def testWithoutProteinPrepare(self):
from htmd.builder.solvate import solvate
# Test without proteinPrepare
pdbids = ['3PTB']
# pdbids = ['3PTB', '1A25', '1GZM', '1U5U']
for pid in pdbids:
np.random.seed(1)
mol = Molecule(pid)
mol.filter('protein')
if mol._checkInsertions():
mol.renumberResidues()
smol = solvate(mol)
ffs = defaultFf()
tmpdir = os.path.join(self.testDir, 'withoutProtPrep', pid)
_ = build(smol, ff=ffs, outdir=tmpdir)
refdir = home(dataDir=join('test-amber-build', 'nopp', pid))
TestAmberBuild._compareResultFolders(refdir, tmpdir, pid)
def testWithProteinPrepare(self):
from htmd.builder.preparation import proteinPrepare
from htmd.builder.solvate import solvate
# Test with proteinPrepare
pdbids = ['3PTB']
# pdbids = ['3PTB', '1A25', '1GZM'] # '1U5U' out because it has AR0 (no parameters)
for pid in pdbids:
np.random.seed(1)
mol = Molecule(pid)
mol.filter('protein')
if mol._checkInsertions():
mol.renumberResidues()
mol = proteinPrepare(mol)
mol.filter(
'protein') # Fix for bad proteinPrepare hydrogen placing
smol = solvate(mol)
ffs = defaultFf()
tmpdir = os.path.join(self.testDir, 'withProtPrep', pid)
_ = build(smol, ff=ffs, outdir=tmpdir)
refdir = home(dataDir=join('test-amber-build', 'pp', pid))
TestAmberBuild._compareResultFolders(refdir, tmpdir, pid)
from htmd.builder.preparation import proteinPrepare
import os
from glob import glob
import numpy as np
# Use pre-prepared files so we can tell whether the error is in prepare or in build
# Inputs are reference outputs of proteinprepare.
preparedInputDir = home(dataDir='test-proteinprepare')
pdbids = ['3PTB', '1A25', '1GZM', '1U5U']
for pdb in pdbids:
inFile = os.path.join(preparedInputDir, pdb,
"{}-prepared.pdb".format(pdb))
mol = Molecule(inFile)
mol.filter('protein') # Fix for bad proteinPrepare hydrogen placing
if mol._checkInsertions():
mol.renumberResidues()
np.random.seed(1) # Needed for ions
smol = solvate(mol)
topos = ['top/top_all36_prot.rtf', 'top/top_water_ions.rtf']
params = ['par/par_all36_prot_mod.prm', 'par/par_water_ions.prm']
tmpdir = tempname()
bmol = build(smol, topo=topos, param=params, outdir=tmpdir)
compareDir = home(dataDir=os.path.join('test-charmm-build', pdb))
assertSameAsReferenceDir(compareDir, tmpdir)
# shutil.rmtree(tmpdir)
from htmd.ui import *
from htmd.util import tempname, assertSameAsReferenceDir
from htmd.builder.preparation import proteinPrepare
import os
from glob import glob
import numpy as np
# Use pre-prepared files so we can tell whether the error is in prepare or in build
# Inputs are reference outputs of proteinprepare.
preparedInputDir = home(dataDir='test-proteinprepare')
pdbids = ['3PTB', '1A25', '1GZM', '1U5U']
for pdb in pdbids:
inFile = os.path.join(preparedInputDir, pdb, "{}-prepared.pdb".format(pdb))
mol = Molecule(inFile)
mol.filter('protein') # Fix for bad proteinPrepare hydrogen placing
if mol._checkInsertions():
mol.renumberResidues()
np.random.seed(1) # Needed for ions
smol = solvate(mol)
topos = ['top/top_all36_prot.rtf', 'top/top_water_ions.rtf']
params = ['par/par_all36_prot_mod.prm', 'par/par_water_ions.prm']
tmpdir = tempname()
bmol = build(smol, topo=topos, param=params, outdir=tmpdir)
compareDir = home(dataDir=os.path.join('test-charmm-build', pdb))
assertSameAsReferenceDir(compareDir, tmpdir)
shutil.rmtree(tmpdir)
from htmd.ui import *
