pele.systems.morse_cluster#
- class pele.systems.morse_cluster.MorseCluster[source]
-
class MorseCluster(AtomicCluster):define the System class for a Morse cluster cluster
- Parameters:
- natomsint
See also
- MorseCluster.draw()[source]
-
def draw(self, coordslinear, index, subtract_com=True):tell the gui how to represent your system using openGL objects
- Parameters:
- coordsarray
- indexint
we can have more than one molecule on the screen at one time. index tells which one to draw. They are viewed at the same time, so they should be visually distinct, e.g. different colors. accepted values are 1 or 2
- MorseCluster.load_coords_pymol()[source]
-
def load_coords_pymol(self, coordslist, oname, index=1):load the coords into pymol
the new object must be named oname so we can manipulate it later
- Parameters:
- coordslistlist of arrays
- onamestr
the new pymol object must be named oname so it can be manipulated later
- indexint
we can have more than one molecule on the screen at one time. index tells which one to draw. They are viewed at the same time, so should be visually distinct, e.g. different colors. accepted values are 1 or 2
Notes
the implementation here is a bit hacky. we create a temporary xyz file from coords and load the molecule in pymol from this file.