def non_solvent(box_vec, system, atomistic_fragments, residue_type):
#### loop through all resids of that residue type
for resid in atomistic_fragments[residue_type]:
skip = os.path.exists(g_var.working_dir + residue_type + '/' +
residue_type + '_' + str(resid) + '.pdb')
if not skip:
pdb_output = gen.create_pdb(
g_var.working_dir + residue_type + '/' + residue_type + '_' +
str(resid) + '.pdb', box_vec)
atomistic_fragments[residue_type][resid] = at_mod.check_hydrogens(
atomistic_fragments[residue_type][resid])
####### check if any atoms in residue overlap #######
coord = []
for atom in atomistic_fragments[residue_type][resid]:
coord.append(
atomistic_fragments[residue_type][resid][atom]['coord'])
coord = at_mod.check_atom_overlap(coord)
for atom_val, atom in enumerate(
atomistic_fragments[residue_type][resid]):
atomistic_fragments[residue_type][resid][atom][
'coord'] = coord[atom_val]
for at_id, atom in enumerate(
atomistic_fragments[residue_type][resid]):
#### write residue out to a pdb file
short_line = atomistic_fragments[residue_type][resid][at_id +
1]
pdb_output.write(g_var.pdbline % (
(at_id + 1, short_line['atom'], short_line['res_type'],
' ', 1, short_line['coord'][0], short_line['coord'][1],
short_line['coord'][2], 0.00, 0.00)) + '\n')
system[residue_type] = int(resid) + 1
return system, atomistic_fragments
def solvent_sol(box_vec, system, atomistic_fragments, residue_type):
#### creates solvent directory and SOL key in system dictionay otherwise it appends solvent molecules to sol pdb
skip = os.path.exists(g_var.working_dir + 'SOL' + '/SOL_0.pdb')
if not skip:
pdb_sol = gen.create_pdb(g_var.working_dir + 'SOL' + '/SOL_0.pdb',
box_vec)
for resid in atomistic_fragments[residue_type]:
####### check if any atoms in residue overlap #######
if not skip:
coord = []
for atom in atomistic_fragments[residue_type][resid]:
coord.append(
atomistic_fragments[residue_type][resid][atom]['coord'])
coord = at_mod.check_atom_overlap(coord)
for atom_val, atom in enumerate(
atomistic_fragments[residue_type][resid]):
atomistic_fragments[residue_type][resid][atom][
'coord'] = coord[atom_val]
for at_id, atom in enumerate(atomistic_fragments[residue_type][resid]):
#### separates out the water molecules from the ion in the fragment
if atomistic_fragments[residue_type][resid][at_id +
1]['frag_mass'] > 1:
system['SOL'] += 1
if not skip:
short_line = atomistic_fragments[residue_type][resid][at_id +
1]
pdb_sol.write(g_var.pdbline % (
(at_id + 1, short_line['atom'], short_line['res_type'],
' ', 1, short_line['coord'][0], short_line['coord'][1],
short_line['coord'][2], 0.00, 0.00)) + '\n')
return system, atomistic_fragments
def solvent_ion(box_vec, 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', box_vec)
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]
pdb_ion.write(g_var.pdbline % (
(at_id + 1, short_line['atom'], short_line['res_type'],
' ', 1, short_line['coord'][0], short_line['coord'][1],
short_line['coord'][2], 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, atomistic_fragments
def merge_minimised(residue_type, np_system, box_vec):
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', box_vec)
if residue_type == 'SOL':
resid_range = 1
else:
resid_range = np_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)
if residue_type != 'SOL':
merge_coords = at_mod.check_atom_overlap(merge_coords)
for line_val, line in enumerate(merge):
pdb_output.write(g_var.pdbline%((int(line['atom_number']), line['atom_name'], line['residue_name'],' ',line['residue_id'],\
merge_coords[line_val][0],merge_coords[line_val][1],merge_coords[line_val][2],1,0))+'\n')
pdb_output.write('TER\nENDMDL')
pdb_output.close()
def merge_system_pdbs(system, protein, cg_residues, box_vec):
os.chdir(g_var.working_dir + 'MERGED')
#### create merged pdb
pdb_output = gen.create_pdb(
g_var.working_dir + 'MERGED/merged_cg2at' + protein + '.pdb', box_vec)
merge = []
merge_coords = []
#### run through every residue type in cg_residues
for segment, residue_type in enumerate(cg_residues):
#### if file contains user input identifier
if residue_type != 'PROTEIN':
input_type = ''
else:
input_type = protein
merge, merge_coords = read_in_merged_pdbs(
merge, merge_coords, g_var.working_dir + residue_type + '/' +
residue_type + input_type + '_merged.pdb')
