id int32 0 165k | repo stringlengths 7 58 | path stringlengths 12 218 | func_name stringlengths 3 140 | original_string stringlengths 73 34.1k | language stringclasses 1
value | code stringlengths 73 34.1k | code_tokens list | docstring stringlengths 3 16k | docstring_tokens list | sha stringlengths 40 40 | url stringlengths 105 339 |
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31,600 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AlternativeAlignment.java | AlternativeAlignment.super_pos_alig | private void super_pos_alig(Atom[]ca1,Atom[]ca2,int[] idx1, int[] idx2, boolean getRMS) throws StructureException{
//System.out.println("superpos alig ");
Atom[] ca1subset = new Atom[idx1.length];
Atom[] ca2subset = new Atom[idx2.length];
for (int i = 0 ; i < idx1.length;i++){
//System.out.println("idx1 "+... | java | private void super_pos_alig(Atom[]ca1,Atom[]ca2,int[] idx1, int[] idx2, boolean getRMS) throws StructureException{
//System.out.println("superpos alig ");
Atom[] ca1subset = new Atom[idx1.length];
Atom[] ca2subset = new Atom[idx2.length];
for (int i = 0 ; i < idx1.length;i++){
//System.out.println("idx1 "+... | [
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@param ca1 Atom set 1
@param ca2 Atom set 2
@param idx1 idx positions in set1
@param idx2 idx positions in set2
@param getRMS a fla... | [
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31,601 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AlternativeAlignment.java | AlternativeAlignment.getAlignedStructure | public Structure getAlignedStructure(Structure s1, Structure s2){
// do not change the original coords ..
Structure s3 = s2.clone();
currentRotMatrix.print(3,3);
Calc.rotate(s3, currentRotMatrix);
Calc.shift( s3, currentTranMatrix);
Structure newpdb = new StructureImpl();
newpdb.setPDBCode("Java");
n... | java | public Structure getAlignedStructure(Structure s1, Structure s2){
// do not change the original coords ..
Structure s3 = s2.clone();
currentRotMatrix.print(3,3);
Calc.rotate(s3, currentRotMatrix);
Calc.shift( s3, currentTranMatrix);
Structure newpdb = new StructureImpl();
newpdb.setPDBCode("Java");
n... | [
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31,602 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AlternativeAlignment.java | AlternativeAlignment.toPDB | public String toPDB(Structure s1, Structure s2){
Structure newpdb = getAlignedStructure(s1, s2);
return newpdb.toPDB();
} | java | public String toPDB(Structure s1, Structure s2){
Structure newpdb = getAlignedStructure(s1, s2);
return newpdb.toPDB();
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each of the structures will be represented as a model.
@param s1
@param s2
@return a PDB file as a String | [
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31,603 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/ChromosomeSequence.java | ChromosomeSequence.addGene | public GeneSequence addGene(AccessionID accession, int bioBegin, int bioEnd, Strand strand) {
GeneSequence geneSequence = new GeneSequence(this, bioBegin, bioEnd, strand);
geneSequence.setAccession(accession);
geneSequenceHashMap.put(accession.toString(), geneSequence);
return geneSequence;
} | java | public GeneSequence addGene(AccessionID accession, int bioBegin, int bioEnd, Strand strand) {
GeneSequence geneSequence = new GeneSequence(this, bioBegin, bioEnd, strand);
geneSequence.setAccession(accession);
geneSequenceHashMap.put(accession.toString(), geneSequence);
return geneSequence;
} | [
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GeneSequence that is returned will have a reference to parent chromosome sequence
which actually contains the sequence data. Strand is important for positive and negative
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31,604 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/AFPChainCoordManager.java | AFPChainCoordManager.getPanelPos | public Point getPanelPos(int aligSeq, int i) {
Point p = new Point();
// get line
// we do integer division since we ignore remainders
int lineNr = i / DEFAULT_LINE_LENGTH;
// but we want to have the reminder for the line position.
int linePos = i % DEFAULT_LINE_LENGTH;
int x = linePos * DEFAULT_CHAR_S... | java | public Point getPanelPos(int aligSeq, int i) {
Point p = new Point();
// get line
// we do integer division since we ignore remainders
int lineNr = i / DEFAULT_LINE_LENGTH;
// but we want to have the reminder for the line position.
int linePos = i % DEFAULT_LINE_LENGTH;
int x = linePos * DEFAULT_CHAR_S... | [
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";... | get the position of the sequence position on the Panel
@param aligSeq 0 or 1 for which of the two sequences to ask for.
@param i sequence position
@return the point on a panel for a sequence position | [
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31,605 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/AFPChainCoordManager.java | AFPChainCoordManager.getLegendPosition | public Point getLegendPosition(int lineNr, int chainNr) {
int x = DEFAULT_X_SPACE ;
int y = lineNr * DEFAULT_Y_STEP + DEFAULT_Y_SPACE;
y += chainNr * DEFAULT_LINE_SEPARATION;
Point p = new Point(x,y);
return p;
} | java | public Point getLegendPosition(int lineNr, int chainNr) {
int x = DEFAULT_X_SPACE ;
int y = lineNr * DEFAULT_Y_STEP + DEFAULT_Y_SPACE;
y += chainNr * DEFAULT_LINE_SEPARATION;
Point p = new Point(x,y);
return p;
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@param lineNr which line is this for
@param chainNr is it chain 0 or 1
@return get the point where to draw the legend | [
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31,606 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriterHelper.java | FastaWriterHelper.writeProteinSequence | public static void writeProteinSequence(File file,
Collection<ProteinSequence> proteinSequences) throws Exception {
FileOutputStream outputStream = new FileOutputStream(file);
BufferedOutputStream bo = new BufferedOutputStream(outputStream);
writeProteinSequence(bo, proteinSequences);
bo.close();
outputStr... | java | public static void writeProteinSequence(File file,
Collection<ProteinSequence> proteinSequences) throws Exception {
FileOutputStream outputStream = new FileOutputStream(file);
BufferedOutputStream bo = new BufferedOutputStream(outputStream);
writeProteinSequence(bo, proteinSequences);
bo.close();
outputStr... | [
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31,607 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriterHelper.java | FastaWriterHelper.writeSequence | public static void writeSequence(File file, Sequence<?> sequence) throws Exception {
FileOutputStream outputStream = new FileOutputStream(file);
BufferedOutputStream bo = new BufferedOutputStream(outputStream);
writeSequences(bo, singleSeqToCollection(sequence));
bo.close();
outputStream.close();
} | java | public static void writeSequence(File file, Sequence<?> sequence) throws Exception {
FileOutputStream outputStream = new FileOutputStream(file);
BufferedOutputStream bo = new BufferedOutputStream(outputStream);
writeSequences(bo, singleSeqToCollection(sequence));
bo.close();
outputStream.close();
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31,608 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriterHelper.java | FastaWriterHelper.writeSequence | public static void writeSequence(OutputStream outputStream, Sequence<?> sequence) throws Exception {
writeSequences(outputStream, singleSeqToCollection(sequence));
} | java | public static void writeSequence(OutputStream outputStream, Sequence<?> sequence) throws Exception {
writeSequences(outputStream, singleSeqToCollection(sequence));
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31,609 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/views/WindowedSequence.java | WindowedSequence.get | public SequenceView<C> get(int index) {
int start = toStartIndex(index);
int end = index + (getWindowSize() - 1);
return getBackingSequence().getSubSequence(start, end);
} | java | public SequenceView<C> get(int index) {
int start = toStartIndex(index);
int end = index + (getWindowSize() - 1);
return getBackingSequence().getSubSequence(start, end);
} | [
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31,610 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorPointGroup.java | JmolSymmetryScriptGeneratorPointGroup.getPolyhedronColor | private Color4f getPolyhedronColor() {
Color4f[] colors = getSymmetryColors(5);
Color4f strongestColor = colors[4];
Color4f complement = new Color4f(Color.WHITE);
complement.sub(strongestColor);
return complement;
} | java | private Color4f getPolyhedronColor() {
Color4f[] colors = getSymmetryColors(5);
Color4f strongestColor = colors[4];
Color4f complement = new Color4f(Color.WHITE);
complement.sub(strongestColor);
return complement;
} | [
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31,611 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java | SequenceMixin.countCompounds | public static <C extends Compound> int countCompounds(
Sequence<C> sequence, C... compounds) {
int count = 0;
