Class BioExt

java.lang.Object
org.jmol.modelsetbio.BioExt

public class BioExt extends Object
  • Field Details

  • Constructor Details

    • BioExt

      public BioExt()
  • Method Details

    • set

      BioExt set(Viewer vwr, ModelSet ms)
    • getAllPolymerInfo

      void getAllPolymerInfo(javajs.util.BS bs, Map<String,javajs.util.Lst<Map<String,Object>>> fullInfo)
    • calculateStraightnessAll

      void calculateStraightnessAll()
    • getPdbData

      private void getPdbData(BioPolymer bp, char ctype, char qtype, int mStep, int derivType, javajs.util.BS bsAtoms, javajs.util.BS bsSelected, boolean bothEnds, boolean isDraw, boolean addHeader, LabelToken[] tokens, javajs.util.OC pdbATOM, javajs.util.SB pdbCONECT, javajs.util.BS bsWritten, javajs.util.P3 ptTemp)
    • getData

      private void getData(int m0, int mStep, BioPolymer p, char ctype, char qtype, int derivType, javajs.util.BS bsAtoms, javajs.util.BS bsSelected, boolean isDraw, boolean isRamachandran, boolean calcRamachandranStraightness, boolean useQuaternionStraightness, boolean writeRamachandranStraightness, boolean quaternionStraightness, float factor, boolean isAmino, boolean isRelativeAlias, LabelToken[] tokens, javajs.util.OC pdbATOM, javajs.util.SB pdbCONECT, javajs.util.BS bsWritten, javajs.util.P3 ptTemp)
      Parameters:
      m0 -
      mStep -
      p -
      ctype -
      qtype -
      derivType -
      bsAtoms -
      bsSelected -
      isDraw -
      isRamachandran -
      calcRamachandranStraightness -
      useQuaternionStraightness -
      writeRamachandranStraightness -
      quaternionStraightness - NOT USED
      factor -
      isAmino -
      isRelativeAlias -
      tokens -
      pdbATOM -
      pdbCONECT -
      bsWritten -
      ptTemp -
    • getQInfo

      private static String getQInfo(javajs.util.Quat q)
    • drawQuat

      static String drawQuat(javajs.util.Quat q, String prefix, String id, javajs.util.P3 ptCenter, float scale)
    • get3DStraightness

      private static float get3DStraightness(String id, javajs.util.Quat dq, javajs.util.Quat dqnext)
      Parameters:
      id - for debugging only
      dq -
      dqnext -
      Returns:
      calculated straightness
    • getQuaternionStraightness

      private static float getQuaternionStraightness(String id, javajs.util.Quat dq, javajs.util.Quat dqnext)
      Parameters:
      id - for debugging only
      dq -
      dqnext -
      Returns:
      straightness
    • getStraightness

      private static float getStraightness(float cosHalfTheta)
    • getPdbDataM

      void getPdbDataM(BioModel m, Viewer vwr, String type, char ctype, boolean isDraw, javajs.util.BS bsSelected, javajs.util.OC out, LabelToken[] tokens, javajs.util.SB pdbCONECT, javajs.util.BS bsWritten)
    • calculateAllstruts

      int calculateAllstruts(Viewer vwr, ModelSet ms, javajs.util.BS bs1, javajs.util.BS bs2)
    • calculateStruts

      private static javajs.util.Lst<Atom[]> calculateStruts(ModelSet modelSet, javajs.util.BS bs1, javajs.util.BS bs2, javajs.util.Lst<Atom> vCA, float thresh, int delta, boolean allowMultiple)
      Algorithm of George Phillips phillips@biochem.wisc.edu originally a contribution to pyMol as struts.py; adapted here by Bob Hanson for Jmol 1/2010 Return a vector of support posts for rapid prototyping models along the lines of George Phillips for Pymol except on actual molecular segments (biopolymers), not PDB chains (which may or may not be continuous). Like George, we go from thresh-4 to thresh in units of 1 Angstrom, but we do not require this threshold to be an integer. In addition, we prevent double-creation of struts by tracking where struts are, and we do not look for any addtional end struts if there is a strut already to an atom at a particular biopolymer end. The three parameters are: set strutDefaultRadius 0.3 set strutSpacingMinimum 6 set strutLengthMaximum 7.0 Struts will be introduced by: calculate struts {atom set A} {atom set B} where the two atom sets are optional and default to the currently selected set. They can be manipulated using the STRUTS command much like any "bond" struts 0.3 color struts opaque pink connect {atomno=3} {atomno=4} strut struts only command
      Parameters:
      modelSet -
      bs1 -
      bs2 -
      vCA -
      thresh -
      delta -
      allowMultiple -
      Returns:
      vector of pairs of atoms
    • strutPoint

      private static int strutPoint(int i, int j, int n)
    • setStrut

      private static void setStrut(int i, int j, int n, javajs.util.Lst<Atom> vCA, javajs.util.BS bs1, javajs.util.BS bs2, javajs.util.Lst<Atom[]> vStruts, javajs.util.BS bsStruts, javajs.util.BS bsNotAvailable, javajs.util.BS bsNearbyResidues, int delta)
    • mutate

      boolean mutate(Viewer vwr, javajs.util.BS bs, String group, String[] sequence, String helixType, float[] phipsi)
      mutate the given group
      Parameters:
      vwr -
      bs -
      group -
      sequence -
      phipsi -
      helixType -
      Returns:
      true if even partially successful
    • createHelix

      private static void createHelix(Viewer vwr, int nRes, int[] gly, float[] phipsi, boolean isTurn)
      Parameters:
      vwr -
      nRes -
      gly -
      phipsi -
      isTurn -
    • getPhiPsiForHelixType

      public float[] getPhiPsiForHelixType(String t)
    • mutateAtom

      private static boolean mutateAtom(Viewer vwr, int iatom, String fileName, boolean addH)
    • replaceMutatedMonomer

      private static void replaceMutatedMonomer(Viewer vwr, AminoMonomer res0, AminoMonomer res1, boolean addH)
    • fixHydrogens

      private static void fixHydrogens(Viewer vwr, AminoMonomer res1)
    • getMutationBackbone

      private static Atom[] getMutationBackbone(AminoMonomer res, Atom[] backbone)
      Parameters:
      res -
      backbone -
      Returns:
      [C O CA N H]
    • getFullPDBHeader

      String getFullPDBHeader(Map<String,Object> auxiliaryInfo)
    • getAminoAcidValenceAndCharge

      boolean getAminoAcidValenceAndCharge(String res, String name, int[] ret)
      returns an array if we have special hybridization or charge
      Parameters:
      res -
      name -
      ret - [0] (target valence) may be reduced by one for sp2 for C or O only [1] will be set to 1 if positive (lysine or terminal N) or -1 if negative (OXT) [2] will be set to 2 if sp2 [3] is supplied covalent bond count
      Returns:
      true for special; false if not