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I found time and have added the .find() function to the molecular c…
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…ontainers.

This lets you easily get the index of atoms in systems etc., e.g.

>>> idxs = mols.atoms().find(mols["element C"])

returns the indexes in `mols` for all of the carbon atoms.
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@chryswoods
chryswoods committed Jan 11, 2023
1 parent 3718493 commit 53880ab
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Showing 31 changed files with 5,119 additions and 4,201 deletions.
221 changes: 110 additions & 111 deletions corelib/src/libs/SireMM/selectorbond.h
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Original file line number Diff line number Diff line change
Expand Up @@ -36,172 +36,171 @@ SIRE_BEGIN_HEADER

namespace SireMM
{
class SelectorBond;
class SelectorBond;
}

SIREMM_EXPORT QDataStream& operator<<(QDataStream&, const SireMM::SelectorBond&);
SIREMM_EXPORT QDataStream& operator>>(QDataStream&, SireMM::SelectorBond&);
SIREMM_EXPORT QDataStream &operator<<(QDataStream &, const SireMM::SelectorBond &);
SIREMM_EXPORT QDataStream &operator>>(QDataStream &, SireMM::SelectorBond &);

namespace SireMM
{

/** This provides a Selector<T>-style interface for multiple bonds */
class SIREMM_EXPORT SelectorBond :
public SireBase::ConcreteProperty<SelectorBond, SireMol::MoleculeView>
{
/** This provides a Selector<T>-style interface for multiple bonds */
class SIREMM_EXPORT SelectorBond : public SireBase::ConcreteProperty<SelectorBond, SireMol::MoleculeView>
{

friend QDataStream& ::operator<<(QDataStream&, const SelectorBond&);
friend QDataStream& ::operator>>(QDataStream&, SelectorBond&);
friend QDataStream & ::operator<<(QDataStream &, const SelectorBond &);
friend QDataStream & ::operator>>(QDataStream &, SelectorBond &);

public:
SelectorBond();
public:
SelectorBond();

SelectorBond(const Bond &bond);
SelectorBond(const Bond &bond);

SelectorBond(const SireMol::MoleculeData &molecule,
const SireBase::PropertyMap &map = SireBase::PropertyMap());
SelectorBond(const SireMol::MoleculeData &molecule,
const SireBase::PropertyMap &map = SireBase::PropertyMap());

SelectorBond(const MoleculeView &molecule,
const SireBase::PropertyMap &map = SireBase::PropertyMap());
SelectorBond(const MoleculeView &molecule,
const SireBase::PropertyMap &map = SireBase::PropertyMap());

SelectorBond(const SireMol::MoleculeData &molecule,
const SireMol::AtomID &atom,
const SireBase::PropertyMap &map = SireBase::PropertyMap());
SelectorBond(const SireMol::MoleculeData &molecule,
const SireMol::AtomID &atom,
const SireBase::PropertyMap &map = SireBase::PropertyMap());

SelectorBond(const SireMol::MoleculeData &molecule,
const SireMol::AtomID &atom0, const SireMol::AtomID &atom1,
const SireBase::PropertyMap &map = SireBase::PropertyMap());
SelectorBond(const SireMol::MoleculeData &molecule,
const SireMol::AtomID &atom0, const SireMol::AtomID &atom1,
const SireBase::PropertyMap &map = SireBase::PropertyMap());

SelectorBond(const SireMol::MoleculeView &molecule,
const SireMol::AtomID &atom,
const SireBase::PropertyMap &map = SireBase::PropertyMap());
SelectorBond(const SireMol::MoleculeView &molecule,
const SireMol::AtomID &atom,
const SireBase::PropertyMap &map = SireBase::PropertyMap());

SelectorBond(const SireMol::MoleculeView &molecule,
const SireMol::BondID &bond,
const SireBase::PropertyMap &map = SireBase::PropertyMap());
SelectorBond(const SireMol::MoleculeView &molecule,
const SireMol::BondID &bond,
const SireBase::PropertyMap &map = SireBase::PropertyMap());

SelectorBond(const SireMol::MoleculeView &molecule,
const QList<SireMol::BondID> &bonds,
const SireBase::PropertyMap &map = SireBase::PropertyMap());
SelectorBond(const SireMol::MoleculeView &molecule,
const QList<SireMol::BondID> &bonds,
const SireBase::PropertyMap &map = SireBase::PropertyMap());

