def SoupFromNamdPsf(psf, in_coor_pdb, in_vel_pdb):
soup = Soup(in_coor_pdb)
load_masses_to_soup(psf, soup)
vel_soup = Soup(in_vel_pdb)
for atom, vel_atom in zip(soup.atoms(), vel_soup.atoms()):
v = vel_atom.pos
atom.vel.set(v.x, v.y, v.z)
return soup
def convert_pdb_to_namd_pdb(standard_pdb, namd_pdb):
soup = Soup(standard_pdb)
for res in soup.residues():
if res.type == "ILE" and res.has_atom('CD1'):
res.atom('CD1').type = 'CD'
if res.has_atom('OXT'):
res.atom('OXT').type = 'OT2'
if res.has_atom('O'):
res.atom('O').type = 'OT1'
for atom in res.atoms():
if atom.type[0].isdigit() and atom.type[1] == "H":
atom.type = atom.type[1:] + atom.type[0]
soup.write_pdb(namd_pdb)
def SoupFromPsf(psf):
"read a psf and parse into protein chains."
f = open(psf, "r")
line = f.readline()
while 'NATOM' not in line:
line = f.readline()
n_atom = int(line[0:8])
lines = [f.readline() for i in range(0, n_atom)]
f.close
# work out the chains in the psf file
chain_info_list = []
chain_char = ""
res_num = -1
chain_type = ""
for i, line in enumerate(lines):
word_list = line.split()
new_chain_type = word_list[1]
new_res_num = int(word_list[2])
if chain_type == "":
chain_type = new_chain_type
res_num = new_res_num
chain_info_list.append([chain_type, i, i+1])
elif chain_type is "WATERS" and new_chain_type is "WATERS" and \
res_num <> new_res_num:
res_num = new_res_num
chain_info_list.append([chain_type, i, i+1])
elif chain_type <> new_chain_type:
chain_type = new_chain_type
chain_info_list.append([chain_type, i, i+1])
else:
chain_info_list[-1][2] = i+1
# make a list of chains using the objects in protein
chains = []
for name, first, last in chain_info_list:
if "WATERS" in name:
chain = polymer.Polymer()
else:
chain = protein.Protein()
curr_res_num = -1
for i, line in enumerate(lines[first:last]):
word_list = line.split()
atom = molecule.Atom()
atom.res_num = int(word_list[2])
atom.res_type = word_list[3][0:3]
atom.type = word_list[4]
atom.element = atom.type[0]
atom.type = atom.type.strip(" ")
atom.num = i + first
try:
atom.mass = float(word_list[7])
except:
atom.mass = 0.0
if curr_res_num != atom.res_num:
res = polymer.Residue(atom.res_type, atom.chain_id, atom.res_num, '')
chain.append_residue_no_renum(res)
curr_res_num = atom.res_num
chain.insert_atom(chain.n_residue()-1, atom)
chains.append(chain)
soup = Soup()
for chain in chains:
soup.append_chain(chain)
# load masses in [a.m.u.]
masses = [float(line[47:60]) for line in open(psf, "r") if "CHAIN" in line]
for a, m in zip(soup.atoms(), masses):
a.mass = m
return soup
def make_namd_from_pdb(pdb, psf, out_pdb):
"""
Creates charmm .pdb and .psf file. Can only make NAMD
generate CHARMM topology files, not OPLS ones - that
requires XPLOR but I don't care. Still, if OPLS
topology files are provided - can still run.
"""
def is_non_water_hetatm(line):
if not line.startswith("HETATM"):
return False
if line[17:20] != 'HOH':
return True
return False
in_pdb = util.temp_fname('.pdb')
txt = open(pdb, 'r').read()
txt = pdbtext.strip_other_nmr_models(txt)
txt = pdbtext.strip_lines(txt, is_non_water_hetatm)
txt = pdbtext.strip_lines(txt, lambda l: l.startswith('ANISOU'))
txt = pdbtext.strip_lines(txt, lambda l: l.startswith('CONECT'))
txt = pdbtext.strip_lines(txt, lambda l: l.startswith('MASTER'))
txt = pdbtext.strip_alternative_atoms(txt)
txt = pdbtext.strip_hydrogens(txt)
txt = pdbtext.renumber_residues(txt)
f = open(in_pdb, 'w')
f.write(txt)
f.close()
name = psf.replace('.psf', '')
psfgen_in = name + ".psfgen.in"
psfgen_out = name + ".psfgen.out"
replace = { 'pdb': in_pdb,
'out_pdb': out_pdb,
'psf': psf,
'module_dir': module_dir,
'topology': 'parms/charmm22.topology'
}
template = _psfgen_template
soup = Soup(in_pdb)
chains = soup.chains()
water_names = ['WAT', "TIP", "TIP3", "HOH"]
waters = [chain for chain in chains
if chain.n_residue() > 0 and chain.residue(0).type in water_names]
chains = [chain for chain in chains if chain.n_residue() > 0 and chain.residue(0).type not in water_names]
if len(waters) > 0:
template = template.replace("# insert water", _water_psfgen_template)
water_pdb = name + ".waters.pdb"
water_soup = Soup()
for water in waters:
water_soup.insert_chain(water)
water_soup.write_pdb(water_pdb)
replace['water_pdb'] = water_pdb
chains_template = ""
for i, chain in enumerate(chains):
id = 'ch%d' % i
pdb = name + '.' + id + '.pdb'
chain_soup = Soup()
chain_soup.append_chain(chain)
chain_soup.write_pdb(pdb)
chain_replace = { 'chain_id': id, 'chain_pdb': pdb }
chain_template = _chain_psfgen_template
chains_template += util.replace_dict(chain_template, chain_replace)
template = template.replace("# insert protein", chains_template)
template = util.replace_dict(template, replace)
open(psfgen_in, "w").write(template)
os.system("psfgen %s > %s" % (psfgen_in, psfgen_out))
os.remove(in_pdb)