Python operations available from the molecule module, used to
load molecules and change their representations.
num():
Returns the number of loaded molecules.
listall():
Returns the molid's of the all the loaded molecules.
structure_type(molid):
Returns the struture file type for the given molecule.
structure_file(molid):
Returns the struture file for the given molecule.
coor_type(molid):
Returns the coordinate file type for the given molecule.
coor_file(molid):
Returns the coordinate file for the given molecule.
load(structure, sfname, coor, cfname):
Load a molecule with structure type structure and filename
sfname. Additionally, a separate coordinate file may be
provided, of type coor and name cfname.
load('pdb','alanin.'pdb')
load('psf','alanin.psf','dcd','alanin.dcd')
cancel(molid):
Cancel loading of coordinates file for the given molecule.
delete(molid):
Delete the specified molecule.
read(molid, type, filename, beg = -1, end = -1, skip = -1):
write(molid, type, filename, beg = -1, end = -1, skip = -1):
Read/write a coordinate file to/from the specified molecule. Optional
arguments beg, end, and skip may be specified with keywords;
the default is to load/save all coordinate frames.
delframe(molid, beg=-1, end=-1, skip=-1):
Delete frames from the specified molecule. Optional
arguments beg, end, and skip may be specified with keywords;
the default is to delete all coordinate frames.
dupframe(molid, frame):
Copy the coordinates from the given frame and append them as a new
frame.
numframes(molid):
Return the number of coordinate frames in the specified molecule.
get_frame(molid):
Return the current coordinate frame for the specified molecule.
set_frame(molid, frame):
Set the current coordinate frames in the specified molecule.
numatoms(molid):
Returns the number of atoms in the specified molecule.
ssrecalc(molid):
Recalculate the secondary structure for the given molecule, using
the current set of coordinates.
get_top(molid):
set_top(molid):
Get/set the molid of the top molecule.