def testWriteCharmm27Top(self):
""" Tests writing a Gromacs topology file with CHARMM 27 FF """
top = load_file(get_fn('1aki.charmm27.top'))
self.assertEqual(top.combining_rule, 'lorentz')
GromacsTopologyFile.write(top,
get_fn('1aki.charmm27.top', written=True))
top2 = load_file(get_fn('1aki.charmm27.top', written=True))
self._charmm27_checks(top)
def test_write_amber99SBILDN(self):
""" Tests writing a Gromacs topology with multiple molecules """
top = load_file(get_fn('ildn.solv.top'))
self.assertEqual(top.combining_rule, 'lorentz')
fn = get_fn('ildn.solv.top', written=True)
GromacsTopologyFile.write(top, fn, combine=None)
top2 = load_file(fn)
self._check_ff99sbildn(top2)
self._check_equal_structures(top, top2)
def apply_forcefield(structure, forcefield, debug=False):
"""Apply a forcefield to a Topology. """
if not structure.bonds:
warn("Structure contains no bonds: \n{}\n".format(structure))
if isinstance(forcefield, string_types):
if forcefield.lower() in ["opls-aa", "oplsaa", "opls"]:
if os.path.isdir("oplsaa.ff"):
ff_path = "oplsaa.ff/forcefield.itp"
else:
ff_path = os.path.join(gmx.GROMACS_TOPDIR, "oplsaa.ff/forcefield.itp")
elif forcefield.lower() in ["trappeua"]:
ff_path = os.path.join(gmx.GROMACS_TOPDIR, "trappeua.ff/forcefield.itp")
else:
ff_path = forcefield
# TODO: this is a patchwork fix until rules and FF files become one
forcefield = forcefield.lower()
for alias in OPLS_ALIASES:
if alias in forcefield:
forcefield = "oplsaa"
ff = GromacsTopologyFile(ff_path, parametrize=False)
find_atomtypes(structure.atoms, forcefield, debug=debug)
if hasattr(structure, "box"):
ff.box = structure.box
ff.atoms = structure.atoms
ff.bonds = structure.bonds
ff.residues = structure.residues
create_bonded_forces(ff)
ff.parametrize()
return ff
def testDuplicateSystemNames(self):
""" Tests that Gromacs topologies never have duplicate moleculetypes """
parm = load_file(get_fn('phenol.prmtop'))
parm = parm * 20 + load_file(get_fn('biphenyl.prmtop')) * 20
top = GromacsTopologyFile.from_structure(parm)
self.assertEqual(top.combining_rule, 'lorentz')
top.write(get_fn('phenol_biphenyl.top', written=True))
top2 = GromacsTopologyFile(get_fn('phenol_biphenyl.top', written=True))
self.assertEqual(len(top.residues), 40)
def _amber_to_gromacs(self):
# Load prmtop and inpcrd as a Structure
parmstruct = load_file(self.outprefix + ".prmtop",
xyz=self.outprefix + ".inpcrd",
structure=True)
# Save .gro coordinate file
GromacsGroFile.write(struct=parmstruct, dest=self.outprefix + ".gro")
# Save .top topology and parameter file
grotop = GromacsTopologyFile.from_structure(parmstruct, copy=False)
grotop.write(dest=self.outprefix + ".top", parameters="inline")
def to_parmed_GromacsTopologyFile(item, atom_indices='all', check=True):
if check:
digest_item(item, 'parmed.Structure')
atom_indices = digest_atom_indices(atom_indices)
from . import extract
from parmed.gromacs import GromacsTopologyFile as GromacsTopologyFile
tmp_item = extract(item,
atom_indices=atom_indices,
copy_if_all=False,
check=False)
tmp_item = GromacsTopologyFile.from_structure(tmp_item)
return tmp_item
def to_parmed_GromacsTopologyFile(item,
molecular_system=None,
atom_indices='all',
structure_indices='all'):
from parmed.gromacs import GromacsTopologyFile
from molsysmt.api_forms.api_parmed_GromacsTopologyFile import to_parmed_GromacsTopologyFile as parmed_GromacsTopologyFile_to_parmed_GromacsTopologyFile
tmp_item = GromacsTopologyFile(item)
if molecular_system is not None:
tmp_molecular_system = molecular_system.combine_with_items(tmp_item)
else:
tmp_molecular_system = None
tmp_item = parmed_GromacsTopologyFile_to_parmed_GromacsTopologyFile(
tmp_item,
molecular_system=tmp_molecular_system,
atom_indices=atom_indices,
structure_indices=structure_indices,
copy_if_all=False)
return tmp_item, tmp_molecular_system