def _run(self, molName):
self.molName = molName
logger.info("Molecule: {}".format(self.molName))
molFile = os.path.join(home("test-charge"), self.molName + ".mol2")
self.mol = Molecule(molFile)
self.new_mols = {}
self.extras = {}
self.new_mols["Gasteiger"] = fitGasteigerCharges(self.mol)
try:
self.new_mols["AM1-BCC"] = fitChargesWithAntechamber(self.mol,
type="bcc")
except:
pass
qm = Psi4()
qm.theory = "B3LYP"
qm.basis = "6-311++G**"
workDir = os.path.join("tmp", self.molName)
os.makedirs(workDir, exist_ok=True)
for factor in [-10, -5, -4, -3, -2, -1]:
logger.info("Factor: {}".format(factor))
key = "ESP b {}".format(factor)
np.random.seed(20181114) # Make ESP grid generation deterministic
self.new_mols[key], self.extras[key] = fitESPCharges(
self.mol, qm, workDir, restraint_factor=10**factor)
def setUp(self):
self.testDir = None
molFile = os.path.join(home("test-qm"), "H2-0.74.mol2")
self.h2_074 = Molecule(molFile)
molFile = os.path.join(home("test-qm"), "H2-1.00.mol2")
self.h2_100 = Molecule(molFile)
molFile = os.path.join(home("test-qm"), "H2O2-90.mol2")
self.h2o2_90 = Molecule(molFile)
molFile = os.path.join(home("test-qm"), "Br.mol2")
self.Br = Molecule(molFile)
self.e_tol = 1e-5 if isinstance(self.qm, TeraChem) else 1e-10
def setUp(self):
self.maxDiff = None
from parameterize.home import home
from moleculekit.molecule import Molecule
molFile = os.path.join(home("test-fftype"), "benzamidine.mol2")
self.mol = Molecule(molFile, guessNE=["bonds"], guess=["angles", "dihedrals"])
def setUp(self):
from parameterize.home import home
from moleculekit.molecule import Molecule
from parameterize.parameterization.detect import detectEquivalentAtoms
from parameterize.parameterization.fftype import fftype
molFile = os.path.join(home("test-param"), "glycol.mol2")
mol = Molecule(molFile)
self.equivalents = detectEquivalentAtoms(mol)
_, self.mol = fftype(mol, method="GAFF2")
def setUp(self):
from parameterize.home import home
from moleculekit.molecule import Molecule
molFile = os.path.join(home("test-param"), "H2O2.mol2")
mol = Molecule(molFile, guessNE="bonds", guess=("angles", "dihedrals"))
self.mol = mol
self.esp = ESP()
self.esp.molecule = self.mol
# Precalculating here for the tests
equivalents = detectEquivalentAtoms(self.esp.molecule)
self.esp._equivalent_atom_groups = equivalents[0]
self.esp._equivalent_group_by_atom = equivalents[2]
def test_rtf_prm(self):
from parameterize.home import home
from parameterize.parameterization.writers import writeRTF, writePRM
refDir = home(dataDir="test-fftype/benzamidine")
with TemporaryDirectory() as resDir:
parameters, mol = fftype(self.mol, method="CGenFF_2b6")
writeRTF(mol, parameters, 0, os.path.join(resDir, "cgenff.rtf"))
writePRM(mol, parameters, os.path.join(resDir, "cgenff.prm"))
for testFile in ("cgenff.rtf", "cgenff.prm"):
with self.subTest(testFile=testFile):
# Get rid of the first linw with parameterize version string
with open(os.path.join(refDir, testFile)) as refFile:
refData = refFile.readlines()[1:]
with open(os.path.join(resDir, testFile)) as resFile:
resData = resFile.readlines()[1:]
self.assertListEqual(refData, resData, msg=testFile)
if old_atom != new_atom:
molecule.atomtype[neighbor] = new_atom
logger.info("Change atom {} type: {} --> {}".format(
neighbor, old_atom, new_atom))
# Change the P--O bond type
bond_index = graph.edges[(node, neighbor)]["index"]
old_bond = molecule.bondtype[bond_index]
if old_bond != new_bond:
molecule.bondtype[bond_index] = new_bond
logger.info("Change bond {}--{} type: {} --> {}".format(
*molecule.bonds[bond_index], old_bond, new_bond))
return molecule
if __name__ == "__main__":
from moleculekit.molecule import Molecule
from parameterize.charge import fitGasteigerCharges
import sys
import doctest
# Prevent HTMD importing inside doctest to fail if importing gives text output
from parameterize.home import home
home()
sys.exit(doctest.testmod().failed)
def setUp(self):
self.maxDiff = None # Make the diff to be complete
self.dataDir = home(dataDir="test-param")
self.testDir = os.environ.get("TESTDIR", tempname())
def setUp(self):
from parameterize.home import home
self.refDir = home(dataDir="test-fftype")
