idx int64 0 41.2k | question stringlengths 74 4.21k | target stringlengths 5 888 |
|---|---|---|
24,400 | private void checkWriteFile ( AFPChain afpChain , Atom [ ] ca1 , Atom [ ] ca2 , boolean dbsearch ) throws IOException , ClassNotFoundException , NoSuchMethodException , InvocationTargetException , IllegalAccessException , StructureException { String output = null ; if ( params . isOutputPDB ( ) ) { if ( ! GuiWrapper . ... | check if the result should be written to the local file system |
24,401 | private Structure fixStructureName ( Structure s , String file ) { if ( s . getName ( ) != null && ( ! s . getName ( ) . equals ( "" ) ) ) return s ; s . setName ( s . getPDBCode ( ) ) ; if ( s . getName ( ) == null || s . getName ( ) . equals ( "" ) ) { File f = new File ( file ) ; s . setName ( f . getName ( ) ) ; } ... | apply a number of rules to fix the name of the structure if it did not get set during loading . |
24,402 | public static void main ( String [ ] args ) throws IOException , StructureException { Structure structure = MmtfActions . readFromWeb ( "4cup" ) ; System . out . println ( structure . getChains ( ) . size ( ) ) ; } | Main function to run the demo |
24,403 | public void runOptimization ( int maxi ) throws StructureException { superimposeBySet ( ) ; if ( debug ) System . err . println ( " initial rmsd " + rmsd ) ; maxKeepStep = 4 ; keepStep = 0 ; optimize ( maxi ) ; } | run the optimization |
24,404 | private void superimposeBySet ( ) throws StructureException { Atom [ ] tmp1 = new Atom [ equLen ] ; Atom [ ] tmp2 = new Atom [ equLen ] ; int i , r1 , r2 ; for ( i = 0 ; i < equLen ; i ++ ) { r1 = equSet [ 0 ] [ i ] ; r2 = equSet [ 1 ] [ i ] ; tmp1 [ i ] = cod1 [ r1 ] ; tmp2 [ i ] = ( Atom ) cod2 [ r2 ] . clone ( ) ; }... | superimpose two structures according to the equivalent residues |
24,405 | private void saveMatrix ( ) { for ( String chainId : currentChainIDs ) { BiologicalAssemblyTransformation transformation = new BiologicalAssemblyTransformation ( ) ; transformation . setRotationMatrix ( currentMatrix . getArray ( ) ) ; transformation . setTranslation ( shift ) ; transformation . setId ( String . valueO... | Saves transformation matrix for the list of current chains |
24,406 | public void setMacromolecularSizes ( ) { for ( BioAssemblyInfo bioAssembly : transformationMap . values ( ) ) { bioAssembly . setMacromolecularSize ( bioAssembly . getTransforms ( ) . size ( ) ) ; } } | Set the macromolecularSize fields of the parsed bioassemblies . This can only be called after the full PDB file has been read so that all the info for all bioassemblies has been gathered . Note that an explicit method to set the field is necessary here because in PDB files the transformations contain only the author ch... |
24,407 | public static < C extends Compound > UniprotProxySequenceReader < C > parseUniprotXMLString ( String xml , CompoundSet < C > compoundSet ) { try { Document document = XMLHelper . inputStreamToDocument ( new ByteArrayInputStream ( xml . getBytes ( ) ) ) ; return new UniprotProxySequenceReader < C > ( document , compound... | The passed in xml is parsed as a DOM object so we know everything about the protein . If an error occurs throw an exception . We could have a bad uniprot id |
24,408 | public ArrayList < AccessionID > getAccessions ( ) throws XPathExpressionException { ArrayList < AccessionID > accessionList = new ArrayList < AccessionID > ( ) ; if ( uniprotDoc == null ) { return accessionList ; } Element uniprotElement = uniprotDoc . getDocumentElement ( ) ; Element entryElement = XMLHelper . select... | Pull uniprot accessions associated with this sequence |
24,409 | public ArrayList < String > getProteinAliases ( ) throws XPathExpressionException { ArrayList < String > aliasList = new ArrayList < String > ( ) ; if ( uniprotDoc == null ) { return aliasList ; } Element uniprotElement = uniprotDoc . getDocumentElement ( ) ; Element entryElement = XMLHelper . selectSingleElement ( uni... | Pull uniprot protein aliases associated with this sequence |
24,410 | public ArrayList < String > getGeneAliases ( ) throws XPathExpressionException { ArrayList < String > aliasList = new ArrayList < String > ( ) ; if ( uniprotDoc == null ) { return aliasList ; } Element uniprotElement = uniprotDoc . getDocumentElement ( ) ; Element entryElement = XMLHelper . selectSingleElement ( unipro... | Pull uniprot gene aliases associated with this sequence |
24,411 | private static HttpURLConnection openURLConnection ( URL url ) throws IOException { final int timeout = 5000 ; final String useragent = "BioJava" ; HttpURLConnection conn = ( HttpURLConnection ) url . openConnection ( ) ; conn . setRequestProperty ( "User-Agent" , useragent ) ; conn . setInstanceFollowRedirects ( true ... | Open a URL connection . |
