include/pdbio.h

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  38
  39 #ifndef _pdbio_h
  40 #define _pdbio_h
  41 #include "visibility.h"
  42 #include "sysstuff.h"
  43 #include "typedefs.h"
  44 #include "symtab.h"
  45 #include "atomprop.h"
  46
  47 #ifdef __cplusplus
  48 extern "C" {
  49 #endif
  50
  51 typedef struct gmx_conect_t *gmx_conect;
  52
  53 /* THE pdb format (for ATOM/HETATOM lines) */
  54 static const char *pdbformat  = "%-6s%5u  %-4.4s%3.3s %c%4d%c   %8.3f%8.3f%8.3f";
  55 static const char *pdbformat4 = "%-6s%5u %-4.4s %3.3s %c%4d%c   %8.3f%8.3f%8.3f";
  56
  57 /* Enumerated type for pdb records. The other entries are ignored
  58  * when reading a pdb file
  59  */
  60 enum {
  61     epdbATOM,   epdbHETATM, epdbANISOU, epdbCRYST1, epdbCOMPND,
  62     epdbMODEL,  epdbENDMDL, epdbTER,    epdbHEADER, epdbTITLE, epdbREMARK,
  63     epdbCONECT, epdbNR
  64 };
  65
  66 /* Enumerated value for indexing an uij entry (anisotropic temperature factors) */
  67 enum {
  68     U11, U22, U33, U12, U13, U23
  69 };
  70
  71 GMX_LIBGMX_EXPORT
  72 void set_pdb_wide_format(gmx_bool bSet);
  73 /* If bSet, use wider format for occupancy and bfactor */
  74
  75 void pdb_use_ter(gmx_bool bSet);
  76 /* set read_pdbatoms to read upto 'TER' or 'ENDMDL' (default, bSet=FALSE).
  77    This function is fundamentally broken as far as thread-safety is concerned.*/
  78
  79 GMX_LIBGMX_EXPORT
  80 void gmx_write_pdb_box(FILE *out, int ePBC, matrix box);
  81 /* write the box in the CRYST1 record,
  82  * with ePBC=-1 the pbc is guessed from the box
  83  * This function is fundamentally broken as far as thread-safety is concerned.
  84  */
  85
  86 GMX_LIBGMX_EXPORT
  87 void write_pdbfile_indexed(FILE *out, const char *title, t_atoms *atoms,
  88                            rvec x[], int ePBC, matrix box, char chain,
  89                            int model_nr, atom_id nindex, atom_id index[],
  90                            gmx_conect conect, gmx_bool bTerSepChains);
  91 /* REALLY low level */
  92
  93 GMX_LIBGMX_EXPORT
  94 void write_pdbfile(FILE *out, const char *title, t_atoms *atoms,
  95                    rvec x[], int ePBC, matrix box, char chain,
  96                    int model_nr, gmx_conect conect, gmx_bool bTerSepChains);
  97 /* Low level pdb file writing routine.
  98  *
  99  *          ONLY FOR SPECIAL PURPOSES,
 100  *
 101  *       USE write_sto_conf WHEN YOU CAN.
 102  *
 103  * override chain-identifiers with chain when chain>0
 104  * write ENDMDL when bEndmodel is TRUE.
 105  *
 106  * If the gmx_conect structure is not NULL its content is dumped as CONECT records
 107  * which may be useful for visualization purposes.
 108  */
 109
 110 GMX_LIBGMX_EXPORT
 111 void get_pdb_atomnumber(t_atoms *atoms, gmx_atomprop_t aps);
 112 /* Routine to extract atomic numbers from the atom names */
 113
 114 int read_pdbfile(FILE *in, char *title, int *model_nr,
 115                  t_atoms *atoms, rvec x[], int *ePBC, matrix box,
 116                  gmx_bool bChange, gmx_conect conect);
 117 /* Function returns number of atoms found.
 118  * ePBC and gmx_conect structure may be NULL.
 119  */
 120
 121 void read_pdb_conf(const char *infile, char *title,
 122                    t_atoms *atoms, rvec x[], int *ePBC, matrix box,
 123                    gmx_bool bChange, gmx_conect conect);
 124 /* Read a pdb file and extract ATOM and HETATM fields.
 125  * Read a box from the CRYST1 line, return 0 box when no CRYST1 is found.
 126  * Change atom names according to protein conventions if wanted.
 127  * ePBC and gmx_conect structure may be NULL.
 128  */
 129
 130 void get_pdb_coordnum(FILE *in, int *natoms);
 131 /* Read a pdb file and count the ATOM and HETATM fields. */
 132
 133 GMX_LIBGMX_EXPORT
 134 gmx_bool is_hydrogen(const char *nm);
 135 /* Return whether atom nm is a hydrogen */
 136
 137 GMX_LIBGMX_EXPORT
 138 gmx_bool is_dummymass(const char *nm);
 139 /* Return whether atom nm is a dummy mass */
 140
 141 /* Routines to handle CONECT records if they have been read in */
 142 void gmx_conect_dump(FILE *fp, gmx_conect conect);
 143
 144 gmx_bool gmx_conect_exist(gmx_conect conect, int ai, int aj);
 145 /* Return TRUE if there is a conection between the atoms */
 146
 147 void gmx_conect_add(gmx_conect conect, int ai, int aj);
 148 /* Add a connection between ai and aj (numbered from 0 to natom-1) */
 149
 150 GMX_LIBGMX_EXPORT
 151 gmx_conect gmx_conect_generate(t_topology *top);
 152 /* Generate a conect structure from a topology */
 153
 154 gmx_conect gmx_conect_init(void);
 155 /* Initiate data structure */
 156
 157 void gmx_conect_done(gmx_conect gc);
 158 /* Free memory */
 159
 160 #ifdef __cplusplus
 161 }
 162 #endif
 163
 164 #endif  /* _pdbio_h */