def measure_dihedral(coords, atoms):
indices = [3 * atom + k for atom in atoms for k in range(3)]
coords_0 = coords[indices[0:3]]
coords_1 = coords[indices[3:6]]
coords_2 = coords[indices[6:9]]
coords_3 = coords[indices[9:12]]
b1 = coords_1 - coords_0
b2 = coords_2 - coords_1
b3 = coords_3 - coords_2
b2_b3 = np.cross(b2, b3)
b1_b2 = np.cross(b1, b2)
angle = np.arctan2(
np.linalg.norm(b2) * np.dot(b1, b2_b3), np.dot(b1_b2, b2_b3))
return angle
if __name__ == "__main__":
import pele.amber.read_amber as amber
import playground.group_rotation.amino_acids as amino
topology_data = amber.read_topology("/home/khs26/coords.prmtop")
parsed = amber.create_atoms_and_residues(topology_data)
test_params = amber.group_rotation_dict(parsed, amino.def_parameters)
test_coords = np.array(
amber.read_amber_coords("/home/khs26/coords.inpcrd"))
testGR = GroupRotation(test_params)
pre_coords = test_coords.copy()
result = testGR.takeStep(test_coords)
print test_coords - pre_coords
# Create a filter, telling it to compress with zlib.
filters = ts.Filters(complib='zlib')
for amino_acid in (amino.amino_acids):
table = fileh.create_table("/RotamerGroupTemplates", amino_acid,
RotamerGroupTemplate,
"Template for {res}".format(res=amino_acid))
# Get the record object associated with the table.
group_template = table.row
# Read in an appropriate topology file and create a molecular graph.
filename = '/scratch/khs26/rotamer_lib_igb2/{res}/{res}/{res}/coords.prmtop'.format(
res=amino_acid)
topology = ra.read_topology(filename)
mol_graph = ra.create_atoms_and_residues(topology)
# Get the residue name for the first residue.
res = next(residue for residue in mol_graph.residues.nodes()
if residue.index == 1)
# Get a list of dihedrals we are interested in for this residue.
dihedrals = sorted([
k[1] for k in amino.def_parameters
if k[0] == amino_acid and not ('C' in k[1] and 'CA' in k[1])
])
# For each pair of atoms in a dihedral, find their highest-ranked neighbours for defining the dihedral angle.
dihedral_atoms = {}
dihedral_moving_atoms = {}
for atom_pair in dihedrals:
# Create a filter, telling it to compress with zlib.
filters = ts.Filters(complib='zlib')
for amino_acid in (amino.amino_acids):
table = fileh.create_table("/RotamerGroupTemplates",
amino_acid,
RotamerGroupTemplate,
"Template for {res}".format(res=amino_acid))
# Get the record object associated with the table.
group_template = table.row
# Read in an appropriate topology file and create a molecular graph.
filename = '/scratch/khs26/rotamer_lib_igb2/{res}/{res}/{res}/coords.prmtop'.format(res=amino_acid)
topology = ra.read_topology(filename)
mol_graph = ra.create_atoms_and_residues(topology)
# Get the residue name for the first residue.
res = next(residue for residue in mol_graph.residues.nodes() if residue.index == 1)
# Get a list of dihedrals we are interested in for this residue.
dihedrals = sorted([k[1] for k in amino.def_parameters if k[0] == amino_acid
and not ('C' in k[1] and 'CA' in k[1])])
# For each pair of atoms in a dihedral, find their highest-ranked neighbours for defining the dihedral angle.
dihedral_atoms = {}
dihedral_moving_atoms = {}
for atom_pair in dihedrals:
atom0 = next(n for n in mol_graph.atoms.nodes() if n.name == atom_pair[0] and n.residue == res)
atom1 = next(n for n in mol_graph.atoms.nodes() if n.name == atom_pair[1] and n.residue == res)
atom_1 = next(atom for atom in chir.chiral_order(mol_graph.atoms, atom0, depth=2) if atom != atom1)
attribute_variance[group] = ((i) * attribute_variance[group] +
diff**2) / float(i + 1)
return attribute_average, attribute_variance
def measure_dihedral(coords, atoms):
indices = [3 * atom + k for atom in atoms for k in range(3)]
coords_0 = coords[indices[0:3]]
coords_1 = coords[indices[3:6]]
coords_2 = coords[indices[6:9]]
coords_3 = coords[indices[9:12]]
b1 = coords_1 - coords_0
b2 = coords_2 - coords_1
b3 = coords_3 - coords_2
b2_b3 = np.cross(b2, b3)
b1_b2 = np.cross(b1, b2)
angle = np.arctan2(np.linalg.norm(b2) * np.dot(b1, b2_b3), np.dot(b1_b2, b2_b3) )
return angle
if __name__ == "__main__":
import pele.amber.read_amber as amber
import playground.group_rotation.amino_acids as amino
topology_data = amber.read_topology("/home/khs26/coords.prmtop")
parsed = amber.create_atoms_and_residues(topology_data)
test_params = amber.group_rotation_dict(parsed, amino.def_parameters)
test_coords = np.array(amber.read_amber_coords("/home/khs26/coords.inpcrd"))
testGR = GroupRotation(test_params)
pre_coords = test_coords.copy()
result = testGR.takeStep(test_coords)
print test_coords-pre_coords