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 2.0
  11  *
  12  * Copyright (c) 1991-1999
  13  * BIOSON Research Institute, Dept. of Biophysical Chemistry
  14  * University of Groningen, The Netherlands
  15  *
  16  * Please refer to:
  17  * GROMACS: A message-passing parallel molecular dynamics implementation
  18  * H.J.C. Berendsen, D. van der Spoel and R. van Drunen
  19  * Comp. Phys. Comm. 91, 43-56 (1995)
  20  *
  21  * Also check out our WWW page:
  22  * http://md.chem.rug.nl/~gmx
  23  * or e-mail to:
  24  * gromacs@chem.rug.nl
  25  *
  26  * And Hey:
  27  * Good ROcking Metal Altar for Chronical Sinners
  28  */
  29
  30 #ifndef _pdbio_h
  31 #define _pdbio_h
  32
  33 static char *SRCID_pdbio_h = "$Id$";
  34
  35 #ifdef HAVE_IDENT
  36 #ident  "@(#) pdbio.h 1.12 7/28/97"
  37 #endif /* HAVE_IDENT */
  38 #include "sysstuff.h"
  39 #include "typedefs.h"
  40 #include "symtab.h"
  41
  42 /* Enumerated type for pdb records. The other entries are ignored
  43  * when reading a pdb file
  44  */
  45 enum { epdbATOM, epdbHETATM, epdbANISOU, epdbCRYST1, epdbCOMPND,
  46        epdbENDMDL, epdbTER, epdbHEADER, epdbTITLE, epdbREMARK, epdbNR };
  47
  48 /* Enumerated value for indexing an uij entry (anisotropic temperature factors) */
  49 enum { U11, U22, U33, U12, U13, U23 };
  50
  51 extern void pdb_use_ter(bool bSet);
  52 /* set read_pdbatoms to read upto 'TER' of 'ENDMDL' (default, bSet=FALSE) */
  53
  54 extern void write_pdbfile_indexed(FILE *out,char *title,
  55                                   t_atoms *atoms,rvec x[],matrix box,
  56                                   char chain, bool bEndmodel,
  57                                   atom_id nindex, atom_id index[]);
  58 /* REALLY low level */
  59
  60 extern void write_pdbfile(FILE *out,char *title,
  61                           t_atoms *atoms,rvec x[],matrix box,char chain,
  62                           bool bEndmodel);
  63 /* Low level pdb file writing routine.
  64  *
  65  *          ONLY FOR SPECIAL PURPOSES,
  66  *
  67  *       USE write_sto_conf WHEN YOU CAN.
  68  *
  69  * override chain-identifiers with chain when chain>0
  70  * write ENDMDL when bEndmodel is TRUE */
  71
  72 void hwrite_pdb_conf_indexed(FILE *out,char *title,
  73                              t_atoms *atoms,rvec x[],matrix box,
  74                              atom_id nindex,atom_id index[]);
  75 /* Write a pdb file to FILE *out
  76  * Use an index to only write out selected atoms. */
  77
  78 extern void write_pdb_confs(char *outfile,
  79                             t_atoms **atoms,rvec *x[],int number);
  80 /* Write multiple chains to one pdb file */
  81
  82 extern int read_pdbfile(FILE *in,char *title,
  83                         t_atoms *atoms,rvec x[],matrix box,bool bChange);
  84 /* Function returns number of atoms found. */
  85
  86 extern void read_pdb_conf(char *infile,char *title,
  87                           t_atoms *atoms,rvec x[],matrix box,bool bChange);
  88 /* Read a pdb file and extract ATOM and HETATM fields.
  89  * Read a box from the CRYST1 line, return 0 box when no CRYST1 is found.
  90  * Change atom names according to protein conventions if wanted
  91  */
  92
  93 extern void get_pdb_coordnum(FILE *in,int *natoms);
  94 /* Read a pdb file and count the ATOM and HETATM fields. */
  95
  96 extern bool is_hydrogen(char *nm);
  97 /* Return whether atom nm is a hydrogen */
  98
  99 extern bool is_dummymass(char *nm);
 100 /* Return whether atom nm is a dummy mass.
 101  * The first character should be an 'M' the last character should be a digit.
 102  */
 103
 104 #endif  /* _pdbio_h */