27 #include <boost/graph/adjacency_list.hpp>
28 #include <boost/smart_ptr.hpp>
29 #include <boost/dynamic_bitset.hpp>
46 typedef boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS,
55 template <
class T1,
class T2>
60 template <
class T1,
class T2>
62 template <
class T1,
class T2>
64 template <
class T1,
class T2>
66 template <
class T1,
class T2>
106 template <
class Graph,
class Vertex,
107 class Iterator =
typename Graph::vertex_iterator>
132 auto vs = boost::vertices(*
graph);
142 template <
class Graph,
class Edge,
143 class Iterator =
typename Graph::edge_iterator>
168 auto vs = boost::edges(*
graph);
187 typedef MolGraph::vertex_descriptor vertex_descriptor;
188 typedef MolGraph::edge_descriptor edge_descriptor;
190 typedef MolGraph::edge_iterator EDGE_ITER;
191 typedef MolGraph::out_edge_iterator OEDGE_ITER;
192 typedef MolGraph::vertex_iterator VERTEX_ITER;
193 typedef MolGraph::adjacency_iterator ADJ_ITER;
194 typedef std::pair<EDGE_ITER, EDGE_ITER> BOND_ITER_PAIR;
195 typedef std::pair<OEDGE_ITER, OEDGE_ITER> OBOND_ITER_PAIR;
196 typedef std::pair<VERTEX_ITER, VERTEX_ITER> ATOM_ITER_PAIR;
197 typedef std::pair<ADJ_ITER, ADJ_ITER> ADJ_ITER_PAIR;
199 typedef std::vector<Atom *> ATOM_PTR_VECT;
200 typedef ATOM_PTR_VECT::iterator ATOM_PTR_VECT_I;
201 typedef ATOM_PTR_VECT::const_iterator ATOM_PTR_VECT_CI;
202 typedef std::vector<Bond *> BOND_PTR_VECT;
203 typedef BOND_PTR_VECT::iterator BOND_PTR_VECT_I;
204 typedef BOND_PTR_VECT::const_iterator BOND_PTR_VECT_CI;
206 typedef std::list<Atom *> ATOM_PTR_LIST;
207 typedef ATOM_PTR_LIST::iterator ATOM_PTR_LIST_I;
208 typedef ATOM_PTR_LIST::const_iterator ATOM_PTR_LIST_CI;
209 typedef std::list<Bond *> BOND_PTR_LIST;
210 typedef BOND_PTR_LIST::iterator BOND_PTR_LIST_I;
211 typedef BOND_PTR_LIST::const_iterator BOND_PTR_LIST_CI;
214 typedef std::list<CONFORMER_SPTR> CONF_SPTR_LIST;
215 typedef CONF_SPTR_LIST::iterator CONF_SPTR_LIST_I;
216 typedef CONF_SPTR_LIST::const_iterator CONF_SPTR_LIST_CI;
217 typedef std::pair<CONF_SPTR_LIST_I, CONF_SPTR_LIST_I> CONFS_I_PAIR;
220 typedef std::map<int, ATOM_PTR_LIST> ATOM_BOOKMARK_MAP;
221 typedef std::map<int, BOND_PTR_LIST> BOND_BOOKMARK_MAP;
229 ConstAromaticAtomIterator;
232 ConstHeteroatomIterator;
235 ConstQueryAtomIterator;
238 ConstMatchingAtomIterator;
240 typedef CONF_SPTR_LIST_I ConformerIterator;
241 typedef CONF_SPTR_LIST_CI ConstConformerIterator;
264 auto pr = getAtomNeighbors(at);
265 return {&d_graph, pr.first, pr.second};
270 auto pr = getAtomNeighbors(at);
271 return {&d_graph, pr.first, pr.second};
276 auto pr = getAtomBonds(at);
277 return {&d_graph, pr.first, pr.second};
282 auto pr = getAtomBonds(at);
283 return {&d_graph, pr.first, pr.second};
314 ROMol(
const ROMol &other,
bool quickCopy =
false,
int confId = -1)
316 dp_ringInfo =
nullptr;
317 initFromOther(other, quickCopy, confId);
318 numBonds = rdcast<unsigned int>(boost::num_edges(d_graph));
323 ROMol(
const std::string &binStr,
unsigned int propertyFlags);
333 return rdcast<unsigned int>(boost::num_vertices(d_graph));
345 return getAtomWithIdx(rdcast<unsigned int>(idx));
350 return getAtomWithIdx(rdcast<unsigned int>(idx));
368 return getBondWithIdx(rdcast<unsigned int>(idx));
373 return getBondWithIdx(rdcast<unsigned int>(idx));
380 template <
class U,
class V>
382 return getBondBetweenAtoms(rdcast<unsigned int>(idx1),
383 rdcast<unsigned int>(idx2));
386 template <
class U,
class V>
