cctk.MOL2File

class cctk.MOL2File(name=None)[source]

Bases: cctk.file.File

Class representing SYBYL .mol2 files.

name

name of file

Type

str

ensemble

Ensemble or ConformationalEnsemble object

Type

Ensemble

__init__(name=None)[source]

Initialize self. See help(type(self)) for accurate signature.

Methods

__init__([name])

Initialize self.

append_to_file(filename, text)

Appends output text to a file.

get_molecule([num])

Returns the last molecule from the ensemble.

read_file(filename[, name])

Reads .mol2 file and generates a MOL2File instance.

write_ensemble_to_file(filename, ensemble)

Write each structure in the specified ensemble to a single mol2 file.

write_file(filename[, molecule])

Write a .mol2 file, using object attributes.

write_molecule_to_file(filename, molecule[, …])

Write a .gjf file using the given molecule.

static append_to_file(filename, text)

Appends output text to a file.

Parameters
  • filename (str) – path to file, including name (e.g. path/to/input.gjf)

  • text (str) – desired contents of file

Returns

True if write succeeded, False otherwise

get_molecule(num=None)[source]

Returns the last molecule from the ensemble.

If num is specified, returns self.ensemble.molecules[num]

classmethod read_file(filename, name=None, **kwargs)[source]

Reads .mol2 file and generates a MOL2File instance.

Parameters
  • filename (str) – path to file

  • name (str) – name of the file

Returns

MOL2File object

classmethod write_ensemble_to_file(filename, ensemble)[source]

Write each structure in the specified ensemble to a single mol2 file.

Parameters
  • filename (str) – where to write the file

  • ensemble (Ensemble) – Ensemble object to write

write_file(filename, molecule=- 1, **kwargs)[source]

Write a .mol2 file, using object attributes.

Parameters
  • filename (str) – path to the new file

  • molecule (int) – which molecule to use – passed to self.get_molecule(). Default is -1 (e.g. the last molecule), but positive integers will select from self.ensemble.molecules (0-indexed). A Molecule object can also be passed, in which case that molecule will be written to the file.

classmethod write_molecule_to_file(filename, molecule, title=None, append=False)[source]

Write a .gjf file using the given molecule.

Parameters
  • filename (str) – path to the new file

  • molecule (Molecule) – which molecule to use – a``Molecule`` object.

  • title (str) – title of the file

  • append (Bool) – whether to write to file normally or append