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 write_pdb(self, pdb, res_type="HOH", atom_type="O", element="O"):
i_res = 1
with open(pdb, 'w') as f:
for i in range(self.n):
for j in range(self.n):
for k in range(self.n):
l = i * self.n_sq + j * self.n + k
if self.array[l]:
atom = pdbatoms.Atom()
atom.pos = self.pos(i, j, k)
atom.type = atom_type
atom.is_hetatm = True
atom.element = element
atom.res_type = res_type
atom.res_num = i_res
atom.num = i_res
f.write(atom.pdb_str() + '\n')
def AtomFromGroLine(line):
"""
Returns an Atom object from a .gro atom line.
"""
atom = pdbatoms.Atom()
atom.res_num = int(line[0:5])
atom.res_type = line[5:8].strip()
atom.type = line[10:15].strip(" ")
atom.element = data.guess_element(atom.res_type, line[12:15])
atom.num = int(line[15:20])
# 10 x multiplier converts from nm to angstroms
x = 10.0 * float(line[20:28])
y = 10.0 * float(line[28:36])
z = 10.0 * float(line[36:44])
v3.set_vector(atom.pos, x, y, z)
if len(line) > 62:
# 10 x multiplier converts from nm to angstroms
x = 10.0 * float(line[44:52])
y = 10.0 * float(line[52:60])
z = 10.0 * float(line[60:68])
v3.set_vector(atom.vel, x, y, z)
return atom
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