def calcDatasetVoxel(self, protPath, ligPath, number, altProtPath,
altLigPath):
dataset = list()
print(ligPath)
try:
sm = SmallMol(ligPath, force_reading=True, fixHs=False)
x = np.mean(sm.get('coords')[:, 0])
y = np.mean(sm.get('coords')[:, 1])
z = np.mean(sm.get('coords')[:, 2])
fs, cs, ns = voxeldescriptors.getVoxelDescriptors(
sm, center=[x, y, z], boxsize=self.boxsize)
except:
# if the normal file is broke, you can use an alternative format
sm = SmallMol(altLigPath, force_reading=True, fixHs=False)
x = np.mean(sm.get('coords')[:, 0])
y = np.mean(sm.get('coords')[:, 1])
z = np.mean(sm.get('coords')[:, 2])
fs, cs, ns = voxeldescriptors.getVoxelDescriptors(
sm, center=[x, y, z], boxsize=self.boxsize)
f, c, n = self.calcProtVoxel(x, y, z, protPath, number, altProtPath)
feature_protein = f
feature_protein_shaped = f.reshape(n[0], n[1], n[2], f.shape[1])
feature_ligand = fs
feature_ligand_shaped = fs.reshape(ns[0], ns[1], ns[2], fs.shape[1])
datapoint = np.concatenate(
(feature_protein_shaped, feature_ligand_shaped),
axis=3).transpose([3, 0, 1, 2])
dataset.append(datapoint)
return np.array(dataset), np.array(c), np.array(
feature_protein), np.array(feature_ligand), np.array(
feature_protein_shaped), np.array(feature_ligand_shaped)
def test_getAtoms(self):
smi = SMILE_SMI
sm = SmallMol(smi)
element_idx_1 = sm.get("element", "idx 1")[0]
neighbors_element_O = sm.get("neighbors", "element O")[0]
btypes_element_O = sm.get("bondtype", "element O",
convertType=False)[0]
self.assertEqual(
element_idx_1,
PHENOL_ELEMENT_IDX_1,
"Element of the first atom does not correspond"
"Expect: {}; Now: {}".format(element_idx_1, PHENOL_ELEMENT_IDX_1),
)
self.assertListEqual(
neighbors_element_O,
PHENOL_ELEMENT_NEIGHBORS_OX,
"Neighbors atoms of the oxygen atom do not correspond"
"Expected: {}; Now: {}".format(PHENOL_ELEMENT_NEIGHBORS_OX,
neighbors_element_O),
)
self.assertListEqual(
btypes_element_O,
PHENOL_BTYPES_OX,
"Bondtypes of the oxygen atom do not correspond:"
"Expeected: {}; Now: {}".format(btypes_element_O,
PHENOL_BTYPES_OX),
)
def test_copy(self):
sm = SmallMol(self.benzamidine_mol2)
sm_copy = sm.copy()
coords = sm.get("coords")
coords_copy = sm_copy.get("coords")
assert np.array_equal(coords, coords_copy)
# Ensure no hydrogens are added in the copy method
sm = SmallMol(self.benzamidine_mol2, removeHs=True, fixHs=False)
sm_copy = sm.copy()
coords = sm.get("coords")
coords_copy = sm_copy.get("coords")
assert np.array_equal(coords, coords_copy)
def test_getAtoms(self):
smi = SMILE_SMI
sm = SmallMol(smi)
element_idx_1 = sm.get('element', 'idx 1')[0]
neighbors_element_O = sm.get('neighbors', 'element O')[0]
btypes_element_O = sm.get('bondtype', 'element O', convertType=False)[0]
self.assertEqual(element_idx_1, PHENOL_ELEMENT_IDX_1, 'Element of the first atom does not correspond'
'Expect: {}; Now: {}'.format(element_idx_1, PHENOL_ELEMENT_IDX_1))
self.assertListEqual(neighbors_element_O, PHENOL_ELEMENT_NEIGHBORS_OX, 'Neighbors atoms of the oxygen atom do not correspond'
