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')