def parseLines(self, lines):
"""Parse list of lines in XYZ format.
Return Structure object or raise StructureFormatError.
"""
linefields = [l.split() for l in lines]
# prepare output structure
stru = Structure()
# find first valid record
start = 0
for field in linefields:
if len(field) == 0 or field[0] == "#":
start += 1
else:
break
# first valid line gives number of atoms
try:
lfs = linefields[start]
w1 = linefields[start][0]
if len(lfs) == 1 and str(int(w1)) == w1:
p_natoms = int(w1)
#try to get lattice vectors from description line
try:
latticeVecs = map(float, linefields[start + 1])
assert len(latticeVecs) == 9
from matter.Lattice import Lattice
reshaped = [
latticeVecs[0:3], latticeVecs[3:6], latticeVecs[6:9]
]
stru.lattice = Lattice(base=reshaped)
needsDescription = True
except:
needsDescription = False
stru.description = lines[start + 1].strip()
start += 2
else:
emsg = ("%d: invalid XYZ format, missing number of atoms" %
(start + 1))
raise StructureFormatError(emsg)
except (IndexError, ValueError):
exc_type, exc_value, exc_traceback = sys.exc_info()
emsg = ("%d: invalid XYZ format, missing number of atoms" %
(start + 1))
raise StructureFormatError, emsg, exc_traceback
# find the last valid record
stop = len(lines)
while stop > start and len(linefields[stop - 1]) == 0:
stop -= 1
# get out for empty structure
if p_natoms == 0 or start >= stop:
return stru
# here we have at least one valid record line
nfields = len(linefields[start])
if nfields != 4 and nfields != 5:
emsg = "%d: invalid XYZ format, expected 4 or 5 columns" % (start +
1)
raise StructureFormatError(emsg)
# now try to read all record lines
try:
p_nl = start
for fields in linefields[start:]:
p_nl += 1
if fields == []:
continue
elif len(fields) != 4 and len(fields) != 5:
emsg = ('%d: all lines must have ' +
'a symbol, position, and optionally charge') % p_nl
raise StructureFormatError(emsg)
symbol = fields[0]
symbol = symbol[0].upper() + symbol[1:].lower()
xyz = [float(f) for f in fields[1:4]]
if len(fields) == 5:
charge = float(fields[4])
else:
charge = 0.0
stru.addNewAtom(symbol, xyz=xyz, charge=charge)
except ValueError:
exc_type, exc_value, exc_traceback = sys.exc_info()
emsg = "%d: invalid number format" % p_nl
raise StructureFormatError, emsg, exc_traceback
# finally check if all the atoms have been read
if p_natoms is not None and len(stru) != p_natoms:
emsg = "expected %d atoms, read %d" % (p_natoms, len(stru))
raise StructureFormatError(emsg)
if needsDescription:
stru.generateDescription()
return stru
def parseLines(self, lines):
"""Parse list of lines in PDB format.
Return Structure instance or raise StructureFormatError.
"""
try:
stru = Structure()
scale = numpy.identity(3, dtype=float)
scaleU = numpy.zeros(3, dtype=float)
p_nl = 0
for line in lines:
p_nl += 1
# skip blank lines
if not line.strip(): continue
# make sure line has 80 characters
if len(line) < 80:
line = "%-80s" % line
words = line.split()
record = words[0]
if record == "TITLE":
continuation = line[8:10]
if continuation.strip():
stru.description += line[10:].rstrip()
else:
stru.description = line[10:].rstrip()
elif record == "CRYST1":
a = float(line[7:15])
b = float(line[15:24])
c = float(line[24:33])
alpha = float(line[33:40])
beta = float(line[40:47])
gamma = float(line[47:54])
stru.lattice.setLatPar(a, b, c, alpha, beta, gamma)
scale = numpy.transpose(stru.lattice.recbase)
elif record == "SCALE1":
sc = numpy.zeros((3,3), dtype=float)
sc[0,:] = [float(x) for x in line[10:40].split()]
scaleU[0] = float(line[45:55])
elif record == "SCALE2":
sc[1,:] = [float(x) for x in line[10:40].split()]
scaleU[1] = float(line[45:55])
elif record == "SCALE3":
sc[2,:] = [float(x) for x in line[10:40].split()]
scaleU[2] = float(line[45:55])
base = numpy.transpose(numpy.linalg.inv(sc))
abcABGcryst = numpy.array(stru.lattice.abcABG())
stru.lattice.setLatBase(base)
abcABGscale = numpy.array(stru.lattice.abcABG())
reldiff = numpy.fabs(1.0 - abcABGscale/abcABGcryst)
if not numpy.all(reldiff < self.epsilon):
emsg = "%d: " % p_nl + \
"SCALE and CRYST1 are not consistent."
raise StructureFormatError(emsg)
if numpy.any(scaleU != 0.0):
emsg = "Origin offset not yet implemented."
