def _process_frame(self, trj, energy, hbonds, entropy):
"""
Frame wise calculation of GIST quantities.
Parameters
----------
trj :
Molecular dynamic trajectory representing current frame.
energy :
If True, solute-water and water-water energies are calculated for each water in each voxel in current
frame.
hbonds : bool
If True, solute-water and water-water hydrogen bonds are calculated for each water in each voxel in current
frame.
entropy : bool
If True, water coordinates and quaternions are stored for each water in each voxel in current frame.
"""
nbr_cutoff_sq = 3.5 ** 2
trj.xyz *= 10.0
coords = trj.xyz
uc = trj.unitcell_vectors[0]*10.
waters = []
calc.assign_voxels(trj.xyz, self.dims, self.gridmax, self.origin, waters, self.wat_oxygen_atom_ids)
for wat in waters:
self.voxeldata[wat[0], 4] += 1
if energy or hbonds:
e_lj_array, e_elec_array = np.copy(self.acoeff), np.copy(self.chg_product)
distance_matrix = np.zeros((self.water_sites, self.all_atom_ids.shape[0]))
calc.get_pairwise_distances(wat, self.all_atom_ids, coords, uc, distance_matrix)
wat_nbrs = self.wat_oxygen_atom_ids[np.where(
(distance_matrix[0, :][self.wat_oxygen_atom_ids] <= nbr_cutoff_sq) & (
distance_matrix[0, :][self.wat_oxygen_atom_ids] > 0.0))]
self.voxeldata[wat[0], 19] += wat_nbrs.shape[0]
calc.calculate_energy(wat[1], distance_matrix, e_elec_array, e_lj_array, self.bcoeff)
if self.prot_atom_ids.shape[0] != 0:
#self.voxeldata[wat[0], 13] += np.sum(e_lj_array[:, self.prot_atom_ids])
#self.voxeldata[wat[0], 13] += np.sum(e_elec_array[:, self.prot_atom_ids])
self.voxeldata[wat[0], 13] += np.sum(e_lj_array[:, self.non_water_atom_ids])
self.voxeldata[wat[0], 13] += np.sum(e_elec_array[:, self.non_water_atom_ids])
self.voxeldata[wat[0], 15] += np.sum(
e_lj_array[:, self.wat_oxygen_atom_ids[0]:wat[1]]) + np.sum(e_lj_array[:, wat[1] + self.water_sites:])
self.voxeldata[wat[0], 15] += np.sum(
e_elec_array[:, self.wat_oxygen_atom_ids[0]:wat[1]]) + np.sum(
e_elec_array[:, wat[1] + self.water_sites:])
e_nbr_list = [np.sum(e_lj_array[:, wat_nbrs + i] + e_elec_array[:, wat_nbrs + i]) for i in
range(self.water_sites)]
self.voxeldata[wat[0], 17] += np.sum(e_nbr_list)
# H-bond calculations
if hbonds:
prot_nbrs_all = self.prot_atom_ids[
np.where(distance_matrix[0, :][self.prot_atom_ids] <= nbr_cutoff_sq)]
prot_nbrs_hb = prot_nbrs_all[np.where(self.prot_hb_types[prot_nbrs_all] != 0)]
if wat_nbrs.shape[0] > 0:
hb_ww = self.calculate_hydrogen_bonds(trj, wat[1], wat_nbrs)
acc_ww = hb_ww[:, 0][np.where(hb_ww[:, 0] == wat[1])].shape[0]
don_ww = hb_ww.shape[0] - acc_ww
self.voxeldata[wat[0], 25] += hb_ww.shape[0]
self.voxeldata[wat[0], 31] += don_ww
self.voxeldata[wat[0], 33] += acc_ww
if wat_nbrs.shape[0] != 0 and hb_ww.shape[0] != 0:
