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 build_multi_residue_atomistic_system(cg_residues, sys_type):
#### initisation of counters
chain_count=0
coord_atomistic={}
g_var.seq_cg={sys_type:{}}
g_var.ter_res={sys_type:{}}
gen.mkdir_directory(g_var.working_dir+sys_type) ### make and change to protein directory
#### for each residue in protein
residue_type={}
residue_type_mass={}
new_chain = True
for cg_residue_id, residue_number in enumerate(cg_residues[sys_type]):
if np.round((cg_residue_id/len(cg_residues[sys_type]))*100,2).is_integer():
print('Converting de_novo '+sys_type+': ',np.round((cg_residue_id/len(cg_residues[sys_type]))*100,2),'%', end='\r')
resname = cg_residues[sys_type][residue_number][next(iter(cg_residues[sys_type][residue_number]))]['residue_name']
if new_chain:
if chain_count not in coord_atomistic:
if sys_type == 'PROTEIN':
g_var.backbone_coords[chain_count]=[]
coord_atomistic[chain_count]={}
g_var.seq_cg[sys_type][chain_count]=[]
g_var.ter_res[sys_type][chain_count]=[resname, False]
new_chain = False
coord_atomistic[chain_count][residue_number]={}
frag_location=gen.fragment_location(resname) ### get fragment location from database
residue_type[resname], residue_type_mass[resname] = at_mod.get_atomistic(frag_location)
g_var.seq_cg[sys_type] = add_to_sequence(g_var.seq_cg[sys_type], resname, chain_count)
new_chain = False
for group in residue_type[resname]:
for key in list(residue_type[resname][group].keys()):
if key not in cg_residues[sys_type][residue_number]:
del residue_type[resname][group][key]
if len(residue_type[resname][group]) > 0:
center, at_frag_centers, cg_frag_centers, group_fit = at_mod.rigid_fit(residue_type[resname][group], residue_type_mass[resname], residue_number, cg_residues[sys_type][residue_number])
at_connect, cg_connect = at_mod.connectivity(cg_residues[sys_type][residue_number], at_frag_centers, cg_frag_centers, group_fit, group)
for group_bead in group_fit:
if group_bead in g_var.res_top[resname]['CONNECT']:
at_connect, cg_connect, new_chain = at_mod.BB_connectivity(at_connect,cg_connect, cg_residues[sys_type], group_fit[group_bead], residue_number, group_bead)
if sys_type == 'PROTEIN':
g_var.backbone_coords[chain_count].append(np.append(cg_residues[sys_type][residue_number][group_bead]['coord'], 1))
xyz_rot_apply = at_mod.get_rotation(cg_connect, at_connect, center, resname, group, residue_number)
coord_atomistic[chain_count] = at_mod.apply_rotations(coord_atomistic[chain_count],residue_number, group_fit, center, xyz_rot_apply)
if new_chain:
g_var.ter_res[sys_type][chain_count][1] = resname
chain_count+=1
print('Completed initial conversion of '+sys_type+'\n')
g_var.system[sys_type]=chain_count
if sys_type == 'PROTEIN':
for chain in range(chain_count):
g_var.skip_disul[chain]=False
return coord_atomistic