if protein in ['_at_rep_user_supplied', '_novo']:
print('checking for atom overlap in : ' + protein[1:])
merge_coords = check_atom_overlap(merge_coords)
for line_val, line in enumerate(merge):
pdb_output.write(g_var.pdbline%((int(line['atom_number']), line['atom_name'], line['residue_name'],' ',line['residue_id'],\
merge_coords[line_val][0],merge_coords[line_val][1],merge_coords[line_val][2],1,0))+'\n')
pdb_output.write('TER\nENDMDL')
pdb_output.close()
def merge_minimised(residue_type, np_system, box_vec):
os.chdir(g_var.working_dir+residue_type+'/min')
print('Merging individual residues : '+residue_type)
#### create merged pdb in min folder
pdb_output=gen.create_pdb(g_var.working_dir+residue_type+'/min/'+residue_type+'_merged.pdb', box_vec)
if residue_type =='SOL':
resid_range=1
else:
resid_range=np_system[residue_type]
merge,merge_coords=[],[]
#### run through every resid
for resid in range(resid_range):
#### check if it exists
merge_temp = []
if os.path.exists(g_var.working_dir+residue_type+'/min/'+residue_type+'_'+str(resid)+'.pdb'):
#### read in resid and write straight to merged pdb
with open(g_var.working_dir+residue_type+'/min/'+residue_type+'_'+str(resid)+'.pdb', 'r') as pdb_input:
for line in pdb_input.readlines():
if line.startswith('ATOM'):
line_sep=gen.pdbatom(line)
merge_temp.append(line_sep)
else:
sys.exit('cannot find minimised residue: \n'+ g_var.working_dir+residue_type+'/'+residue_type+'_merged.pdb')
merge, merge_coords = at_mod.fix_chirality(merge,merge_temp,merge_coords)
if residue_type !='SOL':
merge_coords = at_mod.check_atom_overlap(merge_coords)
for line_val, line in enumerate(merge):
pdb_output.write(g_var.pdbline%((int(line['atom_number']), line['atom_name'], line['residue_name'],' ',line['residue_id'],\
merge_coords[line_val][0],merge_coords[line_val][1],merge_coords[line_val][2],1,0))+'\n')
pdb_output.write('TER\nENDMDL')
pdb_output.close()
def write_to_pdb(cg_residues, box_vec, solvent_dict):
pdb_output = gen.create_pdb(g_var.final_dir + 'AT2CG_merged.pdb', box_vec)
at_count = 1
for residue_type in cg_residues:
if residue_type not in ['PROTEIN', 'SOL', 'ION']:
for resid in cg_residues[residue_type]:
for bead in cg_residues[residue_type][resid]:
coord = cg_residues[residue_type][resid][bead]
pdb_output.write(g_var.pdbline%((at_count, bead, residue_type,' ',resid,\
coord[0],coord[1],coord[2],1,0))+'\n')
at_count += 1
elif residue_type == 'SOL':
for resid, coord in enumerate(cg_residues[residue_type]):
pdb_output.write(g_var.pdbline%((at_count, 'W', residue_type,' ',resid+1,\
coord[0],coord[1],coord[2],1,0))+'\n')
at_count += 1
elif residue_type == 'ION':
for ion_type in cg_residues[residue_type]:
for resid, coord in enumerate(
cg_residues[residue_type][ion_type]):
pdb_output.write(g_var.pdbline%((at_count, ion_type, residue_type,' ',resid+1,\
coord[0],coord[1],coord[2],1,0))+'\n')
at_count += 1
else:
for resid in cg_residues[residue_type]:
for amino_acid in cg_residues[residue_type][resid]:
for bead in cg_residues[residue_type][resid][amino_acid]:
coord = cg_residues[residue_type][resid][amino_acid][
bead]
pdb_output.write(g_var.pdbline%((at_count, bead, amino_acid,' ',resid,\
coord[0],coord[1],coord[2],1,0))+'\n')
at_count += 1
def write_merged_pdb(merge, protein, box_vec):
#### creates merged pdb and writes chains to it
if not os.path.exists(g_var.working_dir+'PROTEIN/PROTEIN'+protein+'_merged.pdb'):
pdb_output=gen.create_pdb(g_var.working_dir+'PROTEIN/PROTEIN'+protein+'_merged.pdb', box_vec)
for line in merge:
pdb_output.write(line)
pdb_output.close()
def finalise_novo_atomistic(atomistic, cg_residues, box_vec):
final_at_residues={}
final_at = {}
for chain in atomistic:
at_number=0
final_at_residues[chain]={}
final_at[chain]={}
coords=[]
skip = os.path.exists(g_var.working_dir+'PROTEIN/PROTEIN_novo_'+str(chain)+'.pdb')
if not skip:
pdb_output = gen.create_pdb(g_var.working_dir+'PROTEIN/PROTEIN_novo_'+str(chain)+'.pdb', box_vec)
for res_index, residue_id in enumerate(atomistic[chain]):
if atomistic[chain][residue_id][1]['res_type'] in f_loc.mod_residues:
atomistic[chain][residue_id] = at_mod.check_hydrogens(atomistic[chain][residue_id])
if res_index < len(atomistic[chain])-2:
atomistic[chain][residue_id] = fix_carbonyl(residue_id, cg_residues, atomistic[chain][residue_id])
else:
