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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docs/scripts/man1/ModifyPDBFiles.1 Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,349 @@ +.\" Automatically generated by Pod::Man 2.25 (Pod::Simple 3.22) +.\" +.\" Standard preamble: +.\" ======================================================================== +.de Sp \" Vertical space (when we can't use .PP) +.if t .sp .5v +.if n .sp +.. +.de Vb \" Begin verbatim text +.ft CW +.nf +.ne \\$1 +.. +.de Ve \" End verbatim text +.ft R +.fi +.. +.\" Set up some character translations and predefined strings. \*(-- will +.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left +.\" double quote, and \*(R" will give a right double quote. \*(C+ will +.\" give a nicer C++. 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Always turn off hyphenation; it makes +.\" way too many mistakes in technical documents. +.if n .ad l +.nh +.SH "NAME" +ModifyPDBFiles.pl \- Modify data in PDBFile(s) +.SH "SYNOPSIS" +.IX Header "SYNOPSIS" +ModifyPDBFiles.pl PDBFile(s)... +.PP +ModifyPDBFiles.pl [\fB\-a, \-\-AtomNumberStart\fR number] [\fB\-c, \-\-ChainIDStart\fR character] +[\fB\-\-ChainIDRenameEmpty\fR yes | no] [\fB\-h, \-\-help\fR] [\fB\-k, \-\-KeepOldRecords\fR yes | no] +[\fB\-m, \-\-mode \fR RenumberAtoms | RenumberResidues | RenumberWaters | RenameChainIDs] +[\fB\-\-ModifyHeader\fR yes | no] [\fB\-o, \-\-overwrite\fR] [\fB\-\-ResidueNumberMode\fR Sequential | PerChain] +[\fB\-\-ResidueNumberStart\fR number] [\fB\-\-ResidueNumberHetatmMode\fR automatic | specify] +[\fB\-\-ResidueNumberStarHetatm\fR number] [\fB\-r, \-\-root\fR rootname] +[\fB\-\-WaterResidueNames\fR Automatic | \*(L"ResidueName, [ResidueName,...]\*(R"] [\fB\-\-WaterResidueStart\fR number] +[\fB\-w, \-\-WorkingDir\fR dirname] PDBFile(s)... +.SH "DESCRIPTION" +.IX Header "DESCRIPTION" +Modify data in \fIPDBFile(s)\fR: renumber atoms, residues, and water residues or assign new +chain IDs. Multiple PDBFile names are separated by spaces. The valid file extension is \fI.pdb\fR. +All other file name extensions are ignored during the wild card expansion. All the \s-1PDB\s0 files +in a current directory can be specified either by \fI*.pdb\fR or the current directory name. +.SH "OPTIONS" +.IX Header "OPTIONS" +.IP "\fB\-a, \-\-AtomNumberStart\fR \fInumber\fR" 4 +.IX Item "-a, --AtomNumberStart number" +Starting atom number to use during \fIRenumberAtoms\fR value of \fB\-m, \-\-mode\fR option. Default: \fI1\fR. +Valid values: positive integers. +.IP "\fB\-c, \-\-ChainIDStart\fR \fIcharacter\fR" 4 +.IX Item "-c, --ChainIDStart character" +A single character to use for starting IDs for chains during \fIRenameChainIDs\fR value of \fB\-m, \-\-mode\fR option. +Default: \fIA\fR. Valid values: \fIA to Z\fR. +.IP "\fB\-\-ChainIDRenameEmpty\fR \fIYes | No\fR" 4 +.IX Item "--ChainIDRenameEmpty Yes | No" +Specify whether to rename empty chain IDs during \fIRenameChainIDs\fR \fB\-m, \-\-mode\fR value. By +default, \s-1ATOM\s0 and \s-1HETATM\s0 records with no chain IDs are left unchanged. Possible values: +\&\fIyes | no\fR. Default: \fINo\fR. +.IP "\fB\-h, \-\-help\fR" 4 +.IX Item "-h, --help" +Print this help message. +.IP "\fB\-k, \-\-KeepOldRecords\fR \fIyes | no\fR" 4 +.IX Item "-k, --KeepOldRecords yes | no" +Specify whether to transfer old non \s-1ATOM\s0 and \s-1HETATM\s0 records from input PDBFile(s) to new +PDBFile(s). By default, except for the \s-1HEADER\s0 record, all records other than \s-1ATOM/HETATM\s0 +are dropped during the generation of new \s-1PDB\s0 files. Possible values: \fIyes | no\fR. +Default: \fIno\fR. +.IP "\fB\-m, \-\-mode \fR \fIRenumberAtoms | RenumberResidues | RenumberWaters | RenameChainIDs\fR" 4 +.IX Item "-m, --mode RenumberAtoms | RenumberResidues | RenumberWaters | RenameChainIDs" +Specify how to modify \fIPDBFile(s)\fR. Possible values: \fIRenumberAtoms | RenumberResidues +| RenumberWaters | RenameChainIDs\fR. Default: \fIRenumberResidues\fR. +.Sp +For \fIRenumberAtoms\fR mode, residue number in \s-1ATOM\s0 and \s-1HETATM\s0 records are reassigned +sequentially starting using value of \fB\-a, \-\-AtomNumberStart\fR option. +.Sp +For \fIRenumberResidues\fR mode, serial number in \s-1ATOM\s0 and \s-1HETATM\s0 records are reassigned +either sequentially or statring from specified values for \s-1ATOM\s0 and \s-1HETATM\s0 records in each +chain. +.Sp +For \fIRenumberWaters\fR mode, residue number for waters are reassigned starting from a specific +value. +.Sp +For \fIRenameChainIDs\fR mode, all the chain IDs are reassigned starting from a specific chain \s-1ID\s0. +.Sp +During the generation of new \s-1PDB\s0 files, unnecessary \s-1CONECT\s0 records are dropped. +.IP "\fB\-\-ModifyHeader\fR \fIyes | no\fR" 4 +.IX Item "--ModifyHeader yes | no" +Specify whether to modify \s-1HEADER\s0 record during the generation of new \s-1PDB\s0 files +Possible values: \fIyes | no\fR. Default: \fIyes\fR. By defailt, Classification data is replaced +by \fIData modified using MayaChemTools\fR before writing out \s-1HEADER\s0 record. +.IP "\fB\-o, \-\-overwrite\fR" 4 +.IX Item "-o, --overwrite" +Overwrite existing files +.IP "\fB\-\-ResidueNumberMode\fR \fISequential | PerChain\fR" 4 +.IX Item "--ResidueNumberMode Sequential | PerChain" +Specify how to renumber residues: renumber residues sequentially across all the chains +or start from the begining for each chain. Possible values: \fISequential | PerChain\fR. Default: +\&\fIPerChain\fR. +.IP "\fB\-\-ResidueNumberStart\fR \fInumber\fR" 4 +.IX Item "--ResidueNumberStart number" +Starting residue number to use for \s-1ATOM\s0 records in chains. Default: \fI1\fR. Valid values +positive integers. +.Sp +For \fISequential\fR value of \fB\-\-ResidueNumberMode\fR option, residue numbers are +assigned sequentially across all the chains starting from the specified value. +.Sp +For \fIPerChain\fR value of \fB\-\-ResidueNumberMode\fR option, residue numbers are +starting again from the specified value for each chain. +.Sp +\&\s-1HETATM\s0 residues with in the chains are numbered using this value as well +.IP "\fB\-\-ResidueNumberHetatmMode\fR \fIautomatic | specify\fR" 4 +.IX Item "--ResidueNumberHetatmMode automatic | specify" +Specify how to start residue number for \s-1HETATM\s0 records: use the next sequential +residue number after the last residue number from \s-1ATOM\s0 records or start from a +specific residue number. Possible values: \fIautomatic | specify\fR. Default: +\&\fIautomatic\fR +.Sp +For \fIautomatic\fR , residue number after highest residue number of \s-1ATOM\s0 +records is used as the starting residue number for \s-1HETATM\s0 records. +.Sp +For \fIspecify\fR, value of option \fB\-\-ResidueNumberStarHetatm\fR is used as the +starting residue number for \s-1HETATM\s0 records. +.Sp +This option along with \fB\-\-ResidueNumberStartHetatm\fR only applies to \s-1HETATM\s0 records +outside the chains. +.IP "\fB\-\-ResidueNumberStartHetatm\fR \fInumber\fR" 4 +.IX Item "--ResidueNumberStartHetatm number" +Starting residue number to use for \s-1HETATM\s0 records. Default: \fI6000\fR. Valid values +positive integers. +.IP "\fB\-r, \-\-root\fR \fIrootname\fR" 4 +.IX Item "-r, --root rootname" +New \s-1PDB\s0 and sequence file name is generated using the root: <Root><Mode>.<Ext>. +Default new file name: <PDBFileName><Mode>.pdb. This option is ignored for multiple +input files. +.ie n .IP "\fB\-\-WaterResidueNames\fR \fIAutomatic | ""ResidueName,[ResidueName,...]""\fR" 4 +.el .IP "\fB\-\-WaterResidueNames\fR \fIAutomatic | ``ResidueName,[ResidueName,...]''\fR" 4 +.IX Item "--WaterResidueNames Automatic | ResidueName,[ResidueName,...]" +Identification of water residues during \fIRenumberWaters\fR value of \fB\-m, \-\-mode\fR option. Possible +values: \fIAutomatic | \*(L"ResidueName,[ResidueName,...]