4 * This source code is part of
8 * GROningen MAchine for Chemical Simulations
11 * Copyright (c) 1991-2001, University of Groningen, The Netherlands
12 * This program is free software; you can redistribute it and/or
13 * modify it under the terms of the GNU General Public License
14 * as published by the Free Software Foundation; either version 2
15 * of the License, or (at your option) any later version.
17 * If you want to redistribute modifications, please consider that
18 * scientific software is very special. Version control is crucial -
19 * bugs must be traceable. We will be happy to consider code for
20 * inclusion in the official distribution, but derived work must not
21 * be called official GROMACS. Details are found in the README & COPYING
22 * files - if they are missing, get the official version at www.gromacs.org.
24 * To help us fund GROMACS development, we humbly ask that you cite
25 * the papers on the package - you can find them in the top README file.
27 * For more info, check our website at http://www.gromacs.org
30 * Getting the Right Output Means no Artefacts in Calculating Stuff
36 static char *SRCID_pdbio_h
= "$Id$";
42 #ident "@(#) pdbio.h 1.12 7/28/97"
43 #endif /* HAVE_IDENT */
48 /* THE pdb format (for ATOM/HETATOM lines) */
49 static char *pdbformat
="%-6s%5u %-4.4s%3.3s %c%4d %8.3f%8.3f%8.3f";
50 static char *pdbformat4
="%-6s%5u %-4.4s %3.3s %c%4d %8.3f%8.3f%8.3f";
52 /* Enumerated type for pdb records. The other entries are ignored
53 * when reading a pdb file
55 enum { epdbATOM
, epdbHETATM
, epdbANISOU
, epdbCRYST1
, epdbCOMPND
,
56 epdbMODEL
, epdbENDMDL
, epdbTER
, epdbHEADER
, epdbTITLE
, epdbREMARK
,
59 /* Enumerated value for indexing an uij entry (anisotropic temperature factors) */
60 enum { U11
, U22
, U33
, U12
, U13
, U23
};
62 extern void set_pdb_wide_format(bool bSet
);
63 /* If bSet, use wider format for occupancy and bfactor */
65 extern void pdb_use_ter(bool bSet
);
66 /* set read_pdbatoms to read upto 'TER' or 'ENDMDL' (default, bSet=FALSE) */
68 extern void write_pdbfile_indexed(FILE *out
,char *title
,t_atoms
*atoms
,
69 rvec x
[],matrix box
,char chain
,
70 int model_nr
,atom_id nindex
,atom_id index
[]);
71 /* REALLY low level */
73 extern void write_pdbfile(FILE *out
,char *title
,t_atoms
*atoms
,
74 rvec x
[],matrix box
,char chain
,int model_nr
);
75 /* Low level pdb file writing routine.
77 * ONLY FOR SPECIAL PURPOSES,
79 * USE write_sto_conf WHEN YOU CAN.
81 * override chain-identifiers with chain when chain>0
82 * write ENDMDL when bEndmodel is TRUE */
84 extern int read_pdbfile(FILE *in
,char *title
,int *model_nr
,
85 t_atoms
*atoms
,rvec x
[],matrix box
,bool bChange
);
86 /* Function returns number of atoms found. */
88 extern void read_pdb_conf(char *infile
,char *title
,
89 t_atoms
*atoms
,rvec x
[],matrix box
,bool bChange
);
90 /* Read a pdb file and extract ATOM and HETATM fields.
91 * Read a box from the CRYST1 line, return 0 box when no CRYST1 is found.
92 * Change atom names according to protein conventions if wanted
95 extern void get_pdb_coordnum(FILE *in
,int *natoms
);
96 /* Read a pdb file and count the ATOM and HETATM fields. */
98 extern bool is_hydrogen(char *nm
);
99 /* Return whether atom nm is a hydrogen */
101 extern bool is_dummymass(char *nm
);
102 /* Return whether atom nm is a dummy mass */
104 #endif /* _pdbio_h */