def non_solvent(system, atomistic_fragments, residue_type):
#### loop through all resids of that residue type
system[residue_type] = len(atomistic_fragments[residue_type])
if not os.path.exists(g_var.working_dir + residue_type + '/' +
residue_type + '_all.pdb') and not os.path.exists(
g_var.working_dir + residue_type + '/' +
residue_type + '_merged.pdb'):
NP = {}
count = 0
coord = []
index_conversion = {}
for resid in atomistic_fragments[residue_type]:
if not os.path.exists(g_var.working_dir + residue_type + '/' +
residue_type + '_merged.pdb'):
atomistic_fragments[residue_type][
resid] = at_mod.check_hydrogens(
atomistic_fragments[residue_type][resid])
for at_id, atom in enumerate(
atomistic_fragments[residue_type][resid], 1):
if not atomistic_fragments[residue_type][resid][at_id][
'atom'].startswith('M'):
index_conversion[count] = len(coord)
coord.append(atomistic_fragments[residue_type][resid]
[at_id]['coord'])
NP[count] = atomistic_fragments[residue_type][resid][at_id]
count += 1
coord = at_mod.check_atom_overlap(coord)
pdb_output_all = gen.create_pdb(g_var.working_dir + residue_type +
'/' + residue_type + '_all.pdb')
atom_counter = 0
for at_val, atom in enumerate(NP):
if at_val in index_conversion:
x, y, z = gen.trunc_coord(coord[index_conversion[at_val]])
else:
x, y, z = gen.trunc_coord([
NP[atom]['coord'][0], NP[atom]['coord'][1],
NP[atom]['coord'][2]
])
if atom_counter >= 99_999:
atom_counter = 1
else:
atom_counter += 1
pdb_output_all.write(g_var.pdbline % (
(atom_counter, NP[atom]['atom'], NP[atom]['res_type'], ' ', 1,
x, y, z, 0.00, 0.00)) + '\n')
return system
def merge_minimised(residue_type):
os.chdir(g_var.working_dir + residue_type + '/MIN')
print('Merging individual residues : ' + residue_type)
#### create merged pdb in min folder
if not os.path.exists(g_var.working_dir + residue_type + '/MIN/' +
residue_type + '_merged.pdb'):
pdb_output = gen.create_pdb(g_var.working_dir + residue_type +
'/MIN/' + residue_type + '_merged.pdb')
if residue_type == 'SOL':
resid_range = 1
else:
resid_range = g_var.system[residue_type]
merge, merge_coords = [], []
#### run through every resid
for resid in range(resid_range):
merge_temp, dump = at_mod.read_in_merged_pdbs(
[], [], g_var.working_dir + residue_type + '/MIN/' +
residue_type + '_' + str(resid) + '.pdb')
merge, merge_coords = at_mod.fix_chirality(merge, merge_temp,
merge_coords,
residue_type)
if residue_type != 'SOL':
merge_coords = at_mod.check_atom_overlap(merge_coords)
for line_val, line in enumerate(merge):
x, y, z = gen.trunc_coord([
merge_coords[line_val][0], merge_coords[line_val][1],
merge_coords[line_val][2]
])
pdb_output.write(g_var.pdbline%((int(line['atom_number']), line['atom_name'], line['residue_name'],' ',line['residue_id'],\
x, y, z,1,0))+'\n')
pdb_output.write('TER\nENDMDL')
pdb_output.close()
def solvent_ion(system, atomistic_fragments, residue_type):
#### creates ion pdb with header
gen.mkdir_directory(g_var.working_dir + 'ION/MIN')
skip = os.path.exists(g_var.working_dir + residue_type + '/' +
residue_type + '_merged.pdb')
if not skip:
pdb_ion = gen.create_pdb(g_var.working_dir + residue_type + '/' +
residue_type + '_merged.pdb')
for resid in atomistic_fragments[residue_type]:
for at_id, atom in enumerate(atomistic_fragments[residue_type][resid]):
#### write ion coordinate out
if not skip:
short_line = atomistic_fragments[residue_type][resid][at_id +
1]
x, y, z = gen.trunc_coord([
short_line['coord'][0], short_line['coord'][1],
short_line['coord'][2]
])
pdb_ion.write(g_var.pdbline % (
(at_id + 1, short_line['atom'], short_line['res_type'],
' ', 1, x, y, z, 0.00, 0.00)) + '\n')
if atomistic_fragments[residue_type][resid][
at_id + 1]['res_type'] != 'SOL':
if atomistic_fragments[residue_type][resid][
at_id + 1]['res_type'] not in system:
system[atomistic_fragments[residue_type][resid][at_id + 1]
['res_type']] = 1
else:
system[atomistic_fragments[residue_type][resid][at_id + 1]
['res_type']] += 1
return system
def write_pdb(merge, merge_coords, index_conversion, write_file):
#### creates merged pdb and writes chains to it
if not os.path.exists(write_file):
pdb_output = gen.create_pdb(write_file)
atom_counter = 1
for line_val, line in enumerate(merge):
if line_val in index_conversion:
x, y, z = gen.trunc_coord(
merge_coords[index_conversion[line_val]])
else:
x, y, z = gen.trunc_coord([line['x'], line['y'], line['z']])
if atom_counter >= 99_999:
atom_counter = 1
else:
atom_counter += 1
