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Be careful about assign or copy from molecules with no layers #806

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Oct 9, 2021
Merged

Be careful about assign or copy from molecules with no layers #806

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26 changes: 19 additions & 7 deletions avogadro/core/molecule.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -43,8 +43,12 @@ Molecule::Molecule(const Molecule& other)
m_residues(other.m_residues), m_graph(other.m_graph),
m_graphDirty(other.m_graphDirty), m_bondPairs(other.m_bondPairs),
m_bondOrders(other.m_bondOrders), m_atomicNumbers(other.m_atomicNumbers),
m_layers(LayerManager::getMoleculeLayer(&other, this))
m_layers(LayerManager::getMoleculeLayer(this))
{
// Copy the layers, if they exist
if (other.m_layers.maxLayer() > 0)
m_layers = LayerManager::getMoleculeLayer(&other, this);

// Copy over any meshes
for (Index i = 0; i < other.meshCount(); ++i) {
Mesh* m = addMesh();
Expand Down Expand Up @@ -79,8 +83,12 @@ Molecule::Molecule(Molecule&& other) noexcept
m_bondPairs(std::move(other.m_bondPairs)),
m_bondOrders(std::move(other.m_bondOrders)),
m_atomicNumbers(std::move(other.m_atomicNumbers)),
m_layers(LayerManager::getMoleculeLayer(&other, this))
m_layers(LayerManager::getMoleculeLayer(this))
{
// Copy the layers, if they exist
if (other.m_layers.maxLayer() > 0)
m_layers = LayerManager::getMoleculeLayer(&other, this);

m_basisSet = other.m_basisSet;
other.m_basisSet = nullptr;

Expand Down Expand Up @@ -134,7 +142,9 @@ Molecule& Molecule::operator=(const Molecule& other)
m_unitCell = other.m_unitCell ? new UnitCell(*other.m_unitCell) : nullptr;
}

m_layers = LayerManager::getMoleculeLayer(&other, this);
// Copy the layers, if they exist
if (other.m_layers.maxLayer() > 0)
m_layers = LayerManager::getMoleculeLayer(&other, this);

return *this;
}
Expand Down Expand Up @@ -176,9 +186,11 @@ Molecule& Molecule::operator=(Molecule&& other) noexcept
delete m_unitCell;
m_unitCell = other.m_unitCell;
other.m_unitCell = nullptr;
}

m_layers = LayerManager::getMoleculeLayer(&other, this);
// Copy the layers, if they exist
if (other.m_layers.maxLayer() > 0)
m_layers = LayerManager::getMoleculeLayer(&other, this);
}

return *this;
}
Expand Down Expand Up @@ -461,8 +473,8 @@ bool Molecule::removeBond(Index index)
if (index >= bondCount())
return false;
if (!m_graphDirty) {
// mark dirty the graph O(n) only if is more efficient than remove an edge
// O(nlogn)
// mark dirty the graph O(n) only if is more efficient than remove
// an edge O(nlogn)
size_t n = atomCount();
size_t m = calcNlogN(m_graph.subgraphCount(m_bondPairs[index].first));
if (m < n) {
Expand Down