# Check to see if AMBERHOME is set.
if "AMBERHOME" in _environ:
_amber_home = _environ.get("AMBERHOME")
else:
_amber_home = None
# Check to see if GROMACS is installed.
import Sire.Base as _SireBase
from os import path as _path
# First, let the user tell us where to find GROMACS. This
# assumes that gromacs is installed in $GROMACSHOME/bin/gmx.
_gmx_exe = None
if "GROMACSHOME" in _environ:
try:
_gmx_exe = _SireBase.findExe("%s/bin/gmx" % _environ.get("GROMACSHOME")) \
.absoluteFilePath()
except:
try:
_gmx_exe = _SireBase.findExe("%s/bin/gmx_mpi" % _environ.get("GROMACSHOME")) \
.absoluteFilePath()
except:
pass
if _gmx_exe is None:
# The user has not told us where it is, so need to look in $PATH.
try:
_gmx_exe = _SireBase.findExe("gmx").absoluteFilePath()
except:
try:
_gmx_exe = _SireBase.findExe("gmx_mpi").absoluteFilePath()
except:
from Sire import Maths as _SireMaths
from Sire import Mol as _SireMol
from Sire import Units as _SireUnits
from BioSimSpace import _isVerbose
from BioSimSpace._Exceptions import AlignmentError as _AlignmentError
from BioSimSpace._Exceptions import MissingSoftwareError as _MissingSoftwareError
from BioSimSpace._SireWrappers import Molecule as _Molecule
from BioSimSpace import IO as _IO
from BioSimSpace import Units as _Units
from BioSimSpace import _Utils as _Utils
# Try to find the FKCOMBU program from KCOMBU: http://strcomp.protein.osaka-u.ac.jp/kcombu
try:
_fkcombu_exe = _SireBase.findExe("fkcombu").absoluteFilePath()
except:
_fkcombu_exe = None
def matchAtoms(molecule0,
molecule1,
scoring_function="rmsd_align",
matches=1,
return_scores=False,
prematch={},
timeout=5 * _Units.Time.second,
property_map0={},
property_map1={}):
"""Find mappings between atom indices in molecule0 to those in molecule1.
Molecules are aligned using a Maximum Common Substructure (MCS) search.
def _find_md_package(system, protocol, gpu_support=False):
"""Find a molecular dynamics package on the system and return
a handle to it as a MDPackage object.
Parameters
----------
system : :class:`System <BioSimSpace._SireWrappers.System>`
The molecular system.
protocol : :class:`Protocol <BioSimSpace.Protocol>`
The simulation protocol.
gpu_support : bool
Whether to use package must have GPU support.
Returns
-------
(package, exe) : (str, str)
The name of the MD package and a path to its executable.
"""
# The input has already been validated in the run method, so no need
# to re-validate here.
# Get the file format of the molecular system.
fileformat = system.fileFormat()
# Make sure that this format is supported.
if not fileformat in _file_extensions:
raise ValueError("Cannot find an MD package that supports format: %s" %
fileformat)
else:
packages = _file_extensions[fileformat]
# Is this a free energy protocol.
if type(protocol) is _Protocol.FreeEnergy:
is_free_energy = True
else:
is_free_energy = False
# Loop over each package that supports the file format.
for package in packages:
# If this is free energy protocol, then check that the package has support.
if not is_free_energy or _free_energy[package]:
# Check whether this package exists on the system and has the desired
# GPU support.
for exe, gpu in _md_packages[package].items():
# If the user has requested GPU support make sure the package
# supports it.
if not gpu_support or gpu:
# AMBER
if package == "AMBER":
# Search AMBERHOME, if set.
if _amber_home is not None:
_exe = "%s/bin/%s" % (_amber_home, exe)
if _os.path.isfile(_exe):
return (package, _exe)
# Search system PATH.
else:
try:
exe = _SireBase.findExe(exe).absoluteFilePath()
return (package, exe)
except:
pass
# GROMACS
elif package == "GROMACS":
if _gmx_exe is not None:
return (package, _gmx_exe)
# SOMD
elif package == "SOMD":
return (package, _SireBase.getBinDir() + "/somd")
# Search system PATH.
else:
try:
exe = _SireBase.findExe(exe).absoluteFilePath()
return (package, exe)
except:
pass
# If we get this far, then no package was found.
raise _MissingSoftwareError("Couldn't find package to support format: %s" %
fileformat)