def test_update_data_file(self):
""" Test writing another CIF file """
# Create a initial data file --
#
myDataList = []
ofh = open(get_fn("test-output-1.cif", written=True), "w")
curContainer = DataContainer("myblock")
aCat = DataCategory("pdbx_seqtool_mapping_ref")
aCat.appendAttribute("ordinal")
aCat.appendAttribute("entity_id")
aCat.appendAttribute("auth_mon_id")
aCat.appendAttribute("auth_mon_num")
aCat.appendAttribute("pdb_chain_id")
aCat.appendAttribute("ref_mon_id")
aCat.appendAttribute("ref_mon_num")
aCat.append((1, 2, 3, 4, 5, 6, 7))
aCat.append((1, 2, 3, 4, 5, 6, 7))
aCat.append((1, 2, 3, 4, 5, 6, 7))
aCat.append((1, 2, 3, 4, 5, 6, 7))
curContainer.append(aCat)
myDataList.append(curContainer)
pdbxW = PdbxWriter(ofh)
pdbxW.write(myDataList)
ofh.close()
self.assertTrue(
diff_files(get_saved_fn('test-output-1.cif'),
get_fn('test-output-1.cif', written=True)))
#
# Read and update the data -
#
myDataList = []
ifh = open(get_fn("test-output-1.cif", written=True), "r")
pRd = PdbxReader(ifh)
pRd.read(myDataList)
ifh.close()
#
myBlock = myDataList[0]
dest = open(get_fn('test_write_1.txt', written=True), 'w')
myBlock.printIt(dest)
myCat = myBlock.getObj('pdbx_seqtool_mapping_ref')
myCat.printIt(dest)
dest.close()
for iRow in range(0, myCat.getRowCount()):
myCat.setValue('some value', 'ref_mon_id', iRow)
myCat.setValue(100, 'ref_mon_num', iRow)
ofh = open(get_fn("test-output-2.cif", written=True), "w")
pdbxW = PdbxWriter(ofh)
pdbxW.write(myDataList)
ofh.close()
self.assertTrue(
diff_files(get_saved_fn('test-output-2.cif'),
get_fn('test-output-2.cif', written=True)))
self.assertTrue(
diff_files(get_saved_fn('test_write_1.txt'),
get_fn('test_write_1.txt', written=True)))
def testUpdateDataFile(self):
""" Test writing another CIF file """
# Create a initial data file --
#
myDataList=[]
ofh = open(get_fn("test-output-1.cif", written=True), "w")
curContainer=DataContainer("myblock")
aCat=DataCategory("pdbx_seqtool_mapping_ref")
aCat.appendAttribute("ordinal")
aCat.appendAttribute("entity_id")
aCat.appendAttribute("auth_mon_id")
aCat.appendAttribute("auth_mon_num")
aCat.appendAttribute("pdb_chain_id")
aCat.appendAttribute("ref_mon_id")
aCat.appendAttribute("ref_mon_num")
aCat.append((1,2,3,4,5,6,7))
aCat.append((1,2,3,4,5,6,7))
aCat.append((1,2,3,4,5,6,7))
aCat.append((1,2,3,4,5,6,7))
curContainer.append(aCat)
myDataList.append(curContainer)
pdbxW=PdbxWriter(ofh)
pdbxW.write(myDataList)
ofh.close()
self.assertTrue(diff_files(get_saved_fn('test-output-1.cif'),
get_fn('test-output-1.cif', written=True)))
#
# Read and update the data -
#
myDataList=[]
ifh = open(get_fn("test-output-1.cif", written=True), "r")
pRd=PdbxReader(ifh)
pRd.read(myDataList)
ifh.close()
#
myBlock=myDataList[0]
dest = open(get_fn('test_write_1.txt', written=True), 'w')
myBlock.printIt(dest)
myCat=myBlock.getObj('pdbx_seqtool_mapping_ref')
myCat.printIt(dest)
dest.close()
for iRow in range(0,myCat.getRowCount()):
myCat.setValue('some value', 'ref_mon_id',iRow)
myCat.setValue(100, 'ref_mon_num',iRow)
ofh = open(get_fn("test-output-2.cif", written=True), "w")
pdbxW=PdbxWriter(ofh)
pdbxW.write(myDataList)
ofh.close()
self.assertTrue(diff_files(get_saved_fn('test-output-2.cif'),
get_fn('test-output-2.cif', written=True)))
