bmolsym.cpp File Reference

A tool to perform symmetry operations on coordinate files. More...

#include "rwmolecule.h"
#include "mol_symmetry.h"
#include "mol_transform.h"
#include "mol_edit.h"
#include "mol_util.h"
#include "utilities.h"
#include "options.h"
#include "timer.h"

Functions
int	main (int argc, char **argv)

Variables
int	verbose
const char *	use []

Detailed Description

A tool to perform symmetry operations on coordinate files.

Author

Bernard Heymann

Date

Created: 19980214

Modified: 20150813

Function Documentation

main()

int main	(	int	argc,
		char **	argv
	)

Variable Documentation

use

const char* use[]

Initial value:

= {
" ",
"Usage: bmolsym [options] in.pdb out.pdb",
"---------------------------------------",
"Performs symmetry operations on molecules.",
" ",
"Actions:",
"-translate 0,-50,22      Translate (angstrom).",
"-rotate 0.5,0,5.8,45     Rotate around a vector (x,y,z) by an angle.",
"-select CA               Atom selection (default all).",
"-apply C5                Apply point group symmetry.",
"-find C5                 Find standard orientation for this point group symmetry.",
"-Bfactor D5              Calculate B factors for this point group symmetry.",
"-pdbsymmetry             Read SMTRY matrices from a PDB file and apply them.",
"-pdbbiomt                Read BIOMT matrices from a PDB file and apply them.",
"-rename D                Rename molecules from the given letter.",
"-show                    Show operational symmetry matrices.",
" ",
"Parameters:",
"-verbose 7               Verbosity of output.",
"-origin 10,-10,20        Origin for rotation (default 0,0,0, can be \"center\" for COM).",
"-reference 0,1.5,-0.2,35 Reference symmetry axis and rotation angle (default 0,0,1,0).",
"-distance 3.5            Distance between overlapping atoms allowed (default 3 angstrom, use with -apply).",
" ",
"Input:",
"-parameters parm.star    Atomic properties parameter file (default atom_prop.star).",
"-similarity sim.star     Residue similarity matrix for finding orientation (default blosum62.star).",
" ",
NULL
}

verbose

int verbose

extern