def _read_vdw(self, f):
""" Reads the van der Waals parameters """
if not hasattr(self, 'atom_list'):
raise AttributeError('Atom definitions must be loaded '
'prior to vdW!')
# Eat the next 3 lines
f.readline()
f.readline()
f.readline()
line = f.readline()
for i in range(self.pointers['natom']):
try:
int(line[0:6])
atnum = int(line[9:15])
self.atom_list[i].add_vdw(
line[22:32],
line[32:42],
line[43:53],
line[53:63],
line[64:74],
)
except ValueError:
raise TinkerError('Error parsing van der Waals term')
line = f.readline()
if atnum != i + 1:
raise TinkerError('Atom number mismatch in vdW [%d vs %d]' %
(i + 1, atnum))
def _read_tortors(self, f):
""" Read the Torsion-Torsion parameters """
self.tortor_list = TorsionTorsionList()
# Eat the next 3 lines
f.readline()
f.readline()
f.readline()
line = f.readline()
for i in range(self.pointers['ntortor']):
try:
int(line[0:6])
at1 = int(line[9:15]) - 1
at2 = int(line[15:21]) - 1
at3 = int(line[21:27]) - 1
at4 = int(line[27:33]) - 1
at5 = int(line[33:39]) - 1
dim1 = int(line[49:55])
dim2 = int(line[55:61])
self.tortor_list.add(self.atom_list[at1], self.atom_list[at2],
self.atom_list[at3], self.atom_list[at4],
self.atom_list[at5], dim1, dim2)
except ValueError:
raise TinkerError('Error parsing torsion-torsion term')
line = f.readline()
# The CMAP section was adjusted to print out the entire torsion
# grid under each tor-tor definition. If this line has 3 words, we
# need to eat the next dim1*dim2 lines
if len(line.split()) == 3:
gridvals = []
for j in range(dim1 * dim2):
gridvals.append(tuple([float(x) for x in line.split()]))
line = f.readline()
self.tortor_list[-1].type = TorsionTorsionGrid.new(gridvals)
def _read_torang(self, f):
""" Read the torsion-angle parameters """
self.torangle_list = TorsionAngleList()
# Eat the next 3 lines
f.readline()
f.readline()
f.readline()
line = f.readline()
for i in range(self.pointers['ntors']):
try:
int(line[0:6])
at1 = int(line[9:15]) - 1
at2 = int(line[15:21]) - 1
at3 = int(line[21:27]) - 1
at4 = int(line[27:33]) - 1
# Get the rest of the terms (replace / with ' ' so we can do a
# simple string split on whitespace)
terms = line[33:].replace('/', ' ').split()
self.torangle_list.add(self.atom_list[at1],
self.atom_list[at2],
self.atom_list[at3],
self.atom_list[at4], terms)
except ValueError:
raise TinkerError('Error parsing torsion angle term')
line = f.readline()
def _read_ureybrad(self, f):
""" Reads the urey-bradley terms """
self.ureybrad_list = UreyBradleyList()
# Eat the next 3 lines
f.readline()
f.readline()
f.readline()
line = f.readline()
for i in range(self.pointers['nurey']):
try:
int(line[0:6])
at1 = int(line[9:15]) - 1
at2 = int(line[15:21]) - 1
# Support older-style analyze output that had all 3 atoms
# involved in the angle. Newer analyze output contains only the
# first and 3rd atoms, so that is all we pass into the
# UreyBradleyList function
try:
at3 = int(line[21:27]) - 1
except ValueError:
at3 = at2
self.ureybrad_list.add(self.atom_list[at1],
self.atom_list[at3], line[34:50],
line[50:60])
except ValueError:
raise TinkerError('Error parsing Urey-Bradley term')
line = f.readline()
def __init__(self, fname):
# The currently recognized/parsed keywords (these are the only ones
# necessary for running Amoeba in Amber)
self.keywords = {
