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Chemical Data Processing Library C++ API - Version 1.1.1
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29 #ifndef CDPL_CHEM_FRAGMENT_HPP
30 #define CDPL_CHEM_FRAGMENT_HPP
33 #include <unordered_map>
36 #include <boost/iterator/indirect_iterator.hpp>
54 typedef std::vector<Atom*> AtomList;
55 typedef std::vector<Bond*> BondList;
71 typedef boost::indirect_iterator<AtomList::iterator, Atom>
AtomIterator;
81 typedef boost::indirect_iterator<BondList::iterator, Bond>
BondIterator;
371 typedef std::unordered_map<const Atom*, std::size_t> AtomIndexMap;
372 typedef std::unordered_map<const Bond*, std::size_t> BondIndexMap;
376 AtomIndexMap atomIndices;
377 BondIndexMap bondIndices;
382 #endif // CDPL_CHEM_FRAGMENT_HPP
std::shared_ptr< MolecularGraph > SharedPointer
A reference-counted smart pointer [SHPTR] for dynamically allocated MolecularGraph instances.
Definition: MolecularGraph.hpp:58
Fragment(const MolecularGraph &molgraph)
Constructs a Fragment instance storing the atoms, bonds and properties of the molecular graph molgrap...
boost::indirect_iterator< BondList::const_iterator, const Bond > ConstBondIterator
A constant random access iterator used to iterate over the stored const Chem::Bond objects.
Definition: Fragment.hpp:76
void orderBonds(const BondCompareFunction &func)
Orders the stored bonds according to criteria implemented by the provided bond comparison function.
void swap(PropertyContainer &cntnr)
Exchanges the properties of this container with the properties of the container cntnr.
std::function< bool(const Chem::Atom &, const Chem::Atom &)> AtomCompareFunction
A generic wrapper class used to store a user-defined atom compare function.
Definition: AtomCompareFunction.hpp:41
Fragment & operator=(const MolecularGraph &molgraph)
Replaces the current set of atoms, bonds and properties by the atoms, bonds and properties of the mol...
Definition of the preprocessor macro CDPL_CHEM_API.
#define CDPL_CHEM_API
Tells the compiler/linker which classes, functions and variables are part of the library API.
boost::indirect_iterator< BondList::iterator, Bond > BondIterator
A mutable random access iterator used to iterate over the stored const Chem::Bond objects.
Definition: Fragment.hpp:81
bool containsBond(const Bond &bond) const
Tells whether the specified bond is part of this fragment.
Bond.
Definition: Bond.hpp:50
void swap(Fragment &frag)
Exchanges the atoms, bonds and properties of this fragment with the atoms, bonds and properties of th...
BondIterator getBondsBegin()
Returns a mutable iterator pointing to the beginning of the stored const Chem::Bond objects.
ConstBondIterator getBondsBegin() const
Returns a constant iterator pointing to the beginning of the stored const Chem::Bond objects.
bool addAtom(const Atom &atom)
Extends the fragment by the specified atom.
A STL compatible random access iterator for container elements accessible by index.
Definition: IndexedElementIterator.hpp:125
Atom.
Definition: Atom.hpp:52
void clear()
Removes all atoms and bonds.
Fragment.
Definition: Fragment.hpp:52
boost::indirect_iterator< AtomList::const_iterator, const Atom > ConstAtomIterator
A constant random access iterator used to iterate over the stored const Chem::Atom objects.
Definition: Fragment.hpp:66
ConstAtomIterator getAtomsEnd() const
Returns a constant iterator pointing to the end of the stored const Chem::Atom objects.
ConstBondIterator getBondsEnd() const
Returns a constant iterator pointing to the end of the stored const Chem::Bond objects.
void reserveMemoryForBonds(std::size_t num_bonds)
Fragment & operator+=(const MolecularGraph &molgraph)
Extends the current set of atoms and bonds by the atoms and bonds in the molecular graph molgraph.
MolecularGraph.
Definition: MolecularGraph.hpp:52
void orderAtoms(const AtomCompareFunction &func)
Orders the stored atoms according to criteria implemented by the provided atom comparison function.
Fragment(const Fragment &frag)
Constructs a copy of the Fragment instance frag.
const Atom & getAtom(std::size_t idx) const
Returns a const reference to the atom at index idx.
std::size_t getNumBonds() const
Returns the number of bonds.
BondIterator getBondsEnd()
Returns a mutable iterator pointing to the end of the stored const Chem::Bond objects.
std::size_t getAtomIndex(const Atom &atom) const
Returns the index of the specified atom.
Definition of the class CDPL::Chem::MolecularGraph.
std::shared_ptr< Fragment > SharedPointer
A reference-counted smart pointer [SHPTR] for dynamically allocated Fragment instances.
Definition: Fragment.hpp:61
std::function< bool(const Chem::Bond &, const Chem::Bond &)> BondCompareFunction
A generic wrapper class used to store a user-defined bond compare function.
Definition: BondCompareFunction.hpp:41
bool removeBond(const Bond &bond)
Removes the specified bond.
Atom & getAtom(std::size_t idx)
Returns a non-const reference to the atom at index idx.
MolecularGraph::SharedPointer clone() const
Creates a copy of the molecular graph.
bool addBond(const Bond &bond)
Extends the fragment by the specified bond.
BondIterator removeBond(const BondIterator &it)
Removes the bond specified by the iterator it.
const Bond & getBond(std::size_t idx) const
Returns a const reference to the bond at index idx.
ConstAtomIterator getAtomsBegin() const
Returns a constant iterator pointing to the beginning of the stored const Chem::Atom objects.
boost::indirect_iterator< AtomList::iterator, Atom > AtomIterator
A mutable random access iterator used to iterate over the stored const Chem::Atom objects.
Definition: Fragment.hpp:71
The namespace of the Chemical Data Processing Library.
std::size_t getNumAtoms() const
Returns the number of atoms.
Fragment()
Constructs an empty Fragment instance.
void removeAtom(std::size_t idx)
Removes the atom at the specified index.
Bond & getBond(std::size_t idx)
Returns a non-const reference to the bond at index idx.
void reserveMemoryForAtoms(std::size_t num_atoms)
void removeBond(std::size_t idx)
Removes the bond at the specified index.
Fragment & operator=(const Fragment &frag)
Replaces the current set of atoms, bonds and properties by the atoms, bonds and properties of the fra...
AtomIterator removeAtom(const AtomIterator &it)
Removes the atom specified by the iterator it.
bool containsAtom(const Atom &atom) const
Tells whether the specified atom is part of this fragment.
AtomIterator getAtomsBegin()
Returns a mutable iterator pointing to the beginning of the stored const Chem::Atom objects.
std::size_t getBondIndex(const Bond &bond) const
Returns the index of the specified bond.
Fragment & operator-=(const MolecularGraph &molgraph)
Removes the atoms and bonds referenced by the molecular graph molgraph from this Fragment instance.
bool removeAtom(const Atom &atom)
Removes the specified atom.
AtomIterator getAtomsEnd()
Returns a mutable iterator pointing to the end of the stored const Chem::Atom objects.