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3 <title>MayaChemTools:Documentation:InfoPDBFiles.pl</title>
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11 </center>
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13 <div class="DocNav">
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14 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./InfoNucleicAcids.html" title="InfoNucleicAcids.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./InfoPeriodicTableElements.html" title="InfoPeriodicTableElements.html">Next</a></td><td width="34%" align="middle"><strong>InfoPDBFiles.pl</strong></td><td width="33%" align="right"><a href="././code/InfoPDBFiles.html" title="View source code">Code</a> | <a href="./../pdf/InfoPDBFiles.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/InfoPDBFiles.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/InfoPDBFiles.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/InfoPDBFiles.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
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16 </table>
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17 </div>
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18 <p>
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19 </p>
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20 <h2>NAME</h2>
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21 <p>InfoPDBFiles.pl - List information about PDB files</p>
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22 <p>
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23 </p>
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24 <h2>SYNOPSIS</h2>
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25 <p>InfoPDBFiles.pl PDBFile(s) PDB(s)...</p>
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26 <p>InfoPDBFiles.pl [<strong>-a, --all</strong>] [<strong>-b, --BoundingBox</strong>]
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27 [<strong>-c, --count</strong> "RecordType, [RecordType,...]" | All] [<strong>--chains</strong>]
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28 [<strong>-d, --detail</strong> infolevel] [<strong>-e, --experiment</strong>] [<strong>-f, --frequency</strong>]
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29 [<strong>-h, --help</strong>] [<strong>--header</strong>] [<strong>m, --MasterCheck</strong>] [<strong>--residues</strong>]
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30 [<strong>--ResiduesMode</strong> InChains | All | Both] [<strong>--ResidueNumbers</strong>]
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31 [<strong>-w, --WorkingDir</strong> dirname] PDBFile(s)...</p>
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32 <p>
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33 </p>
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34 <h2>DESCRIPTION</h2>
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35 <p>List information about contents of <em>PDBFile(s)</em>: number of each record type, number of chains,
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36 count and percent distribution of residues in each chain, bounding box and so on.
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37 Multiple PDBFile names are separated by spaces. The valid file extension is <em>.pdb</em>.
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38 All other file name extensions are ignored during the wild card expansion. All the PDB files
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39 in a current directory can be specified either by <em>*.pdb</em> or the current directory name.</p>
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40 <p>In PDB files containing data for multiple models, all ATOM/HETAM records for chains after the first model
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41 are ignored.</p>
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42 <p>
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43 </p>
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44 <h2>OPTIONS</h2>
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45 <dl>
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46 <dt><strong><strong>-a, --all</strong></strong></dt>
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47 <dd>
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48 <p>List all the available information.</p>
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49 </dd>
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50 <dt><strong><strong>-b, --BoundingBox</strong></strong></dt>
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51 <dd>
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52 <p>List min/max XYZ coordiates of ATOM/HETATM records.</p>
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53 </dd>
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54 <dt><strong><strong>-c, --count</strong> <em>RecordType,[RecordType,...]|All</em></strong></dt>
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55 <dd>
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56 <p>Types of PDB records to count in <em>PDBFile(s)</em>. You can specify a list of any valid PDB
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57 record type or count all record types found in the files. Possible values: Comma delimited list
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58 of valid <em>RecordTypes</em> or <em>All</em>. Default: <em>ATOM,HETATM</em>. And this is also <strong>default behavior</strong>.</p>
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59 <p>The list of valid PDB record types includes: <em>HEADER, OBSLTE, TITLE, CAVEAT, COMPND, SOURCE, KEYWDS,
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60 EXPDTA, AUTHOR, REVDAT, SPRSDE, JRN, REMARK, DBRE, SEQADV, SEQRES, MODRES, HET, HETNAM, HETSYN,
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61 FORMUL, HELIX, SHEET, TURN, SSBOND, LINK, HYDBND, SLTBRG, CISPEP, SITE, CRYST1, ORIGX1, ORIGX2, ORIGX3,
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62 SCALE1, SCALE2, SCALE3, MTRIX1 MTRIX2 MTRIX3, TVECT, MODEL, ATOM, SIGATM, ANISOU, SIGUIJ, TER,
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63 HETATM, ENDMDL, CONECT, MASTER, END</em>.</p>
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64 </dd>
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65 <dt><strong><strong>--chains</strong></strong></dt>
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66 <dd>
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67 <p>Count number of chains.</p>
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68 </dd>
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69 <dt><strong><strong>-d, --detail</strong> <em>infolevel</em></strong></dt>
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70 <dd>
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71 <p>Level of information to print about PDB during various options. Default: <em>1</em>.
