indigo knime nodes · i indigo toolkit api: c#, java, python i bingo for postgresql mikhail...
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Open-source software
Indigo KNIME nodes
Mikhail Rybalkin
KNIME Open Source DaysOctober 6, 2011
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GGA overview
I Saint-Petersburg & Boston since 1995
I 380 employees:
development department: 150content department: 100QA department: 70
I Projects with ...
I http://ggasoftware.com
Mikhail Rybalkin Indigo KNIME nodes October 6, 2011
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GGA projects
- cheminformatics toolkit- database search cartridge
Mass spectrometry
Molecular dynamics
Sequence processing
High-throughput screening
GPGPU, cluster computing
Image analysys and recognition
IndigoBingo
Open-sourceprojects
Proprietarycontract-basedprojects
Mikhail Rybalkin Indigo KNIME nodes October 6, 2011
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History of Indigo projects
I Different algorithms
I Bingo for Oracle
I Bingo for SQL Server
I Ketcher - molecule sketcher:bingo-demo.ggasoftware.com/
I Indigo toolkit API:C#, Java, Python
I Bingo for PostgreSQL
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30M
Mikhail Rybalkin Indigo KNIME nodes October 6, 2011
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History of Indigo projects
I Different algorithms
I Bingo for Oracle
I Bingo for SQL Server
I Ketcher - molecule sketcher:bingo-demo.ggasoftware.com/
I Indigo toolkit API:C#, Java, Python
I Bingo for PostgreSQL
O
O
C
C CCl
Cl
O
OCl
Cl
ON
N
C
O
NN
C
C
O
NN
C
NO
ON
N
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N O
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30M
Mikhail Rybalkin Indigo KNIME nodes October 6, 2011
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History of Indigo projects
I Different algorithms
I Bingo for Oracle
I Bingo for SQL Server
I Ketcher - molecule sketcher:bingo-demo.ggasoftware.com/
I Indigo toolkit API:C#, Java, Python
I Bingo for PostgreSQL
O
O
C
C CCl
Cl
O
OCl
Cl
ON
N
C
O
NN
C
C
O
NN
C
NO
ON
N
N
ON
N
O
N
O
C
C
O
C
N
C
N O
ON
N
C O
O
O
N
NO
O
N
O
N N
NN
OO
OO
30M
Mikhail Rybalkin Indigo KNIME nodes October 6, 2011
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History of Indigo projects
I Different algorithms
I Bingo for Oracle
I Bingo for SQL Server
I Ketcher - molecule sketcher:bingo-demo.ggasoftware.com/
I Indigo toolkit API:C#, Java, Python
I Bingo for PostgreSQL
O
O
C
C CCl
Cl
O
OCl
Cl
ON
N
C
O
NN
C
C
O
NN
C
NO
ON
N
N
ON
N
O
N
O
C
C
O
C
N
C
N O
ON
N
C O
O
O
N
NO
O
N
O
N N
NN
OO
OO
30M
Mikhail Rybalkin Indigo KNIME nodes October 6, 2011
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Why Open Source?
I Bussiness model
I Relationship with the scientific commnity
I Feedback from the commnityI SuggestionsI Testing
I Indigo modules are used in commercial projects
Mikhail Rybalkin Indigo KNIME nodes October 6, 2011
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Why Open Source?
I Bussiness model
I Relationship with the scientific commnity
I Feedback from the commnityI SuggestionsI Testing
I Indigo modules are used in commercial projects
Mikhail Rybalkin Indigo KNIME nodes October 6, 2011
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Why Open Source?
I Bussiness model
I Relationship with the scientific commnity
I Feedback from the commnityI SuggestionsI Testing
I Indigo modules are used in commercial projects
Mikhail Rybalkin Indigo KNIME nodes October 6, 2011
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Introduction
Indigo SDK is an open-source cheminformatics library.
Goals of Indigo
I Easy access to the library of GGA cheminformatics algorithms
I Portability across OS and programming languages
I Extensibility with plugins (incl. third-party)
Mikhail Rybalkin Indigo KNIME nodes October 6, 2011
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Capabilities
I Support of popular data formats:SMILES, SMARTS, Molfile, Rxnfile, SDF, RDF, GZip
I Portability over modern platforms and languages:Linux/Windows/Mac OS X, 32/64 bit, Java/Python/C#
I Outstanding performance:Original algorithms, fast C++ implementation
Mikhail Rybalkin Indigo KNIME nodes October 6, 2011
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Functionality
I Calculation of structure properties:Canonical SMILES, molecular weight, molecular formula
I Rendering of molecules and reactions:SVG, PNG, EMF, PDF, automatic layout, highlighting, ...
