FileParsingParameters (biojava 4.2.1 API)

java.lang.Object
- org.biojava.nbio.structure.io.FileParsingParameters

All Implemented Interfaces:

Serializable
```
public class FileParsingParameters
extends Object
implements Serializable
```
A class that configures parameters that can be sent to the PDB file parsers
- setParseCAOnly(boolean) - parse only the Atom records for C-alpha atoms
- setParseSecStruc(boolean) - a flag if the secondary structure information from the PDB file (author's assignment) should be parsed. If true the assignment can be accessed through AminoAcid.getSecStruc();
- setAlignSeqRes(boolean) - should the AminoAcid sequences from the SEQRES and ATOM records of a PDB file be aligned? (default:yes)
- setHeaderOnly(boolean) - parse only the PDB/mmCIF file header, ignoring coordinates
- setCreateAtomBonds(boolean) - create atom bonds from parsed bonds in PDB/mmCIF files and chemical component files
Author:

Andreas Prlic

See Also:

Serialized Form

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`ATOM_CA_THRESHOLD` The maximum number of atoms that will be parsed before the parser switches to a CA-only representation of the PDB file.
`static int`	`MAX_ATOMS` The maximum number of atoms we will add to a structure, this protects from memory overflows in the few really big protein structures.

Constructor Summary

Constructors
Constructor and Description

FileParsingParameters()

Constructors
Constructor and Description
`FileParsingParameters()`

Method Summary

All Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`String[]`	`getAcceptedAtomNames()` By default the parser will read in all atoms (unless using the CAonly switch).
`int`	`getAtomCaThreshold()` The maximum number of atoms that will be parsed before the parser switches to a CA-only representation of the PDB file.
`int`	`getMaxAtoms()` The maximum numbers of atoms to load in a protein structure (prevents memory overflows)
`boolean`	`isAlignSeqRes()` Flag if the SEQRES amino acids should be aligned with the ATOM amino acids.
`boolean`	`isHeaderOnly()` Parse only the PDB file header out of the files
`boolean`	`isParseBioAssembly()` Should the biological assembly info (REMARK 350) be parsed from the PDB file?
`boolean`	`isParseCAOnly()` The flag if only the C-alpha atoms of the structure should be parsed.
`boolean`	`isParseSecStruc()` Is secondary structure assignment being parsed from the file? default is null
`boolean`	`isUpdateRemediatedFiles()` Deprecated. Properties which impact downloading and caching behavior have been moved to the `StructureIOFile` implementations. See `LocalPDBDirectory#getFetchBehavior(LocalPDBDirectory.FetchBehavior)`
`boolean`	`isUseInternalChainId()` Should we use internal (asym_id) or public facing (author) chain ids
`void`	`setAcceptedAtomNames(String[] fullAtomNames)` By default the parser will read in all atoms (unless using the CAonly switch).
`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.
`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.
`void`	`setCreateAtomBonds(boolean createAtomBonds)` Should we create bonds between atoms when parsing a file.
`void`	`setCreateAtomCharges(boolean createAtomCharges)` Should we create charges on atoms when parsing a file?
`void`	`setDefault()`
`void`	`setHeaderOnly(boolean headerOnly)` Parse only the PDB file header out of the files
`void`	`setMaxAtoms(int maxAtoms)` The maximum numbers of atoms to load in a protein structure (prevents memory overflows)
`void`	`setParseBioAssembly(boolean parseBioAssembly)` Should the biological assembly info (REMARK 350) be parsed from the PDB file?
`void`	`setParseCAOnly(boolean parseCAOnly)` Flag if only the C-alpha atoms of the structure should be parsed.
`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.
`void`	`setUpdateRemediatedFiles(boolean updateRemediatedFiles)` Deprecated. Properties which impact downloading and caching behavior have been moved to the `StructureIOFile` implementations. See `LocalPDBDirectory.setFetchBehavior(LocalPDBDirectory.FetchBehavior)`
`void`	`setUseInternalChainId(boolean useInternalChainId)` Set the useInternalChainId parsing mode.
`boolean`	`shouldCreateAtomBonds()` Should we create bonds between atoms when parsing a file?
`boolean`	`shouldCreateAtomCharges()` Should we create charges on atoms when parsing a file?

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - ATOM_CA_THRESHOLD
```
public static final int ATOM_CA_THRESHOLD
```
    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.
    
    See Also:
    
    Constant Field Values
  - MAX_ATOMS
```
public static final int MAX_ATOMS
```
    The maximum number of atoms we will add to a structure, this protects from memory overflows in the few really big protein structures.
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - FileParsingParameters
```
public FileParsingParameters()
```
- Method Detail
  - 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

Class FileParsingParameters

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

ATOM_CA_THRESHOLD

MAX_ATOMS

Constructor Detail

FileParsingParameters

Method Detail

setDefault

isParseSecStruc

setParseSecStruc

isHeaderOnly

setHeaderOnly

isParseCAOnly

setParseCAOnly

isAlignSeqRes

setAlignSeqRes

isUpdateRemediatedFiles

setUpdateRemediatedFiles

getAcceptedAtomNames

setAcceptedAtomNames

getMaxAtoms

setMaxAtoms

getAtomCaThreshold

setAtomCaThreshold

isParseBioAssembly

setParseBioAssembly

shouldCreateAtomBonds

setCreateAtomBonds

shouldCreateAtomCharges

setCreateAtomCharges

isUseInternalChainId

setUseInternalChainId