29#include <boost/graph/adjacency_list.hpp>
30#include <boost/smart_ptr.hpp>
31#include <boost/dynamic_bitset.hpp>
33#ifdef RDK_USE_BOOST_SERIALIZATION
34#include <boost/serialization/split_member.hpp>
53typedef boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS,
62template <
class T1,
class T2>
67template <
class T1,
class T2>
69template <
class T1,
class T2>
71template <
class T1,
class T2>
73template <
class T1,
class T2>
113template <
class Graph,
class Vertex,
114 class Iterator =
typename Graph::vertex_iterator>
146 auto vs = boost::vertices(*
graph);
156template <
class Graph,
class Edge,
157 class Iterator =
typename Graph::edge_iterator>
189 auto vs = boost::edges(*
graph);
208 typedef MolGraph::vertex_descriptor vertex_descriptor;
209 typedef MolGraph::edge_descriptor edge_descriptor;
211 typedef MolGraph::edge_iterator EDGE_ITER;
212 typedef MolGraph::out_edge_iterator OEDGE_ITER;
213 typedef MolGraph::vertex_iterator VERTEX_ITER;
214 typedef MolGraph::adjacency_iterator ADJ_ITER;
215 typedef std::pair<EDGE_ITER, EDGE_ITER> BOND_ITER_PAIR;
216 typedef std::pair<OEDGE_ITER, OEDGE_ITER> OBOND_ITER_PAIR;
217 typedef std::pair<VERTEX_ITER, VERTEX_ITER> ATOM_ITER_PAIR;
218 typedef std::pair<ADJ_ITER, ADJ_ITER> ADJ_ITER_PAIR;
220 typedef std::vector<Atom *> ATOM_PTR_VECT;
221 typedef ATOM_PTR_VECT::iterator ATOM_PTR_VECT_I;
222 typedef ATOM_PTR_VECT::const_iterator ATOM_PTR_VECT_CI;
223 typedef std::vector<Bond *> BOND_PTR_VECT;
224 typedef BOND_PTR_VECT::iterator BOND_PTR_VECT_I;
225 typedef BOND_PTR_VECT::const_iterator BOND_PTR_VECT_CI;
227 typedef std::list<Atom *> ATOM_PTR_LIST;
228 typedef ATOM_PTR_LIST::iterator ATOM_PTR_LIST_I;
229 typedef ATOM_PTR_LIST::const_iterator ATOM_PTR_LIST_CI;
230 typedef std::list<Bond *> BOND_PTR_LIST;
231 typedef BOND_PTR_LIST::iterator BOND_PTR_LIST_I;
232 typedef BOND_PTR_LIST::const_iterator BOND_PTR_LIST_CI;
235 typedef std::list<CONFORMER_SPTR> CONF_SPTR_LIST;
236 typedef CONF_SPTR_LIST::iterator CONF_SPTR_LIST_I;
237 typedef CONF_SPTR_LIST::const_iterator CONF_SPTR_LIST_CI;
238 typedef std::pair<CONF_SPTR_LIST_I, CONF_SPTR_LIST_I> CONFS_I_PAIR;
241 typedef std::map<int, ATOM_PTR_LIST> ATOM_BOOKMARK_MAP;
242 typedef std::map<int, BOND_PTR_LIST> BOND_BOOKMARK_MAP;
250 ConstAromaticAtomIterator;
253 ConstHeteroatomIterator;
256 ConstQueryAtomIterator;
259 ConstMatchingAtomIterator;
261 typedef CONF_SPTR_LIST_I ConformerIterator;
262 typedef CONF_SPTR_LIST_CI ConstConformerIterator;
285 auto pr = getAtomNeighbors(at);
286 return {&d_graph, pr.first, pr.second};
291 auto pr = getAtomNeighbors(at);
292 return {&d_graph, pr.first, pr.second};
297 auto pr = getAtomBonds(at);
298 return {&d_graph, pr.first, pr.second};
303 auto pr = getAtomBonds(at);
304 return {&d_graph, pr.first, pr.second};
335 ROMol(
const ROMol &other,
bool quickCopy =
false,
int confId = -1)
337 dp_ringInfo =
nullptr;
338 initFromOther(other, quickCopy, confId);
339 numBonds = rdcast<unsigned int>(boost::num_edges(d_graph));
344 ROMol(
const std::string &binStr,
unsigned int propertyFlags);
348 d_graph(std::move(o.d_graph)),
349 d_atomBookmarks(std::move(o.d_atomBookmarks)),
