def buildProtein(sequence, outdir, start_idx=1):
from htmd.builder.preparation import proteinPrepare
from htmd.ui import Molecule, amber
import sys
sys.path.append(
"/home/pablo/PyRosetta4.Release.python36.linux.release-197")
import pyrosetta
pyrosetta.init()
pose = pyrosetta.pose_from_sequence(sequence, 'fa_standard')
pose.dump_pdb('/tmp/test.pdb')
mol = Molecule('/tmp/test.pdb')
mol = proteinPrepare(mol)
mol.resid = mol.resid + start_idx
mol.set('segid', 'P1')
mol.filter('backbone')
_ = amber.build(mol, outdir=outdir, ionize=False
# , caps=None
)
return outdir + '/structure.prmtop'
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')
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)
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')
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)
newResData.data['protonation'] = copy_of_protonation
newResData.data['default_protonation'] = copy_of_default_protonation
newResData.data.loc[list_of_forced_protonations, 'protonation'] = \
d.loc[list_of_forced_protonations, 'forced_protonation']
for cn in keep_pka_columns:
newResData.data[cn] = d[cn]
newResData.pdb2pqr_routines = routines
newResData.pdb2pqr_protein = routines.protein
newResData.missedLigands = self.missedLigands
return newMol, newResData
if __name__ == "__main__":
from htmd.builder.preparation import proteinPrepare
import sys
import doctest
doctest.testmod()
if len(sys.argv) > 1 and sys.argv[1] == 'long-test':
print('LONG TEST')
m = Molecule("3ptb")
mp, dp = proteinPrepare(m, returnDetails=True)
hb = dp.findHbonds()
d = dp.data
d.loc[d.resid == 40, 'forced_protonation'] = 'HIP'
mp2, dp2 = dp.reprepare()
hb2 = dp2.findHbonds()
'Different results produced by amber.build for test {} between {} and {} in files {}.'
.format(pid, compare, tmpdir, mismatch))
for f in deletefiles:
os.remove(f)
# 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 = tempname()
bmol = build(smol, ff=ffs, outdir=tmpdir)
refdir = home(dataDir=os.path.join('test-amber-build', pid))
_compareResultFolders(refdir, tmpdir, pid)
shutil.rmtree(tmpdir)
# Test without proteinPrepare
pdbids = ['3PTB']
# pdbids = ['3PTB', '1A25', '1GZM', '1U5U']
for pid in pdbids:
np.random.seed(1)
match, mismatch, error = filecmp.cmpfiles(tmpdir, compare, files, shallow=False)
if len(mismatch) != 0 or len(error) != 0 or len(match) != len(files):
raise RuntimeError(
'Different results produced by amber.build for test {} between {} and {} in files {}.'.format(pid, compare, tmpdir, mismatch))
for f in deletefiles:
os.remove(f)
# Test with proteinPrepare
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')
mol = proteinPrepare(mol)
mol.filter('protein') # Fix for bad proteinPrepare hydrogen placing
smol = solvate(mol)
ffs = ['leaprc.lipid14', 'leaprc.ff14SB', 'leaprc.gaff']
tmpdir = tempname()
bmol = build(smol, ff=ffs, outdir=tmpdir)
refdir = home(dataDir=os.path.join('test-amber-build', pid))
_compareResultFolders(refdir, tmpdir, pid)
shutil.rmtree(tmpdir)
# Test without proteinPrepare
pdbids = ['3PTB', '1A25', '1GZM', '1U5U']
for pid in pdbids:
np.random.seed(1)
mol = Molecule(pid)
newResData.data['resname'] = copy_of_resname
newResData.data['protonation'] = copy_of_protonation
newResData.data['default_protonation'] = copy_of_default_protonation
newResData.data.loc[list_of_forced_protonations, 'protonation'] = \
d.loc[list_of_forced_protonations, 'forced_protonation']
for cn in keep_pka_columns:
newResData.data[cn] = d[cn]
newResData.pdb2pqr_routines = routines
newResData.pdb2pqr_protein = routines.protein
newResData.missedLigands = self.missedLigands
return newMol, newResData
if __name__ == "__main__":
from htmd.builder.preparation import proteinPrepare
import sys
import doctest
doctest.testmod()
if len(sys.argv) > 1 and sys.argv[0] == 'long-test':
m = Molecule("3ptb")
mp, dp = proteinPrepare(m, returnDetails=True)
hb = dp.findHbonds()
d = dp.data
d.loc[d.resid == 40, 'forced_protonation'] = 'HIP'
mp2, dp2 = dp.reprepare()
hb2 = dp2.findHbonds()