├── rdkit ├── __init__.py ├── utils │ ├── __init__.py │ ├── 12h.gif │ ├── test1.gif │ ├── test2.gif │ ├── test3.gif │ ├── pydoc_local.py │ ├── retest.txt │ └── GUIDs.py ├── Avalon │ └── __init__.py ├── Chem │ ├── MolDb │ │ ├── __init__.py │ │ └── Loader.py │ ├── AtomPairs │ │ ├── __init__.py │ │ ├── test_data │ │ │ ├── mols1000.pkl.gz │ │ │ ├── mols1000.aps.pkl.gz │ │ │ └── mols1000.tts.pkl.gz │ │ └── test_list.py │ ├── ChemUtils │ │ ├── __init__.py │ │ └── test_list.py │ ├── FeatMaps │ │ ├── __init__.py │ │ └── test_list.py │ ├── Features │ │ └── __init__.py │ ├── Pharm3D │ │ ├── __init__.py │ │ ├── test_data │ │ │ ├── cdk2-syn-clip100.pkl.gz │ │ │ ├── mol-r-3.mol │ │ │ ├── mol-s-3.mol │ │ │ ├── mol-r.mol │ │ │ └── mol-s.mol │ │ └── test_list.py │ ├── Scaffolds │ │ ├── __init__.py │ │ └── test_list.py │ ├── Subshape │ │ ├── __init__.py │ │ └── test_list.py │ ├── Suppliers │ │ ├── __init__.py │ │ └── test_list.py │ ├── test_data │ │ ├── Crippen_contribs_regress.pkl │ │ ├── buildingblocks.smi.gz │ │ ├── pubchem-hard-set.sdf.gz │ │ ├── Crippen.csv │ │ └── dative.mol │ ├── Draw │ │ ├── FreeSans.ttf │ │ └── test_list.py │ ├── Fingerprints │ │ ├── __init__.py │ │ └── test_list.py │ ├── MolCatalog.py │ ├── EState │ │ ├── test_list.py │ │ └── __init__.py │ ├── ChemicalForceFields.py │ └── Pharm2D │ │ └── test_list.py ├── Logger │ ├── __init__.py │ └── test_list.py ├── ML │ ├── Cluster │ │ ├── __init__.py │ │ └── test_list.py │ ├── Data │ │ ├── __init__.py │ │ ├── test_data │ │ │ ├── test.qdat │ │ │ └── test.dat │ │ └── test_list.py │ ├── MLUtils │ │ └── __init__.py │ ├── Neural │ │ ├── __init__.py │ │ └── test_list.py │ ├── SLT │ │ ├── __init__.py │ │ └── test_list.py │ ├── Scoring │ │ ├── __init__.py │ │ └── test_list.py │ ├── Composite │ │ ├── __init__.py │ │ ├── test_data │ │ │ ├── composite_base.pkl │ │ │ ├── composite_base.both.pkl │ │ │ ├── composite_base.neural.pkl │ │ │ ├── composite_base.others.pkl │ │ │ ├── composite_base.unitnet.pkl │ │ │ ├── composite_plus_neural.pkl │ │ │ ├── composite_base.others.net.pkl │ │ │ ├── composite_base.unittree.pkl │ │ │ ├── composite_base.others.both.pkl │ │ │ └── composite_base.others.neural.pkl │ │ └── test_list.py │ ├── Descriptors │ │ ├── __init__.py │ │ ├── test_data │ │ │ └── molcalc.dsc │ │ └── test_list.py │ ├── ModelPackage │ │ ├── __init__.py │ │ ├── test_data │ │ │ └── Jan9_build3_model.pkl │ │ └── test_list.py │ ├── FeatureSelect │ │ ├── __init__.py │ │ └── test_list.py │ ├── InfoTheory │ │ ├── __init__.py │ │ └── test_list.py │ ├── DecTree │ │ ├── test_data │ │ │ ├── foo.pdf │ │ │ └── cdk2-few.pkl.gz │ │ ├── __init__.py │ │ └── test_list.py │ ├── test_data │ │ ├── humanoral.1.pkl │ │ ├── humanoral.2.pkl │ │ ├── ferromag_filt_10_3.pkl │ │ └── ferromag_shuffle_10_3.pkl │ ├── KNN │ │ ├── __init__.py │ │ ├── test_data │ │ │ └── sample_pts.csv │ │ └── test_list.py │ ├── NaiveBayes │ │ ├── __init__.py │ │ └── test_list.py │ └── __init__.py ├── sping │ ├── Qt │ │ └── __init__.py │ ├── ReportLab │ │ └── __init__.py │ ├── util │ │ └── __init__.py │ ├── PDF │ │ ├── __init__.py │ │ ├── pdfdoc.py │ │ └── pdfgeom.py │ ├── TK │ │ └── __init__.py │ ├── WX │ │ └── __init__.py │ ├── tests │ │ ├── __init__.py │ │ └── pstests.py │ ├── PIL │ │ ├── __init__.py │ │ └── pilfonts │ │ │ ├── courier-8.pbm │ │ │ ├── courier-8.pil │ │ │ ├── symbol-10.pbm │ │ │ ├── symbol-10.pil │ │ │ ├── symbol-12.pbm │ │ │ ├── symbol-12.pil │ │ │ ├── symbol-14.pbm │ │ │ ├── symbol-14.pil │ │ │ ├── symbol-18.pbm │ │ │ ├── symbol-18.pil │ │ │ ├── symbol-24.pbm │ │ │ ├── symbol-24.pil │ │ │ ├── symbol-8.pbm │ │ │ ├── symbol-8.pil │ │ │ ├── times-10.pbm │ │ │ ├── times-10.pil │ │ │ ├── times-12.pbm │ │ │ ├── times-12.pil │ │ │ ├── times-14.pbm │ │ │ ├── times-14.pil │ │ │ ├── times-18.pbm │ │ │ ├── times-18.pil │ │ │ ├── times-24.pbm │ │ │ ├── times-24.pil │ │ │ ├── times-8.pbm │ │ │ ├── times-8.pil │ │ │ ├── courier-10.pbm │ │ │ ├── courier-10.pil │ │ │ ├── courier-12.pbm │ │ │ ├── courier-12.pil │ │ │ ├── courier-14.pbm │ │ │ ├── courier-14.pil │ │ │ ├── courier-18.pbm │ │ │ ├── courier-18.pil │ │ │ ├── courier-24.pbm │ │ │ ├── courier-24.pil │ │ │ ├── courier-8.pil.1 │ │ │ ├── helvetica-8.pbm │ │ │ ├── helvetica-8.pil │ │ │ ├── courier-bold-8.pbm │ │ │ ├── courier-bold-8.pil │ │ │ ├── helvetica-10.pbm │ │ │ ├── helvetica-10.pil │ │ │ ├── helvetica-12.pbm │ │ │ ├── helvetica-12.pil │ │ │ ├── helvetica-14.pbm │ │ │ ├── helvetica-14.pil │ │ │ ├── helvetica-18.pbm │ │ │ ├── helvetica-18.pil │ │ │ ├── helvetica-24.pbm │ │ │ ├── helvetica-24.pil │ │ │ ├── times-bold-10.pbm │ │ │ ├── times-bold-10.pil │ │ │ ├── times-bold-12.pbm │ │ │ ├── times-bold-12.pil │ │ │ ├── times-bold-14.pbm │ │ │ ├── times-bold-14.pil │ │ │ ├── times-bold-18.pbm │ │ │ ├── times-bold-18.pil │ │ │ ├── times-bold-24.pbm │ │ │ ├── times-bold-24.pil │ │ │ ├── times-bold-8.pbm │ │ │ ├── times-bold-8.pil │ │ │ ├── courier-bold-10.pbm │ │ │ ├── courier-bold-10.pil │ │ │ ├── courier-bold-12.pbm │ │ │ ├── courier-bold-12.pil │ │ │ ├── courier-bold-14.pbm │ │ │ ├── courier-bold-14.pil │ │ │ ├── courier-bold-18.pbm │ │ │ ├── courier-bold-18.pil │ │ │ ├── courier-bold-24.pbm │ │ │ ├── courier-bold-24.pil │ │ │ ├── helvetica-bold-8.pbm │ │ │ ├── helvetica-bold-8.pil │ │ │ ├── helvetica-bold-10.pbm │ │ │ ├── helvetica-bold-10.pil │ │ │ ├── helvetica-bold-12.pbm │ │ │ ├── helvetica-bold-12.pil │ │ │ ├── helvetica-bold-14.pbm │ │ │ ├── helvetica-bold-14.pil │ │ │ ├── helvetica-bold-18.pbm │ │ │ ├── helvetica-bold-18.pil │ │ │ ├── helvetica-bold-24.pbm │ │ │ ├── helvetica-bold-24.pil │ │ │ └── removemedium.py │ ├── PS │ │ ├── __init__.py │ │ └── fontinfo.py │ ├── Pyart │ │ └── __init__.py │ ├── SVG │ │ └── __init__.py │ ├── __init__.py │ └── utils.py ├── Dbase │ ├── Pubmed │ │ ├── __init__.py │ │ ├── test_data │ │ │ ├── counts.xml │ │ │ ├── nohits.xml │ │ │ └── haslinks.xml │ │ └── test_list.py │ ├── test_data │ │ ├── dbtest.csv │ │ ├── dbtest.nulls.csv │ │ ├── dbtest.xls │ │ ├── rdtest.sql │ │ └── dbtest.nulls.xls │ ├── test_list.py │ └── __init__.py ├── VLib │ ├── __init__.py │ ├── NodeLib │ │ ├── __init__.py │ │ └── test_list.py │ └── test_list.py ├── DataManip │ ├── __init__.py │ └── Metric │ │ └── __init__.py ├── DistanceGeometry │ └── __init__.py ├── ForceField │ └── __init__.py ├── Numerics │ └── __init__.py ├── SimDivFilters │ ├── test_list.py │ └── __init__.py ├── Geometry │ └── __init__.py ├── DataStructs │ └── test_list.py ├── epydoc.config └── test_list.py ├── Code ├── GraphMol │ ├── libs │ │ └── .cvskeep │ ├── testExecs │ │ └── .cvskeep │ ├── Depictor │ │ ├── testExecs │ │ │ └── .cvskeep │ │ ├── test_list.py │ │ └── Wrap │ │ │ ├── test_list.py │ │ │ └── CMakeLists.txt │ ├── Subgraphs │ │ ├── testExecs │ │ │ └── .cvskeep │ │ ├── test_list.py │ │ └── CMakeLists.txt │ ├── Substruct │ │ ├── testExecs │ │ │ └── .cvskeep │ │ ├── regress.txt │ │ ├── test_list.py │ │ └── CMakeLists.txt │ ├── FileParsers │ │ ├── testExecs │ │ │ └── .cvskeep │ │ ├── test_data │ │ │ ├── empty2.sdf │ │ │ ├── empty.sdf │ │ │ ├── empty.smi │ │ │ ├── NCI_aids_few.sdf.gz │ │ │ ├── Issue3482695.sdf │ │ │ ├── cdk2_stereo.csv │ │ │ ├── missingCR.sdf │ │ │ ├── Issue269.mol │ │ │ ├── mol_nomol.mol2 │ │ │ ├── bondorder0.mol │ │ │ ├── bondorder9.mol │ │ │ ├── ringcount_0.mol │ │ │ ├── ringcount_2.mol │ │ │ ├── ringcount_3.mol │ │ │ ├── ringcount_4.mol │ │ │ ├── ringcount_star.mol │ │ │ ├── unsaturation.mol │ │ │ ├── mol_noatoms.mol2 │ │ │ ├── v3k.4a.mol │ │ │ ├── v3k.4b.mol │ │ │ ├── lists_plus_values.mol │ │ │ ├── D_in_CTAB.mol │ │ │ ├── T_in_CTAB.mol │ │ │ ├── subst3.mol │ │ │ ├── subst4.mol │ │ │ ├── SkipLines.sdf │ │ │ ├── v3k.rbc.mol │ │ │ ├── v3k.6a.mol │ │ │ ├── v3k.6b.mol │ │ │ ├── Issue142d.mol │ │ │ ├── simple_e.mol │ │ │ ├── simple_z.mol │ │ │ ├── chiral3.mol │ │ │ ├── chiral3a.mol │ │ │ ├── chiral4.mol │ │ │ ├── chiral4a.mol │ │ │ ├── cistrans.1.mol │ │ │ ├── cistrans.1a.mol │ │ │ ├── cistrans.2.mol │ │ │ ├── cistrans.2a.mol │ │ │ ├── cistrans.3.mol │ │ │ ├── simple_either.mol │ │ │ ├── ChiralityAndBondDir1b.mol │ │ │ ├── ChiralityAndBondDir2b.mol │ │ │ ├── AtomProps1.mol │ │ │ ├── three_coordinate_chirality.1.mol │ │ │ ├── three_coordinate_chirality.2.mol │ │ │ ├── three_coordinate_chirality.3.mol │ │ │ ├── three_coordinate_chirality.4.mol │ │ │ ├── three_coordinate_chirality.5.mol │ │ │ ├── three_coordinate_chirality.6.mol │ │ │ ├── radical.mol │ │ │ ├── subst1.mol │ │ │ ├── subst2.mol │ │ │ ├── v3k.5b.mol │ │ │ ├── AtomProps2.mol │ │ │ ├── Issue399a.mol │ │ │ ├── v3k.5a.mol │ │ │ ├── not-list-query.mol │ │ │ ├── ringcount_star2.mol │ │ │ ├── combined.mol │ │ │ ├── conflicting-list-query.mol │ │ │ └── ringcount_star3.mol │ │ └── test_list.py │ ├── Fingerprints │ │ ├── testExecs │ │ │ └── .cvskeep │ │ └── test_list.py │ ├── FragCatalog │ │ ├── testExecs │ │ │ └── .cvskeep │ │ ├── test_data │ │ │ ├── 4mols.smi │ │ │ └── mols.smi │ │ ├── test_list.py │ │ └── Wrap │ │ │ ├── test_list.py │ │ │ ├── rdfragcatalog.h │ │ │ └── CMakeLists.txt │ ├── MolTransforms │ │ ├── testExecs │ │ │ └── .cvskeep │ │ ├── ReadMe │ │ ├── Wrap │ │ │ ├── test_list.py │ │ │ └── CMakeLists.txt │ │ ├── test_list.py │ │ └── CMakeLists.txt │ ├── SmilesParse │ │ ├── regress.txt │ │ ├── testExecs │ │ │ └── .cvskeep │ │ ├── runflex.sh │ │ ├── test_list.py │ │ └── primes.h │ ├── ChemTransforms │ │ ├── testData │ │ │ ├── query_file2.txt │ │ │ ├── ethanol.mol │ │ │ └── oldcrash.mol │ │ └── test_list.py │ ├── regress.txt │ ├── test_data │ │ ├── canonSmiles.v1.pkl │ │ ├── canonSmiles.v2.pkl │ │ ├── Issue2788233.mol │ │ ├── Issue2951221.2.mol │ │ └── Issue2951221.3.mol │ ├── MolDrawing │ │ └── CMakeLists.txt │ ├── MolChemicalFeatures │ │ ├── test_data │ │ │ ├── featDef.txt │ │ │ └── featDef2.txt │ │ ├── Wrap │ │ │ ├── test_list.py │ │ │ └── CMakeLists.txt │ │ └── test_list.py │ ├── ForceFieldHelpers │ │ ├── UFF │ │ │ └── CMakeLists.txt │ │ ├── test_data │ │ │ ├── Issue2378119.2.mol │ │ │ └── Issue2378119.mol │ │ ├── Wrap │ │ │ ├── test_list.py │ │ │ └── CMakeLists.txt │ │ ├── test_list.py │ │ └── CMakeLists.txt │ ├── PartialCharges │ │ ├── CMakeLists.txt │ │ └── Wrap │ │ │ ├── test_list.py │ │ │ ├── CMakeLists.txt │ │ │ └── test_data │ │ │ └── halgren.smi │ ├── MolAlign │ │ ├── Wrap │ │ │ ├── test_list.py │ │ │ └── CMakeLists.txt │ │ ├── test_list.py │ │ └── CMakeLists.txt │ ├── MolCatalog │ │ ├── test_list.py │ │ ├── Wrap │ │ │ ├── test_list.py │ │ │ ├── CMakeLists.txt │ │ │ └── rdMolCatalog.h │ │ ├── CMakeLists.txt │ │ └── MolCatalog.h │ ├── Descriptors │ │ ├── Wrap │ │ │ ├── test_list.py │ │ │ └── CMakeLists.txt │ │ └── test_list.py │ ├── DistGeomHelpers │ │ ├── Wrap │ │ │ ├── test_list.py │ │ │ └── CMakeLists.txt │ │ └── test_list.py │ ├── ShapeHelpers │ │ ├── Wrap │ │ │ ├── test_list.py │ │ │ └── CMakeLists.txt │ │ ├── test_list.py │ │ └── CMakeLists.txt │ ├── SLNParse │ │ ├── Wrap │ │ │ ├── test_list.py │ │ │ └── CMakeLists.txt │ │ └── test_list.py │ ├── ChemReactions │ │ ├── Wrap │ │ │ ├── test_list.py │ │ │ └── CMakeLists.txt │ │ └── test_list.py │ ├── Wrap │ │ ├── test_list.py │ │ ├── test_data │ │ │ └── easy_smiles.txt │ │ ├── rdmolops.h │ │ ├── rdmolfiles.h │ │ └── rdchem.h │ ├── GraphMol.cpp │ └── GraphMol.h ├── Query │ ├── testExecs │ │ └── .cvskeep │ ├── test_list.py │ └── CMakeLists.txt ├── RDGeneral │ ├── testExecs │ │ └── .cvskeep │ ├── test_list.py │ └── versions.h.cmake ├── DataManip │ ├── MetricMatrixCalc │ │ ├── testExecs │ │ │ └── .cvskeep │ │ ├── CMakeLists.txt │ │ ├── test_list.py │ │ └── Wrap │ │ │ ├── test_list.py │ │ │ └── CMakeLists.txt │ └── CMakeLists.txt ├── ML │ ├── Cluster │ │ ├── CMakeLists.txt │ │ └── Murtagh │ │ │ └── CMakeLists.txt │ ├── FeatureSelect │ │ ├── CMakeLists.txt │ │ └── Wrap │ │ │ ├── test_list.py │ │ │ └── CMakeLists.txt │ ├── Data │ │ └── CMakeLists.txt │ ├── CMakeLists.txt │ ├── InfoTheory │ │ ├── Wrap │ │ │ ├── test_list.py │ │ │ └── CMakeLists.txt │ │ └── CMakeLists.txt │ └── test_list.py ├── Demos │ ├── RDKit │ │ ├── Basement │ │ │ ├── xpcom │ │ │ │ ├── demo │ │ │ │ │ ├── rd.js │ │ │ │ │ └── sorttable.js │ │ │ │ ├── IRDKit.xpt │ │ │ │ ├── RDKitImpl.h │ │ │ │ └── RDMolImpl.h │ │ │ ├── BinaryIO │ │ │ │ ├── test_data │ │ │ │ │ └── triazine.mol.gz │ │ │ │ ├── test_list.py │ │ │ │ └── Makefile │ │ │ └── TemplEnum │ │ │ │ └── Makefile │ │ ├── GettingStarted │ │ │ └── CMakeLists.txt │ │ └── Draw │ │ │ └── qtDemo │ │ │ └── qtdraw_demo.pro │ └── boost │ │ ├── cross_module │ │ ├── readme.txt │ │ ├── test.py │ │ ├── moda.cpp │ │ ├── mods.h │ │ └── modb.cpp │ │ ├── any_container │ │ └── Makefile │ │ ├── overloads │ │ └── test.py │ │ ├── numpy │ │ └── test.py │ │ ├── cross_mod_err │ │ └── moduleB.cpp │ │ └── smartPtrsAndIters │ │ └── setup.py ├── Features │ ├── CMakeLists.txt │ ├── test_list.py │ └── Feature.cpp ├── Geometry │ ├── testData │ │ └── grid1.bin │ ├── Wrap │ │ ├── test_list.py │ │ └── CMakeLists.txt │ ├── test_list.py │ └── Transform.h ├── DataStructs │ ├── testData │ │ └── test1.bin │ ├── Wrap │ │ ├── testData │ │ │ ├── isiv.pkl │ │ │ └── lsiv.pkl │ │ ├── DataStructs.h │ │ └── test_list.py │ └── test_list.py ├── PgSQL │ └── rdkit │ │ ├── rdkit.control │ │ └── sql │ │ └── inchi.sql ├── RDBoost │ └── Wrap │ │ └── CMakeLists.txt ├── ForceField │ ├── Wrap │ │ └── CMakeLists.txt │ └── test_list.py ├── JavaWrappers │ └── DiversityPick.i ├── ChemicalFeatures │ ├── Wrap │ │ ├── testData │ │ │ ├── feat.pkl │ │ │ └── featv2.pkl │ │ ├── test_list.py │ │ └── CMakeLists.txt │ ├── test_list.py │ └── CMakeLists.txt ├── Catalogs │ ├── CMakeLists.txt │ ├── Catalog.cpp │ ├── CatalogParams.cpp │ └── CatalogEntry.cpp ├── Numerics │ ├── Alignment │ │ ├── CMakeLists.txt │ │ ├── Wrap │ │ │ ├── test_list.py │ │ │ └── CMakeLists.txt │ │ └── test_list.py │ ├── EigenSolvers │ │ ├── test_list.py │ │ └── CMakeLists.txt │ ├── Optimizer │ │ ├── CMakeLists.txt │ │ ├── test_list.py │ │ ├── BFGSOpt.cpp │ │ └── LinearSearch.cpp │ ├── CMakeLists.txt │ └── test_list.py ├── doxygen │ ├── rdkdocs_footer.html │ └── rdkdocs_header.html ├── DistGeom │ ├── Wrap │ │ ├── test_list.py │ │ └── CMakeLists.txt │ └── test_list.py └── SimDivPickers │ ├── Wrap │ ├── test_list.py │ └── CMakeLists.txt │ ├── CMakeLists.txt │ └── MaxMinPicker.cpp ├── Data ├── RDData.sqlt ├── RDTests.sqlt ├── SmartsLib │ └── tests │ │ ├── mols.1000.pkl.gz │ │ └── fps.1000.counts.pkl.gz └── DTDs │ └── validate.py ├── Docs ├── Book │ ├── RDKit.pdf │ ├── images │ │ ├── indole1.png │ │ ├── cdk2_mol1.png │ │ ├── cdk2_mol2.png │ │ ├── picture_0.png │ │ ├── picture_1.png │ │ ├── picture_2.png │ │ ├── picture_3.png │ │ ├── picture_4.png │ │ ├── picture_5.png │ │ ├── picture_6.png │ │ ├── picture_7.png │ │ ├── picture_8.png │ │ ├── picture_9.png │ │ ├── cdk2_molgrid.png │ │ ├── picture_10.jpg │ │ └── cdk2_molgrid_aligned.png │ └── data │ │ ├── actives_5ht3.sdf.gz │ │ └── bzr.smi ├── Images │ ├── logo.ai │ ├── logo.png │ ├── logo.lrg.png │ └── wiki │ │ └── morganfp_atomenv1.png ├── Design │ ├── Query.dia │ ├── RDKit.dia │ └── RDUtils.dia ├── RDKit_Overview.odp ├── RDKit_Overview.pdf ├── Programs │ └── RDPharm3D │ │ ├── Icon.ico │ │ ├── RDPharm3D.chm │ │ ├── References.htm │ │ ├── Refine-shot1.jpg │ │ ├── Refine-shot2.jpg │ │ ├── AddPoints-shot1.jpg │ │ ├── AddPoints-shot2.jpg │ │ ├── AddPoints-shot3.jpg │ │ ├── RDPharm3D-Splash.jpg │ │ ├── Index.hhk │ │ └── index.htm ├── Code │ ├── Chem │ │ ├── Pharm2D.triangles.ai │ │ ├── Pharm2D.signatures.ai │ │ ├── Pharm2D.signatures.jpg │ │ └── Pharm2D.triangles.jpg │ └── index.html └── Analysis │ ├── ForceField │ ├── UFF Parameters.ods │ └── ForceFieldTerms.new.odt │ └── Descriptors │ └── Correlations │ ├── DrugLikeT80_CorrMat.png │ ├── LeadLikeT80_CorrMat.png │ └── FragmentLikeT80_CorrMat.png ├── External ├── cmim-1.0 │ ├── README │ ├── cmim.cc │ ├── misc.cc │ ├── misc.h │ ├── test.sh │ ├── CMakeLists.txt │ ├── classifier.h │ ├── classifier.cc │ ├── fastentropy.cc │ ├── fastentropy.h │ └── create_samples.cc ├── CMakeLists.txt ├── AvalonTools │ ├── Wrap │ │ ├── test_list.py │ │ └── CMakeLists.txt │ └── test_list.py └── INCHI-API │ └── Wrap │ └── CMakeLists.txt ├── Regress └── Data │ ├── queries.txt.gz │ ├── fptest.pgdump.gz │ ├── mols.1000.sdf.gz │ └── mols.1000.txt.gz ├── Projects ├── CMakeLists.txt ├── DbCLI │ ├── test_list.py │ └── testData │ │ └── README └── test_list.py ├── Contrib ├── mmpa │ ├── sample_mmps_maxratio.csv │ ├── sample_cansmirks.txt │ ├── sample_smirks.txt │ ├── sample_mmps_maxheavy.csv │ ├── sample.smi │ └── sample_mmps_sym_maxheavy.csv └── PBF │ └── Makefile ├── rdkit-config-version.cmake.in ├── rdkit-config.cmake.in └── Web └── RDExtras └── .htaccess /rdkit/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /rdkit/utils/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Code/GraphMol/libs/.cvskeep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /rdkit/Avalon/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /rdkit/Chem/MolDb/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /rdkit/Logger/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /rdkit/ML/Cluster/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /rdkit/ML/Data/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /rdkit/ML/MLUtils/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /rdkit/ML/Neural/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /rdkit/ML/SLT/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /rdkit/ML/Scoring/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /rdkit/sping/Qt/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Code/GraphMol/testExecs/.cvskeep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Code/Query/testExecs/.cvskeep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Code/RDGeneral/testExecs/.cvskeep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /rdkit/Chem/AtomPairs/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /rdkit/Chem/ChemUtils/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /rdkit/Chem/FeatMaps/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /rdkit/Chem/Features/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /rdkit/Chem/Pharm3D/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /rdkit/Chem/Scaffolds/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /rdkit/Chem/Subshape/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /rdkit/Chem/Suppliers/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /rdkit/Dbase/Pubmed/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /rdkit/ML/Composite/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /rdkit/ML/Descriptors/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /rdkit/ML/ModelPackage/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /rdkit/sping/ReportLab/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Code/GraphMol/Depictor/testExecs/.cvskeep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Code/GraphMol/Subgraphs/testExecs/.cvskeep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Code/GraphMol/Substruct/testExecs/.cvskeep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /rdkit/VLib/__init__.py: -------------------------------------------------------------------------------- 1 | __all__ = [] 2 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/testExecs/.cvskeep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/empty2.sdf: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Code/GraphMol/Fingerprints/testExecs/.cvskeep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Code/GraphMol/FragCatalog/testExecs/.cvskeep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Code/GraphMol/MolTransforms/testExecs/.cvskeep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Code/GraphMol/SmilesParse/regress.txt: -------------------------------------------------------------------------------- 1 | test.exe -------------------------------------------------------------------------------- /Code/GraphMol/SmilesParse/testExecs/.cvskeep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /rdkit/sping/util/__init__.py: -------------------------------------------------------------------------------- 1 | # dummy for now 2 | -------------------------------------------------------------------------------- /Code/DataManip/MetricMatrixCalc/testExecs/.cvskeep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Code/GraphMol/Substruct/regress.txt: -------------------------------------------------------------------------------- 1 | test1.exe 2 | -------------------------------------------------------------------------------- /rdkit/Chem/test_data/Crippen_contribs_regress.pkl: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /rdkit/DataManip/__init__.py: -------------------------------------------------------------------------------- 1 | __all__=['Metric'] 2 | -------------------------------------------------------------------------------- /rdkit/sping/PDF/__init__.py: -------------------------------------------------------------------------------- 1 | from pidPDF import * 2 | -------------------------------------------------------------------------------- /rdkit/sping/TK/__init__.py: -------------------------------------------------------------------------------- 1 | from pidTK import * 2 | -------------------------------------------------------------------------------- /rdkit/sping/WX/__init__.py: -------------------------------------------------------------------------------- 1 | from pidWX import * 2 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/empty.sdf: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | -------------------------------------------------------------------------------- /Code/ML/Cluster/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | add_subdirectory(Murtagh) 2 | -------------------------------------------------------------------------------- /Code/ML/FeatureSelect/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | add_subdirectory(Wrap) 2 | -------------------------------------------------------------------------------- /rdkit/DistanceGeometry/__init__.py: -------------------------------------------------------------------------------- 1 | from DistGeom import * 2 | -------------------------------------------------------------------------------- /rdkit/ForceField/__init__.py: -------------------------------------------------------------------------------- 1 | from rdForceField import * 2 | -------------------------------------------------------------------------------- /rdkit/sping/tests/__init__.py: -------------------------------------------------------------------------------- 1 | # dummy package indicator 2 | -------------------------------------------------------------------------------- /Code/DataManip/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | add_subdirectory(MetricMatrixCalc) 2 | -------------------------------------------------------------------------------- /rdkit/sping/PIL/__init__.py: -------------------------------------------------------------------------------- 1 | # package 2 | from pidPIL import * 3 | -------------------------------------------------------------------------------- /rdkit/sping/PS/__init__.py: -------------------------------------------------------------------------------- 1 | # package 2 | from pidPS import * 3 | -------------------------------------------------------------------------------- /Code/Demos/RDKit/Basement/xpcom/demo/rd.js: -------------------------------------------------------------------------------- 1 | var rdMonkeyLock=true; 2 | -------------------------------------------------------------------------------- /Code/GraphMol/ChemTransforms/testData/query_file2.txt: -------------------------------------------------------------------------------- 1 | AcidChloride 2 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/empty.smi: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | -------------------------------------------------------------------------------- /rdkit/sping/Pyart/__init__.py: -------------------------------------------------------------------------------- 1 | # sping:: pyart 2 | 3 | from pidPyart import * 4 | -------------------------------------------------------------------------------- /rdkit/sping/SVG/__init__.py: -------------------------------------------------------------------------------- 1 | # simple __init__.py 2 | 3 | from pidSVG import * 4 | -------------------------------------------------------------------------------- /Data/RDData.sqlt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Data/RDData.sqlt -------------------------------------------------------------------------------- /Data/RDTests.sqlt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Data/RDTests.sqlt -------------------------------------------------------------------------------- /Code/Features/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | rdkit_headers(Feature.h 2 | DEST Features) 3 | -------------------------------------------------------------------------------- /Code/GraphMol/regress.txt: -------------------------------------------------------------------------------- 1 | test1.exe 2 | querytest.exe 3 | molopstest.exe 4 | itertest.exe 5 | -------------------------------------------------------------------------------- /Docs/Book/RDKit.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Book/RDKit.pdf -------------------------------------------------------------------------------- /Docs/Images/logo.ai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Images/logo.ai -------------------------------------------------------------------------------- /Docs/Images/logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Images/logo.png -------------------------------------------------------------------------------- /rdkit/utils/12h.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/utils/12h.gif -------------------------------------------------------------------------------- /Docs/Design/Query.dia: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Design/Query.dia -------------------------------------------------------------------------------- /Docs/Design/RDKit.dia: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Design/RDKit.dia -------------------------------------------------------------------------------- /Docs/Design/RDUtils.dia: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Design/RDUtils.dia -------------------------------------------------------------------------------- /Docs/RDKit_Overview.odp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/RDKit_Overview.odp -------------------------------------------------------------------------------- /Docs/RDKit_Overview.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/RDKit_Overview.pdf -------------------------------------------------------------------------------- /rdkit/Dbase/test_data/dbtest.csv: -------------------------------------------------------------------------------- 1 | int col,floatCol,strCol 2 | 1,1,1 3 | 2,2.4,1 4 | 3,3,fiib 5 | -------------------------------------------------------------------------------- /rdkit/utils/test1.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/utils/test1.gif -------------------------------------------------------------------------------- /rdkit/utils/test2.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/utils/test2.gif -------------------------------------------------------------------------------- /rdkit/utils/test3.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/utils/test3.gif -------------------------------------------------------------------------------- /Docs/Images/logo.lrg.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Images/logo.lrg.png -------------------------------------------------------------------------------- /External/cmim-1.0/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/External/cmim-1.0/README -------------------------------------------------------------------------------- /External/cmim-1.0/cmim.cc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/External/cmim-1.0/cmim.cc -------------------------------------------------------------------------------- /External/cmim-1.0/misc.cc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/External/cmim-1.0/misc.cc -------------------------------------------------------------------------------- /External/cmim-1.0/misc.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/External/cmim-1.0/misc.h -------------------------------------------------------------------------------- /External/cmim-1.0/test.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/External/cmim-1.0/test.sh -------------------------------------------------------------------------------- /rdkit/ML/FeatureSelect/__init__.py: -------------------------------------------------------------------------------- 1 | from rdkit import DataStructs 2 | from rdFeatSelect import * 3 | -------------------------------------------------------------------------------- /rdkit/sping/PDF/pdfdoc.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PDF/pdfdoc.py -------------------------------------------------------------------------------- /Docs/Book/images/indole1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Book/images/indole1.png -------------------------------------------------------------------------------- /Regress/Data/queries.txt.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Regress/Data/queries.txt.gz -------------------------------------------------------------------------------- /rdkit/Chem/Draw/FreeSans.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/Chem/Draw/FreeSans.ttf -------------------------------------------------------------------------------- /rdkit/Dbase/Pubmed/test_data/counts.xml: -------------------------------------------------------------------------------- 1 | 2 | 2 3 | 4 | -------------------------------------------------------------------------------- /rdkit/sping/PDF/pdfgeom.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PDF/pdfgeom.py -------------------------------------------------------------------------------- /rdkit/sping/tests/pstests.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/tests/pstests.py -------------------------------------------------------------------------------- /rdkit/utils/pydoc_local.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/utils/pydoc_local.py -------------------------------------------------------------------------------- /Code/Demos/boost/cross_module/readme.txt: -------------------------------------------------------------------------------- 1 | Demo showing how to deal with BPL-wrapped objects between modules. 2 | -------------------------------------------------------------------------------- /Docs/Book/images/cdk2_mol1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Book/images/cdk2_mol1.png -------------------------------------------------------------------------------- /Docs/Book/images/cdk2_mol2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Book/images/cdk2_mol2.png -------------------------------------------------------------------------------- /Docs/Book/images/picture_0.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Book/images/picture_0.png -------------------------------------------------------------------------------- /Docs/Book/images/picture_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Book/images/picture_1.png -------------------------------------------------------------------------------- /Docs/Book/images/picture_2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Book/images/picture_2.png -------------------------------------------------------------------------------- /Docs/Book/images/picture_3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Book/images/picture_3.png -------------------------------------------------------------------------------- /Docs/Book/images/picture_4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Book/images/picture_4.png -------------------------------------------------------------------------------- /Docs/Book/images/picture_5.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Book/images/picture_5.png -------------------------------------------------------------------------------- /Docs/Book/images/picture_6.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Book/images/picture_6.png -------------------------------------------------------------------------------- /Docs/Book/images/picture_7.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Book/images/picture_7.png -------------------------------------------------------------------------------- /Docs/Book/images/picture_8.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Book/images/picture_8.png -------------------------------------------------------------------------------- /Docs/Book/images/picture_9.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Book/images/picture_9.png -------------------------------------------------------------------------------- /External/cmim-1.0/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | add_library(fastentropy STATIC fastentropy.cc misc.cc) 2 | 3 | 4 | 5 | 6 | -------------------------------------------------------------------------------- /External/cmim-1.0/classifier.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/External/cmim-1.0/classifier.h -------------------------------------------------------------------------------- /Regress/Data/fptest.pgdump.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Regress/Data/fptest.pgdump.gz -------------------------------------------------------------------------------- /Regress/Data/mols.1000.sdf.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Regress/Data/mols.1000.sdf.gz -------------------------------------------------------------------------------- /Regress/Data/mols.1000.txt.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Regress/Data/mols.1000.txt.gz -------------------------------------------------------------------------------- /rdkit/Numerics/__init__.py: -------------------------------------------------------------------------------- 1 | """ A module for Numerics stuff 2 | 3 | """ 4 | import rdAlignment as Alignment 5 | -------------------------------------------------------------------------------- /Code/Geometry/testData/grid1.bin: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Code/Geometry/testData/grid1.bin -------------------------------------------------------------------------------- /Docs/Book/images/cdk2_molgrid.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Book/images/cdk2_molgrid.png -------------------------------------------------------------------------------- /Docs/Book/images/picture_10.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Book/images/picture_10.jpg -------------------------------------------------------------------------------- /Docs/Programs/RDPharm3D/Icon.ico: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Programs/RDPharm3D/Icon.ico -------------------------------------------------------------------------------- /External/cmim-1.0/classifier.cc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/External/cmim-1.0/classifier.cc -------------------------------------------------------------------------------- /External/cmim-1.0/fastentropy.cc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/External/cmim-1.0/fastentropy.cc -------------------------------------------------------------------------------- /External/cmim-1.0/fastentropy.