diff docs/scripts/txt/ModifyPDBFiles.txt @ 0:4816e4a8ae95 draft default tip

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+++ b/docs/scripts/txt/ModifyPDBFiles.txt	Wed Jan 20 09:23:18 2016 -0500
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+NAME
+    ModifyPDBFiles.pl - Modify data in PDBFile(s)
+
+SYNOPSIS
+    ModifyPDBFiles.pl PDBFile(s)...
+
+    ModifyPDBFiles.pl [-a, --AtomNumberStart number] [-c, --ChainIDStart
+    character] [--ChainIDRenameEmpty yes | no] [-h, --help] [-k,
+    --KeepOldRecords yes | no] [-m, --mode RenumberAtoms | RenumberResidues
+    | RenumberWaters | RenameChainIDs] [--ModifyHeader yes | no] [-o,
+    --overwrite] [--ResidueNumberMode Sequential | PerChain]
+    [--ResidueNumberStart number] [--ResidueNumberHetatmMode automatic |
+    specify] [--ResidueNumberStarHetatm number] [-r, --root rootname]
+    [--WaterResidueNames Automatic | "ResidueName, [ResidueName,...]"]
+    [--WaterResidueStart number] [-w, --WorkingDir dirname] PDBFile(s)...
+
+DESCRIPTION
+    Modify data in *PDBFile(s)*: renumber atoms, residues, and water
+    residues or assign new chain IDs. Multiple PDBFile names are separated
+    by spaces. The valid file extension is *.pdb*. All other file name
+    extensions are ignored during the wild card expansion. All the PDB files
+    in a current directory can be specified either by **.pdb* or the current
+    directory name.
+
+OPTIONS
+    -a, --AtomNumberStart *number*
+        Starting atom number to use during *RenumberAtoms* value of -m,
+        --mode option. Default: *1*. Valid values: positive integers.
+
+    -c, --ChainIDStart *character*
+        A single character to use for starting IDs for chains during
+        *RenameChainIDs* value of -m, --mode option. Default: *A*. Valid
+        values: *A to Z*.
+
+    --ChainIDRenameEmpty *Yes | No*
+        Specify whether to rename empty chain IDs during *RenameChainIDs*
+        -m, --mode value. By default, ATOM and HETATM records with no chain
+        IDs are left unchanged. Possible values: *yes | no*. Default: *No*.
+
+    -h, --help
+        Print this help message.
+
+    -k, --KeepOldRecords *yes | no*
+        Specify whether to transfer old non ATOM and HETATM records from
+        input PDBFile(s) to new PDBFile(s). By default, except for the
+        HEADER record, all records other than ATOM/HETATM are dropped during
+        the generation of new PDB files. Possible values: *yes | no*.
+        Default: *no*.
+
+    -m, --mode *RenumberAtoms | RenumberResidues | RenumberWaters |
+    RenameChainIDs*
+        Specify how to modify *PDBFile(s)*. Possible values: *RenumberAtoms
+        | RenumberResidues | RenumberWaters | RenameChainIDs*. Default:
+        *RenumberResidues*.
+
+        For *RenumberAtoms* mode, residue number in ATOM and HETATM records
+        are reassigned sequentially starting using value of -a,
+        --AtomNumberStart option.
+
+        For *RenumberResidues* mode, serial number in ATOM and HETATM
+        records are reassigned either sequentially or statring from
+        specified values for ATOM and HETATM records in each chain.
+
+        For *RenumberWaters* mode, residue number for waters are reassigned
+        starting from a specific value.
+
+        For *RenameChainIDs* mode, all the chain IDs are reassigned starting
+        from a specific chain ID.
+
+        During the generation of new PDB files, unnecessary CONECT records
+        are dropped.
+
+    --ModifyHeader *yes | no*
+        Specify whether to modify HEADER record during the generation of new
+        PDB files Possible values: *yes | no*. Default: *yes*. By defailt,
+        Classification data is replaced by *Data modified using
+        MayaChemTools* before writing out HEADER record.
+
+    -o, --overwrite
+        Overwrite existing files
+
+    --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: *Sequential | PerChain*. Default: *PerChain*.
+
+    --ResidueNumberStart *number*
+        Starting residue number to use for ATOM records in chains. Default:
+        *1*. Valid values positive integers.
+
+        For *Sequential* value of --ResidueNumberMode option, residue
+        numbers are assigned sequentially across all the chains starting
+        from the specified value.
+
+        For *PerChain* value of --ResidueNumberMode option, residue numbers
+        are starting again from the specified value for each chain.
+
+        HETATM residues with in the chains are numbered using this value as
+        well
+
+    --ResidueNumberHetatmMode *automatic | specify*
+        Specify how to start residue number for HETATM records: use the next
+        sequential residue number after the last residue number from ATOM
+        records or start from a specific residue number. Possible values:
+        *automatic | specify*. Default: *automatic*
+
+        For *automatic* , residue number after highest residue number of
+        ATOM records is used as the starting residue number for HETATM
+        records.
