Field Detail

• MODE_PDB

  private static final int MODE_PDB

  See Also:

  Constant Field Values

• MODE_HEX

  private static final int MODE_HEX

  See Also:

  Constant Field Values

• MODE_HYBRID36

  private static final int MODE_HYBRID36

  See Also:

  Constant Field Values

• serMode

  private int serMode

• seqMode

  private int seqMode

• serial

  private int serial

• lineLength

  private int lineLength

• pdbHeader

  private javajs.util.SB pdbHeader

• applySymmetry

  private boolean applySymmetry

• getTlsGroups

  private boolean getTlsGroups

• isMultiModel

  private boolean isMultiModel

• haveMappedSerials

  private boolean haveMappedSerials

• isConnectStateBug

  private boolean isConnectStateBug

• isLegacyModelType

  private boolean isLegacyModelType

• gromacsWideFormat

  protected boolean gromacsWideFormat

• htFormul

  private final java.util.Map<java.lang.String,​java.util.Map<java.lang.String,​java.lang.Boolean>> htFormul

• htHetero

  private java.util.Map<java.lang.String,​java.lang.String> htHetero

• htSites

  private java.util.Map<java.lang.String,​java.util.Map<java.lang.String,​java.lang.Object>> htSites

• htElementsInCurrentGroup

  private java.util.Map<java.lang.String,​java.lang.Boolean> htElementsInCurrentGroup

• htMolIds

  private java.util.Map<java.lang.String,​java.util.Map<java.lang.String,​java.lang.String>> htMolIds

• vCompnds

  private javajs.util.Lst<java.util.Map<java.lang.String,​java.lang.String>> vCompnds

• vBiomolecules

  private javajs.util.Lst<java.util.Map<java.lang.String,​java.lang.Object>> vBiomolecules

• vTlsModels

  private javajs.util.Lst<java.util.Map<java.lang.String,​java.lang.Object>> vTlsModels

• sbTlsErrors

  private javajs.util.SB sbTlsErrors

• biomtChainAtomCounts

  protected int[] biomtChainAtomCounts

• sbIgnored

  private javajs.util.SB sbIgnored

• sbSelected

  private javajs.util.SB sbSelected

• sbConect

  private javajs.util.SB sbConect

• sb

  private javajs.util.SB sb

• ac

  private int ac

• maxSerial

  private int maxSerial

• nUNK

  private int nUNK

• nRes

  private int nRes

• currentCompnd

  private java.util.Map<java.lang.String,​java.lang.String> currentCompnd

• currentGroup3

  private java.lang.String currentGroup3

• currentKey

  private java.lang.String currentKey

• currentResno

  private int currentResno

• configurationPtr

  private int configurationPtr

• resetKey

  private boolean resetKey

• compnd

  private java.lang.String compnd

• conformationIndex

  private int conformationIndex

• fileAtomIndex

  protected int fileAtomIndex

• lastAltLoc

  private char lastAltLoc

• lastGroup

  private int lastGroup

• lastInsertion

  private char lastInsertion

• lastSourceSerial

  private int lastSourceSerial

• lastTargetSerial

  private int lastTargetSerial

• tlsGroupID

  private int tlsGroupID

• atomTypePt0

  private int atomTypePt0

• atomTypeLen

  private int atomTypeLen

• isCourseGrained

  private boolean isCourseGrained

• isbiomol

  private boolean isbiomol

• lineOptions

  private static final java.lang.String lineOptions

  See Also:

  Constant Field Values

• htGroup1

  java.util.Map<java.lang.String,​java.lang.String> htGroup1

• maxLength

  private int maxLength

• pdbID

  private java.lang.String pdbID

• haveDoubleBonds

  private boolean haveDoubleBonds

• cryst1

  private float cryst1

• fileSgName

  private java.lang.String fileSgName

• dataT

  private final float[] dataT

• RAD_PER_DEG

  private static final float RAD_PER_DEG

  See Also:

  Constant Field Values

• _8PI2_

  private static final float _8PI2_

  See Also:

  Constant Field Values

• tlsU

  private java.util.Map<Atom,​float[]> tlsU

• vConnect

  private javajs.util.Lst<int[]> vConnect

• connectNextAtomIndex

  private int connectNextAtomIndex

• connectNextAtomSet

  private int connectNextAtomSet

• connectLast

  private int[] connectLast

Constructor Detail

• PdbReader

  public PdbReader()

Method Detail

• initializeReader

  protected void initializeReader()
                           throws java.lang.Exception

  Overrides:

  initializeReader in class AtomSetCollectionReader

  Throws:

  java.lang.Exception

• checkLine

  protected boolean checkLine()
                       throws java.lang.Exception

  Overrides:

  checkLine in class AtomSetCollectionReader

  Returns:

  true if need to read new line

  Throws:

  java.lang.Exception

• checkRemark

  protected void checkRemark()

• seqAdv

  private void seqAdv()

• readHeader

  private java.lang.String readHeader​(boolean getLine)
                               throws java.lang.Exception

  Throws:

  java.lang.Exception

• finalizeSubclassReader

  protected void finalizeSubclassReader()
                                 throws java.lang.Exception

  Description copied from class: AtomSetCollectionReader
  optional reader-specific method run first.

