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CoordgenMacrocycleBuilder.cpp
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/*
Contributors: Nicola Zonta
Copyright Schrodinger, LLC. All rights reserved
*/
#include <algorithm>
#include <queue>
#include "CoordgenMacrocycleBuilder.h"
#include "CoordgenMinimizer.h"
#include "sketcherMinimizer.h"
#include "sketcherMinimizerMaths.h"
#include "sketcherMinimizerRing.h"
#include "sketcherMinimizerStretchInteraction.h"
#define MAX_MACROCYCLES 40
#define PATH_FAILED -1000
#define HETEROATOM_RESTRAINT 1
#define SUBSTITUTED_ATOM_RESTRAINT 10
#define SUBSTITUENTS_TO_SAME_VERTEX_RESTRAINT 200
#define SUBSTITUENT_CLASH_WITH_PATH_RESTRAINT 400
#define SQRT3HALF 0.8660254037844386
using namespace std;
std::ostream& operator<<(std::ostream& os, const vertexCoords& v)
{
os << "(" << v.x << "," << v.y << "," << v.z << ")";
return os;
}
std::ostream& operator<<(std::ostream& os, const hexCoords& h)
{
os << "(" << h.x << "," << h.y << ")";
return os;
}
Polyomino::Polyomino()
{
resizeGrid(1);
}
Polyomino::Polyomino(const Polyomino& rhs)
{
clear();
pentagonVertices = rhs.pentagonVertices;
resizeGrid(1);
for (auto i : rhs.m_list) {
addHex(i->coords());
}
reassignHexs();
}
Polyomino& Polyomino::operator=(const Polyomino& rhs)
{
clear();
resizeGrid(1);
pentagonVertices = rhs.pentagonVertices;
for (auto i : rhs.m_list) {
addHex(i->coords());
}
reassignHexs();
return *this;
}
Polyomino::~Polyomino()
{
clear();
}
void Polyomino::clear()
{
for (auto& i : m_list) {
delete i;
}
m_list.clear();
}
size_t Polyomino::size() const
{
return m_list.size();
}
void Polyomino::resizeGrid(int i) const
{
m_grid.resize((2 * i + 1) *
(2 * i + 1)); // grid can hold coordinates from -i to i
m_gridSize = i;
reassignHexs();
}
void Polyomino::reassignHexs() const
{
for (auto& j : m_grid) {
j = nullptr;
}
for (auto hex : m_list) {
m_grid[getIndexInList(hex->coords())] = hex;
}
}
bool Polyomino::isTheSameAs(Polyomino& p) const
{
// mirrored polyominoes are considered to be different
if (size() != p.size()) {
return false;
}
vector<hexCoords> targetCoords;
for (Hex* hex : p.m_list) {
targetCoords.push_back(hex->coords());
}
if (targetCoords.empty()) {
return true; // both polyominoes are empty
}
int lowestx = m_list[0]->coords().x;
int lowesty = m_list[0]->coords().y;
for (Hex* hex : m_list) {
int x = hex->coords().x;
int y = hex->coords().y;
if (x < lowestx) {
lowestx = x;
}
if (y < lowesty) {
lowesty = y;
}
}
for (unsigned int i = 0; i < 6;
i++) { // explore 6 possible positions rotating the coordinates 30
// degrees
int lowestTargetX = 0, lowestTargetY = 0;
for (unsigned int j = 0; j < targetCoords.size(); j++) {
if (j == 0 || targetCoords[j].x < lowestTargetX) {
lowestTargetX = targetCoords[j].x;
}
if (j == 0 || targetCoords[j].y < lowestTargetY) {
lowestTargetY = targetCoords[j].y;
}
}
// translate
for (auto& targetCoord : targetCoords) {
targetCoord = hexCoords(targetCoord.x + lowestx - lowestTargetX,
targetCoord.y + lowesty - lowestTargetY);
}
// check
bool same = true;
for (auto targetCoord : targetCoords) {
if (!getHex(targetCoord)) {
same = false;
break;
}
}
if (same) {
return true;
}
// rotate
for (auto& targetCoord : targetCoords) {
targetCoord = targetCoord.rotate30Degrees();
}
}
return false;
}
Hex* Polyomino::getHex(hexCoords coords) const
{
return m_grid[getIndexInList(coords)];
}
void Polyomino::buildSkewedBoxShape(int x, int y, bool pentagon)
{
clear();
for (int yy = 0; yy < y; yy++) {
for (int xx = 0; xx < x; xx++) {
addHex(hexCoords(xx, yy));
}
}
if (pentagon) {
markOneVertexAsPentagon();
