def fix_chirality(merge, merge_temp, merged_coords, residue_type):
#### fixes chiral groups
chiral_atoms, coord = fetch_chiral_coord(merge_temp, residue_type)
for residue in chiral_atoms:
if residue_type in ['PROTEIN', 'OTHER']:
for atom in chiral_atoms[residue]:
resname = merge_temp[chiral_atoms[residue][atom]]['residue_name']
break
else:
resname=residue_type
for chiral_group in g_var.res_top[resname]['CHIRAL']:
if chiral_group != 'atoms':
atom_move = get_atom_move(merge_temp, resname, residue, chiral_group, chiral_atoms)
S_M = atom_move['m'] - atom_move['stat']
rotation = align_to_vector(S_M, [0,0,1])
c1_coord = (atom_move['c1'] - atom_move['stat']).dot(rotation)
c2_coord = (atom_move['c2'] - atom_move['stat']).dot(rotation)
c3_coord = (atom_move['c3'] - atom_move['stat']).dot(rotation)
if gen.angle_clockwise(c1_coord[0:2], c2_coord[0:2]) > gen.angle_clockwise(c1_coord[0:2], c3_coord[0:2]):
for ax_val, axis in enumerate(['x', 'y', 'z']):
merge_temp[chiral_atoms[residue][g_var.res_top[resname]['CHIRAL'][chiral_group]['m']]][axis] = merge_temp[chiral_atoms[residue][g_var.res_top[resname]['CHIRAL'][chiral_group]['m']]][axis] - (3*S_M[ax_val])
merge_temp[chiral_atoms[residue][chiral_group]][axis] = merge_temp[chiral_atoms[residue][chiral_group]][axis] - (S_M[ax_val])
coord[chiral_atoms[residue][g_var.res_top[resname]['CHIRAL'][chiral_group]['m']]] -= (2*S_M) #move_coord -
coord[chiral_atoms[residue][chiral_group]] -= (0.25*S_M)
merge+=merge_temp
merged_coords+=coord
return merge, merged_coords
def fix_chirality(merge, merge_temp, merged_coords):
#### fixes chiral groups
chiral_atoms, coord = fetch_chiral_coord(merge_temp)
for residue in chiral_atoms:
for atom in chiral_atoms[residue]:
resname = merge_temp[chiral_atoms[residue][atom]]['residue_name']
break
for chiral_group in f_loc.chiral[resname]:
if chiral_group != 'atoms':
stat = merge_temp[chiral_atoms[residue][chiral_group]]
move = merge_temp[chiral_atoms[residue][f_loc.chiral[resname]
[chiral_group]['m']]]
c1 = merge_temp[chiral_atoms[residue][f_loc.chiral[resname]
[chiral_group]['c1']]]
c2 = merge_temp[chiral_atoms[residue][f_loc.chiral[resname]
[chiral_group]['c2']]]
c3 = merge_temp[chiral_atoms[residue][f_loc.chiral[resname]
[chiral_group]['c3']]]
stat_coord = np.array([stat['x'], stat['y'], stat['z']])
move_coord = np.array([move['x'], move['y'], move['z']])
S_M = move_coord - stat_coord
rotation = align_to_vector(S_M, [0, 0, 1])
center = stat_coord
c1_coord = (np.array([c1['x'], c1['y'], c1['z']]) -
center).dot(rotation)
c2_coord = (np.array([c2['x'], c2['y'], c2['z']]) -
center).dot(rotation)
c3_coord = (np.array([c3['x'], c3['y'], c3['z']]) -
center).dot(rotation)
C1_C2_a = gen.angle_clockwise(c1_coord[0:2], c2_coord[0:2])
C1_C3_a = gen.angle_clockwise(c1_coord[0:2], c3_coord[0:2])
if C1_C2_a > C1_C3_a:
for ax_val, axis in enumerate(['x', 'y', 'z']):
merge_temp[chiral_atoms[residue][
f_loc.chiral[resname][chiral_group]
['m']]][axis] = merge_temp[chiral_atoms[residue][
f_loc.chiral[resname][chiral_group]
['m']]][axis] - (3 * S_M[ax_val])
merge_temp[chiral_atoms[residue]
[chiral_group]][axis] = merge_temp[
chiral_atoms[residue]
[chiral_group]][axis] - (S_M[ax_val])
coord[chiral_atoms[residue][f_loc.chiral[resname][
chiral_group]['m']]] = move_coord - (3 * S_M)
coord[chiral_atoms[residue]
[chiral_group]] = stat_coord - (1.5 * S_M)
merge += merge_temp
merged_coords += coord
return merge, merged_coords
def fix_chirality(merge, merge_temp, merged_coords, residue_type):
#### fixes chiral groups
r_b_vec, r_b_inv = read_in.real_box_vectors(g_var.box_vec)
chiral_atoms, coord = fetch_chiral_coord(merge_temp, residue_type)
for residue in chiral_atoms:
if residue_type in ['PROTEIN', 'OTHER']:
for atom in chiral_atoms[residue]:
resname = merge_temp[chiral_atoms[residue]
[atom]]['residue_name']
break
else:
resname = residue_type
for chiral_group in g_var.res_top[resname]['CHIRAL']:
if chiral_group != 'atoms':
stat = merge_temp[chiral_atoms[residue][chiral_group]].copy()
atom_move = {
'stat': np.array([stat['x'], stat['y'], stat['z']]),
'm': '',
'c1': '',
'c2': '',
'c3': ''
}
for chir_atom in atom_move:
if chir_atom != 'stat':
test = merge_temp[chiral_atoms[residue]
[g_var.res_top[resname]['CHIRAL']
[chiral_group][chir_atom]]].copy()
atom_move[chir_atom] = np.array(
[test['x'], test['y'], test['z']])
if gen.calculate_distance(atom_move['stat'],
atom_move[chir_atom]) > 10:
atom_move[chir_atom] = np.array(
read_in.brute_mic(atom_move['stat'],
atom_move[chir_atom],
r_b_vec))
S_M = atom_move['m'] - atom_move['stat']
rotation = align_to_vector(S_M, [0, 0, 1])
c1_coord = (atom_move['c1'] - atom_move['stat']).dot(rotation)
c2_coord = (atom_move['c2'] - atom_move['stat']).dot(rotation)
c3_coord = (atom_move['c3'] - atom_move['stat']).dot(rotation)
if gen.angle_clockwise(c1_coord[0:2],
c2_coord[0:2]) > gen.angle_clockwise(
c1_coord[0:2], c3_coord[0:2]):
for ax_val, axis in enumerate(['x', 'y', 'z']):
merge_temp[chiral_atoms[residue][
g_var.res_top[resname]['CHIRAL'][chiral_group]
['m']]][axis] = merge_temp[chiral_atoms[residue][
g_var.res_top[resname]['CHIRAL'][chiral_group]
['m']]][axis] - (3 * S_M[ax_val])
merge_temp[chiral_atoms[residue]
[chiral_group]][axis] = merge_temp[
chiral_atoms[residue]
[chiral_group]][axis] - (S_M[ax_val])
coord[chiral_atoms[residue]
[g_var.res_top[resname]['CHIRAL'][chiral_group]
['m']]] -= (2 * S_M) #move_coord -
coord[chiral_atoms[residue][chiral_group]] -= (
0.25 * S_M) #stat_coord -
merge += merge_temp
merged_coords += coord
return merge, merged_coords