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sketcherMinimizerAtom.cpp
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sketcherMinimizerAtom.cpp
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/*
* sketcherMinimizerAtom.h
*
* Created by Nicola Zonta on 19/10/2010.
* Copyright Schrodinger, LLC. All rights reserved.
*
*/
#include <algorithm>
#include <numeric>
#include <queue>
#include "sketcherMinimizer.h"
#include "sketcherMinimizerAtom.h"
#include "sketcherMinimizerBond.h"
#include "sketcherMinimizerMaths.h"
#include "sketcherMinimizerRing.h"
using namespace std;
bool CIPAtom::operator<(const CIPAtom& rhs) const
{
/* check if this has priority over rhs. An atom is better than another if it
has a parent in the chain that gets priority. Parents are evaluated
starting from the furthest to the closest.
Priority is assigned to the atom with highest atomic number, or has been
found to have priority due to its children in previous iterations of the
algorithm (scores) or in the present iteration (medals)
*/
assert(allParents.size() == rhs.allParents.size());
for (size_t i = 0; i < allParents.size(); i++) {
if (allParents[i]->atomicNumber > rhs.allParents[i]->atomicNumber) {
return true;
}
if (allParents[i]->atomicNumber < rhs.allParents[i]->atomicNumber) {
return false;
}
if ((*scores)[allParents[i]] < (*rhs.scores)[rhs.allParents[i]]) {
return true;
}
if ((*scores)[allParents[i]] > (*rhs.scores)[rhs.allParents[i]]) {
return false;
}
vector<int> meds = (*medals)[allParents[i]];
vector<int> meds2 = (*rhs.medals)[rhs.allParents[i]];
size_t s = (meds.size() < meds2.size()) ? meds.size() : meds2.size();
for (size_t mm = 0; mm < s; mm++) {
if (meds[mm] > meds2[mm]) {
return true;
}
if (meds[mm] < meds2[mm]) {
return false;
}
}
if (meds.size() > meds2.size()) {
return true;
}
if (meds2.size() > meds.size()) {
return false;
}
}
size_t siz = theseAtoms.size();
if (rhs.theseAtoms.size() < siz) {
siz = rhs.theseAtoms.size();
}
for (size_t i = 0; i < siz; i++) {
if (theseAtoms[i].first > rhs.theseAtoms[i].first) {
return true;
}
if (theseAtoms[i].first < rhs.theseAtoms[i].first) {
return false;
}
}
if (theseAtoms.size() > rhs.theseAtoms.size()) {
return true;
}
if (theseAtoms.size() < rhs.theseAtoms.size()) {
return false;
}
return false;
}
bool CIPAtom::operator==(const CIPAtom& rhs) const
{
assert(allParents.size() == rhs.allParents.size());
for (size_t i = 0; i < allParents.size(); i++) {
if (allParents[i]->atomicNumber != rhs.allParents[i]->atomicNumber) {
return false;
}
if ((*scores)[allParents[i]] != (*rhs.scores)[rhs.allParents[i]]) {
return false;
}
}
if (theseAtoms.size() != rhs.theseAtoms.size()) {
return false;
}
for (size_t i = 0; i < theseAtoms.size(); i++) {
if (theseAtoms[i].first != rhs.theseAtoms[i].first) {
return false;
}
}
return true;
}
std::ostream& operator<<(std::ostream& os, const CIPAtom& a)
{
for (size_t i = 0; i < a.allParents.size(); i++) {
os << a.allParents[i]->atomicNumber << "("
<< (*a.scores)[a.allParents[i]] << ")";
if (!(*a.medals)[a.allParents[i]].empty()) {
cerr << "<";
for (int ii : (*a.medals)[a.allParents[i]]) {
cerr << ii << "|";
}
cerr << ">";
}
cerr << " ";
}
os << "-";
for (const auto& theseAtom : a.theseAtoms) {
os << " " << theseAtom.first;
}
return os;
}
bool CIPAtom::isBetter(CIPAtom& rhs,
map<sketcherMinimizerAtom*, unsigned int>* m) const
{
/*
