include/pdbio.h

   1 /*
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  35
  36 #ifndef _pdbio_h
  37 #define _pdbio_h
  38
  39 #ifdef HAVE_CONFIG_H
  40 #include <config.h>
  41 #endif
  42
  43 #include "sysstuff.h"
  44 #include "typedefs.h"
  45 #include "symtab.h"
  46 #include "atomprop.h"
  47
  48 #ifdef __cplusplus
  49 extern "C" {
  50 #endif
  51
  52 typedef struct gmx_conect_t *gmx_conect;
  53
  54 /* THE pdb format (for ATOM/HETATOM lines) */
  55 static const char *pdbformat ="%-6s%5u  %-4.4s%3.3s %c%4d%c   %8.3f%8.3f%8.3f";
  56 static const char *pdbformat4="%-6s%5u %-4.4s %3.3s %c%4d%c   %8.3f%8.3f%8.3f";
  57
  58 /* Enumerated type for pdb records. The other entries are ignored
  59  * when reading a pdb file
  60  */
  61 enum { epdbATOM,   epdbHETATM, epdbANISOU, epdbCRYST1, epdbCOMPND,
  62        epdbMODEL,  epdbENDMDL, epdbTER,    epdbHEADER, epdbTITLE, epdbREMARK,
  63        epdbCONECT, epdbNR };
  64
  65 /* Enumerated value for indexing an uij entry (anisotropic temperature factors) */
  66 enum { U11, U22, U33, U12, U13, U23 };
  67
  68 extern void set_pdb_wide_format(bool bSet);
  69 /* If bSet, use wider format for occupancy and bfactor */
  70
  71 extern void pdb_use_ter(bool bSet);
  72 /* set read_pdbatoms to read upto 'TER' or 'ENDMDL' (default, bSet=FALSE) */
  73
  74 extern void gmx_write_pdb_box(FILE *out,int ePBC,matrix box);
  75 /* write the box in the CRYST1 record,
  76  * with ePBC=-1 the pbc is guessed from the box
  77  */
  78
  79 extern void write_pdbfile_indexed(FILE *out,const char *title,t_atoms *atoms,
  80                                   rvec x[],int ePBC,matrix box,char chain,
  81                                   int model_nr,atom_id nindex,atom_id index[],
  82                                   gmx_conect conect);
  83 /* REALLY low level */
  84
  85 extern void write_pdbfile(FILE *out,const char *title,t_atoms *atoms,
  86                           rvec x[],int ePBC,matrix box,char chain,
  87                           int model_nr,gmx_conect conect);
  88 /* Low level pdb file writing routine.
  89  *
  90  *          ONLY FOR SPECIAL PURPOSES,
  91  *
  92  *       USE write_sto_conf WHEN YOU CAN.
  93  *
  94  * override chain-identifiers with chain when chain>0
  95  * write ENDMDL when bEndmodel is TRUE.
  96  *
  97  * If the gmx_conect structure is not NULL its content is dumped as CONECT records
  98  * which may be useful for visualization purposes.
  99  */
 100
 101 extern void get_pdb_atomnumber(t_atoms *atoms,gmx_atomprop_t aps);
 102 /* Routine to extract atomic numbers from the atom names */
 103
 104 extern int read_pdbfile(FILE *in,char *title,int *model_nr,
 105                         t_atoms *atoms,rvec x[],int *ePBC,matrix box,
 106                         bool bChange,gmx_conect conect);
 107 /* Function returns number of atoms found.
 108  * ePBC and gmx_conect structure may be NULL.
 109  */
 110
 111 extern void read_pdb_conf(const char *infile,char *title,
 112                           t_atoms *atoms,rvec x[],int *ePBC,matrix box,
 113                           bool bChange,gmx_conect conect);
 114 /* Read a pdb file and extract ATOM and HETATM fields.
 115  * Read a box from the CRYST1 line, return 0 box when no CRYST1 is found.
 116  * Change atom names according to protein conventions if wanted.
 117  * ePBC and gmx_conect structure may be NULL.
 118  */
 119
 120 extern void get_pdb_coordnum(FILE *in,int *natoms);
 121 /* Read a pdb file and count the ATOM and HETATM fields. */
 122
 123 extern bool is_hydrogen(const char *nm);
 124 /* Return whether atom nm is a hydrogen */
 125
 126 extern bool is_dummymass(const char *nm);
 127 /* Return whether atom nm is a dummy mass */
 128
 129 /* Routines to handle CONECT records if they have been read in */
 130 extern void gmx_conect_dump(FILE *fp,gmx_conect conect);
 131
 132 extern bool gmx_conect_exist(gmx_conect conect,int ai,int aj);
 133 /* Return TRUE if there is a conection between the atoms */
 134
 135 extern void gmx_conect_add(gmx_conect conect,int ai,int aj);
 136 /* Add a connection between ai and aj (numbered from 0 to natom-1) */
 137
 138 extern gmx_conect gmx_conect_generate(t_topology *top);
 139 /* Generate a conect structure from a topology */
 140
 141 extern gmx_conect gmx_conect_init();
 142 /* Initiate data structure */
 143
 144 extern void gmx_conect_done(gmx_conect gc);
 145 /* Free memory */
 146
 147 #ifdef __cplusplus
 148 }
 149 #endif
 150
 151 #endif  /* _pdbio_h */