def test_MethanolTorsionGaus(self):
print('Testing torsion options')
exampleparentfolder = 'Examples/'
testcasepath = testcaseparentpath + '/' + 'TestMethanolTorsionGaus/'
self.MakeTestCasePath(testcasepath)
examplefolder = 'MethanolTorsionGaus/'
examplestructure = 'methanol.sdf'
examplekeyfilepath = self.GenericCopy(exampleparentfolder,
testcasepath, examplefolder,
examplestructure)
poltype = PolarizableTyper(use_gaus=True,
rotalltors=True,
optpcm=True,
torsppcm=True,
toroptpcm=True,
torsionrestraint=.2,
foldnum=4,
tordatapointsnum=13,
toroptmethod='HF',
torspmethod='MP2',
toroptbasisset='6-311G*',
torspbasisset='6-311++G(2d,2p)',
structure=examplestructure,
numproc=4,
maxmem='5GB',
maxdisk='20GB',
poltypeini=False,
printoutput=True)
self.GenericTest(exampleparentfolder, testcasepath, examplefolder,
examplestructure, poltype, examplekeyfilepath)
def test_ModifiedAminoAcid(self):
print('Testing modified amino acids')
exampleparentfolder = 'Examples/'
testcasepath = testcaseparentpath + '/' + 'TestModifiedAminoAcid/'
self.MakeTestCasePath(testcasepath)
examplefolder = 'ModifiedAminoAcid/'
examplestructure = 'methylamine.sdf'
examplekeyfilepath = self.GenericCopy(exampleparentfolder,
testcasepath, examplefolder,
examplestructure)
poltype = PolarizableTyper(
use_gaus=True,
amoebabioprmpath=
'/home/bdw2292/Tinker-release/params/amoebabio18.prm',
unmodifiedproteinpdbname='SNase_WT_H.pdb',
mutatedresiduenumber='102',
mutatedsidechain='CNC.sdf',
modifiedresiduepdbcode='CNC',
numproc=4,
maxmem='5GB',
maxdisk='20GB',
poltypeini=False,
printoutput=True)
self.GenericTest(exampleparentfolder, testcasepath, examplefolder,
examplestructure, poltype, examplekeyfilepath)
def test_MethylamineDontDoTor(self):
print('Testing dontdotor')
exampleparentfolder = 'Examples/'
testcasepath = testcaseparentpath + '/' + 'TestMethylamineDontDoTor/'
self.MakeTestCasePath(testcasepath)
examplefolder = 'Methylamine/'
examplestructure = 'methylamine.sdf'
examplekeyfilepath = self.GenericCopy(exampleparentfolder,
testcasepath, examplefolder,
examplestructure)
poltype = PolarizableTyper(dontdotor=True,
structure=examplestructure,
numproc=4,
maxmem='5GB',
maxdisk='20GB',
poltypeini=False,
printoutput=True)
def test_Aniline(self):
print('Testing aniline symmetry')
exampleparentfolder = 'Examples/'
testcasepath = testcaseparentpath + '/' + 'TestSymmetryAniline/'
self.MakeTestCasePath(testcasepath)
examplefolder = 'SymmetryAniline/'
examplestructure = 'aniline.sdf'
examplekeyfilepath = self.GenericCopy(exampleparentfolder,
testcasepath, examplefolder,
examplestructure)
poltype = PolarizableTyper(structure=examplestructure,
numproc=4,
maxmem='5GB',
maxdisk='20GB',
poltypeini=False,
printoutput=True)
self.GenericTest(exampleparentfolder, testcasepath, examplefolder,
examplestructure, poltype, examplekeyfilepath)
def test_MethanolFitRotBndsList(self):
print('Testing fitrotbndslist')
exampleparentfolder = 'Examples/'
testcasepath = testcaseparentpath + '/' + 'TestMethanolFitRotBndsList/'
self.MakeTestCasePath(testcasepath)
examplefolder = 'MethanolFitRotBndsList/'
examplestructure = 'methanol.sdf'
examplekeyfilepath = self.GenericCopy(exampleparentfolder,
testcasepath, examplefolder,
examplestructure)
poltype = PolarizableTyper(fitrotbndslist='1 2',
structure=examplestructure,
numproc=4,
maxmem='5GB',
maxdisk='20GB',
poltypeini=False,
printoutput=True)
self.GenericTest(exampleparentfolder, testcasepath, examplefolder,
examplestructure, poltype, examplekeyfilepath)
def test_MethylamineDMAESPOptions(self):
print('Testing DMA and ESP options')
exampleparentfolder = 'Examples/'
testcasepath = testcaseparentpath + '/' + 'TestMethylamineDMAESPOptions/'
self.MakeTestCasePath(testcasepath)
examplefolder = 'Methylamine/'
examplestructure = 'methylamine.sdf'
examplekeyfilepath = self.GenericCopy(exampleparentfolder,
testcasepath, examplefolder,
examplestructure)
poltype = PolarizableTyper(qmonly=True,
espbasisset='aug-cc-pVTZ',
dmabasisset='cc-pVTZ',
structure=examplestructure,
numproc=4,
maxmem='5GB',
maxdisk='20GB',
poltypeini=False,
printoutput=True)
def test_MethylaminePsi4SPOnly(self):
print('Testing Gaussian OPT only')
exampleparentfolder = 'Examples/'
testcasepath = testcaseparentpath + '/' + 'TestMethylamineGausOptOnly/'
self.MakeTestCasePath(testcasepath)
examplefolder = 'MethylamineGausOptOnly/'
examplestructure = 'methylamine.sdf'
examplekeyfilepath = self.GenericCopy(exampleparentfolder,
testcasepath, examplefolder,
examplestructure)
poltype = PolarizableTyper(use_gausoptonly=True,
structure=examplestructure,
numproc=4,
maxmem='5GB',
maxdisk='20GB',
poltypeini=False,
printoutput=True)
self.GenericTest(exampleparentfolder, testcasepath, examplefolder,
examplestructure, poltype, examplekeyfilepath)
def test_MethylamineGeometryOptimizationOptions(self):
print('Testing Geometry Optimization options ')
exampleparentfolder = 'Examples/'
testcasepath = testcaseparentpath + '/' + 'TestMethylamineGeometryOptimizationOptions/'
self.MakeTestCasePath(testcasepath)
examplefolder = 'MethylamineGeometryOptimizationOptions/'
examplestructure = 'methylamine.sdf'
examplekeyfilepath = self.GenericCopy(exampleparentfolder,
testcasepath, examplefolder,
examplestructure)
poltype = PolarizableTyper(structure=examplestructure,
numproc=4,
maxmem='5GB',
maxdisk='20GB',
optbasisset='6-311G*',
gausoptcoords='cartesian',
freq=True,
optpcm=True,
optmaxcycle=500,
optmethod='HF',
poltypeini=False,
printoutput=True)
self.GenericTest(exampleparentfolder, testcasepath, examplefolder,
examplestructure, poltype, examplekeyfilepath)