Package org.jmol.adapter.readers.cif

Class MMTFReader

java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.cif.CifReader
org.jmol.adapter.readers.cif.MMCifReader
org.jmol.adapter.readers.cif.MMTFReader
All Implemented Interfaces:
javajs.api.GenericLineReader
public class MMTFReader extends MMCifReader
JmolData RCSB MMTF (macromolecular transmission format) file reader see https://github.com/rcsb/mmtf/blob/master/spec.md full specification Version: v0.2+dev (as of 2016.08.08) is implemented,including: reading atoms, bonds, and DSSP 1.0 secondary structure load =1f88.mmtf filter "DSSP1" [Note that the filter "DSSP1" is required, since mmtf included DSSP 1.0 calculations, while the standard for Jmol itself is DSSP 2.0. These two calculations differ in their treating of helix kinks as one (1.0) or two (2.0) helices.] reading space groups and unit cells, and using those as per other readers load =1crn.mmtf {1 1 1} reading bioassemblies (biomolecules) and applying all symmetry transformations load =1auy.mmtf FILTER "biomolecule 1;*.CA,*.P" reading both biomolecules and lattices, and loading course-grained using the filter "BYCHAIN" or "BYSYMOP" load =1auy.mmtf {2 2 1} filter "biomolecule 1;bychain";spacefill 30.0; color property symop Many thanks to the MMTF team at RCSB for assistance in this implementation.
Author:
Bob Hanson hansonr@stolaf.edu

  • Field Details

    • haveStructure

      private boolean haveStructure

    • pdbID

      private String pdbID

    • map

      private Map<String,Object> map

    • fileAtomCount

      private int fileAtomCount

    • opCount

      private int opCount

    • groupModels

      private int[] groupModels

    • groupMap

      private int[] groupMap

    • groupDSSP

      private int[] groupDSSP

    • atomGroup

      private int[] atomGroup

    • labelAsymList

      private String[] labelAsymList

    • atomMap

      private Atom[] atomMap

    • entities

      private Object[] entities

    • groupCount

      private int groupCount

    • ac0

      private int ac0

    • bsStructures

      private javajs.util.BS[] bsStructures

  • Constructor Details

    • MMTFReader

      public MMTFReader()

  • Method Details

    • addHeader

      protected void addHeader()
      Overrides:
      addHeader in class CifReader

    • setup

      protected void setup(String fullPath, Map<String,Object> htParams, Object reader)
      standard set up
      Overrides:
      setup in class AtomSetCollectionReader
      Parameters:
      fullPath -
      htParams -
      reader -

    • processBinaryDocument

      protected void processBinaryDocument() throws Exception
      Overrides:
      processBinaryDocument in class AtomSetCollectionReader
      Throws:
      Exception

    • applySymmetryAndSetTrajectory

      public void applySymmetryAndSetTrajectory() throws Exception
      Overrides:
      applySymmetryAndSetTrajectory in class CifReader
      Throws:
      Exception

    • getMMTFAtoms

      private void getMMTFAtoms(boolean doMulti) throws Exception
      set up all atoms, including bonding, within a group
      Parameters:
      doMulti - true to add double bonds
      Throws:
      Exception

    • addMMTFBonds

      private void addMMTFBonds(int[] bo, int[] bi, int a0, boolean doMulti, boolean isInter)

    • setMMTFSymmetry

      private void setMMTFSymmetry()

    • getMMTFBioAssembly

      private void getMMTFBioAssembly()

    • getStructure

      private void getStructure()
      Get and translate the DSSP string from digit format input data

    • addStructureSymmetry

      public void addStructureSymmetry()
      We must add groups to the proper bsStructure element

    • decode

      private Object decode(String key)