}
}
void Polyomino::buildRaggedSmallerBoxShape(
int x, int y,
bool pentagon) // box alternating rows of length x and x-1
{
clear();
int startx = 0;
for (int yy = 0; yy < y; yy++) {
// bigger row
for (int xx = 0; xx < x; xx++) {
addHex(hexCoords(startx + xx, yy));
}
yy++;
if (yy >= y) {
break;
}
for (int xx = 0; xx < x - 1; xx++) {
addHex(hexCoords(startx + xx, yy));
}
startx--;
}
if (pentagon) {
markOneVertexAsPentagon();
}
}
void Polyomino::buildRaggedBiggerBoxShape(
int x, int y,
bool pentagon) // box alternating rows of length x and x+1
{
clear();
int startx = 0;
for (int yy = 0; yy < y; yy++) {
// smaller row
for (int xx = 0; xx < x; xx++) {
addHex(hexCoords(startx + xx, yy));
}
yy++;
if (yy >= y) {
break;
}
for (int xx = 0; xx < x + 1; xx++) {
addHex(hexCoords(startx + xx - 1, yy));
}
startx--;
}
if (pentagon) {
markOneVertexAsPentagon();
}
}
void Polyomino::buildRaggedBoxShape(int x, int y, bool pentagon)
{
clear();
int startx = 0;
for (int yy = 0; yy < y; yy++) {
for (int xx = 0; xx < x; xx++) {
addHex(hexCoords(startx + xx, yy));
}
yy++;
if (yy >= y) {
break;
}
for (int xx = 0; xx < x; xx++) {
addHex(hexCoords(startx + xx, yy));
}
startx--;
}
if (pentagon) {
markOneVertexAsPentagon();
}
}
void Polyomino::buildWithVerticesN(int totVertices)
{
clear();
addHex(hexCoords(0, 0));
addHex(hexCoords(1, 0));
int vertices = 10;
while (vertices < totVertices) { // find a hexagon with 2 neighbors to add.
std::vector<hexCoords> nextCoords = allFreeNeighbors();
int lowestDistance = -1;
unsigned int bestI = 0;
for (unsigned int i = 0; i < nextCoords.size(); i++) {
hexCoords c = nextCoords[i];
if (countNeighbors(c) != 2) {
continue;
}
int distance = c.distanceFrom(hexCoords(0, 0));
if (lowestDistance == -1 || distance < lowestDistance) {
lowestDistance = distance;
bestI = i;
}
}
assert(lowestDistance != -1);
addHex(nextCoords[bestI]);
for (unsigned int i = 0; i < nextCoords.size(); i++) {
if (i == bestI) {
continue;
}
hexCoords c = nextCoords[i];
if (countNeighbors(c) == 3) {
addHex(c);
}
}
vertices += 2;
}
if ((vertices - totVertices) == 1) {
markOneVertexAsPentagon();
}
}
void Polyomino::markOneVertexAsPentagon() // TO DO: should check if one vertex
// is already marked to avoid marking
// it again. Not a problem while we
// only mark one vertex per polyomino
{
vector<vertexCoords> pathV = getPath();
size_t previousMultiplicity = hexagonsAtVertex(pathV[pathV.size() - 1]);
size_t thisMultiplicity = hexagonsAtVertex(pathV[0]);
size_t nextMultiplicity = 0;
for (size_t i = 0; i < pathV.size(); i++) {
size_t nextI = (i >= pathV.size() - 1) ? 0 : i + 1;
nextMultiplicity = hexagonsAtVertex(pathV[nextI]);
if (previousMultiplicity == 2 && thisMultiplicity == 1 &&
nextMultiplicity == 2) {
setPentagon(pathV[i]);
return;
}
previousMultiplicity = thisMultiplicity;
thisMultiplicity = nextMultiplicity;
}
previousMultiplicity = hexagonsAtVertex(pathV[pathV.size() - 1]);
thisMultiplicity = hexagonsAtVertex(pathV[0]);
nextMultiplicity = 0;
for (size_t i = 0; i < pathV.size(); i++) {
size_t nextI = (i >= pathV.size() - 1) ? 0 : i + 1;
nextMultiplicity = hexagonsAtVertex(pathV[nextI]);
if (previousMultiplicity == 1 && thisMultiplicity == 2 &&
nextMultiplicity == 1) {
setPentagon(pathV[i]);
return;
}
previousMultiplicity = thisMultiplicity;
thisMultiplicity = nextMultiplicity;
}
}
void Polyomino::setPentagon(vertexCoords c) // the marked vertex and the
// following one will count as a
// single vertex to turn the hexagon
// into a pentagon
{
pentagonVertices.push_back(c);
}
size_t Polyomino::hexagonsAtVertex(vertexCoords v) const