'PARAMETERS': None,
'A-AXIS': None,
'B-AXIS': None,
'C-AXIS': None,
'ALPHA': None,
'BETA': None,
'GAMMA': None
}
# Parse the file
for line in open(fname, 'r'):
# Skip over any blank lines
if not line.strip(): continue
words = line.split()
key = words[0].upper()
# Get rid of the keyword and all whitespace
result = line.replace(words[0], '').strip()
try:
self.keywords[key] = self._datatypes[key](result)
except KeyError:
pass # All non-keyword lines are ignored comments
except ValueError:
raise TinkerError('Malformed keyword control file! Could not '
'convert the value of %s into type %s' %
(key, self._datatypes[key]))
def _read_multipoles(self, f):
""" Read the atomic multipoles """
self.multipole_list = AtomicMultipoleList()
# Eat the next 3 lines
f.readline()
f.readline()
f.readline()
line = f.readline()
for i in range(self.pointers['npole']):
try:
int(line[0:6])
at = int(line[9:15]) - 1
# Collect the rest of the arguments, kept as strings
frame = [line[16:23], line[23:30], line[30:37]]
typestr = line[40:48]
moments = [line[50:59]]
# Next numbers are on the next line
line = f.readline()
moments.extend([line[50:59], line[59:68], line[68:77]])
line = f.readline()
moments.append(line[50:59])
line = f.readline()
moments.extend([line[50:59], line[59:68]])
line = f.readline()
moments.extend([line[50:59], line[59:68], line[68:77]])
self.multipole_list.add(self.atom_list[at], frame, typestr,
moments)
except ValueError:
raise TinkerError('Error parsing multipole term')
line = f.readline()
def __init__(self, fname, seq=None):
super(XyzFile, self).__init__()
if isinstance(fname, string_types):
fxyz = genopen(fname, 'r')
own_handle_xyz = True
else:
fxyz = fname
own_handle_xyz = False
if seq is not None:
seqstruct = load_file(seq)
# Now parse the file
try:
natom = int(fxyz.readline().split()[0])
except (ValueError, IndexError):
raise TinkerError('Bad XYZ file format; first line')
if seq is not None and natom != len(seqstruct.atoms):
raise ValueError(
'Sequence file %s # of atoms does not match the # '
'of atoms in the XYZ file' % seq)
words = fxyz.readline().split()
if len(words) == 6 and not XyzFile._check_atom_record(words):
self.box = [float(w) for w in words]
words = fxyz.readline().split()
atom = Atom(atomic_number=AtomicNum[element_by_name(words[1])],
name=words[1],
type=words[5])
atom.xx, atom.xy, atom.xz = [float(w) for w in words[2:5]]
residue = Residue('SYS')
residue.number = 1
residue._idx = 0
if seq is not None:
residue = seqstruct.residues[0]
self.add_atom(atom, residue.name, residue.number, residue.chain,
residue.insertion_code, residue.segid)
bond_ids = [[int(w) for w in words[6:]]]
for i, line in enumerate(fxyz):
words = line.split()
atom = Atom(atomic_number=AtomicNum[element_by_name(words[1])],
name=words[1],
type=words[5])
atom.xx, atom.xy, atom.xz = [float(w) for w in words[2:5]]
if seq is not None:
residue = seqstruct.atoms[i + 1].residue
self.add_atom(atom, residue.name, residue.number, residue.chain,
residue.insertion_code, residue.segid)
bond_ids.append([int(w) for w in words[6:]])
# All of the bonds are stored now -- go ahead and make them now
for atom, bonds in zip(self.atoms, bond_ids):
i = atom.idx + 1
for idx in bonds:
if idx > i:
self.bonds.append(Bond(atom, self.atoms[idx - 1]))
if own_handle_xyz:
fxyz.close()
def _read_atom_definitions(self, f):
# Make an atom list
self.atom_list = AtomList()
# Eat 3 lines, then begin
f.readline()
f.readline()
f.readline()
line = f.readline()
for i in range(self.pointers['natom']):
try:
atnum = int(line[:6])
self.atom_list.add(line[11:14], line[14:21], line[21:28],
line[28:34], line[34:44], line[44:49],
line[54:].strip())
except ValueError:
raise TinkerError('Error parsing atomic properties\n\t'
'[%s]' % line.rstrip())
line = f.readline()
if atnum != i + 1:
raise TinkerError('Atom number mismatch [%d vs %d]' %
(i + 1, atnum))
def _read_section(f, container, natom):
"""
Reads a section of an open file into the passed container. The
container should be a 2-dimensional list of length natom x 3
"""
for i in range(natom):
words = f.readline().upper().split()
try:
container[i][0] = float(words[0].replace('D', 'E'))
container[i][1] = float(words[1].replace('D', 'E'))
container[i][2] = float(words[2].replace('D', 'E'))
except (IndexError, ValueError):
raise TinkerError('Could not parse values from dyn file')
def _read_interactions(self, f):
""" Reads the number of interactions present in the system """
# Eat the next line (1 only)
f.readline()
line = f.readline()
while line.strip():
try:
key = TinkerAnalout.atom_inter_flags[line[1:20]]
except KeyError:
raise TinkerError('Unrecognized token in interaction count '
'[%s]' % line[1:20].strip())
self.pointers[key] = int(line[21:])
line = f.readline()
def _read_dipoles(self, f):
""" Read atomic dipole polarizabilities """
self.dipole_list = DipolePolarizabilityList()
# Eat the next 3 lines
f.readline()
f.readline()
f.readline()
line = f.readline()
for i in range(self.pointers['npole']):
try:
int(line[0:6])
at = int(line[9:15]) - 1
self.dipole_list.add(self.atom_list[at], line[25:35],
line[40:].split())
except ValueError:
raise TinkerError('Error parsing dipole polarizabilities')
line = f.readline()
def _read_pitors(self, f):
""" Read the Pi-Orbital Torsion parameters """
self.pitors_list = PiTorsionList()
# Eat the next 3 lines
f.readline()
f.readline()
f.readline()
line = f.readline()
for i in range(self.pointers['npitors']):
try:
int(line[0:6])
at1 = int(line[9:15]) - 1
at2 = int(line[15:21]) - 1
self.pitors_list.add(self.atom_list[at1], self.atom_list[at2],
line[40:50])
except ValueError:
raise TinkerError('Error parsing pi-torsion term')
line = f.readline()
def _read_bonds(self, f):
""" Reads the bond stretching terms """
self.bond_list = BondList()
# Eat the next 3 lines
f.readline()
f.readline()
f.readline()
line = f.readline()
for i in range(self.pointers['nbond']):
try:
int(line[0:6])
at1 = int(line[9:15]) - 1
at2 = int(line[15:21]) - 1
self.bond_list.add(self.atom_list[at1], self.atom_list[at2],
line[40:50], line[50:60])
except ValueError:
raise TinkerError('Error parsing bonded term')
line = f.readline()
def _read_angs(self, f):
""" Reads the angle stretching terms """
self.angle_list = AngleList()
# Eat the next 3 lines
f.readline()
f.readline()
f.readline()
line = f.readline()
for i in range(self.pointers['nangle']):
try:
int(line[0:6])
at1 = int(line[9:15]) - 1
at2 = int(line[15:21]) - 1
at3 = int(line[21:27]) - 1
self.angle_list.add(self.atom_list[at1], self.atom_list[at2],
self.atom_list[at3], line[40:50],
line[50:60], line[60:67], line[69:])
except ValueError:
raise TinkerError('Error parsing angle term')
line = f.readline()
def _read_opdist(self, f):
""" Read the out-of-plane distance parameters """
self.oopdist_list = OutOfPlaneDistList()
# Eat the next 3 lines
f.readline()
f.readline()
f.readline()
line = f.readline()
for i in range(self.pointers['nopdist']):
try:
int(line[0:6])
at1 = int(line[9:15]) - 1
at2 = int(line[15:21]) - 1
at3 = int(line[21:27]) - 1
at4 = int(line[27:33]) - 1
self.oopdist_list.add(self.atom_list[at1], self.atom_list[at2],
self.atom_list[at3], self.atom_list[at4],
line[42:52])
except ValueError:
raise TinkerError('Error parsing out-of-plane distance term')
line = f.readline()
def _read_strbnd(self, f):
""" Reads the stretch-bend terms """
self.stretchbend_list = StretchBendList()
# Eat the next 3 lines
f.readline()
f.readline()
f.readline()
line = f.readline()
for i in range(self.pointers['nstrbnd']):
try:
int(line[0:6])
at1 = int(line[9:15]) - 1
at2 = int(line[15:21]) - 1
at3 = int(line[21:27]) - 1
self.stretchbend_list.add(self.atom_list[at1],
self.atom_list[at2],
self.atom_list[at3], line[27:40],
line[40:50], line[50:60],
line[60:70])
except ValueError:
raise TinkerError('Error parsing stretch-bend term')
line = f.readline()
def read(self, fname):
""" Parses the .dyn file """
f = open(fname, 'r')
try:
if f.readline().strip() != 'Number of Atoms and Title :':
raise TinkerError('%s is not a recognized TINKER .dyn file' %
fname)
line = f.readline()
self.natom, self.title = int(line[0:8].strip()), line[8:].strip()
if f.readline().strip() != 'Periodic Box Dimensions :':
raise TinkerError('No periodic box dimension line')
self.box = [0.0 for i in range(6)]
words = f.readline().upper().split()
self.box[0] = float(words[0].replace('D', 'E'))
self.box[1] = float(words[1].replace('D', 'E'))
self.box[2] = float(words[2].replace('D', 'E'))
words = f.readline().upper().split()
self.box[3] = float(words[0].replace('D', 'E'))
self.box[4] = float(words[1].replace('D', 'E'))
self.box[5] = float(words[2].replace('D', 'E'))
if f.readline().strip() != 'Current Atomic Positions :':
raise TinkerError('No atomic positions in .dyn file')
self.positions = [[0.0, 0.0, 0.0] for i in range(self.natom)]
DynFile._read_section(f, self.positions, self.natom)
line = f.readline().strip()
if line == 'Current Translational Velocities :':
self.rigidbody = True
self.translational_velocities = [[0.0, 0.0, 0.0]
for i in range(self.natom)]
DynFile._read_section(f, self.translational_velocities,
self.natom)
if f.readline().strip() != 'Current Angular Velocities :':
raise TinkerError('Could not find Angular velocity '
'section in .dyn file')
self.angular_velocities = [[0.0, 0.0, 0.0]
for i in range(self.natom)]
DynFile._read_section(f, self.angular_velocities, self.natom)
if f.readline().strip() != 'Current Angular Momenta :':
raise TinkerError('Could not find angular momenta section '
'in .dyn file')
self.angular_momenta = [[0.0, 0.0, 0.0]
for i in range(self.natom)]
DynFile._read_section(f, self.angular_momenta, self.natom)
elif line == 'Current Atomic Velocities :':
self.rigidbody = False
self.velocities = [[0.0, 0.0, 0.0] for i in range(self.natom)]
DynFile._read_section(f, self.velocities, self.natom)
if f.readline().strip() != 'Current Atomic Accelerations :':
raise TinkerError('Could not find accelerations in %s ' %