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/External/cmim-1.0/fastentropy.h -------------------------------------------------------------------------------- /rdkit/Dbase/test_data/dbtest.nulls.csv: -------------------------------------------------------------------------------- 1 | int col,floatCol,strCol 2 | 1,1,1 3 | 2,2.4,1 4 | 3,3,fiib 5 | 4,NA,foo 6 | -------------------------------------------------------------------------------- /rdkit/Dbase/test_data/dbtest.xls: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/Dbase/test_data/dbtest.xls -------------------------------------------------------------------------------- /rdkit/Dbase/test_data/rdtest.sql: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/Dbase/test_data/rdtest.sql -------------------------------------------------------------------------------- /rdkit/ML/InfoTheory/__init__.py: -------------------------------------------------------------------------------- 1 | """ Information Theory functionality 2 | 3 | """ 4 | from rdInfoTheory import * 5 | -------------------------------------------------------------------------------- /Code/DataStructs/testData/test1.bin: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Code/DataStructs/testData/test1.bin -------------------------------------------------------------------------------- /Docs/Book/data/actives_5ht3.sdf.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Book/data/actives_5ht3.sdf.gz -------------------------------------------------------------------------------- /Docs/Code/Chem/Pharm2D.triangles.ai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Code/Chem/Pharm2D.triangles.ai -------------------------------------------------------------------------------- /External/cmim-1.0/create_samples.cc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/External/cmim-1.0/create_samples.cc -------------------------------------------------------------------------------- /rdkit/Chem/Fingerprints/__init__.py: -------------------------------------------------------------------------------- 1 | # 2 | # Copyright (C) 2003 Greg Landrum and Rational Discovery LLC 3 | # 4 | 5 | -------------------------------------------------------------------------------- /rdkit/ML/DecTree/test_data/foo.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/ML/DecTree/test_data/foo.pdf -------------------------------------------------------------------------------- /rdkit/ML/test_data/humanoral.1.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/ML/test_data/humanoral.1.pkl -------------------------------------------------------------------------------- /rdkit/ML/test_data/humanoral.2.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/ML/test_data/humanoral.2.pkl -------------------------------------------------------------------------------- /Data/SmartsLib/tests/mols.1000.pkl.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Data/SmartsLib/tests/mols.1000.pkl.gz -------------------------------------------------------------------------------- /Docs/Code/Chem/Pharm2D.signatures.ai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Code/Chem/Pharm2D.signatures.ai -------------------------------------------------------------------------------- /Docs/Code/Chem/Pharm2D.signatures.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Code/Chem/Pharm2D.signatures.jpg -------------------------------------------------------------------------------- /Docs/Code/Chem/Pharm2D.triangles.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Code/Chem/Pharm2D.triangles.jpg -------------------------------------------------------------------------------- /Docs/Images/wiki/morganfp_atomenv1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Images/wiki/morganfp_atomenv1.png -------------------------------------------------------------------------------- /Docs/Programs/RDPharm3D/RDPharm3D.chm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Programs/RDPharm3D/RDPharm3D.chm -------------------------------------------------------------------------------- /Docs/Programs/RDPharm3D/References.htm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Programs/RDPharm3D/References.htm -------------------------------------------------------------------------------- /External/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | add_subdirectory(cmim-1.0) 2 | add_subdirectory(INCHI-API) 3 | add_subdirectory(AvalonTools) 4 | 5 | -------------------------------------------------------------------------------- /rdkit/Dbase/test_data/dbtest.nulls.xls: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/Dbase/test_data/dbtest.nulls.xls -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/courier-8.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/courier-8.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/courier-8.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/courier-8.pil -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/symbol-10.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/symbol-10.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/symbol-10.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/symbol-10.pil -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/symbol-12.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/symbol-12.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/symbol-12.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/symbol-12.pil -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/symbol-14.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/symbol-14.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/symbol-14.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/symbol-14.pil -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/symbol-18.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/symbol-18.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/symbol-18.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/symbol-18.pil -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/symbol-24.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/symbol-24.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/symbol-24.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/symbol-24.pil -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/symbol-8.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/symbol-8.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/symbol-8.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/symbol-8.pil -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/times-10.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/times-10.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/times-10.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/times-10.pil -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/times-12.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/times-12.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/times-12.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/times-12.pil -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/times-14.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/times-14.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/times-14.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/times-14.pil -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/times-18.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/times-18.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/times-18.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/times-18.pil -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/times-24.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/times-24.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/times-24.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/times-24.pil -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/times-8.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/times-8.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/times-8.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/times-8.pil -------------------------------------------------------------------------------- /Docs/Programs/RDPharm3D/Refine-shot1.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Programs/RDPharm3D/Refine-shot1.jpg -------------------------------------------------------------------------------- /Docs/Programs/RDPharm3D/Refine-shot2.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Programs/RDPharm3D/Refine-shot2.jpg -------------------------------------------------------------------------------- /rdkit/SimDivFilters/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","SimilarityPickers.py",{}), 4 | ] 5 | 6 | longTests=[ 7 | ] 8 | -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/courier-10.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/courier-10.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/courier-10.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/courier-10.pil -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/courier-12.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/courier-12.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/courier-12.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/courier-12.pil -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/courier-14.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/courier-14.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/courier-14.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/courier-14.pil -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/courier-18.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/courier-18.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/courier-18.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/courier-18.pil -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/courier-24.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/courier-24.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/courier-24.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/courier-24.pil -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/courier-8.pil.1: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/courier-8.pil.1 -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/helvetica-8.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/helvetica-8.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/helvetica-8.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/helvetica-8.pil -------------------------------------------------------------------------------- /Code/Demos/RDKit/Basement/xpcom/IRDKit.xpt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Code/Demos/RDKit/Basement/xpcom/IRDKit.xpt -------------------------------------------------------------------------------- /Code/GraphMol/test_data/canonSmiles.v1.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Code/GraphMol/test_data/canonSmiles.v1.pkl -------------------------------------------------------------------------------- /Code/GraphMol/test_data/canonSmiles.v2.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Code/GraphMol/test_data/canonSmiles.v2.pkl -------------------------------------------------------------------------------- /Data/SmartsLib/tests/fps.1000.counts.pkl.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Data/SmartsLib/tests/fps.1000.counts.pkl.gz -------------------------------------------------------------------------------- /Docs/Analysis/ForceField/UFF Parameters.ods: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Analysis/ForceField/UFF Parameters.ods -------------------------------------------------------------------------------- /Docs/Book/images/cdk2_molgrid_aligned.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Book/images/cdk2_molgrid_aligned.png -------------------------------------------------------------------------------- /Docs/Programs/RDPharm3D/AddPoints-shot1.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Programs/RDPharm3D/AddPoints-shot1.jpg -------------------------------------------------------------------------------- /Docs/Programs/RDPharm3D/AddPoints-shot2.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Programs/RDPharm3D/AddPoints-shot2.jpg -------------------------------------------------------------------------------- /Docs/Programs/RDPharm3D/AddPoints-shot3.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Programs/RDPharm3D/AddPoints-shot3.jpg -------------------------------------------------------------------------------- /rdkit/Chem/test_data/buildingblocks.smi.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/Chem/test_data/buildingblocks.smi.gz -------------------------------------------------------------------------------- /rdkit/ML/DecTree/test_data/cdk2-few.pkl.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/ML/DecTree/test_data/cdk2-few.pkl.gz -------------------------------------------------------------------------------- /rdkit/ML/test_data/ferromag_filt_10_3.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/ML/test_data/ferromag_filt_10_3.pkl -------------------------------------------------------------------------------- /rdkit/VLib/NodeLib/__init__.py: -------------------------------------------------------------------------------- 1 | __all__=['SmartsMolFilter','SDSupply','SmartsRemover','SmilesDupeFilter', 2 | 'SmilesOutput'] 3 | -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/courier-bold-8.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/courier-bold-8.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/courier-bold-8.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/courier-bold-8.pil -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/helvetica-10.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/helvetica-10.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/helvetica-10.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/helvetica-10.pil -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/helvetica-12.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/helvetica-12.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/helvetica-12.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/helvetica-12.pil -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/helvetica-14.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/helvetica-14.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/helvetica-14.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/helvetica-14.pil -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/helvetica-18.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/helvetica-18.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/helvetica-18.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/helvetica-18.pil -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/helvetica-24.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/helvetica-24.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/helvetica-24.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/helvetica-24.pil -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/times-bold-10.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/times-bold-10.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/times-bold-10.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/times-bold-10.pil -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/times-bold-12.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/times-bold-12.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/times-bold-12.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/times-bold-12.pil -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/times-bold-14.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/times-bold-14.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/times-bold-14.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/times-bold-14.pil -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/times-bold-18.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/times-bold-18.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/times-bold-18.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/times-bold-18.pil -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/times-bold-24.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/times-bold-24.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/times-bold-24.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/times-bold-24.pil -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/times-bold-8.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/times-bold-8.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/times-bold-8.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/times-bold-8.pil -------------------------------------------------------------------------------- /Code/GraphMol/MolTransforms/ReadMe: -------------------------------------------------------------------------------- 1 | 2 | These are files for doing geometric transformations (rotation, 3 | scaling, etc.) on molecules. 4 | -------------------------------------------------------------------------------- /Docs/Programs/RDPharm3D/RDPharm3D-Splash.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Programs/RDPharm3D/RDPharm3D-Splash.jpg -------------------------------------------------------------------------------- /rdkit/Chem/test_data/pubchem-hard-set.sdf.