public interface Node
Modifier and Type | Method and Description |
---|---|
BS |
findAtomsLike(java.lang.String substring) |
int |
getAtomicAndIsotopeNumber() |
java.lang.String |
getAtomName() |
int |
getAtomNumber() |
int |
getAtomSite() |
java.lang.String |
getAtomType() |
char |
getBioSmilesType() |
java.lang.String |
getBioStructureTypeName() |
int |
getBondCount() |
int |
getBondedAtomIndex(int j) |
int |
getChainID() |
java.lang.String |
getChainIDStr() |
int |
getCovalentBondCount() |
int |
getCovalentBondCountPlusMissingH()
includes actual + missing
|
int |
getCovalentHydrogenCount() |
boolean |
getCrossLinkVector(javajs.util.Lst<java.lang.Integer> vReturn,
boolean crosslinkCovalent,
boolean crosslinkHBond) |
Edge[] |
getEdges() |
int |
getElementNumber() |
float |
getFloatProperty(java.lang.String property) |
int |
getFormalCharge() |
java.lang.String |
getGroup1(char c0) |
java.lang.String |
getGroup3(boolean allowNull) |
void |
getGroupBits(BS bs) |
int |
getImplicitHydrogenCount()
can be > 0 for PDB model with no H atoms or for SMILES string CCC
|
int |
getIndex() |
char |
getInsertionCode() |
int |
getIsotopeNumber() |
int |
getModelIndex() |
int |
getMoleculeNumber(boolean inModel) |
int |
getOffsetResidueAtom(java.lang.String name,
int offset) |
int |
getResno() |
int |
getTotalHydrogenCount() |
int |
getTotalValence() |
int |
getValence() |
boolean |
isCrossLinked(Node node) |
boolean |
isDeleted() |
boolean |
isLeadAtom() |
boolean |
isPurine() |
boolean |
isPyrimidine() |
void |
set(float x,
float y,
float z) |
int getAtomicAndIsotopeNumber()
java.lang.String getAtomName()
int getAtomSite()
int getBondedAtomIndex(int j)
int getCovalentBondCount()
int getCovalentHydrogenCount()
Edge[] getEdges()
int getElementNumber()
int getFormalCharge()
int getIndex()
int getIsotopeNumber()
int getValence()
void set(float x, float y, float z)
int getMoleculeNumber(boolean inModel)
float getFloatProperty(java.lang.String property)
property
- "property_xxxx"BS findAtomsLike(java.lang.String substring)
java.lang.String getAtomType()
int getModelIndex()
int getBondCount()
int getAtomNumber()
int getImplicitHydrogenCount()
int getCovalentBondCountPlusMissingH()
int getTotalHydrogenCount()
int getTotalValence()
java.lang.String getBioStructureTypeName()
java.lang.String getGroup1(char c0)
java.lang.String getGroup3(boolean allowNull)
int getResno()
char getInsertionCode()
int getChainID()
java.lang.String getChainIDStr()
int getOffsetResidueAtom(java.lang.String name, int offset)
boolean getCrossLinkVector(javajs.util.Lst<java.lang.Integer> vReturn, boolean crosslinkCovalent, boolean crosslinkHBond)
void getGroupBits(BS bs)
boolean isLeadAtom()
boolean isCrossLinked(Node node)
boolean isPurine()
boolean isPyrimidine()
boolean isDeleted()
char getBioSmilesType()