def _extensive_checks(self, parm):
# Check the __contains__ methods of the various topologyobjects
atoms = parm.atoms
for bond in parm.bonds:
self.assertEqual(sum([a in bond for a in atoms]), 2)
for angle in parm.angles:
self.assertEqual(sum([a in angle for a in atoms]), 3)
self.assertEqual(sum([b in angle for b in parm.bonds]), 2)
for dihedral in parm.dihedrals:
self.assertEqual(sum([a in dihedral for a in atoms]), 4)
self.assertEqual(sum([b in dihedral for b in parm.bonds]), 3)
for residue in parm.residues:
self.assertTrue(all([a in residue for a in residue.atoms]))
self.assertEqual(sum([a in residue for a in atoms]), len(residue))
if not parm.chamber: return
# Chamber tests now
for ub in parm.urey_bradleys:
self.assertEqual(sum([a in ub for a in atoms]), 2)
self.assertEqual(sum([b in ub for b in parm.bonds]), 2)
for imp in parm.impropers:
self.assertEqual(sum([a in imp for a in atoms]), 4)
self.assertEqual(sum([b in imp for b in parm.bonds]), 3)
if parm.has_cmap:
for cmap in parm.cmaps:
self.assertEqual(sum([a in cmap for a in atoms]), 5)
self.assertEqual(sum([b in cmap for b in parm.bonds]), 4)
def _extensive_checks(self, parm):
# Check the __contains__ methods of the various topologyobjects
atoms = parm.atoms
for bond in parm.bonds:
self.assertEqual(sum([a in bond for a in atoms]), 2)
for angle in parm.angles:
self.assertEqual(sum([a in angle for a in atoms]), 3)
self.assertEqual(sum([b in angle for b in parm.bonds]), 2)
for dihedral in parm.dihedrals:
self.assertEqual(sum([a in dihedral for a in atoms]), 4)
self.assertEqual(sum([b in dihedral for b in parm.bonds]), 3)
for residue in parm.residues:
self.assertTrue(all([a in residue for a in residue.atoms]))
self.assertEqual(sum([a in residue for a in atoms]),
len(residue))
if not parm.chamber: return
# Chamber tests now
for ub in parm.urey_bradleys:
self.assertEqual(sum([a in ub for a in atoms]), 2)
self.assertEqual(sum([b in ub for b in parm.bonds]), 2)
for imp in parm.impropers:
self.assertEqual(sum([a in imp for a in atoms]), 4)
self.assertEqual(sum([b in imp for b in parm.bonds]), 3)
if parm.has_cmap:
for cmap in parm.cmaps:
self.assertEqual(sum([a in cmap for a in atoms]), 5)
self.assertEqual(sum([b in cmap for b in parm.bonds]), 4)
def __init__(self, fname):
self.natom = 0
# Create the list of atoms
self.atom_list = XyzFile._AtomList()
f = open(fname, 'r')
for line in f:
if self.natom == 0:
self.natom = int(line.strip())
# Set up blank positions and connections arrays
self.connections = [[] for i in xrange(self.natom)]
continue
words = line.split()
if len(words) == 6 and all([is_float(x) for x in words]):
# The first line after the number of atoms _could_ be the box
# information. So capture that here and store the info
self.box = [float(x) for x in words]
continue
self.atom_list.add(words[1], words[2], words[3],
words[4], words[5], words[6:])
f.close()
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)
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)