Similar to the < operator, but in estabilishing priorities also considers
scores stored in m
*/
assert(allParents.size() == rhs.allParents.size());
for (size_t i = 0; i < allParents.size(); i++) {
if ((*m)[allParents[i]] > (*m)[rhs.allParents[i]]) {
return true;
}
if ((*m)[allParents[i]] < (*m)[rhs.allParents[i]]) {
return false;
}
if (allParents[i]->atomicNumber > rhs.allParents[i]->atomicNumber) {
return true;
}
if (allParents[i]->atomicNumber < rhs.allParents[i]->atomicNumber) {
return false;
}
if ((*scores)[allParents[i]] < (*rhs.scores)[rhs.allParents[i]]) {
return true;
}
if ((*scores)[allParents[i]] > (*rhs.scores)[rhs.allParents[i]]) {
return false;
}
vector<int> meds = (*medals)[allParents[i]];
vector<int> meds2 = (*rhs.medals)[rhs.allParents[i]];
size_t s = (meds.size() < meds2.size()) ? meds.size() : meds2.size();
for (size_t mm = 0; mm < s; mm++) {
if (meds[mm] > meds2[mm]) {
return true;
}
if (meds[mm] < meds2[mm]) {
return false;
}
}
if (meds.size() > meds2.size()) {
return true;
}
if (meds2.size() > meds.size()) {
return false;
}
}
size_t siz = theseAtoms.size();
if (rhs.theseAtoms.size() < siz) {
siz = rhs.theseAtoms.size();
}
for (size_t i = 0; i < siz; i++) {
if (theseAtoms[i].first > rhs.theseAtoms[i].first) {
return true;
}
if (theseAtoms[i].first < rhs.theseAtoms[i].first) {
return false;
}
}
if (theseAtoms.size() > rhs.theseAtoms.size()) {
return true;
}
if (theseAtoms.size() < rhs.theseAtoms.size()) {
return false;
}
return false;
}
sketcherMinimizerAtom::~sketcherMinimizerAtom() = default;
sketcherMinimizerAtom::sketcherMinimizerAtom()
: crossLayout(false), fixed(false), constrained(false), rigid(false),
isSharedAndInner(false), atomicNumber(6), charge(0), _valence(-10),
_generalUseN(-1), _generalUseN2(-1), m_chmN(-1),
_generalUseVisited(false), _generalUseVisited2(false), fragment(nullptr),
needsCheckForClashes(false), visited(false), coordinatesSet(false),
isR(true), hasStereochemistrySet(false), _hasRingChirality(false)
{
hidden = false;
m_pseudoZ = 0.f;
m_pocketDistance = 0.f;
m_x3D = INVALID_COORDINATES;
m_y3D = INVALID_COORDINATES;
m_z3D = INVALID_COORDINATES;
m_isClashing = false;
m_isLigand = false;
m_isWaterMap = false;
m_clockwiseInvert = false;
m_isStereogenic = false;
m_ignoreRingChirality = false;
}
sketcherMinimizerRing*
sketcherMinimizerAtom::shareARing(const sketcherMinimizerAtom* atom1,
const sketcherMinimizerAtom* atom2)
{
/* return a ring shared by the two atoms. return a non-macrocycle if
* possible */
if (atom1->rings.empty()) {
return nullptr;
}
if (atom2->rings.empty()) {
return nullptr;
}
for (sketcherMinimizerRing* ring : atom1->rings) {
if (ring->isMacrocycle()) {
continue;
}
for (sketcherMinimizerRing* ring2 : atom2->rings) {
if (ring == ring2) {
return ring;
}
}
}
for (sketcherMinimizerRing* ring : atom1->rings) {
for (sketcherMinimizerRing* ring2 : atom2->rings) {
if (ring == ring2) {
return ring;
}
}
}
return nullptr;
}
int sketcherMinimizerAtom::findHsNumber() const
{
int valence = _valence;
if (valence == -10) {
valence = expectedValence(atomicNumber); // valence is not yet set
}
int nBondOrders = 0;
for (auto bond : bonds) {
nBondOrders += bond->bondOrder;
}
if (atomicNumber == 16) { // sulfite & sulfate
int nOs = 0;
for (size_t i = 0; i < neighbors.size(); ++i) {
if (neighbors[i]->atomicNumber == 8 && bonds[i]->bondOrder == 2) {
++nOs;
}
}
if ((nOs) < 3) {
