def load_coords_pymol(self,
coordslist,
oname,
index=1): # pragma: no cover
"""load the coords into pymol
the new object must be named oname so we can manipulate it later
Parameters
----------
coordslist : list of arrays
oname : str
the new pymol object must be named oname so it can be manipulated
later
index : int
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.
"""
# pymol is imported here so you can do, e.g. basinhopping without installing pymol
import pymol
# create the temporary file
suffix = ".xyz"
f = tempfile.NamedTemporaryFile(mode="w", suffix=suffix)
fname = f.name
# write the coords into the xyz file
from pele.mindist import CoMToOrigin
for coords in coordslist:
coords = CoMToOrigin(coords.copy())
write_xyz(f, coords, title=oname, atomtypes=["LA"])
f.flush()
# load the molecule from the temporary file
pymol.cmd.load(fname)
# get name of the object just create and change it to oname
objects = pymol.cmd.get_object_list()
objectname = objects[-1]
pymol.cmd.set_name(objectname, oname)
# set the representation
pymol.cmd.hide("everything", oname)
pymol.cmd.show("spheres", oname)
# set the color according to index
if index == 1:
pymol.cmd.color("red", oname)
else:
pymol.cmd.color("gray", oname)
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
----------
coordslist : list of arrays
oname : str
the new pymol object must be named oname so it can be manipulated
later
index : int
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.
"""
# pymol is imported here so you can do, e.g. basinhopping without installing pymol
import pymol
# create the temporary file
suffix = ".pdb"
f = tempfile.NamedTemporaryFile(mode="w", suffix=suffix)
fname = f.name
from simtk.openmm.app import pdbfile as openmmpdb
# write the coords into pdb file
from pele.mindist import CoMToOrigin
ct = 0
for coords in coordslist:
ct += 1
coords = CoMToOrigin(coords.copy())
self.potential.copyToLocalCoords(coords)
from simtk.unit import angstrom as openmm_angstrom
# openmmpdb.PDBFile.writeFile(self.potential.prmtop.topology , self.potential.localCoords * openmm_angstrom , file=sys.stdout, modelIndex=1)
openmmpdb.PDBFile.writeModel(self.potential.prmtop.topology,
self.potential.localCoords *
openmm_angstrom,
file=f,
modelIndex=ct)
print "closing file"
f.flush()
# load the molecule from the temporary file
pymol.cmd.load(fname)
# get name of the object just created and change it to oname
objects = pymol.cmd.get_object_list()
objectname = objects[-1]
pymol.cmd.set_name(objectname, oname)
# set the representation
pymol.cmd.hide("everything", oname)
pymol.cmd.show("lines", oname)