self.voxeldata[wat[0], 21] += wat_nbrs.shape[0] / hb_ww.shape[0]
if prot_nbrs_hb.shape[0] > 0:
hb_sw = self.calculate_hydrogen_bonds(trj, wat[1], prot_nbrs_hb, water_water=False)
acc_sw = hb_sw[:, 0][np.where(hb_sw[:, 0] == wat[1])].shape[0]
don_sw = hb_sw.shape[0] - acc_sw
self.voxeldata[wat[0], 23] += hb_sw.shape[0]
self.voxeldata[wat[0], 27] += don_sw
self.voxeldata[wat[0], 29] += acc_sw
if entropy:
self.calculate_euler_angles(wat, coords[0, :, :])
def process_chunk(self, begin_chunk, chunk_size, topology, energy, hbonds,
entropy):
nbr_cutoff_sq = 3.5**2
with md.open(self.trajectory) as f:
f.seek(begin_chunk)
trj = f.read_as_traj(topology, n_frames=chunk_size, stride=1)
trj.xyz *= 10.0
pbc = md.utils.in_units_of(trj.unitcell_lengths, "nanometers",
"angstroms")
frame_data = [[] for i in range(trj.n_frames)]
calc.assign_voxels(trj.xyz, self.dims, self.gridmax, self.origin,
frame_data, self.wat_oxygen_atom_ids)
for frame in range(trj.n_frames):
coords = trj.xyz[frame, :, :].reshape(1, trj.xyz.shape[1],
trj.xyz.shape[2])
periodic_box = pbc[frame].reshape(1, pbc.shape[1])
waters = frame_data[frame]
for wat in waters:
self.voxeldata[wat[0], 4] += 1
if energy or hbonds:
e_lj_array, e_elec_array = np.copy(
self.acoeff), np.copy(self.chg_product)
distance_matrix = np.zeros(
(self.water_sites, self.all_atom_ids.shape[0]))
calc.get_pairwise_distances(wat, self.all_atom_ids,
coords, pbc,
distance_matrix)
wat_nbrs = self.wat_oxygen_atom_ids[np.where(
(distance_matrix[0, :][self.wat_oxygen_atom_ids] <=
nbr_cutoff_sq) & (distance_matrix[0, :][
self.wat_oxygen_atom_ids] > 0.0))]
self.voxeldata[wat[0], 17] += wat_nbrs.shape[0]
calc.calculate_energy(wat[1], distance_matrix,
e_elec_array, e_lj_array,
self.bcoeff)
self.voxeldata[wat[0], 11] += np.sum(
e_lj_array[:, :self.wat_oxygen_atom_ids[0]])
self.voxeldata[wat[0], 11] += np.sum(
e_elec_array[:, :self.wat_oxygen_atom_ids[0]])
self.voxeldata[wat[0], 13] += np.sum(
e_lj_array[:, self.wat_oxygen_atom_ids[0]:wat[1]]
) + np.sum(e_lj_array[:, wat[1] + self.water_sites:])
self.voxeldata[wat[0], 13] += np.sum(
e_elec_array[:, self.wat_oxygen_atom_ids[0]:wat[1]]
) + np.sum(e_elec_array[:, wat[1] + self.water_sites:])
e_nbr_list = [
np.sum(e_lj_array[:, wat_nbrs + i] +
e_elec_array[:, wat_nbrs + i])
for i in xrange(self.water_sites)
]
self.voxeldata[wat[0], 15] += np.sum(e_nbr_list)
"""
###DEBUG START###
elj_sw = np.sum(e_lj_array[:, :self.wat_oxygen_atom_ids[0]])
eelec_sw = np.sum(e_elec_array[:, :self.wat_oxygen_atom_ids[0]])
elj_ww = np.sum(e_lj_array[:, self.wat_oxygen_atom_ids[0]:wat[1]]) + np.sum(e_lj_array[:, wat[1] + 1:])
eelec_ww = np.sum(e_elec_array[:, self.wat_oxygen_atom_ids[0]:wat[1]]) + np.sum(e_elec_array[:, wat[1] + self.water_sites:])