fname)
self.accelerations = [[0.0, 0.0, 0.0]
for i in range(self.natom)]
DynFile._read_section(f, self.accelerations, self.natom)
if f.readline().strip() != 'Alternate Atomic Accelerations :':
raise TinkerError(
'Could not find old accelerations in %s' % fname)
self.old_accelerations = [[0.0, 0.0, 0.0]
for i in range(self.natom)]
DynFile._read_section(f, self.old_accelerations, self.natom)
else:
raise TinkerError('No velocities in %s' % fname)
finally:
f.close()
def read(self, fname):
""" Reads the analout file """
self.pointers = dict(natom=0,
norbit=0,
nbond=0,
nbpi=0,
nangle=0,
nstrbnd=0,
nurey=0,
nangang=0,
nopbend=0,
nopdist=0,
niprop=0,
nitors=0,
ntors=0,
npitors=0,
nstrtor=0,
ntortor=0,
nion=0,
ndipole=0,
npole=0,
pair12=0,
pair13=0,
pair14=0,
pair15=0)
self.fname = fname
f = open(self.fname, 'r')
try:
line = f.readline()
# Look for the TINKER watermark
while True:
if not line:
raise TinkerError('Could not find the TINKER watermark '
'in %s' % fname)
if line.lstrip().startswith('### TINKER'):
break
line = f.readline()
# Get the numbers of all parameters
while not line.lstrip().startswith(
'Total Numbers of Atoms and Interactions'):
if not line:
raise TinkerError('Could not find the atom/ixn count')
line = f.readline()
# Eat the next line
f.readline()
line = f.readline()
# Get all of the pointers
while line.strip():
try:
key = TinkerAnalout.atom_inter_flags[line[:27].strip()]
except KeyError:
raise TinkerError('Unrecognized pointer keyword %s' % key)
try:
self.pointers[key] = int(line[27:].strip())
except ValueError:
raise TinkerError('Could not convert pointer %s to int '
'[%s]' % (key, line.rstrip()))
except KeyError:
raise Exception('Should not be here -- internal error')
line = f.readline()
# Check that we read in some pointers
s = 0
for key in self.pointers:
s += self.pointers[key]
if s <= 0:
raise TinkerError('All pointers are 0')
# Get the atoms in the next section
while line.strip() != 'Atom Type Definition Parameters :':
if not line:
raise TinkerError('Unexpected EOF when looking for atom '
'definitions')
line = f.readline()
TinkerAnalout._read_atom_definitions(self, f)
# Get all of the sections defined in _functionmap -- see bottom of
# this file
while True:
line = f.readline()
try:
self._functionmap[line.strip()](self, f)
except KeyError:
break
finally:
f.close()
def load_parameter_file(self, fname):
"""
Parses a parameter file and loads all of the parameters found into data
structures.
"""
self.attributes = dict()
# First load the attributes from the header
f = BookmarkedFile(fname, 'r')
done_with_attributes = False
line = f.readline().replace('\t', ' ')
while line and not done_with_attributes:
if 'Literature References' in line:
done_with_attributes = True
break
line = (line + '#').strip()
line = line[:line.index('#')].strip()
if not line:
line = f.readline().replace('\t', ' ')
continue
words = line.split()
if len(words) != 2: continue
# Now extract the property
if _IS_INT(words[1]):
self.attributes[words[0].lower()] = int(words[1])
elif _IS_FLOAT(words[1]):
self.attributes[words[0].lower()] = float(words[1])
else:
self.attributes[words[0].lower()] = words[1]
line = f.readline().replace('\t', ' ')
if not done_with_attributes:
raise TinkerError('Could not find force field attributes.')