24,412 | public String getGeneName ( ) { if ( uniprotDoc == null ) { return "" ; } try { Element uniprotElement = uniprotDoc . getDocumentElement ( ) ; Element entryElement = XMLHelper . selectSingleElement ( uniprotElement , "entry" ) ; Element geneElement = XMLHelper . selectSingleElement ( entryElement , "gene" ) ; if ( gene... | Get the gene name associated with this sequence . |
24,413 | public ArrayList < String > getKeyWords ( ) { ArrayList < String > keyWordsList = new ArrayList < String > ( ) ; if ( uniprotDoc == null ) { return keyWordsList ; } try { Element uniprotElement = uniprotDoc . getDocumentElement ( ) ; Element entryElement = XMLHelper . selectSingleElement ( uniprotElement , "entry" ) ; ... | Pull UniProt key words which is a mixed bag of words associated with this sequence |
24,414 | public LinkedHashMap < String , ArrayList < DBReferenceInfo > > getDatabaseReferences ( ) { LinkedHashMap < String , ArrayList < DBReferenceInfo > > databaseReferencesHashMap = new LinkedHashMap < String , ArrayList < DBReferenceInfo > > ( ) ; if ( uniprotDoc == null ) { return databaseReferencesHashMap ; } try { Eleme... | The Uniprot mappings to other database identifiers for this sequence |
24,415 | public static AFPChain fastaToAfpChain ( Map < String , ProteinSequence > sequences , Structure structure1 , Structure structure2 ) throws StructureException { if ( sequences . size ( ) != 2 ) { throw new IllegalArgumentException ( "There must be exactly 2 sequences, but there were " + sequences . size ( ) ) ; } if ( s... | Uses two sequences each with a corresponding structure to create an AFPChain corresponding to the alignment . Provided only for convenience since FastaReaders return such maps . |
24,416 | public static AFPChain fastaToAfpChain ( SequencePair < Sequence < AminoAcidCompound > , AminoAcidCompound > alignment , Structure structure1 , Structure structure2 ) throws StructureException { List < AlignedSequence < Sequence < AminoAcidCompound > , AminoAcidCompound > > seqs = alignment . getAlignedSequences ( ) ; ... | Provided only for convenience . |
24,417 | public static void main ( String [ ] args ) throws StructureException , IOException { if ( args . length != 3 ) { System . err . println ( "Usage: FastaAFPChainConverter fasta-file structure-1-name structure-2-name" ) ; return ; } File fasta = new File ( args [ 0 ] ) ; Structure structure1 = StructureTools . getStructu... | Prints out the XML representation of an AFPChain from a file containing exactly two FASTA sequences . |
24,418 | public void put ( Key key , Value val ) { if ( val == null ) st . remove ( key ) ; else st . put ( key , val ) ; } | Put key - value pair into the symbol table . Remove key from table if value is null . |
24,419 | public Key ceil ( Key k ) { SortedMap < Key , Value > tail = st . tailMap ( k ) ; if ( tail . isEmpty ( ) ) return null ; else return tail . firstKey ( ) ; } | Return the smallest key in the table > = k . |
24,420 | public Key floor ( Key k ) { if ( st . containsKey ( k ) ) return k ; SortedMap < Key , Value > head = st . headMap ( k ) ; if ( head . isEmpty ( ) ) return null ; else return head . lastKey ( ) ; } | Return the largest key in the table < = k . |
24,421 | private String [ ] getHeaderValues ( String header ) { String [ ] data = new String [ 0 ] ; ArrayList < String > values = new ArrayList < String > ( ) ; StringBuffer sb = new StringBuffer ( ) ; if ( ! header . startsWith ( "PDB:" ) ) { for ( int i = 0 ; i < header . length ( ) ; i ++ ) { if ( header . charAt ( i ) == '... | Parse out the components where some have a | and others do not |
24,422 | static < E > List < E > getListFromFutures ( List < Future < E > > futures ) { List < E > list = new ArrayList < E > ( ) ; for ( Future < E > f : futures ) { try { list . add ( f . get ( ) ) ; } catch ( InterruptedException e ) { logger . error ( "Interrupted Exception: " , e ) ; } catch ( ExecutionException e ) { logg... | Factory method which retrieves calculated elements from a list of tasks on the concurrent execution queue . |
24,423 | public static < S extends Sequence < C > , C extends Compound > PairwiseSequenceAligner < S , C > getPairwiseAligner ( S query , S target , PairwiseSequenceAlignerType type , GapPenalty gapPenalty , SubstitutionMatrix < C > subMatrix ) { if ( ! query . getCompoundSet ( ) . equals ( target . getCompoundSet ( ) ) ) { thr... | Factory method which constructs a pairwise sequence aligner . |
24,424 | static < S extends Sequence < C > , C extends Compound > PairwiseSequenceScorer < S , C > getPairwiseScorer ( S query , S target , PairwiseSequenceScorerType type , GapPenalty gapPenalty , SubstitutionMatrix < C > subMatrix ) { switch ( type ) { default : case GLOBAL : return getPairwiseAligner ( query , target , Pairw... | Factory method which constructs a pairwise sequence scorer . |
