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// $Id$
//
// Copyright (C) 2013 Greg Landrum
//
// @@ 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 <GraphMol/Descriptors/MolDescriptors.h>
#include <GraphMol/Descriptors/Lipinski.h>
#include <boost/foreach.hpp>
#include <vector>
#include <algorithm>
namespace RDKit{
namespace Descriptors {
std::vector<unsigned int> calcMQNs(const ROMol &mol,
bool force){
// FIX: use force value to enable caching
std::vector<unsigned int> res(42,0);
// ---------------------------------------------------
// atom-centered things
// Note: We're not doing exactly the same thing
// as the original paper on polarity counts
// since we're using different donor and acceptor
// definitions.
ROMol::VERTEX_ITER atBegin,atEnd;
boost::tie(atBegin,atEnd) = mol.getVertices();
while(atBegin!=atEnd){
const ATOM_SPTR at=mol[*atBegin];
++atBegin;
unsigned int nHs = at->getTotalNumHs();
unsigned int nRings=mol.getRingInfo()->numAtomRings(at->getIdx());
switch(at->getAtomicNum()){
case 0:
case 1:
break;
case 6:
res[0]++;break;
case 9:
res[1]++;break;
case 17:
res[2]++;break;
case 35:
res[3]++;break;
case 53:
res[4]++;break;
case 16:
res[5]++;break;
case 15:
res[6]++;break;
case 7:
if(!nRings) res[7]++;
else res[8]++;
if(at->getDegree()!=4){
res[19]++; // number of acceptor sites
res[20]++; // number of acceptor atoms
}
if(nHs){
res[21]+=nHs; // number of donor sites
res[22]++; // number of donor atoms
}
break;
case 8:
if(!nRings) res[9]++;
else res[10]++;
res[20]++; // number of acceptor atoms
if(at->getFormalCharge()!=-1){
res[19]+=2; // number of acceptor sites
} else {
res[19]+=3; // number of acceptor sites
}
if(nHs){
res[21]+=nHs; // number of donor sites
res[22]++; // number of donor atoms
}
break;
default:
res[11]++;break;
}
if(at->getFormalCharge()>0) res[24]++; // positive charges
else if(at->getFormalCharge()<0) res[23]++; // negative charges
if(at->getAtomicNum()!=1){
switch(at->getDegree()){
case 1:
res[25]++;
break;
case 2:
if(!nRings) res[26]++;
else res[29]++;
break;
case 3:
if(!nRings) res[27]++;
else res[30]++;
break;
case 4:
if(!nRings) res[28]++;
else res[31]++;
break;
}
if(nRings>=2) res[40]++;
}
}
// ---------------------------------------------------
// bond counts:
unsigned int nAromatic=0;
ROMol::EDGE_ITER firstB,lastB;
boost::tie(firstB,lastB) = mol.getEdges();
while(firstB!=lastB){
const BOND_SPTR bond = mol[*firstB];
if(bond->getIsAromatic()) ++nAromatic;
unsigned int nRings=mol.getRingInfo()->numBondRings(bond->getIdx());
switch(bond->getBondType()){
case Bond::SINGLE:
if(!nRings) res[12]++;
else res[15]++;
break;
case Bond::DOUBLE:
if(!nRings) res[13]++;
else res[16]++;
break;
case Bond::TRIPLE:
if(!nRings) res[14]++;
else res[17]++;
break;
default:
break;
}
if(nRings>=2) res[41]++;
++firstB;
}
// rather than do the work to kekulize the molecule, we cheat
// by just dividing the number of aromatic bonds evenly among the
// cyclic single bond and cyclic double bond bins and give any
// remainder to the single bonds
res[15] += nAromatic/2;
res[16] += nAromatic/2;
if(nAromatic%2) res[15]++;
res[18] = calcNumRotatableBonds(mol);
// ---------------------------------------------------
// ring size counts
BOOST_FOREACH(const INT_VECT &iv,mol.getRingInfo()->atomRings()){
if(iv.size()<10){
res[iv.size()+29]++;
} else {
res[39]++;
}
}
return res;
}
} // end of namespace Descriptors
} // end of namespace RDKit
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