+
+        For *specify*, value of option --ResidueNumberStarHetatm is used as
+        the starting residue number for HETATM records.
+
+        This option along with --ResidueNumberStartHetatm only applies to
+        HETATM records outside the chains.
+
+    --ResidueNumberStartHetatm *number*
+        Starting residue number to use for HETATM records. Default: *6000*.
+        Valid values positive integers.
+
+    -r, --root *rootname*
+        New PDB 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.
+
+    --WaterResidueNames *Automatic | "ResidueName,[ResidueName,...]"*
+        Identification of water residues during *RenumberWaters* value of
+        -m, --mode option. Possible values: *Automatic |
+        "ResidueName,[ResidueName,...]"*. Default: *Automatic* which
+        corresponds to "HOH,WAT,H20". You can also specify a different comma
+        delimited list of residue names to use for water.
+
+    --WaterResidueStart *number*
+        Starting water residue number to use during *RenumberWaters* -m,
+        --mode value. Default: *8000*. Valid values: positive integers.
+
+    -w, --WorkingDir *dirname*
+        Location of working directory. Default: current directory.
+
+EXAMPLES
+    To renumber ATOM and HETATM residues starting from 1 for each chain with
+    continuation to HETATM residues outside TER records in Sample2.pdb and
+    generate Sample2RenumberResidues.pdb file, type:
+
+        % ModifyPDBFiles.pl Sample1.pdb
+
+    To renumber ATOM and HETATM residues sequentially across all chains
+    starting from 1 with continuation to HETATM residues outside TER records
+    in Sample2.pdb and generate Sample2RenumberResidues.pdb file, type:
+
+        % ModifyPDBFiles.pl --ResidueNumberMode Sequential -o Sample1.pdb
+
+    To renumber ATOM and HETATM residues sequentially across all chains
+    starting from 1 and HETATM residues outside TER records starting from
+    6000 in Sample2.pdb and generate Sample2RenumberResidues.pdb file, type:
+
+        % ModifyPDBFiles.pl --ResidueNumberMode Sequential
+          --ResidueNumberHetatmMode Specify  -o Sample1.pdb
+
+    To renumber ATOM and HETATM residues sequentially across all chains
+    starting from 100 for ATOM/HETATM residues with in TER records and
+    starting from 999 for HETATM residues outside TER records in Sample2.pdb
+    and generate Sample2RenumberResidues.pdb file, type:
+
+        % ModifyPDBFiles.pl --ResidueNumberMode Sequential
+          --ResidueNumberHetatmMode Specify --ResidueNumberStart 100
+          --ResidueNumberStartHetatm 999 -o Sample2.pdb
+
+    To renumber ATOM and HETATM residues from 100 for each chain and
+    starting from 999 for HETATM residues outside TER records in Sample2.pdb
+    and generate Sample2RenumberResidues.pdb file, type:
+
+        % ModifyPDBFiles.pl --ResidueNumberMode PerChain
+          --ResidueNumberHetatmMode Specify --ResidueNumberStart 100
+          --ResidueNumberStartHetatm 999 -o Sample2.pdb
+
+    To renumber ATOM serial numbers sequentially starting from 100 in
+    Sample1.pdb file and generate Sample1RenumberAtoms.pdb file, type:
+
+        % ModifyPDBFiles.pl -m RenumberAtoms --AtomNumberStart 100
+          -o Sample1.pdb
+
+    To renumber water residues identified by "HOH,WAT" starting from residue
+    number 1000 in Sample2.pdb file and generate Sample2RenumberWaters.pdb
+    file, type:
+
+        % ModifyPDBFiles.pl -m RenumberWaters --WaterResidueNames "HOH,WAT"
+          -o --WaterResidueStart 950 Sample2.pdb
+
+    To rename all chain IDs starting from A in Sample1.pdb file and generate
+    Sample1RenameChainIDs.pdb file, type:
+
+        % ModifyPDBFiles.pl -m RenameChainIDs -o Sample1.pdb
+
+    To rename all chain IDs starting from B without assigning any chain IDs
+    to ATOM/HETATOM with no chain IDs in Sample2.pdb file and generate
+    Sample2RenameChainIDs.pdb file, type:
+
+        % ModifyPDBFiles.pl l -m RenameChainIDs -c B --ChainIDRenameEmpty No
+          -o Sample2.pdb
+
+AUTHOR
+    Manish Sud <[e-mail]>
+
+SEE ALSO
+    ExtractFromPDBFiles.pl, InfoPDBFiles.pl
+
+COPYRIGHT
+    Copyright (C) 2015 Manish Sud. All rights reserved.
+
+    This file is part of MayaChemTools.
+
+    MayaChemTools is free software; you can redistribute it and/or modify it
+    under the terms of the GNU Lesser General Public License as published by
+    the Free Software Foundation; either version 3 of the License, or (at
+    your option) any later version.
+