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geometry

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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.

!Get selection
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.
{html}<pre>geometry -s "@~H" foo.xyz</pre>{/html}

!Get selection list
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.
{html}<pre>geometry -S "@H,O" foo.xyz</pre>{/html}

!Explode residues
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.

!Randomize coordinates
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

!Root mean square deviation (RMSD) of coordinates
Option '''-d''' or '''^-^-rmsd'''

Move the second geometry file to minimize its RMSD with the first one.
Prints the RMSD value in {html} &Aring;{/html}, distances between atoms and the fitted geometry

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