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correct_names, new_pqr_line, new_gro_line, pdb2gro)
""" chains_length, chains_res """ else: raise Exception('Input file must be either a pdb or a gro.')
chain, resnumb, x, y, z) = read_pdb_line(line) aname = aname[1:] + aname[0] resname, resnumb, x / 10.0, y / 10, z / 10) box[1] / 10.0, box[2] / 10.0)
resnumb not in done and \ str(resnumb) in sites[chain]:
termini, userff, usernames, inputpqr, outputpqr, sites): """ """
# CTR O1/O2 will be deleted and a O/OXT will be added '--usernames={4} --drop-water -v'.format(pdb2pqr_path, inputpdbfile, inputpqr, userff, usernames))
z, charge, radius) = read_pqr_line(line)
resname, aname, termini, sites_numbs)
resnumb, x, y, z, charge, radius)
# TODO: .sites files should not exist # adapt addHtaut to work without these
'cleaned_tau.pqr'.format(config.script_dir, sites_addHtaut))
chain, resnumb, x, y, z) = read_pdb_line(line) else:
# Read the grofile with only the protein resnumb, x, y, z) else:
# Read the original pdb with the membrane chain, resnumb, x, y, z) = read_pdb_line(line) resnumb, x, y, z)
aname, resname, to_include = convert_FF_atomnames(aname, resname) if to_include: atom_number += 1 x, y, z = x/10, y/10, z/10 new_file_body += new_gro_line(atom_number, aname, resname, resnumb, x, y, z)
popc_resname = config.lipids['POPC'] chol_resname = config.lipids['cholesterol']
lookup = [((' N ', popc_resname), ('NTM', 'CHL')), ((' C12', popc_resname), ('CB ', 'CHL')), ((' C13', popc_resname), ('CN1', 'CHL')), ((' C14', popc_resname), ('CN2', 'CHL')), ((' C15', popc_resname), ('CN3', 'CHL')), ((' C11', popc_resname), ('CA ', 'PJ2')), ((' P ', popc_resname), ('P ', 'PJ2')), ((' O13', popc_resname), ('OG ', 'PJ2')), ((' O14', popc_resname), ('OB ', 'PJ2')), ((' O12', popc_resname), ('OA ', 'PJ2')), ((' O11', popc_resname), ('OD ', 'PJ2')), ((' C1 ', popc_resname), ('CD ', 'POX')), ((' C2 ', popc_resname), ('CE ', 'POX')), ((' O21', popc_resname), ('OE ', 'POX')), ((' C21', popc_resname), ('C1A', 'POX')), ((' O22', popc_resname), ('O1A', 'POX')), ((' C22', popc_resname), ('C1B', 'POX')), ((' C3 ', popc_resname), ('CZ ', 'POX')), ((' O31', popc_resname), ('OZ ', 'POX')), ((' C31', popc_resname), ('C2A', 'POX')), ((' O32', popc_resname), ('O2A', 'POX')), ((' C32', popc_resname), ('C2B', 'POX')), ((' C23', popc_resname), ('C1C', 'POX')), ((' C24', popc_resname), ('C1D', 'POX')), ((' C25', popc_resname), ('C1E', 'POX')), ((' C26', popc_resname), ('C1F', 'POX')), ((' C27', popc_resname), ('C1G', 'POX')), ((' C28', popc_resname), ('C1H', 'POX')), ((' C29', popc_resname), ('C1I', 'POX')), (('0C21', popc_resname), ('C1J', 'POX')), (('1C21', popc_resname), ('C1K', 'POX')), (('2C21', popc_resname), ('C1L', 'POX')), (('3C21', popc_resname), ('C1M', 'POX')), (('4C21', popc_resname), ('C1N', 'POX')), (('5C21', popc_resname), ('C1O', 'POX')), (('6C21', popc_resname), ('C1P', 'POX')), (('7C21', popc_resname), ('C1Q', 'POX')), (('8C21', popc_resname), ('C1R', 'POX')), ((' C33', popc_resname), ('C2C', 'POX')), ((' C34', popc_resname), ('C2D', 'POX')), ((' C35', popc_resname), ('C2E', 'POX')), ((' C36', popc_resname), ('C2F', 'POX')), ((' C37', popc_resname), ('C2G', 'POX')), ((' C38', popc_resname), ('C2H', 'POX')), ((' C39', popc_resname), ('C2I', 'POX')), (('0C31', popc_resname), ('C2J', 'POX')), (('1C31', popc_resname), ('C2K', 'POX')), (('2C31', popc_resname), ('C2L', 'POX')), (('3C31', popc_resname), ('C2M', 'POX')), (('4C31', popc_resname), ('C2N', 'POX')), (('5C31', popc_resname), ('C2O', 'POX')), (('6C31', popc_resname), ('C2P', 'POX')), ((" H3", chol_resname), (" H3", 'CHO')), ((" C3", chol_resname), (" C3", 'CHO')), ((" C2", chol_resname), (" C2", 'CHO')), ((" C1", chol_resname), (" C1", 'CHO')), (("C10", chol_resname), ("C10", 'CHO')), (("C19", chol_resname), ("C19", 'CHO')), ((" C9", chol_resname), (" C9", 'CHO')), (("C11", chol_resname), ("C11", 'CHO')), (("C12", chol_resname), ("C12", 'CHO')), (("C13", chol_resname), ("C13", 'CHO')), (("C18", chol_resname), ("C18", 'CHO')), (("C17", chol_resname), ("C17", 'CHO')), (("C20", chol_resname), ("C20", 'CHO')), (("C22", chol_resname), ("C22", 'CHO')), (("C23", chol_resname), ("C23", 'CHO')), (("C24", chol_resname), ("C24", 'CHO')), (("C25", chol_resname), ("C25", 'CHO')), (("C27", chol_resname), ("C27", 'CHO')), (("C26", chol_resname), ("C26", 'CHO')), (("C21", chol_resname), ("C21", 'CHO')), (("C16", chol_resname), ("C16", 'CHO')), (("C15", chol_resname), ("C15", 'CHO')), (("C14", chol_resname), ("C14", 'CHO')), ((" C8", chol_resname), (" C8", 'CHO')), ((" C7", chol_resname), (" C7", 'CHO')), ((" C6", chol_resname), (" C6", 'CHO')), ((" H6", chol_resname), (" H6", 'CHO')), ((" C5", chol_resname), (" C5", 'CHO')), ((" C4", chol_resname), (" C4", 'CHO')), ((" O3", chol_resname), (" O3", 'CHO')), (("H3'", chol_resname), ("H3'", 'CHO'))]
for swap in lookup: old_aname = swap[0][0].strip() old_resname = swap[0][1] new_aname = swap[1][0].strip() new_resname = swap[1][1] if old_aname == aname and \ old_resname == resname: aname = new_aname resname = new_resname return aname, resname, True
return aname, resname, False |