def get_atom_move(merge_temp, resname, residue, chiral_group, chiral_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]))
return atom_move
def check_ringed_lipids(protein):
print('Checking for ringed lipids')
if not os.path.exists(g_var.merged_directory+'checked_ringed_lipid_de_novo.pdb'):
if not os.path.exists(g_var.merged_directory+'merged_cg2at_threaded.pdb'):
os.chdir(g_var.merged_directory)
merge, merge_coords = read_in_merged_pdbs([], [], protein)
ringed=False
lipid_atoms = []
with open(g_var.merged_directory+'threaded_lipids.dat', 'w') as ring_ouput:
for at_val, atom in enumerate(merge):
resname = get_np_resname(at_val)
if resname in g_var.np_residues:
offset = fetch_start_of_residue_np(at_val, resname)
if atom['atom_number']-offset in g_var.heavy_bond[resname]:
for at_bond in g_var.heavy_bond[resname][atom['atom_number']-offset]:
at_bond -=1
if merge[at_bond+offset]['atom_number'] > merge[at_val]['atom_number']:
merge[at_bond+offset]['x'], merge[at_bond+offset]['y'], merge[at_bond+offset]['z'] = np.array(read_in.brute_mic(merge_coords[at_val],merge_coords[at_bond+offset]))
merge_coords[at_bond+offset] = merge[at_bond+offset]['x'], merge[at_bond+offset]['y'], merge[at_bond+offset]['z']
dist = gen.calculate_distance(merge_coords[at_val], merge_coords[at_bond+offset])
if 2 < dist < 6:
lipid_atoms.append([at_val, at_bond+offset, (np.array(merge_coords[at_val])+np.array(merge_coords[at_bond+offset]))/2])
ring_ouput.write('{0:6}{1:6}{2:2}{3:4}{4:2}{5:7}{6:5}{7:5}{8:5}{9:5}{10:5}{11:5}\n'.format(
'distance: ',str(np.round(dist,2)),'residue: ', merge[at_val]['residue_name'], merge[at_val]['residue_id'],
' atom_1: ', merge[at_val]['atom_name'],
'atom_2: ', merge[at_bond+offset]['atom_name'], 'rough line num: ', at_val, at_bond+offset))
ringed = True
if ringed or os.path.exists(g_var.merged_directory+'merged_cg2at_threaded.pdb'):
print('Found '+str(len(lipid_atoms))+' abnormal bonds, now attempting to fix.')
print('See this file for a complete list: '+g_var.merged_directory+'threaded_lipids.dat')
fix_threaded_lipids(lipid_atoms, merge, merge_coords)
else:
gen.file_copy_and_check(g_var.merged_directory+'MIN/merged_cg2at_de_novo_minimised.pdb', g_var.merged_directory+'checked_ringed_lipid_de_novo.pdb')
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