "HOH,WAT"
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
832 -o --WaterResidueStart 950 Sample2.pdb
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
833
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
834 To rename all chain IDs starting from A in Sample1.pdb file and generate
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
835 Sample1RenameChainIDs.pdb file, type:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
836
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
837 % ModifyPDBFiles.pl -m RenameChainIDs -o Sample1.pdb
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
838
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
839 To rename all chain IDs starting from B without assigning any chain IDs to ATOM/HETATOM
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
840 with no chain IDs in Sample2.pdb file and generate Sample2RenameChainIDs.pdb file, type:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
841
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
842 % ModifyPDBFiles.pl l -m RenameChainIDs -c B --ChainIDRenameEmpty No
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
843 -o Sample2.pdb
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
844
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
845
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
846 =head1 AUTHOR
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
847
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
848 Manish Sud <msud@san.rr.com>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
849
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
850 =head1 SEE ALSO
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
851
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deepakjadmin
parents:
diff changeset
852 ExtractFromPDBFiles.pl, InfoPDBFiles.pl
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
853
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
854 =head1 COPYRIGHT
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
855
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
856 Copyright (C) 2015 Manish Sud. All rights reserved.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
857
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
858 This file is part of MayaChemTools.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
859
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
860 MayaChemTools is free software; you can redistribute it and/or modify it under
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
861 the terms of the GNU Lesser General Public License as published by the Free
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
862 Software Foundation; either version 3 of the License, or (at your option)
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
863 any later version.
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
864
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
865 =cut