388 return getBondBetweenAtoms(rdcast<unsigned int>(idx1),
389 rdcast<unsigned int>(idx2));
399 d_atomBookmarks[mark].push_back(at);
403 d_atomBookmarks[mark].clear();
404 d_atomBookmarks[mark].push_back(at);
427 d_bondBookmarks[mark].push_back(bond);
480 return rdcast<unsigned int>(d_confs.size());
645 bool (*query)(
const Atom *))
const;
656 return d_confs.begin();
659 inline ConstConformerIterator
endConformers()
const {
return d_confs.end(); }
699 return d_stereo_groups;
704 ATOM_BOOKMARK_MAP d_atomBookmarks;
705 BOND_BOOKMARK_MAP d_bondBookmarks;
707 CONF_SPTR_LIST d_confs;
708 std::vector<SubstanceGroup> d_sgroups;
709 std::vector<StereoGroup> d_stereo_groups;
710 std::unique_ptr<boost::dynamic_bitset<>> dp_delAtoms =
nullptr;
711 std::unique_ptr<boost::dynamic_bitset<>> dp_delBonds =
nullptr;
717 void clearSubstanceGroups() { d_sgroups.clear(); }
723 unsigned int numBonds{0};
728 virtual void destroy();
740 unsigned int addAtom(
Atom *atom,
bool updateLabel =
true,
741 bool takeOwnership =
false);
751 unsigned int addBond(
Bond *bond,
bool takeOwnership =
false);
760 void setStereoGroups(std::vector<StereoGroup> stereo_groups);
771 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...
CXXBondIterator< MolGraph, Bond * > bonds()
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...
const Bond * operator[](const edge_descriptor &e) const
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
CXXBondIterator< const MolGraph, Bond *const > bonds() const
void clearAtomBookmark(int mark)
removes a bookmark from our collection
Bond * getBondBetweenAtoms(const U idx1, const V idx2)
This is an overloaded member function, provided for convenience. It differs from the above function o...
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
const Atom * getAtomWithIdx(const U idx) const
This is an overloaded member function, provided for convenience. It differs from the above function o...
unsigned int getNumConformers() const
AtomIterator endAtoms()
get an AtomIterator pointing at the end of our Atoms
Bond * getBondWithIdx(unsigned int idx)
returns a pointer to a particular Bond
RingInfo * getRingInfo() const
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
MolGraph const & getTopology() const
brief returns a pointer to our underlying BGL object
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(const ROMol &other, bool quickCopy=false, int confId=-1)
copy constructor with a twist
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
ATOM_PTR_LIST & getAllAtomsWithBookmark(int mark)
returns all Atoms associated with the bookmark provided
Bond * getBondWithBookmark(int mark)
returns the first Bond associated with the bookmark provided
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...
BOND_BOOKMARK_MAP * getBondBookmarks()
returns a pointer to all of our bond bookmarks
Atom * getAtomWithIdx(const U idx)
This is an overloaded member function, provided for convenience. It differs from the above function o...
const Bond * getBondWithIdx(const U idx) const
This is an overloaded member function, provided for convenience. It differs from the above function o...
QueryAtomIterator endQueryAtoms()
get an AtomIterator pointing at the end of our Atoms
BOND_PTR_LIST & getAllBondsWithBookmark(int mark)
returns all bonds associated with the bookmark provided
unsigned int addConformer(Conformer *conf, bool assignId=false)
Add a new conformation to the molecule.
