Package org.jmol.modelsetbio

Class BioResolver

java.lang.Object
org.jmol.modelsetbio.BioResolver
All Implemented Interfaces:
Comparator<String[]>
public final class BioResolver extends Object implements Comparator<String[]>
a class used by ModelLoader to handle all loading of operations specific to PDB/mmCIF files. By loading only by class name, only loaded if PDB file is called. In addition, constants relating only to PDB files are here -- for coloring by chain, selecting by protein, etc.

  • Field Details

    • htGroup

      public static final Map<String,Short> htGroup

    • vwr

      private Viewer vwr

    • vAB

      private javajs.util.V3 vAB

    • vNorm

      private javajs.util.V3 vNorm

    • plane

      private javajs.util.P4 plane

    • ml

      private ModelLoader ml

    • ms

      private ModelSet ms

    • bsAddedMask

      private javajs.util.BS bsAddedMask

    • lastSetH

      private int lastSetH

    • maxSerial

      private int maxSerial

    • haveHsAlready

      private boolean haveHsAlready

    • bsAddedHydrogens

      private javajs.util.BS bsAddedHydrogens

    • bsAtomsForHs

      private javajs.util.BS bsAtomsForHs

    • htBondMap

      private Map<String,String> htBondMap

    • htGroupBonds

      private Map<String,Boolean> htGroupBonds

    • hNames

      private String[] hNames

    • baseBondIndex

      private int baseBondIndex

    • hasCONECT

      private boolean hasCONECT

    • bsAssigned

      private javajs.util.BS bsAssigned

    • types

      private static STR[] types

    • mytypes

      private static int[] mytypes

    • htPdbBondInfo

      private static Map<String,String[][]> htPdbBondInfo

    • pdbBondInfo

      public static final String[] pdbBondInfo
      pdbBondInfo describes in a compact way what the hydrogen atom names are for each standard amino acid. This list consists of pairs of attached atom/hydrogen atom names, with abbreviations N, C, O, B, D, G, 1, and 2 (for N, C, O, CB, CD, CG, C1', and C2', respectively) given in pdbHAttachments, above. Note that we never add HXT or NH3 "?" here is for methyl groups with H1, H2, H3. "@" indicates a prochiral center, with the assignment order given here

    • pdbHydrogenCount

      private static final int[] pdbHydrogenCount

    • allCarbohydrates

      private static final String allCarbohydrates
      this form is used for counting groups in ModelSet GLX added for 13.1.16
      See Also:

    • group3Count

      private static int group3Count

    • predefinedGroup1Names

      static final char[] predefinedGroup1Names

    • group3NameCount

      public static short group3NameCount

    • predefinedGroup3Names

      private static final String[] predefinedGroup3Names

    • specialAtomNames

      private static final String[] specialAtomNames

    • ATOMID_MAX

      public static final int ATOMID_MAX

    • htSpecialAtoms

      private static Map<String,Byte> htSpecialAtoms

    • argbsAmino

      private static final int[] argbsAmino

    • argbsNucleic

      private static final int[] argbsNucleic

    • argbsChainAtom

      private static final int[] argbsChainAtom
      some pastel colors C0D0FF - pastel blue B0FFB0 - pastel green B0FFFF - pastel cyan FFC0C8 - pink FFC0FF - pastel magenta FFFF80 - pastel yellow FFDEAD - navajowhite FFD070 - pastel gold FF9898 - light coral B4E444 - light yellow-green C0C000 - light olive FF8060 - light tomato 00FF7F - springgreen cpk on; select atomno>100; label %i; color chain; select selected & hetero; cpk off

    • argbsChainHetero

      private static final int[] argbsChainHetero

    • argbsShapely

      private static final int[] argbsShapely

  • Constructor Details

    • BioResolver

      public BioResolver()

  • Method Details

    • setLoader

      public BioResolver setLoader(ModelLoader modelLoader)

    • setViewer

      public BioResolver setViewer(Viewer vwr)

    • getBioModel

      public Model getBioModel(int modelIndex, int trajectoryBaseIndex, String jmolData, Properties modelProperties, Map<String,Object> modelAuxiliaryInfo)

    • distinguishAndPropagateGroup

      public Group distinguishAndPropagateGroup(Chain chain, String group3, int seqcode, int firstAtomIndex, int lastAtomIndex, int[] specialAtomIndexes, Atom[] atoms)

    • setHaveHsAlready

      public void setHaveHsAlready(boolean b)

