public interface Node extends SimpleNode
| Modifier and Type | Method and Description |
|---|---|
javajs.util.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 |
getBondedAtomIndex(int j) |
int |
getChainID() |
java.lang.String |
getChainIDStr() |
java.lang.String |
getCIPChirality(boolean doCalculate) |
int |
getCIPChiralityCode() |
int |
getCovalentBondCount()
Get the total number of covalent bonds, thus not including hydrogen bonds.
|
int |
getCovalentBondCountPlusMissingH()
includes actual + missing
|
int |
getCovalentHydrogenCount() |
boolean |
getCrossLinkVector(javajs.util.Lst<java.lang.Integer> vReturn,
boolean crosslinkCovalent,
boolean crosslinkHBond) |
Edge[] |
getEdges()
Get the bond array, including hydrogen bonds.
|
int |
getElementNumber() |
float |
getFloatProperty(java.lang.String property) |
int |
getFormalCharge() |
java.lang.String |
getGroup1(char c0) |
java.lang.String |
getGroup3(boolean allowNull) |
void |
getGroupBits(javajs.util.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() |
float |
getMass() |
int |
getModelIndex() |
int |
getMoleculeNumber(boolean inModel) |
int |
getOffsetResidueAtom(java.lang.String name,
int offset) |
int |
getResno() |
int |
getTotalHydrogenCount() |
int |
getTotalValence() |
int |
getValence() |
javajs.util.P3 |
getXYZ() |
boolean |
isCrossLinked(Node node) |
boolean |
isDeleted() |
boolean |
isLeadAtom() |
boolean |
isPurine() |
boolean |
isPyrimidine() |
boolean |
modelIsRawPDB() |
void |
set(float x,
float y,
float z) |
void |
setCIPChirality(int c) |
getBondCountint getAtomicAndIsotopeNumber()
java.lang.String getAtomName()
getAtomName in interface SimpleNodeint getAtomSite()
int getBondedAtomIndex(int j)
int getCovalentBondCount()
SimpleNodegetCovalentBondCount in interface SimpleNodeint getCovalentHydrogenCount()
Edge[] getEdges()
SimpleNodegetEdges in interface SimpleNodeint getElementNumber()
getElementNumber in interface SimpleNodeint getFormalCharge()
getFormalCharge in interface SimpleNodeint getIndex()
getIndex in interface SimpleNodeint getIsotopeNumber()
getIsotopeNumber in interface SimpleNodeint getValence()
getValence in interface SimpleNodevoid set(float x,
float y,
float z)
int getMoleculeNumber(boolean inModel)
float getMass()
getMass in interface SimpleNodefloat getFloatProperty(java.lang.String property)
property - "property_xxxx"javajs.util.BS findAtomsLike(java.lang.String substring)
java.lang.String getAtomType()
int getModelIndex()
int getAtomNumber()
int getImplicitHydrogenCount()
int getCovalentBondCountPlusMissingH()
int getTotalHydrogenCount()
int getTotalValence()
java.lang.String getCIPChirality(boolean doCalculate)
int getCIPChiralityCode()
void setCIPChirality(int c)
setCIPChirality in interface SimpleNodejavajs.util.P3 getXYZ()
getXYZ in interface SimpleNodeboolean modelIsRawPDB()
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(javajs.util.BS bs)
boolean isLeadAtom()
boolean isCrossLinked(Node node)
boolean isPurine()
boolean isPyrimidine()
boolean isDeleted()
char getBioSmilesType()