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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 NWFILL_SEEN
#define NWFILL_SEEN
#include "StructAlign.h"
#include "pdbMalloc.h"
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
NWfill(NWtable *nw_table, Cds *cds1, Cds *cds2, double *var);
void
ProcrustesFill(NWtable *nw_table, Cds *cds1, Cds *cds2);
void
SuperDistFill(NWtable *nw_table, Cds *cds1, Cds *cds2, double *var);
void
SimpleChargeFill(NWtable *nw_table, Cds *cds1, Cds *cds2);
void
ContactOrderFill(NWtable *nw_table, Cds *cds1, Cds *cds2);
void
BlosumFill(NWtable *nw_table, Cds *cds1, Cds *cds2);
void
DsspFill(NWtable *nw_table);
void
AnglesFill(NWtable *nw_table, const PDBCds *pdbc1, const PDBCds *pdbc2);
double
Dihedral(const double *atm1, const double *atm2,
const double *atm3, const double *atm4);
void
LogOddsScoresCO(double **mat, int nx, int ny, int convert);
void
MLScores(NWtable *nw_table);
void
MLScoresCO(double **mat, int nx, int ny);
void
LogOddsScores(NWtable *nw_table);
void
BayesScoresCO(double **mat, int nx, int ny);
void
BayesScores(NWtable *nw_table);
#endif
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