27#include <boost/graph/adjacency_list.hpp>
28#include <boost/smart_ptr.hpp>
29#include <boost/dynamic_bitset.hpp>
47typedef boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS,
56template <
class T1,
class T2>
61template <
class T1,
class T2>
63template <
class T1,
class T2>
65template <
class T1,
class T2>
67template <
class T1,
class T2>
107template <
class Graph,
class Vertex,
108 class Iterator =
typename Graph::vertex_iterator>
133 auto vs = boost::vertices(*
graph);
143template <
class Graph,
class Edge,
144 class Iterator =
typename Graph::edge_iterator>
169 auto vs = boost::edges(*
graph);
188 typedef MolGraph::vertex_descriptor vertex_descriptor;
189 typedef MolGraph::edge_descriptor edge_descriptor;
191 typedef MolGraph::edge_iterator EDGE_ITER;
192 typedef MolGraph::out_edge_iterator OEDGE_ITER;
193 typedef MolGraph::vertex_iterator VERTEX_ITER;
194 typedef MolGraph::adjacency_iterator ADJ_ITER;
195 typedef std::pair<EDGE_ITER, EDGE_ITER> BOND_ITER_PAIR;
196 typedef std::pair<OEDGE_ITER, OEDGE_ITER> OBOND_ITER_PAIR;
197 typedef std::pair<VERTEX_ITER, VERTEX_ITER> ATOM_ITER_PAIR;
198 typedef std::pair<ADJ_ITER, ADJ_ITER> ADJ_ITER_PAIR;
200 typedef std::vector<Atom *> ATOM_PTR_VECT;
201 typedef ATOM_PTR_VECT::iterator ATOM_PTR_VECT_I;
202 typedef ATOM_PTR_VECT::const_iterator ATOM_PTR_VECT_CI;
203 typedef std::vector<Bond *> BOND_PTR_VECT;
204 typedef BOND_PTR_VECT::iterator BOND_PTR_VECT_I;
205 typedef BOND_PTR_VECT::const_iterator BOND_PTR_VECT_CI;
207 typedef std::list<Atom *> ATOM_PTR_LIST;
208 typedef ATOM_PTR_LIST::iterator ATOM_PTR_LIST_I;
209 typedef ATOM_PTR_LIST::const_iterator ATOM_PTR_LIST_CI;
210 typedef std::list<Bond *> BOND_PTR_LIST;
211 typedef BOND_PTR_LIST::iterator BOND_PTR_LIST_I;
212 typedef BOND_PTR_LIST::const_iterator BOND_PTR_LIST_CI;
215 typedef std::list<CONFORMER_SPTR> CONF_SPTR_LIST;
216 typedef CONF_SPTR_LIST::iterator CONF_SPTR_LIST_I;
217 typedef CONF_SPTR_LIST::const_iterator CONF_SPTR_LIST_CI;
218 typedef std::pair<CONF_SPTR_LIST_I, CONF_SPTR_LIST_I> CONFS_I_PAIR;
221 typedef std::map<int, ATOM_PTR_LIST> ATOM_BOOKMARK_MAP;
222 typedef std::map<int, BOND_PTR_LIST> BOND_BOOKMARK_MAP;
230 ConstAromaticAtomIterator;
233 ConstHeteroatomIterator;
236 ConstQueryAtomIterator;
239 ConstMatchingAtomIterator;
241 typedef CONF_SPTR_LIST_I ConformerIterator;
242 typedef CONF_SPTR_LIST_CI ConstConformerIterator;
265 auto pr = getAtomNeighbors(at);
266 return {&d_graph, pr.first, pr.second};
271 auto pr = getAtomNeighbors(at);
272 return {&d_graph, pr.first, pr.second};
277 auto pr = getAtomBonds(at);
278 return {&d_graph, pr.first, pr.second};
283 auto pr = getAtomBonds(at);
284 return {&d_graph, pr.first, pr.second};
315 ROMol(
const ROMol &other,
bool quickCopy =
false,
int confId = -1)
317 dp_ringInfo =
nullptr;
318 initFromOther(other, quickCopy, confId);
319 numBonds = rdcast<unsigned int>(boost::num_edges(d_graph));
324 ROMol(
const std::string &binStr,
unsigned int propertyFlags);
328 d_graph(std::move(o.d_graph)),
329 d_atomBookmarks(std::move(o.d_atomBookmarks)),
330 d_bondBookmarks(std::move(o.d_bondBookmarks)),
331 d_confs(std::move(o.d_confs)),
332 d_sgroups(std::move(o.d_sgroups)),
333 d_stereo_groups(std::move(o.d_stereo_groups)),
334 numBonds(o.numBonds) {