valence += nOs * 2;
}
}
if (atomicNumber == 15) { // P
int nOs = 0;
for (size_t i = 0; i < neighbors.size(); ++i) {
if (neighbors[i]->atomicNumber == 8 && bonds[i]->bondOrder == 2) {
++nOs;
}
}
if (nOs < 2) {
valence += nOs * 2;
}
}
int out = valence - nBondOrders + charge;
if (out < 0) {
out = 0;
} else if (out > 4) {
out = 4;
}
return out;
}
unsigned int
sketcherMinimizerAtom::expectedValence(unsigned int atomicNumber) const
{
switch (atomicNumber) {
case 1:
return 1;
case 5:
return 3;
case 6:
return 4;
case 7:
return 3;
case 8:
return 2;
case 9:
return 1;
case 14:
return 4;
case 15:
return 3;
case 16:
return 2;
case 17:
return 1;
case 34:
return 2;
case 35:
return 1;
case 53:
return 1;
default:
return 4;
}
return 4;
}
vector<sketcherMinimizerAtom*>
sketcherMinimizerAtom::clockwiseOrderedNeighbors() const
{
vector<pair<float, sketcherMinimizerAtom*>> rankedNeighbors;
rankedNeighbors.reserve(neighbors.size());
for (auto&& neighbor : neighbors) {
float newAngle = sketcherMinimizerMaths::signedAngle(
neighbors[0]->coordinates, coordinates, neighbor->coordinates);
if (std::isnan(newAngle)) {
newAngle = 361;
} else if (newAngle < 0) {
newAngle += 360;
}
rankedNeighbors.emplace_back(newAngle, neighbor);
}
std::sort(rankedNeighbors.begin(), rankedNeighbors.end());
vector<sketcherMinimizerAtom*> orderedNeighs;
orderedNeighs.reserve(neighbors.size());
for (const auto& rankedNeighbor : rankedNeighbors) {
orderedNeighs.push_back(rankedNeighbor.second);
}
return orderedNeighs;
}
void sketcherMinimizerAtom::writeStereoChemistry() // sets stereochemistry for
// this atom and from
// hasStereochemistrySet and
// isR
{
assert(neighbors.size() == bonds.size());
if (!hasStereochemistrySet) {
return;
}
if (!canBeChiral()) {
hasStereochemistrySet = false;
return;
} else {
sketcherMinimizerAtom dummyH;
dummyH.atomicNumber = 1;
dummyH.molecule = molecule;
sketcherMinimizerAtom dummyLP;
dummyLP.atomicNumber = 0;
dummyLP.molecule = molecule;
sketcherMinimizerAtom* dummy = &dummyH;
vector<sketcherMinimizerAtom*> neighs = neighbors;
vector<sketcherMinimizerAtom*> orderedNeighs;
vector<sketcherMinimizerBond*> bbonds = bonds;
vector<sketcherMinimizerBond*> orderedBonds;
vector<float> angles;
int lastPoppedIndex = 0;
sketcherMinimizerAtom* lastPoppedAtom = neighs[lastPoppedIndex];
orderedNeighs.push_back(lastPoppedAtom);
neighs.erase(neighs.begin() + lastPoppedIndex);
orderedBonds.push_back(bbonds[lastPoppedIndex]);
bbonds.erase(bbonds.begin() + lastPoppedIndex);
// TODO: consider using sketcherMinimizerAtom::clockwiseOrderedNeighbors
while (!neighs.empty()) { // order atoms
float smallestAngle = 361;
for (unsigned int i = 0; i < neighs.size(); i++) {
float newAngle = sketcherMinimizerMaths::signedAngle(
sketcherMinimizerPointF(lastPoppedAtom->coordinates.x(),
lastPoppedAtom->coordinates.y()),
sketcherMinimizerPointF(coordinates.x(), coordinates.y()),
sketcherMinimizerPointF(neighs[i]->coordinates.x(),
neighs[i]->coordinates.y()));
if (newAngle < 0) {
newAngle += 360;
}
if (newAngle < smallestAngle) {
smallestAngle = newAngle;
lastPoppedIndex = i;
}
}
angles.push_back(smallestAngle);
lastPoppedAtom = neighs[lastPoppedIndex];
orderedNeighs.push_back(lastPoppedAtom);
neighs.erase(neighs.begin() + lastPoppedIndex);
orderedBonds.push_back(bbonds[lastPoppedIndex]);
bbonds.erase(bbonds.begin() + lastPoppedIndex);
}
