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52 typedef struct gmx_conect_t
*gmx_conect
;
54 /* THE pdb format (for ATOM/HETATOM lines) */
55 static const char *pdbformat
="%-6s%5u %-4.4s%3.3s %c%4d%c %8.3f%8.3f%8.3f";
56 static const char *pdbformat4
="%-6s%5u %-4.4s %3.3s %c%4d%c %8.3f%8.3f%8.3f";
58 /* Enumerated type for pdb records. The other entries are ignored
59 * when reading a pdb file
61 enum { epdbATOM
, epdbHETATM
, epdbANISOU
, epdbCRYST1
, epdbCOMPND
,
62 epdbMODEL
, epdbENDMDL
, epdbTER
, epdbHEADER
, epdbTITLE
, epdbREMARK
,
65 /* Enumerated value for indexing an uij entry (anisotropic temperature factors) */
66 enum { U11
, U22
, U33
, U12
, U13
, U23
};
68 extern void set_pdb_wide_format(bool bSet
);
69 /* If bSet, use wider format for occupancy and bfactor */
71 extern void pdb_use_ter(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 extern 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 extern 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
,atom_id index
[],
85 /* REALLY low level */
87 extern 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
);
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 extern void get_pdb_atomnumber(t_atoms
*atoms
,gmx_atomprop_t aps
);
104 /* Routine to extract atomic numbers from the atom names */
106 extern int read_pdbfile(FILE *in
,char *title
,int *model_nr
,
107 t_atoms
*atoms
,rvec x
[],int *ePBC
,matrix box
,
108 bool bChange
,gmx_conect conect
);
109 /* Function returns number of atoms found.
110 * ePBC and gmx_conect structure may be NULL.
113 extern void read_pdb_conf(const char *infile
,char *title
,
114 t_atoms
*atoms
,rvec x
[],int *ePBC
,matrix box
,
115 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 extern void get_pdb_coordnum(FILE *in
,int *natoms
);
123 /* Read a pdb file and count the ATOM and HETATM fields. */
125 extern bool is_hydrogen(const char *nm
);
126 /* Return whether atom nm is a hydrogen */
128 extern 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 extern void gmx_conect_dump(FILE *fp
,gmx_conect conect
);
134 extern bool gmx_conect_exist(gmx_conect conect
,int ai
,int aj
);
135 /* Return TRUE if there is a conection between the atoms */
137 extern 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 extern gmx_conect
gmx_conect_generate(t_topology
*top
);
141 /* Generate a conect structure from a topology */
143 extern gmx_conect
gmx_conect_init();
144 /* Initiate data structure */
146 extern void gmx_conect_done(gmx_conect gc
);
153 #endif /* _pdbio_h */