StructureParserOptions (singa-structure 0.3.3 API)

java.lang.Object
- de.bioforscher.singa.structure.parser.pdb.structures.StructureParserOptions

public class StructureParserOptions
extends Object

Options for faster or more detailed parsing.

Author:: cl

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class StructureParserOptions.Setting
Settings that can be passed to the Options.

Nested Classes
Modifier and Type	Class and Description
`static class`	`StructureParserOptions.Setting` Settings that can be passed to the Options.

Constructor Summary

Constructors
Constructor and Description

StructureParserOptions()

Constructors
Constructor and Description
`StructureParserOptions()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`connectHydrogens(boolean connectHydrogens)` Setting this option to `true` will try to connect hydrogen atom tho their respective partners. Default value: `false`
`void`	`createEdges(boolean createEdges)` Setting this option true will connect the molecule with bonds.
`void`	`heteroAtoms(boolean heteroAtoms)`
`void`	`inferIdentifierFromFileName(boolean inferIdentifierFromFileName)` Setting this option to `true` will try parse any pdb identifier from the file name.
`void`	`inferTitleFromFileName(boolean inferTitleFromFileName)` Setting this option to `true` will set the title of the structure to the file name.
`boolean`	`isConnectingHydrogens()` Setting this option to `true` will try to connect hydrogen atom tho their respective partners. Default value: `false`
`boolean`	`isCreatingEdges()` Setting this option true will connect the molecule with bonds.
`boolean`	`isHeteroAtoms()`
`boolean`	`isInferringIdentifierFromFileName()` Setting this option to `true` will try parse any pdb identifier from the file name.
`boolean`	`isInferringTitleFromFileName()` Setting this option to `true` will set the title of the structure to the file name.
`boolean`	`isOmittingHydrogen()` Setting this option to `true` will omit all hydrogen (and eventually deuterium) atoms in amino acids and nucleotides.
`boolean`	`isRetrievingLigandInformation()` Setting this option to `true` will retrieve additional information from cif files from the PDB.
`void`	`omitHydrogens(boolean omitHydrogens)` Setting this option to `true` will omit all hydrogen (and eventually deuterium) atoms in amino acids and nucleotides.
`void`	`retrieveLigandInformation(boolean retrieveLigandInformation)` Setting this option to `true` will retrieve additional information from cif files from the PDB.
`static StructureParserOptions`	`withSettings(StructureParserOptions.Setting... settings)` Create a new Options object using enum constants.

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

- Constructor Detail
  - StructureParserOptions
```
public StructureParserOptions()
```
- Method Detail
  - withSettings
```
public static StructureParserOptions withSettings(StructureParserOptions.Setting... settings)
```
    Create a new Options object using enum constants.
    
    Parameters:
    
    settings - The settings.
    
    Returns:
    
    The options.
  - heteroAtoms
```
public void heteroAtoms(boolean heteroAtoms)
```
  - isHeteroAtoms
```
public boolean isHeteroAtoms()
```
  - isCreatingEdges
```
public boolean isCreatingEdges()
```
    Setting this option true will connect the molecule with bonds. Turning the option false will result in faster parsing, if those information are not strictly required.
    
    Default value: true
    
    Returns:
    
    The value of this option.
  - createEdges
```
public void createEdges(boolean createEdges)
```
    Setting this option true will connect the molecule with bonds. Turning the option false will result in faster parsing, if those information are not strictly required.
    
    Default value: true
    
    Parameters:
    
    createEdges - true to turn this option on, false to turn it off.
  - isRetrievingLigandInformation
```
public boolean isRetrievingLigandInformation()
```
    Setting this option to true will retrieve additional information from cif files from the PDB. This enables the detection modified amino acids and nucleotides als well as the retrieval of additional information for ligands and the connection of ligand atoms. Turning the option false will result in faster parsing, if those information are not strictly required.
    
    Default value: true
    
    Returns:
    
    The value of this option.
  - retrieveLigandInformation
```
public void retrieveLigandInformation(boolean retrieveLigandInformation)
```
    Setting this option to true will retrieve additional information from cif files from the PDB. This enables the detection modified amino acids and nucleotides als well as the retrieval of additional information for ligands and the connection of ligand atoms. Turning the option false will result in faster parsing, if those information are not strictly required.
    
    Default value: true
    
    Parameters:
    
    retrieveLigandInformation - true to turn this option on, false to turn it off.
  - isConnectingHydrogens
```
public boolean isConnectingHydrogens()
```
    Setting this option to true will try to connect hydrogen atom tho their respective partners.
    
    Default value: false
    
    Returns:
    
    The value of this option.
  - connectHydrogens
```
public void connectHydrogens(boolean connectHydrogens)
```
    Setting this option to true will try to connect hydrogen atom tho their respective partners.
    
    Default value: false
    
    Parameters:
    
    connectHydrogens - true to turn this option on, false to turn it off.
  - isOmittingHydrogen
```
public boolean isOmittingHydrogen()
```
    Setting this option to true will omit all hydrogen (and eventually deuterium) atoms in amino acids and nucleotides. Default value: false
    
    Returns:
    
    true to turn this option on, false to turn it off.
  - omitHydrogens
```
public void omitHydrogens(boolean omitHydrogens)
```
    Setting this option to true will omit all hydrogen (and eventually deuterium) atoms in amino acids and nucleotides. Default value: false
    
    Parameters:
    
    omitHydrogens - true to turn this option on, false to turn it off.
  - isInferringTitleFromFileName
```
public boolean isInferringTitleFromFileName()
```
    Setting this option to true will set the title of the structure to the file name. Default value: false
    
    Returns:
    
    true to turn this option on, false to turn it off.
  - inferTitleFromFileName
```
public void inferTitleFromFileName(boolean inferTitleFromFileName)
```
    Setting this option to true will set the title of the structure to the file name. Default value: false
    
    Parameters:
    
    inferTitleFromFileName - true to turn this option on, false to turn it off.
  - isInferringIdentifierFromFileName
```
public boolean isInferringIdentifierFromFileName()
```
    Setting this option to true will try parse any pdb identifier from the file name. Default value: false
    
    Returns:
    
    true to turn this option on, false to turn it off.
  - inferIdentifierFromFileName
```
public void inferIdentifierFromFileName(boolean inferIdentifierFromFileName)
```
    Setting this option to true will try parse any pdb identifier from the file name. Default value: false
    
    Parameters:
    
    inferIdentifierFromFileName - true to turn this option on, false to turn it off.

Class StructureParserOptions

Nested Class Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

StructureParserOptions

Method Detail

withSettings

heteroAtoms

isHeteroAtoms

isCreatingEdges

createEdges

isRetrievingLigandInformation

retrieveLigandInformation

isConnectingHydrogens

connectHydrogens

isOmittingHydrogen

omitHydrogens

isInferringTitleFromFileName

inferTitleFromFileName

isInferringIdentifierFromFileName

inferIdentifierFromFileName