  Overrides:

  finalizeSubclassReader in class AtomSetCollectionReader

  Throws:

  java.lang.Exception

• finalizeReaderPDB

  protected void finalizeReaderPDB()
                            throws java.lang.Exception

  Throws:

  java.lang.Exception

• checkUnitCellParams

  private void checkUnitCellParams()

• checkForResidualBFactors

  private void checkForResidualBFactors​(SymmetryInterface symmetry)

• header

  private void header()

• title

  private void title()

• compnd

  private void compnd​(boolean isSource)

• setBiomoleculeAtomCounts

  private void setBiomoleculeAtomCounts()

• remark350

  private boolean remark350()
                     throws java.lang.Exception

  Throws:

  java.lang.Exception

• remark285

  private boolean remark285()

• remark290

  private boolean remark290()
                     throws java.lang.Exception

  Throws:

  java.lang.Exception

• getSerial

  private int getSerial​(int i,
                        int j)

• getSeqNo

  private int getSeqNo​(int i,
                       int j)

• processAtom

  protected Atom processAtom​(Atom atom,
                             java.lang.String name,
                             char altID,
                             java.lang.String group3,
                             int chainID,
                             int seqNo,
                             char insCode,
                             boolean isHetero,
                             java.lang.String sym)

• processAtom2

  protected void processAtom2​(Atom atom,
                              int serial,
                              float x,
                              float y,
                              float z,
                              int charge)

• atom

  private void atom()

• filterPDBAtom

  protected boolean filterPDBAtom​(Atom atom,
                                  int iAtom)

• setAdditionalAtomParameters

  protected void setAdditionalAtomParameters​(Atom atom)

  adaptable via subclassing

  Parameters:

  atom -

• deduceElementSymbol

  protected java.lang.String deduceElementSymbol​(boolean isHetero)

  The problem here stems from the fact that developers have not fully understood the PDB specifications -- and that those have changed. The actual rules are as follows (using 1-based numbering: 1) Chemical symbols may be in columns 77 and 78 for total disambiguity. 2) Only valid chemical symbols should be in columns 13 and 14 These are the first two characters of a four-character field. 3) Four-character atom names for hydrogen necessarily start in column 13, so when that is the case, if the four-letter name starts with "H" then it is hydrogen regardless of what letter comes next. For example, "HG3 " is mercury (and should be in a HETATM record, not an ATOM record, anyway), but "HG33" is hydrogen, presumably. This leave open the ambiguity of a four-letter H name in a heteroatom set where the symbol is really H, not Hg or Ha, or Ho or Hf, etc.

  Parameters:

  isHetero -

  Returns:

  an atom symbol

• conect

  private void conect()

• structure

  private void structure()

• getModelNumber

  private int getModelNumber()

• model

  protected void model​(int modelNumber)

• checkNotPDB

  private void checkNotPDB()

• cryst1

  private void cryst1()
               throws java.lang.Exception

  Throws:

  java.lang.Exception

• getFloat

  private float getFloat​(int ich,
                         int cch)
                  throws java.lang.Exception

  Throws:

  java.lang.Exception

• scale

  private void scale​(int n)
              throws java.lang.Exception

  Throws:

  java.lang.Exception

• expdta

  private void expdta()

• formul

  private void formul()

• het

  private void het()

• hetnam

  private void hetnam()

• anisou

  private void anisou()

• site

  private void site()

• remarkTls

  private boolean remarkTls()
                     throws java.lang.Exception

  Throws:

  java.lang.Exception

• handleTlsMissingModels

  private void handleTlsMissingModels()

  for now, we just ignore TLS details if user has selected a specific model

• setTlsGroups

  private void setTlsGroups​(int iGroup,
                            int iModel,
                            SymmetryInterface symmetry)

  Sets the atom property property_tlsGroup based on TLS group ranges and adds "TLS" key to model's auxiliaryInfo.

  Parameters:

  iGroup -

  iModel -

  symmetry -

• findAtomForRange

  private int findAtomForRange​(int atom1,
                               int atom2,
                               int chain,
                               int resno,
                               boolean isLast)

• findAtom

  private int findAtom​(int atom1,
                       int atom2,
                       int chain,
                       int resno,
                       boolean isTrue)

• setTlsTensor

  private void setTlsTensor​(Atom atom,
                            java.util.Map<java.lang.String,​java.lang.Object> group,
                            SymmetryInterface symmetry)

• tlsAddError

  private void tlsAddError​(java.lang.String error)

• fixRadius

  protected static float fixRadius​(float r)

• addConnection

  private void addConnection​(int[] is)

• connectAllBad

  private void connectAllBad​(int maxSerial)

• connectAll

  private void connectAll​(int maxSerial,
                          boolean isConnectStateBug)