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.