cctk package

This section describes the cctk API. Please program responsibly.

cctk Core

These are the core classes that represent molecules and collections of molecules in cctk

Molecule	Class representing a single molecular geometry.
Ensemble	Class representing a collection of molecules.
ConformationalEnsemble	Class that representing a group of conformers.

Files

These classes enable input/output functions.

File	Abstract class representing text files.
GaussianFile	Class representing Gaussian input/output files.
MAEFile	Class representing Maestro .mae files.
MOL2File	Class representing SYBYL .mol2 files.
OrcaFile	Generic class for all Orca .inp and .out files.
PDBFile	Generic class for all .pdb files.
SIFile	Class representing Supporting Information files.
XYZFile	Class representing plain .xyz files.

Miscellaneous

Group	Class representing a functional group.
VibrationalMode	Most code adapted from jprogdyn.
helper_functions	Miscellaneous helper functions.
OneIndexedArray	Wrapper for np.ndarray that's indexed from one, not zero, to store atomic numbers and geometries.
LazyLineObject	Instead of storing lines as an array, this object can be used.