    • initializeHydrogenAddition

      public void initializeHydrogenAddition()

    • addImplicitHydrogenAtoms

      public void addImplicitHydrogenAtoms(JmolAdapter adapter, int iGroup, int nH)
      Get bonding info for double bonds and add implicit hydrogen atoms, if needed.
      Parameters:
      adapter -
      iGroup - this group
      nH - legacy quirk

    • getBondInfo

      private void getBondInfo(JmolAdapter adapter, String group3, Object model)

    • getLigandBondInfo

      private String[][] getLigandBondInfo(JmolAdapter adapter, Object model, String group3)
      reads PDB ligand CIF info and creates a bondInfo object.
      Parameters:
      adapter -
      model -
      group3 -
      Returns:
      [[atom1, atom2, order]...]

    • compare

      public int compare(String[] a, String[] b)
      Specified by:
      compare in interface Comparator<String[]>

    • finalizeHydrogens

      public void finalizeHydrogens()

    • addHydrogens

      private void addHydrogens()

    • deleteUnneededAtoms

      private void deleteUnneededAtoms()
      Delete hydrogen atoms that are still in bsAddedHydrogens, because they were not actually added. Also delete ligand hydrogen atoms from CO2- and PO3(2-) Note that we do this AFTER all atoms have been added. That means that this operation will not mess up atom indexing

    • deleteAtoms

      private void deleteAtoms(javajs.util.BS bsDeletedAtoms)
      called from org.jmol.modelsetbio.resolver when adding hydrogens.
      Parameters:
      bsDeletedAtoms -

    • fixAnnotations

      private void fixAnnotations(int i, String name, int type)

    • finalizePdbCharges

      private void finalizePdbCharges()

    • finalizePdbMultipleBonds

      private void finalizePdbMultipleBonds()

    • setHydrogen

      private void setHydrogen(int iTo, int iAtom, String name, javajs.util.P3 pt)

    • fixPropertyValue

      public Object fixPropertyValue(javajs.util.BS bsAtoms, Object data, boolean toHydrogens)

    • allocateBioPolymer

      static BioPolymer allocateBioPolymer(Group[] groups, int firstGroupIndex, boolean checkConnections, int pt0)

    • iterateOverAllNewStructures

      public void iterateOverAllNewStructures(JmolAdapter adapter, Object atomSetCollection)
      Pull in all spans of helix, etc. in the file(s) We do turn first, because sometimes a group is defined twice, and this way it gets marked as helix or sheet if it is both one of those and turn. Jmol 14.3 - adds sequence ANNOTATION
      Parameters:
      adapter -
      atomSetCollection -

    • setStructure

      private void setStructure(JmolAdapterStructureIterator iterStructure)
      note that istart and iend will be adjusted.
      Parameters:
      iterStructure -

    • setGroupLists

      public void setGroupLists(int ipt)

    • isKnownPDBGroup

      public boolean isKnownPDBGroup(String g3, int max)
      Parameters:
      g3 -
      max - max ID (e.g. 20); can be Integer.MAX_VALUE to allow carbohydrate
      Returns:
      true if found

    • lookupSpecialAtomID

      public byte lookupSpecialAtomID(String name)

    • getPdbBondInfo

      private String[][] getPdbBondInfo(String group3, boolean isLegacy)

    • knownGroupID

      public static short knownGroupID(String group3)

    • checkCarbohydrate

      private static final boolean checkCarbohydrate(String group3)
      Parameters:
      group3 - a potential group3 name
      Returns:
      whether this is a carbohydrate from the list

    • isHetero

      public boolean isHetero(String group3)
      MMCif, Gromacs, MdTop, Mol2 readers only
      Parameters:
      group3 -
      Returns:
      true if an identified hetero group

    • toStdAmino3

      public String toStdAmino3(String g1)

    • getGroupID

      public short getGroupID(String g3)

    • getGroupIdFor

      static short getGroupIdFor(String group3)

    • addGroup3Name

      private static short addGroup3Name(String group3)
      These can overrun 3 characters; that is not significant.
      Parameters:
      group3 -
      Returns:
      a short group ID

    • getStandardPdbHydrogenCount

      private static int getStandardPdbHydrogenCount(String group3)

    • getSpecialAtomName

      static final String getSpecialAtomName(int atomID)

    • getArgbs

      public int[] getArgbs(int tok)

    • getBioModelSet

      public BioModelSet getBioModelSet(ModelSet modelSet)