Bond * getBondWithIdx(const U idx)
This is an overloaded member function, provided for convenience. It differs from the above function o...
void clearAllBondBookmarks()
blows out all bond bookmarks
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...
friend RDKIT_GRAPHMOL_EXPORT std::vector< SubstanceGroup > & getSubstanceGroups(ROMol &)
void clearComputedProps(bool includeRings=true) const
clears all of our computed properties
Atom * operator[](const vertex_descriptor &v)
ROMol(const std::string &binStr, unsigned int propertyFlags)
construct a molecule from a pickle string
ConstAtomIterator beginAtoms() const
This is an overloaded member function, provided for convenience. It differs from the above function o...
const Bond * getBondWithIdx(unsigned int idx) 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...
void debugMol(std::ostream &str) const
sends some debugging info to a stream
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...
void setAtomBookmark(Atom *at, int mark)
associates an Atom pointer with a bookmark
const std::vector< StereoGroup > & getStereoGroups() const
Gets a reference to the groups of atoms with relative stereochemistry.
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...
CXXAtomIterator< MolGraph, Atom * > atoms()
C++11 Range iterator.
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
ConstHeteroatomIterator endHeteros() const
This is an overloaded member function, provided for convenience. It differs from the above function o...
Atom * getAtomWithIdx(unsigned int idx)
returns a pointer to a particular Atom
Atom * getAtomWithBookmark(int mark)
returns the first Atom associated with the bookmark provided
CXXAtomIterator< const MolGraph, Atom *const > atoms() const
void replaceAtomBookmark(Atom *at, int mark)
associates an Atom pointer with a bookmark
CXXBondIterator< MolGraph, Bond *, MolGraph::out_edge_iterator > atomBonds(Atom const *at)
unsigned int getAtomDegree(const Atom *at) const
returns the degree (number of neighbors) of an Atom in the graph
AromaticAtomIterator endAromaticAtoms()
get an AtomIterator pointing at the end of our Atoms
void clearAllAtomBookmarks()
blows out all atomic bookmarks
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
CXXBondIterator< const MolGraph, Bond *const, MolGraph::out_edge_iterator > atomBonds(Atom const *at) const
const Atom * operator[](const vertex_descriptor &v) const
HeteroatomIterator endHeteros()
get an AtomIterator pointing at the end of our Atoms
Bond * getBondBetweenAtoms(unsigned int idx1, unsigned int idx2)
returns a pointer to the bond between two atoms, Null on failure
ConstConformerIterator beginConformers() const
void clearBondBookmark(int mark, const Bond *bond)
removes a particular Bond from the list associated with the bookmark
Conformer & getConformer(int id=-1)
friend RDKIT_GRAPHMOL_EXPORT const std::vector< SubstanceGroup > & getSubstanceGroups(const ROMol &)
ATOM_BOOKMARK_MAP * getAtomBookmarks()
returns a pointer to all of our atom bookmarks
MatchingAtomIterator beginMatchingAtoms(bool(*query)(Atom *))
get an AtomIterator pointing at our first Atom that matches query
CXXAtomIterator< const MolGraph, Atom *const, MolGraph::adjacency_iterator > atomNeighbors(Atom const *at) const
bool hasBondBookmark(int mark) const
queries whether or not any bonds are associated with a bookmark
Bond * operator[](const edge_descriptor &e)
CXXAtomIterator< MolGraph, Atom *, MolGraph::adjacency_iterator > atomNeighbors(Atom const *at)
AtomIterator beginAtoms()
get an AtomIterator pointing at our first Atom
Bond * getUniqueBondWithBookmark(int mark)
void removeConformer(unsigned int id)
Delete the conformation with the specified ID.
AromaticAtomIterator beginAromaticAtoms()
get an AtomIterator pointing at our first aromatic Atom
ConstHeteroatomIterator beginHeteros() const
This is an overloaded member function, provided for convenience. It differs from the above function o...
const Conformer & getConformer(int id=-1) const
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
const Atom * getAtomWithIdx(unsigned int idx) const
This is an overloaded member function, provided for convenience. It differs from the above function o...
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(Graph *graph, Iterator pos)
CXXAtomIter & operator++()
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)