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 at_np_solvent(cg_residue_type,cg_residues):
atomistic_fragments={} #### residue dictionary
#### run through every residue in a particular residue type
residue_type={}
residue_type_mass={}
atomistic_fragments_list = []
for cg_resid, cg_residue in enumerate(cg_residues):
atomistic_fragments[cg_resid]={}
frag_location=gen.fragment_location(cg_residue_type) ### get fragment location from database
residue_type[cg_residue_type], residue_type_mass[cg_residue_type] = at_mod.get_atomistic(frag_location, cg_residue_type)
for group in residue_type[cg_residue_type]:
center, at_frag_centers, cg_frag_centers, group_fit = at_mod.rigid_fit(residue_type[cg_residue_type][group],
residue_type_mass[cg_residue_type],
cg_residue, cg_residues[cg_residue])
at_connect, cg_connect = at_mod.connectivity(cg_residues[cg_residue], at_frag_centers, cg_frag_centers, group_fit, group)
xyz_rot_apply=at_mod.get_rotation(cg_connect, at_connect, center, cg_residue_type, group, cg_resid)
atomistic_fragments = at_mod.apply_rotations(atomistic_fragments,cg_resid, group_fit, center, xyz_rot_apply)
if cg_residue_type in g_var.np_residues:
atomistic_fragments[cg_resid] = at_mod.check_hydrogens(atomistic_fragments[cg_resid])
atomistic_fragments_list, sol_p_bead = sort_np_dictionary(atomistic_fragments[cg_resid], atomistic_fragments_list)
if cg_residue_type in g_var.sol_residues:
return atomistic_fragments_list, sol_p_bead*len(cg_residues)
else:
return atomistic_fragments_list, len(atomistic_fragments)
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