This script provides multiple functions working on a geometry file. They are selected by a commandline option. If the output of the action is a geometry, it is printed to standard output by default, in the same format as the input geometry. This can be modified by the option -o (--output) that redirects the output to a file. If file format can be determined from name of the output file, it is used, otherwise the format of the input file is used.
Option -s or --selection
Prints part of the geometry selected by selection expression (see Atom selection expressions) to standard output. The geometry is printed in the same format as was the input geometry (xyz or pdb).
Example: Following command will select all atoms but hydrogens from file foo.xyz.
geometry -s "@~H" foo.xyz
Option -S or --selection-list
Prints list of atom indexes (starting at 1) selected by selection expression (see Atom selection expressions).
Example: Following command will print list of all hydrogens and oxygens in file foo.xyz.
geometry -S "@H,O" foo.xyz
Option -e or --explode [factor]
Moves each residue away from system center of mass by given factor (new distance = old distance * factor). This function was added just to produce animation of molecule broken into pieces.
Option -r or --randomize [amplitude]
Add random numbers with selected max. amplitude to coordinates.
Apart from just making noise, there are two useful applications:
- Breaking symmetry
- Improving the convergence of an optimization when starting from structure that is close to a minimum
Option -d or --rmsd
Move the second geometry file to minimize its RMSD with the first one.
Prints the RMSD value in Å, distances between atoms and the fitted geometry