24,425 | static < S extends Sequence < C > , C extends Compound > ProfileProfileAligner < S , C > getProfileProfileAligner ( Future < ProfilePair < S , C > > profile1 , Future < ProfilePair < S , C > > profile2 , ProfileProfileAlignerType type , GapPenalty gapPenalty , SubstitutionMatrix < C > subMatrix ) { switch ( type ) { de... | Factory method which constructs a profile - profile aligner . |
24,426 | public void process ( ) throws IOException , StructureException { if ( sequences == null ) { LinkedHashMap < String , ProteinSequence > sequenceMap = reader . process ( ) ; sequences = sequenceMap . values ( ) . toArray ( new ProteinSequence [ 0 ] ) ; accessions = new String [ sequences . length ] ; structures = new St... | Parses the fasta file and loads it into memory . |
24,427 | public static void downloadFile ( URL url , File destination ) throws IOException { int count = 0 ; int maxTries = 10 ; int timeout = 60000 ; File tempFile = File . createTempFile ( getFilePrefix ( destination ) , "." + getFileExtension ( destination ) ) ; ReadableByteChannel rbc = null ; FileOutputStream fos = null ; ... | Download the content provided at URL url and store the result to a local file using a temp file to cache the content in case something goes wrong in download |
24,428 | public static String toUnixPath ( String path ) { String uPath = path ; if ( uPath . contains ( "\\" ) ) { uPath = uPath . replaceAll ( "\\\\" , "/" ) ; } if ( uPath . endsWith ( "//" ) ) { uPath = uPath . substring ( 0 , uPath . length ( ) - 1 ) ; } if ( ! uPath . endsWith ( "/" ) ) { uPath = uPath + "/" ; } return uP... | Converts path to Unix convention and adds a terminating slash if it was omitted |
24,429 | public static String expandUserHome ( String file ) { if ( file . startsWith ( "~" + File . separator ) ) { file = System . getProperty ( "user.home" ) + file . substring ( 1 ) ; } return file ; } | Expands ~ in paths to the user s home directory . |
24,430 | public static void deleteDirectory ( Path dir ) throws IOException { if ( dir == null || ! Files . exists ( dir ) ) return ; Files . walkFileTree ( dir , new SimpleFileVisitor < Path > ( ) { public FileVisitResult visitFile ( Path file , BasicFileAttributes attrs ) throws IOException { Files . delete ( file ) ; return ... | Recursively delete a folder & contents |
24,431 | public ChemComp getParent ( ChemComp c ) { if ( c . hasParent ( ) ) { return dictionary . get ( c . getMon_nstd_parent_comp_id ( ) ) ; } return null ; } | Get the parent of a component . If component has no parent return null |
24,432 | public void addChemComp ( ChemComp comp ) { dictionary . put ( comp . getId ( ) , comp ) ; String rep = comp . getPdbx_replaces ( ) ; if ( ( rep != null ) && ( ! rep . equals ( "?" ) ) ) { replaces . put ( comp . getId ( ) , rep ) ; } String isrep = comp . getPdbx_replaced_by ( ) ; if ( ( isrep != null ) && ( ! isrep .... | add a new component to the dictionary |
24,433 | static public LinkedHashMap < String , ChromosomeSequence > loadFastaAddGeneFeaturesFromGeneIDGFF2 ( File fastaSequenceFile , File gffFile ) throws Exception { LinkedHashMap < String , DNASequence > dnaSequenceList = FastaReaderHelper . readFastaDNASequence ( fastaSequenceFile ) ; LinkedHashMap < String , ChromosomeSeq... | Loads Fasta file and GFF2 feature file generated from the geneid prediction algorithm |
24,434 | static public LinkedHashMap < String , ChromosomeSequence > loadFastaAddGeneFeaturesFromGmodGFF3 ( File fastaSequenceFile , File gffFile , boolean lazyloadsequences ) throws Exception { LinkedHashMap < String , DNASequence > dnaSequenceList = FastaReaderHelper . readFastaDNASequence ( fastaSequenceFile , lazyloadsequen... | Lots of variations in the ontology or descriptors that can be used in GFF3 which requires writing a custom parser to handle a GFF3 generated or used by a specific application . Probably could be abstracted out but for now easier to handle with custom code to deal with gff3 elements that are not included but can be extr... |
24,435 | public void setChromosome ( String chr ) throws Exception { if ( twoBitParser == null ) { } twoBitParser . close ( ) ; String [ ] names = twoBitParser . getSequenceNames ( ) ; for ( int i = 0 ; i < names . length ; i ++ ) { if ( names [ i ] . equalsIgnoreCase ( chr ) ) { twoBitParser . setCurrentSequence ( names [ i ] ... | Sets a chromosome for TwoBitParser . |
24,436 | public String getSequence ( String chromosomeName , int start , int end ) throws Exception { twoBitParser . close ( ) ; twoBitParser . setCurrentSequence ( chromosomeName ) ; return twoBitParser . loadFragment ( start , end - start ) ; } | Extract a sequence from a chromosome using chromosomal coordinates |
24,437 | public int compareTo ( StructureName o ) { if ( this . equals ( o ) ) return 0 ; String pdb1 = null ; String pdb2 = null ; try { pdb1 = this . getPdbId ( ) ; } catch ( StructureException e ) { } try { pdb2 = this . getPdbId ( ) ; } catch ( StructureException e ) { } int comp = 0 ; if ( pdb1 == null ) { if ( pdb2 != nul... | Orders identifiers lexicographically by PDB ID and then full Identifier |
