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//
// Copyright (C) 2024 Greg Landrum and other RDKit contributors
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <GraphMol/RDKitBase.h>
#include <map>
#include <string>
#include <strstream>
namespace RDKit {
namespace MolOps {
double getAvgMolWt(const ROMol &mol, bool onlyHeavy) {
double res = 0.0;
const PeriodicTable *table = PeriodicTable::getTable();
for (const auto &atom : mol.atoms()) {
if (!onlyHeavy || atom->getAtomicNum() != 1) {
res += atom->getMass();
}
// add our implicit Hs if we need to:
if (!onlyHeavy) {
res += atom->getTotalNumHs() * table->getAtomicWeight(1);
}
}
return res;
}
double getExactMolWt(const ROMol &mol, bool onlyHeavy) {
double res = 0.0;
int nHsToCount = 0;
const PeriodicTable *table = PeriodicTable::getTable();
for (auto atom : mol.atoms()) {
auto atNum = atom->getAtomicNum();
if (atNum != 1 || !onlyHeavy) {
if (!atom->getIsotope()) {
res += table->getMostCommonIsotopeMass(atNum);
} else {
res += atom->getMass();
}
res -= constants::electronMass * atom->getFormalCharge();
}
// add our implicit Hs if we need to:
if (!onlyHeavy) {
nHsToCount += atom->getTotalNumHs(false);
}
}
if (!onlyHeavy) {
res += nHsToCount * table->getMostCommonIsotopeMass(1);
}
return res;
}
namespace {
bool HillCompare(const std::pair<unsigned int, std::string> &v1,
const std::pair<unsigned int, std::string> &v2) {
bool nCompare = (v1.first < v2.first);
// special cases: Cs, Hs, Ds, and Ts go at the beginning
if (v1.second == "C") {
if (v2.second != "C") {
return true;
}
return nCompare;
} else if (v2.second == "C") {
return false;
}
if (v1.second == "H") {
if (v2.second != "H") {
return true;
}
return nCompare;
} else if (v2.second == "H") {
return false;
}
if (v1.second == "D") {
return true;
} else if (v2.second == "D") {
return false;
}
if (v1.second == "T") {
return true;
} else if (v2.second == "T") {
return false;
}
// finally, just compare the symbols and the isotopes:
if (v1 != v2) {
return v1 < v2;
} else {
return nCompare;
}
}
} // namespace
std::string getMolFormula(const ROMol &mol, bool separateIsotopes,
bool abbreviateHIsotopes) {
std::ostringstream res;
std::map<std::pair<unsigned int, std::string>, unsigned int> counts;
int charge = 0;
unsigned int nHs = 0;
const PeriodicTable *table = PeriodicTable::getTable();
for (const auto atom : mol.atoms()) {
int atNum = atom->getAtomicNum();
std::pair<unsigned int, std::string> key =
std::make_pair(0, table->getElementSymbol(atNum));
if (separateIsotopes) {
unsigned int isotope = atom->getIsotope();
if (abbreviateHIsotopes && atNum == 1 && (isotope == 2 || isotope == 3)) {
if (isotope == 2) {
key.second = "D";
} else {
key.second = "T";
}
} else {
key.first = isotope;
}
}
counts[key] += 1;
nHs += atom->getTotalNumHs();
charge += atom->getFormalCharge();
}
if (nHs) {
counts[{0, "H"}] += nHs;
}
std::list<std::pair<unsigned int, std::string>> ks;
for (const auto &pr : counts) {
ks.push_back(pr.first);
}
ks.sort(HillCompare);
for (const auto &key : ks) {
if (key.first > 0) {
res << "[" << key.first << key.second << "]";
} else {
res << key.second;
}
if (counts[key] > 1) {
res << counts[key];
}
}
if (charge > 0) {
res << "+";
if (charge > 1) {
res << charge;
}
} else if (charge < 0) {
res << "-";
if (charge < -1) {
res << -1 * charge;
}
}
return res.str();
}
} // namespace MolOps
} // namespace RDKit
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