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RDKit
Open-source cheminformatics and machine learning.
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Class for storing atomic queries. More...
#include <QueryAtom.h>
Public Types | |
typedef Queries::Query< int, Atom const *, true > | QUERYATOM_QUERY |
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enum | HybridizationType { UNSPECIFIED =0, S, SP, SP2, SP3, SP3D, SP3D2, OTHER } |
store hybridization More... | |
enum | ChiralType { CHI_UNSPECIFIED =0, CHI_TETRAHEDRAL_CW, CHI_TETRAHEDRAL_CCW, CHI_OTHER } |
store type of chirality More... | |
typedef boost::shared_ptr< Atom > | ATOM_SPTR |
typedef boost::shared_ptr< const Atom > | C_ATOM_SPTR |
typedef Queries::Query< int, Atom const *, true > | QUERYATOM_QUERY |
Public Member Functions | |
QueryAtom () | |
QueryAtom (int num) | |
QueryAtom (const Atom &other) | |
QueryAtom (const QueryAtom &other) | |
~QueryAtom () | |
Atom * | copy () const |
returns a copy of this query, owned by the caller More... | |
bool | hasQuery () const |
void | setQuery (QUERYATOM_QUERY *what) |
replaces our current query with the value passed in More... | |
QUERYATOM_QUERY * | getQuery () const |
returns our current query More... | |
void | expandQuery (QUERYATOM_QUERY *what, Queries::CompositeQueryType how=Queries::COMPOSITE_AND, bool maintainOrder=true) |
expands our current query More... | |
bool | Match (const Atom::ATOM_SPTR &what) const |
returns true if we match Atom what More... | |
bool | Match (Atom const *what) const |
bool | QueryMatch (QueryAtom const *what) const |
returns true if our query details match those of QueryAtom what More... | |
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Atom () | |
Atom (unsigned int num) | |
construct an Atom with a particular atomic number More... | |
Atom (std::string what) | |
construct an Atom with a particular symbol (looked up in the PeriodicTable) More... | |
Atom (const Atom &other) | |
virtual | ~Atom () |
int | getAtomicNum () const |
returns our atomic number More... | |
void | setAtomicNum (int newNum) |
sets our atomic number More... | |
std::string | getSymbol () const |
returns our symbol (determined by our atomic number) More... | |
ROMol & | getOwningMol () const |
returns a reference to the ROMol that owns this Atom More... | |
unsigned int | getIdx () const |
returns our index within the ROMol More... | |
void | setIdx (unsigned int index) |
sets our index within the ROMol More... | |
unsigned int | getDegree () const |
unsigned int | getTotalDegree () const |
unsigned int | getTotalNumHs (bool includeNeighbors=false) const |
returns the total number of Hs (implicit and explicit) that this Atom is bound to More... | |
unsigned int | getTotalValence () const |
returns the total valence (implicit and explicit) for an atom More... | |
unsigned int | getNumImplicitHs () const |
returns the number of implicit Hs this Atom is bound to More... | |
int | getExplicitValence () const |
returns the explicit valence (including Hs) of this atom More... | |
int | getImplicitValence () const |
returns the implicit valence for this Atom More... | |
unsigned int | getNumRadicalElectrons () const |
returns the number of radical electrons for this Atom More... | |
void | setNumRadicalElectrons (unsigned int num) |
int | getFormalCharge () const |
returns the formal charge of this atom More... | |
void | setFormalCharge (int what) |
set's the formal charge of this atom More... | |
void | setNoImplicit (bool what) |
sets our noImplicit flag, indicating whether or not we are allowed to have implicit Hs More... | |
bool | getNoImplicit () const |
returns the noImplicit flag More... | |
void | setNumExplicitHs (unsigned int what) |
sets our number of explict Hs More... | |
unsigned int | getNumExplicitHs () const |
returns our number of explict Hs More... | |
void | setIsAromatic (bool what) |
sets our isAromatic flag, indicating whether or not we are aromatic More... | |
bool | getIsAromatic () const |
returns our isAromatic flag More... | |
double | getMass () const |
returns our mass More... | |
void | setIsotope (unsigned int what) |
sets our isotope number More... | |
unsigned int | getIsotope () const |
returns our isotope number More... | |
void | setChiralTag (ChiralType what) |
sets our chiralTag More... | |
void | invertChirality () |
inverts our chiralTag More... | |
ChiralType | getChiralTag () const |
returns our chiralTag More... | |
void | setHybridization (HybridizationType what) |
sets our hybridization More... | |
HybridizationType | getHybridization () const |
returns our hybridization More... | |
STR_VECT | getPropList () const |
returns a list with the names of our properties More... | |
template<typename T > | |
void | setProp (const char *key, T val, bool computed=false) const |
sets a property value More... | |
template<typename T > | |
