def _to_fml(ds,nmol,sublist):
"""Returns a list of nmol fml.Molecule objects.
* ds :: dataset objects
* nmol :: number of molecules
* sublist :: list of indices of molecules to be converted to
ase Atoms object.
"""
list_of_mol=[]
if nmol==None:
nmol=ds.nmol
if sublist==None:
sublist=ds.list_of_mol[:nmol]
else:
sublist=np.array(ds.list_of_mol)[sublist]
for m in sublist:
fmlm=fml.Molecule()
fmlm.natoms=m.natm
fmlm.atomtypes=m.symb
fmlm.nuclear_charges=m.z
fmlm.coordinates=m.R
list_of_mol.append(fmlm)
return list_of_mol
def create_mols(args):
t = time.time()
filenames = args.input
all_coordinates = []
if len(filenames) == 1:
# trajectory
with open(filenames[0]) as f:
lines = f.readlines()
charges, atom_names, residues, coordinates, remaining_lines = parse_first_frame(
lines)
all_coordinates = parse_trajectory(remaining_lines)
all_coordinates = [coordinates] + all_coordinates
else:
with open(filenames[0]) as f:
lines = f.readlines()
charges, atom_names, residues, coordinates, _ = parse_first_frame(
lines)
all_coordinates.append(coordinates)
for filename in filenames[1:]:
with open(filename) as f:
lines = f.readlines()
all_coordinates.append(parse_frame(lines))
atomtypes = np.asarray([charge_to_atype[charge] for charge in charges])
print "Parsed input in %.1f seconds" % (time.time() - t)
# check if some of the structures have the same coordinates
#for i, coord_i in enumerate(all_coordinates):
# for j, coord_j in enumerate(all_coordinates):
# if j <= i:
# continue
# if np.allclose(coord_i[:50], coord_j[:50]):
# print filenames[i], filenames[j]
t = time.time()
mols = np.empty(len(all_coordinates), dtype=object)
for i in range(mols.size):
mol = fml.Molecule()
mol.natoms = charges.size
mol.atomtypes = atomtypes
mol.atomnames = atom_names
mol.nuclear_charges = charges
mol.coordinates = all_coordinates[i]
mol.residues = residues
generate_descriptor(mol, args)
mols[i] = mol
print "Generated descriptors in %.1f seconds" % (time.time() - t)
return mols
from fml.math.distance import get_l2_distance_arad
from fml.kernels import get_atomic_kernels_arad
if __name__ == "__main__":
# Get list of xyzfilenames
path = "../tests/xyz/"
filenames = os.listdir(path)
mols = []
# Make list of fml.Molecule()
for filename in filenames:
# Initialize molecule
mol = fml.Molecule()
# Read coordinates etc from xyz file
mol.read_xyz(path + filename)
# Generate ARAD descriptor, size = max size of molecule
mol.generate_arad_descriptor(size=20)
# Add mols to list
mols.append(mol)
x1 = []
z1 = []
# Make list of molecules
for mol in mols[:5]:
acti, actj, nacti, nactj, actmax, sigma_space,
pd, r_width, c_width)
# K = np.swapaxes(K,0,5)
# K = np.swapaxes(K,1,4)
# K = np.swapaxes(K,2,3)
# K = np.swapaxes(K,4,5)
return K
if __name__ == "__main__":
import sys
moli = fml.Molecule()
molj = fml.Molecule()
moli.read_xyz(sys.argv[1])
molj.read_xyz(sys.argv[2])
K = pyforce_kernel(moli, molj, 0.5)
# # L = fsingle_force_kernel(moli.coordinates, molj.coordinates, moli.natoms, molj.natoms, 0.5, 0.6)
L = single_force_kernel(moli, molj, 0.5)
print L
# print "K"
# print K
mols = [moli, molj]