350 d_bondBookmarks(std::move(o.d_bondBookmarks)),
351 d_confs(std::move(o.d_confs)),
352 d_sgroups(std::move(o.d_sgroups)),
353 d_stereo_groups(std::move(o.d_stereo_groups)),
354 numBonds(o.numBonds) {
355 for (
auto atom : atoms()) {
356 atom->setOwningMol(
this);
358 for (
auto bond : bonds()) {
359 bond->setOwningMol(
this);
361 for (
auto conf : d_confs) {
362 conf->setOwningMol(
this);
366 dp_ringInfo = std::exchange(o.dp_ringInfo,
nullptr);
367 dp_delAtoms = std::exchange(o.dp_delAtoms,
nullptr);
368 dp_delBonds = std::exchange(o.dp_delBonds,
nullptr);
374 RDProps::operator=(std::move(o));
375 d_graph = std::move(o.d_graph);
376 d_atomBookmarks = std::move(o.d_atomBookmarks);
377 d_bondBookmarks = std::move(o.d_bondBookmarks);
381 dp_ringInfo = std::exchange(o.dp_ringInfo,
nullptr);
383 d_confs = std::move(o.d_confs);
384 d_sgroups = std::move(o.d_sgroups);
385 d_stereo_groups = std::move(o.d_stereo_groups);
386 dp_delAtoms = std::exchange(o.dp_delAtoms,
nullptr);
387 dp_delBonds = std::exchange(o.dp_delBonds,
nullptr);
388 numBonds = o.numBonds;
391 for (
auto atom : atoms()) {
392 atom->setOwningMol(
this);
394 for (
auto bond : bonds()) {
395 bond->setOwningMol(
this);
397 for (
auto conf : d_confs) {
398 conf->setOwningMol(
this);
416 return rdcast<unsigned int>(boost::num_vertices(d_graph));
428 return getAtomWithIdx(rdcast<unsigned int>(idx));
433 return getAtomWithIdx(rdcast<unsigned int>(idx));
451 return getBondWithIdx(rdcast<unsigned int>(idx));
456 return getBondWithIdx(rdcast<unsigned int>(idx));
463 template <
class U,
class V>
465 return getBondBetweenAtoms(rdcast<unsigned int>(idx1),
466 rdcast<unsigned int>(idx2));
469 template <
class U,
class V>
471 return getBondBetweenAtoms(rdcast<unsigned int>(idx1),
472 rdcast<unsigned int>(idx2));
482 d_atomBookmarks[mark].push_back(at);
486 d_atomBookmarks[mark].clear();
487 d_atomBookmarks[mark].push_back(at);
510 d_bondBookmarks[mark].push_back(bond);
563 return rdcast<unsigned int>(d_confs.size());
728 bool (*query)(
const Atom *))
const;
739 return d_confs.begin();
742 inline ConstConformerIterator
endConformers()
const {
return d_confs.end(); }
782 return d_stereo_groups;
794#ifdef RDK_USE_BOOST_SERIALIZATION
797 template <
class Archive>
798 void save(Archive &ar,
const unsigned int version)
const;
799 template <
class Archive>
800 void load(Archive &ar,
const unsigned int version);
801 BOOST_SERIALIZATION_SPLIT_MEMBER()
807 ATOM_BOOKMARK_MAP d_atomBookmarks;
808 BOND_BOOKMARK_MAP d_bondBookmarks;
810 CONF_SPTR_LIST d_confs;
811 std::vector<SubstanceGroup> d_sgroups;
812 std::vector<StereoGroup> d_stereo_groups;
813 std::unique_ptr<boost::dynamic_bitset<>> dp_delAtoms =
nullptr;
814 std::unique_ptr<boost::dynamic_bitset<>> dp_delBonds =
nullptr;
820 void clearSubstanceGroups() { d_sgroups.clear(); }
823 unsigned int numBonds{0};
828 virtual void destroy();
840 unsigned int addAtom(
Atom *atom,
bool updateLabel =
true,
841 bool takeOwnership =
false);
851 unsigned int addBond(
Bond *bond,
bool takeOwnership =
false);
863 void initFromOther(
const ROMol &other,
bool quickCopy,
int confId);
Defines the Atom class and associated typedefs.