if ((atomicNumber == 7 || atomicNumber == 16) && _implicitHs == 0 &&
orderedBonds.size() == 3) {
dummy = &dummyLP;
}
bool four = true;
float totalAngle = std::accumulate(angles.begin(), angles.end(), 0.f);
angles.push_back(360.f - totalAngle);
vector<sketcherMinimizerAtomPriority> atomPriorities,
orderedAtomPriorities;
for (auto& orderedNeigh : orderedNeighs) {
sketcherMinimizerAtomPriority p;
p.a = orderedNeigh;
atomPriorities.push_back(p);
}
if (atomPriorities.size() == 3) {
four = false;
sketcherMinimizerAtomPriority p;
p.a = dummy;
atomPriorities.push_back(p);
}
bool isStereocenter = setCIPPriorities(atomPriorities, this);
if (!isStereocenter) {
if (!m_ignoreRingChirality) {
_hasRingChirality = true;
isStereocenter = setCIPPriorities(atomPriorities, this);
}
}
if (!isStereocenter) {
_hasRingChirality = false;
}
orderedAtomPriorities = atomPriorities;
orderAtomPriorities(orderedAtomPriorities, this);
if (isStereocenter) {
if (!four) {
if (orderedAtomPriorities[0].a == dummy) {
orderedAtomPriorities.push_back(orderedAtomPriorities[0]);
orderedAtomPriorities.insert(orderedAtomPriorities.begin(),
orderedAtomPriorities[3]);
orderedAtomPriorities.erase(orderedAtomPriorities.begin() +
1);
orderedAtomPriorities.erase(orderedAtomPriorities.begin() +
3);
}
}
unsigned int startIndex = 0;
for (unsigned int i = 0; i < atomPriorities.size(); i++) {
if (atomPriorities[i].a == orderedAtomPriorities[0].a) {
startIndex = i;
break;
}
}
for (unsigned int i = 0; i < startIndex; i++) {
atomPriorities.push_back(atomPriorities[0]);
atomPriorities.erase(atomPriorities.begin());
}
if (four) {
if (atomPriorities[1].a == orderedAtomPriorities[3].a) {
atomPriorities.push_back(atomPriorities[0]);
atomPriorities.erase(atomPriorities.begin());
}
}
sketcherMinimizerAtom* mainAtom = nullptr;
if (four) {
if (atomPriorities[0].a == orderedAtomPriorities[0].a) {
mainAtom = atomPriorities[0].a;
}
if (atomPriorities[3].a == orderedAtomPriorities[0].a) {
mainAtom = atomPriorities[3].a;
}
}
bool invert = false;
sketcherMinimizerBond* b1 = bondTo(atomPriorities[0].a);
if (b1) {
if (!four || mainAtom == atomPriorities[0].a ||
(!sketcherMinimizer::sameRing(this, atomPriorities[0].a) &&
!atomPriorities[0].a->hasStereochemistrySet)) {
bool reverse = false;
if (b1->startAtom != this) {
reverse = true;
}
b1->isWedge = !invert;
b1->hasStereochemistryDisplay = true;
b1->isReversed = reverse;
} else {
b1->hasStereochemistryDisplay = false;
}
}
if (four) {
sketcherMinimizerBond* b2 = bondTo(atomPriorities[3].a);
if (b2) {
if (mainAtom == atomPriorities[3].a ||
(!sketcherMinimizer::sameRing(this,
atomPriorities[3].a) &&
!atomPriorities[3].a->hasStereochemistrySet)) {
bool reverse = false;
if (b2->startAtom != this) {
reverse = true;
}
b2->isWedge = invert;
b2->hasStereochemistryDisplay = true;
b2->isReversed = reverse;
} else {
b2->hasStereochemistryDisplay = false;
}
}
}
sketcherMinimizerBond* b3 = bondTo(atomPriorities[1].a);
if (b3) {
b3->hasStereochemistryDisplay = false;
}
sketcherMinimizerBond* b4 = bondTo(atomPriorities[2].a);
if (b4) {
b4->hasStereochemistryDisplay = false;
}
int readS = readStereochemistry(true);
readS = -readS; // inverting stereochemistry cause isR is in
// sketcher coords and readStereo in coordgen coords
// (flipped y)
if ((readS == -1 && isR) || (readS == 1 && !isR)) { // inverting
invert = true;
if (b1) {
