def test_distance2(self):
""" Tests the distance2 calculation """
a1, a2 = Atom(), Atom()
a1.xx = a1.xy = a1.xz = 0
a2.xx = 3
a2.xy = 4
a2.xz = 0
self.assertEqual(geo.distance2(a1, a2), 25)
# Make sure it also works for tuples and a mixture of both
self.assertEqual(geo.distance2((0, 0, 0), (3, 4, 0)), 25)
self.assertEqual(geo.distance2(a1, (3, 4, 0)), 25)
self.assertEqual(geo.distance2((0, 0, 0), a2), 25)
def test_dihedral(self):
""" Tests calculating a torsion angle between 4 points """
a1, a2, a3, a4 = Atom(), Atom(), Atom(), Atom()
a1.xx, a1.xy, a1.xz = 1, 0, 0
a2.xx, a2.xy, a2.xz = 0, 0, 0
a3.xx, a3.xy, a3.xz = 0, 0, 1
a4.xx, a4.xy, a4.xz = 0.1, 0.6, 1
self.assertAlmostEqual(geo.dihedral(a1, a2, a3, a4), 80.537677791974374)
self.assertAlmostEqual(
geo.dihedral([1, 0, 0], [0, 0, 0], [0, 0, 1], [0.1, 0.6, 1]),
80.537677791974374
)
def test_angle(self):
""" Tests the angle calculation """
a1, a2, a3 = Atom(), Atom(), Atom()
a1.xx = a1.xy = a1.xz = 0
a2.xx, a2.xy, a2.xz = 1, 0, 0
a3.xx, a3.xy, a3.xz = 1, 1, 0
self.assertAlmostEqual(geo.angle(a1, a2, a3), 90)
# Check pathological cases
a3.xx, a3.xy, a3.xz = 2, 0, 0
self.assertAlmostEqual(geo.angle(a1, a2, a3), 180)
a3.xx = a3.xy = a3.xz = 0
self.assertAlmostEqual(geo.angle(a1, a2, a3), 0)
def pdb4all2parmed(structure: 'PDB') -> 'Structure':
structure.guess_elements()
struc_pmd = Structure()
for a in structure.pdb:
atom = Atom(atomic_number=Ptable[a['element']]['N'],
name=a['name'],
number=a['serial'])
struc_pmd.add_atom(atom=atom,
resname=a['resName'],
resnum=a['resSeq'],
chain=a['chainID'],
segid=a['segment'])
struc_pmd.coordinates = structure.xyz
struc_pmd.assign_bonds()
return struc_pmd
def test_dihedral(self):
""" Tests calculating a torsion angle between 4 points """
a1, a2, a3, a4 = Atom(), Atom(), Atom(), Atom()
a1.xx, a1.xy, a1.xz = 1, 0, 0
a2.xx, a2.xy, a2.xz = 0, 0, 0
a3.xx, a3.xy, a3.xz = 0, 0, 1
a4.xx, a4.xy, a4.xz = 0.1, 0.6, 1
self.assertAlmostEqual(geo.dihedral(a1, a2, a3, a4), 80.537677791974374)
self.assertAlmostEqual(
geo.dihedral([1, 0, 0], [0, 0, 0], [0, 0, 1], [0.1, 0.6, 1]),
80.537677791974374
)
def _parse_residue(fileobj, name):
"""
Parses the residue information out of the OFF file assuming the file
is pointed at the first line of an atoms table section of the OFF file
Parameters
----------
fileobj : file-like
Assumed to be open for read, this file is parsed until the *next*
atom table is read
name : str
The name of the residue being processed right now
"""
container = ResidueTemplateContainer(name)
nres = 1
templ = ResidueTemplate(name)
line = fileobj.readline()
while line[0] != '!':
nam, typ, typx, resx, flags, seq, elmnt, chg = line.split()
nam = _strip_enveloping_quotes(nam)
typ = _strip_enveloping_quotes(typ)
typx = int(typx)
resx = int(resx)
flags = int(flags)
seq = int(seq)
elmnt = int(elmnt)
chg = float(chg)
atom = Atom(atomic_number=elmnt, type=typ, name=nam, charge=chg)
if resx == nres + 1:
container.append(templ)
nres += 1
templ = ResidueTemplate(name)
templ.add_atom(atom)
line = fileobj.readline()
container.append(templ)
if nres > 1:
start_atoms = []
runsum = 0
for res in container:
start_atoms.append(runsum)
runsum += len(res)
# Make sure we get the next section
rematch = AmberOFFLibrary._sec2re.match(line)
if not rematch:
raise RuntimeError('Expected pertinfo table not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
line = fileobj.readline()
while line[0] != '!':
if not line:
raise RuntimeError('Unexpected EOF in Amber OFF library')
# Not used, just skip
# TODO sanity check
line = fileobj.readline()
rematch = AmberOFFLibrary._sec3re.match(line)
if not rematch:
raise RuntimeError('Expected boundbox table not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
# Only 5 lines
try:
hasbox = float(fileobj.readline().strip())
angle = float(fileobj.readline().strip())