self.assertTrue(diff_files(get_saved_fn('test_write_1.txt'),
get_fn('test_write_1.txt', written=True)))
def testMol3SingleWriteStruct(self):
""" Tests writing mol3 file of single-residue Structure """
mol2 = formats.Mol2File.parse(get_fn('tripos9.mol2'), structure=True)
formats.Mol2File.write(mol2, get_fn('tripos9struct.mol3', written=True),
mol3=True)
self.assertTrue(diff_files(get_fn('tripos9struct.mol3', written=True),
get_saved_fn('tripos9struct.mol3')))
def testMol3SingleWrite(self):
""" Tests writing mol3 file of single ResidueTemplate """
mol2 = formats.Mol2File.parse(get_fn('tripos9.mol2'))
formats.Mol2File.write(mol2, get_fn('tripos9.mol3', written=True),
mol3=True)
self.assertTrue(diff_files(get_fn('tripos9.mol3', written=True),
get_saved_fn('tripos9.mol3')))
def testMol3MultiWriteFromStructure(self):
""" Tests writing mol3 file of multi residues from Structure """
mol2 = formats.Mol2File.parse(get_fn('test_multi.mol2'), structure=True)
formats.Mol2File.write(mol2, get_fn('test_multistruct.mol3', written=True),
mol3=True)
self.assertTrue(diff_files(get_fn('test_multistruct.mol3', written=True),
get_saved_fn('test_multistruct.mol3')))
def test_geometric_combining_rule_energy(self):
""" Tests converting geom. comb. rule energy from Gromacs to Amber """
top = load_file(os.path.join(get_fn('05.OPLS'), 'topol.top'),
xyz=os.path.join(get_fn('05.OPLS'), 'conf.gro'))
self.assertEqual(top.combining_rule, 'geometric')
del top.rb_torsions[:]
parm = load_file(get_saved_fn('opls.parm7'),
xyz=os.path.join(get_fn('05.OPLS'), 'conf.gro'))
self.assertEqual(parm.combining_rule, 'geometric')
self.assertFalse(parm.has_NBFIX())
sysg = top.createSystem()
sysa = parm.createSystem()
cong = mm.Context(sysg, mm.VerletIntegrator(0.001), CPU)
cona = mm.Context(sysa, mm.VerletIntegrator(0.001), CPU)
cong.setPositions(top.positions)
cona.setPositions(top.positions)
self.check_energies(top, cong, parm, cona)
# Make an NBFIX
self.assertFalse(parm.has_NBFIX())
parm.parm_data['LENNARD_JONES_ACOEF'][-4] = 10.0
self.assertTrue(parm.has_NBFIX())
parm.createSystem()
def test_write_data_file(self):
""" Test writing CIF file """
myDataList = []
ofh = open(get_fn("test-output.cif", written=True), "w")
curContainer = DataContainer("myblock")
aCat = DataCategory("pdbx_seqtool_mapping_ref")
aCat.appendAttribute("ordinal")
aCat.appendAttribute("entity_id")
aCat.appendAttribute("auth_mon_id")
aCat.appendAttribute("auth_mon_num")
aCat.appendAttribute("pdb_chain_id")
aCat.appendAttribute("ref_mon_id")
aCat.appendAttribute("ref_mon_num")
aCat.append((1, 2, 3, 4, 5, 6, 7))
aCat.append((1, 2, 3, 4, 5, 6, 7))
aCat.append((1, 2, 3, 4, 5, 6, 7))
aCat.append((1, 2, 3, 4, 5, 6, 7))
curContainer.append(aCat)
myDataList.append(curContainer)
pdbxW = PdbxWriter(ofh)
pdbxW.write(myDataList)
ofh.close()
self.assertTrue(
diff_files(get_saved_fn('test-output.cif'),
get_fn('test-output.cif', written=True)))
def test_geometric_combining_rule_energy(self):
""" Tests converting geom. comb. rule energy from Gromacs to Amber """
top = load_file(os.path.join(get_fn('05.OPLS'), 'topol.top'),
xyz=os.path.join(get_fn('05.OPLS'), 'conf.gro'))
self.assertEqual(top.combining_rule, 'geometric')
del top.rb_torsions[:]
