meshi.molecularElements.extendedAtoms
Class ExtendedAtomsProtein

java.lang.Object
  meshi.molecularElements.Protein
      meshi.molecularElements.extendedAtoms.ExtendedAtomsProtein

public class ExtendedAtomsProtein
extends Protein

An extended atoms model of a protein. This model includes all heavy atoms and most hydrogen atoms that take part in hydrogen bonds.

Nested Class Summary

Nested classes/interfaces inherited from class meshi.molecularElements.Protein

Protein.BackboneFilter

Field Summary

Fields inherited from class meshi.molecularElements.Protein

angles, atoms, bonds, chains, firstResidueIndex, modelNumber, name, residues, torsions

Constructor Summary

ExtendedAtomsProtein(java.lang.String fileName, CommandList commands)
The parameter is expected to be a PDB formatted file.

ExtendedAtomsProtein(java.lang.String fileName, CommandList commands, java.util.List<java.lang.String> chainNames)

Method Summary

Methods inherited from class meshi.molecularElements.Protein

addChain, allYouWantToKnow, atoms, bonds, chain, chains, defrost, firstResidueIndex, firstResidues, freeze, freeze, getAtom, getProteinName, getProteinName, getSequence, missingResidues, modelNumber, name, nowhereAtoms, printAtomsToFile, residue, residue, residueAt, residues, sequence, setName, setSS, setSS, toString

Methods inherited from class java.lang.Object

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

Constructor Detail

ExtendedAtomsProtein

public ExtendedAtomsProtein(java.lang.String fileName,
                            CommandList commands)

The parameter is expected to be a PDB formatted file.

ExtendedAtomsProtein

public ExtendedAtomsProtein(java.lang.String fileName,
                            CommandList commands,
                            java.util.List<java.lang.String> chainNames)