Map<C, Integer> compositon = getComposition(sequence);
for (C compound : compounds) {
if(compositon.containsKey(compound)) {
count = compositon.get(compound) + count;
}
}
return count;
} | java | public static <C extends Compound> int countCompounds(
Sequence<C> sequence, C... compounds) {
int count = 0;
Map<C, Integer> compositon = getComposition(sequence);
for (C compound : compounds) {
if(compositon.containsKey(compound)) {
count = compositon.get(compound) + count;
}
}
return count;
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31,612 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java | SequenceMixin.countGC | public static int countGC(Sequence<NucleotideCompound> sequence) {
CompoundSet<NucleotideCompound> cs = sequence.getCompoundSet();
NucleotideCompound G = cs.getCompoundForString("G");
NucleotideCompound C = cs.getCompoundForString("C");
NucleotideCompound g = cs.getCompoundForString("g");
NucleotideCompound c... | java | public static int countGC(Sequence<NucleotideCompound> sequence) {
CompoundSet<NucleotideCompound> cs = sequence.getCompoundSet();
NucleotideCompound G = cs.getCompoundForString("G");
NucleotideCompound C = cs.getCompoundForString("C");
NucleotideCompound g = cs.getCompoundForString("g");
NucleotideCompound c... | [
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@param sequence The {@link NucleotideCompound} {@link Sequence} to perform
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@return The number of GC compounds in the sequence | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java#L81-L88 |
31,613 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java | SequenceMixin.countAT | public static int countAT(Sequence<NucleotideCompound> sequence) {
CompoundSet<NucleotideCompound> cs = sequence.getCompoundSet();
NucleotideCompound A = cs.getCompoundForString("A");
NucleotideCompound T = cs.getCompoundForString("T");
NucleotideCompound a = cs.getCompoundForString("a");
NucleotideCompound t... | java | public static int countAT(Sequence<NucleotideCompound> sequence) {
CompoundSet<NucleotideCompound> cs = sequence.getCompoundSet();
NucleotideCompound A = cs.getCompoundForString("A");
NucleotideCompound T = cs.getCompoundForString("T");
NucleotideCompound a = cs.getCompoundForString("a");
NucleotideCompound t... | [
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@param sequence The {@link NucleotideCompound} {@link Sequence} to perform
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31,614 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java | SequenceMixin.getComposition | public static <C extends Compound> Map<C, Integer> getComposition(Sequence<C> sequence) {
Map<C, Integer> results = new HashMap<C, Integer>();
for (C currentCompound : sequence) {
Integer currentInteger = results.get(currentCompound);
if ( currentInteger == null)
currentInteger = 0;
currentInteger++;
... | java | public static <C extends Compound> Map<C, Integer> getComposition(Sequence<C> sequence) {
Map<C, Integer> results = new HashMap<C, Integer>();
for (C currentCompound : sequence) {
Integer currentInteger = results.get(currentCompound);
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currentInteger = 0;
currentInteger++;
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@param <C> The type of compound to look for
@param sequence The type of sequence to look over
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31,615 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java | SequenceMixin.write | public static <C extends Compound> void write(Appendable appendable, Sequence<C> sequence) throws IOException {
for(C compound: sequence) {
appendable.append(compound.toString());
}
} | java | public static <C extends Compound> void write(Appendable appendable, Sequence<C> sequence) throws IOException {
for(C compound: sequence) {
appendable.append(compound.toString());
}
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@param <C> Type of compound
@param writer The writer to send data to
@param sequence The sequence to write out
@throws IOException Thrown if we encounter a problem | [
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31,616 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java | SequenceMixin.indexOf | public static <C extends Compound> int indexOf(Sequence<C> sequence,
C compound) {
int index = 1;
for (C currentCompound : sequence) {
if (currentCompound.equals(compound)) {
return index;
}
index++;
}
return 0;
} | java | public static <C extends Compound> int indexOf(Sequence<C> sequence,
C compound) {
int index = 1;
for (C currentCompound : sequence) {
if (currentCompound.equals(compound)) {
return index;
}
index++;
}
return 0;
} | [
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31,617 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java | SequenceMixin.createIterator | public static <C extends Compound> Iterator<C> createIterator(
Sequence<C> sequence) {
return new SequenceIterator<C>(sequence);
} | java | public static <C extends Compound> Iterator<C> createIterator(
Sequence<C> sequence) {
return new SequenceIterator<C>(sequence);
} | [
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31,618 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java | SequenceMixin.createSubSequence | public static <C extends Compound> SequenceView<C> createSubSequence(
Sequence<C> sequence, int start, int end) {
return new SequenceProxyView<C>(sequence, start, end);
} | java | public static <C extends Compound> SequenceView<C> createSubSequence(
Sequence<C> sequence, int start, int end) {
return new SequenceProxyView<C>(sequence, start, end);
} | [
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31,619 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java | SequenceMixin.checksum | public static <C extends Compound> String checksum(Sequence<C> sequence) {
CRC64Checksum checksum = new CRC64Checksum();
for (C compound : sequence) {
checksum.update(compound.getShortName());
}
return checksum.toString();
} | java | public static <C extends Compound> String checksum(Sequence<C> sequence) {
CRC64Checksum checksum = new CRC64Checksum();
for (C compound : sequence) {
checksum.update(compound.getShortName());
}
return checksum.toString();
} | [
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31,620 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java | SequenceMixin.overlappingKmers | public static <C extends Compound> List<SequenceView<C>> overlappingKmers(Sequence<C> sequence, int kmer) {
List<SequenceView<C>> l = new ArrayList<SequenceView<C>>();
List<Iterator<SequenceView<C>>> windows
= new ArrayList<Iterator<SequenceView<C>>>();
for(int i=1; i<=kmer; i++) {
if(i == 1) {
window... | java | public static <C extends Compound> List<SequenceView<C>> overlappingKmers(Sequence<C> sequence, int kmer) {
List<SequenceView<C>> l = new ArrayList<SequenceView<C>>();
List<Iterator<SequenceView<C>>> windows
= new ArrayList<Iterator<SequenceView<C>>>();
for(int i=1; i<=kmer; i++) {
if(i == 1) {
window... | [
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@param <C> Compound to use
@param sequence Sequence to build from
@param kmer Kmer size
@return The list of overlapping K-mers | [
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31,621 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java | SequenceMixin.sequenceEqualityIgnoreCase | public static <C extends Compound> boolean sequenceEqualityIgnoreCase(Sequence<C> source, Sequence<C> target) {
return baseSequenceEquality(source, target, true);
} | java | public static <C extends Compound> boolean sequenceEqualityIgnoreCase(Sequence<C> source, Sequence<C> target) {
return baseSequenceEquality(source, target, true);
} | [
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31,622 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java | SequenceMixin.sequenceEquality | public static <C extends Compound> boolean sequenceEquality(Sequence<C> source, Sequence<C> target) {
return baseSequenceEquality(source, target, false);
} | java | public static <C extends Compound> boolean sequenceEquality(Sequence<C> source, Sequence<C> target) {
return baseSequenceEquality(source, target, false);
} | [
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31,623 | biojava/biojava | biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/LocIterator.java | LocIterator.hasNext | public boolean hasNext( int windowSize, int increment )
{
if( windowSize <= 0 )
{
throw new IllegalArgumentException( "Window size must be positive." );
}
try
{
if( increment > 0 )
{
return windowSize == mBounds.suffix( mPosition ).prefix( windowSize ).length();
}
else
{
if( mPosit... | java | public boolean hasNext( int windowSize, int increment )
{
if( windowSize <= 0 )
{
throw new IllegalArgumentException( "Window size must be positive." );
}
try
{
if( increment > 0 )
{
return windowSize == mBounds.suffix( mPosition ).prefix( windowSize ).length();
}
else
{
if( mPosit... | [
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@param windowSize Size of window. May be smaller or larger than default window size.
