coordgen 0.2.2

/*
 *  sketcherMinimizerMolecule.cpp
 *
 *  Created by Nicola Zonta on 24/05/2011.
 *   Copyright Schrodinger, LLC. All rights reserved.
 *
 */

#include "sketcherMinimizerMolecule.h"
#include "sketcherMinimizerAtom.h"
#include "sketcherMinimizerMaths.h"
#include "sketcherMinimizerRing.h"
#include "sketcherMinimizerBond.h"
#include <queue>

using namespace std;

sketcherMinimizerMolecule::sketcherMinimizerMolecule()
    : fixed(false),

      hasFixedFragments(false), hasConstrainedFragments(false),
      needToAlignNonRingAtoms(false), needToAlignWholeMolecule(false),
      isPlaced(false), m_mainFragment(nullptr), m_requireMinimization(false){};

sketcherMinimizerMolecule::~sketcherMinimizerMolecule()
{
    for (auto ring : _rings) {
        delete ring;
    }
}

sketcherMinimizerAtom* sketcherMinimizerMolecule::addNewAtom()
{
    auto atom = new sketcherMinimizerAtom();
    _atoms.push_back(atom);
    atom->molecule = this;
    return atom;
}

sketcherMinimizerBond*
sketcherMinimizerMolecule::addNewBond(sketcherMinimizerAtom* at1,
                                      sketcherMinimizerAtom* at2)
{
    auto bond = new sketcherMinimizerBond(at1, at2);
    _bonds.push_back(bond);
    return bond;
}

int sketcherMinimizerMolecule::totalCharge()
{
    int charge = 0;
    for (auto& _atom : _atoms) {
        charge += _atom->charge;
    }
    return charge;
}

void sketcherMinimizerMolecule::boundingBox(sketcherMinimizerPointF& min,
                                            sketcherMinimizerPointF& max)
{
    min.setX(0.f);
    min.setY(0.f);
    max.setX(0.f);
    max.setY(0.f);
    if (_atoms.size()) {
        min = _atoms[0]->coordinates;
        max = _atoms[0]->coordinates;
        for (auto a : _atoms) {
            if (a->coordinates.x() < min.x()) {
                min.setX(a->coordinates.x());
            }
            if (a->coordinates.y() < min.y()) {
                min.setY(a->coordinates.y());
            }
            if (a->coordinates.x() > max.x()) {
                max.setX(a->coordinates.x());
            }
            if (a->coordinates.y() > max.y()) {
                max.setY(a->coordinates.y());
            }
        }
    }
}

void sketcherMinimizerMolecule::requireMinimization()
{
    m_requireMinimization = true;
}

bool sketcherMinimizerMolecule::minimizationIsRequired()
{
    return m_requireMinimization;
}

sketcherMinimizerPointF sketcherMinimizerMolecule::center()
{
    if (!_atoms.size()) {
        return sketcherMinimizerPointF(0.f, 0.f);
    }
    sketcherMinimizerPointF c(.0f, .0f);
    for (auto& _atom : _atoms) {
        c += _atom->coordinates;
    }
    return c / _atoms.size();
}

void sketcherMinimizerMolecule::assignBondsAndNeighbors(
    std::vector<sketcherMinimizerAtom*>& atoms,
    std::vector<sketcherMinimizerBond*>& bonds)
{
    for (auto atom : atoms) {
        atom->bonds.clear();
        atom->neighbors.clear();
        atom->residueInteractionPartners.clear();
        atom->residueInteractions.clear();
        atom->rings.clear();
    }

    for (auto bond : bonds) {

        bond->rings.clear();

        if (!bond->isResidueInteraction()) {
            //    bond->_rings.clear ();
            bond->startAtom->bonds.push_back(bond);

            bond->endAtom->neighbors.push_back(bond->startAtom);

            bond->endAtom->bonds.push_back(bond);

            bond->startAtom->neighbors.push_back(bond->endAtom);
        } else {
            bond->startAtom->residueInteractions.push_back(bond);

            bond->endAtom->residueInteractionPartners.push_back(
                bond->startAtom);

            bond->endAtom->residueInteractions.push_back(bond);

