Package org.snpeff.pdb
Class ProteinInteractions
java.lang.Object
org.snpeff.pdb.ProteinInteractions
This class reads a set of protein structure (PDB) files, analyzes
the structures, and creates a interactions file for
a SnpEff genome database (interactions.bin)
- Author:
- pcingola
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Field Summary
Fields -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
boolean
filterTranscript
(String trId) Return true if the transcript passes the criteria (i.e.findTranscriptIds
(String pdbId) int
getByProteinId
(String proteinId) double
double
double
double
getTranscript
(String trId) void
void
void
void
initialize
(Config config) Initialize class (deferred initialization) Note: This is not done at construction because we don't have a 'Config' object ready (loaded) at the timeboolean
isDebug()
boolean
void
void
pdb()
PDB analysisprotected void
Check that protein sequences form PDB matches sequences from Genome Return an IdMapped of confirmed entries (i.e.boolean
run()
Run analysis.boolean
run
(boolean storeResults) void
save
(List<DistanceResult> distResults) Save resultsvoid
setAaMinSeparation
(int aaMinSeparation) void
void
setDebug
(boolean debug) void
setDistanceThreshold
(double distanceThreshold) void
setDistanceThresholdNon
(double distanceThresholdNon) void
setGenomeVer
(String genomeVer) void
setIdMapFile
(String idMapFile) void
setMaxMismatchRate
(double maxMismatchRate) void
void
setPdbOrganismCommon
(String pdbOrganismCommon) void
setPdbOrganismScientific
(String pdbOrganismScientific) void
setPdbResolution
(double pdbResolution) void
setVerbose
(boolean verbose)
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Field Details
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PROTEIN_INTERACTION_FILE
- See Also:
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DEFAULT_PDB_DIR
- See Also:
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DEFAULT_DISTANCE_THRESHOLD
public static final double DEFAULT_DISTANCE_THRESHOLD- See Also:
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DEFAULT_MAX_MISMATCH_RATE
public static final double DEFAULT_MAX_MISMATCH_RATE- See Also:
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DEFAULT_PDB_MIN_AA_SEPARATION
public static final int DEFAULT_PDB_MIN_AA_SEPARATION- See Also:
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DEFAULT_PDB_ORGANISM_COMMON
- See Also:
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DEFAULT_PDB_ORGANISM_SCIENTIFIC
- See Also:
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DEFAULT_PDB_RESOLUTION
public static final double DEFAULT_PDB_RESOLUTION- See Also:
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Constructor Details
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ProteinInteractions
public ProteinInteractions()
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Method Details
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checkParams
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deleteOutputDb
public void deleteOutputDb() -
filterTranscript
Return true if the transcript passes the criteria (i.e. the ID is present in 'trancriptById' map) -
findTranscriptIds
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getAaMinSeparation
public int getAaMinSeparation() -
setAaMinSeparation
public void setAaMinSeparation(int aaMinSeparation) -
getByProteinId
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getDistanceResults
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getDistanceThreshold
public double getDistanceThreshold() -
setDistanceThreshold
public void setDistanceThreshold(double distanceThreshold) -
getDistanceThresholdNon
public double getDistanceThresholdNon() -
setDistanceThresholdNon
public void setDistanceThresholdNon(double distanceThresholdNon) -
getIdMapFile
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setIdMapFile
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getMaxMismatchRate
public double getMaxMismatchRate() -
setMaxMismatchRate
public void setMaxMismatchRate(double maxMismatchRate) -
getPdbOrganismCommon
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setPdbOrganismCommon
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getPdbOrganismScientific
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setPdbOrganismScientific
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getPdbResolution
public double getPdbResolution() -
setPdbResolution
public void setPdbResolution(double pdbResolution) -
getTranscript
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incCountFilesPass
public void incCountFilesPass() -
incCountMapOk
public void incCountMapOk() -
incCountMapError
public void incCountMapError() -
initialize
Initialize class (deferred initialization) Note: This is not done at construction because we don't have a 'Config' object ready (loaded) at the time -
isDebug
public boolean isDebug() -
setDebug
public void setDebug(boolean debug) -
isVerbose
public boolean isVerbose() -
setVerbose
public void setVerbose(boolean verbose) -
loadIdMapper
public void loadIdMapper() -
pdb
public void pdb()PDB analysis -
pdbAnalysis
protected void pdbAnalysis()Check that protein sequences form PDB matches sequences from Genome Return an IdMapped of confirmed entries (i.e. AA sequence matches between transcript and PDB) -
run
public boolean run()Run analysis. -
run
public boolean run(boolean storeResults) -
save
Save results -
setConfig
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setGenomeVer
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setPdbDir
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