# Now get the atom types
while line.lstrip()[:5].lower() != 'atom ':
line = f.readline().replace('\t', ' ')
# Now loop through all atoms
while line.lstrip()[:5].lower() == 'atom ':
rematch = self.atomre.match(line)
num, typenum, name, descrip, anum, mass, val = rematch.groups()
self.atoms[int(num)] = _Atom(typenum, name, descrip,
anum, mass, val)
line = f.readline().replace('\t', ' ')
# Now parse out the van der waals terms
while line.lstrip()[:4].lower() != 'vdw ':
line = f.readline().replace('\t', ' ')
while line.lstrip()[:4].lower() == 'vdw ':
_AtomType.set_vdw_params(*line.split()[1:])
line = f.readline().replace('\t', ' ')
# Now parse out the bonds
while line.lstrip()[:5].lower() != 'bond ':
line = f.readline().replace('\t', ' ')
while line.lstrip()[:5].lower() == 'bond ':
_BondType(*line.split()[1:])
line = f.readline().replace('\t', ' ')
# Now parse out the angles. Handle iring and Fourier terms
rematch = self.anglere.match(line)
while not rematch:
line = f.readline().replace('\t', ' ')
rematch = self.anglere.match(line)
while rematch:
try:
get_angle_type(rematch.groups()[0], *line.split()[1:])
except TypeError as err:
print(repr(rematch.groups()[0]), line.split()[1:])
raise err
line = f.readline().replace('\t', ' ')
rematch = self.anglere.match(line)
# Now parse out the stretch-bend parameters
while line.lstrip()[:7].lower() != 'strbnd ':
line = f.readline().replace('\t', ' ')
while line.lstrip()[:7].lower() == 'strbnd ':
_StretchBendType(*line.split()[1:])
line = f.readline().replace('\t', ' ')
# Get the Urey-Bradley term(s). From here on out, some of the terms may
# not exist in all versions of the force field, so protect for EOF and
# make sure we rewind to avoid missing any terms
f.mark()
while line.lstrip()[:9].lower() != 'ureybrad ' and line:
line = f.readline().replace('\t', ' ')
while line.lstrip()[:9].lower() == 'ureybrad ' and line:
f.mark()
_UreyBradleyType(*line.split()[1:])
line = f.readline().replace('\t', ' ')
# Get the out-of-plane bending
f.rewind(); line = f.readline().replace('\t', ' ')
while line.lstrip()[:7].lower() != 'opbend ' and line:
line = f.readline().replace('\t', ' ')
while line.lstrip()[:7].lower() == 'opbend ' and line:
f.mark()
_OPBendType(*line.split()[1:])
line = f.readline().replace('\t', ' ')
# Get the torsion parameters
f.rewind(); line = f.readline().replace('\t', ' ')
while line.lstrip()[:8].lower() != 'torsion ' and line:
line = f.readline().replace('\t', ' ')
while line.lstrip()[:8].lower() == 'torsion ' and line:
f.mark()
_DihedralType(*line.split()[1:])
line = f.readline().replace('\t', ' ')
# Get the pitorsions
f.rewind(); line = f.readline().replace('\t', ' ')
while line.lstrip()[:7] != 'pitors ' and line:
line = f.readline().replace('\t', ' ')
while line.lstrip()[:7] == 'pitors ' and line:
f.mark()
_PiTorsionType(*line.split()[1:])
line = f.readline().replace('\t', ' ')
# Get the coupled torsions
f.rewind(); line = f.readline().replace('\t', ' ')
while line.lstrip()[:8] != 'tortors ' and line:
line = f.readline().replace('\t', ' ')
while line.lstrip()[:8] == 'tortors ' and line:
words = line.split()
tortor = _TorsionTorsionType(words[1:6], words[6], words[7])
line = f.readline().replace('\t', ' ')
while line.strip():
tortor.add_point(*line.split())
line = f.readline().replace('\t', ' ')
line = f.readline().replace('\t', ' ')
f.mark()
# Get the multipole terms
f.rewind(); line = f.readline().replace('\t', ' ')
while line.lstrip()[:10].lower() != 'multipole ' and line:
line = f.readline().replace('\t', ' ')
while line.lstrip()[:10].lower() == 'multipole ' and line:
words = line.split()
multipole = _MultipoleType(words[1:-1], words[-1])
multipole.add_terms(f.readline().split())
multipole.add_terms(f.readline().split())
multipole.add_terms(f.readline().split())
multipole.add_terms(f.readline().split())
line = f.readline().replace('\t', ' ')
f.mark()
# Get the dipole polarizabilities
f.rewind(); line = f.readline().replace('\t', ' ')
while line.lstrip()[:9] != 'polarize ' and line:
line = f.readline().replace('\t', ' ')
while line.lstrip()[:9] == 'polarize ' and line:
words = line.split()
index = int(words[1])
try:
self.atoms[index].set_polarizability(
words[2], words[3], words[4:]
)
except IndexError:
self.atoms[index].set_polarizability(words[2], words[3], [])
line = f.readline().replace('\t', ' ')
f.close()
# Now clean up so we can load another parameter set
reset()
return