def _vdw_radii(elements):
radii = np.zeros(elements.shape[0], dtype=np.float32)
i = 0
for e in elements:
radii[i] = radiusByElement(e)
i += 1
return radii
def _vdw_radii(elements):
radii = np.zeros(elements.shape[0], dtype=np.float32)
i = 0
for e in elements:
radii[i] = radiusByElement(e)
i += 1
return radii
def _getRadii(mol):
""" Gets vdW radius for each elem in mol.element. Source VMD.
Parameters
----------
mol :
A Molecule object. Needs to be read from Autodock 4 .pdbqt format
Returns
-------
radii : np.ndarray
vdW radius for each element in mol.
"""
mappings = { # Mapping pdbqt representation to element.
'HD': 'H',
'HS': 'H',
'A': 'C',
'NA': 'N',
'NS': 'N',
'OA': 'O',
'OS': 'O',
'MG': 'Mg',
'SA': 'S',
'CL': 'Cl',
'CA': 'Ca',
'MN': 'Mn',
'FE': 'Fe',
'ZN': 'Zn',
'BR': 'Br',
'CS': 'Cs' # Extra added
}
atoms = [
'H', 'C', 'N', 'O', 'F', 'Mg', 'P', 'S', 'Cl', 'Ca', 'Fe', 'Zn', 'Br',
'I'
]
atoms.extend(
['Co', 'Hg', 'Ni', 'Sr', 'Mn', 'K', 'Se', 'Cu', 'Cd', 'Li',
'Na']) # Extra added
for el in atoms:
mappings[el] = el
res = np.zeros(mol.numAtoms)
for a in range(mol.numAtoms):
elem = mol.element[a]
if elem not in mappings:
raise ValueError(
'PDBQT element {} does not exist in mappings.'.format(elem))
elem = mappings[elem]
if elem in vdw.radiidict:
rad = vdw.radiusByElement(elem)
else:
print('Unknown element -', mol.element[a], '- at atom index ', a)
rad = 1.5
res[a] = rad
return res
def _filterPoints(self, points):
# Compute distance threshold for each atom
thresholds = np.array(
[radiusByElement(element) for element in self._molecule.element])
thresholds *= min(self._shell_factors) - 0.001
# Detect the points further away for each atom than its threshold
distances = cdist(points, self._molecule.coords[:, :, 0])
is_valid = np.all(distances > thresholds, axis=1)
return points[is_valid]
def _getRadii(mol):
""" Gets vdW radius for each elem in mol.element. Source VMD.
Parameters
----------
mol :
A Molecule object. Needs to be read from Autodock 4 .pdbqt format
Returns
-------
radii : np.ndarray
vdW radius for each element in mol.
"""
mappings = { # Mapping pdbqt representation to element.
'HD': 'H',
'HS': 'H',
'A': 'C',
'NA': 'N',
'NS': 'N',
'OA': 'O',
'OS': 'O',
'MG': 'Mg',
'SA': 'S',
'CL': 'Cl',
'CA': 'Ca',
'MN': 'Mn',
'FE': 'Fe',
'ZN': 'Zn',
'BR': 'Br'
}
for el in ['H', 'C', 'N', 'O', 'F', 'Mg', 'P', 'S', 'Cl', 'Ca', 'Fe', 'Zn', 'Br', 'I']:
mappings[el] = el
res = np.zeros(mol.numAtoms)
for a in range(mol.numAtoms):
elem = mol.element[a]
if elem not in mappings:
raise ValueError('PDBQT element {} does not exist in mappings.'.format(elem))
elem = mappings[elem]
if elem in vdw.elements:
rad = vdw.radiusByElement(elem)
else:
print('Unknown element -', mol.element[a], '- at atom index ', a)
rad = 1.5
res[a] = rad
return res
def _generatePoints(self):
all_points = []
for element, coord in zip(self._molecule.element,
self._molecule.coords[:, :, 0]):
vdw_radius = radiusByElement(element)
for factor in self._shell_factors:
# Compute the number of point for each shell
radius = factor * vdw_radius
area = 4 / 3 * np.pi * radius**2
num_points = int(self._density * area)
# Generate points
points = radius * randomPointsOnSphere(num_points) + coord
all_points.append(points)
return np.concatenate(all_points)