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48 typedef struct gmx_conect_t *gmx_conect;
50 /* THE pdb format (for ATOM/HETATOM lines) */
51 const char* get_pdbformat(void);
52 const char* get_pdbformat4(void);
54 /* Enumerated type for pdb records. The other entries are ignored
55 * when reading a pdb file
58 epdbATOM, epdbHETATM, epdbANISOU, epdbCRYST1, epdbCOMPND,
59 epdbMODEL, epdbENDMDL, epdbTER, epdbHEADER, epdbTITLE, epdbREMARK,
63 /* Enumerated value for indexing an uij entry (anisotropic temperature factors) */
65 U11, U22, U33, U12, U13, U23
68 void set_pdb_wide_format(gmx_bool bSet);
69 /* If bSet, use wider format for occupancy and bfactor */
71 void pdb_use_ter(gmx_bool bSet);
72 /* set read_pdbatoms to read upto 'TER' or 'ENDMDL' (default, bSet=FALSE).
73 This function is fundamentally broken as far as thread-safety is concerned.*/
75 void gmx_write_pdb_box(FILE *out, int ePBC, matrix box);
76 /* write the box in the CRYST1 record,
77 * with ePBC=-1 the pbc is guessed from the box
78 * This function is fundamentally broken as far as thread-safety is concerned.
81 void write_pdbfile_indexed(FILE *out, const char *title, t_atoms *atoms,
82 rvec x[], int ePBC, matrix box, char chain,
83 int model_nr, atom_id nindex, const atom_id index[],
84 gmx_conect conect, gmx_bool bTerSepChains);
85 /* REALLY low level */
87 void write_pdbfile(FILE *out, const char *title, t_atoms *atoms,
88 rvec x[], int ePBC, matrix box, char chain,
89 int model_nr, gmx_conect conect, gmx_bool bTerSepChains);
90 /* Low level pdb file writing routine.
92 * ONLY FOR SPECIAL PURPOSES,
94 * USE write_sto_conf WHEN YOU CAN.
96 * override chain-identifiers with chain when chain>0
97 * write ENDMDL when bEndmodel is TRUE.
99 * If the gmx_conect structure is not NULL its content is dumped as CONECT records
100 * which may be useful for visualization purposes.
103 void get_pdb_atomnumber(t_atoms *atoms, gmx_atomprop_t aps);
104 /* Routine to extract atomic numbers from the atom names */
106 int read_pdbfile(FILE *in, char *title, int *model_nr,
107 t_atoms *atoms, rvec x[], int *ePBC, matrix box,
108 gmx_bool bChange, gmx_conect conect);
109 /* Function returns number of atoms found.
110 * ePBC and gmx_conect structure may be NULL.
113 void read_pdb_conf(const char *infile, char *title,
114 t_atoms *atoms, rvec x[], int *ePBC, matrix box,
115 gmx_bool bChange, gmx_conect conect);
116 /* Read a pdb file and extract ATOM and HETATM fields.
117 * Read a box from the CRYST1 line, return 0 box when no CRYST1 is found.
118 * Change atom names according to protein conventions if wanted.
119 * ePBC and gmx_conect structure may be NULL.
122 void get_pdb_coordnum(FILE *in, int *natoms);
123 /* Read a pdb file and count the ATOM and HETATM fields. */
125 gmx_bool is_hydrogen(const char *nm);
126 /* Return whether atom nm is a hydrogen */
128 gmx_bool is_dummymass(const char *nm);
129 /* Return whether atom nm is a dummy mass */
131 /* Routines to handle CONECT records if they have been read in */
132 void gmx_conect_dump(FILE *fp, gmx_conect conect);
134 gmx_bool gmx_conect_exist(gmx_conect conect, int ai, int aj);
135 /* Return TRUE if there is a conection between the atoms */
137 void gmx_conect_add(gmx_conect conect, int ai, int aj);
138 /* Add a connection between ai and aj (numbered from 0 to natom-1) */
140 gmx_conect gmx_conect_generate(t_topology *top);
141 /* Generate a conect structure from a topology */
143 gmx_conect gmx_conect_init(void);
144 /* Initiate data structure */
146 void gmx_conect_done(gmx_conect gc);
153 #endif /* _pdbio_h */