Package org.jmol.util
Interface Node
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- All Known Implementing Classes:
Atom
,SmilesAtom
public interface Node
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method 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 + missingint
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 CCCint
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)
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Method Detail
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getAtomicAndIsotopeNumber
int getAtomicAndIsotopeNumber()
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getAtomName
java.lang.String getAtomName()
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getAtomSite
int getAtomSite()
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getBondedAtomIndex
int getBondedAtomIndex(int j)
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getCovalentBondCount
int getCovalentBondCount()
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getCovalentHydrogenCount
int getCovalentHydrogenCount()
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getEdges
Edge[] getEdges()
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getElementNumber
int getElementNumber()
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getFormalCharge
int getFormalCharge()
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getIndex
int getIndex()
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getIsotopeNumber
int getIsotopeNumber()
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getValence
int getValence()
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set
void set(float x, float y, float z)
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getMoleculeNumber
int getMoleculeNumber(boolean inModel)
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getFloatProperty
float getFloatProperty(java.lang.String property)
- Parameters:
property
- "property_xxxx"- Returns:
- value or Float.NaN
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findAtomsLike
BS findAtomsLike(java.lang.String substring)
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getAtomType
java.lang.String getAtomType()
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getModelIndex
int getModelIndex()
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getBondCount
int getBondCount()
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getAtomNumber
int getAtomNumber()
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getImplicitHydrogenCount
int getImplicitHydrogenCount()
can be > 0 for PDB model with no H atoms or for SMILES string CCC- Returns:
- number of missing H atoms
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getCovalentBondCountPlusMissingH
int getCovalentBondCountPlusMissingH()
includes actual + missing- Returns:
- actual + missing
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getTotalHydrogenCount
int getTotalHydrogenCount()
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getTotalValence
int getTotalValence()
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getBioStructureTypeName
java.lang.String getBioStructureTypeName()
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getGroup1
java.lang.String getGroup1(char c0)
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getGroup3
java.lang.String getGroup3(boolean allowNull)
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getResno
int getResno()
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getInsertionCode
char getInsertionCode()
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getChainID
int getChainID()
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getChainIDStr
java.lang.String getChainIDStr()
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getOffsetResidueAtom
int getOffsetResidueAtom(java.lang.String name, int offset)
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getCrossLinkVector
boolean getCrossLinkVector(javajs.util.Lst<java.lang.Integer> vReturn, boolean crosslinkCovalent, boolean crosslinkHBond)
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getGroupBits
void getGroupBits(BS bs)
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isLeadAtom
boolean isLeadAtom()
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isCrossLinked
boolean isCrossLinked(Node node)
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isPurine
boolean isPurine()
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isPyrimidine
boolean isPyrimidine()
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isDeleted
boolean isDeleted()
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getBioSmilesType
char getBioSmilesType()
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