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31,624 | biojava/biojava | biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/LocIterator.java | LocIterator.next | public Location next( int windowSize, int increment )
{
if( windowSize <= 0 )
{
throw new IllegalArgumentException( "Window size must be positive." );
}
if( increment == 0 )
{
throw new IllegalArgumentException( "Increment must be non-zero." );
}
Location r;
try
{
if( increment > 0 )
{... | java | public Location next( int windowSize, int increment )
{
if( windowSize <= 0 )
{
throw new IllegalArgumentException( "Window size must be positive." );
}
if( increment == 0 )
{
throw new IllegalArgumentException( "Increment must be non-zero." );
}
Location r;
try
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if( increment > 0 )
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31,625 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java | AbstractSequence.setProxySequenceReader | public void setProxySequenceReader(SequenceReader<C> proxyLoader) {
this.sequenceStorage = proxyLoader;
if (proxyLoader instanceof FeaturesKeyWordInterface) {
this.setFeaturesKeyWord((FeaturesKeyWordInterface) sequenceStorage);
}
if (proxyLoader instanceof DatabaseReferenceInterface) {
this.setDatabaseRef... | java | public void setProxySequenceReader(SequenceReader<C> proxyLoader) {
this.sequenceStorage = proxyLoader;
if (proxyLoader instanceof FeaturesKeyWordInterface) {
this.setFeaturesKeyWord((FeaturesKeyWordInterface) sequenceStorage);
}
if (proxyLoader instanceof DatabaseReferenceInterface) {
this.setDatabaseRef... | [
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@param proxyLoader | [
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31,626 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java | AbstractSequence.getSource | public String getSource() {
if (source != null) {
return source;
}
if (parentSequence != null) {
return parentSequence.getSource();
}
return null;
} | java | public String getSource() {
if (source != null) {
return source;
}
if (parentSequence != null) {
return parentSequence.getSource();
}
return null;
} | [
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31,627 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java | AbstractSequence.getFeatures | public List<FeatureInterface<AbstractSequence<C>, C>> getFeatures(int bioSequencePosition) {
ArrayList<FeatureInterface<AbstractSequence<C>, C>> featureHits =
new ArrayList<FeatureInterface<AbstractSequence<C>, C>>();
if (features != null) {
for (FeatureInterface<AbstractSequence<C>, C> feature : features) {... | java | public List<FeatureInterface<AbstractSequence<C>, C>> getFeatures(int bioSequencePosition) {
ArrayList<FeatureInterface<AbstractSequence<C>, C>> featureHits =
new ArrayList<FeatureInterface<AbstractSequence<C>, C>>();
if (features != null) {
for (FeatureInterface<AbstractSequence<C>, C> feature : features) {... | [
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31,628 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java | AbstractSequence.addFeature | public void addFeature(int bioStart, int bioEnd, FeatureInterface<AbstractSequence<C>, C> feature) {
SequenceLocation<AbstractSequence<C>, C> sequenceLocation =
new SequenceLocation<AbstractSequence<C>, C>(bioStart, bioEnd, this);
feature.setLocation(sequenceLocation);
addFeature(feature);
} | java | public void addFeature(int bioStart, int bioEnd, FeatureInterface<AbstractSequence<C>, C> feature) {
SequenceLocation<AbstractSequence<C>, C> sequenceLocation =
new SequenceLocation<AbstractSequence<C>, C>(bioStart, bioEnd, this);
feature.setLocation(sequenceLocation);
addFeature(feature);
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31,629 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java | AbstractSequence.addFeature | public void addFeature(FeatureInterface<AbstractSequence<C>, C> feature) {
features.add(feature);
ArrayList<FeatureInterface<AbstractSequence<C>, C>> featureList = groupedFeatures.get(feature.getType());
if (featureList == null) {
featureList = new ArrayList<FeatureInterface<AbstractSequence<C>, C>>();
grou... | java | public void addFeature(FeatureInterface<AbstractSequence<C>, C> feature) {
features.add(feature);
ArrayList<FeatureInterface<AbstractSequence<C>, C>> featureList = groupedFeatures.get(feature.getType());
if (featureList == null) {
featureList = new ArrayList<FeatureInterface<AbstractSequence<C>, C>>();
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31,630 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java | AbstractSequence.removeFeature | public void removeFeature(FeatureInterface<AbstractSequence<C>, C> feature) {
features.remove(feature);
ArrayList<FeatureInterface<AbstractSequence<C>, C>> featureList = groupedFeatures.get(feature.getType());
if (featureList != null) {
featureList.remove(feature);
if (featureList.isEmpty()) {
groupedFe... | java | public void removeFeature(FeatureInterface<AbstractSequence<C>, C> feature) {
features.remove(feature);
ArrayList<FeatureInterface<AbstractSequence<C>, C>> featureList = groupedFeatures.get(feature.getType());
if (featureList != null) {
featureList.remove(feature);
if (featureList.isEmpty()) {
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31,631 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/CrystalCell.java | CrystalCell.getCellIndices | public Point3i getCellIndices(Tuple3d pt) {
Point3d p = new Point3d(pt);
this.transfToCrystal(p);
int x = (int)Math.floor(p.x);
int y = (int)Math.floor(p.y);
int z = (int)Math.floor(p.z);
return new Point3i(x,y,z);
} | java | public Point3i getCellIndices(Tuple3d pt) {
Point3d p = new Point3d(pt);
this.transfToCrystal(p);
int x = (int)Math.floor(p.x);
int y = (int)Math.floor(p.y);
int z = (int)Math.floor(p.z);
return new Point3i(x,y,z);
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Points in the unit cell one unit further along the `a` axis will return (1,0,0),
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@param pt Input point (in orthonormal coordinates)
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31,632 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/CrystalCell.java | CrystalCell.transfToOriginCell | public void transfToOriginCell(Tuple3d[] points, Tuple3d reference) {
reference = new Point3d(reference);//clone
transfToCrystal(reference);
int x = (int)Math.floor(reference.x);
int y = (int)Math.floor(reference.y);
int z = (int)Math.floor(reference.z);
for( Tuple3d point: points ) {
transfToCrystal(p... | java | public void transfToOriginCell(Tuple3d[] points, Tuple3d reference) {
reference = new Point3d(reference);//clone
transfToCrystal(reference);
int x = (int)Math.floor(reference.x);
int y = (int)Math.floor(reference.y);
int z = (int)Math.floor(reference.z);
for( Tuple3d point: points ) {
transfToCrystal(p... | [
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@param points A set of points to transform (in orthonormal coordinates)
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31,633 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/CrystalCell.java | CrystalCell.getMaxDimension | public double getMaxDimension() {
if (maxDimension!=0) {
return maxDimension;
}
Point3d vert0 = new Point3d(0,0,0);
Point3d vert1 = new Point3d(1,0,0);
transfToOrthonormal(vert1);
Point3d vert2 = new Point3d(0,1,0);
transfToOrthonormal(vert2);
Point3d vert3 = new Point3d(0,0,1);
transfToOrthonormal... | java | public double getMaxDimension() {
if (maxDimension!=0) {
return maxDimension;
}
Point3d vert0 = new Point3d(0,0,0);
Point3d vert1 = new Point3d(1,0,0);
transfToOrthonormal(vert1);
Point3d vert2 = new Point3d(0,1,0);
transfToOrthonormal(vert2);
Point3d vert3 = new Point3d(0,0,1);
transfToOrthonormal... | [
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31,634 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsXMLParser.java | SiftsXMLParser.getSiftsSegment | private SiftsSegment getSiftsSegment(Element el) {
String segId = el.getAttribute("segId");
String start = el.getAttribute("start");
String end = el.getAttribute("end");
SiftsSegment seg = new SiftsSegment(segId,start,end);
if ( debug )
System.out.println("parsed " + seg);
// get nodelist of se... | java | private SiftsSegment getSiftsSegment(Element el) {
String segId = el.getAttribute("segId");
String start = el.getAttribute("start");
String end = el.getAttribute("end");
SiftsSegment seg = new SiftsSegment(segId,start,end);
if ( debug )
System.out.println("parsed " + seg);
// get nodelist of se... | [
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@param el
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31,635 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/ColorUtils.java | ColorUtils.rotateHue | public static Color rotateHue (Color color, float fraction) {
float[] af = Color.RGBtoHSB(color.getRed(), color.getGreen(), color.getBlue(), null);
float hue = af[0];
float saturation = af[1];
float brightness = af[2];
float hueNew = hue + fraction;
Color hsb = Color.getHSBColor(hueNew, saturation, bri... | java | public static Color rotateHue (Color color, float fraction) {
float[] af = Color.RGBtoHSB(color.getRed(), color.getGreen(), color.getBlue(), null);
float hue = af[0];
float saturation = af[1];
float brightness = af[2];
float hueNew = hue + fraction;
Color hsb = Color.getHSBColor(hueNew, saturation, bri... | [
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31,636 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/FarmJobRunnable.java | FarmJobRunnable.getAlignmentPairsFromServer | protected PdbPairsMessage getAlignmentPairsFromServer() {
String url = params.getServer();
int nrPairs = params.getStepSize();
if ( maxNrAlignments < nrPairs )
nrPairs = maxNrAlignments;
SortedSet<PdbPair> allPairs = new TreeSet<PdbPair>();
PdbPairsMessage msg = null;
try {
if ( progressListe... | java | protected PdbPairsMessage getAlignmentPairsFromServer() {
String url = params.getServer();
int nrPairs = params.getStepSize();
if ( maxNrAlignments < nrPairs )
nrPairs = maxNrAlignments;
SortedSet<PdbPair> allPairs = new TreeSet<PdbPair>();
PdbPairsMessage msg = null;
try {
if ( progressListe... | [
