libgromacs-dev 2018.1-1 / usr / include / gromacs / fileio / pdbio.h

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#ifndef GMX_FILEIO_PDBIO_H
#define GMX_FILEIO_PDBIO_H

#include <stdio.h>

#include "gromacs/math/vectypes.h"
#include "gromacs/topology/atoms.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"

#ifdef __cplusplus
extern "C" {
#endif

struct gmx_atomprop;
struct t_atoms;
struct t_symtab;
struct t_topology;

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);

/* Enumerated value for indexing an uij entry (anisotropic temperature factors) */
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);
/* 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, gmx_bool bTerSepChains);
/* 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, gmx_bool bTerSepChains);
/* Low level pdb file writing routine.
 *
 *          ONLY FOR SPECIAL PURPOSES,
 *
 *       USE write_sto_conf WHEN YOU CAN.
 *
 * override chain-identifiers with chain when chain>0
 * write ENDMDL when bEndmodel is TRUE.
 *
 * If the gmx_conect structure is not NULL its content is dumped as CONECT records
 * which may be useful for visualization purposes.
 */

void get_pdb_atomnumber(const t_atoms *atoms, struct gmx_atomprop *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);
/* 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);
/* 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);
/* Read a pdb file and count the ATOM and HETATM fields. */

gmx_bool is_hydrogen(const char *nm);
/* Return whether atom nm is a hydrogen */

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);

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);
/* Generate a conect structure from a topology */

gmx_conect gmx_conect_init(void);
/* Initiate data structure */

void gmx_conect_done(gmx_conect gc);
/* Free memory */

#ifdef __cplusplus
}
#endif

#endif  /* GMX_FILEIO_PDBIO_H */