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