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.\" ========================================================================
.\"
.IX Title "MODIFYPDBFILES 1"
.TH MODIFYPDBFILES 1 "2015-03-29" "perl v5.14.2" "MayaChemTools"
.\" For nroff, turn off justification.  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 <[e-mail]>
.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.