Package org.jmol.modelsetbio

Class Monomer

java.lang.Object
org.jmol.modelset.Group
org.jmol.modelsetbio.Monomer
All Implemented Interfaces:
Structure
Direct Known Subclasses:
AlphaMonomer, CarbohydrateMonomer, PhosphorusMonomer
public abstract class Monomer extends Group
A class to maintain information about biomolecule groups that are (potentially) part of biopolymers -- peptides, nucleic acid strands, or complex carbohydrates. Note that it is possible that a monomer is created but is not part of a BioPolymer.

  • Field Details

    • bioPolymer

      public BioPolymer bioPolymer

    • offsets

      protected byte[] offsets

    • monomerIndex

      int monomerIndex

    • phi

      private float phi

    • psi

      private float psi

    • omega

      private float omega

    • straightness

      private float straightness

    • mu

      private float mu

    • theta

      private float theta

    • backboneBlockVis

      public boolean backboneBlockVis

  • Constructor Details

    • Monomer

      public Monomer()

  • Method Details

    • have

      protected static boolean have(byte[] offsets, byte n)

    • set2

      protected Monomer set2(Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, byte[] interestingAtomOffsets)

    • setLeadAtomIndex

      protected void setLeadAtomIndex()

    • setBioPolymer

      void setBioPolymer(BioPolymer polymer, int index)

    • getSelectedMonomerCount

      public int getSelectedMonomerCount()
      Overrides:
      getSelectedMonomerCount in class Group

    • getSelectedMonomerIndex

      public int getSelectedMonomerIndex()
      Overrides:
      getSelectedMonomerIndex in class Group

    • getBioPolymerLength

      public int getBioPolymerLength()
      Overrides:
      getBioPolymerLength in class Group

    • getMonomerIndex

      public int getMonomerIndex()
      Overrides:
      getMonomerIndex in class Group

    • getAtomIndex

      public int getAtomIndex(String name, int offset)
      Overrides:
      getAtomIndex in class Group
      Returns:
      index of atom based on offset

    • getBioPolymerIndexInModel

      public int getBioPolymerIndexInModel()
      Overrides:
      getBioPolymerIndexInModel in class Group

    • scanForOffsets

      protected static byte[] scanForOffsets(int firstAtomIndex, int[] specialAtomIndexes, byte[] interestingAtomIDs)

    • getProteinStructureType

      public STR getProteinStructureType()
      Overrides:
      getProteinStructureType in class Group

    • isHelix

      public boolean isHelix()

    • isSheet

      public boolean isSheet()

    • setStrucNo

      public void setStrucNo(int id)
      Overrides:
      setStrucNo in class Group

    • getAtomFromOffsetIndex

      protected final Atom getAtomFromOffsetIndex(int offsetIndex)

    • getSpecialAtom

      protected final Atom getSpecialAtom(byte[] interestingIDs, byte specialAtomID)

    • getSpecialAtomPoint

      protected final javajs.util.P3 getSpecialAtomPoint(byte[] interestingIDs, byte specialAtomID)

    • isLeadAtom

      public boolean isLeadAtom(int atomIndex)
      Overrides:
      isLeadAtom in class Group
      Returns:
      T/F

    • getLeadAtom

      public final Atom getLeadAtom()
      Overrides:
      getLeadAtom in class Group

    • getWingAtom

      public final Atom getWingAtom()

    • getInitiatorAtom

      Atom getInitiatorAtom()

    • getTerminatorAtom

      Atom getTerminatorAtom()

    • isConnectedAfter

      abstract boolean isConnectedAfter(Monomer possiblyPreviousMonomer)

    • findNearestAtomIndex

      void findNearestAtomIndex(int x, int y, Atom[] closest, short madBegin, short madEnd)
      Selects LeadAtom when this Monomer is clicked iff it is closer to the user.
      Parameters:
      x -
      y -
      closest -
      madBegin -
      madEnd -

    • getMyInfo

      public Map<String,Object> getMyInfo(javajs.util.P3 ptTemp)

    • getStructureId

      public String getStructureId()
      Overrides:
      getStructureId in class Group

    • updateOffsetsForAlternativeLocations

      final void updateOffsetsForAlternativeLocations(Atom[] atoms, javajs.util.BS bsSelected)

    • getMonomerSequenceAtoms

      final void getMonomerSequenceAtoms(javajs.util.BS bsInclude, javajs.util.BS bsResult)

    • checkOptional

      protected static final boolean checkOptional(byte[] offsets, byte atom, int firstAtomIndex, int index)

    • getQuaternionFrameCenter

      javajs.util.P3 getQuaternionFrameCenter(char qtype)
      Parameters:
      qtype -
      Returns:
      center

    • getHelixData2

      protected Object getHelixData2(int tokType, char qType, int mStep)

    • getUniqueID

      public String getUniqueID()

    • isCrossLinked

      public boolean isCrossLinked(Group g)
      Overrides:
      isCrossLinked in class Group
      Returns:
      T/F

    • getCrossLinkVector

      public boolean getCrossLinkVector(javajs.util.Lst<Integer> vReturn, boolean crosslinkCovalent, boolean crosslinkHBond)
      Overrides:
      getCrossLinkVector in class Group
      Returns:
      T/F

    • getCrossLinkGroup

      protected boolean getCrossLinkGroup(int i, javajs.util.Lst<Integer> vReturn, Group group, boolean crosslinkCovalent, boolean crosslinkHBond, boolean isNotCheck)
      Parameters:
      i -
      vReturn - null implies just checking for a specific group
      group - specific group to check or null to indicate just PREVIOUS group (carbohydrates)
      crosslinkCovalent - (S-S)
      crosslinkHBond - (hbond)
      isNotCheck - TODO
      Returns:
      true if there is a cross-link of the allowed type

    • isConnectedPrevious

      public boolean isConnectedPrevious()
      Overrides:
      isConnectedPrevious in class Group

    • setGroupParameter

      void setGroupParameter(int tok, float f)

    • getGroupParameter

      public float getGroupParameter(int tok)
      Description copied from class: Group
      Monomers only
      Overrides:
      getGroupParameter in class Group
      Returns:
      NaN

    • getGroup1

      public char getGroup1()
      Overrides:
      getGroup1 in class Group

    • getGroup1b

      protected char getGroup1b()

    • setGroupID

      public void setGroupID(String group3)
      Overrides:
      setGroupID in class Group

    • toString

      public String toString()
      Overrides:
      toString in class Group