Class Model

  • Direct Known Subclasses:
    BioModel

    public class Model
    extends java.lang.Object
    • Field Detail

      • ms

        public ModelSet ms
        BE CAREFUL: FAILURE TO NULL REFERENCES TO modelSet WILL PREVENT FINALIZATION AND CREATE A MEMORY LEAK.
      • mat4

        public javajs.util.M4 mat4
        mat4 tracks the rotation/translation of the full model using rotateSelected or translateSelected
      • modelIndex

        public int modelIndex
      • fileIndex

        int fileIndex
      • isBioModel

        public boolean isBioModel
      • isPdbWithMultipleBonds

        public boolean isPdbWithMultipleBonds
      • isModelKit

        public boolean isModelKit
      • chains

        public Chain[] chains
      • dssrCache

        public java.util.Map<java.lang.String,​java.lang.Object> dssrCache
      • auxiliaryInfo

        protected java.util.Map<java.lang.String,​java.lang.Object> auxiliaryInfo
      • properties

        public java.util.Properties properties
      • dataFrames

        java.util.Map<java.lang.String,​java.lang.Integer> dataFrames
      • translation

        javajs.util.P3 translation
      • dataSourceFrame

        int dataSourceFrame
      • loadState

        public java.lang.String loadState
      • loadScript

        public javajs.util.SB loadScript
      • hasRasmolHBonds

        public boolean hasRasmolHBonds
      • structureTainted

        public boolean structureTainted
      • isJmolDataFrame

        public boolean isJmolDataFrame
      • isTrajectory

        boolean isTrajectory
      • trajectoryBaseIndex

        public int trajectoryBaseIndex
      • altLocCount

        public int altLocCount
      • insertionCount

        int insertionCount
      • act

        public int act
      • bondCount

        private int bondCount
      • chainCount

        protected int chainCount
      • groupCount

        public int groupCount
      • hydrogenCount

        public int hydrogenCount
      • moleculeCount

        public int moleculeCount
      • biosymmetryCount

        int biosymmetryCount
      • firstAtomIndex

        public int firstAtomIndex
      • firstMoleculeIndex

        int firstMoleculeIndex
      • bsAtoms

        public final BS bsAtoms
      • bsAtomsDeleted

        public final BS bsAtomsDeleted
      • defaultRotationRadius

        float defaultRotationRadius
      • frameDelay

        public long frameDelay
      • selectedTrajectory

        public int selectedTrajectory
      • jmolData

        java.lang.String jmolData
      • jmolFrameType

        java.lang.String jmolFrameType
      • pdbID

        public java.lang.String pdbID
      • bsCheck

        private BS bsCheck
    • Constructor Detail

      • Model

        public Model()
    • Method Detail

      • set

        public Model set​(ModelSet modelSet,
                         int modelIndex,
                         int trajectoryBaseIndex,
                         java.lang.String jmolData,
                         java.util.Properties properties,
                         java.util.Map<java.lang.String,​java.lang.Object> auxiliaryInfo)
      • getTrueAtomCount

        public int getTrueAtomCount()
        not actually accessed -- just pointing out what it is
        Returns:
        true atom count
      • isContainedIn

        public boolean isContainedIn​(BS bs)
        Parameters:
        bs -
        Returns:
        true if all undeleted atom bits in this model are in bs
      • resetBoundCount

        public void resetBoundCount()
      • getBondCount

        public int getBondCount()
      • getChainCount

        public int getChainCount​(boolean countWater)
      • calcSelectedGroupsCount

        void calcSelectedGroupsCount​(BS bsSelected)
      • getGroupCount

        public int getGroupCount()
      • getChainAt

        public Chain getChainAt​(int i)
      • getChain

        Chain getChain​(int chainID)
      • fixIndices

        public void fixIndices​(int modelIndex,
                               int nAtomsDeleted,
                               BS bsDeleted)
      • fixIndicesM

        protected void fixIndicesM​(int modelIndex,
                                   int nAtomsDeleted,
                                   BS bsDeleted)
      • freeze

        public boolean freeze()
      • freezeM

        protected void freezeM()