def filetype(filename):
"""Try to guess the type of the file."""
if os.path.isdir(filename):
# Potentially a BundleTrajectory
if BundleTrajectory.is_bundle(filename):
return 'bundle'
elif os.path.normpath(filename) == 'states':
return 'eon'
else:
raise IOError('Directory: ' + filename)
if filename.startswith('pg://'):
return 'postgresql'
fileobj = open(filename, 'rU')
s3 = fileobj.read(3)
if len(s3) == 0:
raise IOError('Empty file: ' + filename)
if s3.startswith('{"'):
return 'json'
if filename.endswith('.db'):
return 'db'
if filename.lower().endswith('.cmr'):
return 'cmr'
if is_tarfile(filename):
return 'gpw'
if s3 == 'CDF':
from ase.io.pupynere import NetCDFFile
nc = NetCDFFile(filename)
if 'number_of_dynamic_atoms' in nc.dimensions:
return 'dacapo'
history = nc.history
if history == 'GPAW restart file':
return 'gpw-nc'
if history == 'ASE trajectory':
return 'nc'
if history == 'Dacapo':
return 'dacapo'
if hasattr(nc, 'file_format') and nc.file_format.startswith('ETSF'):
return 'etsf'
raise IOError('Unknown netCDF file!')
if is_zipfile(filename):
return 'vnl'
fileobj.seek(0)
lines = fileobj.readlines(1000)
if lines[0].startswith('PickleTrajectory'):
return 'traj'
if (lines[1].startswith('OUTER LOOP:')
or filename.lower().endswith('.cube')):
return 'cube'
if ' ___ ___ ___ _ _ _ \n' in lines:
return 'gpaw-text'
if (' &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&\n'
in lines[:90]):
return 'dacapo-text'
for line in lines:
if line[0] != '#':
word = line.strip()
if word in ['ANIMSTEPS', 'CRYSTAL', 'SLAB', 'POLYMER', 'MOLECULE']:
return 'xsf'
filename_v = os.path.basename(filename)
if 'POSCAR' in filename_v or 'CONTCAR' in filename_v:
return 'vasp'
if 'OUTCAR' in filename_v:
return 'vasp_out'
if filename.lower().endswith('.exi'):
return 'exi'
if filename.lower().endswith('.mol'):
return 'mol'
if filename.lower().endswith('.pdb'):
return 'pdb'
if filename.lower().endswith('.cif'):
return 'cif'
if filename.lower().endswith('.struct'):
return 'struct'
if filename.lower().endswith('.struct_out'):
return 'struct_out'
fileobj.seek(0)
while True:
line = fileobj.readline()
if not line:
break
if 'Invoking FHI-aims ...' in line:
return 'aims_out'
if 'atom' in line:
data = line.split()
try:
Atoms(symbols=[data[4]],
positions=[[
float(data[1]),
float(data[2]),
float(data[3])
]])
return 'aims'
except:
pass
if filename.lower().endswith('.in'):
fileobj.seek(0)
while True:
line = fileobj.readline()
if not line:
break
if ('&system' in line) or ('&SYSTEM' in line):
return 'esp_in'
return 'aims'
if filename.lower().endswith('.cfg'):
return 'cfg'
if os.path.split(filename)[1] == 'atoms.dat':
return 'iwm'
if filename.endswith('I_info'):
return 'Cmdft'
if lines[0].startswith('$coord') or os.path.basename(filename) == 'coord':
return 'tmol'
if (lines[0].startswith('$grad')
or os.path.basename(filename) == 'gradient'):
return 'tmol-gradient'
if lines[0].startswith('Geometry'):
return 'dftb'
if filename.lower().endswith('.geom'):
return 'castep_geom'
if filename.lower().endswith('.castep'):
return 'castep'
if filename.lower().endswith('.cell'):
return 'castep_cell'
if s3 == '<?x':
from ase.io.vtkxml import probe_vtkxml
xmltype = probe_vtkxml(filename)
if xmltype == 'ImageData':
return 'vti'
elif xmltype == 'StructuredGrid':
return 'vts'
elif xmltype == 'UnstructuredGrid':
return 'vtu'
elif xmltype is not None:
raise IOError('Unknown VTK XML file!')
if filename.lower().endswith('.sdf'):
return 'sdf'
if filename.lower().endswith('.gen'):
return 'gen'
if filename.lower().endswith('.con'):
return 'eon'
if 'ITEM: TIMESTEP\n' in lines:
return 'lammps'
if filename.lower().endswith('.gro'):
return 'gromacs'
if filename.lower().endswith('.log'):
return 'gaussian_out'
if filename.lower().endswith('.com'):
return 'gaussian'
if filename.lower().endswith('.g96'):
return 'gromos'
if filename.lower().endswith('.out'):
return 'esp_out'
if filename.endswith('.nw'):
return 'nw'
return 'xyz'
def filetype(filename):
"""Try to guess the type of the file."""
