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1 NAME
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2 InfoPDBFiles.pl - List information about PDB files
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3
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4 SYNOPSIS
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5 InfoPDBFiles.pl PDBFile(s) PDB(s)...
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6
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7 InfoPDBFiles.pl [-a, --all] [-b, --BoundingBox] [-c, --count
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8 "RecordType, [RecordType,...]" | All] [--chains] [-d, --detail
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9 infolevel] [-e, --experiment] [-f, --frequency] [-h, --help] [--header]
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10 [m, --MasterCheck] [--residues] [--ResiduesMode InChains | All | Both]
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11 [--ResidueNumbers] [-w, --WorkingDir dirname] PDBFile(s)...
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12
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13 DESCRIPTION
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14 List information about contents of *PDBFile(s)*: number of each record
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15 type, number of chains, count and percent distribution of residues in
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16 each chain, bounding box and so on. Multiple PDBFile names are separated
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17 by spaces. The valid file extension is *.pdb*. All other file name
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18 extensions are ignored during the wild card expansion. All the PDB files
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19 in a current directory can be specified either by **.pdb* or the current
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20 directory name.
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21
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22 In PDB files containing data for multiple models, all ATOM/HETAM records
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23 for chains after the first model are ignored.
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24
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25 OPTIONS
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26 -a, --all
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27 List all the available information.
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28
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29 -b, --BoundingBox
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30 List min/max XYZ coordiates of ATOM/HETATM records.
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31
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32 -c, --count *RecordType,[RecordType,...]|All*
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33 Types of PDB records to count in *PDBFile(s)*. You can specify a
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34 list of any valid PDB record type or count all record types found in
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35 the files. Possible values: Comma delimited list of valid
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36 *RecordTypes* or *All*. Default: *ATOM,HETATM*. And this is also
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37 default behavior.
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38
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39 The list of valid PDB record types includes: *HEADER, OBSLTE, TITLE,
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40 CAVEAT, COMPND, SOURCE, KEYWDS, EXPDTA, AUTHOR, REVDAT, SPRSDE, JRN,
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41 REMARK, DBRE, SEQADV, SEQRES, MODRES, HET, HETNAM, HETSYN, FORMUL,
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42 HELIX, SHEET, TURN, SSBOND, LINK, HYDBND, SLTBRG, CISPEP, SITE,
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43 CRYST1, ORIGX1, ORIGX2, ORIGX3, SCALE1, SCALE2, SCALE3, MTRIX1
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44 MTRIX2 MTRIX3, TVECT, MODEL, ATOM, SIGATM, ANISOU, SIGUIJ, TER,
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45 HETATM, ENDMDL, CONECT, MASTER, END*.
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46
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47 --chains
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48 Count number of chains.
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49
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50 -d, --detail *infolevel*
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51 Level of information to print about PDB during various options.
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52 Default: *1*. Possible values: *1, 2 or 3*.
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53
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54 -e, --experiment
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55 List experimental technique information along with any applicable
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56 resolution.
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57
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58 -f, --frequency
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59 List distribution of residues: report count and percent of residues
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60 in individual chains and across all the chains, or for all the
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61 residues in the file. The value of option --residuesmode determines
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62 how residues are counted and what is listed. The list is sorted by
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63 frequency in descending order. By default, only residue count values
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64 are reported. To list percent distribution of residues, specify -d,
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65 --detail value of *2* or higher.
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66
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67 -h, --help
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68 Print this help message.
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69
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70 --header
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71 List header information.
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72
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73 m, --MasterCheck
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74 Check master record by explicitly counting the number of REMARK,
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75 HET, HELIX, SHEET, TURN, SITE, ORIGX, SCALE, MTRIX, ATOM, HETATM,
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76 TER, CONECT and SEQRES records and comparing their values against
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77 contents of master record.
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78
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79 --residues
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80 Count residues in *PDBFile(s)*. This is also default behavior.
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81
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82 By default, only residue count values are reported. To list percent
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83 distribution of residues, specify -d, --detail value of *2* or
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84 higher.
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85
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86 --ResiduesMode <InChains | All | Both>
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87 Specify how to count residues in *PDBFile(s)*: Count residue in each
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88 chain and across all the chains, list count iof all the residues in
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89 the file, or list both. Possible values: *InChains, All, or Both*.
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90 Default: *Both*.
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91
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92 --ResidueNumbers
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93 List information about ATOM residue numbers in each chain before TER
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94 record: start and end residue number; gaps in residue numbers
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95 corresponding to non-sequential residue numbers; residue numbers not
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96 in ascending order.
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97
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98 -w, --WorkingDir *dirname*
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99 Location of working directory. Default: current directory.
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100
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101 EXAMPLES
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102 To list total number of records and number of chain(s) residues in PDB
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103 files, type:
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104
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105 % InfoPDBFiles.pl Sample1.pdb
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106 % InfoPDBFiles.pl Sample2.pdb
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107
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108 To list all available information for PDB file Sample2.pdb, type:
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109
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110 % InfoPDBFiles.pl -a Sample2.pdb
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111
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112 To list all available information for PDB file Sample2.pdb with all
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113 available details, type:
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114
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115 % InfoPDBFiles.pl -a -d Sample2.pdb
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116
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117 To count ATOM and HETATM records in Sample2.pdb file, type:
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118
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119 % InfoPDBFiles.pl -c "ATOM,HETATM" Sample2.pdb
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120
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121 To list distribution of residues in chains across the whole PDB file
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122 Sample2.pdb along with percent distribution, type
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123
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124 % InfoPDBFiles.pl --frequency -d 2 Sample2.pdb
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125
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126 To list distribution of residues only across chains in PDB file
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127 Sample2.pdb along with percent distribution, type
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128
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129 % InfoPDBFiles.pl --frequency -d 2 --ResiduesMode InChains Sample2.pdb
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130
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131 To list min/max coordinates of the bounding box which encompasses the
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132 structure in Sample1.pdb file, type:
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133
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134 % InfoPDBFiles.pl -b Sample1.pdb
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135
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136 AUTHOR
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137 Manish Sud <msud@san.rr.com>
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138
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139 SEE ALSO
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140 ExtractFromPDBFiles.pl, InfoAminoAcids.pl, InfoNucleicAcids.pl,
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141 InfoSequenceFiles.pl, ModifyPDBFiles.pl
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142
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143 COPYRIGHT
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144 Copyright (C) 2015 Manish Sud. All rights reserved.
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145
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146 This file is part of MayaChemTools.
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147
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148 MayaChemTools is free software; you can redistribute it and/or modify it
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149 under the terms of the GNU Lesser General Public License as published by
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150 the Free Software Foundation; either version 3 of the License, or (at
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151 your option) any later version.
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152
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