FileParsingParameters (biojava 5.0.0 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
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?
`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. do NOT parse.
`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 -
  - 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:
    
    fullAtomNames - 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

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

getAcceptedAtomNames

setAcceptedAtomNames

getMaxAtoms

setMaxAtoms

getAtomCaThreshold

setAtomCaThreshold

isParseBioAssembly

setParseBioAssembly

shouldCreateAtomBonds

setCreateAtomBonds

shouldCreateAtomCharges

setCreateAtomCharges