e_nbr_list = [np.sum(e_lj_array[:, wat_nbrs + i] + e_elec_array[:, wat_nbrs + i]) for i in xrange(self.water_sites)]
enbr = np.sum(e_nbr_list)
print "Calc: ", elj_sw, eelec_sw, elj_ww, eelec_ww, enbr
distance_matrix = np.sqrt(distance_matrix)
energy_lj, energy_elec = self.calculate_energy(distance_matrix)
test_1 = np.sum(energy_lj[:self.wat_oxygen_atom_ids[0]:])
test_2 = np.sum(energy_elec[:, self.non_water_atom_ids])
test_3 = np.nansum(energy_lj[self.wat_oxygen_atom_ids[0]:])
test_4 = np.sum(energy_elec[:, self.wat_atom_ids[0]:wat[1]]) + np.sum(energy_elec[:, wat[1] + self.water_sites:])
test_5 = 0.0
test_5 += np.sum(energy_lj[self.wat_oxygen_atom_ids[0]:][(wat_nbrs - self.wat_oxygen_atom_ids[0]) / self.water_sites])
for i in range(self.water_sites):
test_5 += np.sum(energy_elec[:, wat_nbrs + i])
print "Ref: ", test_1, test_2, test_3, test_4, test_5
###DEBUG END###
"""
# H-bond calculations
if hbonds:
prot_nbrs_all = self.non_water_atom_ids[np.where(
distance_matrix[0, :][
self.non_water_atom_ids] <= nbr_cutoff_sq)]
prot_nbrs_hb = prot_nbrs_all[np.where(
self.prot_hb_types[prot_nbrs_all] != 0)]
if wat_nbrs.shape[0] != 0 and prot_nbrs_hb.shape[
0] != 0:
# hb_ww, hb_sw = self.calculate_hydrogen_bonds2(coords, wat[1], wat_nbrs, prot_nbrs_hb)
hb_ww, hb_sw = self.calculate_hydrogen_bonds(
trj, wat[1], wat_nbrs, prot_nbrs_hb)
acc_ww = hb_ww[:, 0][np.where(
hb_ww[:, 0] == wat[1])].shape[0]
don_ww = hb_ww.shape[0] - acc_ww
acc_sw = hb_sw[:, 0][np.where(
hb_sw[:, 0] == wat[1])].shape[0]
don_sw = hb_sw.shape[0] - acc_sw
self.voxeldata[wat[0], 23] += hb_sw.shape[0]
self.voxeldata[wat[0], 25] += hb_ww.shape[0]
self.voxeldata[wat[0], 27] += don_sw
self.voxeldata[wat[0], 29] += acc_sw
self.voxeldata[wat[0], 31] += don_ww
self.voxeldata[wat[0], 33] += acc_ww
if wat_nbrs.shape[0] != 0 and hb_ww.shape[
0] != 0:
self.voxeldata[wat[0],
19] += wat_nbrs.shape[
0] / hb_ww.shape[0]
# f_enc = 1.0 - (wat_nbrs.shape[0] / 5.25)
# if f_enc < 0.0:
# f_enc = 0.0
# self.voxeldata[wat[0], 21] += f_enc
if entropy:
self.calculate_euler_angles(wat, coords[0, :, :])
def _process_frame(self, trj, energy, hbonds, entropy):
"""
Frame wise calculation of GIST quantities.
Parameters
----------
trj :
Molecular dynamic trajectory representing current frame.
energy :
If True, solute-water and water-water energies are calculated for each water in each voxel in current
frame.
hbonds : bool
If True, solute-water and water-water hydrogen bonds are calculated for each water in each voxel in current
frame.
entropy : bool
If True, water coordinates and quaternions are stored for each water in each voxel in current frame.
"""
nbr_cutoff_sq = 3.5**2
trj.xyz *= 10.0
coords = trj.xyz
uc = trj.unitcell_vectors[0] * 10.
