Package edu.duke.cs.osprey.structure

Class Molecule

java.lang.Object
edu.duke.cs.osprey.structure.Molecule
All Implemented Interfaces:
Serializable
public class Molecule extends Object implements Serializable
A molecule is a list of Residue and their alternates
See Also:

  • Field Details

  • Constructor Details

    • Molecule

      public Molecule()

    • Molecule

      public Molecule(Residues residues)

    • Molecule

      public Molecule(Molecule other)

    • Molecule

      public Molecule(Molecule other, boolean redoInterResBonds)

  • Method Details

    • getResByPDBResNumber

      public Residue getResByPDBResNumber(String resNum)

    • getResByPDBResNumberOrNull

      public Residue getResByPDBResNumberOrNull(String resNum)

    • getResRangeByPDBResNumber

      public List<Residue> getResRangeByPDBResNumber(String firstResNum, String lastResNum)

    • getResiduesByPDBResNumbers

      public List<Residue> getResiduesByPDBResNumbers(Iterable<String> resNums)

    • getResiduesByPDBResNumbers

      public List<Residue> getResiduesByPDBResNumbers(Set<String> resNums)

    • appendResidue

      public void appendResidue(Residue res)

    • addAlternate

      public void addAlternate(int resIndex, Residue res)

    • getAlternates

      public List<Residue> getAlternates(int resIndex)

    • deleteResidue

      public void deleteResidue(int resIndex)

    • deleteResidues

      public void deleteResidues(Collection<String> resNames)

    • resListFromTermini

      public ArrayList<Residue> resListFromTermini(String[] termini, ArrayList<String> flexibleRes)

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object

    • getResByFullName

      public Residue getResByFullName(String fullName)

    • markInterResBonds

      public void markInterResBonds()