include/pdbio.h

   1 /*
   2  * $Id$
   3  *
   4  *                This source code is part of
   5  *
   6  *                 G   R   O   M   A   C   S
   7  *
   8  *          GROningen MAchine for Chemical Simulations
   9  *
  10  *                        VERSION 3.2.0
  11  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  12  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  13  * Copyright (c) 2001-2004, The GROMACS development team,
  14  * check out http://www.gromacs.org for more information.
  15
  16  * This program is free software; you can redistribute it and/or
  17  * modify it under the terms of the GNU General Public License
  18  * as published by the Free Software Foundation; either version 2
  19  * of the License, or (at your option) any later version.
  20  *
  21  * If you want to redistribute modifications, please consider that
  22  * scientific software is very special. Version control is crucial -
  23  * bugs must be traceable. We will be happy to consider code for
  24  * inclusion in the official distribution, but derived work must not
  25  * be called official GROMACS. Details are found in the README & COPYING
  26  * files - if they are missing, get the official version at www.gromacs.org.
  27  *
  28  * To help us fund GROMACS development, we humbly ask that you cite
  29  * the papers on the package - you can find them in the top README file.
  30  *
  31  * For more info, check our website at http://www.gromacs.org
  32  *
  33  * And Hey:
  34  * Gromacs Runs On Most of All Computer Systems
  35  */
  36
  37 #ifndef _pdbio_h
  38 #define _pdbio_h
  39
  40 #ifdef HAVE_CONFIG_H
  41 #include <config.h>
  42 #endif
  43
  44 #include "sysstuff.h"
  45 #include "typedefs.h"
  46 #include "symtab.h"
  47
  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";
  51
  52 /* Enumerated type for pdb records. The other entries are ignored
  53  * when reading a pdb file
  54  */
  55 enum { epdbATOM, epdbHETATM, epdbANISOU, epdbCRYST1, epdbCOMPND,
  56        epdbMODEL, epdbENDMDL, epdbTER, epdbHEADER, epdbTITLE, epdbREMARK,
  57        epdbNR };
  58
  59 /* Enumerated value for indexing an uij entry (anisotropic temperature factors) */
  60 enum { U11, U22, U33, U12, U13, U23 };
  61
  62 extern void set_pdb_wide_format(bool bSet);
  63 /* If bSet, use wider format for occupancy and bfactor */
  64
  65 extern void pdb_use_ter(bool bSet);
  66 /* set read_pdbatoms to read upto 'TER' or 'ENDMDL' (default, bSet=FALSE) */
  67
  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 */
  72
  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.
  76  *
  77  *          ONLY FOR SPECIAL PURPOSES,
  78  *
  79  *       USE write_sto_conf WHEN YOU CAN.
  80  *
  81  * override chain-identifiers with chain when chain>0
  82  * write ENDMDL when bEndmodel is TRUE */
  83
  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. */
  87
  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
  93  */
  94
  95 extern void get_pdb_coordnum(FILE *in,int *natoms);
  96 /* Read a pdb file and count the ATOM and HETATM fields. */
  97
  98 extern bool is_hydrogen(char *nm);
  99 /* Return whether atom nm is a hydrogen */
 100
 101 extern bool is_dummymass(char *nm);
 102 /* Return whether atom nm is a dummy mass */
 103
 104 #endif  /* _pdbio_h */