waters = []
calc.assign_voxels(trj.xyz, self.dims, self.gridmax, self.origin,
waters, self.wat_oxygen_atom_ids)
distance_matrix = np.zeros(
(self.water_sites, self.all_atom_ids.shape[0]))
for wat in waters:
self.voxeldata[wat[0], 4] += 1
### wat[0]: Voxel index
### wat[1]: water molecule oxygen atom index
if energy or hbonds:
e_lj_array, e_elec_array = np.copy(self.acoeff), np.copy(
self.chg_product)
### Here it is assumed that oxygen atom is always the first atom. Is that always the case?
### We should probably check that somewhere during init?
###
### The self.neighbor_ids array contains atom indices of all atoms that should
### be considered as potential neighbors. Valid_neighbors has same shape as
### self.neighbor_ids and is False at the position where index wat occures in
### self.neighbor_ids, otherwise it is True. neighbor_ids stores the indices of
### the actual neighbor candidates that will be commited to get_pairwise_distances
### routine and has length of self.neighbor_ids-1. wat_nbrs_shell is of length neighbor_ids
### and holds the shell_index of each neighbor candidate atom (0:first shell, 1: beyond first
### shell)
valid_neighbors = np.ones(self.neighbor_ids.shape[0],
dtype=bool)
valid_neighbors[np.where(self.neighbor_ids == wat)] = False
neighbor_ids = self.neighbor_ids[valid_neighbors]
wat_nbrs_shell = self.wat_nbrs_shell[valid_neighbors]
calc.get_pairwise_distances(wat, self.all_atom_ids,
np.array([nbr_cutoff_sq]),
neighbor_ids, wat_nbrs_shell,
coords, uc, distance_matrix, 0)
wat_nbrs = self.all_atom_ids[np.where(wat_nbrs_shell == 0)]
self.voxeldata[wat[0], 19] += wat_nbrs.shape[0]
calc.calculate_energy(wat[1], distance_matrix, e_elec_array,
e_lj_array, self.bcoeff)
if self.prot_atom_ids.shape[0] != 0:
#self.voxeldata[wat[0], 13] += np.sum(e_lj_array[:, self.prot_atom_ids])
#self.voxeldata[wat[0], 13] += np.sum(e_elec_array[:, self.prot_atom_ids])
self.voxeldata[wat[0], 13] += np.sum(
e_lj_array[:, self.non_water_atom_ids])
self.voxeldata[wat[0], 13] += np.sum(
e_elec_array[:, self.non_water_atom_ids])
self.voxeldata[wat[0], 15] += np.sum(
e_lj_array[:,
self.wat_oxygen_atom_ids[0]:wat[1]]) + np.sum(
e_lj_array[:, wat[1] + self.water_sites:])
self.voxeldata[wat[0], 15] += np.sum(
e_elec_array[:, self.wat_oxygen_atom_ids[0]:wat[1]]
) + np.sum(e_elec_array[:, wat[1] + self.water_sites:])
e_nbr_list = [
np.sum(e_lj_array[:, wat_nbrs + i] +
e_elec_array[:, wat_nbrs + i])
for i in range(self.water_sites)
]
self.voxeldata[wat[0], 17] += np.sum(e_nbr_list)
### Might be usefull for API to have the neighbors and shell
### indices available.
self.wat_nbrs_shell[valid_neighbors] = wat_nbrs_shell
self.neighbor_ids[valid_neighbors] = neighbor_ids
"""
###DEBUG START###
elj_sw = np.sum(e_lj_array[:, :self.wat_oxygen_atom_ids[0]])
eelec_sw = np.sum(e_elec_array[:, :self.wat_oxygen_atom_ids[0]])
elj_ww = np.sum(e_lj_array[:, self.wat_oxygen_atom_ids[0]:wat[1]]) + np.sum(e_lj_array[:, wat[1] + 1:])
