FixDupAtomNames

Overview

The FixDupAtomNames utility helps prepare input files for use with programs such as reduce that expect each atom in a residue to have a distinct name. It will identify and rename atoms that have the same name as a previously seen atom. Residue numbers for small molecules may also be altered. See the SZMAP Workflow and chapter MKHetDict for more information about reduce.

Example Commands

If you have structure files with residues having duplicate atom names (not common but some workflows create files like this) and you want to run reduce or another program that expects unique atom names, FixDupAtomNames should be used before running MKHetDict or reduce.

> fixdupatomnames mol.mol2 mol-renamed.pdb
> mkhetdict mol-renamed.pdb mol_hetdict.txt
> reduce -db mol-hetdict.txt -build -rotexist mol-renamed.pdb >molH.pdb

Command Line Help

A description of the command line interface can be obtained by executing FixDupAtomNames with the --help option.

> fixdupatomnames --help

will generate the following output:

Help functions:
  fixdupatomnames --help simple      : Get a list of simple parameters
  fixdupatomnames --help all         : Get a complete list of parameters
  fixdupatomnames --help defaults    : List the defaults for all parameters
  fixdupatomnames --help <parameter> : Get detailed help on a parameter
  fixdupatomnames --help html        : Create an html help file for this program
  fixdupatomnames --help versions    : List the toolkits and versions used in the application

Required Parameters

-input_mol <filename>
-i <filename>

[keyless parameter 1]

Input molecule file.

File type Extension
SDF .sdf .mol .sdf.gz .mol.gz
MOL2 .mol2 .mol2.gz
PDB .pdb .ent .pdb.gz .ent.gz
MacroModel .mmod .mmod.gz
OEBinary .oeb .oeb.gz
-output_mol <filename>
-o <filename>

[keyless parameter 2]

Output molecule file. Duplicate atom names within a residue will be changed.

File type Extension
SDF .sdf .mol .sdf.gz .mol.gz
MOL2 .mol2 .mol2.gz
PDB .pdb .ent .pdb.gz .ent.gz
MacroModel .mmod .mmod.gz
OEBinary .oeb .oeb.gz

Note

If the file is to be used with reduce, then the extension .pdb is required.

Optional Parameters

-verbose
-v

Print additional information to standard-error.