def write_posres(chain):
#### if not posres file exist create one
very_low_posres = posres_header(g_var.working_dir+'PROTEIN/PROTEIN_'+str(chain)+'_very_low_posre.itp')
low_posres = posres_header(g_var.working_dir+'PROTEIN/PROTEIN_'+str(chain)+'_low_posre.itp')
mid_posres = posres_header(g_var.working_dir+'PROTEIN/PROTEIN_'+str(chain)+'_mid_posre.itp')
high_posres = posres_header(g_var.working_dir+'PROTEIN/PROTEIN_'+str(chain)+'_high_posre.itp')
very_high_posres = posres_header(g_var.working_dir+'PROTEIN/PROTEIN_'+str(chain)+'_very_high_posre.itp')
ultra_posres = posres_header(g_var.working_dir+'PROTEIN/PROTEIN_'+str(chain)+'_ultra_posre.itp')
ca_posres = posres_header(g_var.working_dir+'PROTEIN/PROTEIN_'+str(chain)+'_ca_posre.itp')
#### read in each chain from after pdb2gmx
with open(g_var.working_dir+'PROTEIN/PROTEIN_de_novo_'+str(chain)+'_gmx.pdb', 'r') as pdb_input:
at_counter=0
for line in pdb_input.readlines():
if line.startswith('ATOM'):
line_sep = gen.pdbatom(line)
at_counter+=1
#### if atom is in the restraint list for that residue add to position restraint file
if line_sep['atom_name'] == 'CA':
ca_posres.write(str(at_counter)+' 1 1000 1000 1000\n')
if not gen.is_hydrogen(line_sep['atom_name']):
very_low_posres.write(str(at_counter)+' 1 200 200 200\n')
low_posres.write(str(at_counter)+' 1 750 750 750\n')
mid_posres.write(str(at_counter)+' 1 1500 1500 1500\n')
high_posres.write(str(at_counter)+' 1 3000 3000 3000\n')
very_high_posres.write(str(at_counter)+' 1 6000 6000 6000\n')
ultra_posres.write(str(at_counter)+' 1 10000 10000 10000\n')
def read_in_atomistic(protein):
#### reset location and check if pdb exists
os.chdir(g_var.start_dir)
if not os.path.exists(protein):
sys.exit('cannot find atomistic protein : '+protein)
#### read in atomistic fragments into dictionary residue_list[0]=x,y,z,atom_name
atomistic_protein_input={}
if g_var.input_directory in protein:
chain_count=g_var.chain_count
else:
chain_count = 0
#### read in pdb
ter_residues=[]
r_b_vec, r_b_inv = real_box_vectors(g_var.box_vec)
with open(protein, 'r') as pdb_input:
pdb_lines_atoms = filter_input(pdb_input.readlines(), False)
atomistic_protein_input[chain_count]={}
for line_nr, line_sep in enumerate(pdb_lines_atoms):
if line_sep['residue_name'] in g_var.alt_res_name:
line_sep['residue_name'] = g_var.alt_res_name[line_sep['residue_name']]
if not gen.is_hydrogen(line_sep['atom_name']) or line_sep['residue_name'] in g_var.mod_residues:
if line_sep['residue_name'] in g_var.p_residues:
#### sorts out wrong atoms in terminal residues
if line_sep['atom_name'] in ['OT', 'O1', 'O2']:
line_sep['atom_name']='O'
#### makes C_terminal connecting atom variable
if 'prev_atom_coord' in locals():
line_sep['x'],line_sep['y'],line_sep['z'] = brute_mic(prev_atom_coord, [line_sep['x'],line_sep['y'],line_sep['z']], r_b_vec)
if line_sep['atom_name'] in g_var.res_top[line_sep['residue_name']]['CONNECT']['atoms']:
if g_var.res_top[line_sep['residue_name']]['CONNECT']['atoms'][line_sep['atom_name']] > 0:
if 'C_ter' in locals() and len(g_var.res_top[line_sep['residue_name']]['CONNECT']['atoms']) <=1:
