def test_dihedral_5mat(self):
from moleculekit.molecule import Molecule
from moleculekit.home import home
from moleculekit.tools.autosegment import autoSegment
from os import path
mol = Molecule('5MAT')
mol.filter('not insertion A and not altloc A B', _logger=False)
mol = autoSegment(mol, _logger=False)
data = MetricDihedral().project(mol)
dataref = np.load(
path.join(home(dataDir='test-projections'), 'metricdihedral',
'5mat.npy'))
assert np.allclose(
data, dataref, atol=1e-03
), 'Diherdals calculation gave different results from reference'
ref_idx = np.load(
path.join(home(dataDir='test-projections'), 'metricdihedral',
'5mat_mapping_indexes.npy'))
mapping = MetricDihedral().getMapping(mol)
mapping_idx = np.vstack(mapping.atomIndexes.to_numpy())
assert np.array_equal(mapping_idx,
ref_idx), 'Mapping of atom indexes has changed'
def test_dihedral_5mat(self):
from moleculekit.molecule import Molecule
from moleculekit.home import home
from moleculekit.tools.autosegment import autoSegment
from os import path
mol = Molecule('5MAT')
mol.filter('not insertion A and not altloc A B', _logger=False)
mol = autoSegment(mol, _logger=False)
data = MetricDihedral().project(mol)
dataref = np.load(path.join(home(dataDir='test-projections'), 'metricdihedral', '5mat.npy'))
assert np.allclose(data, dataref, atol=1e-03), 'Diherdals calculation gave different results from reference'
def setUpClass(self):
from moleculekit.home import home
from moleculekit.molecule import Molecule
from moleculekit.tools.preparation import proteinPrepare
from moleculekit.tools.autosegment import autoSegment
self.testf = os.path.join(home(), 'test-data', 'test-voxeldescriptors')
mol = Molecule(os.path.join(self.testf, '3PTB.pdb'))
mol.filter('protein')
mol = autoSegment(mol, field='both')
mol = proteinPrepare(mol)
mol.bonds = mol._guessBonds()
self.mol = mol
def setUpClass(self):
from moleculekit.home import home
from moleculekit.molecule import Molecule
from moleculekit.tools.preparation import systemPrepare
from moleculekit.tools.autosegment import autoSegment
self.testf = os.path.join(home(), "test-data", "test-voxeldescriptors")
mol = Molecule(os.path.join(self.testf, "3PTB.pdb"))
mol.filter("protein")
mol = autoSegment(mol, field="both")
mol = systemPrepare(mol, pH=7.0)
mol.bonds = mol._guessBonds()
self.mol = mol
def prepare_protein(chimera: Chimera) -> Molecule:
"""
Builds a water box around the chimera
:param chimera:
:return:
"""
non_standards = Builder.find_nonstandards(chimera)
if non_standards:
raise NotCorrectPDBError(f"PDB presents the non_standards residues {non_standards}."
f" Call remove_residue() or Builder.mutate_nonstandards()"
f" if you wish to minimize.")
mol = proteinPrepare(chimera)
if 'AR0' in mol.resname:
mol.set("resname", "ARG", "resname AR0")
mol = autoSegment(mol)
mol.center()
# D = maxDistance(mol,'all') + 6.0
# smol=solvate(mol,minmax=[[-D, -D, -D], [D, D, D]])
return mol
return rho, phi
angle, _ = cart2pol(xa, ya)
return angle + np.radians(45)
if __name__ == "__main__":
from moleculekit.molecule import Molecule
from moleculekit.tools.autosegment import autoSegment
from htmd.home import home
from os import path
p = Molecule(
path.join(home(), 'data', 'building-protein-membrane', '4dkl.pdb'))
p.filter('(chain B and protein) or water')
p = autoSegment(p, 'protein', 'P')
m = Molecule(
path.join(home(), 'data', 'building-protein-membrane', 'membrane.pdb'))
a = embed(p, m)
print(np.unique(m.get('segid')))
mol = Molecule(
path.join(home(), 'data', 'building-protein-membrane',
'1ITG_clean.pdb'))
ref = Molecule(
path.join(home(), 'data', 'building-protein-membrane', '1ITG.pdb'))
mol = autoSegment(mol, sel='protein')
assert np.all(mol.segid == ref.segid)
mol = Molecule(
path.join(home(), 'data', 'building-protein-membrane',
phi = np.arctan2(y, x)
return rho, phi
angle, _ = cart2pol(xa, ya)
return angle + np.radians(45)
if __name__ == "__main__":
from moleculekit.molecule import Molecule
from moleculekit.tools.autosegment import autoSegment
from htmd.home import home
from os import path
p = Molecule(path.join(home(), "data", "building-protein-membrane", "4dkl.pdb"))
p.filter("(chain B and protein) or water")
p = autoSegment(p, "protein", "P")
m = Molecule(path.join(home(), "data", "building-protein-membrane", "membrane.pdb"))
a = embed(p, m)
print(np.unique(m.get("segid")))
mol = Molecule(
path.join(home(), "data", "building-protein-membrane", "1ITG_clean.pdb")
)
ref = Molecule(path.join(home(), "data", "building-protein-membrane", "1ITG.pdb"))
mol = autoSegment(mol, sel="protein")
assert np.all(mol.segid == ref.segid)
mol = Molecule(
path.join(home(), "data", "building-protein-membrane", "3PTB_clean.pdb")
)
ref = Molecule(path.join(home(), "data", "building-protein-membrane", "3PTB.pdb"))
