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6745264a82
* atoms: radical electrons and presence of a chiral tag * bonds: presence of stereo * add new atom queries to python wrapper * add queries for missing atom chiral tags
504 lines
14 KiB
C++
504 lines
14 KiB
C++
// $Id$
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//
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// Copyright (C) 2003-2008 Greg Landrum and Rational Discovery LLC
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include "QueryOps.h"
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#include <algorithm>
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#include <RDGeneral/types.h>
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namespace RDKit {
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// common general queries
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//! returns a Query for matching atoms with a particular number of ring bonds
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ATOM_EQUALS_QUERY *makeAtomRingBondCountQuery(int what) {
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ATOM_EQUALS_QUERY *res = new AtomRingQuery(what);
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res->setDescription("AtomRingBondCount");
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res->setDataFunc(queryAtomRingBondCount);
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return res;
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};
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ATOM_EQUALS_QUERY *makeAtomInRingOfSizeQuery(int tgt) {
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RANGE_CHECK(3, tgt, 20);
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ATOM_EQUALS_QUERY *res = new ATOM_EQUALS_QUERY;
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res->setVal(tgt);
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switch (tgt) {
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case 3:
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res->setDataFunc(queryAtomIsInRingOfSize<3>);
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break;
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case 4:
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res->setDataFunc(queryAtomIsInRingOfSize<4>);
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break;
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case 5:
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res->setDataFunc(queryAtomIsInRingOfSize<5>);
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break;
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case 6:
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res->setDataFunc(queryAtomIsInRingOfSize<6>);
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break;
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case 7:
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res->setDataFunc(queryAtomIsInRingOfSize<7>);
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break;
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case 8:
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res->setDataFunc(queryAtomIsInRingOfSize<8>);
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break;
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case 9:
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res->setDataFunc(queryAtomIsInRingOfSize<9>);
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break;
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case 10:
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res->setDataFunc(queryAtomIsInRingOfSize<10>);
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break;
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case 11:
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res->setDataFunc(queryAtomIsInRingOfSize<11>);
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break;
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case 12:
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res->setDataFunc(queryAtomIsInRingOfSize<12>);
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break;
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case 13:
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res->setDataFunc(queryAtomIsInRingOfSize<13>);
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break;
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case 14:
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res->setDataFunc(queryAtomIsInRingOfSize<14>);
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break;
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case 15:
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res->setDataFunc(queryAtomIsInRingOfSize<15>);
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break;
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case 16:
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res->setDataFunc(queryAtomIsInRingOfSize<16>);
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break;
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case 17:
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res->setDataFunc(queryAtomIsInRingOfSize<17>);
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break;
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case 18:
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res->setDataFunc(queryAtomIsInRingOfSize<18>);
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break;
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case 19:
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res->setDataFunc(queryAtomIsInRingOfSize<19>);
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break;
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case 20:
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res->setDataFunc(queryAtomIsInRingOfSize<20>);
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break;
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}
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res->setDescription("AtomRingSize");
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return res;
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}
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BOND_EQUALS_QUERY *makeBondInRingOfSizeQuery(int tgt) {
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RANGE_CHECK(3, tgt, 20);
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BOND_EQUALS_QUERY *res = new BOND_EQUALS_QUERY;
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res->setVal(tgt);
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switch (tgt) {
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case 3:
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res->setDataFunc(queryBondIsInRingOfSize<3>);
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break;
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case 4:
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res->setDataFunc(queryBondIsInRingOfSize<4>);
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break;
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case 5:
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res->setDataFunc(queryBondIsInRingOfSize<5>);
