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.

In order to avoid creating small alkane chains (e.g. methane and ethane), TruncationScheme class will raise a warning when an organic group is created as a result of TruncationScheme class.

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()