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/Chem/test_data/pubchem-hard-set.sdf.gz -------------------------------------------------------------------------------- /rdkit/Dbase/Pubmed/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","Searches.py",{}), 4 | ] 5 | 6 | 7 | longTests=[ 8 | 9 | ] 10 | -------------------------------------------------------------------------------- /rdkit/Geometry/__init__.py: -------------------------------------------------------------------------------- 1 | """ A module for Geometry stuff 2 | 3 | """ 4 | from rdkit import DataStructs 5 | from rdGeometry import * 6 | -------------------------------------------------------------------------------- /rdkit/Logger/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","UnitTestLogger.py",{}), 4 | ] 5 | 6 | 7 | 8 | longTests=[ 9 | ] 10 | -------------------------------------------------------------------------------- /rdkit/ML/KNN/__init__.py: -------------------------------------------------------------------------------- 1 | # copyright 2000, greg landrum 2 | """ 3 | 4 | Here is the implementation for K-nearest neighbors 5 | 6 | """ 7 | -------------------------------------------------------------------------------- /rdkit/ML/test_data/ferromag_shuffle_10_3.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/ML/test_data/ferromag_shuffle_10_3.pkl -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/courier-bold-10.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/courier-bold-10.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/courier-bold-10.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/courier-bold-10.pil -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/courier-bold-12.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/courier-bold-12.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/courier-bold-12.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/courier-bold-12.pil -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/courier-bold-14.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/courier-bold-14.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/courier-bold-14.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/courier-bold-14.pil -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/courier-bold-18.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/courier-bold-18.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/courier-bold-18.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/courier-bold-18.pil -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/courier-bold-24.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/courier-bold-24.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/courier-bold-24.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/courier-bold-24.pil -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/helvetica-bold-8.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/helvetica-bold-8.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pil -------------------------------------------------------------------------------- /Docs/Analysis/ForceField/ForceFieldTerms.new.odt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Analysis/ForceField/ForceFieldTerms.new.odt -------------------------------------------------------------------------------- /rdkit/Chem/AtomPairs/test_data/mols1000.pkl.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/Chem/AtomPairs/test_data/mols1000.pkl.gz -------------------------------------------------------------------------------- /rdkit/Chem/MolCatalog.py: -------------------------------------------------------------------------------- 1 | # $Id$ 2 | # 3 | # Copyright (C) 2006 Greg Landrum 4 | # 5 | from rdMolCatalog import * 6 | 7 | 8 | 9 | -------------------------------------------------------------------------------- /rdkit/ML/Composite/test_data/composite_base.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/ML/Composite/test_data/composite_base.pkl -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/helvetica-bold-10.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/helvetica-bold-10.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pil -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/helvetica-bold-12.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/helvetica-bold-12.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pil -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/helvetica-bold-14.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/helvetica-bold-14.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pil -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/helvetica-bold-18.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/helvetica-bold-18.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pil -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/helvetica-bold-24.pbm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pbm -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/helvetica-bold-24.pil: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pil -------------------------------------------------------------------------------- /Code/Demos/RDKit/Basement/xpcom/demo/sorttable.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Code/Demos/RDKit/Basement/xpcom/demo/sorttable.js -------------------------------------------------------------------------------- /rdkit/Chem/AtomPairs/test_data/mols1000.aps.pkl.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/Chem/AtomPairs/test_data/mols1000.aps.pkl.gz -------------------------------------------------------------------------------- /rdkit/Chem/AtomPairs/test_data/mols1000.tts.pkl.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/Chem/AtomPairs/test_data/mols1000.tts.pkl.gz -------------------------------------------------------------------------------- /Projects/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | add_pytest(pythonTestDbCLI 2 | ${CMAKE_CURRENT_SOURCE_DIR}/test_list.py --testDir ${CMAKE_CURRENT_SOURCE_DIR} ) 3 | 4 | -------------------------------------------------------------------------------- /rdkit/Chem/Pharm3D/test_data/cdk2-syn-clip100.pkl.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/Chem/Pharm3D/test_data/cdk2-syn-clip100.pkl.gz -------------------------------------------------------------------------------- /rdkit/ML/Composite/test_data/composite_base.both.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/ML/Composite/test_data/composite_base.both.pkl -------------------------------------------------------------------------------- /rdkit/ML/ModelPackage/test_data/Jan9_build3_model.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/ML/ModelPackage/test_data/Jan9_build3_model.pkl -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/NCI_aids_few.sdf.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Code/GraphMol/FileParsers/test_data/NCI_aids_few.sdf.gz -------------------------------------------------------------------------------- /Contrib/mmpa/sample_mmps_maxratio.csv: -------------------------------------------------------------------------------- 1 | Nc1ccc(-c2cc3ccccc3oc2=O)cc1,O=c1oc2ccccc2cc1-c1ccc(O)cc1,310860,4055843,[*:1]N>>[*:1]O,[*:1]c1ccc(-c2cc3ccccc3oc2=O)cc1 2 | -------------------------------------------------------------------------------- /rdkit/ML/Composite/test_data/composite_base.neural.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/ML/Composite/test_data/composite_base.neural.pkl -------------------------------------------------------------------------------- /rdkit/ML/Composite/test_data/composite_base.others.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/ML/Composite/test_data/composite_base.others.pkl -------------------------------------------------------------------------------- /rdkit/ML/Composite/test_data/composite_base.unitnet.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/ML/Composite/test_data/composite_base.unitnet.pkl -------------------------------------------------------------------------------- /rdkit/ML/Composite/test_data/composite_plus_neural.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/ML/Composite/test_data/composite_plus_neural.pkl -------------------------------------------------------------------------------- /rdkit/ML/Composite/test_data/composite_base.others.net.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/ML/Composite/test_data/composite_base.others.net.pkl -------------------------------------------------------------------------------- /rdkit/ML/Composite/test_data/composite_base.unittree.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/ML/Composite/test_data/composite_base.unittree.pkl -------------------------------------------------------------------------------- /rdkit/utils/retest.txt: -------------------------------------------------------------------------------- 1 | #ignore 2 | foo bar baz grn 3 | foo #bar baz grn 4 | #ignore 5 | foo bar # baz grn 6 | foo bar # baz grn # 7 | foo bar baz grn # 8 | #ignore 9 | -------------------------------------------------------------------------------- /Code/Demos/RDKit/Basement/BinaryIO/test_data/triazine.mol.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Code/Demos/RDKit/Basement/BinaryIO/test_data/triazine.mol.gz -------------------------------------------------------------------------------- /Data/DTDs/validate.py: -------------------------------------------------------------------------------- 1 | import pyRXP 2 | import sys 3 | 4 | parser = pyRXP.Parser() 5 | res = parser.parse(open(sys.argv[1],'r').read()) 6 | if res: 7 | print 'SUCCESS' 8 | -------------------------------------------------------------------------------- /rdkit/ML/Composite/test_data/composite_base.others.both.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/ML/Composite/test_data/composite_base.others.both.pkl -------------------------------------------------------------------------------- /Code/PgSQL/rdkit/rdkit.control: -------------------------------------------------------------------------------- 1 | comment = 'Cheminformatics functionality for PostgreSQL.' 2 | default_version = '3.3' 3 | module_pathname = '$libdir/rdkit' 4 | relocatable = true -------------------------------------------------------------------------------- /Docs/Analysis/Descriptors/Correlations/DrugLikeT80_CorrMat.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_CorrMat.png -------------------------------------------------------------------------------- /Docs/Analysis/Descriptors/Correlations/LeadLikeT80_CorrMat.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Analysis/Descriptors/Correlations/LeadLikeT80_CorrMat.png -------------------------------------------------------------------------------- /rdkit/ML/Composite/test_data/composite_base.others.neural.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/rdkit/ML/Composite/test_data/composite_base.others.neural.pkl -------------------------------------------------------------------------------- /Contrib/mmpa/sample_cansmirks.txt: -------------------------------------------------------------------------------- 1 | [*:1]c1ccc([*:2])o1>>[*:1]c1ccc([*:2])cc1 s1 2 | [*:1]c1ccc([*:2])o1>>[*:1]c1ccc([*:2])cc1 s2 3 | [*:1]c1ccc([*:2])o1>>[*:1]c1ccc([*:2])cc1 s3 4 | -------------------------------------------------------------------------------- /Contrib/mmpa/sample_smirks.txt: -------------------------------------------------------------------------------- 1 | [*:2]c1ccc([*:1])o1>>[*:1]c1ccc([*:2])cc1 s1 2 | [*:1]c1ccc([*:2])o1>>[*:2]c1ccc([*:1])cc1 s2 3 | [*:1]c1ccc([*:2])o1>>[*:2]C1=CC=C([*:1])C=C1 s3 4 | -------------------------------------------------------------------------------- /rdkit/ML/NaiveBayes/__init__.py: -------------------------------------------------------------------------------- 1 | # copyright 2003, Rational Discovery LLC 2 | """ 3 | 4 | An implementation of the Naive Bayes Classifier 5 | 6 | """ 7 | from rdkit import rdBase 8 | -------------------------------------------------------------------------------- /Code/GraphMol/MolDrawing/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | rdkit_headers(DrawingToCairo.h 2 | DrawingToSVG.h 3 | MolDrawing.h 4 | DEST GraphMol/MolDrawing) 5 | 6 | -------------------------------------------------------------------------------- /Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_CorrMat.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rdkit/rdkit-orig/HEAD/Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_CorrMat.png -------------------------------------------------------------------------------- /Code/GraphMol/SmilesParse/runflex.sh: -------------------------------------------------------------------------------- 1 | 2 | bison -t -d smiles.y 3 | mv smiles.tab.c smiles.tab.cpp 4 | flex smiles.flex 5 | grep -v unistd lex.yy.c | sed s/lex.yy.c/lex.yy.cpp/ > lex.yy.cpp 6 | -------------------------------------------------------------------------------- /Code/ML/Data/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | rdkit_python_extension(cQuantize cQuantize.cpp 2 | DEST ML/Data 3 | LINK_LIBRARIES InfoTheory RDGeneral RDBoost ) 4 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/Issue3482695.sdf: -------------------------------------------------------------------------------- 1 | 2 | RDKit 3D 3 | 4 | 0 0 0 0 0 0 0 0 0 0999 V2000 5 | M END 6 | > (1) 7 | some 8 | 9 | $$$$ 10 | -------------------------------------------------------------------------------- /Code/RDBoost/Wrap/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | rdkit_python_extension(rdBase 2 | RDBase.cpp 3 | LINK_LIBRARIES 4 | RDGeneral RDBoost) 5 | 6 | -------------------------------------------------------------------------------- /rdkit/sping/__init__.py: -------------------------------------------------------------------------------- 1 | # package indicator for spin Graphics 2 | # $Id$ 3 | version_maj_number = 1.1 4 | version_min_number = 0 5 | version = "%s.%s" % (version_maj_number , version_min_number) 6 | -------------------------------------------------------------------------------- /rdkit/ML/DecTree/__init__.py: -------------------------------------------------------------------------------- 1 | # copyright 2000, greg landrum 2 | """ 3 | 4 | Here we're implementing the Decision Tree stuff found in Chapter 3 of Tom Mitchell's Machine Learning Book. 5 | 6 | """ 7 | -------------------------------------------------------------------------------- /Code/PgSQL/rdkit/sql/inchi.sql: -------------------------------------------------------------------------------- 1 | select mol_inchi('c1ccccc1'::mol); 2 | select mol_inchikey('c1ccccc1'::mol); 3 | select mol_inchi('Cc1cc(C)[n+]c(C)c1'::mol); 4 | select mol_inchikey('Cc1cc(C)[n+]c(C)c1'::mol); 5 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/cdk2_stereo.csv: -------------------------------------------------------------------------------- 1 | c1cc(Cl)ccc1c(n[o]2)nc2CSC/3=[NH+]/CCN3,mol_14069 2 | [C@@H]12/C=C\[C@@H](C(C(=O)O)C1C(=O)O)c3cccc(c23)[N+]([O-])=O,mol_12186,None,4.50,Scaffold_00,divscreen,0 3 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/missingCR.sdf: -------------------------------------------------------------------------------- 1 | 2 | RDKit 3 | 4 | 1 0 0 0 0 0 0 0 0 0999 V2000 5 | 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | M END 7 | > 8 | OK -------------------------------------------------------------------------------- /rdkit/Chem/test_data/Crippen.csv: -------------------------------------------------------------------------------- 1 | C,0.6361,6.7310 2 | C=C,0.8022,11.2540 3 | C#C,0.2494,9.8900 4 | CO,-0.3915,8.1428 5 | C=O,-0.1849,7.1210 6 | C#[O+],0.0059,5.6315 7 | C(C)(C)(C),1.6623,20.5120 8 | C(C)(C)(C)O,0.7772,21.9718 9 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/Issue269.mol: -------------------------------------------------------------------------------- 1 | 0Lv-4 2 | NextMove09291216262D 3 | 4 | 1 0 0 0 0 0 0 0 0999 V2000 5 | 0.0000 0.0000 0.0000 Lv 0 0 0 0 0 0 0 0 0 0 0 0 6 | M CHG 1 1 -4 7 | M END 8 | -------------------------------------------------------------------------------- /rdkit/ML/KNN/test_data/sample_pts.csv: -------------------------------------------------------------------------------- 1 | id,x,y,val 2 | 1,-4,3,1 3 | 2,-3,3,1.5 4 | 3,-4,2,1.5 5 | 4,-3,2,1 6 | 5,1.5,2,2 7 | 6,3,3,1 8 | 7,4,2,2 9 | 8,3,1,1 10 | 9,3,-1,-1 11 | 10,2,-2.5,-2 12 | 11,4,-2.5,-2 13 | 12,3,-4,-1 14 | -------------------------------------------------------------------------------- /Code/GraphMol/MolChemicalFeatures/test_data/featDef.txt: -------------------------------------------------------------------------------- 1 | DefineFeature HDonor1 [N,O;!H0] 2 | Family HBondDonor 3 | Weights 1.0 4 | EndFeature 5 | DefineFeature HAcceptor1 [N,O] 6 | Family HBondAcceptor 7 | Weights 1.0 8 | EndFeature 9 | -------------------------------------------------------------------------------- /Code/ForceField/Wrap/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | rdkit_python_extension(rdForceField ForceField.cpp 2 | DEST ForceField 3 | LINK_LIBRARIES ForceField Optimizer RDGeneral RDGeometryLib RDBoost) 4 | 5 | 6 | 7 | 8 | 9 | -------------------------------------------------------------------------------- /Code/GraphMol/FragCatalog/test_data/4mols.smi: -------------------------------------------------------------------------------- 1 | S1C2=C(C3=CC=CC4=C3C2=CC=C4)C5=C1C6=C7C(=CC=C6)C=CC=C57 1 2 | C1(/N2)=C/C(C=C3)=N/C3=C\C(N5)=CC=C5\C=C4/N=C(C=C4)/C=C2/C=C1 2 3 | [O-][N+]1=CC2=CC=C[O+]2[Cu]13[O+]4C=CC=C4C=[N+]3[O-] 3 4 | O=C1C=CC(=O)C=C1 4 5 | -------------------------------------------------------------------------------- /Code/Demos/boost/any_container/Makefile: -------------------------------------------------------------------------------- 1 | CXXFLAGS=-g -I$(RDBASE)/External/$(BOOSTBASE) -I$(RDBASE)/Code/GraphMol 2 | 3 | dict.exe: dict.o $(RDBASE)/Code/GraphMol/Invariant/Invariant.o 4 | g++ -o dict.exe $(CFLAGS) dict.o $(RDBASE)/Code/GraphMol/Invariant/Invariant.o -------------------------------------------------------------------------------- /rdkit/Dbase/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","UnitTestDbConnect.py",{}), 4 | ("python","UnitTestDbUtils.py",{}), 5 | ("python","UnitTestDbResultSet.py",{}), 6 | ("python","StorageUtils.py",{}), 7 | ] 8 | 9 | 10 | 11 | longTests=[ 12 | ] 13 | -------------------------------------------------------------------------------- /rdkit/sping/PIL/pilfonts/removemedium.py: -------------------------------------------------------------------------------- 1 | import os 2 | import string 3 | 4 | for fname in filter(lambda x:'-' in x,os.listdir(os.curdir)): 5 | newname = string.replace(fname, '-medium-', '-') 6 | if newname != fname: 7 | print newname 8 | os.rename(fname,newname) 9 | -------------------------------------------------------------------------------- /Code/DataStructs/Wrap/testData/isiv.pkl: -------------------------------------------------------------------------------- 1 | crdkit.DataStructs.cDataStructs 2 | IntSparseIntVect 3 | p1 4 | (S'\x01\x00\x00\x00\x04\x00\x00\x00\x00\x00 \x00\x03\x00\x00\x00\x00\x00\x00\x00\x01\x00\x00\x00\x02\x00\x00\x00\x02\x00\x00\x00\x00\x10\x00\x00\x03\x00\x00\x00' 5 | tRp2 6 | . -------------------------------------------------------------------------------- /Code/JavaWrappers/DiversityPick.i: -------------------------------------------------------------------------------- 1 | 2 | %{ 3 | #include 4 | #include 5 | #include "DiversityPick.h" 6 | %} 7 | 8 | %template(EBV_Vect) std::vector< ExplicitBitVect >; 9 | 10 | %include "DiversityPick.h"; 11 | 12 | -------------------------------------------------------------------------------- /Docs/Programs/RDPharm3D/Index.hhk: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 |
