def setUp(self):
TargetTests.setUp(self)
self.options.update({
'penalty_additive': 0.01,
'jobtype': 'NEWTON',
'forcefield': ['cl4.prm'],
'amoeba_pol': 'direct'})
self.tgt_opt.update({'type':'Interaction_TINKER',
'name':'ccl4-h2o-1',
'energy_denom':1.0,
'attenuate':'True',
'fragment1':'1-5',
'fragment2':'6-8',
'energy-upper':20.0})
self.ff = forcebalance.forcefield.FF(self.options)
self.ffname = self.options['forcefield'][0][:-3]
self.filetype = self.options['forcefield'][0][-3:]
self.mvals = [.5]*self.ff.np
if (which('testgrad') == ''):
self.skipTest("TINKER programs are not in the PATH.")
self.logger.debug("Setting up Interaction_TINKER target\n")
self.target = forcebalance.tinkerio.Interaction_TINKER(self.options, self.tgt_opt, self.ff)
self.addCleanup(os.system, 'rm -rf temp')
def setUp(self):
TargetTests.setUp(self)
self.options.update({
'penalty_additive': 0.01,
'jobtype': 'NEWTON',
'forcefield': ['cl4.prm'],
'amoeba_pol': 'direct'
})
self.tgt_opt.update({
'type': 'Interaction_TINKER',
'name': 'ccl4-h2o-1',
'energy_denom': 1.0,
'attenuate': 'True',
'fragment1': '1-5',
'fragment2': '6-8',
'energy-upper': 20.0
})
self.ff = forcebalance.forcefield.FF(self.options)
self.ffname = self.options['forcefield'][0][:-3]
self.filetype = self.options['forcefield'][0][-3:]
self.mvals = [.5] * self.ff.np
if (which('testgrad') == ''):
self.skipTest("TINKER programs are not in the PATH.")
self.logger.debug("Setting up Interaction_TINKER target\n")
self.target = forcebalance.tinkerio.Interaction_TINKER(
self.options, self.tgt_opt, self.ff)
self.addCleanup(os.system, 'rm -rf temp')
def setUp(self):
TargetTests.setUp(self)
self.options.update({"penalty_additive": 0.01, "jobtype": "NEWTON", "forcefield": ["water.itp"]})
self.tgt_opt.update({"type": "ABINITIO_GMX", "name": "cluster-02"})
self.ff = forcebalance.forcefield.FF(self.options)
self.ffname = self.options["forcefield"][0][:-3]
self.filetype = self.options["forcefield"][0][-3:]
self.target = forcebalance.gmxio.AbInitio_GMX(self.options, self.tgt_opt, self.ff)
self.addCleanup(os.system, "rm -rf temp")
def setUp(self):
TargetTests.setUp(self)
# settings specific to this target
self.options.update({"jobtype": "NEWTON", "forcefield": ["dms.xml"]})
self.tgt_opt.update({"type": "Interaction_OpenMM", "name": "S2EPose", "fragment1": "1-9", "fragment2": "10-18"})
try:
self.ff = forcebalance.forcefield.FF(self.options)
except:
self.skipTest("Unable to create forcefield from dms.xml\n")
self.ffname = self.options["forcefield"][0][:-3]
self.filetype = self.options["forcefield"][0][-3:]
self.target = forcebalance.openmmio.Interaction_OpenMM(self.options, self.tgt_opt, self.ff)
self.addCleanup(os.system, "rm -rf temp")
def setUp(self):
self.skipTest("Needs optimizing to reduce runtime")
TargetTests.setUp(self)
# settings specific to this target
self.options.update({'jobtype': 'NEWTON', 'forcefield': ['dms.xml']})
self.tgt_opt.update({'type': 'LIQUID_OPENMM', 'name': 'dms-liquid'})
self.ff = forcebalance.forcefield.FF(self.options)
self.ffname = self.options['forcefield'][0][:-3]
self.filetype = self.options['forcefield'][0][-3:]
