def add_fake_water_atom(soup, res_type, bfactor): dummy_atom = pdbatoms.Atom() dummy_atom.pos = soup.atoms()[0].pos.copy() dummy_atom.type = "O" dummy_atom.bfactor = bfactor dummy_res = pdbatoms.Residue(res_type, '', 9999) dummy_res.insert_atom(dummy_atom) soup.append_residue(dummy_res)
def soup_from_psf(psf):
"""
Returns a Soup from a .psf file
"""
soup = pdbatoms.Soup()
curr_res_num = None
is_header = True
for line in open(psf):
if is_header:
if "NATOM" in line:
n_atom = int(line.split()[0])
is_header = False
continue
words = line.split()
atom_num = int(words[0])
chain_id = words[1]
res_num = int(words[2])
res_type = words[3]
atom_type = words[4]
charge = float(words[6])
mass = float(words[7])
if chain_id.startswith('WT') or chain_id.startswith('ION'):
is_hetatm = True
chain_id = " "
else:
is_hetatm = False
chain_id = chain_id[0]
if curr_res_num != res_num:
res = pdbatoms.Residue(res_type, chain_id, res_num)
soup.append_residue(res)
curr_res_num = res_num
atom = pdbatoms.Atom()
atom.vel = v3.vector()
atom.chain_id = chain_id
atom.is_hetatm = is_hetatm
atom.num = atom_num
atom.res_num = res_num
atom.res_type = res_type
atom.type = atom_type
atom.mass = mass
atom.charge = charge
atom.element = data.guess_element(res_type, atom_type)
soup.insert_atom(-1, atom)
if len(soup.atoms()) == n_atom:
break
convert_to_pdb_atom_names(soup)
return soup
def soup_from_top_gro(top, gro, skip_solvent=False):
"""
Returns a Soup built from GROMACS restart files.
If skip_solvent=True, will skip all solvent molecules.
"""
util.check_output(top)
util.check_output(gro)
soup = pdbatoms.Soup()
soup.remaining_text = ""
soup.n_remaining_text = 0
atoms = []
# Read from .gro because .top does not contain water
# residue information, which is "inferred"
lines = open(gro, 'r').readlines()
for i_line, line in enumerate(lines[2:-1]):
atom = AtomFromGroLine(line)
if skip_solvent and atom.res_type == "SOL":
soup.remaining_text = "".join(lines[i_line + 2:-1])
soup.n_remaining_text = len(lines[i_line + 2:-1])
break
atoms.append(atom)
soup.box = [float(w) for w in lines[-1].split()]
for atom, (mass, q, chain_id) in zip(atoms, read_top(top)):
atom.mass = mass
atom.charge = q
curr_res_num = -1
for a in atoms:
if curr_res_num != a.res_num:
res = pdbatoms.Residue(a.res_type, a.chain_id, a.res_num)
soup.append_residue(res.copy())
curr_res_num = a.res_num
soup.insert_atom(-1, a)
convert_to_pdb_atom_names(soup)
protein.find_chains(soup)
return soup
def soup_from_topology(topology):
"""
Returns a Soup from a topology dictionary.
"""
soup = pdbatoms.Soup()
chain_id = ''
n_res = topology['NRES']
n_atom = topology['NATOM']
for i_res in range(n_res):
res_type = topology['RESIDUE_LABEL'][i_res].strip()
if res_type == "WAT":
res_type = "HOH"
res = pdbatoms.Residue(res_type, chain_id, i_res + 1)
soup.append_residue(res)
res = soup.residue(i_res)
i_atom_start = topology['RESIDUE_POINTER'][i_res] - 1
if i_res == n_res - 1:
i_atom_end = n_atom
else:
i_atom_end = topology['RESIDUE_POINTER'][i_res + 1] - 1
for i_atom in range(i_atom_start, i_atom_end):
atom = pdbatoms.Atom()
atom.vel = v3.vector()
atom.num = i_atom + 1
atom.res_num = i_res + 1
atom.res_type = res_type
atom.type = topology['ATOM_NAME'][i_atom].strip()
atom.mass = topology['MASS'][i_atom]
atom.charge = topology['CHARGE'][i_atom] / sqrt_of_k
atom.element = data.guess_element(atom.res_type, atom.type)
soup.insert_atom(-1, atom)
convert_to_pdb_atom_names(soup)
if topology['IFBOX'] > 0:
# create dummy dimension to ensure box dimension recognized
soup.box_dimension_str = "1.000000 1.0000000 1.000000"
return soup