def pose_from_params(filename, params_list):
pose = Pose()
rts = pose.conformation().modifiable_residue_type_set_for_conf(
core.chemical.FULL_ATOM_t)
rts.read_files_for_base_residue_types(Vector1(params_list))
pose.conformation().reset_residue_type_set_for_conf(rts)
pose_from_file(pose, pose.residue_type_set_for_pose(), filename)
return pose
def pose_from_pubchem(cid, name, temporary=True):
pose = Pose()
if temporary:
# the temporary solution, create an ephemeral ResidueSet
params_from_pubchem(cid, name)
# Add the new ResidueType to the pose
rts = pose.conformation().modifiable_residue_type_set_for_conf(
core.chemical.FULL_ATOM_t)
rts.add_base_residue_type(name)
pose.conformation().reset_residue_type_set_for_conf(rts)
# fill the pose
pose_from_file(pose, pose.residue_type_set_for_pose(),
name + "_0001.pdb")
else:
# permanent solution, add to .params list
add_cid_to_database(cid, name)
# fill the pose
pose_from_file(pose, name + "_0001.pdb")
return pose