            bond->startAtom->residueInteractionPartners.push_back(
                bond->endAtom);
        }
    }
    for (auto& atom : atoms) {
        if (atom->_implicitHs == -1) {
            atom->_implicitHs = atom->findHsNumber();
        }
    }
}

void sketcherMinimizerMolecule::forceUpdateStruct(
    std::vector<sketcherMinimizerAtom*>& atoms,
    std::vector<sketcherMinimizerBond*>& bonds,
    std::vector<sketcherMinimizerRing*>& rings)
{
    sketcherMinimizerMolecule::assignBondsAndNeighbors(atoms, bonds);

    findRings(bonds, rings);
    for (auto& bond : bonds) {
        for (unsigned int j = 0; j < bond->rings.size(); j++) {
            sketcherMinimizerRing* ring = bond->rings[j];
            bool found = false;
            for (auto& k : bond->startAtom->rings) {
                if (k == ring) {
                    found = true;
                    break;
                }
            }
            if (!found) {
                bond->startAtom->rings.push_back(ring);
            }
            found = false;
            for (auto& k : bond->endAtom->rings) {
                if (k == ring) {
                    found = true;
                    break;
                }
            }
            if (!found) {
                bond->endAtom->rings.push_back(ring);
            }
        }
    }

    for (auto& atom : atoms) {
        for (unsigned int j = 0; j < atom->rings.size(); j++) {
            atom->rings[j]->_atoms.push_back(atom);
        }
    }
}

void sketcherMinimizerMolecule::findRings(
    std::vector<sketcherMinimizerBond*>& bonds,
    std::vector<sketcherMinimizerRing*>& rings)
{
    for (auto& ring : rings) {
        delete ring;
    }
    rings.clear();
    for (unsigned int i = 0; i < bonds.size(); i++) {
        for (auto& bond : bonds) {
            bond->_SSSRVisited = false;
            bond->_SSSRParent = nullptr;
            bond->_SSSRParentAtStart = true;
        }

        sketcherMinimizerBond* bond = bonds[i];

        std::queue<sketcherMinimizerBond*> q;
        bond->_SSSRVisited = true;
        q.push(bond);
        bool closedRing = false;
        while (!q.empty() && !closedRing) {
            sketcherMinimizerBond* lastBond = q.front();
            q.pop();

            sketcherMinimizerAtom* pivotAtom = lastBond->endAtom;
            if (!lastBond->_SSSRParentAtStart) {
                pivotAtom = lastBond->startAtom;
            }
            for (unsigned int j = 0; j < pivotAtom->bonds.size(); j++) {
                sketcherMinimizerBond* nextBond = pivotAtom->bonds[j];
                // sketcherMinimizerAtom *nextAtom = pivotAtom->neighbors[j];
                if (nextBond == lastBond) {
                    continue;
                }
                if (nextBond->_SSSRVisited) {
                    if (nextBond == bond) {
                        addRing(closeRing(lastBond), rings);
                        closedRing = true;
                    }

                } else {
                    if (nextBond->endAtom == pivotAtom) {
                        nextBond->_SSSRParentAtStart = false;
                    }
                    nextBond->_SSSRParent = lastBond;
                    nextBond->_SSSRVisited = true;
                    q.push(nextBond);
                }
            }
        }
    }
    for (auto ring : rings) {
        for (unsigned int j = 0; j < ring->_bonds.size(); j++) {
            sketcherMinimizerBond* bond = ring->_bonds[j];
            bond->rings.push_back(ring);
        }
    }
}

sketcherMinimizerRing*
sketcherMinimizerMolecule::closeRing(sketcherMinimizerBond* bond)
{
    auto* ring = new sketcherMinimizerRing();
    sketcherMinimizerBond* lastBond = bond;
    while (lastBond) {
        ring->_bonds.push_back(lastBond);
        lastBond = lastBond->_SSSRParent;
    }
    return ring;
}

void sketcherMinimizerMolecule::addRing(
    sketcherMinimizerRing* ring, std::vector<sketcherMinimizerRing*>& rings)
{
    bool found = false;
    for (auto& i : rings) {
        if (i->sameAs(ring)) {
            found = true;
            break;
        }
    }
    if (!found) {
        rings.push_back(ring);
    } else {
        delete ring;
    }
}