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RDKit
Open-source cheminformatics and machine learning.
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21 #include <boost/foreach.hpp>
101 explicit Atom(
unsigned int num);
104 explicit Atom(
const std::string &what);
113 virtual Atom *copy()
const;
121 std::string getSymbol()
const;
133 unsigned int getIdx()
const {
return d_index; };
140 void setIdx(
unsigned int index) { d_index = index; };
144 setIdx(rdcast<unsigned int>(index));
152 unsigned int getDegree()
const;
160 unsigned int getTotalDegree()
const;
168 unsigned int getTotalNumHs(
bool includeNeighbors =
false)
const;
176 unsigned int getTotalValence()
const;
183 unsigned int getNumImplicitHs()
const;
186 int getExplicitValence()
const;
193 int getImplicitValence()
const;
202 d_numRadicalElectrons = num;
227 double getMass()
const;
230 void setIsotope(
unsigned int what);
237 void invertChirality();
266 virtual void setQuery(QUERYATOM_QUERY *what);
269 virtual QUERYATOM_QUERY *getQuery()
const;
271 virtual void expandQuery(
272 QUERYATOM_QUERY *what,
274 bool maintainOrder =
true);
308 virtual bool Match(
Atom const *what)
const;
334 int getPerturbationOrder(
INT_LIST probe)
const;
342 void updatePropertyCache(
bool strict =
true);
344 bool needsUpdatePropertyCache()
const;
351 int calcExplicitValence(
bool strict =
true);
358 int calcImplicitValence(
bool strict =
true);
368 !strict || (mapno >= 0 && mapno < 1000),
369 "atom map number out of range [0..1000], use strict=false to override");
386 void setOwningMol(
ROMol *other);
409 void initFromOther(
const Atom &other);
431 const std::string &label);
RDKIT_GRAPHMOL_EXPORT bool isEarlyAtom(int atomicNum)
returns whether or not the atom is to the left of C
std::int8_t d_formalCharge
ChiralType getChiralTag() const
returns our chiralTag
bool hasOwningMol() const
returns whether or not this instance belongs to a molecule
unsigned int getIsotope() const
returns our isotope number
void setIdx(const U index)
overload
RDKIT_GRAPHMOL_EXPORT std::string getAtomValue(const Atom *atom)
std::int8_t d_implicitValence
Pulls in all the query types.
RDKIT_GRAPHMOL_EXPORT int getAtomRLabel(const Atom *atm)
virtual bool hasQuery() const
unsigned int getNumExplicitHs() const
returns our number of explict Hs
HybridizationType
store hybridization
The abstract base class for atom-level monomer info.
RWMol is a molecule class that is intended to be edited.
int getAtomMapNum() const
void setOwningMol(ROMol &other)
sets our owning molecule
ChiralType
store type of chirality
RDKIT_GRAPHMOL_EXPORT void setAtomRLabel(Atom *atm, int rlabel)
Set the atom's MDL integer RLabel.
void setAtomicNum(int newNum)
sets our atomic number
void setAtomMapNum(int mapno, bool strict=true)
Set the atom map Number of the atom.
int getAtomicNum() const
returns our atomic number
unsigned int getIdx() const
returns our index within the ROMol
@ CHI_TETRAHEDRAL_CW
tetrahedral: clockwise rotation (SMILES @@)
RDKIT_GRAPHMOL_EXPORT void setAtomAlias(Atom *atom, const std::string &alias)
Set the atom's MDL atom alias.
The class for representing atoms.
void setMonomerInfo(AtomMonomerInfo *info)
takes ownership of the pointer
void setNumRadicalElectrons(unsigned int num)
Queries::Query< int, Atom const *, true > QUERYATOM_QUERY
void setIsAromatic(bool what)
sets our isAromatic flag, indicating whether or not we are aromatic
RDKIT_GRAPHMOL_EXPORT void setSupplementalSmilesLabel(Atom *atom, const std::string &label)
Sets the supplemental label that will follow the atom when writing.
void setNumExplicitHs(unsigned int what)
sets our number of explict Hs
std::uint8_t d_numExplicitHs
std::uint8_t d_numRadicalElectrons
ROMol & getOwningMol() const
returns a reference to the ROMol that owns this instance
#define RDKIT_GRAPHMOL_EXPORT
void setNoImplicit(bool what)
sets our noImplicit flag, indicating whether or not we are allowed to have implicit Hs
const AtomMonomerInfo * getMonomerInfo() const
int getFormalCharge() const
returns the formal charge of this atom
void setChiralTag(ChiralType what)
sets our chiralTag
HybridizationType getHybridization() const
returns our hybridization
RDKIT_GRAPHMOL_EXPORT void setAtomValue(Atom *atom, const std::string &value)
Set the atom's MDL atom value.
void setIdx(unsigned int index)
sets our index within the ROMol
bool getNoImplicit() const
returns the noImplicit flag
void setFormalCharge(int what)
set's the formal charge of this atom
void setHybridization(HybridizationType what)
sets our hybridization
RDKIT_GRAPHMOL_EXPORT std::ostream & operator<<(std::ostream &target, const RDKit::Atom &at)
allows Atom objects to be dumped to streams
std::list< int > INT_LIST
#define PRECONDITION(expr, mess)
handles pickling (serializing) molecules
unsigned int getNumRadicalElectrons() const
returns the number of radical electrons for this Atom
@ CHI_TETRAHEDRAL_CCW
tetrahedral: counter-clockwise rotation (SMILES
Base class for all queries.
std::uint32_t atomindex_t
bool getIsAromatic() const
returns our isAromatic flag
AtomMonomerInfo * dp_monomerInfo
RDKIT_GRAPHMOL_EXPORT std::string getAtomAlias(const Atom *atom)
AtomMonomerInfo * getMonomerInfo()
const RDKIT_RDGENERAL_EXPORT std::string molAtomMapNumber
RDKIT_GRAPHMOL_EXPORT std::string getSupplementalSmilesLabel(const Atom *atom)