def fchkToGeom(filename):
filename = filename.split('.fchk')[0]
filename = filename.split('.fch')[0]
fileobj = rxgau.GauFile(filename)
fileobj.fchk.read()
geom = rxmol.Molecule('mole')
geom.addatomsFromLists(fileobj.fchk.atomnos, fileobj.fchk.atomcoords[-1])
def setUp(self):
self.file = rxgau.GauFile("samples/testBmat")
gAmber.GauAmberCOM(self.file)
self.file.com.read()
self.file.fchk.read()
self.mole = rxmol.Molecule('12CH')
self.mole.readfromxyz(self.file.com.xyz)
self.mole.readconnectivity(self.file.com.connectivity)
def test_xyzfile(self):
benzene = rxmol.Molecule("benzene")
benfile = rxgau.GauFile("samples/bencom")
benfile.fchk.read()
benzene.addatomsFromLists(benfile.fchk.atomnos,
benfile.fchk.atomcoords[-1])
self.assertEqual(benzene[1].name, 'C1')
self.assertEqual(benzene[12].name, 'H12')
def testmmfile(self):
mmfile = rxgau.GauFile('samples/mmfile')
gAmber.GauAmberCOM(mmfile)
mmfile.com.read()
benmol = rxmol.Molecule('benzene')
benmol.readfromxyz(mmfile.com.xyz)
#benmol.readtypefromlist(mmfile.com.atomtypelist)
#benmol.readchargefromlist(mmfile.com.atomchargelist)
for atom in benmol:
print(atom, atom.atomtype, atom.atomcharge)
benmol.readconnectivity(mmfile.com.connectivity)
print("Bond: ", len(benmol.bondlist.keys()))
print("Angle: ", len(benmol.anglelist.keys()))
print("Dihd: ", len(benmol.dihedrallist.keys()))
def setUp(self):
self.mole = rxmol.Molecule("H2O2")
self.assertTrue(isinstance(self.mole, rxmol.Molecule))
self.mole.addatom('O', np.array([0.0, 0.0, 0.0]), unit='angstrom')
self.mole.addatom('H', np.array([0.0, 1.0, 0.0]), unit='angstrom')
self.mole.addatom('O', np.array([0.0, 0.0, 1.0]))
self.mole.addatom('H', np.array([1.0, 0.0, 0.0]), unit='angstrom')
self.assertTrue(isinstance(self.mole[1], rxmol.Atom))
self.mole.addbond(1, 2)
self.mole.addbond(1, 3)
self.mole.addbond(3, 4)
self.assertTrue(isinstance(self.mole.bond(1, 3), rxmol.Bond))
self.mole.addangle(2, 1, 3)
self.mole.addangle(4, 3, 1)
self.assertTrue(isinstance(self.mole.angle(2, 1, 3), rxmol.Angle))
self.mole.adddihedral(2, 1, 3, 4)
self.assertTrue(
isinstance(self.mole.dihedral(4, 3, 1, 2), rxmol.Dihedral))
self.assertEqual(self.mole.natom, 4)
# def __iter__
ite = iter(self.mole)
for atom in self.mole:
print(atom.name)
# def __next__
self.assertEqual(next(ite).name, 'O1')
self.assertEqual(next(ite).name, 'H2')
ite2 = iter(self.mole)
self.assertEqual(next(ite2).name, 'O1')
self.assertEqual(next(ite2).name, 'H2')
self.assertEqual(next(ite).name, 'O3')
self.assertEqual(next(ite).name, 'H4')
self.assertEqual(next(ite2).name, 'O3')
self.assertEqual(next(ite2).name, 'H4')
# def __getitem__
self.assertEqual(str(self.mole[1].name), 'O1')
def test_readfile(self):
benz = rxmol.Molecule("Benzene")
with open('samples/ben.xyz', 'r') as f:
f = f.read()
benz.readfromxyz(f)
self.assertEqual(benz[1].name, 'C1')
self.assertEqual(benz[12].name, 'H12')
#test_connty
with open('samples/cnnty.com', 'r') as f:
