public class Atom extends RDProps
The chirality of an Atom is determined by two things:
its chiralTag the input order of its bonds (see note below for handling of implicit Hs)
For tetrahedral coordination, the chiralTag tells you what direction you have to rotate to get from bond 2 to bond 3 while looking down bond 1. This is pretty much identical to the SMILES representation of chirality.
NOTE: if an atom has an implicit H, the bond to that H is considered to be at the *end* of the list of other bonds.
Modifier and Type | Class and Description |
---|---|
static class |
Atom.ChiralType |
static class |
Atom.HybridizationType |
Modifier | Constructor and Description |
---|---|
|
Atom() |
|
Atom(Atom other) |
|
Atom(long num) |
protected |
Atom(long cPtr,
boolean cMemoryOwn) |
|
Atom(java.lang.String what) |
clear, clearComputedProps, clearProp, getCPtr, getDict, getPropList, getPropList, getPropList, hasProp, setProp, setProp, updateProps, updateProps
protected Atom(long cPtr, boolean cMemoryOwn)
public Atom()
public Atom(long num)
public Atom(java.lang.String what)
public Atom(Atom other)
protected static long getCPtr(Atom obj)
public Atom copy()
makes a copy of this Atom and returns a pointer to it.
public int getAtomicNum()
public void setAtomicNum(int newNum)
public java.lang.String getSymbol()
public boolean hasOwningMol()
public ROMol getOwningMol()
public long getIdx()
public void setIdx(long index)
sets our index within the ROMol
public long getDegree()
public long getTotalDegree()
public long getTotalNumHs(boolean includeNeighbors)
public long getTotalNumHs()
public long getTotalValence()
public long getNumImplicitHs()
public int getExplicitValence()
public int getImplicitValence()
public long getNumRadicalElectrons()
public void setNumRadicalElectrons(long num)
public int getFormalCharge()
public void setFormalCharge(int what)
public void setNoImplicit(boolean what)
public boolean getNoImplicit()
public void setNumExplicitHs(long what)
public long getNumExplicitHs()
public void setIsAromatic(boolean what)
public boolean getIsAromatic()
public double getMass()
public void setIsotope(long what)
public long getIsotope()
public void setChiralTag(Atom.ChiralType what)
public void invertChirality()
public Atom.ChiralType getChiralTag()
public void setHybridization(Atom.HybridizationType what)
public Atom.HybridizationType getHybridization()
public boolean hasQuery()
public void setQuery(SWIGTYPE_p_Queries__QueryT_int_RDKit__Atom_const_p_true_t what)
public SWIGTYPE_p_Queries__QueryT_int_RDKit__Atom_const_p_true_t getQuery()
public void expandQuery(SWIGTYPE_p_Queries__QueryT_int_RDKit__Atom_const_p_true_t what, CompositeQueryType how, boolean maintainOrder)
public void expandQuery(SWIGTYPE_p_Queries__QueryT_int_RDKit__Atom_const_p_true_t what, CompositeQueryType how)
public void expandQuery(SWIGTYPE_p_Queries__QueryT_int_RDKit__Atom_const_p_true_t what)
public int getPerturbationOrder(Int_List probe)
returns the perturbation order for a list of integers
This value is associated with chirality.
probe
- a list of bond indices. This must be the same length as our number of incoming bonds (our degree).
public void updatePropertyCache(boolean strict)
calculates any of our lazy properties
public void updatePropertyCache()
calculates any of our lazy properties
public boolean needsUpdatePropertyCache()
public int calcExplicitValence(boolean strict)
calculates and returns our explicit valence
public int calcExplicitValence()
calculates and returns our explicit valence
public int calcImplicitValence(boolean strict)
calculates and returns our implicit valence
public int calcImplicitValence()
calculates and returns our implicit valence
public AtomMonomerInfo getMonomerInfo()
public void setMonomerInfo(AtomMonomerInfo info)
public void setAtomMapNum(int mapno, boolean strict)
public void setAtomMapNum(int mapno)
public int getAtomMapNum()
public java.lang.String getProp(java.lang.String key)
public void markConjAtomBonds()
public int numBondsPlusLonePairs()
public boolean atomHasConjugatedBond()
public void transformAtom(Transform3D tform)
public boolean IsInRing()
public boolean IsInRingSize(int size)
public Bond_Vect getBonds()