SelectorBond(const SireMol::MoleculeView &molecule,
const SireMol::AtomID &atom0, const SireMol::AtomID &atom1,
const SireBase::PropertyMap &map = SireBase::PropertyMap());
SelectorBond(const SireMol::MoleculeView &molecule,
const SireMol::AtomID &atom0, const SireMol::AtomID &atom1,
const SireBase::PropertyMap &map = SireBase::PropertyMap());

SelectorBond(const SireMol::Selector<SireMol::Atom> &atoms,
const SireBase::PropertyMap &map = SireBase::PropertyMap());
SelectorBond(const SireMol::Selector<SireMol::Atom> &atoms0,
const SireMol::Selector<SireMol::Atom> &atoms1,
const SireBase::PropertyMap &map = SireBase::PropertyMap());
SelectorBond(const SireMol::Selector<SireMol::Atom> &atoms,
const SireBase::PropertyMap &map = SireBase::PropertyMap());
SelectorBond(const SireMol::Selector<SireMol::Atom> &atoms0,
const SireMol::Selector<SireMol::Atom> &atoms1,
const SireBase::PropertyMap &map = SireBase::PropertyMap());

SelectorBond(const SelectorBond &other);
SelectorBond(const SelectorBond &other);

virtual ~SelectorBond();
virtual ~SelectorBond();

static const char* typeName();
static const char *typeName();

virtual const char* what() const
{
return SelectorBond::typeName();
}
virtual const char *what() const
{
return SelectorBond::typeName();
}

virtual SelectorBond* clone() const
{
return new SelectorBond(*this);
}
virtual SelectorBond *clone() const
{
return new SelectorBond(*this);
}

SelectorBond& operator=(const SelectorBond &bond);
SelectorBond &operator=(const SelectorBond &bond);

bool operator==(const SelectorBond &other) const;
bool operator!=(const SelectorBond &other) const;
bool operator==(const SelectorBond &other) const;
bool operator!=(const SelectorBond &other) const;

QString toString() const;
QString toString() const;

SireMol::MolViewPtr operator[](int i) const;
SireMol::MolViewPtr operator[](const SireBase::Slice &slice) const;
SireMol::MolViewPtr operator[](const QList<qint64> &idxs) const;
SireMol::MolViewPtr operator[](const SireMol::BondID &bond) const;
SireMol::MolViewPtr operator[](int i) const;
SireMol::MolViewPtr operator[](const SireBase::Slice &slice) const;
SireMol::MolViewPtr operator[](const QList<qint64> &idxs) const;
SireMol::MolViewPtr operator[](const SireMol::BondID &bond) const;

Bond operator()(int i) const;
SelectorBond operator()(int i, int j) const;
SelectorBond operator()(const SireBase::Slice &slice) const;
SelectorBond operator()(const QList<qint64> &idxs) const;
SelectorBond operator()(const SireMol::BondID &bond) const;
Bond operator()(int i) const;
SelectorBond operator()(int i, int j) const;
SelectorBond operator()(const SireBase::Slice &slice) const;
SelectorBond operator()(const QList<qint64> &idxs) const;
SelectorBond operator()(const SireMol::BondID &bond) const;

QList<SireMol::MolViewPtr> toList() const;
QList<SireMol::MolViewPtr> toList() const;

bool isSelector() const;
bool isSelector() const;

QList<SireMol::BondID> IDs() const;
QList<SireMol::BondID> IDs() const;

SelectorBond add(const Bond &bond) const;
SelectorBond add(const Bond &bond) const;

int count() const;
int size() const;
int nViews() const;
int count() const;
int size() const;
int nViews() const;

bool isEmpty() const;
bool selectedAll() const;
bool isEmpty() const;
bool selectedAll() const;

SireMol::MolViewPtr toSelector() const;
SireMol::MolViewPtr toSelector() const;

SireMol::AtomSelection selection() const;
SireMol::AtomSelection selection() const;

SelectorBond add(const SelectorBond &other) const;
SelectorBond add(const SelectorBond &other) const;

SelectorBond intersection(const SelectorBond &other) const;
SelectorBond intersection(const SelectorBond &other) const;

