Class PDBMLStructure

java.lang.Object
org.episteme.natural.biology.loaders.pdbml.PDBMLStructure
public class PDBMLStructure extends Object
Represents a macromolecular structure from PDBML.
Since:
1.0
Author:
Silvere Martin-Michiellot, Gemini AI (Google DeepMind)

  • Constructor Details

    • PDBMLStructure

      public PDBMLStructure()

  • Method Details

    • getEntryId

      public String getEntryId()

    • setEntryId

      public void setEntryId(String id)

    • getTitle

      public String getTitle()

    • setTitle

      public void setTitle(String title)

    • getDepositionDate

      public String getDepositionDate()

    • setDepositionDate

      public void setDepositionDate(String date)

    • getExperimentalMethod

      public String getExperimentalMethod()

    • setExperimentalMethod

      public void setExperimentalMethod(String method)

    • getResolution

      public double getResolution()

    • setResolution

      public void setResolution(double r)

    • addAtom

      public void addAtom(AtomSite atom)

    • getAtoms

      public List<AtomSite> getAtoms()

    • addEntity

      public void addEntity(PolymerEntity e)

    • getEntities

      public List<PolymerEntity> getEntities()

    • addSecondaryStructure

      public void addSecondaryStructure(SecondaryStructure ss)

    • getSecondaryStructures

      public List<SecondaryStructure> getSecondaryStructures()

    • getChainIds

      public Set<String> getChainIds()
      Get unique chain IDs.

    • getAtomsForChain

      public List<AtomSite> getAtomsForChain(String chainId)
      Get atoms for a specific chain.

    • getBackboneAtoms

      public List<AtomSite> getBackboneAtoms()
      Get only CA (alpha carbon) atoms for backbone analysis.

    • toString

      public String toString()
      Overrides:
      toString in class Object