a = float(fileobj.readline().strip())
b = float(fileobj.readline().strip())
c = float(fileobj.readline().strip())
except ValueError:
raise RuntimeError('Error processing boundbox table entries')
else:
if hasbox > 0:
angle *= RAD_TO_DEG
container.box = [a, b, c, angle, angle, angle]
# Get the child sequence entry
line = fileobj.readline()
rematch = AmberOFFLibrary._sec4re.match(line)
if not rematch:
raise RuntimeError('Expected childsequence table not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
n = int(fileobj.readline().strip())
if nres + 1 != n:
warnings.warn('Unexpected childsequence (%d); expected %d for '
'residue %s' % (n, nres+1, name), AmberWarning)
elif not isinstance(templ, ResidueTemplate) and n != len(templ) + 1:
raise RuntimeError('child sequence must be 1 greater than the '
'number of residues in the unit')
# Get the CONNECT array to set head and tail
line = fileobj.readline()
rematch = AmberOFFLibrary._sec5re.match(line)
if not rematch:
raise RuntimeError('Expected connect array not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
try:
head = int(fileobj.readline().strip())
tail = int(fileobj.readline().strip())
except ValueError:
raise RuntimeError('Error processing connect table entries')
if head > 0 and nres == 1:
templ.head = templ[head-1]
elif head > 0 and nres > 1:
if head < sum([len(r) for r in container]):
raise RuntimeError('HEAD on multi-residue unit not supported')
if tail > 0 and nres == 1:
templ.tail = templ[tail-1]
elif tail > 0 and nres > 1:
if tail < sum([len(r) for r in container]):
warnings.warn('TAIL on multi-residue unit not supported (%s). '
'Ignored...' % name, AmberWarning)
# Get the connectivity array to set bonds
line = fileobj.readline()
rematch = AmberOFFLibrary._sec6re.match(line)
if not rematch:
raise RuntimeError('Expected connectivity table not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
line = fileobj.readline()
while line[0] != '!':
i, j, flag = line.split()
line = fileobj.readline()
if nres > 1:
# Find which residue we belong in
i = int(i) - 1
j = int(j) - 1
for ii, idx in enumerate(start_atoms):
if idx > i:
ii -= 1
break
start_idx = start_atoms[ii]
container[ii].add_bond(i-start_idx, j-start_idx)
else:
templ.add_bond(int(i)-1, int(j)-1)
# Get the hierarchy table
rematch = AmberOFFLibrary._sec7re.match(line)
if not rematch:
raise RuntimeError('Expected hierarchy table not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
line = fileobj.readline()
while line[0] != '!':
# Skip this section... not used
# TODO turn this into a sanity check
line = fileobj.readline()
# Get the unit name
rematch = AmberOFFLibrary._sec8re.match(line)
if not rematch:
raise RuntimeError('Expected unit name string not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
fileobj.readline() # Skip this... not used
line = fileobj.readline()
# Get the atomic positions
rematch = AmberOFFLibrary._sec9re.match(line)
if not rematch:
raise RuntimeError('Expected unit positions table not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
for res in container:
for atom in res:
x, y, z = fileobj.readline().split()
atom.xx, atom.xy, atom.xz = float(x), float(y), float(z)
line = fileobj.readline()
# Get the residueconnect table
rematch = AmberOFFLibrary._sec10re.match(line)
if not rematch:
raise RuntimeError('Expected unit residueconnect table not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
for i in range(nres):
c1,c2,c3,c4,c5,c6 = [int(x) for x in fileobj.readline().split()]
if templ.head is not None and templ.head is not templ[c1-1]:
warnings.warn('HEAD atom is not connect0')
if templ.tail is not None and templ.tail is not templ[c2-1]:
warnings.warn('TAIL atom is not connect1')
for i in (c3, c4, c5, c6):
if i == 0: continue
templ.connections.append(templ[i-1])
# Get the residues table
line = fileobj.readline()