eelec_ww = np.sum(e_elec_array[:, self.wat_oxygen_atom_ids[0]:wat[1]]) + np.sum(e_elec_array[:, wat[1] + self.water_sites:])
e_nbr_list = [np.sum(e_lj_array[:, wat_nbrs + i] + e_elec_array[:, wat_nbrs + i]) for i in xrange(self.water_sites)]
enbr = np.sum(e_nbr_list)
print "Calc: ", elj_sw, eelec_sw, elj_ww, eelec_ww, enbr
distance_matrix = np.sqrt(distance_matrix)
energy_lj, energy_elec = self.calculate_energy(distance_matrix)
test_1 = np.sum(energy_lj[:self.wat_oxygen_atom_ids[0]:])
test_2 = np.sum(energy_elec[:, self.non_water_atom_ids])
test_3 = np.nansum(energy_lj[self.wat_oxygen_atom_ids[0]:])
test_4 = np.sum(energy_elec[:, self.wat_atom_ids[0]:wat[1]]) + np.sum(energy_elec[:, wat[1] + self.water_sites:])
test_5 = 0.0
test_5 += np.sum(energy_lj[self.wat_oxygen_atom_ids[0]:][(wat_nbrs - self.wat_oxygen_atom_ids[0]) / self.water_sites])
for i in range(self.water_sites):
test_5 += np.sum(energy_elec[:, wat_nbrs + i])
print "Ref: ", test_1, test_2, test_3, test_4, test_5
###DEBUG END###
"""
# H-bond calculations
if hbonds:
prot_nbrs_all = self.prot_atom_ids[np.where(
distance_matrix[0, :][
self.prot_atom_ids] <= nbr_cutoff_sq)]
prot_nbrs_hb = prot_nbrs_all[np.where(
self.prot_hb_types[prot_nbrs_all] != 0)]
if wat_nbrs.shape[0] > 0:
hb_ww = self.calculate_hydrogen_bonds(
trj, wat[1], wat_nbrs)
acc_ww = hb_ww[:, 0][np.where(
hb_ww[:, 0] == wat[1])].shape[0]
don_ww = hb_ww.shape[0] - acc_ww
self.voxeldata[wat[0], 25] += hb_ww.shape[0]
self.voxeldata[wat[0], 31] += don_ww
self.voxeldata[wat[0], 33] += acc_ww
if wat_nbrs.shape[0] != 0 and hb_ww.shape[0] != 0:
self.voxeldata[
wat[0],
21] += wat_nbrs.shape[0] / hb_ww.shape[0]
if prot_nbrs_hb.shape[0] > 0:
hb_sw = self.calculate_hydrogen_bonds(
trj, wat[1], prot_nbrs_hb, water_water=False)
acc_sw = hb_sw[:, 0][np.where(
hb_sw[:, 0] == wat[1])].shape[0]
don_sw = hb_sw.shape[0] - acc_sw
self.voxeldata[wat[0], 23] += hb_sw.shape[0]
self.voxeldata[wat[0], 27] += don_sw
self.voxeldata[wat[0], 29] += acc_sw
if entropy:
self.calculate_euler_angles(wat, coords[0, :, :])
def _process_frame(self, trj, frame_i, energy, hbonds, entropy):
nbr_cutoff_sq = 3.5**2
trj.xyz *= 10.0
coords = trj.xyz
periodic_box = md.utils.in_units_of(trj.unitcell_lengths, "nanometers",
"angstroms")
waters = []
calc.assign_voxels(trj.xyz, self.dims, self.gridmax, self.origin,
waters, self.wat_oxygen_atom_ids)
for wat in waters:
self.voxeldata[wat[0], 4] += 1
if energy or hbonds:
e_lj_array, e_elec_array = np.copy(self.acoeff), np.copy(
self.chg_product)
distance_matrix = np.zeros(
(self.water_sites, self.all_atom_ids.shape[0]))
calc.get_pairwise_distances(wat, self.all_atom_ids, coords,
periodic_box, distance_matrix)
wat_nbrs = self.wat_oxygen_atom_ids[np.where(
(distance_matrix[0, :][self.wat_oxygen_atom_ids] <=
nbr_cutoff_sq)
& (distance_matrix[0, :][self.wat_oxygen_atom_ids] > 0.0))]
self.voxeldata[wat[0], 19] += wat_nbrs.shape[0]
calc.calculate_energy(wat[1], distance_matrix, e_elec_array,
