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/*
Theseus - maximum likelihood superpositioning of macromolecular structures
Copyright (C) 2004-2015 Douglas L. Theobald
This file is part of THESEUS.
THESEUS 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 3 of
the License, or (at your option) any later version.
THESEUS 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 THESEUS in the file 'COPYING'. If not, see
<http://www.gnu.org/licenses/>.
-/_|:|_|_\-
*/
#ifndef STRUCTALIGN_SEEN
#define STRUCTALIGN_SEEN
#include <float.h>
#include <pthread.h>
#include "dssplite.h"
#include "pdbMalloc.h"
#include "DLTutils.h"
#include "msa.h"
typedef struct NWalgo_
{
int fraglen;
int distance;
int blosum;
int gap;
int gapzeron;
int logodds;
int bayes;
int bayespost;
int passes;
int global;
int center_ca;
int KA;
int dsspflag;
int raw_charge;
int corder;
int procrustes;
int convert;
int angles; /* flag to fill by aa psi/phi angle differences */
double open; /* gap open penalty */
double extend; /* gap extension penalty, in terms of the fraction of the open penalty */
/* e.g., default for BLAST blosum62 would be 1/11 = 0.0909 */
double pi_g, pi_m;
double align_dist;
} NWalgo;
typedef struct NWtable_
{
char outfile_name[FILENAME_MAX];
char file1_name[FILENAME_MAX], file2_name[FILENAME_MAX];
char *msa_filename;
int cindex;
double **vmat; /* variance of pair, RMSD^2 */
double **smat; /* dynamic running match score */
double **fmat; /* pairwise scores */
double **gmat; /* 1.0 if gap closed, 0.0 if opened */
char **pmat; /* 'l', 'u', or 'd' -- left, up, or diagonal */
Cds *cds0, *cds1;
PDBCds *pdbc0, *pdbc1;
int nx, ny; /* dimensions of mat */
int **alignment; /* the full traceback alignment */
int **align_nogap;
double *align_score;
int alignlen; /* length of the alignment, including gaps */
double stddev_var; /* the std dev of the average variance */
double cutoff; /* # stddevs allowed for alt alignment scores */
double nw_score;
double gappen;
double Kplus, Evalue, RelEnt;
int mini, minj; /* for Smith-Waterman local alignment traceback start */
int maxi, maxj;
char *ss0, *ss1;
NWalgo *algo;
MSA *msa;
} NWtable;
typedef struct
{
int ii;
int iPartner;
PDBCdsArray *pdbA;
int iCommon;
CdsArray *cdsA, *nwcdsA;
NWtable **nwTableA;
int thrdnum;
} SAData;
extern char aa1[];
extern char aa3[];
extern char ss1[];
extern double s_dssp8[8][8];
extern double s_simple[20][20];
extern double s_simpler[20][20];
extern double s_hsdm[20][20];
extern double s_blosum30[20][20];
extern double s_blosum35[20][20];
extern double s_blosum40[20][20];
extern double s_blosum50[20][20];
extern double s_blosum62[20][20];
extern double s_blosum100[20][20];
void
GetNWCds(CdsArray *nwcdsA, CdsArray *cdsA);
CdsArray
*GetNWCdsSel(const PDBCdsArray *pdbA);
void
StructAlign(PDBCdsArray *pdbA, int iCommon, CdsArray *cdsA, NWtable **nwTableA);
void
StructAlignPth(PDBCdsArray *pdbA, int iCommon, CdsArray *cdsA, NWtable **nwTableA, SAData **sa_data, const int thrdnum);
void
NWscore(NWtable *nw_table);
void
NWscoreTh(NWtable *nw_table);
void
NWtraceback(NWtable *nw_table);
void
NWtracebackTh(NWtable *nw_table);
void
PrintVars(NWtable *nw_table);
void
PrintScores(NWtable *nw_table);
void
PrintSumScores(NWtable *nw_table);
void
PrintTraceback(NWtable *nw_table);
NWtable
*NWinit(void);
void
NWalloc(NWtable *nw_table, int nx, int ny);
void
NWdestroy(NWtable **nw_table_ptr);
NWalgo
*NWalgoInit(void);
char
aa3toaa1(char *aa3_s);
char
*aa1toaa3(char aa1_c);
#endif
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