cn = f.read()
benz.readconnectivity(cn)
self.assertEqual(len(benz.bondlist.values()), 12)
self.assertEqual(len(benz.anglelist.values()), 18)
self.assertEqual(len(benz.dihedrallist.values()), 24)
self.assertAlmostEqual(benz.angle(1, 2, 3).anglevalue,
120.00,
delta=0.1)
os.system(
'rm A* q* Q* p* esout *gaussian* samples/bencom.fchk samples/bencom.chk samples/bencom.log'
)
import rxcclib.utils as utils
import rxcclib.lazy as lazy
import rxcclib.file.Gaussian as rxfile
import rxcclib.geometry.molecules as rxmol
with open('cnnty.com', 'r') as f:
con = f.read()
con = lazy.ConnectivityToConnectionMatrix(con)
con = utils.LTMatrix.newFromUpperMat(con)
benmol = rxmol.Molecule('ben')
benfile = rxfile.GauFile('bencom')
benfile.fchk.read()
benmol.addatomsFromLists(benfile.fchk.atomnos, benfile.fchk.atomcoords[-1])
benmol.readConnectionMatrix(con.fullmat)
def readgeom(inputfile):
# Read info from com
mmcom = inputfile.com
mole = rxmol.Molecule('thisgeometry')
mmcom = GauAmberCOM(inputfile)
mmcom.read()
mole.readfromxyz(mmcom.xyz)
mole.readchargefromlist(mmcom.atomchargelist)
mole.readtypefromlist(mmcom.atomtypelist)
mole.readconnectivity(mmcom.connectivity)
for atom in mole:
atom.vdwradius = float(mmcom.vdwdict[atom.atomtype][0])
atom.vdwwelldepth = float(mmcom.vdwdict[atom.atomtype][1])
# Store and count finalfunc
finalfuncL = []
finalfuncL.extend(sorted(mmcom.bondfunc, key=lambda x: repr(x)))
finalfuncL.extend(sorted(mmcom.anglefunc, key=lambda x: repr(x)))
finalfuncL.extend(sorted(mmcom.dihdfunc, key=lambda x: repr(x)))
finalfuncL.extend(sorted(mmcom.improperfunc, key=lambda x: repr(x)))
for item in mmcom.improperfunc:
for atom3 in mole:
if atom3.atomtype == item.c:
permu = itertools.permutations(atom3.neighbor, 3)
res = []
for tu in permu:
a = tu[0].atomtype == item.a or item.a == '*'
b = tu[1].atomtype == item.b or item.b == '*'
c = tu[2].atomtype == item.d or item.d == '*'
if a and b and c:
res.append([
tu[0].atomnum, tu[1].atomnum, atom3.atomnum,
tu[2].atomnum
])
res = sorted(res, key=lambda x: (str(x[1]) + str(x[3])))
res = res[0]
mole.addimproper(*res)
# Match itnl and finalfunc
itnlcordL = []
itnlcordL.extend(sorted(mole.dihedrallist.values(), key=lambda x: repr(x)))
itnlcordL.extend(sorted(mole.anglelist.values(), key=lambda x: repr(x)))
itnlcordL.extend(sorted(mole.bondlist.values(), key=lambda x: repr(x)))
itnlcordL.extend(sorted(mole.improperlist.values(), key=lambda x: repr(x)))
unkitnlL = []
knownitnlL = []
for item in itnlcordL:
for func in finalfuncL:
if matchitnlwithfinalfunc(item, func):
item.func = func
if type(item) is rxmol.Dihedral:
item.dihdfunctions = copy.deepcopy(func.dihdfunctions)
item.npaths = func.npaths
elif type(item) is rxmol.Improper:
item.forceconst = func.forceconst
item.phase = func.phase
item.periodicity = func.periodicity
else:
item.forceconst = func.forceconst
item.eqvalue = func.eqvalue
break
return finalfuncL, itnlcordL, mole