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31,637 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java | AlignmentTools.alignmentAsMap | public static Map<Integer, Integer> alignmentAsMap(AFPChain afpChain) throws StructureException {
Map<Integer,Integer> map = new HashMap<Integer,Integer>();
if( afpChain.getAlnLength() < 1 ) {
return map;
}
int[][][] optAln = afpChain.getOptAln();
int[] optLen = afpChain.getOptLen();
for(int block = 0; ... | java | public static Map<Integer, Integer> alignmentAsMap(AFPChain afpChain) throws StructureException {
Map<Integer,Integer> map = new HashMap<Integer,Integer>();
if( afpChain.getAlnLength() < 1 ) {
return map;
}
int[][][] optAln = afpChain.getOptAln();
int[] optLen = afpChain.getOptLen();
for(int block = 0; ... | [
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becomes<pre>
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31,638 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java | AlignmentTools.getSymmetryOrder | public static int getSymmetryOrder(Map<Integer, Integer> alignment, Map<Integer,Integer> identity,
final int maxSymmetry, final float minimumMetricChange) {
List<Integer> preimage = new ArrayList<Integer>(alignment.keySet()); // currently unmodified
List<Integer> image = new ArrayList<Integer>(preimage)... | java | public static int getSymmetryOrder(Map<Integer, Integer> alignment, Map<Integer,Integer> identity,
final int maxSymmetry, final float minimumMetricChange) {
List<Integer> preimage = new ArrayList<Integer>(alignment.keySet()); // currently unmodified
List<Integer> image = new ArrayList<Integer>(preimage)... | [
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31,639 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java | AlignmentTools.getSymmetryOrder | public static int getSymmetryOrder(AFPChain afpChain, int maxSymmetry, float minimumMetricChange) throws StructureException {
// alignment comes from the afpChain alignment
Map<Integer,Integer> alignment = AlignmentTools.alignmentAsMap(afpChain);
// Now construct identity to map aligned residues in sequential or... | java | public static int getSymmetryOrder(AFPChain afpChain, int maxSymmetry, float minimumMetricChange) throws StructureException {
// alignment comes from the afpChain alignment
Map<Integer,Integer> alignment = AlignmentTools.alignmentAsMap(afpChain);
// Now construct identity to map aligned residues in sequential or... | [
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31,640 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java | AlignmentTools.guessSequentialAlignment | public static Map<Integer, Integer> guessSequentialAlignment(
Map<Integer,Integer> alignment, boolean inverseAlignment) {
Map<Integer,Integer> identity = new HashMap<Integer,Integer>();
SortedSet<Integer> aligned1 = new TreeSet<Integer>();
SortedSet<Integer> aligned2 = new TreeSet<Integer>();
for(Entry<Int... | java | public static Map<Integer, Integer> guessSequentialAlignment(
Map<Integer,Integer> alignment, boolean inverseAlignment) {
Map<Integer,Integer> identity = new HashMap<Integer,Integer>();
SortedSet<Integer> aligned1 = new TreeSet<Integer>();
SortedSet<Integer> aligned2 = new TreeSet<Integer>();
for(Entry<Int... | [
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31,641 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java | AlignmentTools.createAFPChain | public static AFPChain createAFPChain(Atom[] ca1, Atom[] ca2,
ResidueNumber[] aligned1, ResidueNumber[] aligned2 ) throws StructureException {
//input validation
int alnLen = aligned1.length;
if(alnLen != aligned2.length) {
throw new IllegalArgumentException("Alignment lengths are not equal");
}
... | java | public static AFPChain createAFPChain(Atom[] ca1, Atom[] ca2,
ResidueNumber[] aligned1, ResidueNumber[] aligned2 ) throws StructureException {
//input validation
int alnLen = aligned1.length;
if(alnLen != aligned2.length) {
throw new IllegalArgumentException("Alignment lengths are not equal");
}
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31,642 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java | AlignmentTools.replaceOptAln | public static AFPChain replaceOptAln(int[][][] newAlgn, AFPChain afpChain, Atom[] ca1, Atom[] ca2) throws StructureException {
//The order is the number of groups in the newAlgn
int order = newAlgn.length;
//Calculate the alignment length from all the subunits lengths
int[] optLens = new int[order];
for(int... | java | public static AFPChain replaceOptAln(int[][][] newAlgn, AFPChain afpChain, Atom[] ca1, Atom[] ca2) throws StructureException {
//The order is the number of groups in the newAlgn
int order = newAlgn.length;
//Calculate the alignment length from all the subunits lengths
int[] optLens = new int[order];
for(int... | [
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31,643 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java | AlignmentTools.replaceOptAln | public static AFPChain replaceOptAln(AFPChain afpChain, Atom[] ca1, Atom[] ca2,
Map<Integer, Integer> alignment) throws StructureException {
// Determine block lengths
// Sort ca1 indices, then start a new block whenever ca2 indices aren't
// increasing monotonically.
Integer[] res1 = alignment.keyS... | java | public static AFPChain replaceOptAln(AFPChain afpChain, Atom[] ca1, Atom[] ca2,
Map<Integer, Integer> alignment) throws StructureException {
// Determine block lengths
// Sort ca1 indices, then start a new block whenever ca2 indices aren't
// increasing monotonically.
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31,644 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java | AlignmentTools.toConciseAlignmentString | public static <S,T> String toConciseAlignmentString(Map<S,T> alignment, Map<T,S> identity) {
// Clone input to prevent changes
Map<S,T> alig = new HashMap<S,T>(alignment);
// Generate inverse alignment
Map<S,List<S>> inverse = new HashMap<S,List<S>>();
for(Entry<S,T> e: alig.entrySet()) {
S val = identity... | java | public static <S,T> String toConciseAlignmentString(Map<S,T> alignment, Map<T,S> identity) {
// Clone input to prevent changes
Map<S,T> alig = new HashMap<S,T>(alignment);
// Generate inverse alignment
Map<S,List<S>> inverse = new HashMap<S,List<S>>();
for(Entry<S,T> e: alig.entrySet()) {
S val = identity... | [
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31,645 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java | AlignmentTools.calculateBlockGap | public static int[] calculateBlockGap(int[][][] optAln){
//Initialize the array to be returned
int [] blockGap = new int[optAln.length];
//Loop for every block and look in both chains for non-contiguous residues.
for (int i=0; i<optAln.length; i++){
int gaps = 0; //the number of gaps in that block
int l... | java | public static int[] calculateBlockGap(int[][][] optAln){
//Initialize the array to be returned
int [] blockGap = new int[optAln.length];
//Loop for every block and look in both chains for non-contiguous residues.
for (int i=0; i<optAln.length; i++){
int gaps = 0; //the number of gaps in that block
int l... | [
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31,646 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java | AlignmentTools.getAlignedModel | public static final List<Chain> getAlignedModel(Atom[] ca){
List<Chain> model = new ArrayList<Chain>();
for ( Atom a: ca){
Group g = a.getGroup();
Chain parentC = g.getChain();
Chain newChain = null;
for ( Chain c : model) {
if ( c.getId().equals(parentC.getId())){
newChain = c;
break;... | java | public static final List<Chain> getAlignedModel(Atom[] ca){
List<Chain> model = new ArrayList<Chain>();
for ( Atom a: ca){
Group g = a.getGroup();
Chain parentC = g.getChain();
Chain newChain = null;
for ( Chain c : model) {
if ( c.getId().equals(parentC.getId())){
newChain = c;
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31,647 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java | AlignmentTools.getAlignedStructure | public static final Structure getAlignedStructure(Atom[] ca1, Atom[] ca2) throws StructureException{
/* Previous implementation commented
Structure s = new StructureImpl();
List<Chain>model1 = getAlignedModel(ca1);
List<Chain>model2 = getAlignedModel(ca2);
s.addModel(model1);
s.addModel(model2);
retu... | java | public static final Structure getAlignedStructure(Atom[] ca1, Atom[] ca2) throws StructureException{
/* Previous implementation commented
Structure s = new StructureImpl();
List<Chain>model1 = getAlignedModel(ca1);
List<Chain>model2 = getAlignedModel(ca2);
s.addModel(model1);
s.addModel(model2);
retu... | [
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31,648 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java | AlignmentTools.shiftCA2 | public static void shiftCA2(AFPChain afpChain, Atom[] ca2, Matrix m, Atom shift, Group[] twistedGroups) {
int i = -1;
for (Atom a: ca2){
i++;
Group g = a.getGroup();
Calc.rotate(g,m);
Calc.shift(g, shift);
if (g.hasAltLoc()){
for (Group alt: g.getAltLocs()){
for (Atom alta : alt.getAtoms... | java | public static void shiftCA2(AFPChain afpChain, Atom[] ca2, Matrix m, Atom shift, Group[] twistedGroups) {
int i = -1;
for (Atom a: ca2){
i++;
Group g = a.getGroup();
Calc.rotate(g,m);
Calc.shift(g, shift);
if (g.hasAltLoc()){
for (Group alt: g.getAltLocs()){
for (Atom alta : alt.getAtoms... | [
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31,649 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java | AlignmentTools.fillAlignedAtomArrays | public static void fillAlignedAtomArrays(AFPChain afpChain, Atom[] ca1,
Atom[] ca2, Atom[] ca1aligned, Atom[] ca2aligned) {
int pos=0;
int[] blockLens = afpChain.getOptLen();
int[][][] optAln = afpChain.getOptAln();
assert(afpChain.getBlockNum() <= optAln.length);
for (int block=0; block < afpChain.getBl... | java | public static void fillAlignedAtomArrays(AFPChain afpChain, Atom[] ca1,
Atom[] ca2, Atom[] ca1aligned, Atom[] ca2aligned) {
int pos=0;
int[] blockLens = afpChain.getOptLen();
int[][][] optAln = afpChain.getOptAln();
assert(afpChain.getBlockNum() <= optAln.length);
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31,650 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java | AlignmentTools.deleteHighestDistanceColumn | public static AFPChain deleteHighestDistanceColumn(AFPChain afpChain,
Atom[] ca1, Atom[] ca2) throws StructureException {
