def split_fragment_names(line, residue, resname):
bead = gen.strip_header(line)
group = g_var.res_top[resname]['GROUPS'][bead]
if group not in residue:
residue[group] = {}
if bead not in residue[group]:
residue[group][bead]={}
return residue, group, bead
def read_itp(filename_itp, footer=False):
posre = {}
molecule = {}
mol_type = False
atoms = False
if os.path.exists(filename_itp):
with open(filename_itp, 'r') as itp_input:
for line in itp_input.readlines():
if not (line.isspace()
or len(line) == 0) and not line.startswith(';'):
line_sep = line.split()
if line.startswith('[') and gen.strip_header(
line) == 'moleculetype':
mol_type = True
elif line.startswith('[') and gen.strip_header(
line) == 'atoms':
atoms, mol_type = True, False
elif line.startswith('['):
atoms = False
mol_type = False
elif mol_type:
molecule[line_sep[0]] = []
posre[line_sep[0]] = []
mol = line_sep[0]
elif atoms:
molecule[mol].append(line_sep[4])
if len(line.split()) >= 8:
if int(float(line.split()[7])) > 1:
posre[mol].append(
' {0:5}{1:3}{2:11}{3:11}{4:11}\n'.format(
line.split()[0], 1, 50, 50, 50))
if '#ifdef NP' in line:
footer = True
return molecule, posre, footer
else:
sys.exit('Cannot find itp file: ', filename_itp)
def check_frag_file(directory, molecule):
exists = []
wrong = []
for mol, beads in molecule.items():
beads.sort()
bead_list = []
if os.path.exists(directory + mol + '/' + mol + '.pdb'):
exists.append(mol)
with open(directory + mol + '/' + mol + '.pdb', 'r') as pdb_input:
for line_nr, line in enumerate(pdb_input.readlines()):
if line.startswith('['):
bead_list.append(gen.strip_header(line))
bead_list.sort()
if bead_list == beads:
print(mol, 'Correct')
else:
l1 = mol + ' Incorrect: ' + directory + mol + '/' + mol + '.pdb'
l2 = '\nMartini ' + mol + ': ' + ', '.join(map(str, beads))
l3 = '\nCG2AT2 ' + mol + ': ' + ', '.join(map(str, bead_list))
wrong.append([l1 + l2 + l3])
for residue in wrong:
print(residue)
return exists