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// $Id: mmdb_seqsuperpose.h $
// =================================================================
//
// CCP4 Coordinate Library: support of coordinate-related
// functionality in protein crystallography applications.
//
// Copyright (C) Eugene Krissinel 2000-2013.
//
// This library is free software: you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License version 3, modified in accordance with the provisions
// of the license to address the requirements of UK law.
//
// You should have received a copy of the modified GNU Lesser
// General Public License along with this library. If not, copies
// may be downloaded from http://www.ccp4.ac.uk/ccp4license.php
//
// 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 Lesser General Public License for more details.
//
// =================================================================
//
// 19.09.13 <-- Date of Last Modification.
// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// -----------------------------------------------------------------
//
// **** Module : SeqSuperpose <interface>
// ~~~~~~~~~
// **** Classes : mmdb::SeqSuperpose
// ~~~~~~~~~
//
// (C) E.Krissinel 2005-2013
//
// =================================================================
//
#ifndef __Seq_Superpose__
#define __Seq_Superpose__
#include "mmdb_manager.h"
#include "mmdb_math_align.h"
namespace mmdb {
// =================================================================
enum SEQSP_RC {
SEQSP_Ok = 0,
SEQSP_IterLimit = 100,
SEQSP_SeqThreshold = 101
};
DefineClass(SeqSuperpose);
class SeqSuperpose {
public :
mat44 TMatrix; // superposes Ca1 over Ca2: |T*Ca1 - Ca2|->min
realtype Q; // Q-score
realtype rmsd; // rmsd
realtype seqId; // sequence identity in structure alignment
realtype _seqId; // sequence identity in sequence alignment
int Nalign; // alignment length in structure alignment
ivector c1; // sup-n vector: Ca1[i]->Ca2[c1[i]] if c1[i]>=0
ivector c2; // sup-n vector: Ca2[i]->Ca1[c2[i]] if c2[i]>=0
SeqSuperpose();
~SeqSuperpose();
// Given two sets of atoms, Calpha1 and Calpha2, Superpose(...)
// calculates the rotational-translational matrix TMatrix such
// that |TMatrix*Calpha1 - Calpha2| is minimal in least-square
// terms.
// In difference of a full-scale SSM, this simplified version
// uses initial superposition from sequence alignment, hence
// it should be applied only to similar chains where calculation
// time is crucial. seqThreshold specifies a threshold of
// sequence identity (0<=seqThreshold<=1), below which
// structural alignment is not performed and Superpose(..)
// returns SEQSP_SeqThreshold.
//
// If keepBricks is set True, then space bricks are not
// removed in MMDB and may be used in the next call if
// vector Calpha2 does not change. This saves computation
// time.
//
// The alignment results return in public fields above:
// TMatrix - transformation matrix (1 if not aligned)
// Q - quality Q-score (-1 if not aligned)
// rmsd - r.m.s.d (MaxReal if not aligned)
// seqId - sequence identity in structure alignment
// (0 if not aligned)
// Nalign - alignment length in structure alignment
// (0 if not aligned)
// c1,c2 - atom corrspondences:
// Calpha1[i] <=> Calpha2[c1[i]]
// Calpha2[i] <=> Calpha1[c2[i]]
//
// Upon success, Superpose(...) returns SEQSP_Ok
//
int Superpose ( PManager MMDB,
PPAtom Calpha1, int nCalpha1,
PPAtom Calpha2, int nCalpha2,
realtype seqThreshold,
bool keepBricks );
protected :
math::PAlignment Align;
PManager M; // pointers to
PPAtom Ca1,Ca2; // the input data
int nCa1,nCa2; // copy chain lengths
ivector cn1,cn2; // temporary contact arrays
realtype Rmsd0; // quality optimization parameter
realtype maxContact; // maximal Calpha-pair contact parameter
PContact contact;
int ncontacts;
void SeqSuperposeInit();
void FreeMemory ();
realtype MatchQuality ( int Nalign, realtype Rmsd,
int nres1, int nres2 );
realtype MatchQuality2 ( int Nalign, realtype dist2,
int nres1, int nres2 );
void MakeContacts ( mat44 & TM, realtype cont_est );
int makeStructAlignment ( realtype seqThreshold,
bool keepBricks );
};
} // namespace mmdb
#endif
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