int[][][] optAln = afpChain.getOptAln();
int maxBlock = 0;
int maxPos = 0;
double maxDistance = Double.MIN_VALUE;
for (int b = 0; b < optAln.length; b++) {
for (int p = 0; p < opt... | java | public static AFPChain deleteHighestDistanceColumn(AFPChain afpChain,
Atom[] ca1, Atom[] ca2) throws StructureException {
int[][][] optAln = afpChain.getOptAln();
int maxBlock = 0;
int maxPos = 0;
double maxDistance = Double.MIN_VALUE;
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@param afpChain
original alignment, will be modified
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atom array, will not be modified
@param ca2
atom array, will not be modified
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31,651 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java | AlignmentTools.deleteColumn | public static AFPChain deleteColumn(AFPChain afpChain, Atom[] ca1,
Atom[] ca2, int block, int pos) throws StructureException {
// Check validity of the inputs
if (afpChain.getBlockNum() <= block) {
throw new IndexOutOfBoundsException(String.format(
"Block index requested (%d) is higher than the total nu... | java | public static AFPChain deleteColumn(AFPChain afpChain, Atom[] ca1,
Atom[] ca2, int block, int pos) throws StructureException {
// Check validity of the inputs
if (afpChain.getBlockNum() <= block) {
throw new IndexOutOfBoundsException(String.format(
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atom array, will not be modified
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position index in the block
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31,652 | biojava/biojava | biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java | ProteinModificationIdentifier.identify | public void identify(final Structure structure,
final Set<ProteinModification> potentialModifications) {
if (structure==null) {
throw new IllegalArgumentException("Null structure.");
}
identify(structure.getChains(), potentialModifications);
} | java | public void identify(final Structure structure,
final Set<ProteinModification> potentialModifications) {
if (structure==null) {
throw new IllegalArgumentException("Null structure.");
}
identify(structure.getChains(), potentialModifications);
} | [
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31,653 | biojava/biojava | biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java | ProteinModificationIdentifier.identify | public void identify(final Chain chain,
final Set<ProteinModification> potentialModifications) {
identify(Collections.singletonList(chain), potentialModifications);
} | java | public void identify(final Chain chain,
final Set<ProteinModification> potentialModifications) {
identify(Collections.singletonList(chain), potentialModifications);
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31,654 | biojava/biojava | biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java | ProteinModificationIdentifier.identify | public void identify(final List<Chain> chains,
final Set<ProteinModification> potentialModifications) {
if (chains==null) {
throw new IllegalArgumentException("Null structure.");
}
if (potentialModifications==null) {
throw new IllegalArgumentException("Null potentialModifications.");
}
reset();
... | java | public void identify(final List<Chain> chains,
final Set<ProteinModification> potentialModifications) {
if (chains==null) {
throw new IllegalArgumentException("Null structure.");
}
if (potentialModifications==null) {
throw new IllegalArgumentException("Null potentialModifications.");
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reset();
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31,655 | biojava/biojava | biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java | ProteinModificationIdentifier.identifyAdditionalAttachments | private void identifyAdditionalAttachments(ModifiedCompound mc,
List<Group> ligands, List<Chain> chains) {
if (ligands.isEmpty()) {
return;
}
// TODO: should the additional groups only be allowed to the identified
// ligands or both amino acids and ligands? Currently only on ligands
// ligands to amino... | java | private void identifyAdditionalAttachments(ModifiedCompound mc,
List<Group> ligands, List<Chain> chains) {
if (ligands.isEmpty()) {
return;
}
// TODO: should the additional groups only be allowed to the identified
// ligands or both amino acids and ligands? Currently only on ligands
// ligands to amino... | [
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31,656 | biojava/biojava | biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java | ProteinModificationIdentifier.mergeModComps | private void mergeModComps(List<ModifiedCompound> modComps) {
TreeSet<Integer> remove = new TreeSet<Integer>();
int n = modComps.size();
for (int icurr=1; icurr<n; icurr++) {
ModifiedCompound curr = modComps.get(icurr);
String id = curr.getModification().getId();
if (ProteinModificationRegistry.getById(... | java | private void mergeModComps(List<ModifiedCompound> modComps) {
TreeSet<Integer> remove = new TreeSet<Integer>();
int n = modComps.size();
for (int icurr=1; icurr<n; icurr++) {
ModifiedCompound curr = modComps.get(icurr);
String id = curr.getModification().getId();
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31,657 | biojava/biojava | biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java | ProteinModificationIdentifier.recordUnidentifiableAtomLinkages | private void recordUnidentifiableAtomLinkages(List<ModifiedCompound> modComps,
List<Group> ligands) {
// first put identified linkages in a map for fast query
Set<StructureAtomLinkage> identifiedLinkages = new HashSet<StructureAtomLinkage>();
for (ModifiedCompound mc : modComps) {
identifiedLinkages.addAll... | java | private void recordUnidentifiableAtomLinkages(List<ModifiedCompound> modComps,
List<Group> ligands) {
// first put identified linkages in a map for fast query
Set<StructureAtomLinkage> identifiedLinkages = new HashSet<StructureAtomLinkage>();
for (ModifiedCompound mc : modComps) {
identifiedLinkages.addAll... | [
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31,658 | biojava/biojava | biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java | ProteinModificationIdentifier.getMatchedAtomsOfLinkages | private List<List<Atom[]>> getMatchedAtomsOfLinkages(
ModificationCondition condition, Map<Component, Set<Group>> mapCompGroups) {
List<ModificationLinkage> linkages = condition.getLinkages();
int nLink = linkages.size();
List<List<Atom[]>> matchedAtomsOfLinkages =
new ArrayList<List<Atom[]>>(nLink);
f... | java | private List<List<Atom[]>> getMatchedAtomsOfLinkages(
ModificationCondition condition, Map<Component, Set<Group>> mapCompGroups) {
List<ModificationLinkage> linkages = condition.getLinkages();
int nLink = linkages.size();
List<List<Atom[]>> matchedAtomsOfLinkages =
new ArrayList<List<Atom[]>>(nLink);
f... | [
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31,659 | biojava/biojava | biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java | ProteinModificationIdentifier.assembleLinkages | private void assembleLinkages(List<List<Atom[]>> matchedAtomsOfLinkages,
ProteinModification mod, List<ModifiedCompound> ret) {
ModificationCondition condition = mod.getCondition();
List<ModificationLinkage> modLinks = condition.getLinkages();
int nLink = matchedAtomsOfLinkages.size();
int[] indices = new i... | java | private void assembleLinkages(List<List<Atom[]>> matchedAtomsOfLinkages,
ProteinModification mod, List<ModifiedCompound> ret) {
ModificationCondition condition = mod.getCondition();
List<ModificationLinkage> modLinks = condition.getLinkages();
int nLink = matchedAtomsOfLinkages.size();
int[] indices = new i... | [
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31,660 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/CoordManager.java | CoordManager.getSeqPos | protected int getSeqPos(int panelPos){
int seqPos = Math.round((panelPos - SequenceScalePanel.DEFAULT_X_START) / scale) ;
if ( seqPos < 0)
seqPos = 0;
//int length = chainLength;
//if ( seqPos >= length)
// seqPos = length-1;
return seqPos;
} | java | protected int getSeqPos(int panelPos){
int seqPos = Math.round((panelPos - SequenceScalePanel.DEFAULT_X_START) / scale) ;
if ( seqPos < 0)
seqPos = 0;
//int length = chainLength;
//if ( seqPos >= length)
// seqPos = length-1;
return seqPos;
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31,661 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorCn.java | JmolSymmetryScriptGeneratorCn.getOrientationName | @Override
public String getOrientationName(int index) {
if (getAxisTransformation().getRotationGroup().getPointGroup().equals("C2")) {
if (index == 0) {
return "Front C2 axis";
} else if (index == 2) {
return "Back C2 axis";
}
}
return getPolyhedron().getViewName(index);
} | java | @Override
public String getOrientationName(int index) {
if (getAxisTransformation().getRotationGroup().getPointGroup().equals("C2")) {
if (index == 0) {
return "Front C2 axis";
} else if (index == 2) {
return "Back C2 axis";
}
}
return getPolyhedron().getViewName(index);
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31,662 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/UserConfiguration.java | UserConfiguration.toXML | public XMLWriter toXML(PrintWriter pw)
throws IOException
{
XMLWriter xw = new PrettyXMLWriter( pw);
toXML(xw);
return xw ;
} | java | public XMLWriter toXML(PrintWriter pw)
throws IOException
{
XMLWriter xw = new PrettyXMLWriter( pw);
toXML(xw);
return xw ;
} | [
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31,663 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/UserConfiguration.java | UserConfiguration.toXML | public XMLWriter toXML(XMLWriter xw)
throws IOException
{
xw.printRaw("<?xml version='1.0' standalone='no' ?>");
//xw.printRaw("<!DOCTYPE " + XML_CONTENT_TYPE + " SYSTEM '" + XML_DTD + "' >");
xw.openTag("JFatCatConfig");
xw.openTag("PDBFILEPATH");
// we don;t serialize the tempdir...
String tempdir ... | java | public XMLWriter toXML(XMLWriter xw)
throws IOException
{
xw.printRaw("<?xml version='1.0' standalone='no' ?>");
//xw.printRaw("<!DOCTYPE " + XML_CONTENT_TYPE + " SYSTEM '" + XML_DTD + "' >");
xw.openTag("JFatCatConfig");
xw.openTag("PDBFILEPATH");
// we don;t serialize the tempdir...
