def setup_class(cls):
"""
setup any state specific to the execution of the given class (which usually contains tests).
"""
super(TestAmber99SB, cls).setup_class()
tinkerpath = which('testgrad')
# try to find mdrun_d or gmx_d
# gmx should be built with config -DGMX_DOUBLE=ON
gmxpath = which('mdrun_d') or which('gmx_d')
gmxsuffix = '_d'
# Tests will FAIL if use single precision gromacs
# gmxpath = which('mdrun') or which('gmx')
# gmxsuffix = ''
# self.logger.debug("\nBuilding options for target...\n")
cls.cwd = os.path.dirname(os.path.realpath(__file__))
os.chdir(os.path.join(cls.cwd, "files", "amber_alaglu"))
cls.tmpfolder = os.path.join(cls.cwd, "files", "amber_alaglu", "temp")
if not os.path.exists(cls.tmpfolder):
os.makedirs(cls.tmpfolder)
os.chdir(cls.tmpfolder)
for i in [
"topol.top", "shot.mdp", "a99sb.xml", "a99sb.prm", "all.gro",
"all.arc", "AceGluNme.itp", "AceAlaNme.itp", "a99sb.itp"
]:
os.system("ln -fs ../%s" % i)
cls.engines = OrderedDict()
# Set up GMX engine
if gmxpath != '':
cls.engines['GMX'] = GMX(coords="all.gro",
gmx_top="topol.top",
gmx_mdp="shot.mdp",
gmxpath=gmxpath,
gmxsuffix=gmxsuffix)
else:
logger.warn("GROMACS cannot be found, skipping GMX tests.")
# Set up TINKER engine
if tinkerpath != '':
cls.engines['TINKER'] = TINKER(coords="all.arc",
tinker_key="alaglu.key",
tinkerpath=tinkerpath)
else:
logger.warn("TINKER cannot be found, skipping TINKER tests.")
# Set up OpenMM engine
try:
try:
import openmm
except ImportError:
import simtk.openmm
cls.engines['OpenMM'] = OpenMM(coords="all.gro",
pdb="conf.pdb",
ffxml="a99sb.xml",
platname="Reference",
precision="double")
except:
logger.warn("OpenMM cannot be imported, skipping OpenMM tests.")
def setUp(self):
tinkerpath = which('testgrad')
gmxsuffix = '_d'
gmxpath = which('mdrun' + gmxsuffix)
self.logger.debug("\nBuilding options for target...\n")
self.cwd = os.getcwd()
os.chdir(os.path.join(os.getcwd(), "test", "files", "amber_alaglu"))
if not os.path.exists("temp"): os.makedirs("temp")
os.chdir("temp")
for i in [
"topol.top", "shot.mdp", "a99sb.xml", "a99sb.prm", "all.gro",
"all.arc", "AceGluNme.itp", "AceAlaNme.itp", "a99sb.itp"
]:
os.system("ln -fs ../%s" % i)
self.engines = OrderedDict()
# Set up GMX engine
if gmxpath != '':
self.engines['GMX'] = GMX(coords="all.gro",
gmx_top="topol.top",
gmx_mdp="shot.mdp",
gmxpath=gmxpath,
gmxsuffix=gmxsuffix)
else:
logger.warn("GROMACS cannot be found, skipping GMX tests.")
# Set up TINKER engine
if tinkerpath != '':
self.engines['TINKER'] = TINKER(coords="all.arc",
tinker_key="alaglu.key",
tinkerpath=tinkerpath)
else:
logger.warn("TINKER cannot be found, skipping TINKER tests.")
# Set up OpenMM engine
openmm = False
try:
import simtk.openmm
openmm = True
except:
logger.warn("OpenMM cannot be imported, skipping OpenMM tests.")
if openmm:
self.engines['OpenMM'] = OpenMM(coords="all.gro",
pdb="conf.pdb",
ffxml="a99sb.xml",
platname="Reference",
precision="double")
self.addCleanup(os.system, 'cd .. ; rm -rf temp')
def setup_class(cls):
super(TestAmoebaWater6, cls).setup_class()
#self.logger.debug("\nBuilding options for target...\n")
cls.cwd = os.path.dirname(os.path.realpath(__file__))
os.chdir(os.path.join(cls.cwd, "files", "amoeba_h2o6"))
cls.tmpfolder = os.path.join(cls.cwd, "files", "amoeba_h2o6", "temp")
if not os.path.exists(cls.tmpfolder):
os.makedirs(cls.tmpfolder)
os.chdir(cls.tmpfolder)
os.system("ln -s ../prism.pdb")
os.system("ln -s ../prism.key")
os.system("ln -s ../hex.arc")
os.system("ln -s ../water.prm")
os.system("ln -s ../amoebawater.xml")
cls.O = OpenMM(coords="hex.arc", pdb="prism.pdb", ffxml="amoebawater.xml", precision="double", \
mmopts={'rigidWater':False, 'mutualInducedTargetEpsilon':1e-6})
tinkerpath = which('testgrad')
if tinkerpath:
cls.T = TINKER(coords="hex.arc", tinker_key="prism.key", tinkerpath=tinkerpath)
def setUp(self):
self.logger.debug("\nBuilding options for target...\n")
self.cwd = os.getcwd()
os.chdir(os.path.join(os.getcwd(), "test", "files", "amoeba_h2o6"))
if not os.path.exists("temp"): os.makedirs("temp")
os.chdir("temp")
os.system("ln -s ../prism.pdb")
os.system("ln -s ../prism.key")
os.system("ln -s ../hex.arc")
os.system("ln -s ../water.prm")
os.system("ln -s ../amoebawater.xml")
self.O = OpenMM(coords="hex.arc", pdb="prism.pdb", ffxml="amoebawater.xml", precision="double", \
mmopts={'rigidWater':False, 'mutualInducedTargetEpsilon':1e-6})
tinkerpath = which('testgrad')
if (which('testgrad') != ''):
self.T = TINKER(coords="hex.arc",
tinker_key="prism.key",
tinkerpath=tinkerpath)
os.chdir("..")
self.addCleanup(os.system, 'rm -rf temp')