SelectorBond invert(const SireBase::PropertyMap &map) const;
SelectorBond invert() const;
SelectorBond invert(const SireBase::PropertyMap &map) const;
SelectorBond invert() const;

bool hasProperty(const SireBase::PropertyName &key) const;
bool hasMetadata(const SireBase::PropertyName &key) const;
bool hasMetadata(const SireBase::PropertyName &key,
const SireBase::PropertyName &metakey) const;
bool hasProperty(const SireBase::PropertyName &key) const;
bool hasMetadata(const SireBase::PropertyName &key) const;
bool hasMetadata(const SireBase::PropertyName &key,
const SireBase::PropertyName &metakey) const;

QStringList propertyKeys() const;
QStringList metadataKeys() const;
QStringList metadataKeys(const SireBase::PropertyName &key) const;
QStringList propertyKeys() const;
QStringList metadataKeys() const;
QStringList metadataKeys(const SireBase::PropertyName &key) const;

QList<SireBase::Properties> properties() const;
QList<SireBase::Properties> properties() const;

SireMol::Mover<SelectorBond> move() const;
SireMol::Evaluator evaluate() const;
SireMol::Mover<SelectorBond> move() const;
SireMol::Evaluator evaluate() const;

QList<SireBase::PropertyPtr> property(const SireBase::PropertyName &key) const;
QList<SireBase::PropertyPtr> property(const SireBase::PropertyName &key,
const Property &default_value) const;
QList<SireBase::PropertyPtr> property(const SireBase::PropertyName &key) const;
QList<SireBase::PropertyPtr> property(const SireBase::PropertyName &key,
const Property &default_value) const;

QList<SireUnits::Dimension::Length> lengths() const;
QList<SireUnits::Dimension::Length> lengths(const SireBase::PropertyMap &map) const;
QList<SireUnits::Dimension::Length> lengths() const;
QList<SireUnits::Dimension::Length> lengths(const SireBase::PropertyMap &map) const;

QList<SireUnits::Dimension::Length> measures() const;
QList<SireUnits::Dimension::Length> measures(const SireBase::PropertyMap &map) const;
QList<SireUnits::Dimension::Length> measures() const;
QList<SireUnits::Dimension::Length> measures(const SireBase::PropertyMap &map) const;

QList<SireCAS::Expression> potentials() const;
QList<SireCAS::Expression> potentials(const SireBase::PropertyMap &map) const;
QList<SireCAS::Expression> potentials() const;
QList<SireCAS::Expression> potentials(const SireBase::PropertyMap &map) const;

QList<SireUnits::Dimension::GeneralUnit> energies() const;
QList<SireUnits::Dimension::GeneralUnit> energies(
const SireBase::PropertyMap &map) const;
QList<SireUnits::Dimension::GeneralUnit> energies() const;
QList<SireUnits::Dimension::GeneralUnit> energies(
const SireBase::PropertyMap &map) const;

SireUnits::Dimension::GeneralUnit energy() const;
SireUnits::Dimension::GeneralUnit energy(
const SireBase::PropertyMap &map) const;
SireUnits::Dimension::GeneralUnit energy() const;
SireUnits::Dimension::GeneralUnit energy(
const SireBase::PropertyMap &map) const;

protected:
/** The IDs of the bond (holding AtomIdx IDs) */
QList<SireMol::BondID> bnds;
};
protected:
/** The IDs of the bond (holding AtomIdx IDs) */
QList<SireMol::BondID> bnds;
};

} // end of namespace SireMM

Q_DECLARE_METATYPE( SireMM::SelectorBond )
Q_DECLARE_METATYPE( SireMol::Mover<SireMM::SelectorBond> )
Q_DECLARE_METATYPE(SireMM::SelectorBond)
Q_DECLARE_METATYPE(SireMol::Mover<SireMM::SelectorBond>)

SIRE_EXPOSE_CLASS( SireMM::SelectorBond )
SIRE_EXPOSE_CLASS(SireMM::SelectorBond)

SIRE_EXPOSE_ALIAS( SireMol::Mover<SireMM::SelectorBond>, SireMol::Mover_SelectorBond_ )
SIRE_EXPOSE_ALIAS(SireMol::Mover<SireMM::SelectorBond>, SireMol::Mover_SelectorBond_)

#ifdef SIRE_INSTANTIATE_TEMPLATES

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