def testProteinLigand(self):
from htmd.builder.solvate import solvate
from htmd.parameterization.fftype import fftype, FFTypeMethod
from htmd.parameterization.writers import writeFRCMOD
# Test protein ligand building with parametrized ligand
refdir = home(dataDir=join('test-amber-build', 'protLig'))
tmpdir = os.path.join(self.testDir, 'protLig')
os.makedirs(tmpdir)
mol = Molecule(join(refdir, '3ptb_mod.pdb'))
lig = Molecule(join(refdir, 'benzamidine.pdb'),
guess=('bonds', 'angles', 'dihedrals'))
prm, lig = fftype(lig, method=FFTypeMethod.GAFF2)
writeFRCMOD(lig, prm, join(tmpdir, 'mol.frcmod'))
lig.segid[:] = 'L'
# params =
newmol = Molecule()
newmol.append(lig)
newmol.append(mol)
smol = solvate(newmol)
params = defaultParam() + [
join(tmpdir, 'mol.frcmod'),
]
_ = build(smol, outdir=tmpdir, param=params, ionize=False)
refdir = home(dataDir=join('test-amber-build', 'protLig', 'results'))
TestAmberBuild._compareResultFolders(refdir, tmpdir, '3PTB')
def _get_prmtop(self, mol, prm):
from htmd.parameterization.writers import writeFRCMOD, getAtomTypeMapping
from tempfile import TemporaryDirectory
from subprocess import call
from simtk.openmm import app
with TemporaryDirectory() as tmpDir:
frcFile = os.path.join(tmpDir, 'mol.frcmod')
mapping = getAtomTypeMapping(prm)
writeFRCMOD(mol, prm, frcFile, typemap=mapping)
mol2 = mol.copy()
mol2.atomtype[:] = np.vectorize(mapping.get)(mol2.atomtype)
molFile = os.path.join(tmpDir, 'mol.mol2')
mol2.write(molFile)
with open(os.path.join(tmpDir, 'tleap.inp'), 'w') as file:
file.writelines(
('loadAmberParams %s\n' % frcFile,
'MOL = loadMol2 %s\n' % molFile,
'saveAmberParm MOL mol.prmtop mol.inpcrd\n', 'quit'))
with open(os.path.join(tmpDir, 'tleap.out'), 'w') as out:
call(('tleap', '-f', 'tleap.inp'), cwd=tmpDir, stdout=out)
prmtop = app.AmberPrmtopFile(os.path.join(tmpDir, 'mol.prmtop'))
return prmtop
def testProteinLigand(self):
from htmd.builder.solvate import solvate
from htmd.parameterization.fftype import fftype, FFTypeMethod
from htmd.parameterization.writers import writeFRCMOD
# Test protein ligand building with parametrized ligand
refdir = home(dataDir=join('test-amber-build', 'protLig'))
tmpdir = os.path.join(self.testDir, 'protLig')
os.makedirs(tmpdir)
mol = Molecule(join(refdir, '3ptb_mod.pdb'))
lig = Molecule(join(refdir, 'benzamidine.pdb'), guess=('bonds', 'angles', 'dihedrals'))
prm, lig = fftype(lig, method=FFTypeMethod.GAFF2)
writeFRCMOD(lig, prm, join(tmpdir, 'mol.frcmod'))
lig.segid[:] = 'L'
# params =
newmol = Molecule()
newmol.append(lig)
newmol.append(mol)
smol = solvate(newmol)
params = defaultParam() + [join(tmpdir, 'mol.frcmod'),]
_ = build(smol, outdir=tmpdir, param=params, ionize=False)
refdir = home(dataDir=join('test-amber-build', 'protLig', 'results'))
TestAmberBuild._compareResultFolders(refdir, tmpdir, '3PTB')
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()
if not re.search('HTMD', line)
])
tmpData = sorted([
from htmd.builder.solvate import solvate
from htmd.parameterization.fftype import fftype
from htmd.parameterization.writers import writeFRCMOD
from moleculekit.molecule import Molecule
from htmd.builder.amber import defaultParam, build
# Test protein ligand building with parametrized ligand
refdir = home(dataDir=join('test-amber-build', 'protLig'))
tmpdir = './protLig'
mol = Molecule(join(refdir, '3ptb_mod.pdb'))
mol.center()
lig = Molecule(join(refdir, 'benzamidine.pdb'),
guess=('bonds', 'angles', 'dihedrals'))
prm, lig = fftype(lig, method='GAFF2')
writeFRCMOD(lig, prm, join(tmpdir, 'mol.frcmod'))
lig.segid[:] = 'L'
lig.center()
from moleculekit.util import maxDistance
D = maxDistance(mol, 'all')
D += 6
lig.moveBy([0, 0, D])
newmol = Molecule()
newmol.append(lig)
newmol.append(mol)
smol = solvate(newmol, posz=3)
params = defaultParam() + [
join(tmpdir, 'mol.frcmod'),