String tempdir ... | [
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31,664 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java | BlastXMLParser.mapIds | private void mapIds() {
if (queryReferences != null) {
queryReferencesMap = new HashMap<String,Sequence>(queryReferences.size());
for (int counter=0; counter < queryReferences.size() ; counter ++){
String id = "Query_"+(counter+1);
queryReferencesMap.put(id, queryReferences.get(counter));
}
}
if... | java | private void mapIds() {
if (queryReferences != null) {
queryReferencesMap = new HashMap<String,Sequence>(queryReferences.size());
for (int counter=0; counter < queryReferences.size() ; counter ++){
String id = "Query_"+(counter+1);
queryReferencesMap.put(id, queryReferences.get(counter));
}
}
if... | [
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31,665 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceList.java | StructureInterfaceList.sort | public void sort() {
Collections.sort(list);
int i=1;
for (StructureInterface interf:list) {
interf.setId(i);
i++;
}
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Collections.sort(list);
int i=1;
for (StructureInterface interf:list) {
interf.setId(i);
i++;
}
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31,666 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceList.java | StructureInterfaceList.addNcsEquivalent | public void addNcsEquivalent(StructureInterface interfaceNew, StructureInterface interfaceRef) {
this.add(interfaceNew);
if (clustersNcs == null) {
clustersNcs = new ArrayList<>();
}
if (interfaceRef == null) {
StructureInterfaceCluster newCluster = new StructureInterfaceCluster();
newCluster.addMemb... | java | public void addNcsEquivalent(StructureInterface interfaceNew, StructureInterface interfaceRef) {
this.add(interfaceNew);
if (clustersNcs == null) {
clustersNcs = new ArrayList<>();
}
if (interfaceRef == null) {
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31,667 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceList.java | StructureInterfaceList.calculateInterfaces | public static StructureInterfaceList calculateInterfaces(Structure struc) {
CrystalBuilder builder = new CrystalBuilder(struc);
StructureInterfaceList interfaces = builder.getUniqueInterfaces();
logger.debug("Calculating ASA for "+interfaces.size()+" potential interfaces");
interfaces.calcAsas(StructureInterfac... | java | public static StructureInterfaceList calculateInterfaces(Structure struc) {
CrystalBuilder builder = new CrystalBuilder(struc);
StructureInterfaceList interfaces = builder.getUniqueInterfaces();
logger.debug("Calculating ASA for "+interfaces.size()+" potential interfaces");
interfaces.calcAsas(StructureInterfac... | [
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31,668 | biojava/biojava | biojava-alignment/src/main/java/org/biojava/nbio/phylo/ForesterWrapper.java | ForesterWrapper.getNewickString | public static String getNewickString(Phylogeny phylo,
boolean writeDistances) throws IOException {
PhylogenyWriter w = new PhylogenyWriter();
StringBuffer newickString = w.toNewHampshire(phylo, writeDistances);
return newickString.toString();
} | java | public static String getNewickString(Phylogeny phylo,
boolean writeDistances) throws IOException {
PhylogenyWriter w = new PhylogenyWriter();
StringBuffer newickString = w.toNewHampshire(phylo, writeDistances);
return newickString.toString();
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31,669 | biojava/biojava | biojava-alignment/src/main/java/org/biojava/nbio/phylo/ForesterWrapper.java | ForesterWrapper.cloneDM | public static BasicSymmetricalDistanceMatrix cloneDM(
BasicSymmetricalDistanceMatrix distM) {
int n = distM.getSize();
BasicSymmetricalDistanceMatrix cloneDM =
new BasicSymmetricalDistanceMatrix(n);
for (int i = 0; i < n; i++) {
cloneDM.setIdentifier(i, distM.getIdentifier(i));
for (int j = i + 1; ... | java | public static BasicSymmetricalDistanceMatrix cloneDM(
BasicSymmetricalDistanceMatrix distM) {
int n = distM.getSize();
BasicSymmetricalDistanceMatrix cloneDM =
new BasicSymmetricalDistanceMatrix(n);
for (int i = 0; i < n; i++) {
cloneDM.setIdentifier(i, distM.getIdentifier(i));
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31,670 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GroupContact.java | GroupContact.getContactsWithinDistance | public List<AtomContact> getContactsWithinDistance(double distance) {
List<AtomContact> list = new ArrayList<AtomContact>();
for (AtomContact contact:this.atomContacts) {
if (contact.getDistance()<distance) {
list.add(contact);
}
}
return list;
} | java | public List<AtomContact> getContactsWithinDistance(double distance) {
List<AtomContact> list = new ArrayList<AtomContact>();
for (AtomContact contact:this.atomContacts) {
if (contact.getDistance()<distance) {
list.add(contact);
}
}
return list;
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31,671 | biojava/biojava | biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.java | AminoAcidCompositionTable.computeMolecularWeight | public void computeMolecularWeight(ElementTable eTable){
this.aaSymbol2MolecularWeight = new HashMap<Character, Double>();
for(AminoAcidComposition a:aminoacid){
//Check to ensure that the symbol is of single character
if(a.getSymbol().length() != 1){
throw new Error(a.getSymbol() + " is not allowed. Symb... | java | public void computeMolecularWeight(ElementTable eTable){
this.aaSymbol2MolecularWeight = new HashMap<Character, Double>();
for(AminoAcidComposition a:aminoacid){
//Check to ensure that the symbol is of single character
if(a.getSymbol().length() != 1){
throw new Error(a.getSymbol() + " is not allowed. Symb... | [
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31,672 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GroupContactSet.java | GroupContactSet.hasContact | public boolean hasContact(Group group1, Group group2) {
return hasContact(group1.getResidueNumber(),group2.getResidueNumber());
} | java | public boolean hasContact(Group group1, Group group2) {
return hasContact(group1.getResidueNumber(),group2.getResidueNumber());
} | [
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31,673 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GroupContactSet.java | GroupContactSet.hasContact | public boolean hasContact(ResidueNumber resNumber1, ResidueNumber resNumber2) {
return contacts.containsKey(new Pair<ResidueNumber>(resNumber1, resNumber2));
} | java | public boolean hasContact(ResidueNumber resNumber1, ResidueNumber resNumber2) {
return contacts.containsKey(new Pair<ResidueNumber>(resNumber1, resNumber2));
} | [
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31,674 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GroupContactSet.java | GroupContactSet.getContact | public GroupContact getContact(Group group1, Group group2) {
return contacts.get(
new Pair<ResidueNumber>(group1.getResidueNumber(),group2.getResidueNumber()));
} | java | public GroupContact getContact(Group group1, Group group2) {
return contacts.get(
new Pair<ResidueNumber>(group1.getResidueNumber(),group2.getResidueNumber()));
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31,675 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/Mutator.java | Mutator.mutate | public Structure mutate(Structure struc, String chainId, String pdbResnum, String newType)
throws PDBParseException{
// create a container for the new structure
Structure newstruc = new StructureImpl();
// first we need to find our corresponding chain
// get the chains for model nr. 0
// if structure i... | java | public Structure mutate(Structure struc, String chainId, String pdbResnum, String newType)
throws PDBParseException{
// create a container for the new structure
Structure newstruc = new StructureImpl();
// first we need to find our corresponding chain
// get the chains for model nr. 0
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31,676 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/Mutator.java | Mutator.mutateResidue | public AminoAcid mutateResidue(AminoAcid oldAmino, String newType)
throws PDBParseException {
AminoAcid newgroup = new AminoAcidImpl();
newgroup.setResidueNumber(oldAmino.getResidueNumber());
newgroup.setPDBName(newType);
AtomIterator aiter =new AtomIterator(oldAmino);
while (aiter.hasNext()){
Atom a ... | java | public AminoAcid mutateResidue(AminoAcid oldAmino, String newType)
throws PDBParseException {
AminoAcid newgroup = new AminoAcidImpl();
newgroup.setResidueNumber(oldAmino.getResidueNumber());
newgroup.setPDBName(newType);
AtomIterator aiter =new AtomIterator(oldAmino);
while (aiter.hasNext()){
Atom a ... | [
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31,677 | biojava/biojava | biojava-alignment/src/main/java/org/biojava/nbio/phylo/Comparison.java | Comparison.PID | public final static float PID(String seq1, String seq2) {
return PID(seq1, seq2, 0, seq1.length());
} | java | public final static float PID(String seq1, String seq2) {
return PID(seq1, seq2, 0, seq1.length());
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@param s1
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@param s2
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31,678 | biojava/biojava | biojava-alignment/src/main/java/org/biojava/nbio/phylo/Comparison.java | Comparison.PID | public final static float PID(String seq1, String seq2, int start, int end) {
int s1len = seq1.length();
int s2len = seq2.length();
int len = Math.min(s1len, s2len);
if (end < len) {
len = end;
}
if (len < start) {
start = len - 1; // we just use a single residue for the difference
}
int bad ... | java | public final static float PID(String seq1, String seq2, int start, int end) {
int s1len = seq1.length();
int s2len = seq2.length();
int len = Math.min(s1len, s2len);
if (end < len) {
len = end;
}
if (len < start) {
start = len - 1; // we just use a single residue for the difference
}
int bad ... | [
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31,679 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java | RotationSolver.completeRotationGroup | private boolean completeRotationGroup(Rotation... additionalRots) {