parm = load_file(get_saved_fn('opls.parm7'),
xyz=os.path.join(get_fn('05.OPLS'), 'conf.gro'))
self.assertEqual(parm.combining_rule, 'geometric')
self.assertFalse(parm.has_NBFIX())
sysg = top.createSystem()
sysa = parm.createSystem()
cong = mm.Context(sysg, mm.VerletIntegrator(0.001), CPU)
cona = mm.Context(sysa, mm.VerletIntegrator(0.001), CPU)
cong.setPositions(top.positions)
cona.setPositions(top.positions)
self._check_energies(top, cong, parm, cona)
# Make an NBFIX
self.assertFalse(parm.has_NBFIX())
parm.parm_data['LENNARD_JONES_ACOEF'][-4] = 10.0
self.assertTrue(parm.has_NBFIX())
parm.createSystem()
def testMol2MultiWrite(self):
"""
Tests writing mol2 file of multi residues from ResidueTemplateContainer
"""
mol2 = formats.Mol2File.parse(get_fn('test_multi.mol2'))
formats.Mol2File.write(mol2, get_fn('test_multi.mol2', written=True))
self.assertTrue(diff_files(get_fn('test_multi.mol2', written=True),
get_saved_fn('test_multi.mol2')))
def test_ala_gas(self):
""" Test for alanine dipeptide in gas-phase """
parm = get_fn('ala_gas.prmtop')
rst7 = get_fn('ala_gas.rst7')
output1 = get_fn('ala_gas.field', written=True)
output2 = get_fn('ala_gas.config', written=True)
amber = parmed.load_file(parm, rst7)
amber.save(output1)
self.assertTrue(
diff_files(get_saved_fn('ala_gas.field'),
output1,
absolute_error=1e-6))
amber.save(output2)
self.assertTrue(
diff_files(get_saved_fn('ala_gas.config'),
output2,
absolute_error=1e-6))
def test_ksi_solv(self):
""" Test for ksi protein in solution-phase """
parm = get_fn('ksi_solv.prmtop')
rst7 = get_fn('ksi_solv.rst7')
output1 = get_fn('ksi_solv.field', written=True)
output2 = get_fn('ksi_solv.config', written=True)
amber = parmed.load_file(parm, rst7)
amber.save(output1)
self.assertTrue(
diff_files(get_saved_fn('ksi_solv.field'),
output1,
absolute_error=1e-6))
amber.save(output2)
self.assertTrue(
diff_files(get_saved_fn('ksi_solv.config'),
output2,
absolute_error=1e-6))
def test_simple(self):
""" Tests converting simple Amber system to CHARMM PSF/parameters """
parm = load_file(get_fn('trx.prmtop'), get_fn('trx.inpcrd'))
parm.save(get_fn('amber_to_charmm.psf', written=True))
params = charmm.CharmmParameterSet.from_structure(parm)
params.write(str=get_fn('amber_to_charmm.str', written=True))
self.assertTrue(
diff_files(get_saved_fn('amber_to_charmm.psf'),
get_fn('amber_to_charmm.psf', written=True)
)
)
self.assertTrue(
diff_files(get_saved_fn('amber_to_charmm.str'),
get_fn('amber_to_charmm.str', written=True),
absolute_error=1e-5,
)
)
# Check the PSF file
psf = load_file(get_fn('amber_to_charmm.psf', written=True))
psf.load_parameters(
charmm.CharmmParameterSet(get_fn('amber_to_charmm.str',
written=True))
)
for a1, a2 in zip(psf.atoms, parm.atoms):
self.assertEqual(a1.name, a2.name)
self.assertEqual(a1.atomic_number, a2.atomic_number)
self.assertEqual(a1.mass, a2.mass)
self.assertEqual(len(psf.bonds), len(parm.bonds))
self.assertEqual(len(psf.angles), len(parm.angles))
# Get number of unique torsions
nnormal = nimp = 0
torsfound = set()
for tor in parm.dihedrals:
a1, a2, a3, a4 = tor.atom1, tor.atom2, tor.atom3, tor.atom4
if tor.improper:
nimp += 1
continue
if (a1, a2, a3, a4) in torsfound or (a4, a3, a2, a1) in torsfound:
continue
torsfound.add((a1, a2, a3, a4))
