Package org.jmol.util
Interface Node
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- All Superinterfaces:
SimpleNode
- All Known Implementing Classes:
Atom
,SmilesAtom
public interface Node extends SimpleNode
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method 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 + missingint
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()
int
getExplicitHydrogenCount()
[CH2] for examplefloat
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 CCCint
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)
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Methods inherited from interface org.jmol.util.SimpleNode
getBondCount
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Method Detail
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getAtomicAndIsotopeNumber
int getAtomicAndIsotopeNumber()
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getAtomName
java.lang.String getAtomName()
- Specified by:
getAtomName
in interfaceSimpleNode
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getAtomSite
int getAtomSite()
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getBondedAtomIndex
int getBondedAtomIndex(int j)
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getCovalentBondCount
int getCovalentBondCount()
Description copied from interface:SimpleNode
Get the total number of covalent bonds, thus not including hydrogen bonds.- Specified by:
getCovalentBondCount
in interfaceSimpleNode
- Returns:
- number of bonds
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getCovalentHydrogenCount
int getCovalentHydrogenCount()
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getEdges
Edge[] getEdges()
Description copied from interface:SimpleNode
Get the bond array, including hydrogen bonds.- Specified by:
getEdges
in interfaceSimpleNode
- Returns:
- number of bonds
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getElementNumber
int getElementNumber()
- Specified by:
getElementNumber
in interfaceSimpleNode
- Returns:
- the atomic number for this aotm
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getFormalCharge
int getFormalCharge()
- Specified by:
getFormalCharge
in interfaceSimpleNode
- Returns:
- the formal charge for this atom
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getIndex
int getIndex()
- Specified by:
getIndex
in interfaceSimpleNode
- Returns:
- the unique ID number associated with this atom (which in Jmol is its position in the atoms[] array
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getIsotopeNumber
int getIsotopeNumber()
- Specified by:
getIsotopeNumber
in interfaceSimpleNode
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getValence
int getValence()
- Specified by:
getValence
in interfaceSimpleNode
- Returns:
- the sum of the bond orders for this atom
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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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getMass
float getMass()
- Specified by:
getMass
in interfaceSimpleNode
- Returns:
- the mass or, if specified, the mass number
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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
javajs.util.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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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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getExplicitHydrogenCount
int getExplicitHydrogenCount()
[CH2] for example- Returns:
- number of H atoms in brackets
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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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getCIPChirality
java.lang.String getCIPChirality(boolean doCalculate)
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getCIPChiralityCode
int getCIPChiralityCode()
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setCIPChirality
void setCIPChirality(int c)
- Specified by:
setCIPChirality
in interfaceSimpleNode
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getXYZ
javajs.util.P3 getXYZ()
- Specified by:
getXYZ
in interfaceSimpleNode
- Returns:
- the position of this atom
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modelIsRawPDB
boolean modelIsRawPDB()
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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(javajs.util.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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