atom_types.h

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// -*- mode: c++; -*-
//
//The Biomolecule Toolkit (BTK) is a C++ library for use in the
//modeling, analysis, and design of biological macromolecules.
//Copyright (C) 2004, Christopher Saunders <ctsa@users.sourceforge.net>
//
//This program is free software; you can redistribute it and/or modify
//it under the terms of the GNU Lesser General Public License as published
//by the Free Software Foundation; either version 2.1 of the License, or (at
//your option) any later version.
//
//This program is distributed in the hope that it will be useful,  but
//WITHOUT ANY WARRANTY; without even the implied warranty of
//MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
//Lesser General Public License for more details. 
//
//You should have received a copy of the GNU Lesser General Public License 
//along with this program; if not, write to the Free Software Foundation, 
//Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
//

//@file atom_types.h
// defines and manages default btk atom topology types 
// -- note that these types are based on the most common pdb naming 
// convention for any atom topology
//

#ifndef BTK_ATOM_TYPES_H
#define BTK_ATOM_TYPES_H


#include "element_types.h"

#include <string>

namespace BTK{
  namespace ATOM { 
    // atom topological types from file: top_all27_prot_na.inp distributed with 
    // CHARMM 27 
    // --note that the the charmm symbols have been altered for use in
    // c++ using two subtitutions:
    //   1) s/'/x/ so 1H2' is represented here as 1H2x
    //   2) symbols that start with a digit are prefixed with an 
    //        underscore ...so 1H2x is _1H2x
    // --also note that btk functions do not necessarily 
    // support all of the topological types below
    //
    enum index_t {
      UNKNOWN = -1,
      _1C2x, _1C3x, _1CB, _1H2xx, _1H3x, _1H3xx, _1O2x, _1SG,
      _2C5x, _2CB, _2H5x, _2H5xx, _2O1P, _2O2P, _2O5x, _2P,
      _2SG,
      AC1x, AC2, AC2x, AC3x, AC4, AC4x, AC5, AC5x,
      AC6, AC8, AH1x, AH2, AH2x, AH2T, AH3x, AH3T,
      AH4x, AH5x, AH5s, AH61, AH62, AH8, AN1, AN3,
      AN6, AN7, AN9, AO1, AO1P, AO2, AO2x, AO2P,
      AO2T, AO3x, AO4x, AO5x, AP, AP2,
      C, C1, C1x, C10, C12, C1A, C1B, C1C,
      C1D, C2, C2x, C2A, C2B, C2C, C2D, C3,
      C3x, C3A, C3B, C3C, C3D, C3T, C4, C4x,
      C4A, C4B, C4C, C4D, C5, C5x, C5M, C5T,
      C6, C7, C8, C9, C9B, CA, CAA, CAB,
      CAC, CAD, CAL, CAT, CAY, CB, CBA, CBB,
      CBC, CBD, CD, CD1, CD2, CE, CE1, CE2,
      CE3, CES, CG, CG1, CG2, CGA, CGD, CH2,
      CHA, CHB, CHC, CHD, CLA, CMA, CMB, CMC,
      CMD, CT, CY, CZ, CZ2, CZ3,
      DUM,
      F2x,
      FE,
      H1, H1x, H1xx, H11, H11x, H12, H12x, H13,
      H15, H16, H17, H2, H2x, H2xx, H21, H21x,
      H22, H22x, H23, H3, H3x, H3xx, H31x, H32x,
      H3T, H3T1, H3T2, H3T3, H4, H4x, H4xx, H41,
      H41x, H42, H42x, H5, H5x, H5xx, H51, H51x,
      H52, H52x, H53, H53x, H5M1, H5M2, H5M3, H5T,
      H5T1, H5T2, H5T3, H6, H61, H62, H8, H9,
      H91, H92, H93, H9B1, H9B2, H9B3, HA, HA1,
      HA2, HAA1, HAA2, HAB, HAC, HAD1, HAD2, HB,
      HB1, HB2, HB3, HBA1, HBA2, HBB1, HBB2, HBC1,
      HBC2, HBD1, HBD2, HC, HD, HD1, HD11, HD12,
      HD13, HD2, HD21, HD22, HD23, HD3, HE, HE1,
      HE2, HE21, HE22, HE3, HG, HG1, HG11, HG12,
      HG13, HG2, HG21, HG22, HG23, HH, HH11, HH12,
      HH2, HH21, HH22, HMA1, HMA2, HMA3, HMB1, HMB2,
      HMB3, HMC1, HMC2, HMC3, HMD1, HMD2, HMD3, HN,
      HN1, HN2, HNT, HT1, HT2, HT3, HY1, HY2,
      HY3, HZ, HZ1, HZ2, HZ3,
      MG,
      N, N1,
      N14, N2, N3, N4, N6, N7, N9, NA,
      NB, NC, NC1x, NC2, NC2x, NC3, NC3x, NC4,
      NC4x, NC5, NC5x, NC6, NC7, ND, ND1, ND2,
      NE, NE1, NE2, NH1, NH1x, NH2, NH2x, NH2T,
      NH3x, NH3T, NH4, NH4x, NH42, NH5, NH5x, NH5s,
      NH6, NH71, NH72, NN1, NN7, NO1, NO2, NO2x,
      NO3x, NO4x, NO5x, NO7, NP, NT, NZ,
      O,
      O1, O11, O12, O13, O14, O1A, O1B, O1D,
      O1G, O1P, O1P3, O2, O2x, O21, O22, O23,
      O24, O2A, O2B, O2D, O2G, O2P, O2P3, O3,
      O3x, O31P, O32P, O33P, O3A, O3B, O3G, O3P,
      O3P3, O3T, O4, O4x, O5x, O5T, O6, OD1,
      OD2, OE1, OE2, OG, OG1, OH, OH2, OT1,
      OT2, OY,
      P, P1, P2, P3, PA, PB, PG,
      POT,
      SD, SG,
      SOD,
      ZN,
      SIZE
    };

    index_t pdbname_to_atom_index(const std::string& s); 

    const std::string& atom_index_to_pdbname(index_t i); 

    ELEMENT::index_t atom_index_to_element_index(index_t i);
  }
} 

#endif

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