Package org.jmol.modelsetbio

Class 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 Detail

      • 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

    • Constructor Detail

      • Monomer

        public Monomer()

    • Method Detail

      • have

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

      • set2

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

      • setLeadAtomIndex

        protected void setLeadAtomIndex()

      • setBioPolymer

        void setBioPolymer​(BioPolymer polymer,
                   int index)

      • getAtomIndex

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

      • scanForOffsets

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

      • 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

      • 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 java.util.Map<java.lang.String,​java.lang.Object> getMyInfo​(javajs.util.P3 ptTemp)

      • getStructureId

        public java.lang.String getStructureId()
        Overrides:
        getStructureId in class Group

      • updateOffsetsForAlternativeLocations

        final void updateOffsetsForAlternativeLocations​(Atom[] atoms,
                                                BS bsSelected)

      • getMonomerSequenceAtoms

        final void getMonomerSequenceAtoms​(BS bsInclude,
                                   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 java.lang.Object getHelixData2​(int tokType,
                                         char qType,
                                         int mStep)

      • getUniqueID

        public java.lang.String getUniqueID()

      • getCrossLinkVector

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

      • getCrossLinkGroup

        protected boolean getCrossLinkGroup​(int i,
                                    javajs.util.Lst<java.lang.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

      • 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​(java.lang.String group3)
        Overrides:
        setGroupID in class Group