Class FileParsingParameters

Method Details

• setDefault

  public void setDefault()

• isParseSecStruc

  public boolean isParseSecStruc()

  Is secondary structure assignment being parsed from the file? default is null

  Returns:

  boolean if HELIX STRAND and TURN fields are being parsed

• setParseSecStruc

  public void setParseSecStruc(boolean parseSecStruc)

  A flag to tell the parser to parse the Author's secondary structure assignment from the file default is set to false, i.e. do NOT parse.

  Parameters:

  parseSecStruc - if HELIX STRAND and TURN fields are being parsed

• isHeaderOnly

  public boolean isHeaderOnly()

  Parse only the PDB file header out of the files

  Returns:

  flag

• setHeaderOnly

  public void setHeaderOnly(boolean headerOnly)

  Parse only the PDB file header out of the files

  Parameters:

  headerOnly - flag

• isParseCAOnly

  public boolean isParseCAOnly()

  The flag if only the C-alpha atoms of the structure should be parsed.

  Returns:

  the flag

• setParseCAOnly

  public void setParseCAOnly(boolean parseCAOnly)

  Flag if only the C-alpha atoms of the structure should be parsed.

  Parameters:

  parseCAOnly - boolean flag to enable or disable C-alpha only parsing

• isAlignSeqRes

  public boolean isAlignSeqRes()

  Flag if the SEQRES amino acids should be aligned with the ATOM amino acids.

  Returns:

  flag if SEQRES - ATOM amino acids alignment is enabled

• setAlignSeqRes

  public void setAlignSeqRes(boolean alignSeqRes)

  Define if the SEQRES in the structure should be aligned with the ATOM records if yes, the AminoAcids in structure.getSeqRes will have the coordinates set.

  Parameters:

  alignSeqRes -

• isUpdateRemediatedFiles

  @Deprecated public boolean isUpdateRemediatedFiles()

  Deprecated.

  Properties which impact downloading and caching behavior have been moved to the StructureIOFile implementations. See LocalPDBDirectory#getFetchBehavior(LocalPDBDirectory.FetchBehavior)

  A flag if local files should be replaced with the latest version of remediated PDB files. Default: false

• setUpdateRemediatedFiles

  @Deprecated public void setUpdateRemediatedFiles(boolean updateRemediatedFiles)

  Deprecated.

  Properties which impact downloading and caching behavior have been moved to the StructureIOFile implementations. See LocalPDBDirectory.setFetchBehavior(LocalPDBDirectory.FetchBehavior)

  A flag if local files should be replaced with the latest version of remediated PDB files. Default: false

  Parameters:

  updateRemediatedFiles -

• getAcceptedAtomNames

  public String[] getAcceptedAtomNames()

  By default the parser will read in all atoms (unless using the CAonly switch). This allows to specify a set of atoms to be read. e.g. {"CA", "CB" }. Returns null if all atoms are accepted.

  Returns:

  accepted atom names, or null if all atoms are accepted. default null

• setAcceptedAtomNames

  public void setAcceptedAtomNames(String[] fullAtomNames)

  By default the parser will read in all atoms (unless using the CAonly switch). This allows to specify a set of atoms to be read. e.g. {"CA", "CB" }. Returns null if all atoms are accepted.

  Parameters:

  accepted - atom names, or null if all atoms are accepted. default null

• getMaxAtoms

  public int getMaxAtoms()

  The maximum numbers of atoms to load in a protein structure (prevents memory overflows)

  Returns:

  maximum nr of atoms to load, default Integer.MAX_VALUE;

• setMaxAtoms

  public void setMaxAtoms(int maxAtoms)

  The maximum numbers of atoms to load in a protein structure (prevents memory overflows)

  Parameters:

  maxAtoms - maximun nr of atoms to load

• getAtomCaThreshold

  public int getAtomCaThreshold()

  The maximum number of atoms that will be parsed before the parser switches to a CA-only representation of the PDB file. If this limit is exceeded also the SEQRES groups will be ignored.

  Returns:

  atomCaThreshold.

• setAtomCaThreshold

  public void setAtomCaThreshold(int atomCaThreshold)

  The maximum number of atoms that will be parsed before the parser switches to a CA-only representation of the PDB file. If this limit is exceeded also the SEQRES groups will be ignored.

  Parameters:

  atomCaThreshold - maximum number of atoms for all atom representation.

• isParseBioAssembly

  public boolean isParseBioAssembly()

  Should the biological assembly info (REMARK 350) be parsed from the PDB file?

  Returns:

  boolean flag yes/no

• setParseBioAssembly

  public void setParseBioAssembly(boolean parseBioAssembly)

  Should the biological assembly info (REMARK 350) be parsed from the PDB file?

  Parameters:

  parseBioAssembly - boolean flag yes/no

• shouldCreateAtomBonds

  public boolean shouldCreateAtomBonds()

  Should we create bonds between atoms when parsing a file?

  Returns:

  true if we should create the bonds, false if not

• setCreateAtomBonds

  public void setCreateAtomBonds(boolean createAtomBonds)

  Should we create bonds between atoms when parsing a file. Will create intra-group bonds from information available in chemical component files and some other bonds from struc_conn category in mmCIF file.

  Parameters:

  createAtomBonds - true if we should create the bonds, false if not

  See Also:

  • BondMaker

• shouldCreateAtomCharges

  public boolean shouldCreateAtomCharges()

  Should we create charges on atoms when parsing a file?

  Returns:

  true if we should create the charges, false if not

• setCreateAtomCharges

  public void setCreateAtomCharges(boolean createAtomCharges)

  Should we create charges on atoms when parsing a file?

  Parameters:

  createAtomCharges - true if we should create the charges, false if not

• isUseInternalChainId

  public boolean isUseInternalChainId()

  Should we use internal (asym_id) or public facing (author) chain ids

  Returns:

  Since:

  4.2

• setUseInternalChainId

  public void setUseInternalChainId(boolean useInternalChainId)

  Set the useInternalChainId parsing mode. This is an experimental parsing mode that applies only to the mmCIF parser. It will create chains following the model specified in the mmCIF dictionary where both polymer and non-polymer entities are assigned separate chains. The chain identifiers used are the asym_ids specified in mmCIF file. Some BioJava features might not work properly in this parsing mode.

  Parameters:

  useInternalChainId -

  Since:

  4.2