{
return vertexNeighbors(v).size();
}
vector<hexCoords> Polyomino::freeVertexNeighborPositions(vertexCoords v) const
{
vector<hexCoords> out;
int direction = v.x + v.y + v.z;
if (direction != 1 && direction != -1) {
cerr << "wrong input to free vertex neighbor positions " << v << endl;
return out;
}
Hex* h = getHex(hexCoords(v.x - direction, v.y));
if (!h) {
out.emplace_back(v.x - direction, v.y);
}
h = getHex(hexCoords(v.x, v.y - direction));
if (!h) {
out.emplace_back(v.x, v.y - direction);
}
h = getHex(hexCoords(v.x, v.y)); // z - direction
if (!h) {
out.emplace_back(v.x, v.y);
}
return out;
}
vector<Hex*> Polyomino::vertexNeighbors(vertexCoords v) const
{
vector<Hex*> out;
int direction = v.x + v.y + v.z;
if (direction != 1 && direction != -1) {
cerr << "wrong input to vertex Neighbors " << v << endl;
return out;
}
Hex* h = getHex(hexCoords(v.x - direction, v.y));
if (h) {
out.push_back(h);
}
h = getHex(hexCoords(v.x, v.y - direction));
if (h) {
out.push_back(h);
}
h = getHex(hexCoords(v.x, v.y)); // z - direction
if (h) {
out.push_back(h);
}
return out;
}
vertexCoords Polyomino::findOuterVertex()
const // find an outer vertex. Used to start path around polyomino.
{
// find a hexagon with a free vertex in direction (1, 0, 0). Such a hexagon
// is guarateed to exist in a polyomino.
for (auto h : m_list) {
vertexCoords vert(h->x() + 1, h->y(), h->z());
if (hexagonsAtVertex(vert) == 1) {
return vert;
}
}
cerr << "something went wrong in finding the outer vertex" << endl;
return {0, 0, 0};
}
int Polyomino::countNeighbors(hexCoords h) const
{
int out = 0;
vector<hexCoords> neighs = Hex::neighboringPositions(h);
for (auto neigh : neighs) {
if (getHex(neigh) != nullptr) {
out++;
}
}
return out;
}
std::vector<hexCoords> Polyomino::allFreeNeighbors() const
{
for (auto i : m_list) { // make sure that the grid is big enough to store
// every neighbor
getIndexInList(hexCoords(i->x() + 1, i->y() + 1));
getIndexInList(hexCoords(i->x() - 1, i->y() - 1));
}
std::vector<hexCoords> out;
std::vector<bool> visited(
m_grid.size(),
false); // keep track if a neighbors has already been checked or not
for (auto i : m_list) {
std::vector<hexCoords> neighborsCoords = i->neighbors();
for (auto neighborsCoord : neighborsCoords) {
bool isPresent = (getHex(neighborsCoord) != nullptr);
if (isPresent) {
continue;
}
int index = getIndexInList(neighborsCoord);
if (visited[index]) {
continue;
}
visited[index] = true;
out.push_back(neighborsCoord);
}
}
return out;
}
int Polyomino::getIndexInList(hexCoords coords) const
{
int x = coords.x;
int y = coords.y;
if (abs(x) > m_gridSize) {
resizeGrid(abs(x));
}
if (abs(y) > m_gridSize) {
resizeGrid(abs(y));
}
int a = m_gridSize + x;
int b = m_gridSize + y;
int i = (2 * m_gridSize + 1) * a + b;
return i;
}
void Polyomino::addHex(hexCoords coords)
{
int index = getIndexInList(coords);
assert(m_grid[index] == nullptr);
Hex* h = new Hex(coords);
m_list.push_back(h);
m_grid[index] = h;
}
void Polyomino::removeHex(hexCoords coords)
{
int index = getIndexInList(coords);
Hex* hex = m_grid[getIndexInList(coords)];
assert(hex != nullptr);
for (unsigned int i = 0; i < m_list.size(); i++) {
if (m_list[i] == hex) {
m_list.erase(m_list.begin() + i);
break;
}
}
delete hex;
m_grid[index] = nullptr;
}
bool Polyomino::isEquivalentWithout(hexCoords c) const
{
/* does removing this hexagon yield another polyomino with the same number
of vertices? true if hte hexagon has 3 neighbors all next to each other */
if (countNeighbors(c) != 3) {
return false;
}
vector<hexCoords> neighs = Hex::neighboringPositions(c);
