2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team.
6 * Copyright (c) 2013,2014, by the GROMACS development team, led by
7 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
8 * and including many others, as listed in the AUTHORS file in the
9 * top-level source directory and at http://www.gromacs.org.
11 * GROMACS is free software; you can redistribute it and/or
12 * modify it under the terms of the GNU Lesser General Public License
13 * as published by the Free Software Foundation; either version 2.1
14 * of the License, or (at your option) any later version.
16 * GROMACS is distributed in the hope that it will be useful,
17 * but WITHOUT ANY WARRANTY; without even the implied warranty of
18 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19 * Lesser General Public License for more details.
21 * You should have received a copy of the GNU Lesser General Public
22 * License along with GROMACS; if not, see
23 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
24 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
26 * If you want to redistribute modifications to GROMACS, please
27 * consider that scientific software is very special. Version
28 * control is crucial - bugs must be traceable. We will be happy to
29 * consider code for inclusion in the official distribution, but
30 * derived work must not be called official GROMACS. Details are found
31 * in the README & COPYING files - if they are missing, get the
32 * official version at http://www.gromacs.org.
34 * To help us fund GROMACS development, we humbly ask that you cite
35 * the research papers on the package. Check out http://www.gromacs.org.
38 #ifndef GMX_FILEIO_PDBIO_H
39 #define GMX_FILEIO_PDBIO_H
43 #include "../legacyheaders/atomprop.h"
44 #include "../legacyheaders/types/topology.h"
52 typedef struct gmx_conect_t *gmx_conect;
54 /* THE pdb format (for ATOM/HETATOM lines) */
55 const char* get_pdbformat(void);
56 const char* get_pdbformat4(void);
58 /* Enumerated type for pdb records. The other entries are ignored
59 * when reading a pdb file
62 epdbATOM, epdbHETATM, epdbANISOU, epdbCRYST1, epdbCOMPND,
63 epdbMODEL, epdbENDMDL, epdbTER, epdbHEADER, epdbTITLE, epdbREMARK,
67 /* Enumerated value for indexing an uij entry (anisotropic temperature factors) */
69 U11, U22, U33, U12, U13, U23
72 void set_pdb_wide_format(gmx_bool bSet);
73 /* If bSet, use wider format for occupancy and bfactor */
75 void pdb_use_ter(gmx_bool bSet);
76 /* set read_pdbatoms to read upto 'TER' or 'ENDMDL' (default, bSet=FALSE).
77 This function is fundamentally broken as far as thread-safety is concerned.*/
79 void gmx_write_pdb_box(FILE *out, int ePBC, matrix box);
80 /* write the box in the CRYST1 record,
81 * with ePBC=-1 the pbc is guessed from the box
82 * This function is fundamentally broken as far as thread-safety is concerned.
85 void write_pdbfile_indexed(FILE *out, const char *title, t_atoms *atoms,
86 rvec x[], int ePBC, matrix box, char chain,
87 int model_nr, atom_id nindex, const atom_id index[],
88 gmx_conect conect, gmx_bool bTerSepChains);
89 /* REALLY low level */
91 void write_pdbfile(FILE *out, const char *title, struct t_atoms *atoms,
92 rvec x[], int ePBC, matrix box, char chain,
93 int model_nr, gmx_conect conect, gmx_bool bTerSepChains);
94 /* Low level pdb file writing routine.
96 * ONLY FOR SPECIAL PURPOSES,
98 * USE write_sto_conf WHEN YOU CAN.
100 * override chain-identifiers with chain when chain>0
101 * write ENDMDL when bEndmodel is TRUE.
103 * If the gmx_conect structure is not NULL its content is dumped as CONECT records
104 * which may be useful for visualization purposes.
107 void get_pdb_atomnumber(struct t_atoms *atoms, gmx_atomprop_t aps);
108 /* Routine to extract atomic numbers from the atom names */
110 int read_pdbfile(FILE *in, char *title, int *model_nr,
111 struct t_atoms *atoms, rvec x[], int *ePBC, matrix box,
112 gmx_bool bChange, gmx_conect conect);
113 /* Function returns number of atoms found.
114 * ePBC and gmx_conect structure may be NULL.
117 void read_pdb_conf(const char *infile, char *title,
118 struct t_atoms *atoms, rvec x[], int *ePBC, matrix box,
119 gmx_bool bChange, gmx_conect conect);
120 /* Read a pdb file and extract ATOM and HETATM fields.
121 * Read a box from the CRYST1 line, return 0 box when no CRYST1 is found.
122 * Change atom names according to protein conventions if wanted.
123 * ePBC and gmx_conect structure may be NULL.
126 void get_pdb_coordnum(FILE *in, int *natoms);
127 /* Read a pdb file and count the ATOM and HETATM fields. */
129 gmx_bool is_hydrogen(const char *nm);
130 /* Return whether atom nm is a hydrogen */
132 gmx_bool is_dummymass(const char *nm);
133 /* Return whether atom nm is a dummy mass */
135 /* Routines to handle CONECT records if they have been read in */
136 void gmx_conect_dump(FILE *fp, gmx_conect conect);
138 gmx_bool gmx_conect_exist(gmx_conect conect, int ai, int aj);
139 /* Return TRUE if there is a conection between the atoms */
141 void gmx_conect_add(gmx_conect conect, int ai, int aj);
142 /* Add a connection between ai and aj (numbered from 0 to natom-1) */
144 gmx_conect gmx_conect_generate(t_topology *top);
145 /* Generate a conect structure from a topology */
147 gmx_conect gmx_conect_init(void);
148 /* Initiate data structure */
150 void gmx_conect_done(gmx_conect gc);
157 #endif /* GMX_FILEIO_PDBIO_H */