include/pdbio.h

   1 /*
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  35
  36 #ifndef _pdbio_h
  37 #define _pdbio_h
  38
  39 #include "sysstuff.h"
  40 #include "typedefs.h"
  41 #include "symtab.h"
  42 #include "atomprop.h"
  43
  44 #ifdef __cplusplus
  45 extern "C" {
  46 #endif
  47
  48 typedef struct gmx_conect_t *gmx_conect;
  49
  50 /* THE pdb format (for ATOM/HETATOM lines) */
  51 static const char *pdbformat ="%-6s%5u  %-4.4s%3.3s %c%4d%c   %8.3f%8.3f%8.3f";
  52 static const char *pdbformat4="%-6s%5u %-4.4s %3.3s %c%4d%c   %8.3f%8.3f%8.3f";
  53
  54 /* Enumerated type for pdb records. The other entries are ignored
  55  * when reading a pdb file
  56  */
  57 enum { epdbATOM,   epdbHETATM, epdbANISOU, epdbCRYST1, epdbCOMPND,
  58        epdbMODEL,  epdbENDMDL, epdbTER,    epdbHEADER, epdbTITLE, epdbREMARK,
  59        epdbCONECT, epdbNR };
  60
  61 /* Enumerated value for indexing an uij entry (anisotropic temperature factors) */
  62 enum { U11, U22, U33, U12, U13, U23 };
  63
  64 void set_pdb_wide_format(gmx_bool bSet);
  65 /* If bSet, use wider format for occupancy and bfactor */
  66
  67 void pdb_use_ter(gmx_bool bSet);
  68 /* set read_pdbatoms to read upto 'TER' or 'ENDMDL' (default, bSet=FALSE).
  69    This function is fundamentally broken as far as thread-safety is concerned.*/
  70
  71 void gmx_write_pdb_box(FILE *out,int ePBC,matrix box);
  72 /* write the box in the CRYST1 record,
  73  * with ePBC=-1 the pbc is guessed from the box
  74  * This function is fundamentally broken as far as thread-safety is concerned.
  75  */
  76
  77 void write_pdbfile_indexed(FILE *out,const char *title,t_atoms *atoms,
  78                                   rvec x[],int ePBC,matrix box,char chain,
  79                                   int model_nr,atom_id nindex,atom_id index[],
  80                                   gmx_conect conect,gmx_bool bTerSepChains);
  81 /* REALLY low level */
  82
  83 void write_pdbfile(FILE *out,const char *title,t_atoms *atoms,
  84                           rvec x[],int ePBC,matrix box,char chain,
  85                           int model_nr,gmx_conect conect,gmx_bool bTerSepChains);
  86 /* Low level pdb file writing routine.
  87  *
  88  *          ONLY FOR SPECIAL PURPOSES,
  89  *
  90  *       USE write_sto_conf WHEN YOU CAN.
  91  *
  92  * override chain-identifiers with chain when chain>0
  93  * write ENDMDL when bEndmodel is TRUE.
  94  *
  95  * If the gmx_conect structure is not NULL its content is dumped as CONECT records
  96  * which may be useful for visualization purposes.
  97  */
  98
  99 void get_pdb_atomnumber(t_atoms *atoms,gmx_atomprop_t aps);
 100 /* Routine to extract atomic numbers from the atom names */
 101
 102 int read_pdbfile(FILE *in,char *title,int *model_nr,
 103                         t_atoms *atoms,rvec x[],int *ePBC,matrix box,
 104                         gmx_bool bChange,gmx_conect conect);
 105 /* Function returns number of atoms found.
 106  * ePBC and gmx_conect structure may be NULL.
 107  */
 108
 109 void read_pdb_conf(const char *infile,char *title,
 110                           t_atoms *atoms,rvec x[],int *ePBC,matrix box,
 111                           gmx_bool bChange,gmx_conect conect);
 112 /* Read a pdb file and extract ATOM and HETATM fields.
 113  * Read a box from the CRYST1 line, return 0 box when no CRYST1 is found.
 114  * Change atom names according to protein conventions if wanted.
 115  * ePBC and gmx_conect structure may be NULL.
 116  */
 117
 118 void get_pdb_coordnum(FILE *in,int *natoms);
 119 /* Read a pdb file and count the ATOM and HETATM fields. */
 120
 121 gmx_bool is_hydrogen(const char *nm);
 122 /* Return whether atom nm is a hydrogen */
 123
 124 gmx_bool is_dummymass(const char *nm);
 125 /* Return whether atom nm is a dummy mass */
 126
 127 /* Routines to handle CONECT records if they have been read in */
 128 void gmx_conect_dump(FILE *fp,gmx_conect conect);
 129
 130 gmx_bool gmx_conect_exist(gmx_conect conect,int ai,int aj);
 131 /* Return TRUE if there is a conection between the atoms */
 132
 133 void gmx_conect_add(gmx_conect conect,int ai,int aj);
 134 /* Add a connection between ai and aj (numbered from 0 to natom-1) */
 135
 136 gmx_conect gmx_conect_generate(t_topology *top);
 137 /* Generate a conect structure from a topology */
 138
 139 gmx_conect gmx_conect_init(void);
 140 /* Initiate data structure */
 141
 142 void gmx_conect_done(gmx_conect gc);
 143 /* Free memory */
 144
 145 #ifdef __cplusplus
 146 }
 147 #endif
 148
 149 #endif  /* _pdbio_h */