I Structure and reaction search:Exact, Substructure, Similarity, SMARTS, fingerprints
I Scaffold detection and R-Group decomposition:MCS of arbitrary amount of input structures
I Reaction atom-to-atom mapping
I Combinatorial chemistry:Stereo transformations, intramolecular and multistep reactions
Mikhail Rybalkin Indigo KNIME nodes October 6, 2011
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Functionality
I Calculation of structure properties:Canonical SMILES, molecular weight, molecular formula
I Rendering of molecules and reactions:SVG, PNG, EMF, PDF, automatic layout, highlighting, ...
I Structure and reaction search:Exact, Substructure, Similarity, SMARTS, fingerprints
I Scaffold detection and R-Group decomposition:MCS of arbitrary amount of input structures
I Reaction atom-to-atom mapping
I Combinatorial chemistry:Stereo transformations, intramolecular and multistep reactions
Mikhail Rybalkin Indigo KNIME nodes October 6, 2011
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Indigo Nodes for KNIME
I First release: May 2011
I Intensive communication with the community
Mikhail Rybalkin Indigo KNIME nodes October 6, 2011
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Substructure search
Mikhail Rybalkin Indigo KNIME nodes October 6, 2011
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Atom-to-atom mapping
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Mikhail Rybalkin Indigo KNIME nodes October 6, 2011
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R-Group decomposition
Mikhail Rybalkin Indigo KNIME nodes October 6, 2011
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Combinatorial chemistryI Integrate Legio tool into KNIME
?
Reactionpattern
Monomers Products
Reaction pattern
Monomers
Products
Mikhail Rybalkin Indigo KNIME nodes October 6, 2011
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Technical issues and details
I Cross-platform:
I Linux/Windows/Mac OS X(Solaris is also supported by request)
I 32/64 bit
I Testing:I JenkinsI Python/IronPython/Jython
I C++ core code, plain C API
I Indigo API for Java/C#/PythonSWIG ?
I Hydrogens support.SMARTS: h notation is not supported on purpose.
Mikhail Rybalkin Indigo KNIME nodes October 6, 2011
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Technical issues and details
I Cross-platform:
I Linux/Windows/Mac OS X(Solaris is also supported by request)
I 32/64 bit
I Testing:I JenkinsI Python/IronPython/Jython
I C++ core code, plain C API
I Indigo API for Java/C#/PythonSWIG ?
I Hydrogens support.SMARTS: h notation is not supported on purpose.
Mikhail Rybalkin Indigo KNIME nodes October 6, 2011
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Technical issues and details
I Cross-platform:
I Linux/Windows/Mac OS X(Solaris is also supported by request)
I 32/64 bit
I Testing:I JenkinsI Python/IronPython/Jython
I C++ core code, plain C API
I Indigo API for Java/C#/PythonSWIG ?
I Hydrogens support.SMARTS: h notation is not supported on purpose.
Mikhail Rybalkin Indigo KNIME nodes October 6, 2011
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Design
Core API(C++)
QS_DEF(Molecule, mol); QS_DEF(Array<int>, gross);
MoleculeAutoLoader loader(molfile); loader.loadMolecule(mol);
MoleculeAromatizer::aromatizeBonds(mol); MangoExact::calculateHash(mol, _hash);
MoleculeFingerprintBuilder builder(mol, _context.fp_parameters); builder.process();
_fp.copy(builder.get(), _context.fp_parameters.fingerprintSize()); _fp_sim_bits_count = builder.countBits_Sim(); output.writeBinaryWord((word)_fp_sim_bits_count);
const byte *fp_sim_ptr = builder.getSim(); int fp_sim_size = _context.fp_parameters.fingerprintSizeSim();
// Save gross formula GrossFormula::collect(mol, gross); GrossFormula::toString(gross, _gross_str);
_counted_elems_str.clear();
ArrayOutput ce_output(_counted_elems_str);
for (int i = 0; i < (int)NELEM(counted_elements); i++) ce_output.printf(", %d", gross[counted_elements[i]]);
ce_output.writeByte(0);
// Calculate molecular mass MoleculeMass mass_calulator; mass_calulator.relative_atomic_mass_map = &_context.relative_atomic_mass_map; _molecular_mass = mass_calulator.molecularWeight(mol);
if (outfile_allscafs != 0) { int output = indigoWriteFile(outfile_allscafs); int allscafs = indigoAllScaffolds(scaffold); int item, iter = indigoIterateArray(allscafs);
printf("saving all obtained scaffolds (%d total) to %s\n", indigoArrayCount(allscafs), outfile_allscafs);
while ((item = indigoNext(iter))) { indigoSdfAppend(output, item); indigoFree(item); } indigoFree(iter); indigoFree(output); }
