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 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 extern void set_pdb_wide_format(bool bSet);
  65 /* If bSet, use wider format for occupancy and bfactor */
  66
  67 extern void pdb_use_ter(bool bSet);
  68 /* set read_pdbatoms to read upto 'TER' or 'ENDMDL' (default, bSet=FALSE) */
  69
  70 extern void gmx_write_pdb_box(FILE *out,int ePBC,matrix box);
  71 /* write the box in the CRYST1 record,
  72  * with ePBC=-1 the pbc is guessed from the box
  73  */
  74
  75 extern void write_pdbfile_indexed(FILE *out,const char *title,t_atoms *atoms,
  76                                   rvec x[],int ePBC,matrix box,char chain,
  77                                   int model_nr,atom_id nindex,atom_id index[],
  78                                   gmx_conect conect);
  79 /* REALLY low level */
  80
  81 extern void write_pdbfile(FILE *out,const char *title,t_atoms *atoms,
  82                           rvec x[],int ePBC,matrix box,char chain,
  83                           int model_nr,gmx_conect conect);
  84 /* Low level pdb file writing routine.
  85  *
  86  *          ONLY FOR SPECIAL PURPOSES,
  87  *
  88  *       USE write_sto_conf WHEN YOU CAN.
  89  *
  90  * override chain-identifiers with chain when chain>0
  91  * write ENDMDL when bEndmodel is TRUE.
  92  *
  93  * If the gmx_conect structure is not NULL its content is dumped as CONECT records
  94  * which may be useful for visualization purposes.
  95  */
  96
  97 extern void get_pdb_atomnumber(t_atoms *atoms,gmx_atomprop_t aps);
  98 /* Routine to extract atomic numbers from the atom names */
  99
 100 extern int read_pdbfile(FILE *in,char *title,int *model_nr,
 101                         t_atoms *atoms,rvec x[],int *ePBC,matrix box,
 102                         bool bChange,gmx_conect conect);
 103 /* Function returns number of atoms found.
 104  * ePBC and gmx_conect structure may be NULL.
 105  */
 106
 107 extern void read_pdb_conf(const char *infile,char *title,
 108                           t_atoms *atoms,rvec x[],int *ePBC,matrix box,
 109                           bool bChange,gmx_conect conect);
 110 /* Read a pdb file and extract ATOM and HETATM fields.
 111  * Read a box from the CRYST1 line, return 0 box when no CRYST1 is found.
 112  * Change atom names according to protein conventions if wanted.
 113  * ePBC and gmx_conect structure may be NULL.
 114  */
 115
 116 extern void get_pdb_coordnum(FILE *in,int *natoms);
 117 /* Read a pdb file and count the ATOM and HETATM fields. */
 118
 119 extern bool is_hydrogen(const char *nm);
 120 /* Return whether atom nm is a hydrogen */
 121
 122 extern bool is_dummymass(const char *nm);
 123 /* Return whether atom nm is a dummy mass */
 124
 125 /* Routines to handle CONECT records if they have been read in */
 126 extern void gmx_conect_dump(FILE *fp,gmx_conect conect);
 127
 128 extern bool gmx_conect_exist(gmx_conect conect,int ai,int aj);
 129 /* Return TRUE if there is a conection between the atoms */
 130
 131 extern void gmx_conect_add(gmx_conect conect,int ai,int aj);
 132 /* Add a connection between ai and aj (numbered from 0 to natom-1) */
 133
 134 extern gmx_conect gmx_conect_generate(t_topology *top);
 135 /* Generate a conect structure from a topology */
 136
 137 extern gmx_conect gmx_conect_init();
 138 /* Initiate data structure */
 139
 140 extern void gmx_conect_done(gmx_conect gc);
 141 /* Free memory */
 142
 143 #endif  /* _pdbio_h */