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 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 filter_input(pdb_lines_raw, CG=True):
pdb_lines_atoms = [gen.pdbatom(j) for j in pdb_lines_raw if j.startswith('ATOM ')]
if len(pdb_lines_atoms) == 0:
sys.exit('input coarsegrain structure seems to contain no beads')
if CG:
box_vec = [j for j in pdb_lines_raw if j.startswith('CRYST')]
if len(box_vec) == 0:
sys.exit('The input file is missing the Box vectors')
return pdb_lines_atoms, box_vec
return pdb_lines_atoms
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
def write_posres(chain):
#### if not posres file exist create one
if not os.path.exists(g_var.working_dir+'PROTEIN/PROTEIN_'+str(chain)+'_steered_posre.itp'):
posres_output = open(g_var.working_dir+'PROTEIN/PROTEIN_'+str(chain)+'_steered_posre.itp', 'w')
posres_output.write('[ position_restraints ]\n; atom type fx fy fz\n')
#### read in each chain from after pdb2gmx
with open(g_var.working_dir+'PROTEIN/PROTEIN_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'] in f_loc.backbone[line_sep['residue_name']]['restraint']:
posres_output.write(str(at_counter)+' 1 1000 1000 1000\n')
def read_in_merged_pdbs(merge, merge_coords, location):
if os.path.exists(location):
#### opens pdb files and writes straight to merged_cg2at pdb
with open(location, 'r') as pdb_input:
for line in pdb_input.readlines():
if line.startswith('ATOM'):
line_sep = gen.pdbatom(line)
merge.append(line_sep)
merge_coords.append(
[line_sep['x'], line_sep['y'], line_sep['z']])
return merge, merge_coords
else:
sys.exit('cannot find minimised residue: \n' + g_var.working_dir +
residue_type + '/' + residue_type + input_type +
'_merged.pdb')
def read_in_protein_pdbs(no_chains, file, end):
#### reads in each chain into merge list
merge, merged_coords = [],[]
for chain in range(0,no_chains):
merge_temp = []
if os.path.exists(file+'_'+str(chain)+end):
with open(file+'_'+str(chain)+end, '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 protein chain: '+str(chain))
merge, merge_coords = at_mod.fix_chirality(merge,merge_temp,merged_coords)
merged_coords = at_mod.check_atom_overlap(merge_coords)
merged=[]
for line_val, line in enumerate(merge):
merged.append(g_var.pdbline%((int(line['atom_number']), line['atom_name'], line['residue_name'],' ',line['residue_id'],\
merged_coords[line_val][0],merged_coords[line_val][1],merged_coords[line_val][2],1,0))+'\n')
return merged
def read_initial_cg_pdb():
#### initialisation of dictionaries etc
cg_residues = {
} ## dictionary of CG beads eg cg_residues[residue type(POPE)][resid(1)][bead name(BB)][residue_name(PO4)/coordinates(coord)]
residue_list = {
} ## a dictionary of bead in each residue eg residue_list[bead name(BB)][residue_name(PO4)/coordinates(coord)]
count = 0 ### residue counter initialisation
with open(g_var.input_directory + 'conversion_input.pdb',
'r') as pdb_input:
for line in pdb_input.readlines():
#### separates lines
if line.startswith('ATOM'):
line_sep = gen.pdbatom(line)
line_sep['atom_name'], line_sep['residue_name'] = swap(
line_sep['atom_name'], line_sep['residue_name'],
line_sep['residue_id'])
if line_sep['atom_name'].upper(
) != 'SKIP' or line_sep['residue_name'].upper() != 'SKIP':
#### set up resnames in dictionaries
cg_residues = add_residue_to_dictionary(
cg_residues, line_sep)
#### sets up previous resid id
if 'residue_prev' not in locals():
residue_prev = line_sep['residue_id']
#### if resid the same as previous line
if residue_prev == line_sep[
'residue_id']: ### if resid is the same as the previous line, it adds resname and coordinates to the atom name key in residue_list
residue_list[line_sep['atom_name']] = {
'residue_name':
line_sep['residue_name'],
'coord':
np.array(
[line_sep['x'], line_sep['y'], line_sep['z']])
}
line_sep_prev = line_sep.copy()
#### if resids are different then the residue list is added to cg_residues
else:
if line_sep_prev[
'residue_name'] not in f_loc.p_residues:
cg_residues[line_sep_prev['residue_name']][count] = {
} ### then create sub dictionary cg_residues[resname][count]
cg_residues[line_sep_prev['residue_name']][
count] = residue_list ### adds residue list to dictionary key cg_residues[resname][count]
if line_sep_prev['residue_name'] == 'ION':
cg_residues['SOL'][count] = {}
sol_res_list = {}
sol_res_list[f_loc.water] = residue_list[
line_sep_prev['atom_name']].copy()
sol_res_list[
f_loc.water]['residue_name'] = 'SOL'
cg_residues['SOL'][count] = sol_res_list
else:
for bead in residue_list:
if bead.startswith('B'):
residue_list['BB'] = residue_list.pop(bead)
cg_residues['PROTEIN'][count] = {
} ### then create sub dictionary cg_residues['PROTEIN'][count]
cg_residues['PROTEIN'][
count] = residue_list ### adds residue list to dictionary key cg_residues['PROTEIN'][count]
#### updates dictionaries and counters
residue_list = {} ### resets residue list
count += 1 ### moves counter along to next residue
residue_list[line_sep['atom_name']] = {
'residue_name':
line_sep['residue_name'],
'coord':
np.array(
[line_sep['x'], line_sep['y'], line_sep['z']])
} ### it adds resname and coordinates to the atom name key in residue_list
residue_prev = line_sep[
'residue_id'] ### updates residue_prev with new resid
line_sep_prev = line_sep.copy()
#### finds box vectors
if line.startswith('CRYST'): ### collects box vectors from pdb
box_vec = line
#### adds final residue to cg_residues in the same manner as above
if line_sep['residue_name'] in f_loc.p_residues:
if count not in cg_residues['PROTEIN']:
cg_residues['PROTEIN'][count] = {}
cg_residues['PROTEIN'][count] = residue_list
else:
if count not in cg_residues[line_sep['residue_name']]:
cg_residues[line_sep['residue_name']][count] = {}
cg_residues[line_sep['residue_name']][count] = residue_list
if line_sep['residue_name'] == 'ION':
cg_residues['SOL'][count] = {}
sol_res_list = {}
sol_res_list[f_loc.water] = residue_list[
line_sep['atom_name']].copy()
sol_res_list[f_loc.water]['residue_name'] = 'SOL'
cg_residues['SOL'][count] = sol_res_list
#### checks if box vectors exist
if 'box_vec' not in locals(
): ### stops script if it cannot find box vectors
sys.exit('missing box vectors')
return cg_residues, box_vec
def read_initial_at_pdb():
at_residues = {
} ## dictionary of CG beads eg cg_residues[residue type(POPE)][resid(1)][bead name(BB)][residue_name(PO4)/coordinates(coord)]
residue_list = {
} ## a dictionary of bead in each residue eg residue_list[bead name(BB)][residue_name(PO4)/coordinates(coord)]
count = 0 ### residue counter initialisation
with open(g_var.input_directory + 'conversion_input.pdb',
'r') as pdb_input:
for line in pdb_input.readlines():
if line.startswith('ATOM'):
line_sep = gen.pdbatom(line)
line_sep['atom_name'], line_sep['residue_name'] = swap(
line_sep['atom_name'], line_sep['residue_name'],
line_sep['residue_id'])
if line_sep['atom_name'].upper(
) != 'SKIP' or line_sep['residue_name'].upper() != 'SKIP':
if line_sep['residue_name'] in f_loc.p_residues:
if 'PROTEIN' not in at_residues: ## if protein does not exist add to dict
at_residues['PROTEIN'] = {}
else:
if line_sep['residue_name'] not in at_residues:
at_residues[line_sep['residue_name']] = {}
if 'residue_prev' not in locals():
residue_prev = line_sep['residue_id']
#### if resid the same as previous line
if residue_prev == line_sep[
'residue_id']: ### if resid is the same as the previous line, it adds resname and coordinates to the atom name key in residue_list
residue_list[line_sep['atom_name']] = {
'residue_name':
line_sep['residue_name'],
'coord':
np.array(
[line_sep['x'], line_sep['y'], line_sep['z']])
}
line_sep_prev = line_sep.copy()
else:
if line_sep_prev[
'residue_name'] not in f_loc.p_residues:
at_residues[line_sep_prev['residue_name']][count] = {
} ### then create sub dictionary cg_residues[resname][count]
at_residues[line_sep_prev['residue_name']][
count] = residue_list
else:
at_residues['PROTEIN'][count] = {