pdb_output.write(g_var.pdbline%((atom_counter, line['atom_name'], line['residue_name'],' ',line['residue_id'],\
x,y,z,1,0))+'\n')
pdb_output.close()
def finalise_novo_atomistic(coord_atomistic, sys_type):
final_at_residues = {}
final_at = {}
for chain in coord_atomistic:
at_number = 0
final_at_residues[chain] = {}
final_at[chain] = {}
coords = []
skip = os.path.exists(g_var.working_dir + sys_type + '/' + sys_type +
'_de_novo_' + str(chain) + '.pdb')
if not skip:
pdb_output = gen.create_pdb(g_var.working_dir + sys_type + '/' +
sys_type + '_de_novo_' + str(chain) +
'.pdb')
for res_index, residue_id in enumerate(coord_atomistic[chain]):
if coord_atomistic[chain][residue_id][next(
iter(coord_atomistic[chain][residue_id])
)]['res_type'] in g_var.mod_residues + g_var.o_residues:
coord_atomistic[chain][residue_id] = at_mod.check_hydrogens(
coord_atomistic[chain][residue_id])
if sys_type == 'PROTEIN':
if res_index <= len(coord_atomistic[chain]) - 3:
coord_atomistic[chain][
residue_id], cross_vector = fix_carbonyl(
residue_id, g_var.cg_residues['PROTEIN'],
coord_atomistic[chain][residue_id], False)
elif res_index < len(
coord_atomistic[chain]) and 'cross_vector' in locals():
coord_atomistic[chain][
residue_id], cross_vector = fix_carbonyl(
residue_id, g_var.cg_residues['PROTEIN'],
coord_atomistic[chain][residue_id], cross_vector)
order = np.sort(
np.array(list(coord_atomistic[chain][residue_id].keys())))
for at_val, atom in enumerate(order):
coord_atomistic[chain][residue_id][atom]['resid'] = res_index
coords.append(
coord_atomistic[chain][residue_id][atom]['coord'])
final_at[chain][at_number] = coord_atomistic[chain][
residue_id][atom]
at_number += 1
final_at_residues[chain][res_index] = coord_atomistic[chain][
residue_id]
coords = at_mod.check_atom_overlap(coords)
for atom in final_at[chain]:
final_at[chain][atom]['coord'] = coords[atom]
if not skip:
x, y, z = gen.trunc_coord(final_at[chain][atom]['coord'])
pdb_output.write(g_var.pdbline%((atom,final_at[chain][atom]['atom'],final_at[chain][atom]['res_type'],' ',\
final_at[chain][atom]['resid'],x,y,z,1,0))+'\n')
if 'pdb_output' in locals():
pdb_output.close()
return final_at_residues
def solvent_sol(system, atomistic_fragments, residue_type):
#### creates solvent directory and SOL key in system dictionay otherwise it appends solvent molecules to sol pdb
sol = {}
coord = []
count = 0
index_conversion = {}
if not os.path.exists(g_var.working_dir + 'SOL' + '/SOL_all.pdb'):
pdb_sol = gen.create_pdb(g_var.working_dir + 'SOL' + '/SOL_all.pdb')
for resid in atomistic_fragments[residue_type]:
####### check if any atoms in residue overlap #######
for atom in atomistic_fragments[residue_type][resid]:
if not atomistic_fragments[residue_type][resid][atom][
'atom'].startswith('M'):
index_conversion[count] = len(coord)
coord.append(atomistic_fragments[residue_type][resid][atom]
['coord'])
sol[count] = atomistic_fragments[residue_type][resid][atom]
count += 1
coord = at_mod.check_atom_overlap(coord)
atom_counter = 0
for at_val, atom in enumerate(sol):
if sol[atom]['frag_mass'] > 1:
system['SOL'] += 1
if at_val in index_conversion:
x, y, z = gen.trunc_coord(coord[index_conversion[at_val]])
else:
x, y, z = gen.trunc_coord([
sol[atom]['coord'][0], sol[atom]['coord'][1],
sol[atom]['coord'][2]
])
if atom_counter >= 99_999:
atom_counter = 1
else:
atom_counter += 1
pdb_sol.write(g_var.pdbline % (
(atom_counter, sol[atom]['atom'], sol[atom]['res_type'], ' ',
1, x, y, z, 0.00, 0.00)) + '\n')
return system
def write_user_chains_to_pdb(atomistic_user_supplied, chain):
if not os.path.exists(g_var.working_dir+'PROTEIN/PROTEIN_aligned_'+str(chain)+'.pdb'):
pdb_output = gen.create_pdb(g_var.working_dir+'PROTEIN/PROTEIN_aligned_'+str(chain)+'.pdb')
final_atom={}
at_id=0
coord=[]
for resid in atomistic_user_supplied:
for atom in atomistic_user_supplied[resid]:
coord.append(atomistic_user_supplied[resid][atom]['coord'])
short_line=atomistic_user_supplied[resid][atom]
final_atom[at_id]={'atom':short_line['atom'], 'res_type':short_line['res_type'], 'chain':chain, 'residue':resid,\
'x':short_line['coord'][0],'y':short_line['coord'][1],'z':short_line['coord'][2]}
at_id+=1
merge_coords=at_mod.check_atom_overlap(coord)
for at_id, coord in enumerate(merge_coords):
x, y, z = gen.trunc_coord(coord)
pdb_output.write(g_var.pdbline%((at_id+1,final_atom[at_id]['atom'],final_atom[at_id]['res_type'],'A',final_atom[at_id]['residue'],
x,y,z,1,0))+'\n')