Defines the class StereoGroup which stores relationships between the absolute configurations of atoms...
Defines the SubstanceGroup class.
Iterate over aromatic atoms, this is bidirectional.
A general random access iterator.
The class for representing atoms.
iterator for a molecule's bonds, currently BiDirectional, but it theoretically ought to be RandomAcce...
class for representing a bond
const iterator for a molecule's bonds, currently BiDirectional, but it theoretically ought to be Rand...
Iterate over heteroatoms, this is bidirectional.
Iterate over atoms matching a query function. This is bidirectional.
handles pickling (serializing) molecules
Iterate over atoms matching a query. This is bidirectional.
Class for storing atomic queries.
Class for storing Bond queries.
ConstAromaticAtomIterator endAromaticAtoms() const
This is an overloaded member function, provided for convenience. It differs from the above function o...
ADJ_ITER_PAIR getAtomNeighbors(Atom const *at) const
provides access to all neighbors around an Atom
ConstQueryAtomIterator endQueryAtoms() const
This is an overloaded member function, provided for convenience. It differs from the above function o...
bool needsUpdatePropertyCache() const
OBOND_ITER_PAIR getAtomBonds(Atom const *at) const
provides access to all Bond objects connected to an Atom
unsigned int getNumBonds(bool onlyHeavy=1) const
returns our number of Bonds
CXXAtomIterator< const MolGraph, Atom *const > atoms() const
void clearAtomBookmark(int mark)
removes a bookmark from our collection
unsigned int getNumHeavyAtoms() const
returns our number of heavy atoms (atomic number > 1)
void clearAtomBookmark(int mark, const Atom *atom)
removes a particular Atom from the list associated with the bookmark
Atom * getAtomWithIdx(unsigned int idx)
returns a pointer to a particular Atom
unsigned int getNumConformers() const
AtomIterator endAtoms()
get an AtomIterator pointing at the end of our Atoms
BOND_PTR_LIST & getAllBondsWithBookmark(int mark)
returns all bonds associated with the bookmark provided
const std::vector< StereoGroup > & getStereoGroups() const
Gets a reference to the groups of atoms with relative stereochemistry.
ConstAtomIterator endAtoms() const
This is an overloaded member function, provided for convenience. It differs from the above function o...
BondIterator beginBonds()
get a BondIterator pointing at our first Bond
bool hasAtomBookmark(int mark) const
queries whether or not any atoms are associated with a bookmark
Atom * getAtomWithIdx(const U idx)
This is an overloaded member function, provided for convenience. It differs from the above function o...
ConstQueryAtomIterator beginQueryAtoms(QueryAtom const *) const
This is an overloaded member function, provided for convenience. It differs from the above function o...
unsigned int getNumAtoms() const
returns our number of atoms
ConstConformerIterator endConformers() const
ConstMatchingAtomIterator beginMatchingAtoms(bool(*query)(const Atom *)) const
This is an overloaded member function, provided for convenience. It differs from the above function o...
ROMol & operator=(ROMol &&o) noexcept
ROMol(const ROMol &other, bool quickCopy=false, int confId=-1)
copy constructor with a twist
ROMol & operator=(const ROMol &)=delete
Bond * getUniqueBondWithBookmark(int mark)
ConstMatchingAtomIterator endMatchingAtoms() const
This is an overloaded member function, provided for convenience. It differs from the above function o...
BOND_ITER_PAIR getEdges()
returns an iterator pair for looping over all Bonds
void clearConformers()
Clear all the conformations on the molecule.
void setBondBookmark(Bond *bond, int mark)
associates a Bond pointer with a bookmark
void updatePropertyCache(bool strict=true)
calculates any of our lazy properties
CXXAtomIterator< MolGraph, Atom * > atoms()
C++11 Range iterator.