for (unsigned int i = 0; i < neighs.size(); i++) {
int i2 = (i - 1 + 6) % 6;
int i3 = (i - 2 + 6) % 6;
if (getHex(neighs[i]) != nullptr && getHex(neighs[i2]) != nullptr &&
getHex(neighs[i3]) != nullptr) {
return true;
}
}
return false;
}
vertexCoords Polyomino::coordinatesOfSubstituent(const vertexCoords pos) const
{
vector<Hex*> neighbors = vertexNeighbors(pos);
assert(!neighbors.empty());
assert(neighbors.size() < 3);
vertexCoords out = pos;
if (neighbors.size() == 1) {
/*
the vertex coordinates differ from its parent's by a single +1 or -1
(d). The substituent will be along the same direction, so the other two
coordinates will be incremented by -d. e.g. (1, 0, 0)-> (1, -1, -1)
or (0, -1, 0)-> (1, -1, 1)
*/
vertexCoords parentCoords = neighbors[0]->coords().toVertexCoords();
vertexCoords v = pos - parentCoords;
int d = -1;
if (v.x + v.y + v.z > 0) {
d = 1;
}
if (v.x == 0) {
v.x -= d;
}
if (v.y == 0) {
v.y -= d;
}
if (v.z == 0) {
v.z -= d;
}
out = parentCoords + v;
} else if (neighbors.size() == 2) {
/*
the two parents share two vertices. One is pos, the other one is the
neighbor we are looking for
*/
vertexCoords parent1Coords = neighbors[0]->coords().toVertexCoords();
vertexCoords v = pos - parent1Coords;
vertexCoords parent2Coords = neighbors[1]->coords().toVertexCoords();
out = parent2Coords - v;
}
return out;
}
vector<vertexCoords> Polyomino::getPath() const
{
vector<vertexCoords> out;
vertexCoords firstVertex = findOuterVertex();
vertexCoords currentVertex = firstVertex;
vector<Hex*> neighbors = vertexNeighbors(firstVertex);
assert(neighbors.size() == 1);
Hex* currentHex = neighbors[0];
vertexCoords nextVertex = currentHex->followingVertex(currentVertex);
do {
bool skip = false;
if (!pentagonVertices.empty()) {
for (auto pentagonVertice : pentagonVertices) {
if (pentagonVertice == currentVertex) {
skip = true;
break;
}
}
}
if (!skip) {
out.push_back(currentVertex);
}
currentVertex = nextVertex;
neighbors = vertexNeighbors(currentVertex);
assert(neighbors.size() <= 2);
if (neighbors.size() == 2) {
currentHex =
(neighbors[0] != currentHex ? neighbors[0] : neighbors[1]);
}
nextVertex = currentHex->followingVertex(currentVertex);
} while (currentVertex != firstVertex);
return out;
}
vector<hexCoords> Hex::neighboringPositions(hexCoords h)
{
int xx = h.x;
int yy = h.y;
vector<hexCoords> out;
out.emplace_back(xx + 1, yy); // z-1
out.emplace_back(xx + 1, yy - 1);
out.emplace_back(xx, yy - 1); // z+1
out.emplace_back(xx - 1, yy); // z+1
out.emplace_back(xx - 1, yy + 1);
out.emplace_back(xx, yy + 1); // z-1
return out;
}
vector<hexCoords> Hex::neighbors() const
{
return neighboringPositions(m_coords);
}
vertexCoords Hex::followingVertex(vertexCoords v) const
{
int dx = v.x - x();
int dy = v.y - y();
int dz = v.z - z();
if (dx + dy + dz != 1 && dx + dy + dz != -1) {
cerr << "wrong input to transform to following vertex" << endl;
}
if (dx == 0 && dy == 0) {
dx = -dz;
dy = 0;
dz = 0;
} else if (dx == 0 && dz == 0) {
dz = -dy;
dx = 0;
dy = 0;
} else if (dy == 0 && dz == 0) {
dy = -dx;
dx = 0;
dz = 0;
} else {
cerr << "wrong input to transform to following vertex" << endl;
}
return {x() + dx, y() + dy, z() + dz};
}
float CoordgenMacrocycleBuilder::getPrecision() const
{
return m_precision;
}
void CoordgenMacrocycleBuilder::setPrecision(float f)
{
m_precision = f;
}
vector<sketcherMinimizerPointF> CoordgenMacrocycleBuilder::newMacrocycle(
sketcherMinimizerRing* ring, vector<sketcherMinimizerAtom*> atoms) const
{
// TODO the coordinates should be built on the returned vector, never saved
// to the atoms in atoms.
