core

This is the core package of PQAnalysis.

It consists of all classes and functions that are used to handle atomic systems, atoms, elements and cells. Additionally it contains some functions that are used to compute properties of atomic systems within the api module, but can be used directly from the core package.

Submodules

• api
• exceptions
• residue

Subpackages

• core.atom
• core.cell

Summary

__all__ Exceptions:

AtomError	Exception raised for errors related to the Atom class
CellError	Exception raised for errors related to the Cell class
ElementNotFoundError	Exception raised if the given element id is not valid
ResidueError	Exception raised for errors related to the Residue class
ResidueWarning	Warning raised for problems related to the Residue class

__all__ Classes:

Atom	A class used to represent an atom in a molecule.
Cell	Class for storing unit cell parameters.
CustomElement	A class representing a custom element it inherits from the Element class.
Element	A class representing an element.
QMResidue	A class for representing a QM residue type (mol type).
Residue	A class for representing a residue type (mol type).

__all__ Functions:

distance

Returns the distances between all combinations of two position arrays.

__all__ Data:

Atoms	Type variable.
Cells	NewType creates simple unique types with almost zero runtime overhead.
Elements	NewType creates simple unique types with almost zero runtime overhead.
Residues	Type variable.

Reference