Class PdbReader

Method Details

• initializeReader

  protected void initializeReader() throws Exception

  Overrides:

  initializeReader in class AtomSetCollectionReader

  Throws:

  Exception

• checkLine

  protected boolean checkLine() throws Exception

  Overrides:

  checkLine in class AtomSetCollectionReader

  Returns:

  true if need to read new line

  Throws:

  Exception

• checkRemark

  protected void checkRemark()

• seqAdv

  private void seqAdv()

• readHeader

  private String readHeader(boolean getLine) throws Exception

  Throws:

  Exception

• finalizeSubclassReader

  protected void finalizeSubclassReader() throws Exception

  Description copied from class: AtomSetCollectionReader

  optional reader-specific method run first.

  Overrides:

  finalizeSubclassReader in class AtomSetCollectionReader

  Throws:

  Exception

• finalizeReaderPDB

  protected void finalizeReaderPDB() throws Exception

  Throws:

  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 Exception

  Throws:

  Exception

• remark285

  private boolean remark285()

• remark290

  private boolean remark290() throws Exception

  Throws:

  Exception

• getSerial

  private int getSerial(int i, int j)

• getSeqNo

  private int getSeqNo(int i, int j)

• processAtom

  protected Atom processAtom(Atom atom, String name, char altID, String group3, int chainID, int seqNo, char insCode, boolean isHetero, 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 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()

• getModelName

  private String getModelName()

  A Jmol add-on -- allows for model name on MODEL line starting in column 15 (0-based)

  Returns:

  name or null

• model

  protected void model(int modelNumber, String name)

• checkNotPDB

  private void checkNotPDB()

• cryst1

  private void cryst1() throws Exception

  Throws:

  Exception

• getFloat

  private float getFloat(int ich, int cch) throws Exception

  Throws:

  Exception

• scale

  private void scale(int n) throws Exception

  Throws:

  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 Exception

  Throws:

  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, Map<String,Object> group, SymmetryInterface symmetry)

• tlsAddError

  private void tlsAddError(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)