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72 Possible values: <em>1, 2 or 3</em>.</p>
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73 </dd>
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74 <dt><strong><strong>-e, --experiment</strong></strong></dt>
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75 <dd>
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76 <p>List experimental technique information along with any applicable resolution.</p>
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77 </dd>
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78 <dt><strong><strong>-f, --frequency</strong></strong></dt>
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79 <dd>
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80 <p>List distribution of residues: report count and percent of residues in individual chains and
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81 across all the chains, or for all the residues in the file. The value of option <strong>--residuesmode</strong>
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82 determines how residues are counted and what is listed. The list is sorted by frequency in
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83 descending order. By default, only residue count values are reported. To list percent distribution
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84 of residues, specify <strong>-d, --detail</strong> value of <em>2</em> or higher.</p>
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85 </dd>
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86 <dt><strong><strong>-h, --help</strong></strong></dt>
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87 <dd>
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88 <p>Print this help message.</p>
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89 </dd>
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90 <dt><strong><strong>--header</strong></strong></dt>
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91 <dd>
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92 <p>List header information.</p>
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93 </dd>
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94 <dt><strong><strong>m, --MasterCheck</strong></strong></dt>
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95 <dd>
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96 <p>Check master record by explicitly counting the number of REMARK, HET, HELIX, SHEET, TURN, SITE,
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97 ORIGX, SCALE, MTRIX, ATOM, HETATM, TER, CONECT and SEQRES records and comparing their
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98 values against contents of master record.</p>
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99 </dd>
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100 <dt><strong><strong>--residues</strong></strong></dt>
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101 <dd>
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102 <p>Count residues in <em>PDBFile(s)</em>. This is also <strong>default behavior</strong>.</p>
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103 <p>By default, only residue count values are reported. To list percent distribution of residues,
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104 specify <strong>-d, --detail</strong> value of <em>2</em> or higher.</p>
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105 </dd>
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106 <dt><strong><strong>--ResiduesMode</strong> <InChains | All | Both></strong></dt>
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107 <dd>
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108 <p>Specify how to count residues in <em>PDBFile(s)</em>: Count residue in each chain and across all the chains,
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109 list count iof all the residues in the file, or list both. Possible values: <em>InChains, All, or Both</em>.
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110 Default: <em>Both</em>.</p>
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111 </dd>
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112 <dt><strong><strong>--ResidueNumbers</strong></strong></dt>
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113 <dd>
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114 <p>List information about ATOM residue numbers in each chain before TER record: start and end residue
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115 number; gaps in residue numbers corresponding to non-sequential residue numbers; residue
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116 numbers not in ascending order.</p>
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117 </dd>
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118 <dt><strong><strong>-w, --WorkingDir</strong> <em>dirname</em></strong></dt>
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119 <dd>
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120 <p>Location of working directory. Default: current directory.</p>
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121 </dd>
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122 </dl>
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123 <p>
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124 </p>
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125 <h2>EXAMPLES</h2>
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126 <p>To list total number of records and number of chain(s) residues in PDB files, type:</p>
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127 <div class="ExampleBox">
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128 % InfoPDBFiles.pl Sample1.pdb
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129 <br/>% InfoPDBFiles.pl Sample2.pdb</div>
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130 <p>To list all available information for PDB file Sample2.pdb, type:</p>
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131 <div class="ExampleBox">
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132 % InfoPDBFiles.pl -a Sample2.pdb</div>
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133 <p>To list all available information for PDB file Sample2.pdb with all available details, type:</p>
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134 <div class="ExampleBox">
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135 % InfoPDBFiles.pl -a -d Sample2.pdb</div>
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136 <p>To count ATOM and HETATM records in Sample2.pdb file, type:</p>
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137 <div class="ExampleBox">
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138 % InfoPDBFiles.pl -c "ATOM,HETATM" Sample2.pdb</div>
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139 <p>To list distribution of residues in chains across the whole PDB file Sample2.pdb along with
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140 percent distribution, type</p>
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141 <div class="ExampleBox">
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142 % InfoPDBFiles.pl --frequency -d 2 Sample2.pdb</div>
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143 <p>To list distribution of residues only across chains in PDB file Sample2.pdb along with
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144 percent distribution, type</p>
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145 <div class="ExampleBox">
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146 % InfoPDBFiles.pl --frequency -d 2 --ResiduesMode InChains Sample2.pdb</div>
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147 <p>To list min/max coordinates of the bounding box which encompasses the structure in Sample1.pdb
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148 file, type:</p>
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149 <div class="ExampleBox">
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150 % InfoPDBFiles.pl -b Sample1.pdb</div>
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151 <p>
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152 </p>
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153 <h2>AUTHOR</h2>
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154 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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155 <p>
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156 </p>
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157 <h2>SEE ALSO</h2>
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158 <p><a href="./ExtractFromPDBFiles.html">ExtractFromPDBFiles.pl</a>, <a href="./InfoAminoAcids.html">InfoAminoAcids.pl</a>, <a href="./InfoNucleicAcids.html">InfoNucleicAcids.pl</a>, <a href="./InfoSequenceFiles.html">InfoSequenceFiles.pl</a>, <a href="./ModifyPDBFiles.html">ModifyPDBFiles.pl</a>
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159 </p>
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160 <p>
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161 </p>
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162 <h2>COPYRIGHT</h2>
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163 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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164 <p>This file is part of MayaChemTools.</p>
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165 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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166 the terms of the GNU Lesser General Public License as published by the Free
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167 Software Foundation; either version 3 of the License, or (at your option)
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168 any later version.</p>
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169 <p> </p><p> </p><div class="DocNav">
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170 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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171 <tr align="left" valign="top"><td width="33%" align="left"><a href="./InfoNucleicAcids.html" title="InfoNucleicAcids.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./InfoPeriodicTableElements.html" title="InfoPeriodicTableElements.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>InfoPDBFiles.pl</strong></td></tr>
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172 </table>
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173 </div>
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174 <br />
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175 <center>
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176 <img src="../../images/h2o2.png">
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177 </center>
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178 </body>
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179 </html>
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