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//
// Copyright (C) 2020 Guillaume GODIN
// @@ 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.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// Adding ATOM FEATURES descriptors by Guillaume Godin
#include <GraphMol/RDKitBase.h>
#include <iostream>
#include "AtomFeat.h"
#include <GraphMol/PartialCharges/GasteigerCharges.h>
#include <GraphMol/PartialCharges/GasteigerParams.h>
#include <GraphMol/Atom.h>
#include <GraphMol/MolOps.h>
#include <cmath>
#include <vector>
namespace RDKit {
namespace Descriptors {
namespace {
std::vector<Atom::ChiralType> RS{Atom::CHI_TETRAHEDRAL_CW,
Atom::CHI_TETRAHEDRAL_CCW, Atom::CHI_OTHER};
std::vector<std::string> Symbols{"B", "C", "N", "O", "S", "F", "Si",
"P", "Cl", "Br", "I", "H", "*"};
std::vector<Atom::HybridizationType> HS{Atom::SP, Atom::SP2, Atom::SP3,
Atom::SP3D, Atom::SP3D2};
void AtomFeatVector(const RDKit::Atom *atom, const ROMol *mol,
std::vector<double> &feats, bool addchiral) {
PRECONDITION(atom, "bad atom");
PRECONDITION(mol, "bad mol");
if (addchiral) {
feats.reserve(52);
} else {
feats.reserve(49);
}
// initiate ring info if not already done
if (!mol->getRingInfo()->isSssrOrBetter()) {
RDKit::MolOps::findSSSR(*mol);
}
// one hot atom symbols
std::string s = atom->getSymbol();
bool inlist = false;
int indx = 0;
for (auto ind : Symbols) {
if (ind == s) {
feats[indx] = 1;
inlist = true;
} else {
feats[indx] = 0;
}
++indx;
}
// write UNK type if not found in the symbol list
feats[indx] = (inlist ? 0 : 1);
++indx;
// one hot degree
int d = atom->getDegree();
for (int i = 0; i < 7; i++) {
feats[indx] = d == i;
++indx;
}
Atom::HybridizationType hs = atom->getHybridization();
// one hot hybridization type
for (auto hsquery : HS) {
feats[indx] = hs == hsquery;
++indx;
}
// one hot Implicit Valence
int IV = atom->getValence(Atom::ValenceType::IMPLICIT);
for (int i = 0; i < 7; ++i) {
feats[indx] = IV == i;
++indx;
}
// one hot getFormalCharge
int fc = atom->getFormalCharge();
for (int i = -1; i < 2; i++) {
feats[indx] = fc == i;
++indx;
}
// one hot ring size
int atomid = atom->getIdx();
for (unsigned int i = 3; i < 9; i++) {
feats[indx] = mol->getRingInfo()->isAtomInRingOfSize(atomid, i);
++indx;
}
// Is aromatic
feats[indx] = (atom->getIsAromatic());
++indx;
// one hot Total NumH
unsigned int toth = atom->getTotalNumHs(false);
for (unsigned int i = 0; i < 5; ++i) {
feats[indx] = toth == i;
++indx;
}
// add numatoms
feats[indx] = 1. / mol->getNumAtoms();
++indx;
// put if here
if (addchiral) {
Atom::ChiralType rs = atom->getChiralTag();
// one hot getChiralTag type
for (auto rsquery : RS) {
feats[indx] = rs == rsquery;
++indx;
}
}
}
} // end of anonymous namespace
// entry point
void AtomFeatVect(const ROMol &mol, std::vector<double> &res, int atomid,
bool addchiral) {
res.clear();
if (addchiral) {
res.resize(52);
} else {
res.resize(49);
}
AtomFeatVector(mol.getAtomWithIdx(atomid), &mol, res, addchiral);
}
} // namespace Descriptors
} // namespace RDKit
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