Package schrodinger :: Package application :: Package desmond :: Module meta :: Class CVrmsd

Class CVrmsd

CV --+
     |
    CVrmsd

rmsd collective variable

Instance Methods

[hide private]

__init__(self, atomlist, xyz_coords_ref, width, rmsd_weights=None, superpos_weights=None)

getMExpr(self, model, cvname)

Class Variables

[hide private]

cvrmsd_template = '\n# rmsd definition\n%(cvname)s_sel = %(ato...

cvrmsd_weights_template = '\n# rmsd definition\n%(cvname)s_sel...

Method Details

[hide private]

init(self, atomlist, xyz_coords_ref, width, rmsd_weights=None, superpos_weights=None)
(Constructor)

Overrides: CV.__init__

getMExpr(self, model, cvname)

Overrides: CV.getMExpr

Class Variable Details

[hide private]

cvrmsd_template

Value:

'''
# rmsd definition
%(cvname)s_sel = %(atomlist)s;
%(cvname)s_ref = array( %(xyz_ref)s );
%(cvname)s = rmsd( %(cvname)s_ref,  %(cvname)s_sel );
print ("%(cvname)s", %(cvname)s);
# the width for %(cvname)s will be set to: %(width)s
'''

cvrmsd_weights_template

Value:

'''
# rmsd definition
%(cvname)s_sel = %(atomlist)s;
%(cvname)s_ref = array( %(xyz_ref)s );
%(cvname)s_rmsd_weights = array( %(rmsd_weights)s );
%(cvname)s_superpos_weights = array( %(superpos_weights)s );
%(cvname)s = rmsd( %(cvname)s_ref,  %(cvname)s_sel, %(cvname)s_rmsd_we
ights, %(cvname)s_superpos_weights );
...

Class CVrmsd

__init__(self, atomlist, xyz_coords_ref, width, rmsd_weights=None, superpos_weights=None) (Constructor)

getMExpr(self, model, cvname)

cvrmsd_template

cvrmsd_weights_template

init(self, atomlist, xyz_coords_ref, width, rmsd_weights=None, superpos_weights=None)
(Constructor)