Package org.jmol.modelset
Class Chain
java.lang.Object
org.jmol.modelset.Chain
- All Implemented Interfaces:
Structure
A Model is a collection of Chains of Groups of Atoms.
Chains hold overall information relating to a Monomer,
particularly whether this monomer is RNA or DNA.
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Field Summary
FieldsModifier and TypeFieldDescriptionint
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 is for information purposes only; retrieved by {atoms}.chainNoint
Group[]
Groups form the essence of what a Chain is.int
Calculated just prior to coloring by group so that the range is appropriate for each chain. -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescription(package private) void
calcSelectedGroupsCount
(javajs.util.BS bsSelected) prior to coloring by group, we need the chain count per chain that is selected(package private) void
fixIndices
(int atomsDeleted, javajs.util.BS bsDeleted) getIDStr()
void
setAtomBits
(javajs.util.BS bs) void
setAtomBitsAndClear
(javajs.util.BS bs, javajs.util.BS bsOut)
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Field Details
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model
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chainID
public int chainIDchainID 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 -
chainNo
public int chainNochainNo is for information purposes only; retrieved by {atoms}.chainNo -
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. -
groupCount
public int groupCount -
selectedGroupCount
public int selectedGroupCountCalculated just prior to coloring by group so that the range is appropriate for each chain.
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Constructor Details
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Chain
Chain(Model model, int chainID, int chainNo)
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Method Details
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getIDStr
- Returns:
- actual string form of the chain identifier
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calcSelectedGroupsCount
void calcSelectedGroupsCount(javajs.util.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, javajs.util.BS bsDeleted) -
setAtomBits
public void setAtomBits(javajs.util.BS bs) - Specified by:
setAtomBits
in interfaceStructure
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setAtomBitsAndClear
public void setAtomBitsAndClear(javajs.util.BS bs, javajs.util.BS bsOut) - Specified by:
setAtomBitsAndClear
in interfaceStructure
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