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38 #ifndef GMX_FILEIO_PDBIO_H
39 #define GMX_FILEIO_PDBIO_H
43 #include "../legacyheaders/types/simple.h"
53 typedef struct gmx_conect_t *gmx_conect;
55 /* THE pdb format (for ATOM/HETATOM lines) */
56 const char* get_pdbformat(void);
57 const char* get_pdbformat4(void);
59 /* Enumerated type for pdb records. The other entries are ignored
60 * when reading a pdb file
63 epdbATOM, epdbHETATM, epdbANISOU, epdbCRYST1, epdbCOMPND,
64 epdbMODEL, epdbENDMDL, epdbTER, epdbHEADER, epdbTITLE, epdbREMARK,
68 /* Enumerated value for indexing an uij entry (anisotropic temperature factors) */
70 U11, U22, U33, U12, U13, U23
73 void set_pdb_wide_format(gmx_bool bSet);
74 /* If bSet, use wider format for occupancy and bfactor */
76 void pdb_use_ter(gmx_bool bSet);
77 /* set read_pdbatoms to read upto 'TER' or 'ENDMDL' (default, bSet=FALSE).
78 This function is fundamentally broken as far as thread-safety is concerned.*/
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.
86 void write_pdbfile_indexed(FILE *out, const char *title, struct t_atoms *atoms,
87 rvec x[], int ePBC, matrix box, char chain,
88 int model_nr, atom_id nindex, const atom_id index[],
89 gmx_conect conect, gmx_bool bTerSepChains);
90 /* REALLY low level */
92 void write_pdbfile(FILE *out, const char *title, struct t_atoms *atoms,
93 rvec x[], int ePBC, matrix box, char chain,
94 int model_nr, gmx_conect conect, gmx_bool bTerSepChains);
95 /* Low level pdb file writing routine.
97 * ONLY FOR SPECIAL PURPOSES,
99 * USE write_sto_conf WHEN YOU CAN.
101 * override chain-identifiers with chain when chain>0
102 * write ENDMDL when bEndmodel is TRUE.
104 * If the gmx_conect structure is not NULL its content is dumped as CONECT records
105 * which may be useful for visualization purposes.
108 void get_pdb_atomnumber(struct t_atoms *atoms, struct gmx_atomprop *aps);
109 /* Routine to extract atomic numbers from the atom names */
111 int read_pdbfile(FILE *in, char *title, int *model_nr,
112 struct t_atoms *atoms, rvec x[], int *ePBC, matrix box,
113 gmx_bool bChange, gmx_conect conect);
114 /* Function returns number of atoms found.
115 * ePBC and gmx_conect structure may be NULL.
118 void read_pdb_conf(const char *infile, char *title,
119 struct t_atoms *atoms, rvec x[], int *ePBC, matrix box,
120 gmx_bool bChange, gmx_conect conect);
121 /* Read a pdb file and extract ATOM and HETATM fields.
122 * Read a box from the CRYST1 line, return 0 box when no CRYST1 is found.
123 * Change atom names according to protein conventions if wanted.
124 * ePBC and gmx_conect structure may be NULL.
127 void get_pdb_coordnum(FILE *in, int *natoms);
128 /* Read a pdb file and count the ATOM and HETATM fields. */
130 gmx_bool is_hydrogen(const char *nm);
131 /* Return whether atom nm is a hydrogen */
133 gmx_bool is_dummymass(const char *nm);
134 /* Return whether atom nm is a dummy mass */
136 /* Routines to handle CONECT records if they have been read in */
137 void gmx_conect_dump(FILE *fp, gmx_conect conect);
139 gmx_bool gmx_conect_exist(gmx_conect conect, int ai, int aj);
140 /* Return TRUE if there is a conection between the atoms */
142 void gmx_conect_add(gmx_conect conect, int ai, int aj);
143 /* Add a connection between ai and aj (numbered from 0 to natom-1) */
145 gmx_conect gmx_conect_generate(struct t_topology *top);
146 /* Generate a conect structure from a topology */
148 gmx_conect gmx_conect_init(void);
149 /* Initiate data structure */
151 void gmx_conect_done(gmx_conect gc);
158 #endif /* GMX_FILEIO_PDBIO_H */