sketcherMinimizerBond.h

/*
 *  sketcherMinimizerBond.h
 *
 *  Created by Nicola Zonta on 03/05/2010.
 *   Copyright Schrodinger, LLC. All rights reserved.
 *
 */

#ifndef sketcherMINIMIZERBOND_H
#define sketcherMINIMIZERBOND_H

#include "CoordgenConfig.hpp"
#include <cstddef>
#include <vector>

class sketcherMinimizerRing;
class sketcherMinimizerAtom;

struct sketcherMinimizerBondStereoInfo {
    enum sketcherMinimizerBondStereo { cis, trans, unspecified };

    sketcherMinimizerAtom* atom1 = nullptr;
    sketcherMinimizerAtom* atom2 = nullptr;
    sketcherMinimizerBondStereo stereo = unspecified;
};

/* class to represent a covalent bond */
class EXPORT_COORDGEN sketcherMinimizerBond
{
  public:
    sketcherMinimizerBond() : rings() {}
    sketcherMinimizerBond(sketcherMinimizerAtom* at1,
                          sketcherMinimizerAtom* at2)
        : sketcherMinimizerBond()
    {
        startAtom = at1;
        endAtom = at2;
    }

    virtual ~sketcherMinimizerBond() = default;

    virtual bool isResidueInteraction() { return false; }
    sketcherMinimizerAtom* startAtom = nullptr;
    sketcherMinimizerAtom* endAtom = nullptr;
    sketcherMinimizerAtom* getStartAtom() const { return startAtom; }
    sketcherMinimizerAtom* getEndAtom() const { return endAtom; }

    /* return bond order */
    int getBondOrder() const { return bondOrder; }

    void setBondOrder(int order) { bondOrder = order; }

    void setStereoChemistry(sketcherMinimizerBondStereoInfo stereo)
    {
        m_stereo = stereo;
    }

    void setAbsoluteStereoFromStereoInfo();

    /* return true if the bond is part of a small ring (i.e. 8 members or less)
     */
    bool isInSmallRing() const;

    /* return true if the bond is part of a macrocycle */
    bool isInMacrocycle() const;

    /* return true if the bond is to a terminal atom */
    bool isTerminal() const;

    /*
     does this bond separate two rigid fragments?
     i.e. is bond a single rotatable bond to a non-terminal atom?
     */
    bool isInterFragment() const;
    bool isStereo() const;

    /* given atom1 and atom2 as substituents on the two sides of a double bond,
     should they be put in cis?
     */
    bool markedAsCis(sketcherMinimizerAtom* atom1,
                     sketcherMinimizerAtom* atom2) const;

    /* flip the current bond, mirroring the coordinates of all the atoms on one
     * side of it */
    void flip();

    /* get the atom bound to the start atom of the bond with the highest CIP
     * priority */
    sketcherMinimizerAtom* startAtomCIPFirstNeighbor() const;

    /* get the atom bound to the end atom of the bond with the highest CIP
     * priority */
    sketcherMinimizerAtom* endAtomCIPFirstNeighbor() const;

    /* return true if the E/Z stereochemistry as read from the atoms coordinates
     * matches the label */
    bool checkStereoChemistry() const;
    int bondOrder{1};
    bool skip{false};
    bool isZEActive{false}; // does it have  a Z and E form?
    bool isZ{false}; // used for double bonds to distinguish Z from E form.
                     // bonds default to E

    int m_chmN =
        -1; // idx of the corresponding ChmAtom if molecule comes from 3d

    sketcherMinimizerBondStereoInfo m_stereo;

    bool isWedge{false};
    bool isReversed{false};
    bool hasStereochemistryDisplay{false};
    bool _SSSRVisited{false};
    bool _SSSRParentAtStart{true};
    bool m_ignoreZE{false};
    sketcherMinimizerBond* _SSSRParent{nullptr};

    /*this modifies the penalty for crossing this bond. scores < 1 indicate bonds that can be crossed without compromising aesthetics too much (e.g. residue interactions) */
    float crossingBondPenaltyMultiplier{1.f};
    std::vector<sketcherMinimizerRing*> rings;
};

#endif // sketcherMINIMIZERBOND_H