def test_convertFromMolecule(self):
from moleculekit.molecule import mol_equal
mol = Molecule(self.benzamidine_mol2)
sm = SmallMol(mol)
assert mol_equal(sm, mol, exceptFields=['serial', 'name'], _logger=False)
mol = Molecule(self.indole_mol2)
sm = SmallMol(mol, force_reading=True)
# Force reading writes to sdf which loses atomtypes and charges
assert mol_equal(sm, mol, exceptFields=['serial', 'name', 'atomtype', 'charge'], _logger=False)
def test_channels_with_metals(self):
from moleculekit.home import home
from moleculekit.molecule import Molecule, mol_equal
from os.path import join
ref_channels = np.load(
join(home(dataDir='test-voxeldescriptors'), '1ATL_channels.npy'))
ref_mol = Molecule(
join(home(dataDir='test-voxeldescriptors'),
'1ATL_atomtyped.psf')) # Need PSF to store the atomtypes!
ref_mol.read(
join(home(dataDir='test-voxeldescriptors'), '1ATL_atomtyped.pdb'))
mol = Molecule(
join(
home(dataDir='test-voxeldescriptors'),
'1ATL_prepared.psf')) # Need PSF to store the correct charges!
mol.read(
join(home(dataDir='test-voxeldescriptors'), '1ATL_prepared.pdb'))
channels, mol_atomtyped = getChannels(mol)
assert np.array_equal(ref_channels, channels)
assert mol_equal(mol_atomtyped, ref_mol)
def test_convertToMolecule(self):
from moleculekit.molecule import mol_equal
sm = SmallMol(self.benzamidine_mol2)
mol = sm.toMolecule(formalcharges=False)
assert mol_equal(sm, mol, exceptFields=['serial', 'name'], _logger=False)
def _singleMolfile(sims):
from moleculekit.molecule import mol_equal
from htmd.util import ensurelist
if isinstance(sims, Molecule):
return False, []
elif isinstance(sims, np.ndarray):
molfiles = []
for s in sims:
molfiles.append(tuple(ensurelist(s.molfile)))
uqmolfiles = list(set(molfiles))
if len(uqmolfiles) == 0:
raise RuntimeError('No molfiles found in simlist')
elif len(uqmolfiles) == 1:
return True, uqmolfiles[0]
elif len(
uqmolfiles
) > 1: # If more than one molfile load them and see if they are different Molecules
ref = Molecule(uqmolfiles[0], _logger=False)
for i in range(1, len(uqmolfiles)):
mol = Molecule(uqmolfiles[i], _logger=False)
if not mol_equal(ref, mol, exceptFields=['coords']):
return False, []
return True, uqmolfiles[0]
return False, []
def test_crystalpacking_biological_unit(self):
from moleculekit.home import home
from os.path import join
from moleculekit.molecule import mol_equal
mol = generateCrystalPacking('1out')
refmol = Molecule(join(home(dataDir='test-crystalpacking'), '1out_packing.pdb'))
assert mol_equal(mol, refmol, fieldPrecision={'coords': 1e-3})
def test_preparation(self):
from moleculekit.home import home
from moleculekit.molecule import Molecule, mol_equal
from os import path
mol = Molecule(path.join(home(dataDir='test-voxeldescriptors'), '1ATL.pdb'))
ref = Molecule(path.join(home(dataDir='test-voxeldescriptors'), '1ATL_prepared.pdb'))
mol2 = prepareProteinForAtomtyping(mol, verbose=False)
assert mol_equal(mol2, ref, exceptFields=('coords',))
def test_convertFromMolecule(self):
from moleculekit.molecule import mol_equal
mol = Molecule(self.benzamidine_mol2)
sm = SmallMol(mol)
assert mol_equal(sm,
mol,
exceptFields=['serial', 'name'],
_logger=False)
def test_convertToMolecule(self):
from moleculekit.molecule import mol_equal
sm = SmallMol(self.benzamidine_mol2)
mol = sm.toMolecule()
assert mol_equal(sm,
mol,
exceptFields=["serial", "name"],
_logger=False)
def test_preparation(self):
from moleculekit.home import home
from moleculekit.molecule import Molecule, mol_equal
from os import path
mol = Molecule(path.join(home(dataDir="test-atomtyper"), "1ATL.pdb"))
mol.remove('resname "0QI"')
ref = Molecule(
path.join(home(dataDir="test-atomtyper"), "1ATL_prepared.pdb"))
mol2 = prepareProteinForAtomtyping(mol, pH=7.0, verbose=False)
assert mol_equal(mol2, ref, exceptFields=("coords", ))
def _monitoringThread():
global pymolViewingMols
global showing
from pymol import cmd
import time
def _view(mol, viewname):
topo = tempname(suffix=".cif")
xtc = tempname(suffix=".xtc")
mol.write(topo)
mol.write(xtc)
cmd.delete(viewname)
cmd.load(topo, viewname)
cmd.load_traj(xtc, viewname, state=1)
cmd.dss() # Guess SS
os.remove(topo)
os.remove(xtc)
showing[viewname] = True
curr_mols = {key: val.copy() for key, val in pymolViewingMols.items()}
for viewname in curr_mols:
_view(curr_mols[viewname], viewname)
while True:
# print("KEYS", curr_mols.keys())
new_keys = np.setdiff1d(list(pymolViewingMols.keys()),
list(curr_mols.keys()))
for viewname in new_keys:
curr_mols[viewname] = pymolViewingMols[viewname].copy()
_view(curr_mols[viewname], viewname)
# print("viewed new mol")
for viewname in curr_mols:
if not mol_equal(curr_mols[viewname],
pymolViewingMols[viewname],
_logger=False):
curr_mols[viewname] = pymolViewingMols[viewname].copy()
_view(curr_mols[viewname], viewname)
# print("updated existing mol")
time.sleep(_checkFrequency)
# Check if molecule which was showing before does not exist in viewer anymore
# If it doesn't remove it from our lists here to clean-up
pymol_objects = cmd.get_object_list("all")
todelete = []
for key in showing:
if key not in pymol_objects:
todelete.append(key)
for key in todelete:
del showing[key]
del curr_mols[key]
del pymolViewingMols[key]