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break;
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case 6:
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res->setDataFunc(queryBondIsInRingOfSize<6>);
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break;
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case 7:
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res->setDataFunc(queryBondIsInRingOfSize<7>);
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break;
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case 8:
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res->setDataFunc(queryBondIsInRingOfSize<8>);
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break;
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case 9:
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res->setDataFunc(queryBondIsInRingOfSize<9>);
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break;
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case 10:
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res->setDataFunc(queryBondIsInRingOfSize<10>);
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break;
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case 11:
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res->setDataFunc(queryBondIsInRingOfSize<11>);
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break;
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case 12:
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res->setDataFunc(queryBondIsInRingOfSize<12>);
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break;
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case 13:
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res->setDataFunc(queryBondIsInRingOfSize<13>);
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break;
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case 14:
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res->setDataFunc(queryBondIsInRingOfSize<14>);
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break;
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case 15:
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res->setDataFunc(queryBondIsInRingOfSize<15>);
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break;
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case 16:
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res->setDataFunc(queryBondIsInRingOfSize<16>);
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break;
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case 17:
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res->setDataFunc(queryBondIsInRingOfSize<17>);
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break;
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case 18:
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res->setDataFunc(queryBondIsInRingOfSize<18>);
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break;
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case 19:
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res->setDataFunc(queryBondIsInRingOfSize<19>);
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break;
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case 20:
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res->setDataFunc(queryBondIsInRingOfSize<20>);
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break;
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}
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res->setDescription("BondRingSize");
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return res;
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}
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ATOM_EQUALS_QUERY *makeAtomMinRingSizeQuery(int tgt) {
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RANGE_CHECK(3, tgt, 20);
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ATOM_EQUALS_QUERY *res = new ATOM_EQUALS_QUERY;
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res->setVal(tgt);
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res->setDataFunc(queryAtomMinRingSize);
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res->setDescription("AtomMinRingSize");
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return res;
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}
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BOND_EQUALS_QUERY *makeBondMinRingSizeQuery(int tgt) {
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RANGE_CHECK(3, tgt, 20);
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BOND_EQUALS_QUERY *res = new BOND_EQUALS_QUERY;
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res->setVal(tgt);
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res->setDataFunc(queryBondMinRingSize);
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res->setDescription("BondMinRingSize");
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return res;
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}
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unsigned int queryAtomBondProduct(Atom const *at) {
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ROMol::OEDGE_ITER beg, end;
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boost::tie(beg, end) = at->getOwningMol().getAtomBonds(at);
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unsigned int prod = 1;
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while (beg != end) {
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prod *= static_cast<unsigned int>(
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firstThousandPrimes[at->getOwningMol()[*beg]->getBondType()]);
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++beg;
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}
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return prod;
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}
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unsigned int queryAtomAllBondProduct(Atom const *at) {
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ROMol::OEDGE_ITER beg, end;
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boost::tie(beg, end) = at->getOwningMol().getAtomBonds(at);
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unsigned int prod = 1;
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while (beg != end) {
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prod *= static_cast<unsigned int>(
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firstThousandPrimes[at->getOwningMol()[*beg]->getBondType()]);
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++beg;
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}
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for (unsigned int i = 0; i < at->getTotalNumHs(); i++) {
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prod *= static_cast<unsigned int>(firstThousandPrimes[Bond::SINGLE]);
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}
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return prod;
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}
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ATOM_EQUALS_QUERY *makeAtomImplicitValenceQuery(int what) {
