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Copy pathsketcherMinimizerFragment.h
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sketcherMinimizerFragment.h
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/*
*
*
* Created by Nicola Zonta on 03/05/2010.
* Copyright Schrodinger, LLC. All rights reserved.
*
*/
#ifndef sketcherMINIMIZERFRAGMENT
#define sketcherMINIMIZERFRAGMENT
#include "sketcherMinimizerMaths.h"
#include <cassert>
#include <iostream>
#include <map>
#include <vector>
#include "CoordgenConfig.hpp"
class sketcherMinimizerAtom;
class sketcherMinimizerBond;
class sketcherMinimizerRing;
class sketcherMinimizerFragment;
/*
abstract class for fragment degree of freedom
*/
class CoordgenFragmentDOF
{
public:
CoordgenFragmentDOF(sketcherMinimizerFragment* fragment);
virtual ~CoordgenFragmentDOF();
/* set the current value as the optimal value for this DOF */
void storeCurrentValueAsOptimal();
/* load the optimal value */
void setToOptimalValue();
/* cycle through the various possible values of this DOF */
void changeState();
/* add the given atom to the DoF */
void addAtom(sketcherMinimizerAtom* atom);
/* get the penalty associated with the current state */
virtual float getCurrentPenalty() const;
/* return the number of states */
virtual int numberOfStates() const = 0;
/* return the tier of this DoF. Lower tier DoFs are considered first in the
* minimization */
virtual int tier() const = 0;
/* apply the current DoF value to the atoms coordinates */
virtual void apply() const = 0;
/* return the fragment this DoF refers to */
sketcherMinimizerFragment* getFragment() const;
/* return the current state */
short unsigned int getCurrentState();
/* set the given state as current */
void setState(short unsigned int state);
short unsigned int m_currentState, m_optimalState;
protected:
std::vector<sketcherMinimizerAtom*> m_atoms;
sketcherMinimizerFragment* m_fragment;
};
/*
change the angle of the fragment wrt its parent
*/
class CoordgenRotateFragmentDOF : public CoordgenFragmentDOF
{
public:
CoordgenRotateFragmentDOF(sketcherMinimizerFragment* fragment);
int numberOfStates() const override;
int tier() const override;
void apply() const override;
float getCurrentPenalty() const override;
};
/*
flip the fragment along the bond to its parent
*/
class CoordgenFlipFragmentDOF : public CoordgenFragmentDOF
{
public:
CoordgenFlipFragmentDOF(sketcherMinimizerFragment* fragment);
int numberOfStates() const override;
int tier() const override;
void apply() const override;
float getCurrentPenalty() const override;
};
/*
scale the coordinates of the given atoms
*/
class CoordgenScaleAtomsDOF : public CoordgenFragmentDOF
{
public:
CoordgenScaleAtomsDOF(sketcherMinimizerAtom* pivotAtom);
int numberOfStates() const override;
int tier() const override;
void apply() const override;
float getCurrentPenalty() const override;
private:
sketcherMinimizerAtom* m_pivotAtom;
};
/*
scale the coordinates of the whole fragment
*/
class CoordgenScaleFragmentDOF : public CoordgenFragmentDOF
{
public:
CoordgenScaleFragmentDOF(sketcherMinimizerFragment* fragment);
int numberOfStates() const override;
int tier() const override;
void apply() const override;
float getCurrentPenalty() const override;
};
/*
extend or shorten the bond to the parent fragment
*/
class CoordgenChangeParentBondLengthFragmentDOF : public CoordgenFragmentDOF
{
public:
CoordgenChangeParentBondLengthFragmentDOF(
sketcherMinimizerFragment* fragment);
int numberOfStates() const override;
int tier() const override;
void apply() const override;
float getCurrentPenalty() const override;
};
/*
Invert the direction of a bond (e.g. a substituent to a macrocycle can be
placed towards the inside
of the ring)
*/
class CoordgenInvertBondDOF : public CoordgenFragmentDOF
{
public:
CoordgenInvertBondDOF(sketcherMinimizerAtom* pivotAtom,
sketcherMinimizerAtom* boundAtom);
int numberOfStates() const override;
int tier() const override;
void apply() const override;
float getCurrentPenalty() const override;
private:
