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