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ATOM_EQUALS_QUERY *res =
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makeAtomSimpleQuery<ATOM_EQUALS_QUERY>(what, queryAtomImplicitValence);
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res->setDescription("AtomImplicitValence");
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return res;
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}
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ATOM_EQUALS_QUERY *makeAtomExplicitValenceQuery(int what) {
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ATOM_EQUALS_QUERY *res =
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makeAtomSimpleQuery<ATOM_EQUALS_QUERY>(what, queryAtomExplicitValence);
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res->setDescription("AtomExplicitValence");
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return res;
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}
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ATOM_EQUALS_QUERY *makeAtomTotalValenceQuery(int what) {
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ATOM_EQUALS_QUERY *res =
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makeAtomSimpleQuery<ATOM_EQUALS_QUERY>(what, queryAtomTotalValence);
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res->setDescription("AtomTotalValence");
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return res;
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}
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ATOM_EQUALS_QUERY *makeAtomNumQuery(int what) {
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return makeAtomSimpleQuery<ATOM_EQUALS_QUERY>(what, queryAtomNum,
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"AtomAtomicNum");
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}
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ATOM_EQUALS_QUERY *makeAtomExplicitDegreeQuery(int what) {
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ATOM_EQUALS_QUERY *res =
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makeAtomSimpleQuery<ATOM_EQUALS_QUERY>(what, queryAtomExplicitDegree);
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res->setDescription("AtomExplicitDegree");
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return res;
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}
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ATOM_EQUALS_QUERY *makeAtomTotalDegreeQuery(int what) {
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ATOM_EQUALS_QUERY *res =
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makeAtomSimpleQuery<ATOM_EQUALS_QUERY>(what, queryAtomTotalDegree);
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res->setDescription("AtomTotalDegree");
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return res;
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}
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ATOM_EQUALS_QUERY *makeAtomHCountQuery(int what) {
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ATOM_EQUALS_QUERY *res =
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makeAtomSimpleQuery<ATOM_EQUALS_QUERY>(what, queryAtomHCount);
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res->setDescription("AtomHCount");
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return res;
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}
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ATOM_EQUALS_QUERY *makeAtomImplicitHCountQuery(int what) {
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ATOM_EQUALS_QUERY *res =
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makeAtomSimpleQuery<ATOM_EQUALS_QUERY>(what, queryAtomImplicitHCount);
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res->setDescription("AtomImplicitHCount");
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return res;
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}
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ATOM_EQUALS_QUERY *makeAtomHasImplicitHQuery() {
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ATOM_EQUALS_QUERY *res =
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makeAtomSimpleQuery<ATOM_EQUALS_QUERY>(true, queryAtomHasImplicitH);
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res->setDescription("AtomHasImplicitH");
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return res;
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}
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ATOM_EQUALS_QUERY *makeAtomAromaticQuery() {
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ATOM_EQUALS_QUERY *res =
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makeAtomSimpleQuery<ATOM_EQUALS_QUERY>(true, queryAtomAromatic);
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res->setDescription("AtomIsAromatic");
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return res;
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}
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ATOM_EQUALS_QUERY *makeAtomAliphaticQuery() {
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ATOM_EQUALS_QUERY *res =
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makeAtomSimpleQuery<ATOM_EQUALS_QUERY>(true, queryAtomAliphatic);
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res->setDescription("AtomIsAliphatic");
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return res;
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}
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ATOM_EQUALS_QUERY *makeAtomUnsaturatedQuery() {
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ATOM_EQUALS_QUERY *res =
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makeAtomSimpleQuery<ATOM_EQUALS_QUERY>(true, queryAtomUnsaturated);
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res->setDescription("AtomUnsaturated");
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return res;
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}
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ATOM_EQUALS_QUERY *makeAtomMassQuery(int what) {
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ATOM_EQUALS_QUERY *res = makeAtomSimpleQuery<ATOM_EQUALS_QUERY>(
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massIntegerConversionFactor * what, queryAtomMass);
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res->setDescription("AtomMass");
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return res;
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}
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ATOM_EQUALS_QUERY *makeAtomIsotopeQuery(int what) {
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ATOM_EQUALS_QUERY *res =
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makeAtomSimpleQuery<ATOM_EQUALS_QUERY>(what, queryAtomIsotope);
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res->setDescription("AtomIsotope");
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return res;
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}
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ATOM_EQUALS_QUERY *makeAtomFormalChargeQuery(int what) {
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ATOM_EQUALS_QUERY *res =
