struct t_symtab;
struct t_topology;
-typedef struct gmx_conect_t *gmx_conect;
+typedef struct gmx_conect_t* gmx_conect;
/* Write a PDB line with an ATOM or HETATM record directly to a file pointer.
*
* Returns the number of characters printed.
*/
-int
-gmx_fprintf_pdb_atomline(FILE * fp,
- enum PDB_record record,
- int atom_seq_number,
- const char * atom_name,
- char alternate_location,
- const char * res_name,
- char chain_id,
- int res_seq_number,
- char res_insertion_code,
- real x,
- real y,
- real z,
- real occupancy,
- real b_factor,
- const char * element);
+int gmx_fprintf_pdb_atomline(FILE* fp,
+ enum PDB_record record,
+ int atom_seq_number,
+ const char* atom_name,
+ char alternate_location,
+ const char* res_name,
+ char chain_id,
+ int res_seq_number,
+ char res_insertion_code,
+ real x,
+ real y,
+ real z,
+ real occupancy,
+ real b_factor,
+ const char* element);
/* Enumerated value for indexing an uij entry (anisotropic temperature factors) */
-enum {
- U11, U22, U33, U12, U13, U23
+enum
+{
+ U11,
+ U22,
+ U33,
+ U12,
+ U13,
+ U23
};
void pdb_use_ter(gmx_bool bSet);
/* set read_pdbatoms to read upto 'TER' or 'ENDMDL' (default, bSet=FALSE).
This function is fundamentally broken as far as thread-safety is concerned.*/
-void gmx_write_pdb_box(FILE *out, int ePBC, const matrix box);
+void gmx_write_pdb_box(FILE* out, int ePBC, const matrix box);
/* write the box in the CRYST1 record,
* with ePBC=-1 the pbc is guessed from the box
* This function is fundamentally broken as far as thread-safety is concerned.
*/
-void write_pdbfile_indexed(FILE *out, const char *title, const t_atoms *atoms,
- const rvec x[], int ePBC, const matrix box, char chain,
- int model_nr, int nindex, const int index[],
- gmx_conect conect,
- bool usePqrFormat);
+void write_pdbfile_indexed(FILE* out,
+ const char* title,
+ const t_atoms* atoms,
+ const rvec x[],
+ int ePBC,
+ const matrix box,
+ char chain,
+ int model_nr,
+ int nindex,
+ const int index[],
+ gmx_conect conect,
+ bool usePqrFormat);
/* REALLY low level */
-void write_pdbfile(FILE *out, const char *title, const t_atoms *atoms,
- const rvec x[], int ePBC, const matrix box, char chain,
- int model_nr, gmx_conect conect);
+void write_pdbfile(FILE* out,
+ const char* title,
+ const t_atoms* atoms,
+ const rvec x[],
+ int ePBC,
+ const matrix box,
+ char chain,
+ int model_nr,
+ gmx_conect conect);
/* Low level pdb file writing routine.
*
* ONLY FOR SPECIAL PURPOSES,
* which may be useful for visualization purposes.
*/
-void get_pdb_atomnumber(const t_atoms *atoms, AtomProperties *aps);
+void get_pdb_atomnumber(const t_atoms* atoms, AtomProperties* aps);
/* Routine to extract atomic numbers from the atom names */
-int read_pdbfile(FILE *in, char *title, int *model_nr,
- struct t_atoms *atoms, struct t_symtab *symtab,
- rvec x[], int *ePBC, matrix box,
- gmx_bool bChange, gmx_conect conect);
+int read_pdbfile(FILE* in,
+ char* title,
+ int* model_nr,
+ struct t_atoms* atoms,
+ struct t_symtab* symtab,
+ rvec x[],
+ int* ePBC,
+ matrix box,
+ gmx_bool bChange,
+ gmx_conect conect);
/* Function returns number of atoms found.
* ePBC and gmx_conect structure may be NULL.
*/
-void gmx_pdb_read_conf(const char *infile,
- t_symtab *symtab, char **name, t_atoms *atoms,
- rvec x[], int *ePBC, matrix box);
+void gmx_pdb_read_conf(const char* infile, t_symtab* symtab, char** name, t_atoms* atoms, rvec x[], int* ePBC, matrix box);
/* Read a pdb file and extract ATOM and HETATM fields.
* Read a box from the CRYST1 line, return 0 box when no CRYST1 is found.
* ePBC may be NULL.
*
* If name is not nullptr, gmx_strdup the title string into it. */
-void get_pdb_coordnum(FILE *in, int *natoms);
+void get_pdb_coordnum(FILE* in, int* natoms);
/* Read a pdb file and count the ATOM and HETATM fields. */
-gmx_bool is_hydrogen(const char *nm);
+gmx_bool is_hydrogen(const char* nm);
/* Return whether atom nm is a hydrogen */
-gmx_bool is_dummymass(const char *nm);
+gmx_bool is_dummymass(const char* nm);
/* Return whether atom nm is a dummy mass */
/* Routines to handle CONECT records if they have been read in */
-void gmx_conect_dump(FILE *fp, gmx_conect conect);
+void gmx_conect_dump(FILE* fp, gmx_conect conect);
gmx_bool gmx_conect_exist(gmx_conect conect, int ai, int aj);
/* Return TRUE if there is a conection between the atoms */
void gmx_conect_add(gmx_conect conect, int ai, int aj);
/* Add a connection between ai and aj (numbered from 0 to natom-1) */
-gmx_conect gmx_conect_generate(const t_topology *top);
+gmx_conect gmx_conect_generate(const t_topology* top);
/* Generate a conect structure from a topology */
gmx_conect gmx_conect_init();
void gmx_conect_done(gmx_conect gc);
/* Free memory */
-#endif /* GMX_FILEIO_PDBIO_H */
+#endif /* GMX_FILEIO_PDBIO_H */
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff