def get_random_configuration(self):
"""set coordinates before calling BH etc."""
""" returns a 1-D numpy array of length 3xNatoms """
# using pele.amber.read_amber and inpcrd
from pele.amber.read_amber import read_amber_coords
coords = read_amber_coords(self.inpcrdFname)
print "amberSystem> Number of coordinates:", len(coords)
coords = np.reshape(np.transpose(coords), len(coords), 1)
# -- OpenMM
# from simtk.unit import angstrom as openmm_angstrom
## using pdb
# from simtk.openmm.app import pdbfile as openmmpdbReader
# pdb = openmmpdbReader.PDBFile('coords.pdb') # todo: coords.pdb is hardcoded
# coords = pdb.getPositions() / openmm_angstrom
# coords = np.reshape(np.transpose(coords), 3*len(coords),1 )
## using input inpcrd
# from simtk.openmm.app import AmberInpcrdFile
# inpcrd = AmberInpcrdFile( self.inpcrdFname )
# coords = inpcrd.getPositions() / openmm_angstrom
# coords = np.reshape(np.transpose(coords), 3*len(coords),1 )
return coords
def get_random_configuration(self):
"""set coordinates before calling BH etc."""
""" returns a 1-D numpy array of length 3xNatoms """
# using pele.amber.read_amber and inpcrd
from pele.amber.read_amber import read_amber_coords
coords = read_amber_coords(self.inpcrdFname)
print "amberSystem> Number of coordinates:", len(coords)
coords = np.reshape(np.transpose(coords), len(coords), 1)
# -- OpenMM
# from simtk.unit import angstrom as openmm_angstrom
## using pdb
# from simtk.openmm.app import pdbfile as openmmpdbReader
# pdb = openmmpdbReader.PDBFile('coords.pdb') # todo: coords.pdb is hardcoded
# coords = pdb.getPositions() / openmm_angstrom
# coords = np.reshape(np.transpose(coords), 3*len(coords),1 )
## using input inpcrd
# from simtk.openmm.app import AmberInpcrdFile
# inpcrd = AmberInpcrdFile( self.inpcrdFname )
# coords = inpcrd.getPositions() / openmm_angstrom
# coords = np.reshape(np.transpose(coords), 3*len(coords),1 )
return coords
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
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)
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
for dihedral in unmapped_dihedrals:
# We need to convert "N-1" to the N neighbouring "C0". The others can be converted using the map.
atom_map = residue_atom_map[residue]
mapped_dihedral = [[nb for nb in nx.neighbors(residue.molecule.atoms, atom_map["C0"]) if nb.element == "N"][0]
if atom_name == "N-1" else atom_map[atom_name] for atom_name in dihedral]
mapped_dihedrals.append(mapped_dihedral)
dihedral_dict[residue] = mapped_dihedrals
return dihedral_dict
if __name__ == "__main__":
import os.path
import numpy as np
from playground.rotamer.measure_dihedral import dihedrals_with_symmetry
import cProfile
# pr = cProfile.Profile()
# pr.enable()
topology_data = amber.read_topology(os.path.normpath("/home/khs26/flu.prmtop"))
coords = np.array(amber.read_amber_coords(os.path.normpath("/home/khs26/flu.inpcrd"))).reshape((-1, 3))
molecule = amber.create_molecule(topology_data)
ress, maps = molecule.identify_residues()
dihedrals = []
for v in map_dihedrals(ress, maps).values():
for dihedral in v:
dihedrals.append(Dihedral(dihedral))
for dihe in sorted(dihedrals, key=lambda x: x.residue.index):
if dihe.residue.identity in symmetric_atoms:
print dihe.residue, dihe.atoms, dihe.residue.atoms
print "Angle:", dihe.measure_dihedral(coords) * 180.0 / np.pi
# pr.disable()
# pr.print_stats('cumulative')