24,438 | private String printPDBConnections ( ) { StringBuilder str = new StringBuilder ( ) ; for ( Chain c : structure . getChains ( ) ) { for ( Group g : c . getAtomGroups ( ) ) { for ( Atom a : g . getAtoms ( ) ) { if ( a . getBonds ( ) != null ) { for ( Bond b : a . getBonds ( ) ) { str . append ( String . format ( "CONECT%... | Prints the connections in PDB style |
24,439 | public static String toPDB ( Atom a ) { StringBuffer w = new StringBuffer ( ) ; toPDB ( a , w ) ; return w . toString ( ) ; } | Prints the content of an Atom object as a PDB formatted line . |
24,440 | public static String toPDB ( Chain chain ) { StringBuffer w = new StringBuffer ( ) ; int nrGroups = chain . getAtomLength ( ) ; for ( int h = 0 ; h < nrGroups ; h ++ ) { Group g = chain . getAtomGroup ( h ) ; toPDB ( g , w ) ; } return w . toString ( ) ; } | Convert a Chain object to PDB representation |
24,441 | public static String toPDB ( Group g ) { StringBuffer w = new StringBuffer ( ) ; toPDB ( g , w ) ; return w . toString ( ) ; } | Convert a Group object to PDB representation |
24,442 | private static boolean hasInsertionCode ( String pdbserial ) { try { Integer . parseInt ( pdbserial ) ; } catch ( NumberFormatException e ) { return true ; } return false ; } | test if pdbserial has an insertion code |
24,443 | private static String toSingleLoopLineMmCifString ( Object record , Field [ ] fields , int [ ] sizes ) { StringBuilder str = new StringBuilder ( ) ; Class < ? > c = record . getClass ( ) ; if ( fields == null ) fields = getFields ( c ) ; if ( sizes . length != fields . length ) throw new IllegalArgumentException ( "The... | Given a mmCIF bean produces a String representing it in mmCIF loop format as a single record line |
24,444 | private static < T > int [ ] getFieldSizes ( List < T > list , Field [ ] fields ) { if ( list . isEmpty ( ) ) throw new IllegalArgumentException ( "List of beans is empty!" ) ; if ( fields == null ) fields = getFields ( list . get ( 0 ) . getClass ( ) ) ; int [ ] sizes = new int [ fields . length ] ; for ( T a : list )... | Finds the max length of each of the String values contained in each of the fields of the given list of beans . Useful for producing mmCIF loop data that is aligned for all columns . |
24,445 | private static int getMaxStringLength ( String [ ] names ) { int size = 0 ; for ( String s : names ) { if ( s . length ( ) > size ) { size = s . length ( ) ; } } return size ; } | Finds the max length of a list of strings Useful for producing mmCIF single - record data that is aligned for all values . |
24,446 | public String toXML ( boolean hasResult ) throws IOException { StringWriter swriter = new StringWriter ( ) ; PrintWriter writer = new PrintWriter ( swriter ) ; PrettyXMLWriter xml = new PrettyXMLWriter ( writer ) ; xml . openTag ( "alignment" ) ; xml . attribute ( "hasResult" , String . valueOf ( hasResult ) ) ; xml . ... | return flag if the server has a result |
24,447 | public List < StructureIdentifier > getRepeatsID ( ) throws StructureException { if ( ! isRefined ( ) ) return null ; List < StructureIdentifier > repeats = new ArrayList < StructureIdentifier > ( numRepeats ) ; String pdbId = structureId . toCanonical ( ) . getPdbId ( ) ; Block align = multipleAlignment . getBlocks ( ... | Return the symmetric repeats as structure identifiers if the result is symmetric and it was refined return null otherwise . |
24,448 | public String getReason ( ) { double tm = selfAlignment . getTMScore ( ) ; if ( tm < params . getUnrefinedScoreThreshold ( ) ) { return String . format ( "Insignificant self-alignment (TM=%.2f)" , tm ) ; } if ( numRepeats == 1 ) { return String . format ( "Order detector found asymmetric alignment (TM=%.2f)" , tm ) ; }... | Return a String describing the reasons for the CE - Symm final decision in this particular result . |
24,449 | private static List < Integer > initializeEligible ( Map < Integer , Integer > alignment , Map < Integer , Double > scores , List < Integer > eligible , int k , NavigableSet < Integer > forwardLoops , NavigableSet < Integer > backwardLoops ) { if ( eligible == null ) { eligible = new LinkedList < Integer > ( alignment ... | Helper method to initialize eligible residues . |
24,450 | private static Map < Integer , Double > initializeScores ( Map < Integer , Integer > alignment , Map < Integer , Double > scores , int k ) { if ( scores == null ) { scores = new HashMap < Integer , Double > ( alignment . size ( ) ) ; } else { scores . clear ( ) ; } Map < Integer , Integer > alignK = AlignmentTools . ap... | Calculates all scores for an alignment |