PermutationGroup g = new PermutationGroup();
for (Rotation s : rotations) {
g.addPermutation(s.getPermutation());
}
for( Rotation s : additionalRots) {
g.addPermutation(s.getPermutation());
// inputs should not have been added already
... | java | private boolean completeRotationGroup(Rotation... additionalRots) {
PermutationGroup g = new PermutationGroup();
for (Rotation s : rotations) {
g.addPermutation(s.getPermutation());
}
for( Rotation s : additionalRots) {
g.addPermutation(s.getPermutation());
// inputs should not have been added already
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31,680 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java | RotationSolver.getAngles | private List<Double> getAngles() {
int n = subunits.getSubunitCount();
// for spherical symmetric cases, n cannot be higher than 60
if (n % 60 == 0 && isSpherical()) {
n = 60;
}
List<Integer> folds = subunits.getFolds();
List<Double> angles = new ArrayList<Double>(folds.size()-1);
// note this loop s... | java | private List<Double> getAngles() {
int n = subunits.getSubunitCount();
// for spherical symmetric cases, n cannot be higher than 60
if (n % 60 == 0 && isSpherical()) {
n = 60;
}
List<Integer> folds = subunits.getFolds();
List<Double> angles = new ArrayList<Double>(folds.size()-1);
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31,681 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java | RotationSolver.isValidPermutation | private Rotation isValidPermutation(List<Integer> permutation) {
if (permutation.size() == 0) {
return null;
}
// cached value
if (evaluatedPermutations.containsKey(permutation)) {
return evaluatedPermutations.get(permutation);
}
// check if permutation is allowed
if (! isAllowedPermutation(permut... | java | private Rotation isValidPermutation(List<Integer> permutation) {
if (permutation.size() == 0) {
return null;
}
// cached value
if (evaluatedPermutations.containsKey(permutation)) {
return evaluatedPermutations.get(permutation);
}
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31,682 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java | RotationSolver.isAllowedPermutation | private boolean isAllowedPermutation(List<Integer> permutation) {
List<Integer> seqClusterId = subunits.getClusterIds();
int selfaligned = 0;
for (int i = 0; i < permutation.size(); i++) {
int j = permutation.get(i);
if ( seqClusterId.get(i) != seqClusterId.get(j)) {
return false;
}
if(i == j ) {
... | java | private boolean isAllowedPermutation(List<Integer> permutation) {
List<Integer> seqClusterId = subunits.getClusterIds();
int selfaligned = 0;
for (int i = 0; i < permutation.size(); i++) {
int j = permutation.get(i);
if ( seqClusterId.get(i) != seqClusterId.get(j)) {
return false;
}
if(i == j ) {
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31,683 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java | RotationSolver.getPermutation | private List<Integer> getPermutation() {
List<Integer> permutation = new ArrayList<Integer>(transformedCoords.length);
double sum = 0.0f;
for (Point3d t: transformedCoords) {
List<Integer> neighbors = box.getNeighborsWithCache(t);
int closest = -1;
double minDist = Double.MAX_VALUE;
for (int j : ne... | java | private List<Integer> getPermutation() {
List<Integer> permutation = new ArrayList<Integer>(transformedCoords.length);
double sum = 0.0f;
for (Point3d t: transformedCoords) {
List<Integer> neighbors = box.getNeighborsWithCache(t);
int closest = -1;
double minDist = Double.MAX_VALUE;
for (int j : ne... | [
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31,684 | biojava/biojava | biojava-structure-gui/src/main/java/demo/DemoShowLargeAssembly.java | DemoShowLargeAssembly.readStructure | public static Structure readStructure(String pdbId, int bioAssemblyId) {
// pre-computed files use lower case PDB IDs
pdbId = pdbId.toLowerCase();
// we just need this to track where to store PDB files
// this checks the PDB_DIR property (and uses a tmp location if not set)
AtomCache cache = new AtomCache(... | java | public static Structure readStructure(String pdbId, int bioAssemblyId) {
// pre-computed files use lower case PDB IDs
pdbId = pdbId.toLowerCase();
// we just need this to track where to store PDB files
// this checks the PDB_DIR property (and uses a tmp location if not set)
AtomCache cache = new AtomCache(... | [
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@param bioAssemblyId .. the first assembly has the bioAssemblyId 1
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31,685 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucCalc.java | SecStrucCalc.calculate | public List<SecStrucState> calculate(Structure s, boolean assign)
throws StructureException {
List<SecStrucState> secstruc = new ArrayList<SecStrucState>();
for(int i=0; i<s.nrModels(); i++) {
// Reinitialise the global vars
ladders = new ArrayList<Ladder>();
bridges = new ArrayList<BetaBridge>();
g... | java | public List<SecStrucState> calculate(Structure s, boolean assign)
throws StructureException {
List<SecStrucState> secstruc = new ArrayList<SecStrucState>();
for(int i=0; i<s.nrModels(); i++) {
// Reinitialise the global vars
ladders = new ArrayList<Ladder>();
bridges = new ArrayList<BetaBridge>();
g... | [
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@param s Structure to predict the SS
@param assign sets the SS information to the Groups of s
@return a List of SS annotation objects | [
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31,686 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucCalc.java | SecStrucCalc.initContactSet | private void initContactSet() {
// Initialise an array of atoms
atoms = new Atom[groups.length];
// Remake this local var
indResMap = new HashMap<>();
for (int i=0 ; i < groups.length ; i++){
SecStrucGroup one = groups[i];
indResMap.put(one.getResidueNumber(), i);
atoms[i] = one.getCA();
}
Grid ... | java | private void initContactSet() {
// Initialise an array of atoms
atoms = new Atom[groups.length];
// Remake this local var
indResMap = new HashMap<>();
for (int i=0 ; i < groups.length ; i++){
SecStrucGroup one = groups[i];
indResMap.put(one.getResidueNumber(), i);
atoms[i] = one.getCA();
}
Grid ... | [
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31,687 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucCalc.java | SecStrucCalc.printDSSP | public String printDSSP() {
StringBuffer buf = new StringBuffer();
String nl = System.getProperty("line.separator");
//Header Line
buf.append("==== Secondary Structure Definition by BioJava"
+ " DSSP implementation, Version October 2015 ===="+nl);
//First line with column definition
buf.append(" # ... | java | public String printDSSP() {
StringBuffer buf = new StringBuffer();
String nl = System.getProperty("line.separator");
//Header Line
buf.append("==== Secondary Structure Definition by BioJava"
+ " DSSP implementation, Version October 2015 ===="+nl);
//First line with column definition
buf.append(" # ... | [
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31,688 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucCalc.java | SecStrucCalc.printFASTA | public String printFASTA() {
StringBuffer buf = new StringBuffer();
String nl = System.getProperty("line.separator");
buf.append(">"+groups[0].getChain().getStructure().getIdentifier()+nl);
for (int g = 0; g < groups.length; g++){
buf.append(getSecStrucState(g).getType());
}
return buf.toString();
} | java | public String printFASTA() {
StringBuffer buf = new StringBuffer();
String nl = System.getProperty("line.separator");
buf.append(">"+groups[0].getChain().getStructure().getIdentifier()+nl);
for (int g = 0; g < groups.length; g++){
buf.append(getSecStrucState(g).getType());
}
return buf.toString();
} | [
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31,689 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucCalc.java | SecStrucCalc.calculateHAtoms | private void calculateHAtoms() throws StructureException {
for ( int i = 0 ; i < groups.length-1 ; i++) {
SecStrucGroup a = groups[i];
SecStrucGroup b = groups[i+1];
if ( !b.hasAtom("H") ) {
//Atom H = calc_H(a.getC(), b.getN(), b.getCA());
Atom H = calcSimple_H(a.getC(), a.getO(), b.getN());
... | java | private void calculateHAtoms() throws StructureException {
for ( int i = 0 ; i < groups.length-1 ; i++) {
SecStrucGroup a = groups[i];
SecStrucGroup b = groups[i+1];
if ( !b.hasAtom("H") ) {
//Atom H = calc_H(a.getC(), b.getN(), b.getCA());
Atom H = calcSimple_H(a.getC(), a.getO(), b.getN());
... | [
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31,690 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucCalc.java | SecStrucCalc.calculateHBonds | private void calculateHBonds() {
/**
* More efficient method for calculating C-Alpha pairs
*/
if (groups.length < 5) return;
Iterator<AtomContact> otu = contactSet.iterator();
while(otu.hasNext()){
AtomContact ac = otu.next();
Pair<Atom> pair = ac.getPair();
Group g1 = pair.getFirst().getGroup();... | java | private void calculateHBonds() {
/**
* More efficient method for calculating C-Alpha pairs
*/
if (groups.length < 5) return;
Iterator<AtomContact> otu = contactSet.iterator();
while(otu.hasNext()){
AtomContact ac = otu.next();
Pair<Atom> pair = ac.getPair();
Group g1 = pair.getFirst().getGroup();... | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucCalc.java#L775-L794 |
31,691 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucCalc.java | SecStrucCalc.trackHBondEnergy | private void trackHBondEnergy(int i, int j, double energy) {
if (groups[i].getPDBName().equals("PRO")) {
logger.debug("Ignore: PRO {}",groups[i].getResidueNumber());
return;
}
SecStrucState stateOne = getSecStrucState(i);
SecStrucState stateTwo = getSecStrucState(j);
double acc1e = stateOne.getAccep... | java | private void trackHBondEnergy(int i, int j, double energy) {
if (groups[i].getPDBName().equals("PRO")) {
logger.debug("Ignore: PRO {}",groups[i].getResidueNumber());
return;
}
SecStrucState stateOne = getSecStrucState(i);
SecStrucState stateTwo = getSecStrucState(j);
double acc1e = stateOne.getAccep... | [
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... | Store Hbonds in the Groups.
