Package org.jmol.util
Interface Node
- All Superinterfaces:
SimpleNode
- All Known Implementing Classes:
Atom
,SmilesAtom
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Method Summary
Modifier and TypeMethodDescriptionjavajs.util.BS
findAtomsLike
(String substring) int
int
int
char
int
getBondedAtomIndex
(int j) int
getCIPChirality
(boolean doCalculate) int
int
Get the total number of covalent bonds, thus not including hydrogen bonds.int
includes actual + missingint
boolean
getCrossLinkVector
(javajs.util.Lst<Integer> vReturn, boolean crosslinkCovalent, boolean crosslinkHBond) Edge[]
getEdges()
Get the bond array, including hydrogen bonds.int
int
[CH2] for examplefloat
getFloatProperty
(String property) int
getGroup1
(char c0) getGroup3
(boolean allowNull) void
getGroupBits
(javajs.util.BS bs) int
can be > 0 for PDB model with no H atoms or for SMILES string CCCint
getIndex()
char
int
float
getMass()
int
int
getMoleculeNumber
(boolean inModel) int
getOffsetResidueAtom
(String name, int offset) int
getResno()
int
int
int
javajs.util.P3
getXYZ()
boolean
isCrossLinked
(Node node) boolean
boolean
boolean
isPurine()
boolean
boolean
void
set
(float x, float y, float z) void
setCIPChirality
(int c) Methods inherited from interface org.jmol.util.SimpleNode
getBondCount
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Method Details
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getAtomicAndIsotopeNumber
int getAtomicAndIsotopeNumber() -
getAtomName
String getAtomName()- Specified by:
getAtomName
in interfaceSimpleNode
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getAtomSite
int getAtomSite() -
getBondedAtomIndex
int getBondedAtomIndex(int j) -
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() -
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) -
getMoleculeNumber
int getMoleculeNumber(boolean inModel) -
getMass
float getMass()- Specified by:
getMass
in interfaceSimpleNode
- Returns:
- the mass or, if specified, the mass number
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getFloatProperty
- Parameters:
property
- "property_xxxx"- Returns:
- value or Float.NaN
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findAtomsLike
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getAtomType
String getAtomType() -
getModelIndex
int getModelIndex() -
getAtomNumber
int getAtomNumber() -
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() -
getTotalValence
int getTotalValence() -
getCIPChirality
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getCIPChiralityCode
int getCIPChiralityCode() -
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() -
getBioStructureTypeName
String getBioStructureTypeName() -
getGroup1
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getGroup3
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getResno
int getResno() -
getInsertionCode
char getInsertionCode() -
getChainID
int getChainID() -
getChainIDStr
String getChainIDStr() -
getOffsetResidueAtom
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getCrossLinkVector
boolean getCrossLinkVector(javajs.util.Lst<Integer> vReturn, boolean crosslinkCovalent, boolean crosslinkHBond) -
getGroupBits
void getGroupBits(javajs.util.BS bs) -
isLeadAtom
boolean isLeadAtom() -
isCrossLinked
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isPurine
boolean isPurine() -
isPyrimidine
boolean isPyrimidine() -
isDeleted
boolean isDeleted() -
getBioSmilesType
char getBioSmilesType()
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