def from_mol2(f):
path = str(datapath / f)
u = Universe(path)
elements = [guess_atom_element(n) for n in u.atoms.names]
u.add_TopologyAttr("elements", np.array(elements, dtype=object))
u.atoms.types = np.array([x.upper() for x in u.atoms.types], dtype=object)
return Molecule.from_mda(u, force=True)
def assign_name(u: Universe, names: np.ndarray):
"""
Assign resnames to residues in a MDAnalysis.universe object. The function will not overwrite existing names.
Args:
u: The universe object to assign resnames to.
names: The element name array.
"""
u.add_TopologyAttr("name", values=names)
def assign_resname(u: Universe, res_dict: Dict[str, str]):
"""
Assign resnames to residues in a MDAnalysis.universe object. The function will not overwrite existing resnames.
Args:
u: The universe object to assign resnames to.
res_dict: A dictionary of resnames, where each resname is a key
and the corresponding values are the selection language.
"""
u.add_TopologyAttr("resname")
for key, val in res_dict.items():
res_group = u.select_atoms(val)
res_names = res_group.residues.resnames
res_names[res_names == ""] = key
res_group.residues.resnames = res_names
def write_betafactor(u:mda.Universe,data:np.ndarray,pdb_name:str, selection=None, skip=1):
"""
write cosine theta data for all atoms into a multi frame pdb file
"""
u.add_TopologyAttr("tempfactors")
with mda.Writer(pdb_name, multiframe=True, bonds=None, n_atoms=len(u.atoms)) as PDB:
for i in range(0,len(data),skip):
index = int(data[i,0])
print("printing frame {}".format(index))
u.trajectory[index]
atoms = u.atoms
if selection:
atoms = u.select_atoms("resname {}".format(selection))
atoms.tempfactors = data[i,1:]
PDB.write(atoms)
