scripps.vvm.manager
Class ExInterpreter

java.lang.Object
  |
  +--scripps.vvm.manager.ExInterpreter

public class ExInterpreter

extends java.lang.Object

Constructor Summary

ExInterpreter()

Method Summary

TreeNodeSet	interpret(java.lang.String ex, Molecule mol)
AtomSet	interpretAtomExpression(AtomSet subSet, java.lang.String ex)
ChainSet	interpretChainExpression(ChainSet defSet, java.lang.String ex)
ResidueSet	interpretResidueExpression(ResidueSet subSet, java.lang.String ex) Return a subset of given set based on expression.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ExInterpreter

public ExInterpreter()

Method Detail

interpret

public TreeNodeSet interpret(java.lang.String ex,
                             Molecule mol)

interpretChainExpression

public ChainSet interpretChainExpression(ChainSet defSet,
                                         java.lang.String ex)

interpretResidueExpression

public ResidueSet interpretResidueExpression(ResidueSet subSet,
                                             java.lang.String ex)

Return a subset of given set based on expression. "all": all residues in subset "all helix/strand/turn/loop": all of given secondary structure type a letter, number or anything not a residue name: is a chain chainId means all residue of chain anything else is broken up by comma resType: all residues of type in molecule.... (chain?) chainId resId: single residue of that name (chainId resId)-(chainId resId): range

interpretAtomExpression

public AtomSet interpretAtomExpression(AtomSet subSet,
                                       java.lang.String ex)