rematch = AmberOFFLibrary._sec11re.match(line)
if not rematch:
raise RuntimeError('Expected unit residues table not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
for i in range(nres):
resname, id, next, start, typ, img = fileobj.readline().split()
resname = _strip_enveloping_quotes(resname)
id = int(id)
start = int(start)
next = int(next)
typ = _strip_enveloping_quotes(typ)
img = int(img)
if next - start != len(container[i]):
warnings.warn('residue table predicted %d, not %d atoms for '
'residue %s' % (next-start, len(container[i]),
name), AmberWarning)
if typ == 'p':
container[i].type = PROTEIN
elif typ == 'n':
container[i].type = NUCLEIC
elif typ == 'w':
container[i].type = SOLVENT
elif typ != '?':
warnings.warn('Unknown residue type "%s"' % typ,
AmberWarning)
if nres > 1:
container[i].name = resname
# Get the residues sequence table
line = fileobj.readline()
rematch = AmberOFFLibrary._sec12re.match(line)
if not rematch:
raise RuntimeError('Expected residue sequence number not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
for i in range(nres):
#TODO sanity check
fileobj.readline()
line = fileobj.readline()
# Get the solventcap array
rematch = AmberOFFLibrary._sec13re.match(line)
if not rematch:
raise RuntimeError('Expected unit solventcap array not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
# Ignore the solvent cap
fileobj.readline()
fileobj.readline()
fileobj.readline()
fileobj.readline()
fileobj.readline()
# Velocities
line = fileobj.readline()
rematch = AmberOFFLibrary._sec14re.match(line)
if not rematch:
raise RuntimeError('Expected unit solventcap array not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
for res in container:
for atom in res:
vx, vy, vz = [float(x) for x in fileobj.readline().split()]
atom.vx, atom.vy, atom.vz = vx, vy, vz
if nres > 1:
return container
return templ
def _parse_residue(fileobj, name):
"""
Parses the residue information out of the OFF file assuming the file
is pointed at the first line of an atoms table section of the OFF file
Parameters
----------
fileobj : file-like
Assumed to be open for read, this file is parsed until the *next*
atom table is read
name : str
The name of the residue being processed right now
"""
container = ResidueTemplateContainer(name)
nres = 1
templ = ResidueTemplate(name)
line = fileobj.readline()
while line[0] != '!':
nam, typ, typx, resx, flags, seq, elmnt, chg = line.split()
nam = _strip_enveloping_quotes(nam)
typ = _strip_enveloping_quotes(typ)
typx = int(typx)
resx = int(resx)
flags = int(flags)
seq = int(seq)
elmnt = int(elmnt)
chg = float(chg)
atom = Atom(atomic_number=elmnt, type=typ, name=nam, charge=chg)
if resx == nres + 1:
container.append(templ)
nres += 1
templ = ResidueTemplate(name)
templ.add_atom(atom)
line = fileobj.readline()
# Skip blank lines
while line and not line.strip():
line = fileobj.readline()
container.append(templ)
if nres > 1:
start_atoms = []
runsum = 0
for res in container:
start_atoms.append(runsum)
runsum += len(res)
# Make sure we get the next section
rematch = AmberOFFLibrary._sec2re.match(line)
if not rematch:
raise RuntimeError('Expected pertinfo table not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
line = fileobj.readline()
while line[0] != '!':
if not line:
raise RuntimeError('Unexpected EOF in Amber OFF library')
# Not used, just skip
# TODO sanity check
line = fileobj.readline()
rematch = AmberOFFLibrary._sec3re.match(line)
if not rematch:
raise RuntimeError('Expected boundbox table not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
# Only 5 lines
try:
hasbox = float(fileobj.readline().strip())
angle = float(fileobj.readline().strip())
a = float(fileobj.readline().strip())
b = float(fileobj.readline().strip())
c = float(fileobj.readline().strip())
except ValueError:
raise RuntimeError('Error processing boundbox table entries')
else:
if hasbox > 0:
if angle < 3.15:
# No box is this acute -- must be in radians
angle *= RAD_TO_DEG
container.box = [a, b, c, angle, angle, angle]
# Get the child sequence entry
line = fileobj.readline()
rematch = AmberOFFLibrary._sec4re.match(line)
if not rematch:
raise RuntimeError('Expected childsequence table not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
n = int(fileobj.readline().strip())
if nres + 1 != n:
warnings.warn('Unexpected childsequence (%d); expected %d for '
'residue %s' % (n, nres+1, name), AmberWarning)
elif not isinstance(templ, ResidueTemplate) and n != len(templ) + 1:
raise RuntimeError('child sequence must be 1 greater than the '
'number of residues in the unit')
# Get the CONNECT array to set head and tail
line = fileobj.readline()
rematch = AmberOFFLibrary._sec5re.match(line)
if not rematch:
raise RuntimeError('Expected connect array not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
try:
head = int(fileobj.readline().strip())
tail = int(fileobj.readline().strip())
except ValueError:
raise RuntimeError('Error processing connect table entries')
if head > 0 and nres == 1:
templ.head = templ[head-1]
elif head > 0 and nres > 1:
if head < sum((len(r) for r in container)):
raise RuntimeError('HEAD on multi-residue unit not supported')
if tail > 0 and nres == 1:
templ.tail = templ[tail-1]
elif tail > 0 and nres > 1:
if tail < sum((len(r) for r in container)):
warnings.warn('TAIL on multi-residue unit not supported (%s). '
'Ignored...' % name, AmberWarning)
# Get the connectivity array to set bonds
line = fileobj.readline()
if len(templ.atoms) > 1:
rematch = AmberOFFLibrary._sec6re.match(line)
if not rematch:
raise RuntimeError('Expected connectivity table not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
line = fileobj.readline()
while line[0] != '!':
i, j, flag = line.split()
line = fileobj.readline()
if nres > 1:
# Find which residue we belong in
i = int(i) - 1
j = int(j) - 1
for ii, idx in enumerate(start_atoms):
if idx > i:
ii -= 1
break
start_idx = start_atoms[ii]
container[ii].add_bond(i-start_idx, j-start_idx)
else:
templ.add_bond(int(i)-1, int(j)-1)
# Get the hierarchy table
rematch = AmberOFFLibrary._sec7re.match(line)
if not rematch:
raise RuntimeError('Expected hierarchy table not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
line = fileobj.readline()
while line[0] != '!':
# Skip this section... not used
# TODO turn this into a sanity check
line = fileobj.readline()
# Get the unit name
rematch = AmberOFFLibrary._sec8re.match(line)
if not rematch:
raise RuntimeError('Expected unit name string not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
fileobj.readline() # Skip this... not used
line = fileobj.readline()
# Get the atomic positions
rematch = AmberOFFLibrary._sec9re.match(line)
if not rematch:
raise RuntimeError('Expected unit positions table not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
for res in container:
for atom in res:
x, y, z = fileobj.readline().split()
atom.xx, atom.xy, atom.xz = float(x), float(y), float(z)
line = fileobj.readline()
# Get the residueconnect table
rematch = AmberOFFLibrary._sec10re.match(line)
if not rematch:
raise RuntimeError('Expected unit residueconnect table not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
for i in range(nres):
c1,c2,c3,c4,c5,c6 = (int(x) for x in fileobj.readline().split())
if (c1 > 0 and templ.head is not None and
templ.head is not templ[c1-1]):
raise RuntimeError('HEAD atom is not connect0')
if (c2 > 0 and templ.tail is not None and
templ.tail is not templ[c2-1]):
raise RuntimeError('TAIL atom is not connect1')
for i in (c3, c4, c5, c6):
if i == 0: continue
templ.connections.append(templ[i-1])
# Get the residues table
line = fileobj.readline()