nnormal += 1
# Make sure that written psf only contains unique torsions.
self.assertEqual(nnormal+nimp, len(psf.dihedrals))
def test_simple(self):
""" Tests converting simple Amber system to CHARMM PSF/parameters """
parm = load_file(get_fn('trx.prmtop'), get_fn('trx.inpcrd'))
parm.save(get_fn('amber_to_charmm.psf', written=True))
params = charmm.CharmmParameterSet.from_structure(parm)
params.write(str=get_fn('amber_to_charmm.str', written=True))
self.assertTrue(
diff_files(get_saved_fn('amber_to_charmm.psf'),
get_fn('amber_to_charmm.psf', written=True)
)
)
self.assertTrue(
diff_files(get_saved_fn('amber_to_charmm.str'),
get_fn('amber_to_charmm.str', written=True),
absolute_error=1e-5,
)
)
# Check the PSF file
psf = load_file(get_fn('amber_to_charmm.psf', written=True))
psf.load_parameters(
charmm.CharmmParameterSet(get_fn('amber_to_charmm.str',
written=True))
)
for a1, a2 in zip(psf.atoms, parm.atoms):
self.assertEqual(a1.name, a2.name)
self.assertEqual(a1.atomic_number, a2.atomic_number)
self.assertEqual(a1.mass, a2.mass)
self.assertEqual(len(psf.bonds), len(parm.bonds))
self.assertEqual(len(psf.angles), len(parm.angles))
# Get number of unique torsions
nnormal = nimp = 0
torsfound = set()
for tor in parm.dihedrals:
a1, a2, a3, a4 = tor.atom1, tor.atom2, tor.atom3, tor.atom4
if tor.improper:
nimp += 1
continue
if (a1, a2, a3, a4) in torsfound or (a4, a3, a2, a1) in torsfound:
continue
torsfound.add((a1, a2, a3, a4))
nnormal += 1
# Make sure that written psf only contains unique torsions.
self.assertEqual(nnormal+nimp, len(psf.dihedrals))
def test_chamber(self):
""" Tests converting standard Gromacs system into Chamber prmtop """
top = load_file(get_fn('1aki.charmm27.solv.top'),
xyz=get_fn('1aki.charmm27.solv.gro'))
parm = amber.ChamberParm.from_structure(top)
parm.write_parm(get_fn('1aki.charmm27_fromgmx.parm7', written=True))
self.assertTrue(diff_files(get_fn('1aki.charmm27_fromgmx.parm7',
written=True),
get_saved_fn('1aki.charmm27_fromgmx.parm7'),
relative_error=1e-8)
)
def testGeometricCombiningRule(self):
""" Tests converting geom. comb. rule from Gromacs to Amber """
top = load_file(os.path.join(get_fn('05.OPLS'), 'topol.top'),
xyz=os.path.join(get_fn('05.OPLS'), 'conf.gro'))
self.assertEqual(top.combining_rule, 'geometric')
del top.rb_torsions[:]
parm = amber.AmberParm.from_structure(top)
self.assertEqual(parm.combining_rule, 'geometric')
parm.write_parm(get_fn('opls.parm7', written=True))
self.assertTrue(diff_files(get_fn('opls.parm7', written=True),
get_saved_fn('opls.parm7'))
)
def testMol2MultiWrite(self):
"""
Tests writing mol2 file of multi residues from ResidueTemplateContainer
"""
mol2 = formats.Mol2File.parse(get_fn('test_multi.mol2'))
formats.Mol2File.write(mol2, get_fn('test_multi.mol2', written=True))
formats.Mol2File.write(mol2, get_fn('test_multi_sep.mol2', written=True),
split=True)
self.assertTrue(diff_files(get_saved_fn('test_multi.mol2'),
get_fn('test_multi.mol2', written=True)))
self.assertTrue(diff_files(get_saved_fn('test_multi_sep.mol2'),
get_fn('test_multi_sep.mol2', written=True)))
mol22 = formats.Mol2File.parse(get_fn('test_multi_sep.mol2', written=True))