24,451 | private static AFPChain partitionAFPchain ( AFPChain afpChain , Atom [ ] ca1 , Atom [ ] ca2 , int order ) throws StructureException { int [ ] [ ] [ ] newAlgn = new int [ order ] [ ] [ ] ; int repeatLen = afpChain . getOptLength ( ) / order ; List < Integer > alignedRes = new ArrayList < Integer > ( ) ; for ( int su = 0... | Partitions an afpChain alignment into order blocks of aligned residues . |
24,452 | private static SubstitutionMatrix < AminoAcidCompound > getAminoAcidMatrix ( String file ) { if ( ! aminoAcidMatrices . containsKey ( file ) ) { aminoAcidMatrices . put ( file , new SimpleSubstitutionMatrix < AminoAcidCompound > ( AminoAcidCompoundSet . getAminoAcidCompoundSet ( ) , getReader ( file ) , file ) ) ; } re... | reads in an amino acid substitution matrix if necessary |
24,453 | private static SubstitutionMatrix < NucleotideCompound > getNucleotideMatrix ( String file ) { if ( ! nucleotideMatrices . containsKey ( file ) ) { nucleotideMatrices . put ( file , new SimpleSubstitutionMatrix < NucleotideCompound > ( AmbiguityDNACompoundSet . getDNACompoundSet ( ) , getReader ( file ) , file ) ) ; } ... | reads in a nucleotide substitution matrix if necessary |
24,454 | private static InputStreamReader getReader ( String file ) { String resourcePathPrefix = "matrices/" ; return new InputStreamReader ( SubstitutionMatrixHelper . class . getResourceAsStream ( String . format ( "/%s.txt" , resourcePathPrefix + file ) ) ) ; } | reads in a substitution matrix from a resource file |
24,455 | private Group getNewGroup ( String recordName , Character aminoCode1 , String aminoCode3 ) { Group g = ChemCompGroupFactory . getGroupFromChemCompDictionary ( aminoCode3 ) ; if ( g != null && ! g . getChemComp ( ) . isEmpty ( ) ) return g ; Group group ; if ( aminoCode1 == null || StructureTools . UNKNOWN_GROUP_LABEL =... | initiate new resNum either Hetatom Nucleotide or AminoAcid |
24,456 | private void pdb_JRNL_Handler ( String line ) { if ( line . substring ( line . length ( ) - 8 , line . length ( ) - 4 ) . equals ( pdbId ) ) { logger . debug ( "trimming legacy PDB id from end of JRNL section line" ) ; line = line . substring ( 0 , line . length ( ) - 8 ) ; journalLines . add ( line ) ; } else { journa... | JRNL handler . The JRNL record contains the primary literature citation that describes the experiment which resulted in the deposited coordinate set . There is at most one JRNL reference per entry . If there is no primary reference then there is no JRNL reference . Other references are given in REMARK 1 . |
24,457 | private void pdb_SOURCE_Handler ( String line ) { String continuationNr = line . substring ( 9 , 10 ) . trim ( ) ; logger . debug ( "current continuationNo is " + continuationNr ) ; logger . debug ( "previousContinuationField is " + previousContinuationField ) ; logger . debug ( "current continuationField is " + ... | Handler for SOURCE Record format |
24,458 | private void pdb_REMARK_Handler ( String line ) { if ( line == null || line . length ( ) < 11 ) return ; if ( line . startsWith ( "REMARK 800" ) ) { pdb_REMARK_800_Handler ( line ) ; } else if ( line . startsWith ( "REMARK 350" ) ) { if ( params . isParseBioAssembly ( ) ) { if ( bioAssemblyParser == null ) { bioAssembl... | Handler for REMARK lines |
24,459 | private Integer conect_helper ( String line , int start , int end ) { if ( line . length ( ) < end ) return null ; String sbond = line . substring ( start , end ) . trim ( ) ; int bond = - 1 ; Integer b = null ; if ( ! sbond . equals ( "" ) ) { bond = Integer . parseInt ( sbond ) ; b = new Integer ( bond ) ; } return b... | safes repeating a few lines ... |
24,460 | private void pdb_SSBOND_Handler ( String line ) { if ( params . isHeaderOnly ( ) ) return ; if ( line . length ( ) < 36 ) { logger . info ( "SSBOND line has length under 36. Ignoring it." ) ; return ; } String chain1 = line . substring ( 15 , 16 ) ; String seqNum1 = line . substring ( 17 , 21 ) . trim ( ) ; String icod... | Process the disulfide bond info provided by an SSBOND record |
24,461 | private static Chain isKnownChain ( String chainID , List < Chain > chains ) { for ( int i = 0 ; i < chains . size ( ) ; i ++ ) { Chain testchain = chains . get ( i ) ; if ( chainID . equals ( testchain . getName ( ) ) ) { return testchain ; } } return null ; } | Finds in the given list of chains the first one that has as name the given chainID . If no such Chain can be found it returns null . |
24,462 | private void makeCompounds ( List < String > compoundList , List < String > sourceList ) { for ( String line : compoundList ) { if ( compoundList . indexOf ( line ) + 1 == compoundList . size ( ) ) { isLastCompndLine = true ; } pdb_COMPND_Handler ( line ) ; } if ( entities . size ( ) == 0 ) { current_compound = new Ent... | This is the new method for building the COMPND and SOURCE records . Now each method is self - contained . |
