cctk.XYZFile

class cctk.XYZFile(ensemble, titles)

Bases: File

Class representing plain .xyz files.

titles

the title or titles from the file

Type:

list of str

ensemble

Ensemble instance

Type:

Ensemble

molecule

Molecule instance representing the first molecule in the file. deprecated, but present for backwards compatibility.

Type:

Molecule

__init__(ensemble, titles)

Methods

__init__(ensemble, titles)
append_to_file(filename, text)	Appends output text to a file.
get_molecule([num])	Returns a given molecule.
mol_from_lines(lines[, charge, multiplicity])
read_ensemble(filename, **kwargs)	Post refactoring, just an alias for XYZFile.read_file().
read_file(filename[, charge, multiplicity, ...])	Factory method to create new XYZFile instances.
read_trajectory(filename, **kwargs)	Post refactoring, just an alias for XYZFile.read_file().
write_ensemble_to_file(filename, ensemble[, ...])	Write a cctk.Ensemble to a single .xyz file.
write_file(filename[, idx])	Write an .xyz file, using object attributes.
write_molecule_to_file(filename, molecule[, ...])	Write an .xyz file, using object attributes.

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)

Returns a given molecule.

If num is specified, returns self.ensemble.molecule_list()[num]

classmethod mol_from_lines(lines, charge=0, multiplicity=1)

classmethod read_ensemble(filename, **kwargs)

Post refactoring, just an alias for XYZFile.read_file().

classmethod read_file(filename, charge=0, multiplicity=1, conformational=False)

Factory method to create new XYZFile instances.

Parameters:

• filename (str) – path to .xyz file

• charge (int) – charge of resultant molecule

• multiplicity (int) – multiplicity of resultant molecule

• conformational (bool) – whether or not it’s a conformational ensemble

classmethod read_trajectory(filename, **kwargs)

Post refactoring, just an alias for XYZFile.read_file().

classmethod write_ensemble_to_file(filename, ensemble, titles=None)

Write a cctk.Ensemble to a single .xyz file. Can be viewed in MOLDEN.

Parameters:

• filename (str) – path to .xyz file

• ensemble (Ensemble) – the collection of structures to write

• titles (None, str, or list of str) – if None, the titles of the Molecules will be used; if one str, then the same name will be used for all molecules; if iterable, then the titles are assumed to parallel the indexing of the list

write_file(filename, idx=-1)

Write an .xyz file, using object attributes.

Parameters:

idx (int) – the index of the molecule to write

classmethod write_molecule_to_file(filename, molecule, title='title', append=False)

Write an .xyz file, using object attributes.

Parameters:

• filename (str) – path to the new file

• molecule (Molecule) – molecule to write

• title (str) – title of file

• append (Bool) – whether or not to append to file