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    This function is fundamentally broken as far as thread-safety is concerned.*/
  74
  75 extern void gmx_write_pdb_box(FILE *out,int ePBC,matrix box);
  76 /* write the box in the CRYST1 record,
  77  * with ePBC=-1 the pbc is guessed from the box
  78  * This function is fundamentally broken as far as thread-safety is concerned.
  79  */
  80
  81 extern void write_pdbfile_indexed(FILE *out,const char *title,t_atoms *atoms,
  82                                   rvec x[],int ePBC,matrix box,char chain,
  83                                   int model_nr,atom_id nindex,atom_id index[],
  84                                   gmx_conect conect,bool bTerSepChains);
  85 /* REALLY low level */
  86
  87 extern void write_pdbfile(FILE *out,const char *title,t_atoms *atoms,
  88                           rvec x[],int ePBC,matrix box,char chain,
  89                           int model_nr,gmx_conect conect,bool bTerSepChains);
  90 /* Low level pdb file writing routine.
  91  *
  92  *          ONLY FOR SPECIAL PURPOSES,
  93  *
  94  *       USE write_sto_conf WHEN YOU CAN.
  95  *
  96  * override chain-identifiers with chain when chain>0
  97  * write ENDMDL when bEndmodel is TRUE.
  98  *
  99  * If the gmx_conect structure is not NULL its content is dumped as CONECT records
 100  * which may be useful for visualization purposes.
 101  */
 102
 103 extern void get_pdb_atomnumber(t_atoms *atoms,gmx_atomprop_t aps);
 104 /* Routine to extract atomic numbers from the atom names */
 105
 106 extern int read_pdbfile(FILE *in,char *title,int *model_nr,
 107                         t_atoms *atoms,rvec x[],int *ePBC,matrix box,
 108                         bool bChange,gmx_conect conect);
 109 /* Function returns number of atoms found.
 110  * ePBC and gmx_conect structure may be NULL.
 111  */
 112
 113 extern void read_pdb_conf(const char *infile,char *title,
 114                           t_atoms *atoms,rvec x[],int *ePBC,matrix box,
 115                           bool bChange,gmx_conect conect);
 116 /* Read a pdb file and extract ATOM and HETATM fields.
 117  * Read a box from the CRYST1 line, return 0 box when no CRYST1 is found.
 118  * Change atom names according to protein conventions if wanted.
 119  * ePBC and gmx_conect structure may be NULL.
 120  */
 121
 122 extern void get_pdb_coordnum(FILE *in,int *natoms);
 123 /* Read a pdb file and count the ATOM and HETATM fields. */
 124
 125 extern bool is_hydrogen(const char *nm);
 126 /* Return whether atom nm is a hydrogen */
 127
 128 extern bool is_dummymass(const char *nm);
 129 /* Return whether atom nm is a dummy mass */
 130
 131 /* Routines to handle CONECT records if they have been read in */
 132 extern void gmx_conect_dump(FILE *fp,gmx_conect conect);
 133
 134 extern bool gmx_conect_exist(gmx_conect conect,int ai,int aj);
 135 /* Return TRUE if there is a conection between the atoms */
 136
 137 extern void gmx_conect_add(gmx_conect conect,int ai,int aj);
 138 /* Add a connection between ai and aj (numbered from 0 to natom-1) */
 139
 140 extern gmx_conect gmx_conect_generate(t_topology *top);
 141 /* Generate a conect structure from a topology */
 142
 143 extern gmx_conect gmx_conect_init();
 144 /* Initiate data structure */
 145
 146 extern void gmx_conect_done(gmx_conect gc);
 147 /* Free memory */
 148
 149 #ifdef __cplusplus
 150 }
 151 #endif
 152
 153 #endif  /* _pdbio_h */