Atom * getAtomWithBookmark(int mark)
returns the first Atom associated with the bookmark provided
CXXAtomIterator< const MolGraph, Atom *const, MolGraph::adjacency_iterator > atomNeighbors(Atom const *at) const
BOND_BOOKMARK_MAP * getBondBookmarks()
returns a pointer to all of our bond bookmarks
Conformer & getConformer(int id=-1)
QueryAtomIterator endQueryAtoms()
get an AtomIterator pointing at the end of our Atoms
const Conformer & getConformer(int id=-1) const
unsigned int addConformer(Conformer *conf, bool assignId=false)
Add a new conformation to the molecule.
const Atom * operator[](const vertex_descriptor &v) const
void clearAllBondBookmarks()
blows out all bond bookmarks
const Atom * getAtomWithIdx(const U idx) const
This is an overloaded member function, provided for convenience. It differs from the above function o...
CXXBondIterator< MolGraph, Bond * > bonds()
ATOM_ITER_PAIR getVertices()
returns an iterator pair for looping over all Atoms
BOND_ITER_PAIR getEdges() const
This is an overloaded member function, provided for convenience. It differs from the above function o...
void clearComputedProps(bool includeRings=true) const
clears all of our computed properties
const Bond * getBondWithIdx(const U idx) const
This is an overloaded member function, provided for convenience. It differs from the above function o...
ATOM_PTR_LIST & getAllAtomsWithBookmark(int mark)
returns all Atoms associated with the bookmark provided
const Bond * getBondBetweenAtoms(unsigned int idx1, unsigned int idx2) const
This is an overloaded member function, provided for convenience. It differs from the above function o...
ROMol(const std::string &binStr, unsigned int propertyFlags)
construct a molecule from a pickle string
Bond * getBondWithIdx(const U idx)
This is an overloaded member function, provided for convenience. It differs from the above function o...
ATOM_BOOKMARK_MAP * getAtomBookmarks()
returns a pointer to all of our atom bookmarks
ConstAtomIterator beginAtoms() const
This is an overloaded member function, provided for convenience. It differs from the above function o...
ConstAromaticAtomIterator beginAromaticAtoms() const
This is an overloaded member function, provided for convenience. It differs from the above function o...
CXXAtomIterator< MolGraph, Atom *, MolGraph::adjacency_iterator > atomNeighbors(Atom const *at)
void debugMol(std::ostream &str) const
const Bond * getBondBetweenAtoms(const U idx1, const V idx2) const
This is an overloaded member function, provided for convenience. It differs from the above function o...
void setAtomBookmark(Atom *at, int mark)
associates an Atom pointer with a bookmark
MatchingAtomIterator endMatchingAtoms()
get an AtomIterator pointing at the end of our Atoms
ConstBondIterator beginBonds() const
This is an overloaded member function, provided for convenience. It differs from the above function o...
BondIterator endBonds()
get a BondIterator pointing at the end of our Bonds
ROMol(const std::string &binStr)
construct a molecule from a pickle string
Atom * getUniqueAtomWithBookmark(int mark)
QueryAtomIterator beginQueryAtoms(QueryAtom const *query)
get an AtomIterator pointing at our first Atom that matches query
friend RDKIT_GRAPHMOL_EXPORT std::vector< SubstanceGroup > & getSubstanceGroups(ROMol &)
ConstHeteroatomIterator endHeteros() const
This is an overloaded member function, provided for convenience. It differs from the above function o...
void replaceAtomBookmark(Atom *at, int mark)
associates an Atom pointer with a bookmark
Bond * getBondWithBookmark(int mark)
returns the first Bond associated with the bookmark provided
CXXBondIterator< const MolGraph, Bond *const, MolGraph::out_edge_iterator > atomBonds(Atom const *at) const
unsigned int getAtomDegree(const Atom *at) const
returns the degree (number of neighbors) of an Atom in the graph
void setStereoGroups(std::vector< StereoGroup > stereo_groups)
Sets groups of atoms with relative stereochemistry.