    8 |
9 | 10 | -------------------------------------------------------------------------------- /rdkit/ML/Data/test_data/test.qdat: -------------------------------------------------------------------------------- 1 | # Testing data 2 | # ---------- 3 | # Variable Table 4 | # foo1 [] 5 | # foo2 [] 6 | # foo3 [] 7 | # foo4 [] 8 | # res [] 9 | # --------- 10 | p1 0 0 0 0 0 11 | p2 0 0 0 1 0 12 | p3 1 0 0 0 1 13 | p4 2 1 0 0 1 14 | p5 2 2 1 0 1 15 | 16 | -------------------------------------------------------------------------------- /Code/Demos/boost/overloads/test.py: -------------------------------------------------------------------------------- 1 | import overloads 2 | 3 | assert overloads.f1(1)==4 4 | assert overloads.f1(1,4)==5 5 | assert overloads.f1(1.)==4. 6 | assert overloads.f1(1.,5)==6. 7 | 8 | assert overloads.f2(1)==4 9 | assert overloads.f2(1,12)==13 10 | 11 | 12 | 13 | -------------------------------------------------------------------------------- /Code/GraphMol/FragCatalog/test_data/mols.smi: -------------------------------------------------------------------------------- 1 | OCCC 1 2 | CCC 2 3 | C=CC 3 4 | OC=CC 4 5 | CC(O)C 5 6 | C=C(O)C 6 7 | OCCCC 7 8 | CC(O)CC 8 9 | C=CCC 9 10 | CC=CC 10 11 | OC=CCC 11 12 | CC=C(O)C 12 13 | OCC=CC 13 14 | C=C(O)CC 14 15 | C=CC(O)C 15 16 | C=CCCO 16 17 | 18 | 19 | -------------------------------------------------------------------------------- /rdkit/SimDivFilters/__init__.py: -------------------------------------------------------------------------------- 1 | # 2 | # Copyright (C) 2004 Rational Discovery LLC 3 | # All Rights Reserved 4 | # 5 | from rdkit import rdBase 6 | try: 7 | import rdSimDivPickers 8 | from rdSimDivPickers import * 9 | except ImportError: 10 | rdSimDivPickers=None 11 | -------------------------------------------------------------------------------- /Code/ChemicalFeatures/Wrap/testData/feat.pkl: -------------------------------------------------------------------------------- 1 | crdkit.Chem.rdChemicalFeatures 2 | FreeChemicalFeature 3 | p1 4 | (S'\x10\x00\x00\x00\x0b\x00\x00\x00HBondDonor\x00\x0c\x00\x00\x00HBondDonor1\x00\x00\x00\x00\x00\x00\x00\xf0?\x00\x00\x00\x00\x00\x00\x00@\x00\x00\x00\x00\x00\x00\x08@' 5 | tRp2 6 | . -------------------------------------------------------------------------------- /Code/GraphMol/ForceFieldHelpers/UFF/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | rdkit_library(ForceFieldHelpers AtomTyper.cpp Builder.cpp 2 | LINK_LIBRARIES SmilesParse SubstructMatch ForceField) 3 | 4 | rdkit_headers(AtomTyper.h 5 | Builder.h DEST GraphMol/ForceFieldHelpers/UFF) 6 | 7 | -------------------------------------------------------------------------------- /Code/GraphMol/test_data/Issue2788233.mol: -------------------------------------------------------------------------------- 1 | 2 | Marvin 06010908082D 3 | 4 | 2 0 0 0 0 0 999 V2000 5 | -1.2494 1.5483 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 6 | -1.0123 0.7592 0.0000 Cr 0 0 0 0 0 0 0 0 0 0 0 0 7 | M END 8 | -------------------------------------------------------------------------------- /Code/ChemicalFeatures/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("testExecs/main.exe","",{}), 4 | 5 | ] 6 | 7 | 8 | if __name__=='__main__': 9 | import sys 10 | from rdkit import TestRunner 11 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 12 | sys.exit(len(failed)) 13 | -------------------------------------------------------------------------------- /Code/Catalogs/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | rdkit_library(Catalogs 2 | Catalog.cpp CatalogParams.cpp CatalogEntry.cpp 3 | LINK_LIBRARIES RDGeneral) 4 | 5 | rdkit_headers(CatalogEntry.h 6 | Catalog.h 7 | CatalogParams.h DEST Catalogs) 8 | 9 | 10 | -------------------------------------------------------------------------------- /Code/Demos/boost/cross_module/test.py: -------------------------------------------------------------------------------- 1 | import moda 2 | import modb 3 | 4 | ca = moda.ClassA() 5 | print 'ca:',ca.Get4() 6 | 7 | cb = modb.ClassB() 8 | print 'cb:',cb.Get3() 9 | 10 | newca = cb.ReturnOther() 11 | print 'new:',newca.Get4() 12 | 13 | print 'arg:',cb.AcceptOther(newca) 14 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/mol_nomol.mol2: -------------------------------------------------------------------------------- 1 | # Name: benzene 2 | # Creating user name: stiefni2 3 | # Creation time: Thu May 15 13:14:53 2008 4 | 5 | # Modifying user name: stiefni2 6 | # Modification time: Thu May 15 13:16:20 2008 7 | 8 | @ATOM 9 | whatever 10 | 11 | 12 | -------------------------------------------------------------------------------- /Code/ChemicalFeatures/Wrap/testData/featv2.pkl: -------------------------------------------------------------------------------- 1 | crdkit.Chem.rdChemicalFeatures 2 | FreeChemicalFeature 3 | p1 4 | (S' \x00\x00\x00{\x00\x00\x00\x0b\x00\x00\x00HBondDonor\x00\x0c\x00\x00\x00HBondDonor1\x00\x00\x00\x00\x00\x00\x00\xf0?\x00\x00\x00\x00\x00\x00\x00@\x00\x00\x00\x00\x00\x00\x08@' 5 | tRp2 6 | . -------------------------------------------------------------------------------- /Code/DataManip/MetricMatrixCalc/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | ### Template library 2 | rdkit_headers(MetricFuncs.h 3 | MetricMatrixCalc.h DEST DataManip/MetricMatrixCalc) 4 | 5 | rdkit_test(testMatCalc testMatCalc.cpp LINK_LIBRARIES RDGeneral) 6 | 7 | add_subdirectory(Wrap) 8 | 9 | 10 | 11 | -------------------------------------------------------------------------------- /Code/GraphMol/ForceFieldHelpers/test_data/Issue2378119.2.mol: -------------------------------------------------------------------------------- 1 | 2 | RDKit 3D 3 | 4 | 2 0 0 0 0 0 0 0 0 0999 V2000 5 | 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | 3.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | M END 8 | 9 | -------------------------------------------------------------------------------- /Code/Query/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("testExecs/test.exe","",{}), 4 | ] 5 | 6 | 7 | 8 | longTests=[] 9 | 10 | if __name__=='__main__': 11 | import sys 12 | from rdkit import TestRunner 13 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 14 | sys.exit(len(failed)) 15 | -------------------------------------------------------------------------------- /Code/DataStructs/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("testExecs/test.exe","",{}), 4 | ] 5 | 6 | 7 | 8 | longTests=[] 9 | 10 | if __name__=='__main__': 11 | import sys 12 | from rdkit import TestRunner 13 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 14 | sys.exit(len(failed)) 15 | -------------------------------------------------------------------------------- /Code/ML/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | if(RDK_BIG_ENDIAN) 2 | message("Skipping build of clustering and cmim libraries on big endian system") 3 | else(RDK_BIG_ENDIAN) 4 | add_subdirectory(Cluster) 5 | add_subdirectory(FeatureSelect) 6 | endif(RDK_BIG_ENDIAN) 7 | add_subdirectory(InfoTheory) 8 | add_subdirectory(Data) 9 | -------------------------------------------------------------------------------- /Code/ML/InfoTheory/Wrap/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","testRanker.py",{}), 4 | ] 5 | 6 | longTests=[] 7 | 8 | if __name__=='__main__': 9 | import sys 10 | from rdkit import TestRunner 11 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 12 | sys.exit(len(failed)) 13 | -------------------------------------------------------------------------------- /Code/Numerics/Alignment/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | rdkit_library(Alignment AlignPoints.cpp LINK_LIBRARIES RDGeometryLib) 2 | 3 | rdkit_headers(AlignPoints.h DEST Numerics/Alignment) 4 | 5 | rdkit_test(testAlignment testAlignment.cpp LINK_LIBRARIES Alignment RDGeometryLib RDGeneral ) 6 | 7 | add_subdirectory(Wrap) 8 | -------------------------------------------------------------------------------- /Code/RDGeneral/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("testExecs/testDict.exe","",{}), 4 | ] 5 | 6 | 7 | 8 | longTests=[] 9 | 10 | if __name__=='__main__': 11 | import sys 12 | from rdkit import TestRunner 13 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 14 | sys.exit(len(failed)) 15 | -------------------------------------------------------------------------------- /Code/doxygen/rdkdocs_footer.html: -------------------------------------------------------------------------------- 1 |
2 | Generated on $datetime for $projectname by doxygen $doxygenversion
3 | 4 | 5 | -------------------------------------------------------------------------------- /Code/Demos/boost/numpy/test.py: -------------------------------------------------------------------------------- 1 | from Numeric import * 2 | import linalg 3 | 4 | print linalg.GetFirstElement(array([1,0,2],Int)) 5 | print linalg.GetFirstElement(array([1,0,2],Float)) 6 | print linalg.GetFirstElement(array([1,0,2],Float64)) 7 | print linalg.GetFirstElement(array([1,0,2],Complex)) # will be zero 8 | -------------------------------------------------------------------------------- /Code/DistGeom/Wrap/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","rough_test.py",{}) 4 | ] 5 | 6 | 7 | 8 | longTests=[] 9 | 10 | if __name__=='__main__': 11 | import sys 12 | from rdkit import TestRunner 13 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 14 | sys.exit(len(failed)) 15 | -------------------------------------------------------------------------------- /Code/Geometry/Wrap/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","testGeometry.py",{}) 4 | ] 5 | 6 | 7 | 8 | longTests=[] 9 | 10 | if __name__=='__main__': 11 | import sys 12 | from rdkit import TestRunner 13 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 14 | sys.exit(len(failed)) 15 | -------------------------------------------------------------------------------- /Code/GraphMol/Depictor/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("testExecs/testDepictor.exe","",{}), 4 | ] 5 | 6 | longTests = [] 7 | 8 | if __name__=='__main__': 9 | import sys 10 | from rdkit import TestRunner 11 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 12 | sys.exit(len(failed)) 13 | -------------------------------------------------------------------------------- /Code/GraphMol/ForceFieldHelpers/Wrap/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","testHelpers.py",{}), 4 | ] 5 | 6 | longTests=[] 7 | 8 | if __name__=='__main__': 9 | import sys 10 | import TestRunner 11 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 12 | sys.exit(len(failed)) 13 | -------------------------------------------------------------------------------- /Code/GraphMol/PartialCharges/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | rdkit_library(PartialCharges 2 | GasteigerCharges.cpp GasteigerParams.cpp 3 | LINK_LIBRARIES GraphMol) 4 | 5 | rdkit_headers(GasteigerCharges.h 6 | GasteigerParams.h DEST GraphMol/PartialCharges) 7 | 8 | add_subdirectory(Wrap) 9 | -------------------------------------------------------------------------------- /Code/ML/FeatureSelect/Wrap/test_list.py: -------------------------------------------------------------------------------- 1 | tests=[ 2 | ("python","testCMIM.py",{}), 3 | ] 4 | 5 | longTests=[] 6 | 7 | if __name__=='__main__': 8 | import sys 9 | from rdkit import TestRunner 10 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 11 | sys.exit(len(failed)) 12 | -------------------------------------------------------------------------------- /Code/ML/InfoTheory/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | add_library(InfoTheory STATIC InfoBitRanker.cpp) 2 | 3 | rdkit_python_extension(cEntropy cEntropy.cpp 4 | DEST ML/InfoTheory 5 | LINK_LIBRARIES 6 | InfoTheory RDGeneral RDBoost) 7 | 8 | add_subdirectory(Wrap) 9 | -------------------------------------------------------------------------------- /Contrib/mmpa/sample_mmps_maxheavy.csv: -------------------------------------------------------------------------------- 1 | Nc1ccc(-c2cc3ccccc3oc2=O)cc1,O=c1oc2ccccc2cc1-c1ccc(O)cc1,310860,4055843,[*:1]N>>[*:1]O,[*:1]c1ccc(-c2cc3ccccc3oc2=O)cc1 2 | O=C(O)c1ccc(NC(=O)C2COc3ccccc3O2)cc1,NC(=O)c1ccc(NC(=O)C2COc3ccccc3O2)cc1,2881039,2787356,[*:1]C(=O)O>>[*:1]C(N)=O,[*:1]c1ccc(NC(=O)C2COc3ccccc3O2)cc1 3 | -------------------------------------------------------------------------------- /rdkit/ML/SLT/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","UnitTestRisk.py",{}), 4 | ] 5 | 6 | 7 | 8 | longTests=[ 9 | ] 10 | if __name__=='__main__': 11 | import sys 12 | from rdkit import TestRunner 13 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 14 | sys.exit(len(failed)) 15 | -------------------------------------------------------------------------------- /rdkit/ML/Scoring/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","UnitTestScoring.py",{}), 4 | ] 5 | 6 | longTests=[ 7 | ] 8 | 9 | if __name__=='__main__': 10 | import sys 11 | from rdkit import TestRunner 12 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 13 | sys.exit(len(failed)) 14 | -------------------------------------------------------------------------------- /Code/DataManip/MetricMatrixCalc/test_list.py: -------------------------------------------------------------------------------- 1 | tests=[ 2 | ("testExecs/testMatCalc.exe","", {}) 3 | ] 4 | 5 | longTests=[] 6 | 7 | if __name__=='__main__': 8 | import sys 9 | from rdkit import TestRunner 10 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 11 | sys.exit(len(failed)) 12 | -------------------------------------------------------------------------------- /Code/Demos/RDKit/Basement/BinaryIO/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("testExecs/iotest.exe","",{}), 4 | ] 5 | 6 | 7 | 8 | longTests=[] 9 | 10 | if __name__=='__main__': 11 | import sys 12 | import TestRunner 13 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 14 | sys.exit(len(failed)) 15 | -------------------------------------------------------------------------------- /Code/GraphMol/Fingerprints/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("testExecs/test1.exe","",{}) 4 | ] 5 | 6 | 7 | 8 | longTests=[] 9 | 10 | if __name__=='__main__': 11 | import sys 12 | from rdkit import TestRunner 13 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 14 | sys.exit(len(failed)) 15 | -------------------------------------------------------------------------------- /Code/GraphMol/FragCatalog/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("testExecs/test1.exe","",{}) 4 | ] 5 | 6 | 7 | 8 | longTests=[] 9 | 10 | if __name__=='__main__': 11 | import sys 12 | from rdkit import TestRunner 13 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 14 | sys.exit(len(failed)) 15 | -------------------------------------------------------------------------------- /Code/GraphMol/MolAlign/Wrap/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","testMolAlign.py",{}), 4 | ] 5 | 6 | longTests=[] 7 | 8 | if __name__=='__main__': 9 | import sys 10 | from rdkit import TestRunner 11 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 12 | sys.exit(len(failed)) 13 | -------------------------------------------------------------------------------- /Code/GraphMol/MolCatalog/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("testExecs/test1.exe","",{}) 4 | ] 5 | 6 | 7 | 8 | longTests=[] 9 | 10 | if __name__=='__main__': 11 | import sys 12 | from rdkit import TestRunner 13 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 14 | sys.exit(len(failed)) 15 | -------------------------------------------------------------------------------- /rdkit/Chem/Draw/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","UnitTestDraw.py",{}), 4 | ] 5 | 6 | 7 | 8 | longTests=[ 9 | ] 10 | 11 | if __name__=='__main__': 12 | import sys 13 | from rdkit import TestRunner 14 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 15 | sys.exit(len(failed)) 16 | -------------------------------------------------------------------------------- /rdkit/ML/Neural/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","UnitTestTrainer.py",{}), 4 | ] 5 | 6 | 7 | 8 | longTests=[ 9 | ] 10 | if __name__=='__main__': 11 | import sys 12 | from rdkit import TestRunner 13 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 14 | sys.exit(len(failed)) 15 | -------------------------------------------------------------------------------- /Code/ChemicalFeatures/Wrap/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","testFeatures.py",{}) 4 | ] 5 | 6 | 7 | 8 | longTests=[] 9 | 10 | if __name__=='__main__': 11 | import sys 12 | from rdkit import TestRunner 13 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 14 | sys.exit(len(failed)) 15 | -------------------------------------------------------------------------------- /Code/GraphMol/Descriptors/Wrap/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","testMolDescriptors.py",{}), 4 | ] 5 | 6 | longTests=[] 7 | 8 | if __name__=='__main__': 9 | import sys 10 | from rdkit import TestRunner 11 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 12 | sys.exit(len(failed)) 13 | -------------------------------------------------------------------------------- /Code/GraphMol/DistGeomHelpers/Wrap/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","testDistGeom.py",{}), 4 | ] 5 | 6 | longTests=[] 7 | 8 | if __name__=='__main__': 9 | import sys 10 | from rdkit import TestRunner 11 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 12 | sys.exit(len(failed)) 13 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/bondorder0.mol: -------------------------------------------------------------------------------- 1 | 2 | Marvin 11240808252D 3 | 4 | 2 1 0 0 0 0 999 V2000 5 | -2.4455 2.3277 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | -1.6205 2.3277 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 1 2 0 0 0 0 0 8 | M END 9 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/bondorder9.mol: -------------------------------------------------------------------------------- 1 | 2 | Marvin 11240808262D 3 | 4 | 2 1 0 0 0 0 999 V2000 5 | -2.4455 2.3277 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | -1.6205 2.3277 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 1 2 9 0 0 0 0 8 | M END 9 | -------------------------------------------------------------------------------- /Code/GraphMol/FragCatalog/Wrap/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","rough_test.py",{}) 4 | ] 5 | 6 | 7 | 8 | longTests=[] 9 | 10 | if __name__=='__main__': 11 | import sys 12 | from rdkit import TestRunner 13 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 14 | sys.exit(len(failed)) 15 | -------------------------------------------------------------------------------- /Code/GraphMol/MolCatalog/Wrap/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","rough_test.py",{}) 4 | ] 5 | 6 | 7 | 8 | longTests=[] 9 | 10 | if __name__=='__main__': 11 | import sys 12 | from rdkit import TestRunner 13 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 14 | sys.exit(len(failed)) 15 | -------------------------------------------------------------------------------- /Code/GraphMol/ShapeHelpers/Wrap/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","testShapeHelpers.py",{}), 4 | ] 5 | 6 | longTests=[] 7 | 8 | if __name__=='__main__': 9 | import sys 10 | from rdkit import TestRunner 11 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 12 | sys.exit(len(failed)) 13 | -------------------------------------------------------------------------------- /Code/Numerics/Alignment/Wrap/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","testAlignment.py",{}) 4 | ] 5 | 6 | 7 | 8 | longTests=[] 9 | 10 | if __name__=='__main__': 11 | import sys 12 | from rdkit import TestRunner 13 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 14 | sys.exit(len(failed)) 15 | -------------------------------------------------------------------------------- /rdkit/Chem/Subshape/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","UnitTestSubshape.py",{}), 4 | ] 5 | 6 | 7 | 8 | longTests=[ 9 | ] 10 | if __name__=='__main__': 11 | import sys 12 | from rdkit import TestRunner 13 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 14 | sys.exit(len(failed)) 15 | -------------------------------------------------------------------------------- /rdkit/ML/Composite/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","UnitTestComposite.py",{}), 4 | ] 5 | 6 | 7 | 8 | longTests=[ 9 | ] 10 | if __name__=='__main__': 11 | import sys 12 | from rdkit import TestRunner 13 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 14 | sys.exit(len(failed)) 15 | -------------------------------------------------------------------------------- /rdkit/ML/FeatureSelect/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","UnitTestCMIM.py",{}), 4 | ] 5 | 6 | 7 | 8 | longTests=[ 9 | ] 10 | if __name__=='__main__': 11 | import sys 12 | from rdkit import TestRunner 13 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 14 | sys.exit(len(failed)) 15 | -------------------------------------------------------------------------------- /rdkit/ML/ModelPackage/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","UnitTestPackage.py",{}), 4 | ] 5 | 6 | 7 | 8 | longTests=[ 9 | ] 10 | if __name__=='__main__': 11 | import sys 12 | from rdkit import TestRunner 13 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 14 | sys.exit(len(failed)) 15 | -------------------------------------------------------------------------------- /rdkit/ML/NaiveBayes/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","UnitTestNB.py",{}), 4 | 5 | ] 6 | 7 | 8 | 9 | longTests=[ 10 | ] 11 | if __name__=='__main__': 12 | import sys 13 | from rdkit import TestRunner 14 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 15 | sys.exit(len(failed)) 16 | -------------------------------------------------------------------------------- /rdkit/VLib/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","Node.py",{}), 4 | ("python","Filter.py",{}), 5 | ("python","Output.py",{}), 6 | ("python","Supply.py",{}), 7 | ("python","Transform.py",{}), 8 | ("python","test_list.py",{'dir':'NodeLib'}), 9 | ] 10 | 11 | 12 | 13 | longTests=[ 14 | 15 | ] 16 | -------------------------------------------------------------------------------- /Code/DataManip/MetricMatrixCalc/Wrap/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","testMatricCalc.py",{}), 4 | ] 5 | 6 | longTests=[] 7 | 8 | if __name__=='__main__': 9 | import sys 10 | from rdkit import TestRunner 11 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 12 | sys.exit(len(failed)) 13 | -------------------------------------------------------------------------------- /Code/Demos/boost/cross_module/moda.cpp: -------------------------------------------------------------------------------- 1 | // 2 | // Copyright (C) 2003 Rational Discovery LLC 3 | // 4 | 5 | #include "mods.h" 6 | 7 | namespace python = boost::python; 8 | 9 | BOOST_PYTHON_MODULE(moda) 10 | { 11 | python::class_("ClassA") 12 | .def("Get4",&ClassA::get4) 13 | ; 14 | 15 | } 16 | -------------------------------------------------------------------------------- /Code/Features/test_list.py: -------------------------------------------------------------------------------- 1 | import sys 2 | 3 | tests=[ 4 | ("testExecs/testFeatures.exe","",{}), 5 | ] 6 | 7 | longTests=[ 8 | ] 9 | 10 | if __name__=='__main__': 11 | import sys 12 | from rdkit import TestRunner 13 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 14 | sys.exit(len(failed)) 15 | -------------------------------------------------------------------------------- /Code/GraphMol/Depictor/Wrap/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python", "testDepictor.py", {}), 4 | ] 5 | 6 | longTests = [] 7 | 8 | 9 | if __name__=='__main__': 10 | import sys 11 | from rdkit import TestRunner 12 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 13 | sys.exit(len(failed)) 14 | -------------------------------------------------------------------------------- /Code/GraphMol/MolChemicalFeatures/test_data/featDef2.txt: -------------------------------------------------------------------------------- 1 | AtomType a1 [N,O;!H0] 2 | AtomType a2 \ 3 | [N,O] 4 | DefineFeature HDonor1 [{a1}] 5 | Family HBondDonor 6 | Weights 1.0 7 | EndFeature 8 | DefineFeature HAcceptor1 [{a2}] 9 | Family \ 10 | HBondAcceptor 11 | Weights 1.0 12 | EndFeature 13 | -------------------------------------------------------------------------------- /Code/GraphMol/MolTransforms/Wrap/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","testMolTransforms.py",{}), 4 | ] 5 | 6 | longTests=[] 7 | 8 | if __name__=='__main__': 9 | import sys 10 | from rdkit import TestRunner 11 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 12 | sys.exit(len(failed)) 13 | -------------------------------------------------------------------------------- /Code/GraphMol/PartialCharges/Wrap/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","testPartialCharges.py",{}), 4 | ] 5 | 6 | longTests=[] 7 | 8 | if __name__=='__main__': 9 | import sys 10 | from rdkit import TestRunner 11 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 12 | sys.exit(len(failed)) 13 | -------------------------------------------------------------------------------- /Code/ForceField/test_list.py: -------------------------------------------------------------------------------- 1 | import sys 2 | 3 | tests=[ 4 | ("testExecs/testForceField.exe","",{}), 5 | ] 6 | 7 | longTests=[ 8 | ] 9 | 10 | if __name__=='__main__': 11 | import sys 12 | from rdkit import TestRunner 13 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 14 | sys.exit(len(failed)) 15 | -------------------------------------------------------------------------------- /Code/GraphMol/ChemTransforms/test_list.py: -------------------------------------------------------------------------------- 1 | import sys 2 | 3 | tests=[ 4 | ("testExecs/main.exe","",{}), 5 | ] 6 | 7 | longTests=[ 8 | ] 9 | 10 | if __name__=='__main__': 11 | import sys 12 | from rdkit import TestRunner 13 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 14 | sys.exit(len(failed)) 15 | -------------------------------------------------------------------------------- /Code/GraphMol/MolChemicalFeatures/Wrap/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","testChemicalFeatures.py",{}), 4 | ] 5 | 6 | longTests=[] 7 | 8 | if __name__=='__main__': 9 | import sys 10 | from rdkit import TestRunner 11 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 12 | sys.exit(len(failed)) 13 | -------------------------------------------------------------------------------- /Code/GraphMol/SLNParse/Wrap/test_list.py: -------------------------------------------------------------------------------- 1 | import sys 2 | 3 | tests=[ 4 | ("python", "testSLN.py",{}), 5 | ] 6 | 7 | longTests=[ 8 | ] 9 | 10 | if __name__=='__main__': 11 | import sys 12 | from rdkit import TestRunner 13 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 14 | sys.exit(len(failed)) 15 | -------------------------------------------------------------------------------- /Code/Numerics/Alignment/Wrap/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | rdkit_python_extension(rdAlignment 2 | rdAlignment.cpp 3 | DEST Numerics 4 | LINK_LIBRARIES Alignment RDGeneral RDGeometryLib RDBoost) 5 | 6 | add_pytest(pyAlignment ${CMAKE_CURRENT_SOURCE_DIR}/testAlignment.py) 7 | 8 | -------------------------------------------------------------------------------- /Code/Numerics/EigenSolvers/test_list.py: -------------------------------------------------------------------------------- 1 | import sys 2 | 3 | tests=[ 4 | ("testExecs/main.exe","",{}), 5 | ] 6 | 7 | longTests=[ 8 | ] 9 | 10 | if __name__=='__main__': 11 | import sys 12 | from rdkit import TestRunner 13 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 14 | sys.exit(len(failed)) 15 | -------------------------------------------------------------------------------- /External/AvalonTools/Wrap/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","testAvalonTools.py",{}), 4 | ] 5 | 6 | 7 | 8 | longTests=[] 9 | if __name__=='__main__': 10 | import sys 11 | from rdkit import TestRunner 12 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 13 | sys.exit(len(failed)) 14 | 15 | 16 | -------------------------------------------------------------------------------- /Code/DistGeom/Wrap/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | rdkit_python_extension(DistGeom DistGeom.cpp 2 | DEST DistanceGeometry 3 | LINK_LIBRARIES DistGeometry EigenSolvers ForceField Optimizer RDGeneral RDGeometryLib RDBoost ) 4 | 5 | 6 | add_pytest(pyDistGeom ${CMAKE_CURRENT_SOURCE_DIR}/rough_test.py) 7 | 8 | 9 | 10 | 11 | -------------------------------------------------------------------------------- /Code/ML/Cluster/Murtagh/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | # add_library(hc STATIC hc.c hcdriver.c) 2 | rdkit_library(hc hc.c hcdriver.c) 3 | 4 | rdkit_python_extension(Clustering Clustering.cpp 5 | DEST ML/Cluster 6 | LINK_LIBRARIES 7 | hc RDGeneral RDBoost) 8 | 9 | 10 | 11 | -------------------------------------------------------------------------------- /Code/Numerics/Optimizer/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | rdkit_library(Optimizer 2 | BFGSOpt.cpp LinearSearch.cpp 3 | LINK_LIBRARIES RDGeometryLib) 4 | 5 | rdkit_headers(BFGSOpt.h DEST Numerics/Optimizer) 6 | 7 | rdkit_test(testOptimizer testOptimizer.cpp LINK_LIBRARIES Optimizer RDGeometryLib RDGeneral ) 8 | 9 | 10 | -------------------------------------------------------------------------------- /Code/Numerics/Optimizer/test_list.py: -------------------------------------------------------------------------------- 1 | import sys 2 | 3 | tests=[ 4 | ("testExecs/testOptimizer.exe","",{}), 5 | ] 6 | 7 | longTests=[ 8 | ] 9 | 10 | if __name__=='__main__': 11 | import sys 12 | from rdkit import TestRunner 13 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 14 | sys.exit(len(failed)) 15 | -------------------------------------------------------------------------------- /Projects/DbCLI/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","TestDbCLI.py",{}), 4 | ] 5 | 6 | 7 | 8 | longTests=[ 9 | 10 | ] 11 | 12 | if __name__=='__main__': 13 | import sys 14 | from rdkit import TestRunner 15 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 16 | sys.exit(len(failed)) 17 | -------------------------------------------------------------------------------- /rdkit/Dbase/Pubmed/test_data/nohits.xml: -------------------------------------------------------------------------------- 1 | 2 | Can't run executor 3 | 4 | penzotti je, grootenhuis pd[Author] 5 | 6 | 7 | No items found. 