} ### then create sub dictionary cg_residues['PROTEIN'][count]
at_residues['PROTEIN'][
count] = residue_list ### adds residue list to dictionary key cg_residues['PROTEIN'][count]
#### updates dictionaries and counters
residue_list = {} ### resets residue list
count += 1 ### moves counter along to next residue
residue_list[line_sep['atom_name']] = {
'residue_name':
line_sep['residue_name'],
'coord':
np.array(
[line_sep['x'], line_sep['y'], line_sep['z']])
} ### it adds resname and coordinates to the atom name key in residue_list
residue_prev = line_sep[
'residue_id'] ### updates residue_prev with new resid
line_sep_prev = line_sep.copy()
#### finds box vectors
if line.startswith('CRYST'): ### collects box vectors from pdb
box_vec = line
#### adds final residue to cg_residues in the same manner as above
if line_sep['residue_name'] in f_loc.p_residues:
if count not in at_residues['PROTEIN']:
at_residues['PROTEIN'][count] = {}
at_residues['PROTEIN'][count] = residue_list
else:
if count not in at_residues[line_sep['residue_name']]:
at_residues[line_sep['residue_name']][count] = {}
at_residues[line_sep['residue_name']][count] = residue_list
if 'box_vec' not in locals(
): ### stops script if it cannot find box vectors
sys.exit('missing box vectors')
return at_residues, box_vec
def read_in_atomistic(protein, cg_chain_count, sequence, check_alignment):
#### 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={}
chain_count=0
#### read in pdb
ter_residues=[]
with open(protein, 'r') as pdb_input:
atomistic_protein_input[chain_count]={}
for line_nr, line in enumerate(pdb_input.readlines()):
#### separate line
run=False ## turns to true is line is a bead/atom
if line.startswith('ATOM'):
line_sep = gen.pdbatom(line)
# print(line_sep['atom_name'])
if line_sep['residue_name'] in f_loc.mod_residues:
run=True
elif str.isdigit(line_sep['atom_name'][0]) and line_sep['atom_name'][1] != 'H':
run=True
elif not str.isdigit(line_sep['atom_name'][0]) and not line_sep['atom_name'].startswith('H'):
run=True
#### if line is correct
if run:
if line_sep['residue_name'] in f_loc.p_residues or line_sep['residue_name'] in f_loc.mod_residues:
if not line_sep['atom_name'].startswith('H') or line_sep['residue_name'] in f_loc.mod_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 line_sep['atom_name'] == f_loc.backbone[line_sep['residue_name']]['C_ter']:
C_ter=[line_sep['x'],line_sep['y'],line_sep['z']]
C_resid=line_sep['residue_id']
C=True
try:
#### tries to make a N_terminal connecting atom variable
if line_sep['atom_name'] == f_loc.backbone[line_sep['residue_name']]['N_ter']:
N_resid=line_sep['residue_id']
N_ter=[line_sep['x'],line_sep['y'],line_sep['z']]
N=True
#### measures distance between N and C atoms. if the bond is over 3 A it counts as a new protein
dist=gen.calculate_distance(N_ter, C_ter)
if N and C and C_resid != N_resid and dist > 3.5:# and aas[line_sep['residue_name']] != sequence[chain_count][line_sep['residue_id']]:
N_ter, C_ter=False, False
ter_residues.append(line_sep['residue_id'])
chain_count+=1
atomistic_protein_input[chain_count]={} ### new chain key
except:
pass
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 f_loc.backbone[line_sep['residue_name']]['atoms']:
for atom in line_sep['atom_name']:
if atom in g_var.mass:
atomistic_protein_input[chain_count][line_sep['residue_id']][line_sep['atom_number']]['frag_mass']=g_var.mass[atom]
else:
if check_alignment:
sys.exit('The residue '+line_sep['residue_name']+' does not exist in the fragment database')
if check_alignment:
seq_user = check_sequence(atomistic_protein_input, chain_count+1)
atomistic_protein_input = align_chains(atomistic_protein_input, seq_user, sequence)
#### check if number of monomers is the same
elif chain_count+1 != cg_chain_count:
sys.exit('number of chains in atomistic protein input ('+str(chain_count+1)+') does not match CG representation ('+str(cg_chain_count)+')')
return atomistic_protein_input