e_lj_array, self.bcoeff)
if self.prot_atom_ids.shape[0] != 0:
self.voxeldata[wat[0], 13] += np.sum(
e_lj_array[:, self.prot_atom_ids])
self.voxeldata[wat[0], 13] += np.sum(
e_elec_array[:, self.prot_atom_ids])
self.voxeldata[wat[0], 15] += np.sum(
e_lj_array[:,
self.wat_oxygen_atom_ids[0]:wat[1]]) + np.sum(
e_lj_array[:, wat[1] + self.water_sites:])
self.voxeldata[wat[0], 15] += np.sum(
e_elec_array[:, self.wat_oxygen_atom_ids[0]:wat[1]]
) + np.sum(e_elec_array[:, wat[1] + self.water_sites:])
e_nbr_list = [
np.sum(e_lj_array[:, wat_nbrs + i] +
e_elec_array[:, wat_nbrs + i])
for i in xrange(self.water_sites)
]
self.voxeldata[wat[0], 17] += np.sum(e_nbr_list)
"""
###DEBUG START###
elj_sw = np.sum(e_lj_array[:, :self.wat_oxygen_atom_ids[0]])
eelec_sw = np.sum(e_elec_array[:, :self.wat_oxygen_atom_ids[0]])
elj_ww = np.sum(e_lj_array[:, self.wat_oxygen_atom_ids[0]:wat[1]]) + np.sum(e_lj_array[:, wat[1] + 1:])
eelec_ww = np.sum(e_elec_array[:, self.wat_oxygen_atom_ids[0]:wat[1]]) + np.sum(e_elec_array[:, wat[1] + self.water_sites:])
e_nbr_list = [np.sum(e_lj_array[:, wat_nbrs + i] + e_elec_array[:, wat_nbrs + i]) for i in xrange(self.water_sites)]
enbr = np.sum(e_nbr_list)
print "Calc: ", elj_sw, eelec_sw, elj_ww, eelec_ww, enbr
distance_matrix = np.sqrt(distance_matrix)
energy_lj, energy_elec = self.calculate_energy(distance_matrix)
test_1 = np.sum(energy_lj[:self.wat_oxygen_atom_ids[0]:])
test_2 = np.sum(energy_elec[:, self.non_water_atom_ids])
test_3 = np.nansum(energy_lj[self.wat_oxygen_atom_ids[0]:])
test_4 = np.sum(energy_elec[:, self.wat_atom_ids[0]:wat[1]]) + np.sum(energy_elec[:, wat[1] + self.water_sites:])
test_5 = 0.0
test_5 += np.sum(energy_lj[self.wat_oxygen_atom_ids[0]:][(wat_nbrs - self.wat_oxygen_atom_ids[0]) / self.water_sites])
for i in range(self.water_sites):
test_5 += np.sum(energy_elec[:, wat_nbrs + i])
print "Ref: ", test_1, test_2, test_3, test_4, test_5
###DEBUG END###
"""
# H-bond calculations
if hbonds:
prot_nbrs_all = self.non_water_atom_ids[np.where(
distance_matrix[0, :][
self.non_water_atom_ids] <= nbr_cutoff_sq)]
prot_nbrs_hb = prot_nbrs_all[np.where(
self.prot_hb_types[prot_nbrs_all] != 0)]
if wat_nbrs.shape[0] > 0:
hb_ww = self.calculate_hydrogen_bonds(
trj, wat[1], wat_nbrs)
acc_ww = hb_ww[:, 0][np.where(
hb_ww[:, 0] == wat[1])].shape[0]
don_ww = hb_ww.shape[0] - acc_ww
self.voxeldata[wat[0], 25] += hb_ww.shape[0]
self.voxeldata[wat[0], 31] += don_ww
self.voxeldata[wat[0], 33] += acc_ww
if wat_nbrs.shape[0] != 0 and hb_ww.shape[0] != 0:
self.voxeldata[
wat[0],
21] += wat_nbrs.shape[0] / hb_ww.shape[0]
if prot_nbrs_hb.shape[0] > 0:
hb_sw = self.calculate_hydrogen_bonds(
trj, wat[1], prot_nbrs_hb, water_water=False)
acc_sw = hb_sw[:, 0][np.where(
hb_sw[:, 0] == wat[1])].shape[0]
don_sw = hb_sw.shape[0] - acc_sw
self.voxeldata[wat[0], 23] += hb_sw.shape[0]
self.voxeldata[wat[0], 27] += don_sw
self.voxeldata[wat[0], 29] += acc_sw
if entropy:
self.calculate_euler_angles(wat, coords[0, :, :])