void | setProp (const std::string &key, T val, bool computed=false) const |
template<typename T > | |
void | getProp (const char *key, T &res) const |
allows retrieval of a particular property value More... | |
template<typename T > | |
void | getProp (const std::string &key, T &res) const |
template<typename T > | |
T | getProp (const char *key) const |
template<typename T > | |
T | getProp (const std::string &key) const |
template<typename T > | |
bool | getPropIfPresent (const char *key, T &res) const |
template<typename T > | |
bool | getPropIfPresent (const std::string &key, T &res) const |
bool | hasProp (const char *key) const |
returns whether or not we have a property with name key More... | |
bool | hasProp (const std::string &key) const |
void | clearProp (const char *key) const |
clears the value of a property More... | |
void | clearProp (const std::string &key) const |
void | clearComputedProps () const |
clears all of our computed properties More... | |
int | getPerturbationOrder (INT_LIST probe) const |
returns the perturbation order for a list of integers More... | |
void | updatePropertyCache (bool strict=true) |
calculates any of our lazy properties More... | |
bool | needsUpdatePropertyCache () const |
int | calcExplicitValence (bool strict=true) |
calculates and returns our explicit valence More... | |
int | calcImplicitValence (bool strict=true) |
calculates and returns our implicit valence More... | |
AtomMonomerInfo * | getMonomerInfo () |
const AtomMonomerInfo * | getMonomerInfo () const |
void | setMonomerInfo (AtomMonomerInfo *info) |
takes ownership of the pointer More... | |
Additional Inherited Members | |
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void | setOwningMol (ROMol *other) |
sets our owning molecule More... | |
void | setOwningMol (ROMol &other) |
sets our owning molecule More... | |
void | initAtom () |
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bool | df_isAromatic |
bool | df_noImplicit |
boost::uint8_t | d_numExplicitHs |
boost::int8_t | d_formalCharge |
boost::uint8_t | d_atomicNum |
boost::int8_t | d_implicitValence |
boost::int8_t | d_explicitValence |
boost::uint8_t | d_numRadicalElectrons |
boost::uint8_t | d_chiralTag |
boost::uint8_t | d_hybrid |
atomindex_t | d_index |
boost::uint16_t | d_isotope |
ROMol * | dp_mol |
Dict * | dp_props |
AtomMonomerInfo * | dp_monomerInfo |
Class for storing atomic queries.
QueryAtom objects are derived from Atom objects, so they can be added to molecules and the like, but they have much fancier querying capabilities.
Definition at line 26 of file QueryAtom.h.
typedef Queries::Query<int,Atom const *,true> RDKit::QueryAtom::QUERYATOM_QUERY |
Definition at line 28 of file QueryAtom.h.
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inline |
Definition at line 30 of file QueryAtom.h.
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inlineexplicit |
Definition at line 31 of file QueryAtom.h.
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inlineexplicit |
Definition at line 32 of file QueryAtom.h.
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inline |
Definition at line 33 of file QueryAtom.h.
References copy(), Queries::Query< MatchFuncArgType, DataFuncArgType, needsConversion >::copy(), and ~QueryAtom().
RDKit::QueryAtom::~QueryAtom | ( | ) |
Referenced by QueryAtom().
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virtual |
returns a copy of this query, owned by the caller
Reimplemented from RDKit::Atom.
Referenced by QueryAtom().
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virtual |
expands our current query
what | the Queries::Query to be added |
how | the operator to be used in the expansion |
maintainOrder | (optional) flags whether the relative order of the queries needs to be maintained, if this is false, the order is reversed Notes:
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Reimplemented from RDKit::Atom.
Referenced by getQuery().
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inlinevirtual |
returns our current query
Reimplemented from RDKit::Atom.
Definition at line 48 of file QueryAtom.h.
References Queries::COMPOSITE_AND, expandQuery(), Match(), and QueryMatch().
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inlinevirtual |
Reimplemented from RDKit::Atom.
Definition at line 43 of file QueryAtom.h.
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virtual |
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virtual |
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
Reimplemented from RDKit::Atom.
bool RDKit::QueryAtom::QueryMatch | ( | QueryAtom const * | what | ) | const |
returns true if our query details match those of QueryAtom what
Referenced by getQuery().
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inlinevirtual |
replaces our current query with the value passed in
Reimplemented from RDKit::Atom.
Definition at line 46 of file QueryAtom.h.