atomistic[chain][residue_id] = atomistic[chain][residue_id]
for at_val, atom in enumerate(atomistic[chain][residue_id]):
atomistic[chain][residue_id][at_val+1]['resid'] = res_index
coords.append(atomistic[chain][residue_id][at_val+1]['coord'])
final_at[chain][at_number]=atomistic[chain][residue_id][at_val+1]
at_number+=1
final_at_residues[chain][res_index]=atomistic[chain][residue_id]
coords = at_mod.check_atom_overlap(coords)
for atom in final_at[chain]:
final_at[chain][atom]['coord']=coords[atom]
final_at_residues[chain][final_at[chain][atom]['resid']][atom]=final_at[chain][atom]
if not skip:
pdb_output.write(g_var.pdbline%((atom,final_at[chain][atom]['atom'],final_at[chain][atom]['res_type'],ascii_uppercase[chain],\
final_at[chain][atom]['resid'],final_at[chain][atom]['coord'][0],final_at[chain][atom]['coord'][1],final_at[chain][atom]['coord'][2],1,0))+'\n')
if 'pdb_output' in locals():
pdb_output.close()
return final_at_residues
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 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 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')
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 hybridise_protein_inputs(final_coordinates_atomistic, atomistic_protein_centered, cg_com, xyz_rot_apply, chain, box_vec):
pdb_output = gen.create_pdb(g_var.working_dir+'PROTEIN/PROTEIN_at_rep_user_supplied_'+str(chain)+'.pdb', box_vec)
final_atom={}
coord=[]
at_id=0
for residue in final_coordinates_atomistic:
exists=False
for initial_index in final_coordinates_atomistic[residue]:
if final_coordinates_atomistic[residue][initial_index]['res_type'] in f_loc.mod_residues:
for atom in final_coordinates_atomistic[residue]:
short_line=final_coordinates_atomistic[residue][atom]
final_atom[at_id]={'atom':short_line['atom'], 'res_type':short_line['res_type'], 'chain':ascii_uppercase[chain], 'residue':residue,\
'x':short_line['coord'][0],'y':short_line['coord'][1],'z':short_line['coord'][2]}
at_id+=1
coord.append(short_line['coord'])
elif final_coordinates_atomistic[residue][initial_index]['res_type'] not in f_loc.mod_residues:
for part_val, part in enumerate(atomistic_protein_centered):
if residue in atomistic_protein_centered[part]:
exists=True
for atom in atomistic_protein_centered[part][residue]:
if atomistic_protein_centered[part][residue][atom]['res_type'] != final_coordinates_atomistic[residue][initial_index]['res_type']:
print('de_novo' , final_coordinates_atomistic[residue][initial_index]['res_type'],'at_user', atomistic_protein_centered[part][residue][atom]['res_type'])
sys.exit('de novo and at user supplied don\'t match')
atomistic_protein_centered[part][residue][atom]['coord'] = at_mod.rotate_atom(atomistic_protein_centered[part][residue][atom]['coord'], cg_com[part_val], xyz_rot_apply[part_val])
short_line = atomistic_protein_centered[part][residue][atom]
final_atom[at_id]={'atom':short_line['atom'], 'res_type':short_line['res_type'], 'chain':ascii_uppercase[chain], 'residue':residue,\
'x':short_line['coord'][0],'y':short_line['coord'][1],'z':short_line['coord'][2]}
at_id+=1
coord.append(short_line['coord'])
if not exists:
for atom in final_coordinates_atomistic[residue]:
short_line=final_coordinates_atomistic[residue][atom]
final_atom[at_id]={'atom':short_line['atom'], 'res_type':short_line['res_type'], 'chain':ascii_uppercase[chain], 'residue':residue,\
'x':short_line['coord'][0],'y':short_line['coord'][1],'z':short_line['coord'][2]}
at_id+=1
coord.append(short_line['coord'])
break
merge_coords = at_mod.check_atom_overlap(coord)
for at_id, coord in enumerate(merge_coords):
pdb_output.write(g_var.pdbline%((at_id+1,final_atom[at_id]['atom'],final_atom[at_id]['res_type'],final_atom[at_id]['chain'],final_atom[at_id]['residue'],
coord[0],coord[1],coord[2],1,0))+'\n')
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 at_id, atom in enumerate(atomistic_fragments[residue_type]):
#### write ion coordinate out
if not skip:
x, y, z = gen.trunc_coord(
[atom['coord'][0], atom['coord'][1], atom['coord'][2]])
pdb_ion.write(g_var.pdbline %
((at_id + 1, atom['atom_name'], atom['residue_name'],
' ', 1, x, y, z, 0.00, 0.00)) + '\n')
if atom['residue_name'] not in system:
system[atom['residue_name']] = 1
else:
system[atom['residue_name']] += 1
return system
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
