Fit3D (singa-structure 0.3.3 API)

All Known Implementing Classes:

Fit3DAlignment, Fit3DAlignmentBatch, Fit3DSiteAlignment
```
public interface Fit3D
```
Represents an instance of the Fit3D algorithm. This can either be a one target one alignment (Fit3DAlignment) or an alignment batch (Fit3DAlignmentBatch).

Author:

fk

Field Summary

Fields
Modifier and Type Field and Description

static org.slf4j.Logger logger

Fields
Modifier and Type	Field and Description
`static org.slf4j.Logger`	`logger`

Method Summary

All Methods Instance Methods Abstract Methods Default Methods
Modifier and Type	Method and Description
`default String`	`getAlignmentString()` Returns a string that represents the alignment.
`default double`	`getFraction()` Returns the fraction of residues that were aligned.
`List<Fit3DMatch>`	`getMatches()` Returns the matches that were found by this Fit3D search.
`default PsScore`	`getPsScore()` Returns the `PsScore` of aligned residues (only available for `Fit3DSiteAlignment`.
`default XieScore`	`getXieScore()` Returns the `XieScore` of aligned residues (only available for `Fit3DSiteAlignment`.
`default void`	`writeMatches(Path outputDirectory)` Writes the matches that were found by this Fit3D search to the specified directory.
`default void`	`writeMatches(Path outputDirectory, double rmsdCutoff)` Writes the matches that were found by this Fit3D search to the specified directory.
`default void`	`writeSummaryFile(Path summaryFilePath)` Writes a CSV summary file of the matches obtained by `Fit3D`i.

- Field Detail
  - logger
```
static final org.slf4j.Logger logger
```
- Method Detail
  - getMatches
```
List<Fit3DMatch> getMatches()
```
    Returns the matches that were found by this Fit3D search.
    
    Returns:
    
    The matches found in the target structure(s).
  - getFraction
```
default double getFraction()
```
    Returns the fraction of residues that were aligned.
    
    Returns:
    
    The fractions of matches that were aligned.
  - getXieScore
```
default XieScore getXieScore()
```
    Returns the XieScore of aligned residues (only available for Fit3DSiteAlignment.
    
    Returns:
    
    The XieScore of residues that were aligned.
  - getPsScore
```
default PsScore getPsScore()
```
    Returns the PsScore of aligned residues (only available for Fit3DSiteAlignment.
    
    Returns:
    
    The PsScore of residues that were aligned.
  - writeMatches
```
default void writeMatches(Path outputDirectory,
                          double rmsdCutoff)
```
    Writes the matches that were found by this Fit3D search to the specified directory. All matches are aligned to the query motif. Only matches up to the specified RMSD cutoff are reported.
    
    Parameters:
    
    outputDirectory - The directory where the matches should be written.
    
    rmsdCutoff - The cutoff up to which matches should be written.
  - writeMatches
```
default void writeMatches(Path outputDirectory)
```
    Writes the matches that were found by this Fit3D search to the specified directory. All matches are aligned to the query motif.
    
    Parameters:
    
    outputDirectory - The directory where the matches should be written.
  - writeSummaryFile
```
default void writeSummaryFile(Path summaryFilePath)
                       throws IOException
```
    Writes a CSV summary file of the matches obtained by Fit3Di.
    
    Parameters:
    
    summaryFilePath - The Path to which the file should be written.
    
    Throws:
    
    IOException - If writing of the summary file fails.
  - getAlignmentString
```
default String getAlignmentString()
```
    Returns a string that represents the alignment. This is only available for the Fit3DSiteAlignment.
    
    Returns:
    
    The alignment in string representation.

Interface Fit3D

Field Summary

Method Summary

Field Detail

logger

Method Detail

getMatches

getFraction

getXieScore

getPsScore

writeMatches

writeMatches

writeSummaryFile

getAlignmentString