def soup_from_top_and_crd_or_rst(top, crd_or_rst):
"""
Returns a Soup from AMBER .top and .crd/.rst files.
"""
topology = read_top(top)
soup = soup_from_topology(topology)
load_crd_or_rst_into_soup(soup, crd_or_rst)
protein.find_chains(soup)
if topology['IFBOX'] > 0:
# if periodic cells are in .crd or .rst then save
# for later, if we need to write modified .crd or .rst
lines = open(crd_or_rst, "r").readlines()
lines = [l for l in reversed(lines) if l.strip()]
soup.box_dimension_str = lines[0].rstrip()
return soup
def soup_from_top_and_crd_or_rst(top, crd_or_rst):
"""
Returns a Soup from AMBER .top and .crd/.rst files.
"""
topology = read_top(top)
soup = soup_from_topology(topology)
load_crd_or_rst_into_soup(soup, crd_or_rst)
protein.find_chains(soup)
if topology['IFBOX'] > 0:
# if periodic cells are in .crd or .rst then save
# for later, if we need to write modified .crd or .rst
lines = open(crd_or_rst, "r").readlines()
lines = [l for l in reversed(lines) if l.strip()]
soup.box_dimension_str = lines[0].rstrip()
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_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