\*(R"\fR. Default: \fIAutomatic\fR which corresponds +to \*(L"\s-1HOH\s0,WAT,H20\*(R". You can also specify a different comma delimited list of residue names +to use for water. +.IP "\fB\-\-WaterResidueStart\fR \fInumber\fR" 4 +.IX Item "--WaterResidueStart number" +Starting water residue number to use during \fIRenumberWaters\fR \fB\-m, \-\-mode\fR value. +Default: \fI8000\fR. Valid values: positive integers. +.IP "\fB\-w, \-\-WorkingDir\fR \fIdirname\fR" 4 +.IX Item "-w, --WorkingDir dirname" +Location of working directory. Default: current directory. +.SH "EXAMPLES" +.IX Header "EXAMPLES" +To renumber \s-1ATOM\s0 and \s-1HETATM\s0 residues starting from 1 for each chain with continuation to +\&\s-1HETATM\s0 residues outside \s-1TER\s0 records in Sample2.pdb and generate +Sample2RenumberResidues.pdb file, type: +.PP +.Vb 1 +\& % ModifyPDBFiles.pl Sample1.pdb +.Ve +.PP +To renumber \s-1ATOM\s0 and \s-1HETATM\s0 residues sequentially across all chains starting from 1 with +continuation to \s-1HETATM\s0 residues outside \s-1TER\s0 records in Sample2.pdb and generate +Sample2RenumberResidues.pdb file, type: +.PP +.Vb 1 +\& % ModifyPDBFiles.pl \-\-ResidueNumberMode Sequential \-o Sample1.pdb +.Ve +.PP +To renumber \s-1ATOM\s0 and \s-1HETATM\s0 residues sequentially across all chains starting from 1 and +\&\s-1HETATM\s0 residues outside \s-1TER\s0 records starting from 6000 in Sample2.pdb and generate +Sample2RenumberResidues.pdb file, type: +.PP +.Vb 2 +\& % ModifyPDBFiles.pl \-\-ResidueNumberMode Sequential +\& \-\-ResidueNumberHetatmMode Specify \-o Sample1.pdb +.Ve +.PP +To renumber \s-1ATOM\s0 and \s-1HETATM\s0 residues sequentially across all chains starting from 100 for +\&\s-1ATOM/HETATM\s0 residues with in \s-1TER\s0 records and starting from 999 for \s-1HETATM\s0 residues +outside \s-1TER\s0 records in Sample2.pdb and generate Sample2RenumberResidues.pdb file, type: +.PP +.Vb 3 +\& % ModifyPDBFiles.pl \-\-ResidueNumberMode Sequential +\& \-\-ResidueNumberHetatmMode Specify \-\-ResidueNumberStart 100 +\& \-\-ResidueNumberStartHetatm 999 \-o Sample2.pdb +.Ve +.PP +To renumber \s-1ATOM\s0 and \s-1HETATM\s0 residues from 100 for each chain and starting from 999 for +\&\s-1HETATM\s0 residues outside \s-1TER\s0 records in Sample2.pdb and generate Sample2RenumberResidues.pdb +file, type: +.PP +.Vb 3 +\& % ModifyPDBFiles.pl \-\-ResidueNumberMode PerChain +\& \-\-ResidueNumberHetatmMode Specify \-\-ResidueNumberStart 100 +\& \-\-ResidueNumberStartHetatm 999 \-o Sample2.pdb +.Ve +.PP +To renumber \s-1ATOM\s0 serial numbers sequentially starting from 100 in Sample1.pdb file and generate +Sample1RenumberAtoms.pdb file, type: +.PP +.Vb 2 +\& % ModifyPDBFiles.pl \-m RenumberAtoms \-\-AtomNumberStart 100 +\& \-o Sample1.pdb +.Ve +.PP +To renumber water residues identified by \*(L"\s-1HOH\s0,WAT\*(R" starting from residue number 1000 +in Sample2.pdb file and generate Sample2RenumberWaters.pdb file, type: +.PP +.Vb 2 +\& % ModifyPDBFiles.pl \-m RenumberWaters \-\-WaterResidueNames "HOH,WAT" +\& \-o \-\-WaterResidueStart 950 Sample2.pdb +.Ve +.PP +To rename all chain IDs starting from A in Sample1.pdb file and generate +Sample1RenameChainIDs.pdb file, type: +.PP +.Vb 1 +\& % ModifyPDBFiles.pl \-m RenameChainIDs \-o Sample1.pdb +.Ve +.PP +To rename all chain IDs starting from B without assigning any chain IDs to \s-1ATOM/HETATOM\s0 +with no chain IDs in Sample2.pdb file and generate Sample2RenameChainIDs.pdb file, type: +.PP +.Vb 2 +\& % ModifyPDBFiles.pl l \-m RenameChainIDs \-c B \-\-ChainIDRenameEmpty No +\& \-o Sample2.pdb +.Ve +.SH "AUTHOR" +.IX Header "AUTHOR" +Manish Sud <msud@san.rr.com> +.SH "SEE ALSO" +.IX Header "SEE ALSO" +ExtractFromPDBFiles.pl, InfoPDBFiles.pl +.SH "COPYRIGHT" +.IX Header "COPYRIGHT" +Copyright (C) 2015 Manish Sud. All rights reserved. +.PP +This file is part of MayaChemTools. +.PP +MayaChemTools is free software; you can redistribute it and/or modify it under +the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free +Software Foundation; either version 3 of the License, or (at your option) +any later version.