335 for (
auto atom : atoms()) {
336 atom->setOwningMol(
this);
338 for (
auto bond : bonds()) {
339 bond->setOwningMol(
this);
341 for (
auto conf : d_confs) {
342 conf->setOwningMol(
this);
346 dp_ringInfo = std::exchange(o.dp_ringInfo,
nullptr);
347 dp_delAtoms = std::exchange(o.dp_delAtoms,
nullptr);
348 dp_delBonds = std::exchange(o.dp_delBonds,
nullptr);
355 d_graph = std::move(o.d_graph);
356 d_atomBookmarks = std::move(o.d_atomBookmarks);
357 d_bondBookmarks = std::move(o.d_bondBookmarks);
361 dp_ringInfo = std::exchange(o.dp_ringInfo,
nullptr);
363 d_confs = std::move(o.d_confs);
364 d_sgroups = std::move(o.d_sgroups);
365 d_stereo_groups = std::move(o.d_stereo_groups);
366 dp_delAtoms = std::exchange(o.dp_delAtoms,
nullptr);
367 dp_delBonds = std::exchange(o.dp_delBonds,
nullptr);
368 numBonds = o.numBonds;
371 for (
auto atom : atoms()) {
372 atom->setOwningMol(
this);
374 for (
auto bond : bonds()) {
375 bond->setOwningMol(
this);
377 for (
auto conf : d_confs) {
378 conf->setOwningMol(
this);
396 return rdcast<unsigned int>(boost::num_vertices(d_graph));
408 return getAtomWithIdx(rdcast<unsigned int>(idx));
413 return getAtomWithIdx(rdcast<unsigned int>(idx));
431 return getBondWithIdx(rdcast<unsigned int>(idx));
436 return getBondWithIdx(rdcast<unsigned int>(idx));
443 template <
class U,
class V>
445 return getBondBetweenAtoms(rdcast<unsigned int>(idx1),
446 rdcast<unsigned int>(idx2));
449 template <
class U,
class V>
451 return getBondBetweenAtoms(rdcast<unsigned int>(idx1),
452 rdcast<unsigned int>(idx2));
462 d_atomBookmarks[mark].push_back(at);
466 d_atomBookmarks[mark].clear();
467 d_atomBookmarks[mark].push_back(at);
490 d_bondBookmarks[mark].push_back(bond);
543 return rdcast<unsigned int>(d_confs.size());
708 bool (*query)(
const Atom *))
const;
719 return d_confs.begin();
722 inline ConstConformerIterator
endConformers()
const {
return d_confs.end(); }
762 return d_stereo_groups;
776 ATOM_BOOKMARK_MAP d_atomBookmarks;
777 BOND_BOOKMARK_MAP d_bondBookmarks;
779 CONF_SPTR_LIST d_confs;
780 std::vector<SubstanceGroup> d_sgroups;
781 std::vector<StereoGroup> d_stereo_groups;
782 std::unique_ptr<boost::dynamic_bitset<>> dp_delAtoms =
nullptr;
783 std::unique_ptr<boost::dynamic_bitset<>> dp_delBonds =
nullptr;
789 void clearSubstanceGroups() { d_sgroups.clear(); }
792 unsigned int numBonds{0};
797 virtual void destroy();
809 unsigned int addAtom(
Atom *atom,
bool updateLabel =
true,
810 bool takeOwnership =
false);
820 unsigned int addBond(
Bond *bond,
bool takeOwnership =
false);
832 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.
RDProps & operator=(const RDProps &rhs)
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
sends some debugging info to a stream
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
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
CXXAtomIter & operator++()
CXXAtomIter(Graph *graph, Iterator pos)
bool operator!=(const CXXAtomIter &it) const
CXXAtomIterator(Graph *graph, Iterator start, Iterator end)
CXXAtomIterator(Graph *graph)
CXXBondIter(Graph *graph, Iterator pos)
bool operator!=(const CXXBondIter &it) const
CXXBondIter & operator++()
CXXBondIterator(Graph *graph)
CXXBondIterator(Graph *graph, Iterator start, Iterator end)