Package org.jmol.modelset
Class Chain
- java.lang.Object
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- org.jmol.modelset.Chain
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Field Summary
Fields Modifier and Type Field Description int
chainID
chainID is either the integer form of a single character or a pointer into a map held in Viewer that allows retrieval of a longer stringint
chainNo
chainNo is for information purposes only; retrieved by {atoms}.chainNoint
groupCount
Group[]
groups
Groups form the essence of what a Chain is.Model
model
int
selectedGroupCount
Calculated just prior to coloring by group so that the range is appropriate for each chain.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description (package private) void
calcSelectedGroupsCount(BS bsSelected)
prior to coloring by group, we need the chain count per chain that is selected(package private) void
fixIndices(int atomsDeleted, BS bsDeleted)
java.lang.String
getIDStr()
void
setAtomBits(BS bs)
void
setAtomBitsAndClear(BS bs, BS bsOut)
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Field Detail
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model
public Model model
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chainID
public int chainID
chainID is either the integer form of a single character or a pointer into a map held in Viewer that allows retrieval of a longer string
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chainNo
public int chainNo
chainNo is for information purposes only; retrieved by {atoms}.chainNo
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groups
public Group[] groups
Groups form the essence of what a Chain is. This number will be 0 if there is no chain designation in the PDB or CIF file or when the file is not of a type that would have chain designations.
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groupCount
public int groupCount
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selectedGroupCount
public int selectedGroupCount
Calculated just prior to coloring by group so that the range is appropriate for each chain.
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Constructor Detail
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Chain
Chain(Model model, int chainID, int chainNo)
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Method Detail
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getIDStr
public java.lang.String getIDStr()
- Returns:
- actual string form of the chain identifier
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calcSelectedGroupsCount
void calcSelectedGroupsCount(BS bsSelected)
prior to coloring by group, we need the chain count per chain that is selected- Parameters:
bsSelected
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fixIndices
void fixIndices(int atomsDeleted, BS bsDeleted)
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setAtomBits
public void setAtomBits(BS bs)
- Specified by:
setAtomBits
in interfaceStructure
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setAtomBitsAndClear
public void setAtomBitsAndClear(BS bs, BS bsOut)
- Specified by:
setAtomBitsAndClear
in interfaceStructure
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