cctk.PDBFile

class cctk.PDBFile(molecule, title=None)

Bases: File

Generic class for all .pdb files.

__init__(molecule, title=None)

Methods

__init__(molecule[, title])
append_to_file(filename, text)	Appends output text to a file.
read_file(filename)	Reads a file and parses into lines.
write_ensemble_to_trajectory(filename, ensemble)	Writes a ConformationalEnsemble to a trajectory file.
write_file(filename, text[, overwrite_existing])	Writes output text to a file.
write_molecule_to_file(filename, molecule[, ...])	Write a .pdb 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

classmethod read_file(filename)

Reads a file and parses into lines.

Parameters:

filename (str) – The path to the file.

Returns:

A list containing all the lines in the file.

classmethod write_ensemble_to_trajectory(filename, ensemble)

Writes a ConformationalEnsemble to a trajectory file.

Parameters:

• filename (str) – where to write the file

• ensemble (Ensemble) – Ensemble object to write

static write_file(filename, text, overwrite_existing=True)

Writes 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

• overwrite_existing (Bool) – whether any existing files should be overwritten or not

Returns:

True if write succeeded, False otherwise

classmethod write_molecule_to_file(filename, molecule, num=1, append=False)

Write a .pdb file, using object attributes.

Parameters:

• filename (str) – path to the new file

• molecule (Molecule) – Molecule object

• num (int) – model number

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