raise NotImplementedError(emsg)
elif record in ("ATOM", "HETATM"):
name = line[12:16].strip()
rc = [float(x) for x in line[30:54].split()]
xyz = numpy.dot(scale, rc) + scaleU
try:
occupancy = float(line[54:60])
except ValueError:
occupancy = 1.0
try:
B = float(line[60:66])
U = numpy.identity(3)*B/(8*pi**2)
except ValueError:
U = numpy.zeros((3,3), dtype=float)
symbol = line[76:78].strip()
if symbol == "":
# get symbol from the first 2 characters of name
symbol = line[12:14].strip()
symbol = symbol[0].upper() + symbol[1:].lower()
#stru.addNewAtom(symbol, occupancy=occupancy, name=name, U=U)
stru.addNewAtom(symbol, occupancy=occupancy, label=name, U=U)
last_atom = stru.getLastAtom()
last_atom.xyz_cartn = rc
elif record == "SIGATM":
sigrc = [float(x) for x in line[30:54].split()]
sigxyz = numpy.dot(scale, sigrc)
try:
sigo = float(line[54:60])
except ValueError:
sigo = 0.0
try:
sigB = float(line[60:66])
sigU = numpy.identity(3)*sigB/(8*pi**2)
except ValueError:
sigU = numpy.zeros((3,3), dtype=float)
last_atom.sigxyz = sigxyz
last_atom.sigo = sigo
last_atom.sigU = sigU
elif record == "ANISOU":
Uij = [ float(x)*1.0e-4 for x in line[28:70].split() ]
for i in range(3):
last_atom.U[i,i] = Uij[i]
last_atom.U[0,1] = last_atom.U[1,0] = Uij[3]
last_atom.U[0,2] = last_atom.U[2,0] = Uij[4]
last_atom.U[1,2] = last_atom.U[2,1] = Uij[5]
elif record == "SIGUIJ":
sigUij = [ float(x)*1.0e-4 for x in line[28:70].split() ]
for i in range(3):
last_atom.sigU[i,i] = sigUij[i]
last_atom.sigU[0,1] = last_atom.sigU[1,0] = sigUij[3]
last_atom.sigU[0,2] = last_atom.sigU[2,0] = sigUij[4]
last_atom.sigU[1,2] = last_atom.sigU[2,1] = sigUij[5]
elif record in P_pdb.validRecords:
pass
else:
emsg = "%d: invalid record name '%r'" % (p_nl, record)
raise StructureFormatError(emsg)
except (ValueError, IndexError):
emsg = "%d: invalid PDB record" % p_nl
exc_type, exc_value, exc_traceback = sys.exc_info()
raise StructureFormatError, emsg, exc_traceback
return stru
def parseLines(self, lines):
"""Parse list of lines in XYZ format.
Return Structure object or raise StructureFormatError.
"""
linefields = [l.split() for l in lines]
# prepare output structure
stru = Structure()
# find first valid record
start = 0
for field in linefields:
if len(field) == 0 or field[0] == "#":
start += 1
else:
break
# first valid line gives number of atoms
try:
lfs = linefields[start]
w1 = linefields[start][0]
if len(lfs) == 1 and str(int(w1)) == w1:
p_natoms = int(w1)
#try to get lattice vectors from description line
try:
latticeVecs = map(float, linefields[start+1])
assert len(latticeVecs)==9
from matter.Lattice import Lattice
reshaped = [latticeVecs[0:3], latticeVecs[3:6], latticeVecs[6:9]]
stru.lattice = Lattice(base=reshaped)
needsDescription = True
except:
needsDescription = False
stru.description = lines[start+1].strip()
start += 2
else:
emsg = ("%d: invalid XYZ format, missing number of atoms" %
(start + 1))
raise StructureFormatError(emsg)
except (IndexError, ValueError):
exc_type, exc_value, exc_traceback = sys.exc_info()
emsg = ("%d: invalid XYZ format, missing number of atoms" %
(start + 1))
raise StructureFormatError, emsg, exc_traceback
# find the last valid record
stop = len(lines)
while stop > start and len(linefields[stop-1]) == 0:
stop -= 1
# get out for empty structure
if p_natoms == 0 or start >= stop:
return stru
# here we have at least one valid record line
nfields = len(linefields[start])
if nfields != 4 and nfields != 5:
emsg = "%d: invalid XYZ format, expected 4 or 5 columns" % (start + 1)
raise StructureFormatError(emsg)
# now try to read all record lines
try:
p_nl = start
for fields in linefields[start:] :
p_nl += 1
if fields == []:
continue
elif len(fields) != 4 and len(fields) !=5:
emsg = ('%d: all lines must have ' +
'a symbol, position, and optionally charge') % p_nl
raise StructureFormatError(emsg)
symbol = fields[0]
symbol = symbol[0].upper() + symbol[1:].lower()
xyz = [ float(f) for f in fields[1:4] ]
if len(fields)==5:
charge = float(fields[4])
else:
charge = 0.0
stru.addNewAtom(symbol, xyz=xyz, charge=charge)
except ValueError:
exc_type, exc_value, exc_traceback = sys.exc_info()
emsg = "%d: invalid number format" % p_nl
raise StructureFormatError, emsg, exc_traceback
# finally check if all the atoms have been read
if p_natoms is not None and len(stru) != p_natoms:
emsg = "expected %d atoms, read %d" % (p_natoms, len(stru))
raise StructureFormatError(emsg)
if needsDescription:
stru.generateDescription()
return stru