24,463 | private static List < List < Chain > > findChains ( String chainName , List < List < Chain > > polyModels ) { List < List < Chain > > models = new ArrayList < > ( ) ; for ( List < Chain > chains : polyModels ) { List < Chain > matchingChains = new ArrayList < > ( ) ; models . add ( matchingChains ) ; for ( Chain c : ch... | Gets all chains with given chainName from given models list |
24,464 | private void assignAsymIds ( List < List < Chain > > polys , List < List < Chain > > nonPolys , List < List < Chain > > waters ) { for ( int i = 0 ; i < polys . size ( ) ; i ++ ) { String asymId = "A" ; for ( Chain poly : polys . get ( i ) ) { poly . setId ( asymId ) ; asymId = getNextAsymId ( asymId ) ; } for ( Chain ... | Assign asym ids following the rules used by the PDB to assign asym ids in mmCIF files |
24,465 | private void linkSitesToGroups ( ) { if ( siteMap == null || siteToResidueMap == null ) { logger . info ( "Sites can not be linked to residues!" ) ; return ; } List < Site > sites = null ; if ( structure . getChains ( ) . isEmpty ( ) ) { sites = new ArrayList < Site > ( siteMap . values ( ) ) ; logger . info ( "No chai... | Links the Sites in the siteMap to the Groups in the Structure via the siteToResidueMap ResidueNumber . |
24,466 | public Sequence < AminoAcidCompound > translate ( Sequence < NucleotideCompound > dna ) { Map < Frame , Sequence < AminoAcidCompound > > trans = multipleFrameTranslation ( dna , Frame . ONE ) ; return trans . get ( Frame . ONE ) ; } | Quick method to let you go from a CDS to a Peptide quickly . It assumes you are translating only in the first frame |
24,467 | public Map < Frame , Sequence < AminoAcidCompound > > multipleFrameTranslation ( Sequence < NucleotideCompound > dna , Frame ... frames ) { Map < Frame , Sequence < AminoAcidCompound > > results = new EnumMap < Frame , Sequence < AminoAcidCompound > > ( Frame . class ) ; for ( Frame frame : frames ) { Sequence < Nucleo... | A way of translating DNA in a number of frames |
24,468 | public boolean isIdenticalTo ( SubunitCluster other ) { String thisSequence = this . subunits . get ( this . representative ) . getProteinSequenceString ( ) ; String otherSequence = other . subunits . get ( other . representative ) . getProteinSequenceString ( ) ; return thisSequence . equals ( otherSequence ) ; } | Tells whether the other SubunitCluster contains exactly the same Subunit . This is checked by String equality of their residue one - letter sequences . |
24,469 | public void actionPerformed ( ActionEvent evt ) { logStatus ( "terminating" ) ; logStatus ( " Total alignments processed: " + alignmentsProcessed ) ; stopButton . setEnabled ( false ) ; setCursor ( Cursor . getPredefinedCursor ( Cursor . WAIT_CURSOR ) ) ; progressBar . setIndeterminate ( true ) ; progressBar . setStrin... | Invoked when the user presses the stop button . |
24,470 | private static < T > void permuteArray ( T [ ] arr , int cp ) { if ( cp == 0 ) { return ; } if ( cp < 0 ) { cp = arr . length + cp ; } if ( cp < 0 || cp >= arr . length ) { throw new ArrayIndexOutOfBoundsException ( "Permutation point (" + cp + ") must be between -ca2.length and ca2.length-1" ) ; } List < T > temp = ne... | Circularly permutes arr in place . |
24,471 | private static void permuteAFPChain ( AFPChain afpChain , int cp ) { int ca2len = afpChain . getCa2Length ( ) ; if ( cp == 0 ) { return ; } if ( cp < 0 ) { cp = ca2len + cp ; } if ( cp < 0 || cp >= ca2len ) { throw new ArrayIndexOutOfBoundsException ( "Permutation point (" + cp + ") must be between -ca2.length and ca2.... | Permute the second protein of afpChain by the specified number of residues . |
24,472 | public int getSeqPos ( int aligSeq , Point p ) { int x = p . x - DEFAULT_X_SPACE - DEFAULT_LEGEND_SIZE ; int y = p . y - DEFAULT_Y_SPACE ; y -= ( DEFAULT_LINE_SEPARATION * aligSeq ) - DEFAULT_CHAR_SIZE ; int lineNr = y / DEFAULT_Y_STEP ; int linePos = x / DEFAULT_CHAR_SIZE ; return lineNr * DEFAULT_LINE_LENGTH + linePo... | Convert from an X position in the JPanel to the position in the sequence alignment . |
24,473 | public Point getPanelPos ( int structure , int pos ) { Point p = new Point ( ) ; int lineNr = pos / DEFAULT_LINE_LENGTH ; int linePos = pos % DEFAULT_LINE_LENGTH ; int x = linePos * DEFAULT_CHAR_SIZE + DEFAULT_X_SPACE + DEFAULT_LEGEND_SIZE ; int y = lineNr * DEFAULT_Y_STEP + DEFAULT_Y_SPACE ; y += DEFAULT_LINE_SEPARATI... | Get the X position on the Panel of a particular sequence position . |
24,474 | public int getAligSeq ( Point point ) { for ( int pos = 0 ; pos < alignmentSize ; pos ++ ) { int i = getSeqPos ( pos , point ) ; Point t = getPanelPos ( pos , i ) ; if ( Math . abs ( t . x - point . x ) <= DEFAULT_CHAR_SIZE && Math . abs ( t . y - point . y ) < DEFAULT_CHAR_SIZE ) return pos ; } return - 1 ; } | Returns the index of the structure for a given point in the Panel . Returns - 1 if not over a position in the sequence alignment . |