ter_residues.append(line_sep['residue_id'])
chain_count+=1
atomistic_protein_input[chain_count]={}
C_ter=[line_sep['x'],line_sep['y'],line_sep['z']]
C_resid=line_sep['residue_id']
elif 'C_ter' in locals():
N_resid=line_sep['residue_id']
N_ter=[line_sep['x'],line_sep['y'],line_sep['z']]
dist=gen.calculate_distance(N_ter, C_ter)
if C_resid != N_resid and dist > 3.5:
del N_ter, C_ter
ter_residues.append(line_sep['residue_id'])
chain_count+=1
atomistic_protein_input[chain_count]={} ### new chain key
prev_atom_coord = [line_sep['x'],line_sep['y'],line_sep['z']]
if line_sep['residue_id'] not in atomistic_protein_input[chain_count]: ## if protein does not exist add to dict
atomistic_protein_input[chain_count][line_sep['residue_id']]={}
#### adds atom to dictionary, every atom is given a initial mass of zero
atomistic_protein_input[chain_count][line_sep['residue_id']][line_sep['atom_number']]={'coord':np.array([line_sep['x'],line_sep['y'],line_sep['z']]),'atom':line_sep['atom_name'], 'res_type':line_sep['residue_name'],'frag_mass':0, 'resid':line_sep['residue_id']}
#### if atom is in the backbone list then its mass is updated to the correct one
if line_sep['atom_name'] in g_var.res_top[line_sep['residue_name']]['ATOMS']:
if line_sep['atom_name'] in line_sep['atom_name'] in g_var.res_top[line_sep['residue_name']]['atom_masses']:
atomistic_protein_input[chain_count][line_sep['residue_id']][line_sep['atom_number']]['frag_mass']=g_var.res_top[line_sep['residue_name']]['atom_masses'][line_sep['atom_name']]
return atomistic_protein_input, chain_count+1
def get_atomistic(frag_location, resname=False):
if not resname:
resname = frag_location.split('/')[-1][:-4]
#### read in atomistic fragments into dictionary
residue = {
} ## a dictionary of bead in each residue eg residue[group][bead][atom number(1)][residue_name(ASP)/coordinates(coord)/atom name(C)/connectivity(2)/atom_mass(12)]
fragment_mass = {}
with open(frag_location, 'r') as pdb_input:
for line_nr, line in enumerate(pdb_input.readlines()):
if line.startswith('['):
residue, group, bead = split_fragment_names(
line, residue, resname)
fragment_mass[bead] = []
if line.startswith('ATOM'):
line_sep = gen.pdbatom(line) ## splits up pdb line
residue[group][bead][line_sep['atom_number']] = {
'coord':
np.array([
line_sep['x'] * g_var.sf, line_sep['y'] * g_var.sf,
line_sep['z'] * g_var.sf
]),
'atom':
line_sep['atom_name'],
'resid':
1,
'resid_ori':
line_sep['residue_id'],
'res_type':
line_sep['residue_name'],
'frag_mass':
1
}
#### updates fragment mass
if not gen.is_hydrogen(line_sep['atom_name']):
if line_sep['atom_name'] in g_var.res_top[resname][
'atom_masses']:
residue[group][bead][line_sep['atom_number']][
'frag_mass'] = g_var.res_top[resname][
'atom_masses'][line_sep[
'atom_name']] ### updates atom masses with crude approximations
fragment_mass[bead].append([
line_sep['x'] * g_var.sf, line_sep['y'] * g_var.sf,
line_sep['z'] * g_var.sf, g_var.res_top[resname]
['atom_masses'][line_sep['atom_name']]
])
else:
fragment_mass[bead].append([
line_sep['x'] * g_var.sf, line_sep['y'] * g_var.sf,
line_sep['z'] * g_var.sf, 1
])
return residue, fragment_mass