cctk.PDBFile

class cctk.PDBFile(molecule, title=None)[source]

Bases: cctk.file.File

Generic class for all .pdb files.

__init__(molecule, title=None)[source]

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

Methods

__init__(molecule[, title])

Initialize self.

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)[source]

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)[source]

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)[source]

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