rematch = AmberOFFLibrary._sec11re.match(line)
if not rematch:
raise RuntimeError('Expected unit residues table not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
for i in range(nres):
resname, id, next, start, typ, img = fileobj.readline().split()
resname = _strip_enveloping_quotes(resname)
id = int(id)
start = int(start)
next = int(next)
typ = _strip_enveloping_quotes(typ)
img = int(img)
if next - start != len(container[i]):
warnings.warn('residue table predicted %d, not %d atoms for '
'residue %s' % (next-start, len(container[i]),
name), AmberWarning)
if typ == 'p':
container[i].type = PROTEIN
elif typ == 'n':
container[i].type = NUCLEIC
elif typ == 'w':
container[i].type = SOLVENT
elif typ != '?':
warnings.warn('Unknown residue type "%s"' % typ, AmberWarning)
if nres > 1:
container[i].name = resname
# Get the residues sequence table
line = fileobj.readline()
rematch = AmberOFFLibrary._sec12re.match(line)
if not rematch:
raise RuntimeError('Expected residue sequence number not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
for i in range(nres):
#TODO sanity check
fileobj.readline()
line = fileobj.readline()
# Get the solventcap array
rematch = AmberOFFLibrary._sec13re.match(line)
if not rematch:
raise RuntimeError('Expected unit solventcap array not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
# Ignore the solvent cap
fileobj.readline()
fileobj.readline()
fileobj.readline()
fileobj.readline()
fileobj.readline()
# Velocities
line = fileobj.readline()
rematch = AmberOFFLibrary._sec14re.match(line)
if not rematch:
raise RuntimeError('Expected unit solventcap array not found')
elif rematch.groups()[0] != name:
raise RuntimeError('Found residue %s while processing residue %s' %
(rematch.groups()[0], name))
for res in container:
for atom in res:
vx, vy, vz = (float(x) for x in fileobj.readline().split())
atom.vx, atom.vy, atom.vz = vx, vy, vz
if nres > 1:
return container
return templ
def __init__(self, psf_name):
"""
Opens and parses a PSF file, then instantiates a CharmmPsfFile
instance from the data.
"""
global _resre
Structure.__init__(self)
conv = CharmmPsfFile._convert
# Open the PSF and read the first line. It must start with "PSF"
with closing(genopen(psf_name, 'r')) as psf:
self.name = psf_name
line = psf.readline()
if not line.startswith('PSF'):
raise CharmmError('Unrecognized PSF file. First line is %s' %
line.strip())
# Store the flags
psf_flags = line.split()[1:]
# Now get all of the sections and store them in a dict
psf.readline()
# Now get all of the sections
psfsections = _ZeroDict()
while True:
try:
sec, ptr, data = CharmmPsfFile._parse_psf_section(psf)
except _FileEOF:
break
psfsections[sec] = (ptr, data)
# store the title
self.title = psfsections['NTITLE'][1]
# Next is the number of atoms
natom = conv(psfsections['NATOM'][0], int, 'natom')
# Parse all of the atoms
for i in range(natom):
words = psfsections['NATOM'][1][i].split()
atid = int(words[0])
if atid != i + 1:
raise CharmmError('Nonsequential atoms detected!')
segid = words[1]
rematch = _resre.match(words[2])
if not rematch:
raise RuntimeError('Could not interpret residue number %s' %
words[2])
resid, inscode = rematch.groups()
resid = conv(resid, int, 'residue number')
resname = words[3]
name = words[4]
attype = words[5]
# Try to convert the atom type to an integer a la CHARMM
try:
attype = int(attype)
except ValueError:
pass
charge = conv(words[6], float, 'partial charge')
mass = conv(words[7], float, 'atomic mass')
props = words[8:]
atom = Atom(name=name, type=attype, charge=charge, mass=mass)
atom.segid = segid
atom.props = props
self.add_atom(atom,resname,resid,chain=segid,inscode=inscode)
# Now get the number of bonds
nbond = conv(psfsections['NBOND'][0], int, 'number of bonds')
if len(psfsections['NBOND'][1]) != nbond * 2:
raise CharmmError('Got %d indexes for %d bonds' %
