Functions and classes for standard amino acids¶

The AminoAcid enum¶

class AminoAcid¶

The amino acid enum enumerates all 20 standard amino acid and the special value XXX, to signify an unknown amino acid. The amino acid enum supports the following values:

ALA, ARG, ASN, ASP, GLN, GLU, LYS, SER, CYS, MET TRP, TYR, THR, VAL, ILE, LEU, GLY, PRO, HIS, PHE XXX

Converter functions¶

ResidueToAminoAcid(residue)¶

ResidueNameToAminoAcid(rname)¶

OneLetterCodeNameToAminoAcid(olc)¶

Returns:	Amino acid from residue, residue name (three-letter-code) or one-letter-code. Returns XXX if residue, residue name or one-letter-code is not one of the 20 standard amino acids.
Return type:	AminoAcid

OneLetterCodeToResidueName(olc)¶

AminoAcidToResidueName(amino_acid)¶

Returns:	Residue name from one-letter-code or amino_acid. For invalid one-letter-codes or XXX, ‘UNK’ is returned.
Return type:	str
Parameters:	olc (str) – One-letter-code amino_acid (AminoAcid) – Amino acid type

ResidueNameToOneLetterCode(rname)¶

Returns:	One-letter-code for the given residue name. Returns ‘X’ if residue name is not one of the 20 standard amino acids.
Return type:	str
Parameters:	rname (str) – Residue name

class AminoAcidSet¶

A set of amino acids, with constant-time access

static CreatePolarSet()¶

static CreateAromaticSet()¶

static CreateApolarSet()¶

Returns a set containing all polar, aromatic or apolar amino acids, respectively.

Add(amino_acid)¶

Add amino acid to the set.

Remove(amino_acid)¶

Remove amino acid from the set

Empty()¶

Whether the set is empty, i.e. doesn’t contain any amino acids.

Mapping functions¶

The following functions help to convert one residue into another by reusing as much as possible from the present atoms. They are mainly meant to map from standard amino acid to other standard amino acids or from modified amino acids to standard amino acids.

CopyResidue(src_res, dst_res, editor)¶

Copies the atoms of src_res to dst_res using the residue names as guide to decide which of the atoms should be copied. If src_res and dst_res have the same name, or src_res is a modified version of dst_res (i.e. have the same single letter code), CopyConserved will be called, otherwise CopyNonConserved will be called.

Parameters:	src_res (ResidueHandle) – The source residue dst_res (ResidueHandle) – The destination residue
Returns:	true if the residue could be copied, false if not.

CopyConserved(src_res, dst_res, editor)¶

Copies the atoms of src_res to dst_res assuming that the parent amino acid of src_res (or src_res itself) are identical to dst_res.

If src_res and dst_res are identical, all heavy atoms are copied to dst_res. If src_res is a modified version of dst_res and the modification is a pure addition (e.g. the phosphate group of phosphoserine), the modification is stripped off and all other heavy atoms are copied to dst_res. If the modification is not a pure addition, only the backbone heavy atoms are copied to dst_res.

Additionally, the selenium atom of MSE is converted to sulphur.

Parameters:	src_res (ResidueHandle) – The source residue dst_res (ResidueHandle) – The destination residue
Returns:	a tuple of bools stating whether the residue could be copied and whether the Cbeta atom was inserted into the dst_res.

CopyNonConserved(src_res, dst_res, editor)¶

Copies the heavy backbone atoms and Cbeta (except for GLY) of src_res to dst_res.

Parameters:	src_res (ResidueHandle) – The source residue dst_res (ResidueHandle) – The destination residue
Returns:	a tuple of bools stating whether the residue could be copied and whether the Cbeta atom was inserted into the dst_res.