org.jmol.modelsetbio
public abstract class ProteinStructure extends Object
Field Summary | |
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AlphaPolymer | apolymer |
Point3f | axisA |
Point3f | axisB |
Vector3f | axisUnitVector |
static int | globalSerialID |
int | monomerCount |
int | monomerIndexFirst |
int | monomerIndexLast |
Point3f[] | segments |
byte | type |
int | uniqueID |
Vector3f | vectorProjection |
Constructor Summary | |
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ProteinStructure(AlphaPolymer apolymer, byte type, int monomerIndex, int monomerCount) |
Method Summary | |
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void | addMonomer(int index)
Note that this method does not check to see
that there are no overlapping protein structures.
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void | calcAxis() |
void | calcSegments() |
Point3f | getAxisEndPoint() |
Point3f | getAxisStartPoint() |
int | getIndex(Monomer monomer) |
void | getInfo(Hashtable info) |
int | getMonomerCount() |
int | getMonomerIndex() |
Point3f[] | getSegments() |
Point3f | getStructureMidPoint(int index) |
boolean | lowerNeighborIsHelixOrSheet() |
int | removeMonomer(int monomerIndex)
should be OK here to remove the first -- we just get a
monomerCount of 0; but we don't remove monomers that aren't
part of this structure.
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void | resetAxes() |
boolean | upperNeighborIsHelixOrSheet() |
Parameters: index
Parameters: monomerIndex
Returns: the number of monomers AFTER this one that have been abandoned