8 | 9 | 10 | -------------------------------------------------------------------------------- /Code/GraphMol/Descriptors/test_list.py: -------------------------------------------------------------------------------- 1 | import sys 2 | 3 | tests=[ 4 | ("testExecs/testDescriptors.exe","",{}), 5 | ] 6 | 7 | longTests=[ 8 | ] 9 | 10 | if __name__=='__main__': 11 | import sys 12 | from rdkit import TestRunner 13 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 14 | sys.exit(len(failed)) 15 | -------------------------------------------------------------------------------- /Code/GraphMol/ForceFieldHelpers/test_list.py: -------------------------------------------------------------------------------- 1 | import sys 2 | 3 | tests=[ 4 | ("testExecs/testHelpers.exe","",{}), 5 | ] 6 | 7 | longTests=[ 8 | ] 9 | 10 | if __name__=='__main__': 11 | import sys 12 | from rdkit import TestRunner 13 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 14 | sys.exit(len(failed)) 15 | -------------------------------------------------------------------------------- /Projects/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","TestDbCLI.py",{'dir':'DbCLI'}), 4 | ] 5 | 6 | 7 | 8 | longTests=[ 9 | 10 | ] 11 | 12 | if __name__=='__main__': 13 | import sys 14 | from rdkit import TestRunner 15 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 16 | sys.exit(len(failed)) 17 | -------------------------------------------------------------------------------- /Code/GraphMol/ChemReactions/Wrap/test_list.py: -------------------------------------------------------------------------------- 1 | import sys 2 | 3 | tests=[ 4 | ("python", "testReactionWrapper.py",{}), 5 | ] 6 | 7 | longTests=[ 8 | ] 9 | 10 | if __name__=='__main__': 11 | import sys 12 | from rdkit import TestRunner 13 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 14 | sys.exit(len(failed)) 15 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/ringcount_0.mol: -------------------------------------------------------------------------------- 1 | 2 | -ISIS- 02260813282D 3 | 4 | 2 1 0 0 0 0 0 0 0 0999 V2000 5 | 2.4625 -4.4708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | 2.4583 -3.6458 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 1 2 1 0 0 0 0 8 | M RBC 1 1 -1 9 | M END 10 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/ringcount_2.mol: -------------------------------------------------------------------------------- 1 | 2 | -ISIS- 02260813302D 3 | 4 | 2 1 0 0 0 0 0 0 0 0999 V2000 5 | 2.4625 -4.4708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | 2.4583 -3.6458 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 1 2 1 0 0 0 0 8 | M RBC 1 1 2 9 | M END 10 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/ringcount_3.mol: -------------------------------------------------------------------------------- 1 | 2 | -ISIS- 02260813302D 3 | 4 | 2 1 0 0 0 0 0 0 0 0999 V2000 5 | 2.4625 -4.4708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | 2.4583 -3.6458 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 1 2 1 0 0 0 0 8 | M RBC 1 1 3 9 | M END 10 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/ringcount_4.mol: -------------------------------------------------------------------------------- 1 | 2 | -ISIS- 02260813282D 3 | 4 | 2 1 0 0 0 0 0 0 0 0999 V2000 5 | 2.4625 -4.4708 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 6 | 2.4583 -3.6458 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 1 2 1 0 0 0 0 8 | M RBC 1 1 4 9 | M END 10 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/ringcount_star.mol: -------------------------------------------------------------------------------- 1 | 2 | -ISIS- 02260813302D 3 | 4 | 2 1 0 0 0 0 0 0 0 0999 V2000 5 | 2.4625 -4.4708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | 2.4583 -3.6458 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 1 2 1 0 0 0 0 8 | M RBC 1 1 -2 9 | M END 10 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/unsaturation.mol: -------------------------------------------------------------------------------- 1 | 2 | -ISIS- 02260817032D 3 | 4 | 2 1 0 0 0 0 0 0 0 0999 V2000 5 | 2.9000 -4.0958 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | 3.6145 -3.6833 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7 | 1 2 8 0 0 0 0 8 | M UNS 1 1 1 9 | M END 10 | -------------------------------------------------------------------------------- /Code/SimDivPickers/Wrap/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","testPickers.py",{}), 4 | ("python","testMaxMin.py",{}) 5 | ] 6 | 7 | longTests=[] 8 | 9 | if __name__=='__main__': 10 | import sys 11 | from rdkit import TestRunner 12 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 13 | sys.exit(len(failed)) 14 | -------------------------------------------------------------------------------- /External/INCHI-API/Wrap/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | rdkit_python_extension(rdinchi 2 | pyInchi.cpp 3 | DEST Chem 4 | LINK_LIBRARIES 5 | RDInchiLib ${INCHI_LIBRARIES} SmilesParse SubstructMatch Depictor 6 | GraphMol DataStructs RDGeometryLib RDGeneral RDBoost) 7 | -------------------------------------------------------------------------------- /Code/Geometry/Wrap/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | rdkit_python_extension(rdGeometry 2 | Point.cpp UniformGrid3D.cpp rdGeometry.cpp 3 | DEST Geometry 4 | LINK_LIBRARIES RDGeometryLib DataStructs RDGeneral RDBoost) 5 | 6 | add_pytest(testPyGeometry ${CMAKE_CURRENT_SOURCE_DIR}/testGeometry.py) 7 | 8 | -------------------------------------------------------------------------------- /Code/GraphMol/Wrap/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","rough_test.py",{}), 4 | ("python","testConformer.py",{}), 5 | ] 6 | 7 | 8 | 9 | longTests=[] 10 | 11 | if __name__=='__main__': 12 | import sys 13 | from rdkit import TestRunner 14 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 15 | sys.exit(len(failed)) 16 | -------------------------------------------------------------------------------- /Code/Numerics/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | add_subdirectory(Alignment) 2 | add_subdirectory(EigenSolvers) 3 | add_subdirectory(Optimizer) 4 | 5 | rdkit_headers(Matrix.h 6 | SquareMatrix.h 7 | SymmMatrix.h 8 | Vector.h DEST Numerics) 9 | 10 | rdkit_test(testMatrices testMatrices.cpp LINK_LIBRARIES RDGeneral) 11 | -------------------------------------------------------------------------------- /rdkit/ML/InfoTheory/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","testCorrMatGen.py",{}), 4 | ] 5 | 6 | longTests=[ 7 | ("python","testBitRanker.py",{}), 8 | ] 9 | if __name__=='__main__': 10 | import sys 11 | from rdkit import TestRunner 12 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 13 | sys.exit(len(failed)) 14 | -------------------------------------------------------------------------------- /rdkit/VLib/NodeLib/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","SDSupply.py",{}), 4 | ("python","SmartsMolFilter.py",{}), 5 | ("python","SmartsRemover.py",{}), 6 | ("python","SmilesDupeFilter.py",{}), 7 | ("python","SmilesOutput.py",{}), 8 | ("python","SmilesSupply.py",{}), 9 | ] 10 | 11 | 12 | 13 | longTests=[ 14 | 15 | ] 16 | -------------------------------------------------------------------------------- /Code/DataStructs/Wrap/testData/lsiv.pkl: -------------------------------------------------------------------------------- 1 | crdkit.DataStructs.cDataStructs 2 | LongSparseIntVect 3 | p1 4 | (S'\x01\x00\x00\x00\x08\x00\x00\x00\x00\x00\x00\x00\x00\x04\x00\x00\x03\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x01\x00\x00\x00\x02\x00\x00\x00\x00\x00\x00\x00\x02\x00\x00\x00\x00\x00\x00\x00\x08\x00\x00\x00\x03\x00\x00\x00' 5 | tRp2 6 | . -------------------------------------------------------------------------------- /Code/Geometry/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("testExecs/testTransforms.exe","",{}), 4 | ("testExecs/testGrid.exe","",{}), 5 | ] 6 | 7 | 8 | 9 | longTests=[] 10 | 11 | if __name__=='__main__': 12 | import sys 13 | from rdkit import TestRunner 14 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 15 | sys.exit(len(failed)) 16 | -------------------------------------------------------------------------------- /Code/GraphMol/SmilesParse/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("testExecs/test.exe","",{}), 4 | ("testExecs/smatest.exe", "",{}) 5 | ] 6 | 7 | 8 | 9 | longTests=[] 10 | 11 | if __name__=='__main__': 12 | import sys 13 | from rdkit import TestRunner 14 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 15 | sys.exit(len(failed)) 16 | -------------------------------------------------------------------------------- /Code/GraphMol/Subgraphs/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("testExecs/test1.exe","",{}), 4 | ("testExecs/test2.exe","",{}), 5 | ] 6 | 7 | 8 | 9 | longTests=[] 10 | 11 | if __name__=='__main__': 12 | import sys 13 | from rdkit import TestRunner 14 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 15 | sys.exit(len(failed)) 16 | -------------------------------------------------------------------------------- /External/AvalonTools/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("testExecs/test1.exe","",{}), 4 | ("python","test_list.py",{"dir":"Wrap"}), 5 | ] 6 | 7 | 8 | 9 | longTests=[] 10 | if __name__=='__main__': 11 | import sys 12 | import TestRunner 13 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 14 | sys.exit(len(failed)) 15 | 16 | 17 | -------------------------------------------------------------------------------- /rdkit/ML/KNN/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","UnitTestKNN.py",{}), 4 | ("python","DistFunctions.py",{}), 5 | 6 | ] 7 | 8 | 9 | 10 | longTests=[ 11 | ] 12 | if __name__=='__main__': 13 | import sys 14 | from rdkit import TestRunner 15 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 16 | sys.exit(len(failed)) 17 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/mol_noatoms.mol2: -------------------------------------------------------------------------------- 1 | # Name: benzene 2 | # Creating user name: stiefni2 3 | # Creation time: Thu May 15 13:14:53 2008 4 | 5 | # Modifying user name: stiefni2 6 | # Modification time: Thu May 15 13:16:20 2008 7 | 8 | @MOLECULE 9 | mol 10 | 12 0 1 0 0 11 | SMALL 12 | NO_CHARGES 13 | 14 | 15 | -------------------------------------------------------------------------------- /Code/GraphMol/Substruct/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("testExecs/test1.exe","",{}) 4 | ] 5 | 6 | 7 | 8 | longTests=[ 9 | ("testExecs/test1.exe","-l",{}), 10 | ] 11 | 12 | if __name__=='__main__': 13 | import sys 14 | from rdkit import TestRunner 15 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 16 | sys.exit(len(failed)) 17 | -------------------------------------------------------------------------------- /rdkit/ML/Data/test_data/test.dat: -------------------------------------------------------------------------------- 1 | # Testing data 2 | # ---------- 3 | # Variable Table 4 | # foo1 [] 5 | # foo2 [] 6 | # foo3 [] 7 | # foo4 [] 8 | # res [2,4] 9 | # --------- 10 | p1 foo 1 1.0 1 1.1 11 | p2 foo 2 1.0 1 2.1 12 | p3 foo 3 1.2 1.1 3.1 13 | p4 foo 4 1.0 1 4.1 14 | p5 foo 5 1.1 1 5.1 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | -------------------------------------------------------------------------------- /Code/DistGeom/test_list.py: -------------------------------------------------------------------------------- 1 | import sys 2 | 3 | tests=[ 4 | ("testExecs/main.exe","",{}), 5 | ("python","test_list.py",{'dir':'Wrap'}), 6 | ] 7 | 8 | longTests=[ 9 | ] 10 | 11 | if __name__=='__main__': 12 | import sys 13 | from rdkit import TestRunner 14 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 15 | sys.exit(len(failed)) 16 | -------------------------------------------------------------------------------- /rdkit/ML/Cluster/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","UnitTestCluster.py",{}), 4 | ("python","UnitTestButina.py",{}), 5 | 6 | ] 7 | 8 | 9 | 10 | longTests=[ 11 | ] 12 | if __name__=='__main__': 13 | import sys 14 | from rdkit import TestRunner 15 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 16 | sys.exit(len(failed)) 17 | -------------------------------------------------------------------------------- /Code/DataManip/MetricMatrixCalc/Wrap/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | rdkit_python_extension(rdMetricMatrixCalc rdMetricMatrixCalc.cpp 2 | DEST DataManip/Metric 3 | LINK_LIBRARIES 4 | RDGeneral DataStructs RDBoost) 5 | 6 | add_pytest(pyMatCalc ${CMAKE_CURRENT_SOURCE_DIR}/testMatricCalc.py) 7 | 8 | 9 | 10 | 11 | -------------------------------------------------------------------------------- /rdkit/Chem/Scaffolds/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","test_MurckoScaffold.py",{}), 4 | ("python","MurckoScaffold.py",{}), 5 | ] 6 | 7 | 8 | 9 | longTests=[ 10 | ] 11 | 12 | if __name__=='__main__': 13 | import sys 14 | from rdkit import TestRunner 15 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 16 | sys.exit(len(failed)) 17 | -------------------------------------------------------------------------------- /Code/Numerics/Alignment/test_list.py: -------------------------------------------------------------------------------- 1 | import sys 2 | 3 | tests=[ 4 | ("testExecs/main.exe","",{}), 5 | ("python","test_list.py",{'dir':'Wrap'}), 6 | ] 7 | 8 | longTests=[ 9 | ] 10 | 11 | if __name__=='__main__': 12 | import sys 13 | from rdkit import TestRunner 14 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 15 | sys.exit(len(failed)) 16 | -------------------------------------------------------------------------------- /Code/SimDivPickers/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | rdkit_library(SimDivPickers 2 | DistPicker.cpp MaxMinPicker.cpp HierarchicalClusterPicker.cpp 3 | LINK_LIBRARIES hc RDGeneral) 4 | 5 | rdkit_headers(DistPicker.h 6 | HierarchicalClusterPicker.h 7 | MaxMinPicker.h DEST SimDivPickers) 8 | 9 | add_subdirectory(Wrap) 10 | 11 | 12 | -------------------------------------------------------------------------------- /rdkit-config-version.cmake.in: -------------------------------------------------------------------------------- 1 | set (PACKAGE_VERSION "@RDKit_VERSION@") 2 | if (NOT "${PACKAGE_FIND_VERSION}" VERSION_GREATER "@RDKit_VERSION@") 3 | set (PACKAGE_VERSION_COMPATIBLE 1) # assuming backward compatible 4 | if ("$PACKAGE_FIND_VERSION}" VERSION_EQUAL "@RDKit_VERSION@") 5 | set (PACKAGE_VERSION_EXACT 1) # matches exactly 6 | endif () 7 | endif () 8 | -------------------------------------------------------------------------------- /Code/ChemicalFeatures/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | rdkit_library(ChemicalFeatures FreeChemicalFeature.cpp) 2 | 3 | rdkit_headers(ChemicalFeature.h 4 | FreeChemicalFeature.h DEST ChemicalFeatures) 5 | 6 | rdkit_test(testChemicalFeatures testChemicalFeatures.cpp 7 | LINK_LIBRARIES ChemicalFeatures RDGeneral) 8 | 9 | add_subdirectory(Wrap) 10 | 11 | 12 | 13 | -------------------------------------------------------------------------------- /Code/DataStructs/Wrap/DataStructs.h: -------------------------------------------------------------------------------- 1 | // 2 | // Copyright (c) 2001-2006 greg Landrum and Rational Discovery LLC 3 | // 4 | // @@ All Rights Reserved @@ 5 | // This file is part of the RDKit. 6 | // The contents are covered by the terms of the BSD license 7 | // which is included in the file license.txt, found at the root 8 | // of the RDKit source tree. 9 | // 10 | 11 | -------------------------------------------------------------------------------- /Code/GraphMol/Depictor/Wrap/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | rdkit_python_extension(rdDepictor 2 | rdDepictor.cpp 3 | DEST Chem 4 | LINK_LIBRARIES 5 | Depictor SmilesParse FileParsers SubstructMatch GraphMol RDGeometryLib RDGeneral RDBoost ) 6 | 7 | add_pytest(pyDepictor ${CMAKE_CURRENT_SOURCE_DIR}/testDepictor.py) 8 | -------------------------------------------------------------------------------- /Code/GraphMol/DistGeomHelpers/test_list.py: -------------------------------------------------------------------------------- 1 | import sys 2 | 3 | tests=[ 4 | ("testExecs/main.exe","",{}), 5 | ("python","test_list.py",{'dir':'Wrap'}), 6 | ] 7 | 8 | longTests=[ 9 | ] 10 | 11 | if __name__=='__main__': 12 | import sys 13 | from rdkit import TestRunner 14 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 15 | sys.exit(len(failed)) 16 | -------------------------------------------------------------------------------- /Code/GraphMol/MolAlign/test_list.py: -------------------------------------------------------------------------------- 1 | import sys 2 | 3 | tests=[ 4 | ("testExecs/testMolAlign.exe","",{}), 5 | ("python","test_list.py",{'dir':'Wrap'}), 6 | ] 7 | 8 | longTests=[ 9 | ] 10 | 11 | if __name__=='__main__': 12 | import sys 13 | from rdkit import TestRunner 14 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 15 | sys.exit(len(failed)) 16 | -------------------------------------------------------------------------------- /Code/GraphMol/PartialCharges/Wrap/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | rdkit_python_extension(rdPartialCharges 2 | rdPartialCharges.cpp 3 | DEST Chem 4 | LINK_LIBRARIES PartialCharges 5 | GraphMol RDGeometryLib RDGeneral DataStructs 6 | RDBoost) 7 | 8 | add_pytest(pyPartialCharges ${CMAKE_CURRENT_SOURCE_DIR}/testPartialCharges.py) 9 | -------------------------------------------------------------------------------- /Code/GraphMol/ShapeHelpers/test_list.py: -------------------------------------------------------------------------------- 1 | import sys 2 | 3 | tests=[ 4 | ("testExecs/main.exe","",{}), 5 | ("python","test_list.py",{'dir':'Wrap'}), 6 | ] 7 | 8 | longTests=[ 9 | ] 10 | 11 | if __name__=='__main__': 12 | import sys 13 | from rdkit import TestRunner 14 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 15 | sys.exit(len(failed)) 16 | -------------------------------------------------------------------------------- /Code/ML/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","test_list.py",{'dir':'InfoTheory/Wrap'}), 4 | ("python","test_list.py",{'dir':'FeatureSelect/Wrap'}), 5 | ] 6 | 7 | longTests = [ 8 | ] 9 | 10 | if __name__=='__main__': 11 | import sys 12 | from rdkit import TestRunner 13 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 14 | sys.exit(len(failed)) 15 | -------------------------------------------------------------------------------- /Code/SimDivPickers/Wrap/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | rdkit_python_extension(rdSimDivPickers 2 | MaxMinPicker.cpp HierarchicalClusterPicker.cpp 3 | rdSimDivPickers.cpp 4 | DEST SimDivFilters 5 | LINK_LIBRARIES SimDivPickers 6 | hc DataStructs 7 | RDGeneral RDBoost) 8 | 9 | 10 | 11 | 12 | 13 | -------------------------------------------------------------------------------- /Projects/DbCLI/testData/README: -------------------------------------------------------------------------------- 1 | Source of data: 2 | 3 | 1) bzr.sdf and bzr.smi : compounds from the publication: 4 | "Spline-Fitting with a Genetic Algorithm: A Method for Developing 5 | Classification Structure-Activity Relationships" J.J. Sutherland, 6 | L.A. O'Brien, D.F. Weaver JCICS:43 1906-15 (2003). 