/home/slemaign/softs-local/BioMove3D-git/BioTools/Translators/Protein/protein.h

#ifndef PROTEIN_H
#define PROTEIN_H

#define MAX_NAME_LENGTH 50


typedef enum {
  ALA, ARG, ASN, ASP, CYS, GLN, GLU, GLY, HIS, ILE, 
  LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL,
  ALAH, ARGH, ASNH, ASPH, CYSH, GLNH, GLUH, GLYH, HISH, ILEH, 
  LEUH, LYSH, METH, PHEH, PROH, SERH, THRH, TRPH, TYRH, VALH 
} residueTypes;

typedef enum {
 SULPHUR, SULPHUR_H, OXYGEN, OXYGEN_H, NITROGEN, NITROGEN_H, NITROGEN_FULL,
 CARBON, HYDROGEN, HYDROGEN_P, BROMINE, IODINE, FLUORINE, PHOSPHORUS, CHLORINE
} atomTypes;


/**********************************************************************
 *                Protein Structure Format (PSF)                      *
 **********************************************************************/

typedef struct s_atom {
  struct s_residue *residuePt;
  int serial;
  char name[5];
  atomTypes atomType;
  double pos[3];
  int changedpos; // indicates if pos has been modified
  int inapc;      // indicates if the atom is in an articulated chain (NECESSARY ???)
  double vdwR;
  int nbondedA;
  struct s_atom **bondedAlist;
  int amber_index;
} atom;


typedef struct s_residue {
  struct s_AAchain *chainPt;
  char chainID[2];
  int subchainind;
  int resSeq;
  char resName[4];
  residueTypes resType;
  int flagH;    // indicates if it contains hydrogen atoms
  int flagCterm;// indicates if it is a C terminal residue with OXT
  int flagNterm;// indicates if it is a N terminal residue with 3 H atoms
  // NOTE : use pseudo backbone and side-chain
  int nbkbatoms;
  int nschatoms;
  // NOTE : atoms in lists have precise order (defined for BCD)
  struct s_atom **bkbAlist;
  struct s_atom **schAlist;
  struct s_residue *next;
  struct s_residue *prev;
} residue;


typedef struct s_AAchain {
  struct s_protein *proteinPt;
  int nresidues;
  struct s_residue **reslist;
  //struct s_AAchain *next;
} AAchain;


typedef struct s_protein {
  char name[MAX_NAME_LENGTH];
  int nchains;
  struct s_AAchain **chainlist;
} protein;

#endif