self.assertEqual(len(mol2), len(mol22))
self.assertEqual([r.name for r in mol2], [r.name for r in mol22])
for r1, r2 in zip(mol2, mol22):
self.assertEqual(len(r1.bonds), len(r2.bonds))
self.assertEqual(len(r1.atoms), len(r2.atoms))
self.assertFalse(r1.head is None and r1.tail is None)
self.assertTrue(r2.head is None and r2.tail is None)
f = StringIO()
formats.Mol2File.write(mol2, f, mol3=True, split=True)
f.seek(0)
mol3 = formats.Mol2File.parse(f)
self.assertEqual(len(mol2), len(mol3))
self.assertEqual([r.name for r in mol2], [r.name for r in mol3])
for r1, r2 in zip(mol2, mol3):
self.assertEqual(len(r1.bonds), len(r2.bonds))
self.assertEqual(len(r1.atoms), len(r2.atoms))
self.assertFalse(r1.head is None and r1.tail is None)
self.assertFalse(r2.head is None and r2.tail is None)
if r1.head is None:
self.assertIs(r2.head, None)
else:
self.assertEqual(r1.head.name, r2.head.name)
if r1.tail is None:
self.assertIs(r2.tail, None)
else:
self.assertEqual(r1.tail.name, r2.tail.name)
def test_chamber(self):
""" Tests converting standard Gromacs system into Chamber prmtop """
fn = get_fn('1aki.charmm27_fromgmx.parm7')
top = load_file(get_fn('1aki.charmm27.solv.top'),
xyz=get_fn('1aki.charmm27.solv.gro'))
parm = amber.ChamberParm.from_structure(top)
parm.write_parm(fn)
self.assertTrue(
diff_files(fn, get_saved_fn('1aki.charmm27_fromgmx.parm7'),
relative_error=1e-8)
)
parm.fill_LJ()
self.assertTrue(0 in parm.LJ_14_radius)
self.assertTrue(0 in parm.LJ_14_depth)
def test_chamber(self):
""" Tests converting standard Gromacs system into Chamber prmtop """
fn = get_fn('1aki.charmm27_fromgmx.parm7', written=True)
top = load_file(get_fn('1aki.charmm27.solv.top'),
xyz=get_fn('1aki.charmm27.solv.gro'))
self.assertGreater(len(top.urey_bradleys), 0)
self.assertGreater(len(top.urey_bradley_types), 0)
parm = amber.ChamberParm.from_structure(top)
parm.write_parm(fn)
self.assertTrue(
diff_files(fn,
get_saved_fn('1aki.charmm27_fromgmx.parm7'),
relative_error=1e-8))
parm.fill_LJ()
self.assertTrue(0 in parm.LJ_14_radius)
self.assertTrue(0 in parm.LJ_14_depth)
def test_geometric_combining_rule(self):
""" Tests converting geom. comb. rule from Gromacs to Amber """
top = load_file(os.path.join(get_fn('05.OPLS'), 'topol.top'),
xyz=os.path.join(get_fn('05.OPLS'), 'conf.gro'))
self.assertEqual(top.combining_rule, 'geometric')
del top.rb_torsions[:]
parm = amber.AmberParm.from_structure(top)
parm.box = None # Get rid of the unit cell
self.assertEqual(parm.combining_rule, 'geometric')
parm.write_parm(get_fn('opls.parm7', written=True))
self.assertTrue(diff_files(get_fn('opls.parm7', written=True),
get_saved_fn('opls.parm7'))
)
# Make sure recalculate_LJ works
acoef = np.array(parm.parm_data['LENNARD_JONES_ACOEF'])
bcoef = np.array(parm.parm_data['LENNARD_JONES_BCOEF'])
parm.recalculate_LJ()
np.testing.assert_allclose(acoef, parm.parm_data['LENNARD_JONES_ACOEF'])
np.testing.assert_allclose(bcoef, parm.parm_data['LENNARD_JONES_BCOEF'])
def test_geometric_combining_rule(self):
""" Tests converting geom. comb. rule from Gromacs to Amber """
