TruncationSchemes

Module containing functions to truncate a QMzymeRegion based on some logic/scheme.

class QMzyme.TruncationSchemes.TruncationScheme(region, name)

Bases: ABC

Base class for defining QM region truncation methodologies.

A truncation scheme defines the specific rule for how protein amino acid residues in the QMzymeModel is truncated to create the desired QM region.

abstractmethod truncate()

return_region()

class QMzyme.TruncationSchemes.TerminalAlphaCarbon(region, name)

Bases: TruncationScheme

The TerminalAlphaCarbon scheme will 1) remove N-terminal backbone atoms (N and H) if the preceding sequence residue (resid-1) is not included in the region and add a hydrogen atom along the CA-N backbone bond vector; and 2) remove C-terminal backbone atoms (C and O) if the following sequence residue (resid+1) is not included in the region and add a hydrogen atom along the CA-C backbone bond vector. In the case of Proline, if the preceding sequence residue is not present the Proline N atom is kept and a hydrogen is added along the N-(resid-1)C backbone bond vector.

truncate()

class QMzyme.TruncationSchemes.AlphaCarbon(region, name)

Bases: TruncationScheme

Function to truncate a QMzymeRegion according to the AlphaCarbon scheme. This method is still under development.

truncate()

class QMzyme.TruncationSchemes.BetaCarbon(region, alanine_mutation, name)

Bases: TruncationScheme

The Beta Carbon scheme will select for atoms that are within 2Å from CB, remove all non-backbone atoms that are outside of 2Å distance, and remove non-hydrogen and non-backbone atoms and replace it with hydrogen along the CB-X vector. In the case of Proline and Glycine, it skips and returns a warning message.

truncate()