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/*
Theseus - maximum likelihood superpositioning of macromolecular structures
Copyright (C) 2004-2014 Douglas L. Theobald
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the:
Free Software Foundation, Inc.,
59 Temple Place, Suite 330,
Boston, MA 02111-1307 USA
-/_|:|_|_\-
*/
#ifndef PDBCOORDS_SEEN
#define PDBCOORDS_SEEN
#include "msa.h"
#include "Cds.h"
typedef struct Seq2PDB Seq2PDB;
typedef struct PDBCds PDBCds;
typedef struct PDBCdsArray PDBCdsArray;
/* A structure for mapping sequence names in an alignment to their corresponding
pdbfiles */
struct Seq2PDB
{
int seqnum;
char **pdbfile_name;
char **seqname;
char *pdbfile_name_space;
char *seqname_space;
int *map;
MSA *msa;
int *singletons;
};
/* PDBCds is mostly for reading/writing PDB files */
struct PDBCds
{
char filename[FILENAME_MAX];
int model;
int vlen; /* number of coordinates */
double **matrix;
double *translation;
double scale;
/* PDB ATOM/HETATM fields */
char **record; /* ATOM or HETATM */
unsigned int *serial; /* atom number */
char *Hnum;
char **name; /* atom name, e.g. CA */
char *altLoc; /* alternate location identifier, usu A, B, or C */
char **resName; /* residue name, e.g. ALA, TYR, PHE, etc. */
char *xchainID;
char *chainID;
int *resSeq; /* residue number */
char *iCode;
double *x; /* x,y,z atomic coordinates */
double *y;
double *z;
double *occupancy;
double *tempFactor; /* B-factor */
char **segID;
char **element;
char **charge;
int *nu;
/* not to be accessed - for space only */
char *record_space;
char *name_space;
char *resName_space;
char *segID_space;
char *element_space;
char *charge_space;
};
struct PDBCdsArray
{
PDBCds **cds; /* pointer to an array of cnum pointers to Cds */
PDBCds *avecds; /* average Cds of all in CdsArray */
struct CdsArray *cdsA; /* associated CdsArray - do not free */
struct CdsArray *scratchA; /* do not free */
int vlen; /* number of coordinates */
int cnum; /* number of Cds in array */
int *upper, *lower;
int range_num;
Seq2PDB *seq2pdb;
};
#endif
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