if (!four || mainAtom == atomPriorities[0].a ||
(!sketcherMinimizer::sameRing(this,
atomPriorities[0].a) &&
!atomPriorities[0].a->hasStereochemistrySet)) {
// cerr << "and setting it "<<endl;
bool reverse = false;
if (b1->startAtom != this) {
reverse = true;
}
b1->isWedge = !invert;
b1->hasStereochemistryDisplay = true;
b1->isReversed = reverse;
} else {
b1->hasStereochemistryDisplay = false;
}
}
if (four) {
sketcherMinimizerBond* b2 = bondTo(atomPriorities[3].a);
if (b2) {
if (mainAtom == atomPriorities[3].a ||
(!sketcherMinimizer::sameRing(
this, atomPriorities[3].a) &&
!atomPriorities[3].a->hasStereochemistrySet)) {
bool reverse = false;
if (b2->startAtom != this) {
reverse = true;
}
b2->isWedge = invert;
b2->hasStereochemistryDisplay = true;
b2->isReversed = reverse;
} else {
b2->hasStereochemistryDisplay = false;
}
}
}
}
}
else {
for (auto b : bonds) {
b->hasStereochemistryDisplay = false;
}
}
}
}
sketcherMinimizerAtomChiralityInfo::sketcherMinimizerChirality
sketcherMinimizerAtom::getRelativeStereo(sketcherMinimizerAtom* lookingFrom,
sketcherMinimizerAtom* atom1,
sketcherMinimizerAtom* atom2)
{
readStereochemistry(); // to set m_RSPriorities
auto RSpriorities = m_RSPriorities;
if (RSpriorities.size() < 3) {
return sketcherMinimizerAtomChiralityInfo::unspecified;
}
vector<int> priorities(4, 3);
/* order the CIP priority of the atoms in the following order
atom1 - atom2 - atom3 - atomLookingFrom
*/
for (unsigned int nn = 0; nn < neighbors.size(); nn++) {
sketcherMinimizerAtom* n = neighbors[nn];
if (n == atom1) {
priorities[0] = RSpriorities[nn];
} else if (n == atom2) {
priorities[1] = RSpriorities[nn];
} else if (n == lookingFrom) {
priorities[3] = RSpriorities[nn];
} else {
priorities[2] = RSpriorities[nn];
}
}
vector<int> can(4);
for (unsigned int i = 0; i < 4; i++) {
can[i] = i;
}
/*
this represents a molecule with
atom1 (priority 0 - highest)
atom2 (priority 1)
atom3 (priority 2)
atomLookingFrom (priority 3 -lowest)
which is the opposite of the CIP rules, where the the lowest priority atom
is AWAY from the observer. This is the reason why we return CCW for R and
CW for S.
*/
bool match = sketcherMinimizerAtom::matchCIPSequence(priorities, can);
bool isClockWise = (match ? !isR : isR);
if (isClockWise) {
return sketcherMinimizerAtomChiralityInfo::clockwise;
}
return sketcherMinimizerAtomChiralityInfo::counterClockwise;
}
bool sketcherMinimizerAtom::setAbsoluteStereoFromChiralityInfo()
{
auto info = m_chiralityInfo;
if (info.direction == sketcherMinimizerAtomChiralityInfo::unspecified) {
return true;
}
readStereochemistry(); // to set m_RSPriorities
auto RSpriorities = m_RSPriorities;
if (RSpriorities.size() < 3) {
cerr << "CHMMol-> sketcher stereo error: wrong number for RSpriorities"
<< endl;
return false;
}
vector<int> priorities(4, 5);
bool at3 = false;
for (unsigned int nn = 0; nn < neighbors.size(); nn++) {
sketcherMinimizerAtom* n = neighbors[nn];
if (n == info.atom1) {
priorities[0] = RSpriorities[nn];
} else if (n == info.atom2) {
priorities[1] = RSpriorities[nn];
} else if (n == info.lookingFrom) {
priorities[3] = RSpriorities[nn];
} else {
if (at3) {
cerr << "CHMMol-> sketcher stereo error: more than 1 atom not "
"matching"
<< endl;
return false;
} else {
at3 = true;
priorities[2] = RSpriorities[nn];
}
}
}
int addingHN = 0;
if (priorities[0] == 5) {
priorities[0] = 3;
addingHN++;
}
if (priorities[1] == 5) {
