def save_to_ligand(self, mol_input, name=None, input_type='input'):
"""
Public access to private file_handlers.py file.
Users shouldn't ever need to interface with file_handlers.py directly.
All parameters will be set from a file (or other input) via this public method.
Don't bother updating name, topology or atoms if they are already stored.
Do bother updating coords and rdkit_mol
:param mol_input:
:param name:
:param input_type: "input", "mm", "qm", "traq", or "temp"
"""
ligand = ReadInput(mol_input, name)
if ligand.name is not None and self.name is None:
self.name = ligand.name
if ligand.topology is not None and self.topology is None:
self.topology = ligand.topology
if ligand.atoms is not None and self.atoms is None:
self.atoms = ligand.atoms
if ligand.coords is not None:
self.coords[input_type] = ligand.coords
if ligand.rdkit_mol is not None:
self.rdkit_mol = ligand.rdkit_mol
def save_to_protein(self, mol_input, name=None, input_type='input'):
"""
Public access to private file_handlers.py file.
Users shouldn't ever need to interface with file_handlers.py directly.
All parameters will be set from a file (or other input) via this public method.
* Don't bother updating name, topology or atoms if they are already stored.
* Do bother updating coords, rdkit_mol, residues, Residues, pdb_names
"""
protein = ReadInput(mol_input, name, is_protein=True)
if protein.name is not None and self.name is None:
self.name = protein.name
if protein.topology is not None and self.topology is None:
self.topology = protein.topology
if protein.atoms is not None and self.atoms is None:
self.atoms = protein.atoms
if protein.coords is not None:
self.coords[input_type] = protein.coords
if protein.rdkit_mol is not None:
self.rdkit_mol = protein.rdkit_mol
if protein.residues is not None:
self.residues = protein.residues
if protein.Residues is not None:
self.Residues = protein.Residues
if protein.pdb_names is not None:
self.pdb_names = protein.pdb_names
if not self.topology.edges:
print(
'No connections found in pdb file; topology will be inferred by OpenMM.'
)
return
self.find_angles()
self.find_dihedrals()
self.find_rotatable_dihedrals()
self.find_impropers()
self.get_dihedral_values(input_type)
self.find_bond_lengths(input_type)
self.get_angle_values(input_type)
# this creates the dictionary of terms that should be symmetrise
self.symmetrise_from_topology()