C++ (Cpp) Mol::addAtom Examples

Programming Language: C++ (Cpp)

Class/Type: Mol

Method/Function: addAtom

Examples at hotexamples.com: 5

C++ (Cpp) Mol::addAtom - 5 examples found. These are the top rated real world C++ (Cpp) examples of Mol::addAtom extracted from open source projects. You can rate examples to help us improve the quality of examples.

Frequently Used Methods

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addBond(5)

addAtom(5)

getAtomWithIdx(4)

beginBonds(3)

DoingAO(3)

getBondWithIdx(3)

IsReady(3)

endBonds(3)

beginAtoms(2)

beginQueryAtoms(2)

endAtoms(2)

SetColMode(2)

ReadPdb(2)

ResetAO(2)

PrepareAOstep(2)

endQueryAtoms(2)

GetMolName(2)

Draw(2)

endHeteros(1)

endAromaticAtoms(1)

getBondBetweenAtoms(1)

getDefaultViewRotation(1)

beginHeteros(1)

AddNewAtom(1)

SetSpaceFill(1)

beginAromaticAtoms(1)

Transform(1)

DecentAO(1)

SetLicorice(1)

SetBallAndSticks(1)

ScaleTransl(1)

PrepareAOSingleView(1)

PredictAO(1)

GetFilenameSnap(1)

DrawOnTexture(1)

DrawHalos(1)

hasDefaultView(1)

Example #1

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File: querytest.cpp Project: abradle/rdkit

void test2() {
  BOOST_LOG(rdErrorLog) << "---------------------- Test2" << std::endl;
  Mol qM;
  Mol m;

  Atom *a = new Atom(6);
  // we copy in addAtom, so this is safe
  m.addAtom(a);
  m.addAtom(a);
  m.addAtom(a);
  delete a;
  m.addBond(0, 1, Bond::TRIPLE);
  m.addBond(1, 2, Bond::SINGLE);
  a = new Atom(8);
  m.addAtom(a);
  delete a;
  m.addBond(2, 3, Bond::DOUBLE);
  MolOps::sanitizeMol(m);

  QueryBond *qB;
  qB = new QueryBond(Bond::SINGLE);

  CHECK_INVARIANT(!qB->Match(m.getBondWithIdx(0)), "");
  CHECK_INVARIANT(qB->Match(m.getBondWithIdx(1)), "");
  CHECK_INVARIANT(!qB->Match(m.getBondWithIdx(2)), "");

  BOND_EQUALS_QUERY *newQ = makeBondOrderEqualsQuery(Bond::DOUBLE);
  qB->expandQuery(newQ, Queries::COMPOSITE_OR);
  CHECK_INVARIANT(!qB->Match(m.getBondWithIdx(0)), "");
  CHECK_INVARIANT(qB->Match(m.getBondWithIdx(1)), "");
  CHECK_INVARIANT(qB->Match(m.getBondWithIdx(2)), "");

  BOOST_LOG(rdErrorLog) << "Done!" << std::endl;
}

Example #2

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File: querytest.cpp Project: abradle/rdkit

void test4() {
  BOOST_LOG(rdErrorLog) << "---------------------- Test4" << std::endl;
  Mol m;

  Atom *a = new Atom(6);
  // we copy in addAtom, so this is safe
  m.addAtom(a);
  m.addAtom(a);
  m.addAtom(a);
  m.addAtom(a);
  m.addAtom(a);
  m.addAtom(a);
  m.addAtom(a);
  delete a;
  m.addBond(0, 1, Bond::SINGLE);
  m.addBond(1, 2, Bond::DOUBLE);
  m.addBond(2, 3, Bond::SINGLE);
  m.addBond(3, 4, Bond::DOUBLE);
  m.addBond(4, 5, Bond::SINGLE);
  m.addBond(5, 0, Bond::DOUBLE);
  m.addBond(5, 6, Bond::SINGLE);
  MolOps::sanitizeMol(m);

  ATOM_NULL_QUERY *aeq = makeAtomNullQuery();
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(0)), "");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(1)), "");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(5)), "");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(6)), "");
  delete aeq;

  BOOST_LOG(rdErrorLog) << "Done!" << std::endl;
}

Example #3

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File: querytest.cpp Project: teng-lin/rdkit

void test5(){
  BOOST_LOG(rdErrorLog) << "---------------------- Test5" << std::endl;
  Mol m;