priorities[1] = 3;
addingHN++;
}
if (priorities[2] == 5) {
priorities[2] = 3;
addingHN++;
}
if (priorities[3] == 5) {
priorities[3] = 3;
addingHN++;
}
if (addingHN > 1) {
cerr << "CHMMol-> sketcher stereo error: more than 1 H on chiral center"
<< endl;
return false;
}
bool invert = false;
vector<int> can(4);
for (unsigned int i = 0; i < 4; i++) {
can[i] = i;
}
if (!sketcherMinimizerAtom::matchCIPSequence(priorities, can)) {
invert = !invert;
}
bool isRBool = true;
if (info.direction == sketcherMinimizerAtomChiralityInfo::clockwise) {
isRBool = false;
}
if (invert) {
isRBool = !isRBool;
}
isR = isRBool;
hasStereochemistrySet = true;
return true;
}
bool sketcherMinimizerAtom::matchCIPSequence(vector<int>& v1, vector<int>& v2)
{
if (v1.size() < v2.size()) {
v1.push_back(3);
} else if (v2.size() < v1.size()) {
v2.push_back(3);
}
int outofPlaceNs = 0;
for (unsigned int i = 0; i < v1.size(); i++) {
if (v1[i] != v2[i]) {
outofPlaceNs++;
}
}
if (outofPlaceNs == 2) {
return false;
} else if (outofPlaceNs == 4) {
int n1 = v1[0];
int index2 = 0;
for (unsigned int j = 0; j < v2.size(); j++) {
if (v2[j] == n1) {
index2 = j;
break;
}
}
if (v1[index2] != v2[0]) {
return false;
}
}
return true;
}
void sketcherMinimizerAtom::setCoordinates(sketcherMinimizerPointF coords)
{
coordinates = std::move(coords);
coordinates.round();
coordinatesSet = true;
}
bool sketcherMinimizerAtom::hasNoStereoActiveBonds() const
{
for (auto bond : bonds) {
if (bond->isStereo()) {
return false;
}
}
return true;
}
void sketcherMinimizerAtom::orderAtomPriorities(
vector<sketcherMinimizerAtomPriority>& atomPriorities,
sketcherMinimizerAtom* center) // orders trying to keep long chains in
// position 2 and 3 and side substituents in
// 1 and 4
{
assert(atomPriorities.size() == 4);
vector<float> weights(4);
for (unsigned int i = 0; i < 4; i++) {
queue<sketcherMinimizerAtom*> q;
for (auto& _atom : center->molecule->_atoms) {
_atom->_generalUseVisited = false;
}
q.push(atomPriorities[i].a);
center->_generalUseVisited = true;
atomPriorities[i].a->_generalUseVisited = true;
int counter = 0;
while (!q.empty()) {
counter++;
sketcherMinimizerAtom* at = q.front();
q.pop();
for (auto n : at->neighbors) {
if (!n->_generalUseVisited) {
q.push(n);
n->_generalUseVisited = true;
}
}
}
weights[i] = static_cast<float>(counter);
sketcherMinimizerBond* b = center->bondTo(atomPriorities[i].a);
if (b) {
if (b->bondOrder == 2) {
weights[i] -=
0.25; // so that =O get lower priority than -OH in phosphate
}
if (center->atomicNumber == 16 && b->bondOrder == 2) {
weights[i] += 2000; // forcing the wedge away from double bond
}
// in sulphoxide
if (sketcherMinimizer::sameRing(b->startAtom, b->endAtom)) {
weights[i] +=
500; // force same ring atoms to be in position 3 and 4
}
}
if (atomPriorities[i].a->atomicNumber == 6) {
weights[i] += 0.5; // carbons get priority over other heavy atoms
}
if (atomPriorities[i].a->atomicNumber == 1) {
weights[i] -= 0.5;
}
if (atomPriorities[i].a->isSharedAndInner &&
!center->isSharedAndInner) {
weights[i] -= 2000; // forced bond to shared and inner
}
if (center->crossLayout) {
if (atomPriorities[i].a->neighbors.size() > 1) {
weights[i] += 200;
}
}
if (/* atomPriorities[i].a->isStereogenic && */ atomPriorities[i]
.a->hasStereochemistrySet) {
weights[i] += 10000; // to avoid problems with wedges when 2
}
// stereocenters are near
