/ . / Trajectory / DCD / MDToolsMarch97 / md_AtomGroup.py / Molecule 

Complete interface for pdb/psf molecule files.

Data: pdbfile, psffile, pdbremarks, psfremarks _bonds, _angles, _dihedrals, _impropers, _donors, _acceptors optionally: bonds, angles, dihedrals, impropers, donors, acceptors

Methods: m = Molecule([pdb],[psf]) - read molecule from file(s) m.buildrefs() - assigns molecule for segments (done on creation) m.delrefs() - removes references to allow deletion (must be done by user) m.buildstructure() - adds structure lists to molecule and atoms m.writepdb([file]) - write pdb to file (pdbfile by default) m.view() - launch a pdb viewer with the current coordinates

See also: Segment, pdbdisplayfunction

delrefs ( self )

buildstructure ( self )

writepdb ( self,  pdbfile=None )

__repr__ ( self )

buildrefs ( self )

__init__ (
        self,
        pdb=None,
        psf=None,
        )

view ( self )