24,475 | public String toPDB ( ) { StringBuffer buf = new StringBuffer ( ) ; toPDB ( buf ) ; return buf . toString ( ) ; } | Convert the DBRef object to a DBREF record as it is used in PDB files |
24,476 | public void toPDB ( StringBuffer buf ) { Formatter formatter = new Formatter ( new StringBuilder ( ) , Locale . UK ) ; formatter . format ( "DBREF %4s %1s %4d%1s %4d%1s %-6s %-8s %-12s%6d%1c%6d%1c " , idCode , chainName , seqbegin , insertBegin , seqEnd , insertEnd , database , dbAccession , dbIdCode , dbSe... | Append the PDB representation of this DBRef to the provided StringBuffer |
24,477 | public static final List < String > getPDBresnum ( int aligPos , AFPChain afpChain , Atom [ ] ca ) { List < String > lst = new ArrayList < String > ( ) ; if ( aligPos > 1 ) { System . err . println ( "multiple alignments not supported yet!" ) ; return lst ; } int blockNum = afpChain . getBlockNum ( ) ; int [ ] optLen =... | Return a list of pdb Strings corresponding to the aligned positions of the molecule . Only supports a pairwise alignment with the AFPChain DS . |
24,478 | public static final Atom getAtomForAligPos ( AFPChain afpChain , int chainNr , int aligPos , Atom [ ] ca , boolean getPrevious ) throws StructureException { int [ ] optLen = afpChain . getOptLen ( ) ; if ( optLen == null ) return null ; if ( chainNr < 0 || chainNr > 1 ) { throw new StructureException ( "So far only pai... | Return the atom at alignment position aligPos . at the present only works with block 0 |
24,479 | public static final Atom [ ] getAtomArray ( Atom [ ] ca , List < Group > hetatms ) throws StructureException { List < Atom > atoms = new ArrayList < Atom > ( ) ; Collections . addAll ( atoms , ca ) ; logger . debug ( "got {} hetatoms" , hetatms . size ( ) ) ; for ( Group g : hetatms ) { if ( g . size ( ) < 1 ) continue... | Returns the first atom for each group |
24,480 | public static Structure createArtificalStructure ( AFPChain afpChain , Atom [ ] ca1 , Atom [ ] ca2 ) throws StructureException { if ( afpChain . getNrEQR ( ) < 1 ) { return AlignmentTools . getAlignedStructure ( ca1 , ca2 ) ; } Group [ ] twistedGroups = AlignmentTools . prepareGroupsForDisplay ( afpChain , ca1 , ca2 ) ... | Create a fake Structure objects that contains the two sets of atoms aligned on top of each other . |
24,481 | public int getOverlapLength ( HmmerResult other ) { int overlap = 0 ; for ( HmmerDomain d1 : getDomains ( ) ) { for ( HmmerDomain d2 : other . getDomains ( ) ) { overlap += getOverlap ( d1 , d2 ) ; } } return overlap ; } | Get the overlap between two HmmerResult objects |
24,482 | public static File getPath ( ) { if ( path == null ) { UserConfiguration config = new UserConfiguration ( ) ; path = new File ( config . getCacheFilePath ( ) ) ; } return path ; } | Get this provider s cache path |
24,483 | public void checkDoFirstInstall ( ) { if ( ! downloadAll ) { return ; } File dir = new File ( getPath ( ) , CHEM_COMP_CACHE_DIRECTORY ) ; File f = new File ( dir , "components.cif.gz" ) ; if ( ! f . exists ( ) ) { downloadAllDefinitions ( ) ; } else { FilenameFilter filter = new FilenameFilter ( ) { public boolean acce... | Checks if the chemical components already have been installed into the PDB directory . If not will download the chemical components definitions file and split it up into small subfiles . |
24,484 | private void writeID ( String contents , String currentID ) throws IOException { String localName = getLocalFileName ( currentID ) ; try ( PrintWriter pw = new PrintWriter ( new GZIPOutputStream ( new FileOutputStream ( localName ) ) ) ) { pw . print ( contents ) ; pw . flush ( ) ; } } | Output chemical contents to a file |
24,485 | public boolean isEquivalent ( CrystalTransform other ) { Matrix4d mul = new Matrix4d ( ) ; mul . mul ( this . matTransform , other . matTransform ) ; if ( mul . epsilonEquals ( IDENTITY , 0.0001 ) ) { return true ; } return false ; } | Returns true if the given CrystalTransform is equivalent to this one . Two crystal transforms are equivalent if one is the inverse of the other i . e . their transformation matrices multiplication is equal to the identity . |
24,486 | public String toXYZString ( ) { StringBuilder str = new StringBuilder ( ) ; for ( int i = 0 ; i < 3 ; i ++ ) { boolean emptyRow = true ; double coef ; coef = matTransform . getElement ( i , 0 ) ; if ( abs ( coef ) > 1e-6 ) { if ( abs ( abs ( coef ) - 1 ) < 1e-6 ) { if ( coef < 0 ) { str . append ( "-" ) ; } } else { st... | Expresses this transformation in terms of x y z fractional coordinates . |
24,487 | private String formatCoef ( double coef ) { double tol = 1e-6 ; if ( Math . abs ( coef ) < tol ) { return "0" ; } long num = Math . round ( coef ) ; if ( Math . abs ( num - coef ) < tol ) { return Long . toString ( num ) ; } for ( int denom = 2 ; denom < 12 ; denom ++ ) { num = Math . round ( coef * denom ) ; if ( num ... | helper function to format simple fractions into rationals |
