Field Detail

• vwr

  private Viewer vwr

• ms

  private ModelSet ms

• qColor

  private static final java.lang.String[] qColor

• pdbRecords

  private static final java.lang.String[] pdbRecords

• naNoH

  private static final java.lang.String naNoH

  See Also:

  Constant Field Values

• aaSp2

  private static final java.lang.String aaSp2

  See Also:

  Constant Field Values

• aaSp21

  private static final java.lang.String aaSp21

  See Also:

  Constant Field Values

• aaPlus

  private static final java.lang.String aaPlus

  See Also:

  Constant Field Values

Constructor Detail

• BioExt

  public BioExt()

Method Detail

• set

  BioExt set​(Viewer vwr,
             ModelSet ms)

• getAllPolymerInfo

  void getAllPolymerInfo​(BS bs,
                         java.util.Map<java.lang.String,​javajs.util.Lst<java.util.Map<java.lang.String,​java.lang.Object>>> fullInfo)

• calculateStraightnessAll

  void calculateStraightnessAll()

• getPdbData

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

• getData

  private void getData​(int m0,
                       int mStep,
                       BioPolymer p,
                       char ctype,
                       char qtype,
                       int derivType,
                       BS bsAtoms,
                       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,
                       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 java.lang.String getQInfo​(javajs.util.Quat q)

• drawQuat

  static java.lang.String drawQuat​(javajs.util.Quat q,
                                   java.lang.String prefix,
                                   java.lang.String id,
                                   javajs.util.P3 ptCenter,
                                   float scale)

• get3DStraightness

  private static float get3DStraightness​(java.lang.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​(java.lang.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,
                   java.lang.String type,
                   char ctype,
                   boolean isDraw,
                   BS bsSelected,
                   javajs.util.OC out,
                   LabelToken[] tokens,
                   javajs.util.SB pdbCONECT,
                   BS bsWritten)

• calculateAllstruts

  int calculateAllstruts​(Viewer vwr,
                         ModelSet ms,
                         BS bs1,
                         BS bs2)

• calculateStruts

  private static javajs.util.Lst<Atom[]> calculateStruts​(ModelSet modelSet,
                                                         BS bs1,
                                                         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,
                               BS bs1,
                               BS bs2,
                               javajs.util.Lst<Atom[]> vStruts,
                               BS bsStruts,
                               BS bsNotAvailable,
                               BS bsNearbyResidues,
                               int delta)

• mutate

  boolean mutate​(Viewer vwr,
                 BS bs,
                 java.lang.String group,
                 java.lang.String[] sequence)

• mutateAtom

  private static boolean mutateAtom​(Viewer vwr,
                                    int iatom,
                                    java.lang.String fileName)

• replaceMutatedMonomer

  private static void replaceMutatedMonomer​(Viewer vwr,
                                            AminoMonomer res0,
                                            AminoMonomer res1)

• getMutationBackbone

  private static Atom[] getMutationBackbone​(AminoMonomer res1,
                                            Atom[] backbone)

  Parameters:

  res1 -

  backbone -

  Returns:

  [C O CA N H]

• getFullPDBHeader

  java.lang.String getFullPDBHeader​(java.util.Map<java.lang.String,​java.lang.Object> auxiliaryInfo)

• getAminoAcidValenceAndCharge

  boolean getAminoAcidValenceAndCharge​(java.lang.String res,
                                       java.lang.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