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RotamerID

The sidechain module has its own definition of amino acids to satisfy custom requirements for the implemented sidechain construction algorithms. As an example there are histidine in two possible protonation states, that affect the hbond term or different versions of proline/cysteine.

The RotamerID

class promod3.sidechain.RotamerID

Enumerates the amino acids. Possible values:

  • ARG - Arginine
  • ASN - Asparagine
  • ASP - Aspartate
  • GLN - Glutamine
  • GLU - Glutamate
  • LYS - Lysine
  • SER - Serine
  • CYS - Cystein
  • CYH - “free” Cystein
  • CYD - disulfid bonded Cystein
  • MET - Methionine
  • TRP - Tryptophane
  • TYR - Tyrosine
  • THR - Threonine
  • VAL - Valine
  • ILE - Isoleucine
  • LEU - Leucine
  • PRO - Proline
  • CPR - cis-Proline
  • TPR - trans-Proline
  • HIS - Histidine
  • HSD - d-protonated Histidine
  • HSE - e-protonated Histidine
  • PHE - Phenylalanine
  • GLY - Glycine
  • ALA - Alanine
  • XXX - Invalid

The RotamerID enum can be accessed either directly as promod3.sidechain.ARG or as promod3.sidechain.RotamerID.ARG.

How can I get an ID?

The RotamerID enum can directly be accessed from Python. Two convenient functions exist to get RotamerIDs from the ost.conop.AminoAcid enum or from amino acid three letter codes.

promod3.sidechain.TLCToRotID(tlc)

Directly translates the three letter code into a RotamerID. Following exactly the naming convention defined above.

Parameters:tlc (str) – Three letter code of amino acid
Returns:RotamerID, XXX if tlc cannot be recoginzed.
promod3.sidechain.AAToRotID(aa)

Directly translates aa into a RotamerID. Note, that it is not possible to generate special IDs this way (e.g. HSD, HSE or the special prolines/cysteins) since they’re simply not defined in ost.conop.AminoAcid

Parameters:aa (ost.conop.AminoAcid) – AA enum of amino acid
Returns:RotamerID, XXX if aa is invalid.

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