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makeAtomSimpleQuery<ATOM_EQUALS_QUERY>(what, queryAtomFormalCharge);
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res->setDescription("AtomFormalCharge");
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return res;
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}
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ATOM_EQUALS_QUERY *makeAtomHybridizationQuery(int what) {
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ATOM_EQUALS_QUERY *res =
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makeAtomSimpleQuery<ATOM_EQUALS_QUERY>(what, queryAtomHybridization);
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res->setDescription("AtomHybridization");
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return res;
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}
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ATOM_EQUALS_QUERY *makeAtomNumRadicalElectronsQuery(int what) {
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ATOM_EQUALS_QUERY *res = makeAtomSimpleQuery<ATOM_EQUALS_QUERY>(
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what, queryAtomNumRadicalElectrons);
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res->setDescription("AtomNumRadicalElectrons");
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return res;
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}
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ATOM_EQUALS_QUERY *makeAtomHasChiralTagQuery() {
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ATOM_EQUALS_QUERY *res =
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makeAtomSimpleQuery<ATOM_EQUALS_QUERY>(true, queryAtomHasChiralTag);
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res->setDescription("AtomHasChiralTag");
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return res;
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}
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ATOM_EQUALS_QUERY *makeAtomMissingChiralTagQuery() {
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ATOM_EQUALS_QUERY *res =
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makeAtomSimpleQuery<ATOM_EQUALS_QUERY>(true, queryAtomMissingChiralTag);
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res->setDescription("AtomMissingChiralTag");
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return res;
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}
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ATOM_EQUALS_QUERY *makeAtomInRingQuery() {
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ATOM_EQUALS_QUERY *res =
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makeAtomSimpleQuery<ATOM_EQUALS_QUERY>(true, queryIsAtomInRing);
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res->setDescription("AtomInRing");
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return res;
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}
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ATOM_EQUALS_QUERY *makeAtomHasRingBondQuery() {
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ATOM_EQUALS_QUERY *res =
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makeAtomSimpleQuery<ATOM_EQUALS_QUERY>(true, queryAtomHasRingBond);
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res->setDescription("AtomHasRingBond");
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return res;
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}
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ATOM_EQUALS_QUERY *makeAtomInNRingsQuery(int what) {
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ATOM_EQUALS_QUERY *res;
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res = makeAtomSimpleQuery<ATOM_EQUALS_QUERY>(what, queryIsAtomInNRings);
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res->setDescription("AtomInNRings");
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return res;
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}
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BOND_EQUALS_QUERY *makeBondOrderEqualsQuery(Bond::BondType what) {
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BOND_EQUALS_QUERY *res = new BOND_EQUALS_QUERY;
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res->setVal(what);
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res->setDataFunc(queryBondOrder);
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res->setDescription("BondOrder");
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return res;
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}
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BOND_EQUALS_QUERY *makeBondDirEqualsQuery(Bond::BondDir what) {
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BOND_EQUALS_QUERY *res = new BOND_EQUALS_QUERY;
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res->setVal(what);
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res->setDataFunc(queryBondDir);
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res->setDescription("BondDir");
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return res;
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}
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BOND_EQUALS_QUERY *makeBondHasStereoQuery() {
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BOND_EQUALS_QUERY *res = new BOND_EQUALS_QUERY;
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res->setVal(true);
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res->setDataFunc(queryBondHasStereo);
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res->setDescription("BondStereo");
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return res;
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}
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BOND_EQUALS_QUERY *makeBondIsInRingQuery() {
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BOND_EQUALS_QUERY *res = new BOND_EQUALS_QUERY;
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res->setVal(true);
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res->setDataFunc(queryIsBondInRing);
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res->setDescription("BondInRing");
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return res;
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}
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BOND_EQUALS_QUERY *makeBondInNRingsQuery(int what) {
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BOND_EQUALS_QUERY *res = new BOND_EQUALS_QUERY;
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res->setVal(what);
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res->setDataFunc(queryIsBondInNRings);
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res->setDescription("BondInNRings");
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return res;
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}
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BOND_NULL_QUERY *makeBondNullQuery() {
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BOND_NULL_QUERY *res = new BOND_NULL_QUERY;
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res->setDataFunc(nullDataFun);
