def to_mdtraj_Topology(item, atom_indices='all', check=True):
if check:
digest_item(item, 'file:mol2')
atom_indices = digest_atom_indices(atom_indices)
from mdtraj import load_mol2
from ..mdtraj_Topology import extract as extract_mdtraj_Topology
tmp_item = load_mol2(item).topology
tmp_item = extract_mdtraj_Topology(tmp_item)
return tmp_item
def to_mdtraj_Trajectory(item,
atom_indices='all',
structure_indices='all',
check=True):
if check:
digest_item(item, 'file:mol2')
atom_indices = digest_atom_indices(atom_indices)
structure_indices = digest_structure_indices(structure_indices)
from mdtraj import load_mol2
from ..mdtraj_Trajectory import extract as extract_mdtraj_Trajectory
tmp_item = load_mol2(item)
tmp_item = extract_mdtraj_Trajectory(tmp_item)
return tmp_item
def test_mol2_without_bonds(get_fn):
trj = md.load_mol2(get_fn('li.mol2'))
assert trj.topology.n_bonds == 0
def test_mol2_status_bits(get_fn):
trj = md.load_mol2(get_fn('status-bits.mol2'))
eq(trj.topology.n_atoms, 18)
eq(trj.topology.n_bonds, 18)
def test_mol2_warnings(get_fn):
trj = md.load_mol2(get_fn('lysozyme-ligand-tripos.mol2'))
def test_mol2_status_bits():
trj = md.load_mol2(get_fn('status-bits.mol2'))
eq(trj.topology.n_atoms, 18)
eq(trj.topology.n_bonds, 18)
def test_mol2_warnings():
trj = md.load_mol2(get_fn('lysozyme-ligand-tripos.mol2'))
def test_mol2_without_bonds():
trj = md.load_mol2(get_fn('li.mol2'))
assert trj.topology.n_bonds == 0
def _create_pdb_and_topology(molecule, file_path):
"""Creates a uniform PDB file and `mdtraj.Topology` from an
openeye molecule.
Parameters
----------
molecule: openeye.oechem.OEChem
The component to create the PDB and topology for.
file_path: str
The path pointing to where the PDB file should be created.
Returns
-------
mdtraj.Topology
The topology of the created PDB file.
"""
import mdtraj
from mdtraj.core import residue_names
from openeye import oechem
# Create a temporary mol2 file using OE, change its
# residue name (sometimes OE assigns the molecule an
# amino acid residue name even if that molecule is not
# an amino acid, e.g. C(CO)N is not Gly), save the
# altered object as a pdb.
with tempfile.NamedTemporaryFile(suffix='.mol2') as mol2_file:
mol2_flavor = oechem.OEOFlavor_MOL2_DEFAULT
ofs = oechem.oemolostream(mol2_file.name)
ofs.SetFlavor(oechem.OEFormat_MOL2, mol2_flavor)
oechem.OEWriteConstMolecule(ofs, molecule)
ofs.close()
# Load in the OE created mol2 file.
oe_mol2 = mdtraj.load_mol2(mol2_file.name)
smiles = oechem.OEMolToSmiles(molecule)
# Choose a random residue name.
residue_map = {}
for residue in oe_mol2.topology.residues:
residue_map[residue.name] = None
if smiles == 'O':
residue_map[residue.name] = 'HOH'
elif smiles == '[Cl-]':
residue_map[residue.name] = 'Cl-'
for atom in residue.atoms:
atom.name = 'Cl-'
elif smiles == '[Na+]':
residue_map[residue.name] = 'Na+'
for atom in residue.atoms:
atom.name = 'Na+'
for original_residue_name in residue_map:
if residue_map[original_residue_name] is not None:
continue
# Make sure the residue is not already reserved, as this can occasionally
# result in bonds being automatically added in the wrong places when
# loading the pdb file either through mdtraj or openmm
forbidden_residue_names = [
*residue_names._AMINO_ACID_CODES,
*residue_names._SOLVENT_TYPES, *residue_names._WATER_RESIDUES,
'ADE', 'CYT', 'CYX', 'DAD', 'DGU', 'FOR', 'GUA', 'HID', 'HIE',
'HIH', 'HSD', 'HSH', 'HSP', 'NMA', 'THY', 'URA'
]
new_residue_name = ''.join(
[random.choice(string.ascii_uppercase) for _ in range(3)])
while new_residue_name in forbidden_residue_names:
# Re-choose the residue name until we find a safe one.
new_residue_name = ''.join(
[random.choice(string.ascii_uppercase) for _ in range(3)])
residue_map[original_residue_name] = new_residue_name
for residue in oe_mol2.topology.residues:
residue.name = residue_map[residue.name]
# Create the final pdb file.
oe_mol2.save_pdb(file_path)
return oe_mol2.topology
def mol2_to_pdb(mol2_filename):
#convert PDB file with this name, to be used for Packmol input
struct = md.load_mol2(mol2_filename)
struct.save_pdb(mol2_filename[:-4] + 'pdb')
def test_load_all_mol2(mol2_file, get_fn):
trj = md.load_mol2(get_fn(mol2_file))
def test_mol2_element_name(get_fn):
trj = md.load_mol2(get_fn('cl.mol2'))
top, bonds = trj.top.to_dataframe()
assert top.iloc[0]['element'] == 'Cl'
def test_load_all_mol2(mol2_file, get_fn):
trj = md.load_mol2(get_fn(mol2_file))
def test_mol2_element_name(get_fn):
trj = md.load_mol2(get_fn('cl.mol2'))
top, bonds = trj.top.to_dataframe()
assert top.iloc[0]['element'] == 'Cl'