int natoms = static_cast<int>(atoms.size());
Polyomino p;
p.buildWithVerticesN(natoms);
vector<Polyomino> pols;
pols.push_back(p);
vector<Polyomino> squarePols = buildSquaredShapes(natoms);
for (unsigned int i = 0; i < squarePols.size(); i++) {
assert(squarePols[i].getPath().size() == atoms.size());
}
pols.reserve(pols.size() + squarePols.size());
pols.insert(pols.end(), squarePols.begin(), squarePols.end());
pols = removeDuplicates(pols);
bool found = false;
pathRestraints pr = getPathRestraints(atoms);
pathConstraints pc = getPathConstraints(atoms);
int scoreOfChosen = PATH_FAILED;
int startOfChosen = 0;
int bestStart = 0;
int bestScore = PATH_FAILED;
Polyomino chosenP = pols[0];
int acceptableScore = acceptableShapeScore(natoms);
int checkedMacrocycles = 0;
if (!m_forceOpenMacrocycles) {
do {
int bestP = 0;
found = matchPolyominoes(pols, pc, pr, bestP, bestScore, bestStart,
checkedMacrocycles);
if (bestScore > scoreOfChosen) {
startOfChosen = bestStart;
scoreOfChosen = bestScore;
chosenP = pols[bestP];
if (bestScore > acceptableScore) {
break;
}
}
if (checkedMacrocycles > MAX_MACROCYCLES) {
break;
}
pols = listOfEquivalents(pols);
pols = removeDuplicates(pols);
} while (!pols.empty());
}
if (found) {
vector<vertexCoords> path = chosenP.getPath();
writePolyominoCoordinates(path, atoms, startOfChosen);
if (!chosenP.pentagonVertices.empty()) {
atoms.at(0)->molecule->requireMinimization();
}
} else { // could not find a shape. fallback methods
if (!openCycleAndGenerateCoords(ring)) {
vector<sketcherMinimizerPointF> coords =
CoordgenFragmentBuilder::listOfCoordinatesFromListofRingAtoms(
atoms);
int i = 0;
for (sketcherMinimizerAtom* atom : atoms) {
atom->setCoordinates(coords[i]);
++i;
}
}
atoms.at(0)->molecule->requireMinimization();
}
vector<sketcherMinimizerPointF> coordinates;
coordinates.reserve(atoms.size());
for (sketcherMinimizerAtom* atom : atoms) {
coordinates.push_back(atom->getCoordinates());
}
return coordinates;
}
sketcherMinimizerBond*
CoordgenMacrocycleBuilder::findBondToOpen(sketcherMinimizerRing* ring) const
{
sketcherMinimizerBond* bestBond = nullptr;
float bestScore = 0.f;
for (sketcherMinimizerBond* bond : ring->_bonds) {
float score = 0.f;
if (ring->isMacrocycle()) {
if (bond->getBondOrder() != 1) {
continue;
}
bool nextToMultipleBond = false;
for (auto otherBond : bond->getStartAtom()->bonds) {
if (otherBond->isStereo()) {
nextToMultipleBond = true;
break;
}
}
for (auto otherBond : bond->getEndAtom()->bonds) {
if (otherBond->isStereo()) {
nextToMultipleBond = true;
break;
}
}
if (nextToMultipleBond) {
continue;
}
}
score += bond->rings.size() * 10;
score += bond->getStartAtom()->neighbors.size();
score += bond->getEndAtom()->neighbors.size();
score /= bond->crossingBondPenaltyMultiplier;
if (bestBond == nullptr || score < bestScore) {
bestScore = score;
bestBond = bond;
}
}
return bestBond;
}
bool CoordgenMacrocycleBuilder::openCycleAndGenerateCoords(
sketcherMinimizerRing* ring) const // generate coordinates of whole fragment
// by opening one bond of the macrocycle
{
map<sketcherMinimizerAtom*, sketcherMinimizerAtom*> atomMap;
