java.lang.Object
- org.jmol.modelset.Chain

All Implemented Interfaces:

Structure
```
public final class Chain
extends java.lang.Object
implements 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.

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 string
`int`	`chainNo`	chainNo is for information purposes only; retrieved by {atoms}.chainNo
`int`	`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.

Constructor Summary

Constructors
Constructor Description

Chain(Model model, int chainID, int chainNo)

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)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - model
```
public Model model
```
  - 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
  - chainNo
```
public int chainNo
```
    chainNo is for information purposes only; retrieved by {atoms}.chainNo
  - 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.
  - groupCount
```
public int groupCount
```
  - selectedGroupCount
```
public int selectedGroupCount
```
    Calculated just prior to coloring by group so that the range is appropriate for each chain.
- Constructor Detail
  - Chain
```
Chain(Model model,
      int chainID,
      int chainNo)
```
- Method Detail
  - getIDStr
```
public java.lang.String getIDStr()
```
    Returns:
    
    actual string form of the chain identifier
  - calcSelectedGroupsCount
```
void calcSelectedGroupsCount(BS bsSelected)
```
    prior to coloring by group, we need the chain count per chain that is selected
    
    Parameters:
    
    bsSelected -
  - fixIndices
```
void fixIndices(int atomsDeleted,
                BS bsDeleted)
```
  - setAtomBits
```
public void setAtomBits(BS bs)
```
    Specified by:
    
    setAtomBits in interface Structure
  - setAtomBitsAndClear
```
public void setAtomBitsAndClear(BS bs,
                                BS bsOut)
```
    Specified by:
    
    setAtomBitsAndClear in interface Structure

Class Chain

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

model

chainID

chainNo

groups

groupCount

selectedGroupCount

Constructor Detail

Chain

Method Detail

getIDStr

calcSelectedGroupsCount

fixIndices

setAtomBits

setAtomBitsAndClear