24,488 | public Matrix4d getGeometicCenterTransformation ( ) { run ( ) ; Matrix4d geometricCentered = new Matrix4d ( reverseTransformationMatrix ) ; geometricCentered . setTranslation ( new Vector3d ( getGeometricCenter ( ) ) ) ; return geometricCentered ; } | Returns a transformation matrix transform polyhedra for Cn structures . The center in this matrix is the geometric center rather then the centroid . In Cn structures those are usually not the same . |
24,489 | public Point3d getGeometricCenter ( ) { run ( ) ; Point3d geometricCenter = new Point3d ( ) ; Vector3d translation = new Vector3d ( ) ; reverseTransformationMatrix . get ( translation ) ; if ( rotationGroup . getPointGroup ( ) . startsWith ( "C" ) ) { Vector3d corr = new Vector3d ( 0 , 0 , minBoundary . z + getDimensio... | Returns the geometric center of polyhedron . In the case of the Cn point group the centroid and geometric center are usually not identical . |
24,490 | private Matrix4d alignAxes ( Vector3d [ ] axisVectors , Vector3d [ ] referenceVectors ) { Matrix4d m1 = new Matrix4d ( ) ; AxisAngle4d a = new AxisAngle4d ( ) ; Vector3d axis = new Vector3d ( ) ; Vector3d v1 = new Vector3d ( axisVectors [ 0 ] ) ; Vector3d v2 = new Vector3d ( referenceVectors [ 0 ] ) ; double dot = v1 .... | Returns a transformation matrix that rotates refPoints to match coordPoints |
24,491 | private void refineReferenceVector ( ) { referenceVector = new Vector3d ( Y_AXIS ) ; if ( rotationGroup . getPointGroup ( ) . startsWith ( "C" ) ) { referenceVector = getReferenceAxisCylicWithSubunitAlignment ( ) ; } else if ( rotationGroup . getPointGroup ( ) . startsWith ( "D" ) ) { referenceVector = getReferenceAxis... | Returns a normalized vector that represents a minor rotation axis except for Cn this represents an axis orthogonal to the principal axis . |
24,492 | private Vector3d getReferenceAxisCylicWithSubunitAlignment ( ) { if ( rotationGroup . getPointGroup ( ) . equals ( "C2" ) ) { return referenceVector ; } List < List < Integer > > orbits = getOrbitsByXYWidth ( ) ; List < Integer > widestOrbit = orbits . get ( orbits . size ( ) - 1 ) ; List < Point3d > centers = subunits... | Returns a reference vector for the alignment of Cn structures . |
24,493 | private void init ( String svcUrl ) { try { serviceUrl = new URL ( svcUrl ) ; } catch ( MalformedURLException e ) { throw new RuntimeException ( "It looks like the URL for remote NCBI BLAST service (" + svcUrl + ") is wrong. Cause: " + e . getMessage ( ) , e ) ; } } | Initialize the serviceUrl data member |
24,494 | private URLConnection setQBlastServiceProperties ( URLConnection conn ) { conn . setDoOutput ( true ) ; conn . setUseCaches ( false ) ; conn . setRequestProperty ( "User-Agent" , "Biojava/NCBIQBlastService" ) ; conn . setRequestProperty ( "Connection" , "Keep-Alive" ) ; conn . setRequestProperty ( "Content-type" , "app... | Sets properties for given URLConnection |
24,495 | public SortedSet < String > getDomainNames ( String name ) { if ( name . length ( ) < 4 ) throw new IllegalArgumentException ( "Can't interpret IDs that are shorter than 4 residues!" ) ; String url = String . format ( "%srepresentativeDomains?cluster=%s&structureId=%s" , base , cutoff , name ) ; return requestRepresent... | Gets a list of domain representatives for a given PDB ID . |
24,496 | public SortedSet < String > getRepresentativeDomains ( ) { String url = base + "representativeDomains?cluster=" + cutoff ; return requestRepresentativeDomains ( url ) ; } | Gets a list of all domain representatives |
24,497 | private SortedSet < String > requestRepresentativeDomains ( String url ) { try { final SortedSet < String > results = new TreeSet < String > ( ) ; DefaultHandler handler = new DefaultHandler ( ) { public void startElement ( String uri , String localName , String qName , Attributes attributes ) throws SAXException { if ... | Handles fetching and parsing XML from representativeDomains requests |
24,498 | private static void handleRestRequest ( String url , DefaultHandler handler ) throws SAXException , IOException , ParserConfigurationException { URL u = new URL ( url ) ; InputStream response = URLConnectionTools . getInputStream ( u ) ; InputSource xml = new InputSource ( response ) ; SAXParserFactory factory = SAXPar... | Handles fetching and processing REST requests . The actual XML parsing is handled by the handler which is also in charge of storing interesting data . |
24,499 | private double getDensity ( Atom [ ] ca1subset , Atom [ ] ca2subset ) throws StructureException { Atom centroid1 = Calc . getCentroid ( ca1subset ) ; Atom centroid2 = Calc . getCentroid ( ca2subset ) ; double d1 = 0 ; double d2 = 0 ; for ( int i = 0 ; i < ca1subset . length ; i ++ ) { double dd1 = Calc . getDistance ( ... | this is probably useless |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.