sketcherMinimizer min(getPrecision());
min.setSkipMinimization(true);
min.setForceOpenMacrocycles(true);
sketcherMinimizerBond* bondToBreak = findBondToOpen(ring);
if (!bondToBreak) {
return false;
}
auto* minMol = new sketcherMinimizerMolecule;
sketcherMinimizerAtom* a = ring->_atoms[0];
// vector<sketcherMinimizerAtom*> atoms = a->getFragment()->getAtoms();
vector<sketcherMinimizerAtom*> atoms = a->molecule->getAtoms();
for (sketcherMinimizerAtom* at : atoms) {
if (at->isResidue()) {
continue;
}
auto* new_at = new sketcherMinimizerAtom;
atomMap[at] = new_at;
new_at->templateCoordinates = at->coordinates;
new_at->coordinates = at->coordinates;
new_at->atomicNumber = at->atomicNumber;
new_at->_generalUseN = at->_generalUseN;
new_at->molecule = minMol;
new_at->_implicitHs = at->_implicitHs;
minMol->_atoms.push_back(new_at);
}
// vector<sketcherMinimizerBond*> bonds = a->getFragment()->getBonds();
vector<sketcherMinimizerBond*> bonds = a->molecule->getBonds();
for (sketcherMinimizerBond* bo : bonds) {
if (bo == bondToBreak || bo->isResidueInteraction()) {
continue;
}
auto* new_bo = new sketcherMinimizerBond;
new_bo->bondOrder = bo->bondOrder;
new_bo->startAtom = atomMap[bo->startAtom];
new_bo->endAtom = atomMap[bo->endAtom];
new_bo->isZ = bo->isZ;
new_bo->m_ignoreZE = bo->m_ignoreZE;
minMol->_bonds.push_back(new_bo);
}
min.initialize(minMol);
min.findFragments();
min.buildFromFragments(true);
auto* brokenBond = new sketcherMinimizerBond;
brokenBond->bondOrder = bondToBreak->bondOrder;
brokenBond->startAtom = atomMap[bondToBreak->startAtom];
brokenBond->endAtom = atomMap[bondToBreak->endAtom];
brokenBond->isZ = bondToBreak->isZ;
minMol->_bonds.push_back(brokenBond);
minMol->forceUpdateStruct(minMol->_atoms, minMol->_bonds, minMol->_rings);
std::vector<sketcherMinimizerInteraction*> extraInteractions;
extraInteractions.push_back(new sketcherMinimizerStretchInteraction(
brokenBond->startAtom, brokenBond->endAtom));
min.avoidClashesOfMolecule(minMol, extraInteractions);
for (sketcherMinimizerAtom* atom : atoms) {
sketcherMinimizerAtom* otherAtom = atomMap[atom];
if (otherAtom->rigid) {
atom->rigid = true;
}
atom->setCoordinates(otherAtom->getCoordinates());
}
for (auto r : ring->getAtoms()[0]->fragment->getRings()) {
r->coordinatesGenerated = true;
}
for (auto bondRing : bondToBreak->rings) {
if (!bondRing->isMacrocycle() && bondRing != ring) {
bondRing->coordinatesGenerated = false;
}
}
delete brokenBond;
return true;
}
vector<Polyomino>
CoordgenMacrocycleBuilder::listOfEquivalents(const vector<Polyomino>& l) const
{
vector<Polyomino> out;
for (const auto& i : l) {
vector<Polyomino> newV = listOfEquivalent(i);
out.reserve(out.size() + newV.size());
out.insert(out.end(), newV.begin(), newV.end());
}
return out;
}
vector<Polyomino>
CoordgenMacrocycleBuilder::listOfEquivalent(const Polyomino& p)
const // build a list of polyominoes with the same number of
// vertices by removing hexagons with 3 neighbors
{
vector<Polyomino> out;
vector<Hex*> l = p.m_list;
size_t pentagonVs = p.pentagonVertices.size();
for (auto& i : l) {
hexCoords c = i->coords();
if (p.isEquivalentWithout(c)) {
