Field Detail

• vwr

  private Viewer vwr

• ms

  private ModelSet ms

• ext

  private BioExt ext

• unitIdSets

  private java.util.Map<java.lang.String,​javajs.util.BS>[] unitIdSets

Constructor Detail

• BioModelSet

  public BioModelSet()

Method Detail

• getBioExt

  BioExt getBioExt()

• set

  public BioModelSet set​(Viewer vwr,
                         ModelSet ms)

• calcAllRasmolHydrogenBonds

  public void calcAllRasmolHydrogenBonds​(javajs.util.BS bsA,
                                         javajs.util.BS bsB,
                                         javajs.util.Lst<Bond> vHBonds,
                                         boolean nucleicOnly,
                                         int nMax,
                                         boolean dsspIgnoreHydrogens,
                                         javajs.util.BS bsHBonds,
                                         int dsspVersion)

  only for base models, not trajectories

  Parameters:

  bsA -

  bsB -

  vHBonds - will be null for autobonding

  nucleicOnly -

  nMax -

  dsspIgnoreHydrogens -

  bsHBonds -

  dsspVersion - 1 or 2

• calcSelectedMonomersCount

  public void calcSelectedMonomersCount()

• calculateAllPolymers

  public void calculateAllPolymers​(Group[] groups,
                                   int groupCount,
                                   int baseGroupIndex,
                                   javajs.util.BS modelsExcluded)

• calculateAllStructuresExcept

  public java.lang.String calculateAllStructuresExcept​(javajs.util.BS alreadyDefined,
                                                       boolean asDSSP,
                                                       boolean doReport,
                                                       boolean dsspIgnoreHydrogen,
                                                       boolean setStructure,
                                                       boolean includeAlpha,
                                                       int version)

• calculateAllStuctures

  public java.lang.String calculateAllStuctures​(javajs.util.BS bsAtoms,
                                                boolean asDSSP,
                                                boolean doReport,
                                                boolean dsspIgnoreHydrogen,
                                                boolean setStructure,
                                                int version)

• calculateStraightnessAll

  public void calculateStraightnessAll()

• calculateStruts

  public int calculateStruts​(javajs.util.BS bs1,
                             javajs.util.BS bs2)

• getAllDefaultStructures

  public java.lang.String getAllDefaultStructures​(javajs.util.BS bsAtoms,
                                                  javajs.util.BS bsModified)

• getAllHeteroList

  public java.util.Map<java.lang.String,​java.lang.String> getAllHeteroList​(int modelIndex)

• getAllPolymerInfo

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

• getAllPolymerPointsAndVectors

  public void getAllPolymerPointsAndVectors​(javajs.util.BS bs,
                                            javajs.util.Lst<javajs.util.P3[]> vList,
                                            boolean isTraceAlpha,
                                            float sheetSmoothing)

• getAllSequenceBits

  public javajs.util.BS getAllSequenceBits​(java.lang.String specInfo,
                                           javajs.util.BS bsAtoms,
                                           javajs.util.BS bsResult)

• getAtomBitsBS

  public javajs.util.BS getAtomBitsBS​(int tokType,
                                      javajs.util.BS bsInfo,
                                      javajs.util.BS bs)

• getAtomBitsStr

  public javajs.util.BS getAtomBitsStr​(int tokType,
                                       java.lang.String specInfo,
                                       javajs.util.BS bs)

• getBioPolymerCountInModel

  public int getBioPolymerCountInModel​(int modelIndex)

  Parameters:

  modelIndex -

  Returns:

  number of polymers

• getFullProteinStructureState

  public java.lang.String getFullProteinStructureState​(javajs.util.BS bsAtoms,
                                                       int mode)

• getGroupsWithinAll

  public javajs.util.BS getGroupsWithinAll​(int nResidues,
                                           javajs.util.BS bs)

• getIdentifierOrNull

  public javajs.util.BS getIdentifierOrNull​(java.lang.String identifier)

• mutate

  public boolean mutate​(javajs.util.BS bs,
                        java.lang.String group,
                        java.lang.String[] sequence)

• recalculateAllPolymers

  public void recalculateAllPolymers​(javajs.util.BS bsModelsExcluded,
                                     Group[] groups)

• recalculatePoints

  public void recalculatePoints​(int modelIndex)

• setAllConformation

  public void setAllConformation​(javajs.util.BS bsAtoms)

• setAllProteinType

  public void setAllProteinType​(javajs.util.BS bs,
                                STR type)

• setAllStructureList

  public void setAllStructureList​(java.util.Map<STR,​float[]> structureList)

• getAllBasePairBits

  private javajs.util.BS getAllBasePairBits​(java.lang.String specInfo)

• getAllUnitIds

  private javajs.util.BS getAllUnitIds​(java.lang.String specInfo,
                                       javajs.util.BS bsSelected,
                                       javajs.util.BS bsResult)

• checkMap

  private javajs.util.BS checkMap​(java.util.Map<java.lang.String,​javajs.util.BS> map,
                                  java.lang.String key,
                                  javajs.util.BS bsAtoms)

  Ensure that if two models have the same name or number, we appropriately OR their bitsets.

  Parameters:

  map -

  key -

  bsAtoms -

  Returns:

  current BS

• addUnit

  private boolean addUnit​(int tok,
                          java.lang.String key,
                          javajs.util.BS bsTemp,
                          java.util.Map<java.lang.String,​javajs.util.BS> map)

  Repetitively AND unit components to get the final set of atoms

  Parameters:

  tok -

  key -

  bsTemp -

  map -

  Returns:

  true if there are still atoms to consider

• getAnnotationBits

  private javajs.util.BS getAnnotationBits​(java.lang.String name,
                                           int tok,
                                           java.lang.String specInfo)

• getStructureLines

  private int getStructureLines​(javajs.util.BS bsAtoms,
                                javajs.util.SB cmd,
                                javajs.util.Lst<ProteinStructure> lstStr,
                                STR type,
                                boolean scriptMode,
                                int mode)

• modelsOf

  private javajs.util.BS modelsOf​(javajs.util.BS bsAtoms,
                                  javajs.util.BS bsAtomsRet)

  general purpose; return models associated with specific atoms

  Parameters:

  bsAtoms -

  bsAtomsRet - all atoms associated with these models.

  Returns:

  bitset of base models

• setAllDefaultStructure

  private void setAllDefaultStructure​(javajs.util.BS bsModels)

• getAminoAcidValenceAndCharge

  public boolean getAminoAcidValenceAndCharge​(java.lang.String s,
                                              java.lang.String atomName,
                                              int[] aaRet)