'Expected: {}; Now: {}'.format(PHENOL_ELEMENT_NEIGHBORS_OX, neighbors_element_O))
self.assertListEqual(btypes_element_O, PHENOL_BTYPES_OX, 'Bondtypes of the oxygen atom do not correspond:'
'Expeected: {}; Now: {}'.format(btypes_element_O, PHENOL_BTYPES_OX))
def calcFeatures(number, ligPath, altLigPath, protPath, altProtPath,
boxsize, targetpath):
features = {}
try:
sm = SmallMol(ligPath, force_reading=True, fixHs=False)
x = np.mean(sm.get('coords')[:, 0])
y = np.mean(sm.get('coords')[:, 1])
z = np.mean(sm.get('coords')[:, 2])
smallChannels, sm = voxeldescriptors.getChannels(sm)
except:
sm = SmallMol(altLigPath, force_reading=True, fixHs=False)
x = np.mean(sm.get('coords')[:, 0])
y = np.mean(sm.get('coords')[:, 1])
z = np.mean(sm.get('coords')[:, 2])
smallChannels, sm = voxeldescriptors.getChannels(sm)
features['smallChannels'] = smallChannels
features['sm'] = sm
try:
prot = Molecule(protPath)
if prot.numAtoms > 50000:
factorx = boxsize[0] * 2.5
factory = boxsize[1] * 2.5
factorz = boxsize[2] * 2.5
prot.filter('z < ' + format(z + factorz) + ' and z > ' +
format(z - factorz))
prot.filter('x < ' + format(x + factorx) + ' and x > ' +
format(x - factorx))
prot.filter('y < ' + format(y + factory) + ' and y > ' +
format(y - factory))
prot.filter('protein')
prot.bonds = prot._getBonds()
prot = prepareProteinForAtomtyping(prot)
prot.set(value='Se', field='element', sel='name SE')
protChannels, prot = voxeldescriptors.getChannels(prot)
except:
try:
prot = Molecule(altProtPath)
if prot.numAtoms > 50000:
factorx = boxsize[0] * 2.5
factory = boxsize[1] * 2.5
factorz = boxsize[2] * 2.5
prot.filter('z < ' + format(z + factorz) + ' and z > ' +
format(z - factorz))
prot.filter('x < ' + format(x + factorx) + ' and x > ' +
format(x - factorx))
prot.filter('y < ' + format(y + factory) + ' and y > ' +
format(y - factory))
prot.filter('protein')
prot.bonds = prot._getBonds()
prot = prepareProteinForAtomtyping(prot)
prot.set(value='Se', field='element', sel='name SE')
protChannels, prot = voxeldescriptors.getChannels(prot)
except:
try:
prot = Molecule(protPath)
if prot.numAtoms > 50000:
factorx = boxsize[0] * 2.5
factory = boxsize[1] * 2.5
factorz = boxsize[2] * 2.5
prot.filter('z < ' + format(z + factorz) +
' and z > ' + format(z - factorz))
prot.filter('x < ' + format(x + factorx) +
' and x > ' + format(x - factorx))
prot.filter('y < ' + format(y + factory) +
' and y > ' + format(y - factory))
prot.filter('protein')
prot.filter('not resname 3EB')
prot = proteinPrepare(prot)
prot = autoSegment(prot)
# Residues are not supported
try:
prot.mutateResidue('resname TPO', 'THR')
except:
pass
try:
prot.mutateResidue('resname MSE', 'MET')
except:
pass
try:
prot.mutateResidue('resname SEP', 'SER')
except:
pass
prot = charmm.build(prot, ionize=False)
protChannels, prot = voxeldescriptors.getChannels(prot)
except:
f = open("../../Data/prep_log.txt", "a")
f.writelines('Protein ' + protPath +
' leads to errors! Proteinnumber: ' +
str(number) + '\n')
f.close()
protChannels = None
features['protChannels'] = protChannels
features['prot'] = prot
return features