Polyomino newP = p;
newP.pentagonVertices.clear();
newP.removeHex(c);
for (size_t i = 0; i < pentagonVs; i++) {
newP.markOneVertexAsPentagon();
}
out.push_back(newP);
}
}
return out;
}
pathConstraints CoordgenMacrocycleBuilder::getPathConstraints(
vector<sketcherMinimizerAtom*>& atoms) const
{
pathConstraints pc;
pc.doubleBonds = getDoubleBondConstraints(atoms);
pc.ringConstraints = getRingConstraints(atoms);
return pc;
}
vector<ringConstraint> CoordgenMacrocycleBuilder::getRingConstraints(
vector<sketcherMinimizerAtom*>& atoms) const
{
vector<ringConstraint> out;
for (int i = 0; i < static_cast<int>(atoms.size()); i++) {
sketcherMinimizerAtom* a = atoms[i];
if (a->rings.size() > 1) {
for (unsigned int rr = 0; rr < a->rings.size(); rr++) {
sketcherMinimizerRing* r = a->rings[rr];
if (r->_atoms.size() < MACROCYCLE) { // this excludes the
// current cycle and all
// fused macrocycles
bool forceOutside = false;
for (auto n : a->neighbors) {
if (find(atoms.begin(), atoms.end(), n) ==
atoms.end()) {
if (r->containsAtom(n)) {
forceOutside = true;
}
break;
}
}
out.emplace_back(i, r, forceOutside);
}
}
}
}
return out;
}
vector<doubleBondConstraint>
CoordgenMacrocycleBuilder::getDoubleBondConstraints(
vector<sketcherMinimizerAtom*>& atoms) const
{
vector<doubleBondConstraint> out;
if (atoms.size() >= MACROCYCLE) {
for (unsigned int i = 0; i < atoms.size(); i++) {
unsigned int index = i;
unsigned int index2 = (i + 1) % atoms.size();
sketcherMinimizerBond* b =
sketcherMinimizer::getBond(atoms[i], atoms[index2]);
if (!b) {
cerr << "bad input to get double bond constraints" << endl;
break;
}
if (b->bondOrder != 2) {
continue;
}
bool smallRingBond = false;
if (b->rings.size() > 1) {
for (auto& ring : b->rings) {
if (ring->_atoms.size() < MACROCYCLE) {
smallRingBond = true;
break;
}
}
}
if (smallRingBond) {
continue;
}
int previousI =
static_cast<int>((i + atoms.size() - 1) % atoms.size());
int followingI = (i + 2) % atoms.size();
bool isTrans = !b->isZ; // is the atom trans in the ring? (isZ
// stores the absolute chirality)
if (b->startAtom !=
atoms[i]) { // atoms[i] could be the end atom of b
int swap = previousI;
previousI = followingI;
followingI = swap;
index = index2;
index2 = i;
}
if (b->startAtomCIPFirstNeighbor() != atoms[previousI]) {
isTrans = !isTrans;
}
if (b->endAtomCIPFirstNeighbor() != atoms[followingI]) {
isTrans = !isTrans;
}
doubleBondConstraint constraint;
constraint.trans = isTrans;
constraint.atom1 = index;
constraint.atom2 = index2;
constraint.previousAtom = previousI;
constraint.followingAtom = followingI;
out.push_back(constraint);
}
}
return out;
}
int CoordgenMacrocycleBuilder::getNumberOfChildren(
sketcherMinimizerAtom* a, sketcherMinimizerAtom* parent) const
{
int n = 0;
map<sketcherMinimizerAtom*, bool> visited;
queue<sketcherMinimizerAtom*> q;
q.push(a);
visited[parent] = true;
while (!q.empty()) {
sketcherMinimizerAtom* thisA = q.front();
q.pop();
visited[thisA] = true;
n++;
for (auto n : thisA->neighbors) {
if (visited[n]) {
continue;
}
q.push(n);
}
}
return n;
}
pathRestraints CoordgenMacrocycleBuilder::getPathRestraints(