sketcherMinimizerAtom* m_pivotAtom;
sketcherMinimizerAtom* m_boundAtom;
};
/* flip a ring fused with another with more than 2 bonds (e.g. ring in a
* macrocycle) */
class CoordgenFlipRingDOF : public CoordgenFragmentDOF
{
public:
CoordgenFlipRingDOF(sketcherMinimizerRing* ring,
const std::vector<sketcherMinimizerAtom*>& fusionAtoms);
int numberOfStates() const override;
int tier() const override;
void apply() const override;
float getCurrentPenalty() const override;
private:
sketcherMinimizerAtom* m_pivotAtom1;
sketcherMinimizerAtom* m_pivotAtom2;
int m_penalty;
};
/* class that represents a rigid molecular fragment */
class EXPORT_COORDGEN sketcherMinimizerFragment
{
public:
sketcherMinimizerFragment();
~sketcherMinimizerFragment();
/* return the total weight of the fragment */
unsigned int totalWeight() const;
/* return the number of double bonds in the fragment */
unsigned int countDoubleBonds() const;
/* return the number of heavy atoms in the fragment */
unsigned int countHeavyAtoms() const;
/* return the number of constrained atoms in the fragment */
unsigned int countConstrainedAtoms() const;
/* return the number of fixed atoms in the fragment */
unsigned int countFixedAtoms() const;
/* add an atom to this fragment */
void addAtom(sketcherMinimizerAtom* atom);
/* add a bond to this fragment */
void addBond(sketcherMinimizerBond* bond);
/* add a ring to this fragment */
void addRing(sketcherMinimizerRing* ring);
/* add a degree of freedom to this fragment */
void addDof(CoordgenFragmentDOF* dof);
/* get all degrees of freedom of this fragment */
const std::vector<CoordgenFragmentDOF*>& getDofs();
/* mark the given bond as interfragment */
void addInterFragmentBond(sketcherMinimizerBond* bond)
{
_interFragmentBonds.push_back(bond);
}
std::vector<sketcherMinimizerAtom*> getAtoms() const { return m_atoms; }
std::vector<sketcherMinimizerBond*> getBonds() const { return m_bonds; }
std::vector<sketcherMinimizerRing*> getRings() const { return m_rings; }
std::vector<sketcherMinimizerAtom*>& atoms() { return m_atoms; }
std::vector<sketcherMinimizerBond*>& bonds() { return m_bonds; }
std::vector<sketcherMinimizerRing*>& rings() { return m_rings; }
/* return the parent fragment */
sketcherMinimizerFragment* getParent() const { return m_parent; }
/* set the given fragment as parent */
void setParent(sketcherMinimizerFragment* parent) { m_parent = parent; }
/* add the given degree of freedom to the given atom which will be modified
* by it */
void addDofToAtom(sketcherMinimizerAtom* atom, CoordgenFragmentDOF* dof)
{
m_dofsForAtom[atom].push_back(dof);
}
/* return the degrees of freedom that would modify the given atom */
std::vector<CoordgenFragmentDOF*>&
getDofsOfAtom(sketcherMinimizerAtom* atom)
{
return m_dofsForAtom[atom];
}
/* set the coordinates of each atom to the template coordinates */
void setAllCoordinatesToTemplate();
/* save coordinates information */
void storeCoordinateInformation();
std::vector<sketcherMinimizerBond*> _interFragmentBonds;
std::vector<sketcherMinimizerFragment*> _children;
std::map<sketcherMinimizerAtom*, sketcherMinimizerPointF> _coordinates;
sketcherMinimizerPointF _bondToParentCoordinatesStart;
sketcherMinimizerPointF _bondToParentCoordinatesEnd;
bool fixed, isTemplated, constrained, constrainedFlip;
bool isChain;
sketcherMinimizerBond* _bondToParent;
float longestChainFromHere;
size_t numberOfChildrenAtoms;
float numberOfChildrenAtomsRank;
/* translate and rotate the fragment and set the resulting coordinates to
* every atom */
void setCoordinates(const sketcherMinimizerPointF& position, float angle);
/* get the dof that refers to flipping this fragment */
CoordgenFragmentDOF* getFlipDof() const { return m_dofs[0]; }
private:
sketcherMinimizerFragment* m_parent;
std::vector<sketcherMinimizerAtom*> m_atoms;
std::vector<sketcherMinimizerBond*> m_bonds;
std::vector<sketcherMinimizerRing*> m_rings;
std::vector<CoordgenFragmentDOF*> m_dofs;
std::map<sketcherMinimizerAtom*, std::vector<CoordgenFragmentDOF*>>
m_dofsForAtom;
};
#endif // sketcherMINIMIZERFRAGMENT