def test_rtf_prm(self):
from htmd.home import home
from htmd.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 HTMD 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)
# BUG: MATCH does not work on Mac!
if 'TRAVIS_OS_NAME' in os.environ:
if os.environ['TRAVIS_OS_NAME'] == 'osx':
sys.exit(0)
molFile = os.path.join(home('building-protein-ligand'), 'benzamidine.mol2')
refDir = home(dataDir='test-fftype/benzamidine')
mol = Molecule(molFile)
mol = canonicalizeAtomNames(mol)
mol, equivalents, all_dihedrals = getEquivalentsAndDihedrals(mol)
with TemporaryDirectory() as tmpDir:
parameters, mol = fftype(mol, method=FFTypeMethod.CGenFF_2b6)
writeRTF(mol, parameters, 0, os.path.join(tmpDir, 'cgenff.rtf'))
writePRM(mol, parameters, os.path.join(tmpDir, 'cgenff.prm'))
parameters, mol = fftype(mol, method=FFTypeMethod.GAFF)
writeFRCMOD(mol, parameters, os.path.join(tmpDir, 'gaff.frcmod'))
parameters, mol = fftype(mol, method=FFTypeMethod.GAFF2)
writeFRCMOD(mol, parameters, os.path.join(tmpDir, 'gaff2.frcmod'))
for testFile in os.listdir(refDir):
print(testFile)
with open(os.path.join(refDir, testFile)) as refFile:
with open(os.path.join(tmpDir, testFile)) as tmpFile:
# The line order for antechamber is unstable, so the files are sorted.
# Also, it get rids of HTMD version string
refData = sorted([
line for line in refFile.readlines()