def test_customDisulfideBonds(self):
from htmd.molecule.molecule import Molecule
from htmd.builder.solvate import solvate
from htmd.home import home
from htmd.util import tempname, assertSameAsReferenceDir
import os
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')
pdb = '1GZM'
inFile = os.path.join(preparedInputDir, pdb,
"{}-prepared.pdb".format(pdb))
mol = Molecule(inFile)
mol.filter('protein') # Fix for bad proteinPrepare hydrogen placing
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']
disu = [['segid 1 and resid 110', 'segid 1 and resid 187'],
['segid 0 and resid 110', 'segid 0 and resid 187']]
tmpdir = tempname()
_ = build(smol,
topo=topos,
param=params,
outdir=tmpdir,
disulfide=disu)
compareDir = home(dataDir=os.path.join('test-charmm-build', pdb))
assertSameAsReferenceDir(compareDir, tmpdir)
# TODO: Remove this after deprecation
from htmd.builder.builder import DisulfideBridge
np.random.seed(1) # Needed for ions
disu = [
DisulfideBridge('1', 110, '1', 187),
DisulfideBridge('0', 110, '0', 187)
]
tmpdir = tempname()
_ = build(smol,
topo=topos,
param=params,
outdir=tmpdir,
disulfide=disu)
compareDir = home(dataDir=os.path.join('test-charmm-build', pdb))
assertSameAsReferenceDir(compareDir, tmpdir)
def test_customDisulfideBonds(self):
from moleculekit.molecule import Molecule
from htmd.builder.solvate import solvate
from htmd.home import home
from htmd.util import tempname, assertSameAsReferenceDir
import os
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")
pdb = "1GZM"
inFile = os.path.join(preparedInputDir, pdb, "{}-prepared.pdb".format(pdb))
mol = Molecule(inFile)
mol.filter("protein") # Fix for bad proteinPrepare hydrogen placing
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.prm", "par/par_water_ions.prm"]
disu = [
["segid 1 and resid 110", "segid 1 and resid 187"],
["segid 0 and resid 110", "segid 0 and resid 187"],
]
tmpdir = tempname()
_ = build(smol, topo=topos, param=params, outdir=tmpdir, disulfide=disu)
compareDir = home(dataDir=os.path.join("test-charmm-build", pdb))
assertSameAsReferenceDir(compareDir, tmpdir)
# TODO: Remove this after deprecation
from htmd.builder.builder import DisulfideBridge
np.random.seed(1) # Needed for ions
disu = [
DisulfideBridge("1", 110, "1", 187),
DisulfideBridge("0", 110, "0", 187),
]
tmpdir = tempname()
_ = build(smol, topo=topos, param=params, outdir=tmpdir, disulfide=disu)
compareDir = home(dataDir=os.path.join("test-charmm-build", pdb))
assertSameAsReferenceDir(compareDir, tmpdir)