  Atom *a = new Atom(6);
  // we copy in addAtom, so this is safe
  m.addAtom(a);
  m.addAtom(a);
  m.addAtom(a);
  m.addAtom(a);
  m.addAtom(a);
  m.addAtom(a);
  m.addAtom(a);
  delete a;
  m.addBond(0,1,Bond::SINGLE);
  m.addBond(1,2,Bond::DOUBLE);
  m.addBond(2,3,Bond::SINGLE);
  m.addBond(3,4,Bond::DOUBLE);
  m.addBond(4,5,Bond::SINGLE);
  m.addBond(5,0,Bond::DOUBLE);
  m.addBond(5,6,Bond::SINGLE);
  MolOps::sanitizeMol(m);
  
  unsigned int valenceProd;
  valenceProd=queryAtomBondProduct(m.getAtomWithIdx(0));
  TEST_ASSERT(valenceProd==1681);  // aromatic*aromatic = 41 * 41 = 1681
  valenceProd=queryAtomBondProduct(m.getAtomWithIdx(1));
  TEST_ASSERT(valenceProd==1681);
  
  valenceProd=queryAtomBondProduct(m.getAtomWithIdx(5));
  TEST_ASSERT(valenceProd==5043);

  valenceProd=queryAtomBondProduct(m.getAtomWithIdx(6));
  TEST_ASSERT(valenceProd==3);
  
  valenceProd=queryAtomAllBondProduct(m.getAtomWithIdx(6));
  TEST_ASSERT(valenceProd==81);
  

  BOOST_LOG(rdErrorLog) << "Done!" << std::endl;
}

Example #4

Show file

File: querytest.cpp Project: abradle/rdkit

void test1() {
  BOOST_LOG(rdErrorLog) << "---------------------- Test1" << std::endl;
  Mol qM;
  Mol m;

  Atom *a = new Atom(6);
  // we copy in addAtom, so this is safe
  m.addAtom(a);
  m.addAtom(a);
  delete a;
  m.addBond(0, 1, Bond::SINGLE);
  a = new Atom(8);
  m.addAtom(a);
  delete a;
  m.addBond(1, 2, Bond::DOUBLE);
  MolOps::sanitizeMol(m);

  QueryAtom *qA = new QueryAtom(6);
  CHECK_INVARIANT(qA->Match(m.getAtomWithIdx(0)), "");
  CHECK_INVARIANT(qA->Match(m.getAtomWithIdx(1)), "");
  CHECK_INVARIANT(!qA->Match(m.getAtomWithIdx(2)), "");
  qA->expandQuery(makeAtomImplicitValenceQuery(3));
  CHECK_INVARIANT(qA->Match(m.getAtomWithIdx(0)), "");
  CHECK_INVARIANT(!qA->Match(m.getAtomWithIdx(1)), "");
  CHECK_INVARIANT(!qA->Match(m.getAtomWithIdx(2)), "");

  qM.addAtom(qA);
  delete qA;
  qA = new QueryAtom(6);
  qA->expandQuery(makeAtomNumQuery(8), Queries::COMPOSITE_OR);
  qM.addAtom(qA);
  delete qA;
  qM.addAtom(new QueryAtom(8), true, true);
  // Atom::ATOM_SPTR qA(new QueryAtom(6));

  QueryBond *qB;
  qB = new QueryBond(Bond::UNSPECIFIED);
  qB->setOwningMol(qM);
  qB->setBeginAtomIdx(0);
  qB->setEndAtomIdx(1);

  CHECK_INVARIANT(qB->Match(m.getBondWithIdx(0)), "");
  CHECK_INVARIANT(qB->Match(m.getBondWithIdx(1)), "");
  qM.addBond(qB, true);
  qB = new QueryBond(Bond::DOUBLE);
  qB->setOwningMol(qM);
  qB->setBeginAtomIdx(1);
  qB->setEndAtomIdx(2);
  qM.addBond(qB, true);

  CHECK_INVARIANT(qM.getAtomWithIdx(0)->Match(m.getAtomWithIdx(0)), "");
  CHECK_INVARIANT(!qM.getAtomWithIdx(0)->Match(m.getAtomWithIdx(1)), "");
  CHECK_INVARIANT(!qM.getAtomWithIdx(0)->Match(m.getAtomWithIdx(2)), "");
  CHECK_INVARIANT(qM.getAtomWithIdx(1)->Match(m.getAtomWithIdx(0)), "");
  CHECK_INVARIANT(qM.getAtomWithIdx(1)->Match(m.getAtomWithIdx(1)), "");
  CHECK_INVARIANT(qM.getAtomWithIdx(1)->Match(m.getAtomWithIdx(2)), "");
  CHECK_INVARIANT(!qM.getAtomWithIdx(2)->Match(m.getAtomWithIdx(0)), "");
  CHECK_INVARIANT(!qM.getAtomWithIdx(2)->Match(m.getAtomWithIdx(1)), "");
  CHECK_INVARIANT(qM.getAtomWithIdx(2)->Match(m.getAtomWithIdx(2)), "");