printf("decomposing the structures... "); deco = indigoDecomposeMolecules(scaffold, structures);
if (outfile_hl != 0) { int output = indigoWriteFile(outfile_hl); int item, iter = indigoIterateDecomposedMolecules(deco);
printf("saving the highlighted structures to %s\n", outfile_hl);
while ((item = indigoNext(iter))) { indigoSdfAppend(output, indigoDecomposedMoleculeHighlighted(item)); indigoFree(item); }
indigoFree(iter); indigoFree(output); }
Simplified API(plain C)
zlib
IndigoObject query = indigo.loadSmarts("[NX3;H2,H1;!$(NC=O)]"); for (IndigoObject item : indigo.iterateSDFile("thiazolidines.sdf")) { item.aromatize(); IndigoObject match = indigo.matchSubstructure(query, item);
if (match != null) System.out.println(match.matchHighlight().smiles()); else System.out.println("no match"); }
Java wrapper
C# wrapperIndigoObject rxn = indigo.loadReactionFromFile("test.rxn");
foreach (IndigoObject iter in rxn2.iterateReactants()){ System.Console.WriteLine(iter.smiles()); System.Console.WriteLine(iter.molecularWeight()); System.Console.WriteLine(iter.mostAbundantMass()); System.Console.WriteLine(iter.monoisotopicMass()); System.Console.WriteLine(iter.grossFormula());}
arr = indigo.createArray(); for item in indigo.iterateSDFile("thiazolidines.sdf"): item.aromatize(); item.cisTransClear(); arr.arrayAdd(item);
scaf = indigo.extractCommonScaffold(arr, "exact") deco = indigo.decomposeMolecules(scaf, arr) scaff = deco.decomposedMoleculeScaffold() for item in deco.iterateDecomposedMolecules(): print item.decomposedMoleculeHighlighted().smiles()
Pythonwrapper
RendererC++ plugin
cairo
Javawrapper
C# wrapper
Pythonwrapper
Open for third-party plugins(either C, C++, Java, C#, or Python)
Renderer C API
RenderParams& rp = renderer_self.renderParams
Array<int> mapping; if (obj->getBaseMolecule().isQueryMolecule()) rp.mol.reset(new QueryMolecule()); else rp.mol.reset(new Molecule()); rp.mol->clone(self.getObject(object)-> getBaseMolecule(), &mapping, 0); GraphHighlighting* hl = self.getObject(object)->getMoleculeHighlighting(); if (hl != 0 && hl->numVertices() > 0) { rp.molhl.init(*rp.mol.get()); rp.molhl.copy(*hl, mapping); } rp.rmode = RENDER_MOL; RenderParamInterface::render(rp);
Mikhail Rybalkin Indigo KNIME nodes October 6, 2011
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Indigo API
Indigo i n d i g o = new Indigo ( ) ;
IndigoObject r x n = i n d i g o . c r e a t e R e a c t i o n ( ) ;r x n . addReactant ( mol1 ) ;r x n . addReactant ( mol2 ) ;r x n . addProduct ( i n d i g o . l o a d M o l e c u l e ( ”ClC1CCCCC1” ) ) ;r x n . automap ( ” d i s c a r d ” ) ;
System . out . p r i n t l n ( r x n . s m i l e s ( ) ) ;fo r ( IndigoObject i t em : r x n . i t e r a t e R e a c t a n t s ( ) )
System . out . p r i n t l n ( i tem . m o l f i l e ( ) ) ;
Mikhail Rybalkin Indigo KNIME nodes October 6, 2011
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Plans
1. Add reaction support into KNIME:I automatic atom-to-atom mapping (already available)I substructure and exact seachI combinatorial chemistryI reaction-based transformations
2. Add reaction readers into KNIME core
3. Add other additional nodes (community requests)
4. Multithreading
5. Testing workflows
Mikhail Rybalkin Indigo KNIME nodes October 6, 2011
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Other open-source projects
Ketcher — web-based chemical structure editor
Imago — 2D chemical structure image recognition toolkit
Mikhail Rybalkin Indigo KNIME nodes October 6, 2011
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Acknowledgnents
I Indigo community
I KNIME community
I KNIME Open Source Days organizers
I Dmitry Pavlov
Mikhail Rybalkin Indigo KNIME nodes October 6, 2011
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Community
I Web Site:http://ggasoftware.com/opensource
I Google groups:http://groups.google.com/group/indigo-general
http://groups.google.com/group/indigo-dev
http://groups.google.com/group/indigo-bugs
I Complete source code on GitHub:http://github.com/ggasoftware/indigo
I Chemistry Toolkit Rosetta (code examples):http://ctr.wikia.com
I KNIME Community:http://tech.knime.org/forum/indigo
Mikhail Rybalkin Indigo KNIME nodes October 6, 2011
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Suggestions to KNIME
I Pipes between knodes to avoid intermediate data
I Automatic node conversion to a newer version
I Universal domain-specific language for table processing
Mikhail Rybalkin Indigo KNIME nodes October 6, 2011