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) |
getBondCount
int getAtomicAndIsotopeNumber()
java.lang.String getAtomName()
getAtomName
in interface SimpleNode
int getAtomSite()
int getBondedAtomIndex(int j)
int getCovalentBondCount()
SimpleNode
getCovalentBondCount
in interface SimpleNode
int getCovalentHydrogenCount()
Edge[] getEdges()
SimpleNode
getEdges
in interface SimpleNode
int getElementNumber()
getElementNumber
in interface SimpleNode
int getFormalCharge()
getFormalCharge
in interface SimpleNode
int getIndex()
getIndex
in interface SimpleNode
int getIsotopeNumber()
getIsotopeNumber
in interface SimpleNode
int getValence()
getValence
in interface SimpleNode
void set(float x, float y, float z)
int getMoleculeNumber(boolean inModel)
float getMass()
getMass
in interface SimpleNode
float 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 SimpleNode
javajs.util.P3 getXYZ()
getXYZ
in interface SimpleNode
boolean 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()