top = load_file(os.path.join(get_fn('05.OPLS'), 'topol.top'),
xyz=os.path.join(get_fn('05.OPLS'), 'conf.gro'))
self.assertEqual(top.combining_rule, 'geometric')
del top.rb_torsions[:]
parm = amber.AmberParm.from_structure(top)
parm.box = None # Get rid of the unit cell
self.assertEqual(parm.combining_rule, 'geometric')
parm.write_parm(get_fn('opls.parm7', written=True))
self.assertTrue(diff_files(get_fn('opls.parm7', written=True),
get_saved_fn('opls.parm7'))
)
# Make sure recalculate_LJ works
acoef = np.array(parm.parm_data['LENNARD_JONES_ACOEF'])
bcoef = np.array(parm.parm_data['LENNARD_JONES_BCOEF'])
parm.recalculate_LJ()
np.testing.assert_allclose(acoef, parm.parm_data['LENNARD_JONES_ACOEF'])
np.testing.assert_allclose(bcoef, parm.parm_data['LENNARD_JONES_BCOEF'])
def test_benzene_cyclohexane(self):
""" Test converting binary liquid from Amber prmtop to Gromacs top """
parm = load_file(get_fn('benzene_cyclohexane_10_500.prmtop'),
get_fn('benzene_cyclohexane_10_500.inpcrd'))
top = gromacs.GromacsTopologyFile.from_structure(parm)
self.assertEqual(top.combining_rule, 'lorentz')
groname = get_fn('benzene_cyclohexane_10_500.gro', written=True)
gromacs.GromacsGroFile.write(parm, groname, precision=8)
gro = gromacs.GromacsGroFile.parse(groname)
self.assertEqual(len(gro.atoms), len(parm.atoms))
np.testing.assert_allclose(gro.box, parm.box)
for a1, a2 in zip(gro.atoms, parm.atoms):
self.assertEqual(a1.residue.name, a2.residue.name)
self.assertEqual(a1.residue.idx, a2.residue.idx)
self.assertEqual(a1.name, a2.name)
self.assertAlmostEqual(a1.xx, a2.xx)
self.assertAlmostEqual(a1.xy, a2.xy)
self.assertAlmostEqual(a1.xz, a2.xz)
top.write(get_fn('benzene_cyclohexane_10_500.top', written=True))
saved = GromacsFile(get_saved_fn('benzene_cyclohexane_10_500.top'))
written = GromacsFile(
get_fn('benzene_cyclohexane_10_500.top', written=True))
self.assertTrue(diff_files(saved, written))
# Check that Gromacs topology is given the correct box information when
# generated from a Structure
gromacs.GromacsGroFile.write(top, groname, precision=8)
gro = gromacs.GromacsGroFile.parse(groname)
self.assertEqual(len(gro.atoms), len(parm.atoms))
for a1, a2 in zip(gro.atoms, parm.atoms):
self.assertEqual(a1.residue.name, a2.residue.name)
self.assertEqual(a1.residue.idx, a2.residue.idx)
self.assertEqual(a1.name, a2.name)
self.assertAlmostEqual(a1.xx, a2.xx)
self.assertAlmostEqual(a1.xy, a2.xy)
self.assertAlmostEqual(a1.xz, a2.xz)
np.testing.assert_allclose(gro.box, parm.box)
np.testing.assert_allclose(top.box, parm.box)
def testReadWriteHighPrecisionGroFile(self):
""" Tests reading/writing high-precision GRO files """
gro = GromacsGroFile.parse(get_fn('1aki.ff99sbildn.gro'))
GromacsGroFile.write(gro, get_fn('1aki.ff99sbildn_highprec.gro',
written=True),
precision=6)
self.assertTrue(diff_files(get_saved_fn('1aki.ff99sbildn_highprec.gro'),
get_fn('1aki.ff99sbildn_highprec.gro',
written=True)
)
)
gro2 = GromacsGroFile.parse(get_fn('1aki.ff99sbildn_highprec.gro',
written=True))
gro3 = load_file(get_fn('1aki.ff99sbildn_highprec.gro', written=True))
self.assertIsInstance(gro3, Structure)
for a1, a2, a3 in zip(gro.atoms, gro2.atoms, gro3.atoms):