for (unsigned int j = 0; j < atomPriorities[i].a->bonds.size(); j++) {
if (atomPriorities[i].a->bonds[j]->bondOrder == 2) {
weights[i] += 100;
break;
}
}
}
float lowestWeight = weights[0];
int index = 0;
sketcherMinimizerAtomPriority firstAtom = atomPriorities[0];
for (unsigned int i = 1; i < 4; i++) {
if (weights[i] < lowestWeight) {
lowestWeight = weights[i];
index = i;
}
}
firstAtom = atomPriorities[index];
atomPriorities.erase(atomPriorities.begin() + index);
weights.erase(weights.begin() + index);
index = 0;
lowestWeight = weights[0];
sketcherMinimizerAtomPriority secondAtom = atomPriorities[0];
for (unsigned int i = 1; i < 3; i++) {
if (weights[i] < lowestWeight) {
lowestWeight = weights[i];
index = i;
}
}
secondAtom = atomPriorities[index];
atomPriorities.erase(atomPriorities.begin() + index);
if ((center->atomicNumber != 16 && center->atomicNumber != 15) ||
center->neighbors.size() != 4) {
atomPriorities.push_back(secondAtom);
atomPriorities.insert(atomPriorities.begin(), firstAtom);
} else {
atomPriorities.insert(atomPriorities.begin() + 1, secondAtom);
atomPriorities.insert(atomPriorities.begin(), firstAtom);
}
}
bool sketcherMinimizerAtom::setCIPPriorities(
vector<sketcherMinimizerAtomPriority>& atomPriorities,
sketcherMinimizerAtom* center)
{
for (auto& atomPrioritie : atomPriorities) {
atomPrioritie.priority = 3;
}
if (atomPriorities.size() != 4) {
// cerr << "coordgen: stereo error. (wrong number of atom priorities:
// "<< atomPriorities.size () << ")"<<endl; // commented for
// Ev:134037
return false;
}
for (unsigned int i = 0; i < atomPriorities.size() - 1; i++) {
for (unsigned int j = i + 1; j < atomPriorities.size(); j++) {
sketcherMinimizerAtom* res =
CIPPriority(atomPriorities[i].a, atomPriorities[j].a, center);
if (res == atomPriorities[i].a) {
atomPriorities[i].priority--;
} else if (res == atomPriorities[j].a) {
atomPriorities[j].priority--;
}
}
}
vector<bool> found(4, false);
for (auto& atomPrioritie : atomPriorities) {
if (found[atomPrioritie.priority]) {
return false; // two atoms have the same priority
}
found[atomPrioritie.priority] = true;
}
return true;
}
sketcherMinimizerAtom*
sketcherMinimizerAtom::CIPPriority(sketcherMinimizerAtom* at1,
sketcherMinimizerAtom* at2,
sketcherMinimizerAtom* center)
{
assert(center->molecule);
assert(at1->molecule == center->molecule);
assert(at2->molecule == center->molecule);
assert(!center->molecule->_atoms.empty());
assert(at1);
assert(at2);
if (at1->atomicNumber > at2->atomicNumber) {
return at1;
} else if (at2->atomicNumber > at1->atomicNumber) {
return at2;
}
if (center->_hasRingChirality && !center->m_ignoreRingChirality) {
if (sketcherMinimizer::sameRing(center, at1, at2)) {
if (at1->_generalUseN > at2->_generalUseN) {
return at1;
} else {
return at2;
}
}
}
vector<CIPAtom> AN1, AN2;
map<sketcherMinimizerAtom*, int> score1,
score2; // used to keep track if a parent atom has been found to have
// priority over another
map<sketcherMinimizerAtom*, vector<int>> medals1,
medals2; // marks if an atom is a parent of the atoms being evaluated in
// the current iteration
map<sketcherMinimizerAtom*, int> visited1,
visited2; // marks at which iteration this atom was evaluated
visited1[center] = 1;
visited2[center] = 1;
visited1[at1] = 2;
visited2[at2] = 2;
vector<pair<int, sketcherMinimizerAtom*>> v1, v2;
v1.emplace_back(at1->atomicNumber, at1);