if os.path.isdir(filename):
# Potentially a BundleTrajectory
if BundleTrajectory.is_bundle(filename):
return 'bundle'
else:
raise IOError('Directory: ' + filename)
fileobj = open(filename)
s3 = fileobj.read(3)
if len(s3) == 0:
raise IOError('Empty file: ' + filename)
if is_tarfile(filename):
return 'gpw'
if s3 == 'CDF':
from ase.io.pupynere import NetCDFFile
nc = NetCDFFile(filename)
if 'number_of_dynamic_atoms' in nc.dimensions:
return 'dacapo'
history = nc.history
if history == 'GPAW restart file':
return 'gpw-nc'
if history == 'ASE trajectory':
return 'nc'
if history == 'Dacapo':
return 'dacapo'
if hasattr(nc, 'file_format') and nc.file_format.startswith('ETSF'):
return 'etsf'
raise IOError('Unknown netCDF file!')
if is_zipfile(filename):
return 'vnl'
fileobj.seek(0)
lines = fileobj.readlines(1000)
if lines[0].startswith('PickleTrajectory'):
return 'traj'
if lines[1].startswith('OUTER LOOP:') or filename.lower().endswith(
'.cube'):
return 'cube'
if ' ___ ___ ___ _ _ _ \n' in lines:
return 'gpaw-text'
if (' &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&\n'
in lines[:90]):
return 'dacapo-text'
for line in lines:
if line[0] != '#':
word = line.strip()
if word in ['ANIMSTEPS', 'CRYSTAL', 'SLAB', 'POLYMER', 'MOLECULE']:
return 'xsf'
filename_v = basename(filename)
if 'POSCAR' in filename_v or 'CONTCAR' in filename_v:
return 'vasp'
if 'OUTCAR' in filename_v:
return 'vasp_out'
if filename.lower().endswith('.exi'):
return 'exi'
if filename.lower().endswith('.mol'):
return 'mol'
if filename.lower().endswith('.pdb'):
return 'pdb'
if filename.lower().endswith('.cif'):
return 'cif'
if filename.lower().endswith('.struct'):
return 'struct'
if filename.lower().endswith('.in'):
return 'aims'
if filename.lower().endswith('.out'):
return 'aims_out'
if filename.lower().endswith('.cfg'):
return 'cfg'
if os.path.split(filename)[1] == 'atoms.dat':
return 'iwm'
if filename.endswith('I_info'):
return 'Cmdft'
if lines[0].startswith('$coord'):
return 'tmol'
if lines[0].startswith('Geometry'):
return 'dftb'
if s3 == '<?x':
from ase.io.vtkxml import probe_vtkxml
xmltype = probe_vtkxml(filename)
if xmltype == 'ImageData':
return 'vti'
elif xmltype == 'StructuredGrid':
return 'vts'
elif xmltype == 'UnstructuredGrid':
return 'vtu'
elif xmltype is not None:
raise IOError('Unknown VTK XML file!')
if filename.lower().endswith('.sdf'):
return 'sdf'
return 'xyz'
def filetype(filename):
"""Try to guess the type of the file."""
if os.path.isdir(filename):
# Potentially a BundleTrajectory
if BundleTrajectory.is_bundle(filename):
return 'bundle'
elif os.path.normpath(filename) == 'states':
return 'eon'
else:
raise IOError('Directory: ' + filename)
if filename.startswith('pg://'):
return 'postgresql'
fileobj = open(filename, 'rb')
s3 = fileobj.read(3)
if len(s3) == 0:
raise IOError('Empty file: ' + filename)
if s3.startswith(b'{"'):
return 'json'
if filename.endswith('.db'):
return 'db'
if filename.lower().endswith('.cmr'):
return 'cmr'
if is_tarfile(filename):
return 'gpw'
if s3 == 'CDF':
from ase.io.pupynere import NetCDFFile
nc = NetCDFFile(filename)
if 'number_of_dynamic_atoms' in nc.dimensions:
return 'dacapo'
history = nc.history
if history == 'GPAW restart file':
return 'gpw-nc'
if history == 'ASE trajectory':
return 'nc'
if history == 'Dacapo':
return 'dacapo'
if hasattr(nc, 'file_format') and nc.file_format.startswith('ETSF'):
return 'etsf'
raise IOError('Unknown netCDF file!')