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res->setMatchFunc(nullQueryFun);
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res->setDescription("BondNull");
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return res;
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}
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ATOM_NULL_QUERY *makeAtomNullQuery() {
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ATOM_NULL_QUERY *res = new ATOM_NULL_QUERY;
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res->setDataFunc(nullDataFun);
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res->setMatchFunc(nullQueryFun);
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res->setDescription("AtomNull");
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return res;
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}
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bool isComplexQuery(const Bond *b) {
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if (!b->hasQuery()) return false;
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// negated things are always complex:
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if (b->getQuery()->getNegation()) return true;
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std::string descr = b->getQuery()->getDescription();
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if (descr == "BondOrder") return false;
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if (descr == "BondAnd" || descr == "BondXor") return true;
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if (descr == "BondOr") {
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// detect the types of queries that appear for unspecified bonds in SMARTS:
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if (b->getQuery()->endChildren() - b->getQuery()->beginChildren() == 2) {
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for (Bond::QUERYBOND_QUERY::CHILD_VECT_CI child =
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b->getQuery()->beginChildren();
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child != b->getQuery()->endChildren(); ++child) {
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if ((*child)->getDescription() != "BondOrder" ||
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(*child)->getNegation())
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return true;
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if (static_cast<BOND_EQUALS_QUERY *>(child->get())->getVal() !=
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Bond::SINGLE &&
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static_cast<BOND_EQUALS_QUERY *>(child->get())->getVal() !=
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Bond::AROMATIC)
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return true;
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return false;
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}
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}
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}
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return true;
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}
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bool _complexQueryHelper(Atom::QUERYATOM_QUERY const *query, bool &hasAtNum) {
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if (!query) return false;
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if (query->getNegation()) return true;
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std::string descr = query->getDescription();
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// std::cerr<<" |"<<descr;
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if (descr == "AtomAtomicNum") {
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hasAtNum = true;
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return false;
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}
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if (descr == "AtomOr" || descr == "AtomXor") return true;
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if (descr == "AtomAnd") {
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Queries::Query<int, Atom const *, true>::CHILD_VECT_CI childIt =
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query->beginChildren();
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while (childIt != query->endChildren()) {
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if (_complexQueryHelper(childIt->get(), hasAtNum)) return true;
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++childIt;
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}
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}
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return false;
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}
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bool isComplexQuery(const Atom *a) {
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if (!a->hasQuery()) return false;
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// std::cerr<<"\n"<<a->getIdx();
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// negated things are always complex:
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if (a->getQuery()->getNegation()) return true;
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std::string descr = a->getQuery()->getDescription();
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// std::cerr<<" "<<descr;
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if (descr == "AtomAtomicNum") return false;
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if (descr == "AtomOr" || descr == "AtomXor") return true;
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if (descr == "AtomAnd") {
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bool hasAtNum = false;
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if (_complexQueryHelper(a->getQuery(), hasAtNum)) return true;
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if (hasAtNum)
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return false;
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else
|
|
return true;
|
|
}
|
|
|
|
return true;
|
|
}
|
|
bool isAtomAromatic(const Atom *a) {
|
|
bool res = false;
|
|
if (!a->hasQuery()) {
|
|
res = a->getIsAromatic();
|
|
} else {
|
|
std::string descr = a->getQuery()->getDescription();
|
|
if (descr == "AtomAtomicNum") {
|
|
res = a->getIsAromatic();
|
|
} else if (descr == "AtomIsAromatic") {
|
|
res = true;
|
|
if (a->getQuery()->getNegation()) res = !res;
|
|
} else if (descr == "AtomIsAliphatic") {
|
|
res = false;
|
|
if (a->getQuery()->getNegation()) res = !res;
|
|
} else if (descr == "AtomAnd") {
|
|
Queries::Query<int, Atom const *, true>::CHILD_VECT_CI childIt =
|
|
a->getQuery()->beginChildren();
|
|
if ((*childIt)->getDescription() == "AtomAtomicNum") {
|
|
if (a->getQuery()->getNegation()) {
|
|
res = false;
|
|
} else if ((*(childIt + 1))->getDescription() == "AtomIsAliphatic") {
|
|
res = false;
|
|
} else if ((*(childIt + 1))->getDescription() == "AtomIsAromatic") {
|
|
res = true;
|
|
}
|
|
}
|
|
}
|
|
}
|
|
return res;
|
|
}
|
|
};
|