self.assertEqual(a1.name, a2.name)
self.assertEqual(a3.name, a2.name)
self.assertEqual(a1.xx, a2.xx)
self.assertEqual(a3.xx, a2.xx)
self.assertEqual(a1.xy, a2.xy)
self.assertEqual(a3.xy, a2.xy)
self.assertEqual(a1.xz, a2.xz)
self.assertEqual(a3.xz, a2.xz)
def testWriteDataFile(self):
""" Test writing CIF file """
myDataList=[]
ofh = open(get_fn("test-output.cif", written=True), "w")
curContainer=DataContainer("myblock")
aCat=DataCategory("pdbx_seqtool_mapping_ref")
aCat.appendAttribute("ordinal")
aCat.appendAttribute("entity_id")
aCat.appendAttribute("auth_mon_id")
aCat.appendAttribute("auth_mon_num")
aCat.appendAttribute("pdb_chain_id")
aCat.appendAttribute("ref_mon_id")
aCat.appendAttribute("ref_mon_num")
aCat.append((1,2,3,4,5,6,7))
aCat.append((1,2,3,4,5,6,7))
aCat.append((1,2,3,4,5,6,7))
aCat.append((1,2,3,4,5,6,7))
curContainer.append(aCat)
myDataList.append(curContainer)
pdbxW=PdbxWriter(ofh)
pdbxW.write(myDataList)
ofh.close()
self.assertTrue(diff_files(get_saved_fn('test-output.cif'),
get_fn('test-output.cif', written=True)))
def test_benzene_cyclohexane(self):
""" Test converting binary liquid from Amber prmtop to Gromacs top """
parm = load_file(get_fn('benzene_cyclohexane_10_500.prmtop'),
get_fn('benzene_cyclohexane_10_500.inpcrd'))
top = gromacs.GromacsTopologyFile.from_structure(parm)
self.assertEqual(top.combining_rule, 'lorentz')
groname = get_fn('benzene_cyclohexane_10_500.gro', written=True)
gromacs.GromacsGroFile.write(parm, groname, precision=8)
gro = gromacs.GromacsGroFile.parse(groname)
self.assertEqual(len(gro.atoms), len(parm.atoms))
np.testing.assert_allclose(gro.box, parm.box)
for a1, a2 in zip(gro.atoms, parm.atoms):
self.assertEqual(a1.residue.name, a2.residue.name)
self.assertEqual(a1.residue.idx, a2.residue.idx)
self.assertEqual(a1.name, a2.name)
self.assertAlmostEqual(a1.xx, a2.xx)
self.assertAlmostEqual(a1.xy, a2.xy)
self.assertAlmostEqual(a1.xz, a2.xz)
top.write(get_fn('benzene_cyclohexane_10_500.top', written=True))
saved = GromacsFile(get_saved_fn('benzene_cyclohexane_10_500.top'))
written = GromacsFile(get_fn('benzene_cyclohexane_10_500.top', written=True))
self.assertTrue(diff_files(saved, written))
# Check that Gromacs topology is given the correct box information when
# generated from a Structure
gromacs.GromacsGroFile.write(top, groname, precision=8)
gro = gromacs.GromacsGroFile.parse(groname)
self.assertEqual(len(gro.atoms), len(parm.atoms))
for a1, a2 in zip(gro.atoms, parm.atoms):
self.assertEqual(a1.residue.name, a2.residue.name)
self.assertEqual(a1.residue.idx, a2.residue.idx)
self.assertEqual(a1.name, a2.name)
self.assertAlmostEqual(a1.xx, a2.xx)
self.assertAlmostEqual(a1.xy, a2.xy)
self.assertAlmostEqual(a1.xz, a2.xz)
np.testing.assert_allclose(gro.box, parm.box)
np.testing.assert_allclose(top.box, parm.box)
def testPDBWriteFormat(self):
""" Test PDB atom names are properly justified per PDB standard """
pdbfile = read_PDB(self.format_test)
f = get_fn('pdb_format_test.pdb', written=True)
pdbfile.write_pdb(f, write_anisou=True)
self.assertTrue(diff_files(get_saved_fn('SCM_A_formatted.pdb'), f))