DSSP allows two HBonds per aminoacids to allow bifurcated bonds. | [
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31,692 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucCalc.java | SecStrucCalc.calculateTurns | private void calculateTurns(){
for (int i = 0 ; i< groups.length; i++){
for (int turn = 3; turn <= 5; turn++) {
if (i+turn >= groups.length) continue;
//Check for H bond from NH(i+n) to CO(i)
if (isBonded(i, i+turn)) {
logger.debug("Turn at ({},{}) turn {}",i,(i+turn),turn);
getSecStrucSta... | java | private void calculateTurns(){
for (int i = 0 ; i< groups.length; i++){
for (int turn = 3; turn <= 5; turn++) {
if (i+turn >= groups.length) continue;
//Check for H bond from NH(i+n) to CO(i)
if (isBonded(i, i+turn)) {
logger.debug("Turn at ({},{}) turn {}",i,(i+turn),turn);
getSecStrucSta... | [
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... | Detect helical turn patterns. | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucCalc.java#L940-L961 |
31,693 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucCalc.java | SecStrucCalc.calc_H | @SuppressWarnings("unused")
private static Atom calc_H(Atom C, Atom N, Atom CA)
throws StructureException {
Atom nc = Calc.subtract(N,C);
Atom nca = Calc.subtract(N,CA);
Atom u_nc = Calc.unitVector(nc) ;
Atom u_nca = Calc.unitVector(nca);
Atom added = Calc.add(u_nc,u_nca);
Atom U = Calc.unitVect... | java | @SuppressWarnings("unused")
private static Atom calc_H(Atom C, Atom N, Atom CA)
throws StructureException {
Atom nc = Calc.subtract(N,C);
Atom nca = Calc.subtract(N,CA);
Atom u_nc = Calc.unitVector(nc) ;
Atom u_nca = Calc.unitVector(nca);
Atom added = Calc.add(u_nc,u_nca);
Atom U = Calc.unitVect... | [
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")"... | Use unit vectors NC and NCalpha Add them. Calc unit vector and
substract it from N.
C coordinates are from amino acid i-1
N, CA atoms from amino acid i
@link http://openbioinformatics.blogspot.com/
2009/08/how-to-calculate-h-atoms-for-nitrogens.html | [
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... | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucCalc.java#L1011-L1032 |
31,694 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucCalc.java | SecStrucCalc.setSecStrucType | private void setSecStrucType(int pos, SecStrucType type){
SecStrucState ss = getSecStrucState(pos);
if (type.compareTo(ss.getType()) < 0) ss.setType(type);
} | java | private void setSecStrucType(int pos, SecStrucType type){
SecStrucState ss = getSecStrucState(pos);
if (type.compareTo(ss.getType()) < 0) ss.setType(type);
} | [
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current residue SS type.
@param pos
@param type | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucCalc.java#L1137-L1140 |
31,695 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeMain.java | CeMain.align | @Override
public AFPChain align(Atom[] ca1, Atom[] ca2, Object param) throws StructureException{
if ( ! (param instanceof CeParameters))
throw new IllegalArgumentException("CE algorithm needs an object of call CeParameters as argument.");
params = (CeParameters) param;
// we don't want to rotate input atoms... | java | @Override
public AFPChain align(Atom[] ca1, Atom[] ca2, Object param) throws StructureException{
if ( ! (param instanceof CeParameters))
throw new IllegalArgumentException("CE algorithm needs an object of call CeParameters as argument.");
params = (CeParameters) param;
// we don't want to rotate input atoms... | [
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... | Align ca2 onto ca1. | [
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"."
] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeMain.java#L86-L136 |
31,696 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/Site.java | Site.remark800toPDB | public void remark800toPDB(StringBuffer stringBuffer) {
//REMARK 800 SITE_IDENTIFIER: CAT
//REMARK 800 EVIDENCE_CODE: UNKNOWN
//REMARK 800 SITE_DESCRIPTION: ACTIVE SITE
stringBuffer.append(String.format(Locale.UK, "REMARK 800 SITE_IDENTIFIER: %-52s%s", siteID, lineEnd));
stringBuffer.append(String.format(Loc... | java | public void remark800toPDB(StringBuffer stringBuffer) {
//REMARK 800 SITE_IDENTIFIER: CAT
//REMARK 800 EVIDENCE_CODE: UNKNOWN
//REMARK 800 SITE_DESCRIPTION: ACTIVE SITE
stringBuffer.append(String.format(Locale.UK, "REMARK 800 SITE_IDENTIFIER: %-52s%s", siteID, lineEnd));
stringBuffer.append(String.format(Loc... | [
"public",
"void",
"remark800toPDB",
"(",
"StringBuffer",
"stringBuffer",
")",
"{",
"//REMARK 800 SITE_IDENTIFIER: CAT",
"//REMARK 800 EVIDENCE_CODE: UNKNOWN",
"//REMARK 800 SITE_DESCRIPTION: ACTIVE SITE",
"stringBuffer",
".",
"append",
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"String",
".",
"format",
"(",
"Locale... | Appends the REMARK 800 section pertaining to the site onto the end of the
StringBuffer provided.
For example in pdb 1a4w:
REMARK 800 SITE_IDENTIFIER: CAT
REMARK 800 EVIDENCE_CODE: UNKNOWN
REMARK 800 SITE_DESCRIPTION: ACTIVE SITE
@param stringBuffer | [
"Appends",
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/Site.java#L139-L148 |
31,697 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/SigEva.java | SigEva.normScore | private double normScore(double score, double rmsd, int optLen, int r)
{
//double score1 = modScore(score, r);
double score1 = score;
if(r > 0) score1 /= Math.sqrt(r + 1);
//it is tested that flexible score is more linear relevant to 1/r2 than 1/r
if(rmsd < 0.5) score1 *= Math.sqrt((optLen) /... | java | private double normScore(double score, double rmsd, int optLen, int r)
{
//double score1 = modScore(score, r);
double score1 = score;
if(r > 0) score1 /= Math.sqrt(r + 1);
//it is tested that flexible score is more linear relevant to 1/r2 than 1/r
if(rmsd < 0.5) score1 *= Math.sqrt((optLen) /... | [
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... | the chaining score is normalized by rmsd, twist and optimal alignment length | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/SigEva.java#L201-L210 |
31,698 | biojava/biojava | biojava-protein-disorder/src/main/java/org/biojava/nbio/data/sequence/SequenceUtil.java | SequenceUtil.cleanSequence | public static String cleanSequence(String sequence) {
assert sequence != null;
final Matcher m = SequenceUtil.WHITE_SPACE.matcher(sequence);
sequence = m.replaceAll("").toUpperCase();
return sequence;
} | java | public static String cleanSequence(String sequence) {
assert sequence != null;
final Matcher m = SequenceUtil.WHITE_SPACE.matcher(sequence);
sequence = m.replaceAll("").toUpperCase();
return sequence;
} | [
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... | Removes all whitespace chars in the sequence string
@param sequence
@return cleaned up sequence | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-protein-disorder/src/main/java/org/biojava/nbio/data/sequence/SequenceUtil.java#L149-L154 |
31,699 | biojava/biojava | biojava-protein-disorder/src/main/java/org/biojava/nbio/data/sequence/SequenceUtil.java | SequenceUtil.deepCleanSequence | public static String deepCleanSequence(String sequence) {
sequence = SequenceUtil.cleanSequence(sequence);
sequence = SequenceUtil.DIGIT.matcher(sequence).replaceAll("");
sequence = SequenceUtil.NONWORD.matcher(sequence).replaceAll("");
final Pattern othernonSeqChars = Pattern.compile("[_-]+");
sequence = othernon... | java | public static String deepCleanSequence(String sequence) {
sequence = SequenceUtil.cleanSequence(sequence);
sequence = SequenceUtil.DIGIT.matcher(sequence).replaceAll("");
sequence = SequenceUtil.NONWORD.matcher(sequence).replaceAll("");
final Pattern othernonSeqChars = Pattern.compile("[_-]+");
sequence = othernon... | [
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... | Removes all special characters and digits as well as whitespace chars
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@param sequence
@return cleaned up sequence | [
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