resinfo.hpp

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// Copyright 2018 Global Phasing Ltd.
//
// List of common residues with basic data.
 
#ifndef GEMMI_RESINFO_HPP_
#define GEMMI_RESINFO_HPP_
 
#include <cstdint>  // for uint8_t
#include <string>
#include <vector>
#include "fail.hpp"
 
namespace gemmi {
 
// Simple approximate classification.
// AA - aminoacid
// AAD - D-aminoacid
// PAA - proline-like aminoacid
// MAA - methylated aminoacid
// RNA, DNA - nucleic acids
// HOH - water or heavy water (OH, H3O, D3O are not included here)
// PYR - pyranose according to the refmac dictionary
// KET - ketopyranose according to the refmac dictionary
// BUF - agent from crystallization buffer according to PISA agents.dat
// ELS - something else (ligand).
enum class ResidueKind : unsigned char {
  // when changing this list update check_polymer_type()
  UNKNOWN=0, AA, AAD, PAA, MAA, RNA, DNA, BUF, HOH, PYR, KET, ELS
};
 
struct ResidueInfo {
  ResidueKind kind;
  // linking type: 0=n/a, 1=peptide-linking, 2=nucl.-linking, 3=(2|1)
  std::uint8_t linking_type;
  // one-letter code or space (uppercase iff it is a standard residues)
  char one_letter_code;
  // rough count of hydrogens used to estimate mass with implicit hydrogens
  std::uint8_t hydrogen_count;
  // molecular weight
  float weight;
 
  bool found() const { return kind != ResidueKind::UNKNOWN; }
  bool is_water() const { return kind == ResidueKind::HOH; }
  bool is_dna() const { return kind == ResidueKind::DNA; }
  bool is_rna() const { return kind == ResidueKind::RNA; }
  bool is_nucleic_acid() const { return is_dna() || is_rna(); }
  bool is_amino_acid() const {
    return kind == ResidueKind::AA || kind == ResidueKind::AAD ||
           kind == ResidueKind::PAA || kind == ResidueKind::MAA;
  }
  bool is_buffer_or_water() const {
    return kind == ResidueKind::HOH || kind == ResidueKind::BUF;
  }
  // PDB format has non-standard residues (modified AA) marked as HETATM.
  bool is_standard() const { return (one_letter_code & 0x20) == 0; }
  char fasta_code() const { return is_standard() ? one_letter_code : 'X'; }
  bool is_peptide_linking() const { return (linking_type & 1); }
  bool is_na_linking() const { return (linking_type & 2); }
};
 
GEMMI_DLL ResidueInfo find_tabulated_residue(const std::string& name);
 
inline const char* expand_one_letter(char c, ResidueKind kind) {
  static const char* names =
    // amino-acids (all letters but J are used)
    "ALA\0ASX\0CYS\0ASP\0GLU\0PHE\0GLY\0HIS\0ILE\0\0   LYS\0LEU\0MET\0"  // A-M
    "ASN\0PYL\0PRO\0GLN\0ARG\0SER\0THR\0SEC\0VAL\0TRP\0UNK\0TYR\0GLX\0"  // N-Z
    // DNA
    "DA\0 \0\0  DC\0 \0\0  \0\0  \0\0  DG\0 \0\0  DI\0 \0\0  \0\0  \0\0  \0\0  "   // A-M
    "DN\0 \0\0  \0\0  \0\0  \0\0  \0\0  DT\0 DU\0 \0\0  \0\0  \0\0  \0\0  \0\0  "; // N-Z
  c &= ~0x20;
  const char* ret = nullptr;
  if (c >= 'A' && c <= 'Z') {
    ret = &names[4 * (c - 'A')];
    if (kind == ResidueKind::AA) {
      // ret is already set
    } else if (kind == ResidueKind::DNA) {
      ret += 4 * 26;
    } else if (kind == ResidueKind::RNA && c != 'T') {
      ret += 4 * 26 + 1;
    } else {
      ret = nullptr;
    }
  }
  return (ret && *ret) ? ret : nullptr;
}
 
GEMMI_DLL std::vector<std::string> expand_one_letter_sequence(const std::string& seq,
                                                              ResidueKind kind);
 
// deprecated
inline const char* expand_protein_one_letter(char c) {
  return expand_one_letter(c, ResidueKind::AA);
}
// deprecated
inline std::vector<std::string> expand_protein_one_letter_string(const std::string& s) {
  return expand_one_letter_sequence(s, ResidueKind::AA);
}
 
 
} // namespace gemmi
#endif