def testWriteVmd(self):
""" Test writing VMD-style PSF files """
# Test writing VMD-style PSFs
cpsf = psf.CharmmPsfFile(get_fn('dhfr_cmap_pbc.psf'))
cpsf.write_psf(get_fn('dhfr_cmap_pbc.psf', written=True), vmd=True)
cpsf2 = psf.CharmmPsfFile(get_fn('dhfr_cmap_pbc.psf', written=True))
for attr in dir(cpsf):
if attr.startswith('_'): continue
if attr in ('topology', 'positions', 'box_vectors', 'velocities',
'name'):
continue
if callable(getattr(cpsf, attr)): continue
if hasattr(getattr(cpsf, attr), '__len__'):
self.assertEqual(len(getattr(cpsf, attr)),
len(getattr(cpsf2, attr)))
else:
self.assertEqual(getattr(cpsf, attr), getattr(cpsf2, attr))
f = open(get_fn('dhfr_cmap_pbc.psf', written=True), 'r')
try:
has_key = False
for line in f:
if '!MOLNT' in line:
has_key = True
break
finally:
f.close()
self.assertFalse(has_key)
def testInscodePSF(self):
""" Test PSF with insertion code as part of residue number """
cpsf = psf.CharmmPsfFile(get_fn('4TVP-dmj_wat-ion.psf'))
self.assertEqual(len(cpsf.atoms), 66264)
self.assertEqual(len(cpsf.residues), 20169)
self.assertEqual(len(cpsf.bonds), 46634)
self.assertEqual(len(cpsf.angles), 32739)
self.assertEqual(len(cpsf.dihedrals), 19104)
self.assertEqual(len(cpsf.impropers), 1257)
self.assertEqual(len(cpsf.cmaps), 447)
self.assertEqual(cpsf.residues[281].insertion_code, 'A')
def testCharmmGuiBuilder(self):
""" Test parsing of CHARMM PSF from CHARMM-GUI """
cpsf = psf.CharmmPsfFile(get_fn('parv.psf'))
self.assertEqual(len(cpsf.acceptors), 0)
self.assertEqual(len(cpsf.angles), 3004)
self.assertEqual(len(cpsf.atoms), 1659)
self.assertEqual(len(cpsf.bonds), 1671)
self.assertEqual(len(cpsf.cmaps), 107)
self.assertEqual(len(cpsf.dihedrals), 4377)
self.assertEqual(len(cpsf.donors), 0)
self.assertEqual(len(cpsf.flags), 3)
self.assertEqual(len(cpsf.groups), 1)
self.assertEqual(len(cpsf.impropers), 295)
self.assertEqual(len(cpsf.residues), 109)
self.assertEqual(len(cpsf.title), 3)
def testCharmmPsf(self):
""" Test CHARMM PSF file parsing """
cpsf = psf.CharmmPsfFile(get_fn('ala_ala_ala.psf'))
self.assertEqual(len(cpsf.atoms), 33)
for i, atom in enumerate(cpsf.atoms):
self.assertEqual(atom.idx, i)
self.assertEqual(atom.residue.name, 'ALA')
self.assertTrue(atom in atom.residue) # tests __contains__
# Check the bond, angle, and torsion partners of the first N atom
a = cpsf.atoms[0]
for atom in a.bond_partners:
self.assertTrue(atom.name in ['HT3', 'HT2', 'CA', 'HT1'])
self.assertEqual(atom.residue.idx, 0)
self.assertTrue(atom.type in [2, 22])
for atom in a.angle_partners:
self.assertTrue(atom.name in ['HA', 'CB', 'C'])
self.assertTrue(atom.type in [6, 24, 20])
self.assertEqual(atom.residue.idx, 0)
for atom in a.dihedral_partners:
self.assertTrue(atom.name in ['HB1', 'HB2', 'HB3', 'O', 'N'])
if atom.name == 'N':
self.assertEqual(atom.residue.idx, 1)
else:
self.assertEqual(atom.residue.idx, 0)
self.assertTrue(atom.type in [3, 70, 54])
# Check some atom properties
self.assertRaises(exceptions.MissingParameter,
lambda: str(a.atom_type))
self.assertTrue(all([isinstance(b, to.Bond) for b in a.bonds]))
self.assertTrue(all([isinstance(an, to.Angle) for an in a.angles]))
self.assertTrue(all([isinstance(d, to.Dihedral) for d in a.dihedrals]))
self.assertEqual(len(a.angle_partners), 3)
self.assertEqual(len(a.angles), 9)
self.assertEqual(len(a.bond_partners), 4)
self.assertEqual(len(a.bonds), 4)
self.assertEqual(len(a.cmaps), 0)
self.assertEqual(len(a.dihedral_partners), 5)
self.assertEqual(len(a.dihedrals), 14)
self.assertEqual(len(a.impropers), 0)
self.assertEqual(len(a.name), 1)
self.assertEqual(len(a.props), 3)
self.assertEqual(len(a.residue), 12)
self.assertEqual(len(a.segid), 3)
self.assertEqual(len(a.urey_bradleys), 0)
# Check attributes of the psf file
self.assertEqual(len(cpsf.acceptors), 4)
self.assertEqual(len(cpsf.angles), 57)
self.assertEqual(len(cpsf.atoms), 33)
self.assertEqual(len(cpsf.bonds), 32)
self.assertEqual(len(cpsf.cmaps), 1)
self.assertEqual(len(cpsf.dihedrals), 74)
self.assertEqual(len(cpsf.donors), 5)
self.assertEqual(len(cpsf.flags), 2)
self.assertEqual(len(cpsf.groups), 9)
self.assertEqual(len(cpsf.impropers), 5)
self.assertEqual(len(cpsf.residues), 3)
self.assertEqual(len(cpsf.title), 2)
# Check the __contains__ methods of valence terms (make sure the correct
# number of atoms are in each valence term)
atoms = cpsf.atoms
bonds = cpsf.bonds
for bond in cpsf.bonds:
self.assertEqual(sum([int(a in bond) for a in atoms]), 2)
# Other valence terms can also contain bonds
for i, angle in enumerate(cpsf.angles):
self.assertEqual(sum([int(a in angle) for a in atoms]), 3)
self.assertEqual(sum([int(b in angle) for b in bonds]), 2)
for dih in cpsf.dihedrals:
self.assertEqual(sum([int(a in dih) for a in atoms]), 4)
self.assertEqual(sum([int(b in dih) for b in bonds]), 3)
for imp in cpsf.impropers:
self.assertEqual(sum([int(a in imp) for a in atoms]), 4)
self.assertEqual(sum([int(b in imp) for b in bonds]), 3)
for cmap in cpsf.cmaps:
self.assertEqual(sum([int(a in cmap) for a in atoms]), 5)
self.assertEqual(sum([int(b in cmap) for b in bonds]), 4)