rxnutils.chem.protection package

Submodules

rxnutils.chem.protection.amino_acids module

Module to attach protection groups to amino acids

rxnutils.chem.protection.amino_acids.preprocess_amino_acids(original_smiles)

Remove all charges of the amino acids so that the protection reaction can be applied.

Parameters:

original_smiles (str)

Return type:

str

rxnutils.chem.protection.amino_acids.remove_backbone_charges(original_smiles)

Remove the backbone charges of the amino acid, this is needed for the protection chemistry.

Parameters:

original_smiles (str)

Return type:

str

class rxnutils.chem.protection.amino_acids.ProtectedAminoAcid(smiles, protection_groups)

Bases: object

An output from the protection strategy on an amino acid

Parameters:

  • smiles (str) – the protected amino acid SMILES

  • protection_groups (Tuple[str, ...]) – the protection groups that was used to generate the amino acid

smiles: str
protection_groups: Tuple[str, ...]
class rxnutils.chem.protection.amino_acids.AminoAcidProtectionEngine(smartslib_path, reaction_rules_path, protection_groups_path)

Bases: object

Engine for protecting amino acids

The file with protection reactions, specified with reaction_rules_path should have the following columns:

  • functional_group - the functional group that can be protected by this reaction

  • protection_group - the name of the protection group

  • primary_reaction - the first reaction SMARTS to apply

  • secondary_reaction - a second, optional reaction SMARTS to apply

The file with the protection groups, specified with `protection_groups_path`should have the following columns:

  • name - the name of the protection group

  • smiles - the SMILES of the group

  • smarts - the SMARTS of the group

Parameters:

  • smartslib_path (str) – the path to a file with SMARTS patterns for functional group

  • reaction_rules_path (str) – the path to the file with the protection reaction SMARTS

  • protection_groups – the path to the file with SMILES for protection groups.

  • protection_groups_path (str)

protect(smiles)

Protect the given SMILES.

The SMILES need to have neutralized backbone charges

Parameters:

smiles (str) – the smiles of an amino acid

Returns:

a list of possible protected amino acids

Return type:

List[ProtectedAminoAcid]

Module contents