  CHECK_INVARIANT(qM.getBondWithIdx(0)->Match(m.getBondWithIdx(0)), "");
  CHECK_INVARIANT(qM.getBondWithIdx(0)->Match(m.getBondWithIdx(1)), "");
  CHECK_INVARIANT(!qM.getBondWithIdx(1)->Match(m.getBondWithIdx(0)), "");
  CHECK_INVARIANT(qM.getBondWithIdx(1)->Match(m.getBondWithIdx(1)), "");

  BOOST_LOG(rdErrorLog) << "Done!" << std::endl;
}

Example #5

Show file

File: querytest.cpp Project: abradle/rdkit

void test3() {
  BOOST_LOG(rdErrorLog) << "---------------------- Test3" << std::endl;
  Mol m;

  Atom *a = new Atom(6);
  // we copy in addAtom, so this is safe
  m.addAtom(a);
  m.addAtom(a);
  m.addAtom(a);
  m.addAtom(a);
  m.addAtom(a);
  m.addAtom(a);
  m.addAtom(a);
  delete a;
  m.addBond(0, 1, Bond::SINGLE);
  m.addBond(1, 2, Bond::DOUBLE);
  m.addBond(2, 3, Bond::SINGLE);
  m.addBond(3, 4, Bond::DOUBLE);
  m.addBond(4, 5, Bond::SINGLE);
  m.addBond(5, 0, Bond::DOUBLE);
  m.addBond(5, 6, Bond::SINGLE);
  MolOps::sanitizeMol(m);

  ATOM_EQUALS_QUERY *aeq = makeAtomExplicitDegreeQuery(3);
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(0)), "");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(1)), "");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(5)), "");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(6)), "");
  delete aeq;
  aeq = makeAtomExplicitDegreeQuery(2);
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(0)), "");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(1)), "");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(5)), "");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(6)), "");
  delete aeq;

  aeq = makeAtomHCountQuery(1);
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(0)), "");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(1)), "");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(5)), "");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(6)), "");
  delete aeq;

  aeq = makeAtomInNRingsQuery(1);
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(0)), "");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(1)), "");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(5)), "");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(6)), "");
  delete aeq;

  aeq = makeAtomInNRingsQuery(0);
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(0)), "");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(1)), "");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(5)), "");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(6)), "");
  delete aeq;

  aeq = makeAtomAromaticQuery();
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(0)), "");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(1)), "");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(5)), "");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(6)), "");
  delete aeq;

  aeq = makeAtomAliphaticQuery();
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(0)), "");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(1)), "");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(5)), "");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(6)), "");
  delete aeq;

  aeq = makeAtomInRingQuery();
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(0)), "");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(1)), "");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(5)), "");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(6)), "");
  aeq->setNegation(true);
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(0)), "");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(1)), "");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(5)), "");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(6)), "");
  delete aeq;

  aeq = makeAtomInRingOfSizeQuery(6);
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(0)), "");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(1)), "");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(5)), "");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(6)), "");
  aeq->setNegation(true);
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(0)), "");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(1)), "");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(5)), "");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(6)), "");
  delete aeq;

  aeq = makeAtomInRingOfSizeQuery(5);
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(0)), "");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(1)), "");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(5)), "");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(6)), "");
  aeq->setNegation(true);
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(0)), "");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(1)), "");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(5)), "");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(6)), "");
  delete aeq;

  BOND_EQUALS_QUERY *beq = makeBondIsInRingQuery();
  CHECK_INVARIANT(beq->Match(m.getBondWithIdx(0)), "");
  CHECK_INVARIANT(!beq->Match(m.getBondWithIdx(6)), "");
  CHECK_INVARIANT(beq->Match(m.getBondBetweenAtoms(0, 1)), "");
  CHECK_INVARIANT(beq->Match(m.getBondBetweenAtoms(1, 0)), "");
  CHECK_INVARIANT(!beq->Match(m.getBondBetweenAtoms(5, 6)), "");
  CHECK_INVARIANT(!beq->Match(m.getBondBetweenAtoms(6, 5)), "");

  BOOST_LOG(rdErrorLog) << "Done!" << std::endl;
}