src/gromacs/fileio/pdbio.h

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  37
  38 #ifndef GMX_FILEIO_PDBIO_H
  39 #define GMX_FILEIO_PDBIO_H
  40
  41 #include <stdio.h>
  42
  43 #include "gromacs/math/vectypes.h"
  44 #include "gromacs/topology/atoms.h"
  45 #include "gromacs/utility/basedefinitions.h"
  46 #include "gromacs/utility/real.h"
  47
  48 #ifdef __cplusplus
  49 extern "C" {
  50 #endif
  51
  52 struct gmx_atomprop;
  53 struct t_atoms;
  54 struct t_symtab;
  55 struct t_topology;
  56
  57 typedef struct gmx_conect_t *gmx_conect;
  58
  59 /* Write a PDB line with an ATOM or HETATM record directly to a file pointer.
  60  *
  61  * Returns the number of characters printed.
  62  */
  63 int
  64 gmx_fprintf_pdb_atomline(FILE *            fp,
  65                          enum PDB_record   record,
  66                          int               atom_seq_number,
  67                          const char *      atom_name,
  68                          char              alternate_location,
  69                          const char *      res_name,
  70                          char              chain_id,
  71                          int               res_seq_number,
  72                          char              res_insertion_code,
  73                          real              x,
  74                          real              y,
  75                          real              z,
  76                          real              occupancy,
  77                          real              b_factor,
  78                          const char *      element);
  79
  80 /* Enumerated value for indexing an uij entry (anisotropic temperature factors) */
  81 enum {
  82     U11, U22, U33, U12, U13, U23
  83 };
  84
  85 void pdb_use_ter(gmx_bool bSet);
  86 /* set read_pdbatoms to read upto 'TER' or 'ENDMDL' (default, bSet=FALSE).
  87    This function is fundamentally broken as far as thread-safety is concerned.*/
  88
  89 void gmx_write_pdb_box(FILE *out, int ePBC, const matrix box);
  90 /* write the box in the CRYST1 record,
  91  * with ePBC=-1 the pbc is guessed from the box
  92  * This function is fundamentally broken as far as thread-safety is concerned.
  93  */
  94
  95 void write_pdbfile_indexed(FILE *out, const char *title, const t_atoms *atoms,
  96                            const rvec x[], int ePBC, const matrix box, char chain,
  97                            int model_nr, int nindex, const int index[],
  98                            gmx_conect conect, gmx_bool bTerSepChains);
  99 /* REALLY low level */
 100
 101 void write_pdbfile(FILE *out, const char *title, const t_atoms *atoms,
 102                    const rvec x[], int ePBC, const matrix box, char chain,
 103                    int model_nr, gmx_conect conect, gmx_bool bTerSepChains);
 104 /* Low level pdb file writing routine.
 105  *
 106  *          ONLY FOR SPECIAL PURPOSES,
 107  *
 108  *       USE write_sto_conf WHEN YOU CAN.
 109  *
 110  * override chain-identifiers with chain when chain>0
 111  * write ENDMDL when bEndmodel is TRUE.
 112  *
 113  * If the gmx_conect structure is not NULL its content is dumped as CONECT records
 114  * which may be useful for visualization purposes.
 115  */
 116
 117 void get_pdb_atomnumber(const t_atoms *atoms, struct gmx_atomprop *aps);
 118 /* Routine to extract atomic numbers from the atom names */
 119
 120 int read_pdbfile(FILE *in, char *title, int *model_nr,
 121                  struct t_atoms *atoms, struct t_symtab *symtab,
 122                  rvec x[], int *ePBC, matrix box,
 123                  gmx_bool bChange, gmx_conect conect);
 124 /* Function returns number of atoms found.
 125  * ePBC and gmx_conect structure may be NULL.
 126  */
 127
 128 void gmx_pdb_read_conf(const char *infile,
 129                        t_symtab *symtab, char ***name, t_atoms *atoms,
 130                        rvec x[], int *ePBC, matrix box);
 131 /* Read a pdb file and extract ATOM and HETATM fields.
 132  * Read a box from the CRYST1 line, return 0 box when no CRYST1 is found.
 133  * ePBC may be NULL.
 134  */
 135
 136 void get_pdb_coordnum(FILE *in, int *natoms);
 137 /* Read a pdb file and count the ATOM and HETATM fields. */
 138
 139 gmx_bool is_hydrogen(const char *nm);
 140 /* Return whether atom nm is a hydrogen */
 141
 142 gmx_bool is_dummymass(const char *nm);
 143 /* Return whether atom nm is a dummy mass */
 144
 145 /* Routines to handle CONECT records if they have been read in */
 146 void gmx_conect_dump(FILE *fp, gmx_conect conect);
 147
 148 gmx_bool gmx_conect_exist(gmx_conect conect, int ai, int aj);
 149 /* Return TRUE if there is a conection between the atoms */
 150
 151 void gmx_conect_add(gmx_conect conect, int ai, int aj);
 152 /* Add a connection between ai and aj (numbered from 0 to natom-1) */
 153
 154 gmx_conect gmx_conect_generate(const t_topology *top);
 155 /* Generate a conect structure from a topology */
 156
 157 gmx_conect gmx_conect_init(void);
 158 /* Initiate data structure */
 159
 160 void gmx_conect_done(gmx_conect gc);
 161 /* Free memory */
 162
 163 #ifdef __cplusplus
 164 }
 165 #endif
 166
 167 #endif  /* GMX_FILEIO_PDBIO_H */