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/*
A* -------------------------------------------------------------------
B* This file contains source code for the PyMOL computer program
C* Copyright (c) Schrodinger, LLC.
D* -------------------------------------------------------------------
E* It is unlawful to modify or remove this copyright notice.
F* -------------------------------------------------------------------
G* Please see the accompanying LICENSE file for further information.
H* -------------------------------------------------------------------
I* Additional authors of this source file include:
-*
-*
-*
Z* -------------------------------------------------------------------
*/
#ifndef _H_Match
#define _H_Match
#include "PyMOLGlobals.h"
typedef struct {
PyMOLGlobals *G;
float **smat;
float **mat;
float **da, **db;
int na, nb;
int *pair;
float score; /* result */
int n_pair;
} CMatch;
CMatch *MatchNew(PyMOLGlobals * G, unsigned int na, unsigned int nb, int dist_mats);
int MatchResidueToCode(CMatch * I, int *vla, int n);
int MatchMatrixFromFile(CMatch * I, const char *fname, int quiet);
int MatchPreScore(CMatch * I, int *vla1, int n1, int *vla2, int n2, int quiet);
void MatchFree(CMatch * I);
int MatchAlign(CMatch * I, float gap_penalty, float ext_penalty,
int max_gap, int max_skip, int quiet, int window, float ante);
#endif
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