self.mvals = [.5] * self.ff.np
self.target = forcebalance.openmmio.Liquid_OpenMM(
self.options, self.tgt_opt, self.ff)
self.target.stage(self.mvals)
self.addCleanup(os.system, 'rm -rf temp')
def setUp(self):
self.skipTest("Not Implemented")
TargetTests.setUp(self)
# settings specific to this target
self.options.update({"jobtype": "NEWTON", "forcefield": ["dms.xml"]})
self.tgt_opt.update({"type": "LIQUID_OPENMM", "name": "dms-liquid"})
try:
self.ff = forcebalance.forcefield.FF(self.options)
except:
self.skipTest("Unable to create forcefield from dms.xml\n")
self.ffname = self.options["forcefield"][0][:-3]
self.filetype = self.options["forcefield"][0][-3:]
self.target = forcebalance.openmmio.Liquid_OpenMM(self.options, self.tgt_opt, self.ff)
self.addCleanup(os.system, "rm -rf temp")
def setUp(self):
TargetTests.setUp(self)
self.options.update({
'penalty_additive': 0.01,
'jobtype': 'NEWTON',
'forcefield': ['water.itp']})
self.tgt_opt.update({'type':'ABINITIO_GMX',
'name':'cluster-02'})
self.ff = forcebalance.forcefield.FF(self.options)
self.ffname = self.options['forcefield'][0][:-3]
self.filetype = self.options['forcefield'][0][-3:]
self.mvals = [.5]*self.ff.np
self.logger.debug("Setting up AbInitio_GMX target\n")
self.target = forcebalance.gmxio.AbInitio_GMX(self.options, self.tgt_opt, self.ff)
self.addCleanup(os.system, 'rm -rf temp')
def setUp(self):
TargetTests.setUp(self)
# settings specific to this target
self.options.update({
'jobtype': 'NEWTON',
'forcefield': ['dms.xml']})
self.tgt_opt.update({"type" : "Interaction_OpenMM",
"name" : "S2EPose",
"fragment1" : "1-9",
"fragment2" : "10-18"})
self.ff = forcebalance.forcefield.FF(self.options)
self.ffname = self.options['forcefield'][0][:-3]
self.filetype = self.options['forcefield'][0][-3:]
self.mvals = [.5]*self.ff.np
self.target = forcebalance.openmmio.Interaction_OpenMM(self.options, self.tgt_opt, self.ff)
self.addCleanup(os.system, 'rm -rf temp')
def setUp(self):
self.skipTest("Needs optimizing to reduce runtime")
TargetTests.setUp(self)
# settings specific to this target
self.options.update({
'jobtype': 'NEWTON',
'forcefield': ['dms.xml']})
self.tgt_opt.update({'type':'LIQUID_OPENMM',
'name':'dms-liquid'})
self.ff = forcebalance.forcefield.FF(self.options)
self.ffname = self.options['forcefield'][0][:-3]
self.filetype = self.options['forcefield'][0][-3:]
self.mvals = [.5]*self.ff.np
self.target = forcebalance.openmmio.Liquid_OpenMM(self.options, self.tgt_opt, self.ff)
self.target.stage(self.mvals)
self.addCleanup(os.system, 'rm -rf temp')
def setUp(self):
TargetTests.setUp(self)
# settings specific to this target
self.options.update({'jobtype': 'NEWTON', 'forcefield': ['dms.xml']})
self.tgt_opt.update({
"type": "Interaction_OpenMM",
"name": "S2EPose",
"fragment1": "1-9",
"fragment2": "10-18"
})
self.ff = forcebalance.forcefield.FF(self.options)
self.ffname = self.options['forcefield'][0][:-3]
self.filetype = self.options['forcefield'][0][-3:]
self.mvals = [.5] * self.ff.np
self.target = forcebalance.openmmio.Interaction_OpenMM(
self.options, self.tgt_opt, self.ff)
self.addCleanup(os.system, 'rm -rf temp')
