def energy_decomposition_system(structure,
system,
platform=None,
nrg=u.kilocalories_per_mole):
"""
This function computes the energy contribution for all of the different
force groups.
Parameters
----------
structure : Structure
The Structure with the coordinates for this system
system : mm.System
The OpenMM System object to get decomposed energies from
platform : str
The platform to use. Options are None (default), 'CPU', 'Reference',
'CUDA', and 'OpenCL'. None will pick default OpenMM platform for this
installation and computer
nrg : energy unit, optional
The unit to convert all energies into. Default is kcal/mol
Returns
-------
energies : list of tuple
Each entry is a tuple with the name of the force followed by its
contribution
"""
import simtk.openmm as mm
# First get all of the old force groups so we can restore them
old_groups = [f.getForceGroup() for f in system.getForces()]
old_recip_group = []
def _ene(context, grp):
st = context.getState(getEnergy=True, groups=1 << grp)
return (type(system.getForce(grp)).__name__,
st.getPotentialEnergy().value_in_unit(nrg))
try:
for i, f in enumerate(system.getForces()):
if isinstance(f, mm.NonbondedForce):
old_recip_group.append(f.getReciprocalSpaceForceGroup())
f.setReciprocalSpaceForceGroup(i)
f.setForceGroup(i)
if platform is None:
con = mm.Context(system, mm.VerletIntegrator(0.001))
else:
con = mm.Context(system, mm.VerletIntegrator(0.001),
mm.Platform.getPlatformByName(platform))
con.setPositions(structure.positions)
if structure.box is not None:
con.setPeriodicBoxVectors(*structure.box_vectors)
return list(map(lambda x: _ene(con, x), range(system.getNumForces())))
finally:
idx = 0
for grp, force in zip(old_groups, system.getForces()):
if isinstance(force, mm.NonbondedForce):
force.setReciprocalSpaceForceGroup(old_recip_group[idx])
idx += 1
force.setForceGroup(grp)
def energy_decomposition_system(structure, system, platform=None,
nrg=u.kilocalories_per_mole):
"""
This function computes the energy contribution for all of the different
force groups.
Parameters
----------
structure : Structure
The Structure with the coordinates for this system
system : mm.System
The OpenMM System object to get decomposed energies from
platform : str
The platform to use. Options are None (default), 'CPU', 'Reference',
'CUDA', and 'OpenCL'. None will pick default OpenMM platform for this
installation and computer
nrg : energy unit, optional
The unit to convert all energies into. Default is kcal/mol
Returns
-------
energies : list of tuple
Each entry is a tuple with the name of the force followed by its
contribution
"""
import simtk.openmm as mm
# First get all of the old force groups so we can restore them
old_groups = [f.getForceGroup() for f in system.getForces()]
old_recip_group = []
def _ene(context, grp):
st = context.getState(getEnergy=True, groups=1<<grp)
return (type(system.getForce(grp)).__name__,
st.getPotentialEnergy().value_in_unit(nrg))
try:
for i, f in enumerate(system.getForces()):
if isinstance(f, mm.NonbondedForce):
old_recip_group.append(f.getReciprocalSpaceForceGroup())
f.setReciprocalSpaceForceGroup(i)
f.setForceGroup(i)
if platform is None:
con = mm.Context(system, mm.VerletIntegrator(0.001))
else:
con = mm.Context(system, mm.VerletIntegrator(0.001),
mm.Platform.getPlatformByName(platform))
con.setPositions(structure.positions)
if structure.box is not None:
con.setPeriodicBoxVectors(*structure.box_vectors)
return list(map(lambda x: _ene(con, x), range(system.getNumForces())))
finally:
idx = 0
for grp, force in zip(old_groups, system.getForces()):
if isinstance(force, mm.NonbondedForce):
force.setReciprocalSpaceForceGroup(old_recip_group[idx])
idx += 1
force.setForceGroup(grp)
def from_leaprc(cls, fname, search_oldff=False):
""" Load a parameter set from a leaprc file
Parameters
----------
fname : str or file-like
Name of the file or open file-object from which a leaprc-style file
will be read
search_oldff : bool, optional, default=False
If True, search the oldff directories in the main Amber leap
folders. Default is False
Notes
-----
This does not read all parts of a leaprc file -- only those pertinent to
defining force field information. For instance, the following sections
and commands are processed:
- addAtomTypes
- loadAmberParams
- loadOFF
- loadMol2
- loadMol3
"""
params = cls()
if isinstance(fname, string_types):
f = genopen(fname, 'r')
own_handle = True
else:
f = fname
own_handle = False
# To make parsing easier, and because leaprc files are usually quite
# short, I'll read the whole file into memory
def joinlines(lines):
newlines = []
composite = []
for line in lines:
if line.endswith('\\\n'):
composite.append(line[:-2])
continue
else:
composite.append(line)
newlines.append(''.join(composite))
composite = []
if composite:
newlines.append(''.join(composite))
return newlines
lines = joinlines(map(lambda line:
line if '#' not in line else line[:line.index('#')], f))
text = ''.join(lines)
if own_handle: f.close()
lowertext = text.lower() # commands are case-insensitive
# Now process the parameter files
def process_fname(fname):
if fname[0] in ('"', "'"):
fname = fname[1:-1]
fname = fname.replace('_BSTOKEN_', r'\ ').replace(r'\ ', ' ')
return fname
for line in lines:
line = line.replace(r'\ ', '_BSTOKEN_')
if _loadparamsre.findall(line):
fname = process_fname(_loadparamsre.findall(line)[0])
params.load_parameters(_find_amber_file(fname, search_oldff))
elif _loadoffre.findall(line):
fname = process_fname(_loadoffre.findall(line)[0])
params.residues.update(
AmberOFFLibrary.parse(_find_amber_file(fname, search_oldff))
)
elif _loadmol2re.findall(line):
(resname, fname), = _loadmol2re.findall(line)
residue = Mol2File.parse(_find_amber_file(fname, search_oldff))
if isinstance(residue, ResidueTemplateContainer):
warnings.warn('Multi-residue mol2 files not supported by '
'tleap. Loading anyway using names in mol2',
AmberWarning)
for res in residue:
params.residues[res.name] = res
else:
params.residues[resname] = residue
# Now process the addAtomTypes
try:
idx = lowertext.index('addatomtypes')
except ValueError:
# Does not exist in this file
atom_types_str = ''
else:
i = idx + len('addatomtypes')
while i < len(text) and text[i] != '{':
if text[i] not in '\r\n\t ':
raise ParameterError('Unsupported addAtomTypes syntax in '
'leaprc file')
i += 1
if i == len(text):
raise ParameterError('Unsupported addAtomTypes syntax in '
'leaprc file')
# We are at our first brace
chars = []
nopen = 1
i += 1
while i < len(text):
char = text[i]
if char == '{':
nopen += 1
elif char == '}':
nopen -= 1
if nopen == 0: break
elif char == '\n':
char = ' '
chars.append(char)
i += 1
atom_types_str = ''.join(chars).strip()
for _, name, symb, hyb in _atomtypere.findall(atom_types_str):
if symb not in AtomicNum:
raise ParameterError('%s is not a recognized element' % symb)
if name in params.atom_types:
params.atom_types[name].atomic_number = AtomicNum[symb]
return params