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/* -------------------------------------------------------------------------- *
* MMB (MacroMoleculeBuilder) *
* -------------------------------------------------------------------------- *
* *
* Copyright (c) 2011-12 by the Author. *
* Author: Samuel Flores *
* *
* See RNABuilder.cpp for the copyright and usage agreement. *
* -------------------------------------------------------------------------- */
#ifndef AtomSpringContainer_H_
#define AtomSpringContainer_H_
#include "Utils.h"
#include "Threading.h"
#include <seqan/align.h>
//#include <Superpose.h>
class BiopolymerClassContainer;
typedef seqan::String<char> TSequence; // sequence type
typedef seqan::Align<TSequence,seqan::ArrayGaps> TAlign;
class MMB_EXPORT AtomSpringContainer {
private:
std::vector <AtomSpring> atomSpringVector;
std::vector <ThreadingStruct> threadingStructVector;
std::vector <ThreadingStruct> gappedThreadingStructVector;
public:
void clear();
AtomSpringContainer() {clear(); };
double calcRmsd (State & state, BiopolymerClassContainer & biopolymerClassContainer);
float calcKabschRmsd(State & state, BiopolymerClassContainer & biopolymerClassContainer);
//void printAtomSpring (const AtomSpring atomSpring);
void printAtomSpring (int atomSpringIndex);
void printAtomSprings ();
void validateAtomSpring(const AtomSpring & atomSpring );// , BiopolymerClassContainer & myBiopolymerContainer);
void validateAtomSpring(const AtomSpring & atomSpring, BiopolymerClassContainer & myBiopolymerContainer);
AtomSpring & initializeAtomSpring(AtomSpring & atomSpring);
void add(AtomSpring & atomSpring ){validateAtomSpring(atomSpring); atomSpringVector.push_back(atomSpring); };
void addAtomSpring(const AtomSpring & atomSpring, BiopolymerClassContainer & myBiopolymerContainer);
AtomSpring & updAtomSpring(int atomSpringIndex) {return atomSpringVector[atomSpringIndex]; };
const AtomSpring getAtomSpring(int atomSpringIndex) {return atomSpringVector[atomSpringIndex]; };
int numAtomSprings() {return atomSpringVector.size(); };
const std::vector <AtomSpring> getAtomSpringVector( ){return atomSpringVector; };
void deleteAtomSpring(const int atomSpringIndex);
void updateAtomSpring(const int atomSpringIndex, const AtomSpring & newSpring, BiopolymerClassContainer & myBiopolymerClassContainer);
void clearThreading();
std::vector<ThreadingStruct> & getThreadingVector() { return threadingStructVector; }
void validateThreading(const ThreadingStruct & threadingStruct, BiopolymerClassContainer & myBiopolymerClassContainer);
void addThreading(const ThreadingStruct & threadingStruct, BiopolymerClassContainer & myBiopolymerClassContainer);
void addThreading(String chain1, ResidueID resStart1, ResidueID resEnd1, String chain2, ResidueID resStart2, ResidueID resEnd2, double forceConstant, bool backboneOnly, BiopolymerClassContainer & myBiopolymerClassContainer);
void deleteThreading(int id);
void updateThreading(int id, const ThreadingStruct & threadingStruct, BiopolymerClassContainer & myBiopolymerClassContainer);
void updateThreading(int id, String chain1, ResidueID resStart1, ResidueID resEnd1, String chain2, ResidueID resStart2, ResidueID resEnd2, double forceConstant, bool backboneOnly, BiopolymerClassContainer & myBiopolymerClassContainer);
void createSpringsFromThreading(BiopolymerClassContainer & myBiopolymerClassContainer);
void clearGappedThreading();
std::vector<ThreadingStruct> & getGappedThreadingVector() { return gappedThreadingStructVector; }
void createSpringsFromGappedThreading(BiopolymerClassContainer & myBiopolymerClassContainer);
void addGappedThreading(const ThreadingStruct & threadingStruct, BiopolymerClassContainer & myBiopolymerClassContainer);
void addGappedThreading(String chain1, String chain2, double forceConstant, bool backboneOnly, BiopolymerClassContainer & myBiopolymerClassContainer,double gapPenalty, String scoringScheme);
void addGappedThreading(String chain1, ResidueID startResidue1, ResidueID endResidue1, String chain2, ResidueID startResidue2, ResidueID endResidue2, double forceConstant, bool backboneOnly,
BiopolymerClassContainer & myBiopolymerClassContainer,double gapPenalty, String scoringScheme);
void deleteGappedThreading(int id);
void updateGappedThreading(int id, const ThreadingStruct & threadingStruct, BiopolymerClassContainer & myBiopolymerClassContainer);
void updateGappedThreading(int id, String chain1, String chain2, double forceConstant, bool backboneOnly, BiopolymerClassContainer & myBiopolymerClassContainer,double gapPenalty, String scoringScheme);
static ThreadingStruct createGappedThreading(String chain1, String chain2, double forceConstant, bool backboneOnly, BiopolymerClassContainer & myBiopolymerClassContainer1, BiopolymerClassContainer & myBiopolymerClassContainer2,double gapPenalty, String scoringScheme );
static ThreadingStruct createGappedThreading(String chain1, String chain2, double forceConstant, bool backboneOnly, BiopolymerClassContainer & myBiopolymerClassContainer,double gapPenalty, String scoringScheme) {return createGappedThreading( chain1, chain2, forceConstant, backboneOnly, myBiopolymerClassContainer, myBiopolymerClassContainer, gapPenalty, scoringScheme);}; // For backward compatibility. Just calls its two-BiopolymerClassContainer counterpart with both BiopolymerClassContainer's set to the same object.
static ThreadingStruct createGappedThreading(String chain1, ResidueID startResidue1, ResidueID endResidue1, String chain2, ResidueID startResidue2, ResidueID endResidue2, double forceConstant, bool backboneOnly, BiopolymerClassContainer & myBiopolymerClassContainer1,BiopolymerClassContainer & myBiopolymerClassContainer2,double gapPenalty, String myScoringScheme ) ;
static ThreadingStruct createGappedThreading(String chain1, ResidueID startResidue1, ResidueID endResidue1, String chain2, ResidueID startResidue2, ResidueID endResidue2, double forceConstant, bool backboneOnly, BiopolymerClassContainer & myBiopolymerClassContainer,double gapPenalty, String scoringScheme) {return createGappedThreading(chain1, startResidue1, endResidue1, chain2, startResidue2, endResidue2, forceConstant, backboneOnly, myBiopolymerClassContainer , myBiopolymerClassContainer, gapPenalty, scoringScheme);}; // For backward compatibility. Just calls its two-BiopolymerClassContainer counterpart with both BiopolymerClassContainer's set to the same object.
void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
};
#endif
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