CXXBondIterator< MolGraph, Bond *, MolGraph::out_edge_iterator > atomBonds(Atom const *at)
AromaticAtomIterator endAromaticAtoms()
get an AtomIterator pointing at the end of our Atoms
RingInfo * getRingInfo() const
void clearAllAtomBookmarks()
blows out all atomic bookmarks
const Bond * operator[](const edge_descriptor &e) const
Bond * operator[](const edge_descriptor &e)
Bond * getBondWithIdx(unsigned int idx)
returns a pointer to a particular Bond
ConformerIterator beginConformers()
ConstBondIterator endBonds() const
This is an overloaded member function, provided for convenience. It differs from the above function o...
unsigned int getNumAtoms(bool onlyExplicit) const
HeteroatomIterator endHeteros()
get an AtomIterator pointing at the end of our Atoms
ROMol(ROMol &&o) noexcept
Bond * getBondBetweenAtoms(const U idx1, const V idx2)
This is an overloaded member function, provided for convenience. It differs from the above function o...
ConstConformerIterator beginConformers() const
void clearBondBookmark(int mark, const Bond *bond)
removes a particular Bond from the list associated with the bookmark
MatchingAtomIterator beginMatchingAtoms(bool(*query)(Atom *))
get an AtomIterator pointing at our first Atom that matches query
MolGraph const & getTopology() const
brief returns a pointer to our underlying BGL object
bool hasBondBookmark(int mark) const
queries whether or not any bonds are associated with a bookmark
const Bond * getBondWithIdx(unsigned int idx) const
This is an overloaded member function, provided for convenience. It differs from the above function o...
AtomIterator beginAtoms()
get an AtomIterator pointing at our first Atom
const Atom * getAtomWithIdx(unsigned int idx) const
This is an overloaded member function, provided for convenience. It differs from the above function o...
void removeConformer(unsigned int id)
Delete the conformation with the specified ID.
AromaticAtomIterator beginAromaticAtoms()
get an AtomIterator pointing at our first aromatic Atom
Atom * operator[](const vertex_descriptor &v)
ConstHeteroatomIterator beginHeteros() const
This is an overloaded member function, provided for convenience. It differs from the above function o...
friend RDKIT_GRAPHMOL_EXPORT const std::vector< SubstanceGroup > & getSubstanceGroups(const ROMol &)
ConformerIterator endConformers()
ATOM_ITER_PAIR getVertices() const
This is an overloaded member function, provided for convenience. It differs from the above function o...
void clearBondBookmark(int mark)
removes a bookmark from our collection
HeteroatomIterator beginHeteros()
get an AtomIterator pointing at our first hetero Atom
Bond * getBondBetweenAtoms(unsigned int idx1, unsigned int idx2)
returns a pointer to the bond between two atoms, Null on failure
CXXBondIterator< const MolGraph, Bond *const > bonds() const
RWMol is a molecule class that is intended to be edited.
A class to store information about a molecule's rings.
#define RDKIT_GRAPHMOL_EXPORT
std::vector< ROMol > MOL_VECT
MOL_PTR_VECT::const_iterator MOL_PTR_VECT_CI
RDKIT_GRAPHMOL_EXPORT const int ci_RIGHTMOST_ATOM
RDKIT_GRAPHMOL_EXPORT const int ci_ATOM_HOLDER
bool rdvalue_is(const RDValue_cast_t)
std::vector< ROMol * > MOL_PTR_VECT
boost::shared_ptr< ROMol > ROMOL_SPTR
MOL_PTR_VECT::iterator MOL_PTR_VECT_I
boost::adjacency_list< boost::vecS, boost::vecS, boost::undirectedS, Atom *, Bond * > MolGraph
This is the BGL type used to store the topology:
std::vector< boost::shared_ptr< ROMol > > MOL_SPTR_VECT
RDKIT_GRAPHMOL_EXPORT const int ci_LEADING_BOND
std::forward_iterator_tag iterator_category
std::ptrdiff_t difference_type
CXXAtomIter & operator++()
bool operator==(const CXXAtomIter &it) const
CXXAtomIter(Graph *graph, Iterator pos)
bool operator!=(const CXXAtomIter &it) const
CXXAtomIterator(Graph *graph, Iterator start, Iterator end)
CXXAtomIterator(Graph *graph)
std::forward_iterator_tag iterator_category
CXXBondIter(Graph *graph, Iterator pos)
bool operator==(const CXXBondIter &it) const
std::ptrdiff_t difference_type
bool operator!=(const CXXBondIter &it) const
CXXBondIter & operator++()
CXXBondIterator(Graph *graph)
CXXBondIterator(Graph *graph, Iterator start, Iterator end)