(len(psfsections['NBOND'][1]), nbond))
it = iter(psfsections['NBOND'][1])
for i, j in zip(it, it):
self.bonds.append(Bond(self.atoms[i-1], self.atoms[j-1]))
# Now get the number of angles and the angle list
ntheta = conv(psfsections['NTHETA'][0], int, 'number of angles')
if len(psfsections['NTHETA'][1]) != ntheta * 3:
raise CharmmError('Got %d indexes for %d angles' %
(len(psfsections['NTHETA'][1]), ntheta))
it = iter(psfsections['NTHETA'][1])
for i, j, k in zip(it, it, it):
self.angles.append(
Angle(self.atoms[i-1], self.atoms[j-1], self.atoms[k-1])
)
self.angles[-1].funct = 5 # urey-bradley
# Now get the number of torsions and the torsion list
nphi = conv(psfsections['NPHI'][0], int, 'number of torsions')
if len(psfsections['NPHI'][1]) != nphi * 4:
raise CharmmError('Got %d indexes for %d torsions' %
(len(psfsections['NPHI']), nphi))
it = iter(psfsections['NPHI'][1])
for i, j, k, l in zip(it, it, it, it):
self.dihedrals.append(
Dihedral(self.atoms[i-1], self.atoms[j-1],
self.atoms[k-1], self.atoms[l-1])
)
self.dihedrals.split = False
# Now get the number of improper torsions
nimphi = conv(psfsections['NIMPHI'][0], int, 'number of impropers')
if len(psfsections['NIMPHI'][1]) != nimphi * 4:
raise CharmmError('Got %d indexes for %d impropers' %
(len(psfsections['NIMPHI'][1]), nimphi))
it = iter(psfsections['NIMPHI'][1])
for i, j, k, l in zip(it, it, it, it):
self.impropers.append(
Improper(self.atoms[i-1], self.atoms[j-1],
self.atoms[k-1], self.atoms[l-1])
)
# Now handle the donors (what is this used for??)
ndon = conv(psfsections['NDON'][0], int, 'number of donors')
if len(psfsections['NDON'][1]) != ndon * 2:
raise CharmmError('Got %d indexes for %d donors' %
(len(psfsections['NDON'][1]), ndon))
it = iter(psfsections['NDON'][1])
for i, j in zip(it, it):
self.donors.append(
AcceptorDonor(self.atoms[i-1], self.atoms[j-1])
)
# Now handle the acceptors (what is this used for??)
nacc = conv(psfsections['NACC'][0], int, 'number of acceptors')
if len(psfsections['NACC'][1]) != nacc * 2:
raise CharmmError('Got %d indexes for %d acceptors' %
(len(psfsections['NACC'][1]), nacc))
it = iter(psfsections['NACC'][1])
for i, j in zip(it, it):
self.acceptors.append(
AcceptorDonor(self.atoms[i-1], self.atoms[j-1])
)
# Now get the group sections
try:
ngrp, nst2 = psfsections['NGRP NST2'][0]
except ValueError:
raise CharmmError('Could not unpack GROUP pointers')
tmp = psfsections['NGRP NST2'][1]
self.groups.nst2 = nst2
# Now handle the groups
if len(psfsections['NGRP NST2'][1]) != ngrp * 3:
raise CharmmError('Got %d indexes for %d groups' %
(len(tmp), ngrp))
it = iter(psfsections['NGRP NST2'][1])
for i, j, k in zip(it, it, it):
self.groups.append(Group(i, j, k))
# Assign all of the atoms to molecules recursively
tmp = psfsections['MOLNT'][1]
set_molecules(self.atoms)
molecule_list = [a.marked for a in self.atoms]
if len(tmp) == len(self.atoms):
if molecule_list != tmp:
warnings.warn('Detected PSF molecule section that is WRONG. '
'Resetting molecularity.', CharmmWarning)
# We have a CHARMM PSF file; now do NUMLP/NUMLPH sections
numlp, numlph = psfsections['NUMLP NUMLPH'][0]
if numlp != 0 or numlph != 0:
raise NotImplementedError('Cannot currently handle PSFs with '
'lone pairs defined in the NUMLP/'
'NUMLPH section.')
# Now do the CMAPs
ncrterm = conv(psfsections['NCRTERM'][0], int, 'Number of cross-terms')
if len(psfsections['NCRTERM'][1]) != ncrterm * 8:
raise CharmmError('Got %d CMAP indexes for %d cmap terms' %
(len(psfsections['NCRTERM']), ncrterm))
it = iter(psfsections['NCRTERM'][1])
for i, j, k, l, m, n, o, p in zip(it, it, it, it, it, it, it, it):
self.cmaps.append(
Cmap.extended(self.atoms[i-1], self.atoms[j-1],
self.atoms[k-1], self.atoms[l-1],
self.atoms[m-1], self.atoms[n-1],
self.atoms[o-1], self.atoms[p-1])
)
self.unchange()
self.flags = psf_flags