if is_zipfile(filename):
return 'vnl'
fileobj.seek(0)
lines = fileobj.readlines(1000)
if lines[0].startswith(b'AFFormatASE-Trajectory'):
return 'traj'
if lines[0].startswith(b'PickleTrajectory'):
return 'trj'
if (lines[1].startswith(b'OUTER LOOP:') or
filename.lower().endswith('.cube')):
return 'cube'
if b' ___ ___ ___ _ _ _ \n' in lines:
return 'gpaw-text'
if (b' &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&\n'
in lines[:90]):
return 'dacapo-text'
for line in lines:
if line[0] != b'#':
word = line.strip()
if word in ['ANIMSTEPS', 'CRYSTAL', 'SLAB', 'POLYMER', 'MOLECULE']:
return 'xsf'
filename_v = os.path.basename(filename)
if 'POSCAR' in filename_v or 'CONTCAR' in filename_v:
return 'vasp'
if 'OUTCAR' in filename_v:
return 'vasp_out'
if 'XDATCAR' in filename_v:
return 'vasp_xdatcar'
if filename.lower().endswith('.exi'):
return 'exi'
if filename.lower().endswith('.mol'):
return 'mol'
if filename.lower().endswith('.pdb'):
return 'pdb'
if filename.lower().endswith('.cif'):
return 'cif'
if filename.lower().endswith('.struct'):
return 'struct'
if filename.lower().endswith('.struct_out'):
return 'struct_out'
fileobj.seek(0)
while True:
line = fileobj.readline()
if not line:
break
if b'Invoking FHI-aims ...' in line:
return 'aims_out'
if b'atom' in line:
data = line.split()
try:
Atoms(symbols=[data[4]],
positions=[[float(data[1]),
float(data[2]),
float(data[3])]])
return 'aims'
except:
pass
if filename.lower().endswith('.in'):
fileobj.seek(0)
while True:
line = fileobj.readline()
if not line:
break
if ('&system' in line) or ('&SYSTEM' in line):
return 'esp_in'
return 'aims'
if filename.lower().endswith('.cfg'):
return 'cfg'
if os.path.split(filename)[1] == 'atoms.dat':
return 'iwm'
if filename.endswith('I_info'):
return 'Cmdft'
if lines[0].startswith(b'$coord') or os.path.basename(filename) == 'coord':
return 'tmol'
if (lines[0].startswith(b'$grad') or
os.path.basename(filename) == 'gradient'):
return 'tmol-gradient'
if lines[0].startswith(b'Geometry'):
return 'dftb'
if filename.lower().endswith('.geom'):
return 'castep_geom'
if filename.lower().endswith('.castep'):
return 'castep'
if filename.lower().endswith('.cell'):
return 'castep_cell'
if s3 == '<?x' and not filename.endswith('xsd'):
from ase.io.vtkxml import probe_vtkxml
xmltype = probe_vtkxml(filename)
if xmltype == 'ImageData':
return 'vti'
elif xmltype == 'StructuredGrid':
return 'vts'
elif xmltype == 'UnstructuredGrid':
return 'vtu'
elif xmltype is not None:
raise IOError('Unknown VTK XML file!')
if filename.lower().endswith('.sdf'):
return 'sdf'
if filename.lower().endswith('.gen'):
return 'gen'
if filename.lower().endswith('.con'):
return 'eon'
if 'ITEM: TIMESTEP\n' in lines:
return 'lammps'
if filename.lower().endswith('.gro'):
return 'gromacs'
if filename.lower().endswith('.log'):
return 'gaussian_out'
if filename.lower().endswith('.com'):
return 'gaussian'
if filename.lower().endswith('.g96'):
return 'gromos'
if filename.lower().endswith('.out'):
return 'esp_out'
if filename.endswith('.nw'):
return 'nw'
if filename.endswith('xsd'):
return 'xsd'
return 'xyz'
def filetype(filename):
"""Try to guess the type of the file."""
fileobj = open(filename)
s3 = fileobj.read(3)
if len(s3) == 0:
raise IOError('Empty file: ' + filename)
if is_tarfile(filename):
return 'gpw'
if s3 == 'CDF':
from ase.io.pupynere import NetCDFFile
nc = NetCDFFile(filename)
if 'number_of_dynamic_atoms' in nc.dimensions:
return 'dacapo'
history = nc.history
if history == 'GPAW restart file':
return 'gpw-nc'
if history == 'ASE trajectory':
return 'nc'
if history == 'Dacapo':
return 'dacapo'
raise IOError('Unknown netCDF file!')
if s3 == '<?x':
from ase.io.vtkxml import probe_vtkxml
xmltype = probe_vtkxml(filename)
if xmltype == 'ImageData':
return 'vti'
elif xmltype == 'StructuredGrid':
return 'vts'
elif xmltype == 'UnstructuredGrid':
return 'vtu'
elif xmltype is not None:
raise IOError('Unknown VTK XML file!')
if is_zipfile(filename):
return 'vnl'
fileobj.seek(0)
lines = fileobj.readlines(1000)
if lines[0].startswith('PickleTrajectory'):
return 'traj'
if lines[1].startswith('OUTER LOOP:') or filename.lower().endswith('.cube'):
return 'cube'
if ' ___ ___ ___ _ _ _ \n' in lines:
return 'gpaw-text'
if (' &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&\n'
in lines[:90]):
return 'dacapo-text'
for word in ['ANIMSTEPS', 'CRYSTAL', 'SLAB', 'POLYMER', 'MOLECULE']:
if lines[0].startswith(word):
return 'xsf'
filename_v = basename(filename)
if 'POSCAR' in filename_v or 'CONTCAR' in filename_v:
return 'vasp'
if filename.lower().endswith('.mol'):
return 'mol'
if filename.lower().endswith('.pdb'):
return 'pdb'
if filename.lower().endswith('.cif'):
return 'cif'
if os.path.split(filename)[1] == 'atoms.dat':
return 'iwm'
if filename.endswith('I_info'):
return 'Cmdft'
return 'xyz'