def read_coords(self, inpcrd_filename):
""" Reads coordinates from a file into the Atoms of the Molecule. """
coords = np.array(read_amber_restart(inpcrd_filename)).reshape((-1, 3))
# Sanity check that there are 3 coordinates per atom
if len(coords) != self.num_atoms():
raise ex.RuntimeError("Incorrect number of coordinates read into molecule.")
# Now run through the list of atoms (sorted by index) and coordinates
for atom, xyz in itertools.izip(sorted(self.atoms.nodes(), key=op.attrgetter("index")), coords):
atom.coords = xyz
import os
import site
import sys
# Add
site.addsitedir(os.path.normpath(sys.argv[0] + "/../.."))
import rotamer.io.amber as amber_io
import rotamer.io.gmin as gmin_io
if __name__ == "__main__":
if sys.argv[1] == "init":
pass
elif sys.argv[1] == "move":
coords = amber_io.read_amber_restart(".coords_before_rotamer.rst")
coords = coords * 100
gmin_io.write_coords(coords, ".coords_after_rotamer.rst")
ress, maps = molecule.identify_residues()
sc_dihedrals = []
for k, v in map_dihedrals(ress, maps).items():
for idx, dihedral in enumerate(v):
k.dihedrals["chi" + str(idx + 1)] = Dihedral(dihedral)
sc_dihedrals.append(dihedral)
return sc_dihedrals
if __name__ == "__main__":
import os.path
import numpy as np
topology_data = amber.read_topology(
os.path.normpath("../tests/data/ARG_LYS_ASN.prmtop"))
coords = np.array(
read_amber_restart(
os.path.normpath("../tests/data/ARG_LYS_ASN.inpcrd"))).reshape(
(-1, 3))
molecule = amber.create_molecule(topology_data)
phi_psi_dihedrals(molecule)
sidechain_dihedrals(molecule)
for res in sorted(molecule.residues, key=lambda x: x.index)[1:4]:
print "========================"
print res
for k, v in res.dihedrals.items():
# print k, v.measure_dihedral(coords) * 180.0 / np.pi
new_coords = v.set_dihedral(coords, -45.0 * np.pi / 180.0)
print k, v.measure_dihedral(
coords) * 180.0 / np.pi, v.measure_dihedral(
new_coords) * 180.0 / np.pi