7 | 8 | 2) pubchem.200.sdf : 200 arbitrary pubchem compounds 9 | 10 | -------------------------------------------------------------------------------- /rdkit/Chem/Suppliers/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","UnitTestSDMolSupplier.py",{}), 4 | ("python","UnitTestSmilesMolSupplier.py",{}), 5 | ] 6 | 7 | 8 | 9 | longTests=[ 10 | ] 11 | if __name__=='__main__': 12 | import sys 13 | from rdkit import TestRunner 14 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 15 | sys.exit(len(failed)) 16 | -------------------------------------------------------------------------------- /Code/GraphMol/MolCatalog/Wrap/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | rdkit_python_extension(rdMolCatalog rdMolCatalog.cpp 2 | DEST Chem 3 | LINK_LIBRARIES 4 | MolCatalog FileParsers Catalogs SmilesParse GraphMol DataStructs RDGeneral RDGeometryLib 5 | RDBoost) 6 | 7 | add_pytest(pyMolCatalog ${CMAKE_CURRENT_SOURCE_DIR}/rough_test.py) 8 | 9 | 10 | 11 | -------------------------------------------------------------------------------- /rdkit-config.cmake.in: -------------------------------------------------------------------------------- 1 | # Compute installation prefix relative to this file 2 | get_filename_component (_dir "${CMAKE_CURRENT_LIST_FILE}" PATH) 3 | get_filename_component (_prefix "${_dir}/.." ABSOLUTE) 4 | 5 | # Import the targets 6 | include ("${_prefix}/lib@LIB_SUFFIX@/@RDKit_EXPORTED_TARGETS@.cmake") 7 | 8 | # Report other info 9 | set (RDKit_INCLUDE_DIRS "${_prefix}/@RDKit_HdrDir@") -------------------------------------------------------------------------------- /Code/Demos/RDKit/Basement/xpcom/RDKitImpl.h: -------------------------------------------------------------------------------- 1 | #ifndef _RDKITIMPL_H_ 2 | #define _RDKITIMPL_H_ 3 | #include "IRDKit.h" 4 | 5 | /* Header file */ 6 | class RDKitImpl : public IRDKit 7 | { 8 | public: 9 | NS_DECL_ISUPPORTS 10 | NS_DECL_IRDKIT 11 | 12 | RDKitImpl(); 13 | 14 | private: 15 | ~RDKitImpl(); 16 | 17 | protected: 18 | /* additional members */ 19 | }; 20 | #endif 21 | -------------------------------------------------------------------------------- /Code/GraphMol/ChemReactions/test_list.py: -------------------------------------------------------------------------------- 1 | import sys 2 | 3 | tests=[ 4 | ("testExecs/testReaction.exe","",{}), 5 | ("python","test_list.py",{'dir':'Wrap'}), 6 | ] 7 | 8 | longTests=[ 9 | ] 10 | 11 | if __name__=='__main__': 12 | import sys 13 | from rdkit import TestRunner 14 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 15 | sys.exit(len(failed)) 16 | -------------------------------------------------------------------------------- /Code/GraphMol/SLNParse/Wrap/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | rdkit_python_extension(rdSLNParse rdSLNParse.cpp 2 | DEST Chem 3 | LINK_LIBRARIES 4 | SLNParse SmilesParse SubstructMatch GraphMol 5 | RDGeometryLib RDGeneral DataStructs RDBoost) 6 | 7 | add_pytest(pySLNParse ${CMAKE_CURRENT_SOURCE_DIR}/testSLN.py) 8 | 9 | -------------------------------------------------------------------------------- /Code/ML/FeatureSelect/Wrap/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | include_directories(${CMAKE_SOURCE_DIR}/External/cmim-1.0) 2 | 3 | rdkit_python_extension(rdFeatSelect rdFeatSelect.cpp 4 | DEST ML/FeatureSelect 5 | LINK_LIBRARIES 6 | fastentropy DataStructs RDGeneral RDBoost) 7 | 8 | add_pytest(pyCMIM ${CMAKE_CURRENT_SOURCE_DIR}/testCMIM.py) 9 | -------------------------------------------------------------------------------- /Code/GraphMol/MolChemicalFeatures/test_list.py: -------------------------------------------------------------------------------- 1 | import sys 2 | 3 | tests=[ 4 | ("testExecs/testFeatures.exe","",{}), 5 | ("python","test_list.py",{'dir':'Wrap'}), 6 | ] 7 | 8 | longTests=[ 9 | ] 10 | 11 | if __name__=='__main__': 12 | import sys 13 | from rdkit import TestRunner 14 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 15 | sys.exit(len(failed)) 16 | -------------------------------------------------------------------------------- /Code/GraphMol/MolTransforms/test_list.py: -------------------------------------------------------------------------------- 1 | import sys 2 | 3 | tests=[ 4 | ("testExecs/testMolTransform.exe","",{}), 5 | ("python","test_list.py",{'dir':'Wrap'}), 6 | ] 7 | 8 | 9 | longTests=[ 10 | ] 11 | 12 | if __name__=='__main__': 13 | import sys 14 | from rdkit import TestRunner 15 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 16 | sys.exit(len(failed)) 17 | -------------------------------------------------------------------------------- /Docs/Code/index.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | RD Source Docs 5 | 6 | 7 | 8 | 9 | 10 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | -------------------------------------------------------------------------------- /rdkit/ML/Descriptors/test_data/molcalc.dsc: -------------------------------------------------------------------------------- 1 | (irdkit.ML.Descriptors.MoleculeDescriptors 2 | MolecularDescriptorCalculator 3 | p1 4 | (dp2 5 | S'simpleList' 6 | p3 7 | (S'MolLogP' 8 | p4 9 | S'Chi1v' 10 | p5 11 | tp6 12 | sS'descriptorVersions' 13 | p7 14 | (lp8 15 | S'1.1.0' 16 | p9 17 | aS'1.0.0' 18 | p10 19 | asS'descriptorNames' 20 | p11 21 | g6 22 | sS'compoundList' 23 | p12 24 | Nsb. 25 | -------------------------------------------------------------------------------- /rdkit/Chem/ChemUtils/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","SDFToCSV.py --test",{}), 4 | ] 5 | 6 | 7 | 8 | longTests=[ 9 | ] 10 | 11 | if __name__=='__main__': 12 | import sys 13 | from rdkit import TestRunner 14 | doLong = 0 15 | if '-l' in sys.argv: 16 | doLong=1 17 | failed,tests = TestRunner.RunScript('test_list.py',doLong,1) 18 | sys.exit(len(failed)) 19 | 20 | -------------------------------------------------------------------------------- /rdkit/Chem/Pharm3D/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","EmbedLib.py",{}), 4 | ("python","UnitTestEmbed.py",{}), 5 | ("python","UnitTestPharmacophore.py",{}), 6 | ] 7 | 8 | 9 | 10 | longTests=[] 11 | 12 | if __name__=='__main__': 13 | import sys 14 | from rdkit import TestRunner 15 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 16 | sys.exit(len(failed)) 17 | -------------------------------------------------------------------------------- /rdkit/sping/PS/fontinfo.py: -------------------------------------------------------------------------------- 1 | # Adobe's official Names for Acrobat's (?) fonts 2 | StandardRomanFonts = [ 3 | 'Courier', 'Courier-Bold', 'Courier-Oblique', 'Courier-BoldOblique', 4 | 'Helvetica', 'Helvetica-Bold', 'Helvetica-Oblique', 5 | 'Helvetica-BoldOblique', 6 | 'Times-Roman', 'Times-Bold', 'Times-Italic', 'Times-BoldItalic' ] 7 | 8 | 9 | NonRomanFonts = ["Symbol", "ZapfDingbats"] 10 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/v3k.4a.mol: -------------------------------------------------------------------------------- 1 | 2 | Marvin 06050906242D 3 | 4 | 0 0 0 0 0 999 V3000 5 | M V30 BEGIN CTAB 6 | M V30 COUNTS 2 1 0 0 0 7 | M V30 BEGIN ATOM 8 | M V30 1 C 0.7476 -1.4581 0 0 9 | M V30 2 O 1.6627 -0.2009 0 0 10 | M V30 END ATOM 11 | M V30 BEGIN BOND 12 | M V30 1 1 1 2 TOPO=1 13 | M V30 END BOND 14 | M V30 END CTAB 15 | M END 16 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/v3k.4b.mol: -------------------------------------------------------------------------------- 1 | 2 | Marvin 06050906242D 3 | 4 | 0 0 0 0 0 999 V3000 5 | M V30 BEGIN CTAB 6 | M V30 COUNTS 2 1 0 0 0 7 | M V30 BEGIN ATOM 8 | M V30 1 C 0.7476 -1.4581 0 0 9 | M V30 2 O 1.6627 -0.2009 0 0 10 | M V30 END ATOM 11 | M V30 BEGIN BOND 12 | M V30 1 1 1 2 TOPO=2 13 | M V30 END BOND 14 | M V30 END CTAB 15 | M END 16 | -------------------------------------------------------------------------------- /Code/GraphMol/MolTransforms/Wrap/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | rdkit_python_extension(rdMolTransforms 2 | rdMolTransforms.cpp 3 | DEST Chem 4 | LINK_LIBRARIES MolTransforms 5 | EigenSolvers 6 | GraphMol DataStructs RDGeometryLib RDGeneral 7 | RDBoost) 8 | 9 | add_pytest(pyMolTransforms ${CMAKE_CURRENT_SOURCE_DIR}/testMolTransforms.py) 10 | -------------------------------------------------------------------------------- /rdkit/ML/__init__.py: -------------------------------------------------------------------------------- 1 | # 2 | # Copyright (C) 2000-2006 greg Landrum and Rational Discovery LLC 3 | # 4 | # @@ All Rights Reserved @@ 5 | # This file is part of the RDKit. 6 | # The contents are covered by the terms of the BSD license 7 | # which is included in the file license.txt, found at the root 8 | # of the RDKit source tree. 9 | # 10 | """ module containing machine learning code """ 11 | -------------------------------------------------------------------------------- /Code/DataStructs/Wrap/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","testBV.py",{}), 4 | ("python","testDiscreteValueVect.py",{}), 5 | ("python","testSparseIntVect.py",{}), 6 | ] 7 | 8 | 9 | 10 | longTests=[] 11 | if __name__=='__main__': 12 | import sys 13 | from rdkit import TestRunner 14 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 15 | sys.exit(len(failed)) 16 | 17 | 18 | -------------------------------------------------------------------------------- /Code/GraphMol/Wrap/test_data/easy_smiles.txt: -------------------------------------------------------------------------------- 1 | test1 CCC 2 | test2 C1CCC1 3 | test3 C1CCC1.CCC 4 | test4 C1CCC1.C=CC 5 | test5 C1CC=C1.CCC 6 | test6 C(CC)CCC 7 | test7 C(CO)CCC 8 | test8 C(C=O)CCC 9 | test9 C(C=O)CCC.[Na+].[Cl-] 10 | test10 C(C=O)CCC.CCC.C(CC)C 11 | TR435 C(C)(C)(C)c1cc(Sc2cc(c(O)cc2C)C(C)(C)C)c(C)cc1O 12 | dbl1 C/C=C\C 13 | dbl2 C\C=C/C 14 | dbl3 C/C=C/C 15 | dbl4 C\C=C\C 16 | -------------------------------------------------------------------------------- /Code/ML/InfoTheory/Wrap/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | rdkit_python_extension(rdInfoTheory 2 | InfoBitRanker.cpp BitCorrMatGenerator.cpp 3 | rdInfoTheory.cpp 4 | DEST ML/InfoTheory 5 | LINK_LIBRARIES 6 | InfoTheory RDGeneral DataStructs RDBoost) 7 | 8 | add_pytest(pyRanker ${CMAKE_CURRENT_SOURCE_DIR}/testRanker.py) 9 | -------------------------------------------------------------------------------- /rdkit/Chem/Fingerprints/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","UnitTestFingerprints.py",{}), 4 | ("python","UnitTestSimScreener.py",{}), 5 | ("python","DbFpSupplier.py",{}), 6 | ] 7 | 8 | 9 | 10 | longTests=[ 11 | ] 12 | if __name__=='__main__': 13 | import sys 14 | from rdkit import TestRunner 15 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 16 | sys.exit(len(failed)) 17 | -------------------------------------------------------------------------------- /rdkit/Dbase/__init__.py: -------------------------------------------------------------------------------- 1 | # 2 | # Copyright (C) 2001-2006 greg Landrum and Rational Discovery LLC 3 | # 4 | # @@ All Rights Reserved @@ 5 | # This file is part of the RDKit. 6 | # The contents are covered by the terms of the BSD license 7 | # which is included in the file license.txt, found at the root 8 | # of the RDKit source tree. 9 | # 10 | """ a module for interacting with databases 11 | """ 12 | -------------------------------------------------------------------------------- /Code/Demos/boost/cross_module/mods.h: -------------------------------------------------------------------------------- 1 | // 2 | // Copyright (C) 2003 Rational Discovery LLC 3 | // 4 | 5 | #include 6 | 7 | 8 | class ClassA{ 9 | public: 10 | int get4() { return 4; }; 11 | }; 12 | 13 | class ClassB{ 14 | public: 15 | ClassA *returnOther() { return new ClassA; }; 16 | int get3() { return 3; }; 17 | int acceptOther(ClassA *other) { return other->get4();}; 18 | }; 19 | -------------------------------------------------------------------------------- /Code/GraphMol/ShapeHelpers/Wrap/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | rdkit_python_extension(rdShapeHelpers rdShapeHelpers.cpp 2 | DEST Chem 3 | LINK_LIBRARIES 4 | ShapeHelpers 5 | MolTransforms EigenSolvers 6 | DataStructs GraphMol RDGeometryLib RDGeneral 7 | RDBoost) 8 | 9 | add_pytest(pyShapeHelpers 10 | ${CMAKE_CURRENT_SOURCE_DIR}/testShapeHelpers.py) 11 | 12 | 13 | -------------------------------------------------------------------------------- /rdkit/Chem/Pharm3D/test_data/mol-r-3.mol: -------------------------------------------------------------------------------- 1 | mol-r.mol 2 | 3 | 4 | 4 3 0 0 0 1 V2000 5 | -0.7657 1.1135 1.2900 F 0 0 0 0 0 6 | -0.1332 0.6558 0.1671 C 0 0 0 0 0 7 | -0.9081 1.2867 -1.2835 Cl 0 0 0 0 0 8 | -0.1304 -1.2874 0.1637 Br 0 0 0 0 0 9 | 1 2 1 6 0 0 10 | 2 3 1 6 0 0 11 | 2 4 1 0 0 0 12 | M END 13 | -------------------------------------------------------------------------------- /rdkit/Chem/Pharm3D/test_data/mol-s-3.mol: -------------------------------------------------------------------------------- 1 | mol-s.mol 2 | 3 | 4 | 4 3 0 0 0 1 V2000 5 | -0.7375 1.0123 1.3585 F 0 0 0 0 0 6 | -0.0942 0.5332 0.2506 C 0 0 0 0 0 7 | -0.9459 1.2280 -1.3520 Br 0 0 0 0 0 8 | -0.0907 -1.2282 0.2487 Cl 0 0 0 0 0 9 | 1 2 1 6 0 0 10 | 2 3 1 6 0 0 11 | 2 4 1 0 0 0 12 | M END 13 | -------------------------------------------------------------------------------- /Code/ChemicalFeatures/Wrap/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | rdkit_python_extension(rdChemicalFeatures 2 | rdChemicalFeatures.cpp FreeChemicalFeature.cpp 3 | DEST Chem 4 | LINK_LIBRARIES 5 | ChemicalFeatures GraphMol RDGeometryLib RDGeneral RDBoost) 6 | 7 | add_pytest(pyFeatures ${CMAKE_CURRENT_SOURCE_DIR}/testFeatures.py) 8 | 9 | 10 | 11 | -------------------------------------------------------------------------------- /Code/GraphMol/ChemTransforms/testData/ethanol.mol: -------------------------------------------------------------------------------- 1 | 2 | Mrv0541 12131105162D 3 | 4 | 3 2 0 0 0 0 999 V2000 5 | -3.7714 1.9446 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | -3.0570 2.3571 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | -2.3425 1.9446 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8 | 1 2 1 0 0 0 0 9 | 2 3 1 0 0 0 0 10 | M END 11 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/lists_plus_values.mol: -------------------------------------------------------------------------------- 1 | 2 | -ISIS- 05260916352D 3 | 4 | 2 1 1 0 0 0 0 0 0 0999 V2000 5 | 5.0167 0.2042 0.0000 R# 0 0 0 0 0 0 0 0 0 4 0 0 6 | 5.5255 0.4979 0.0000 L 0 0 0 0 0 0 0 0 0 0 0 0 7 | 1 2 1 0 0 0 0 8 | 2 F 2 35 53 9 | V 2 halogen 10 | M RGP 1 1 3 11 | M ALS 2 2 F Br I 12 | M END 13 | 14 | -------------------------------------------------------------------------------- /Code/Numerics/EigenSolvers/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | rdkit_library(EigenSolvers PowerEigenSolver.cpp LINK_LIBRARIES RDGeneral) 2 | 3 | rdkit_headers(PowerEigenSolver.h DEST Numerics/EigenSolvers) 4 | 5 | IF (LAPACK_FOUND) 6 | include_directories(${CMAKE_SOURCE_DIR}/External/boost-numeric-bindings) 7 | rdkit_test(tesEigensolvers testEigenSolvers.cpp 8 | LINK_LIBRARIES EigenSolvers RDGeneral ) 9 | ENDIF (LAPACK_FOUND) 10 | -------------------------------------------------------------------------------- /rdkit/Chem/AtomPairs/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","Utils.py",{}), 4 | ("python","Torsions.py",{}), 5 | ("python","Pairs.py",{}), 6 | ("python","UnitTestDescriptors.py",{}), 7 | ] 8 | 9 | 10 | 11 | longTests=[ 12 | ] 13 | 14 | if __name__=='__main__': 15 | import sys 16 | from rdkit import TestRunner 17 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 18 | sys.exit(len(failed)) 19 | -------------------------------------------------------------------------------- /rdkit/DataManip/Metric/__init__.py: -------------------------------------------------------------------------------- 1 | # $Id$ 2 | # 3 | # Copyright (C) 2004-2006 Rational Discovery LLC 4 | # 5 | # @@ All Rights Reserved @@ 6 | # This file is part of the RDKit. 7 | # The contents are covered by the terms of the BSD license 8 | # which is included in the file license.txt, found at the root 9 | # of the RDKit source tree. 10 | # 11 | from rdkit import rdBase 12 | from rdMetricMatrixCalc import * 13 | -------------------------------------------------------------------------------- /rdkit/ML/Descriptors/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","UnitTestParser.py",{}), 4 | ("python","UnitTestMolDescriptors.py",{}), 5 | ("python","UnitTestDescriptors.py",{}), 6 | 7 | 8 | ] 9 | 10 | 11 | 12 | longTests=[ 13 | ] 14 | if __name__=='__main__': 15 | import sys 16 | from rdkit import TestRunner 17 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 18 | sys.exit(len(failed)) 19 | -------------------------------------------------------------------------------- /Code/Features/Feature.cpp: -------------------------------------------------------------------------------- 1 | // $Id$ 2 | // 3 | // Copyright (C) 2004-2006 Rational Discovery LLC 4 | // 5 | // @@ All Rights Reserved @@ 6 | // This file is part of the RDKit. 7 | // The contents are covered by the terms of the BSD license 8 | // which is included in the file license.txt, found at the root 9 | // of the RDKit source tree. 10 | // 11 | #include 12 | namespace RDFeatures { 13 | 14 | } 15 | -------------------------------------------------------------------------------- /Code/GraphMol/SLNParse/test_list.py: -------------------------------------------------------------------------------- 1 | import sys 2 | 3 | tests=[ 4 | ("testExecs/test.exe","",{}), 5 | ("python","test_list.py",{'dir':'Wrap'}), 6 | ] 7 | 8 | if sys.platform != 'win32': 9 | pass 10 | 11 | 12 | 13 | longTests=[ 14 | ] 15 | 16 | if __name__=='__main__': 17 | import sys 18 | from rdkit import TestRunner 19 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 20 | sys.exit(len(failed)) 21 | -------------------------------------------------------------------------------- /rdkit/Chem/test_data/dative.mol: -------------------------------------------------------------------------------- 1 | dative.mol 2 | ChemDraw04240109292D 3 | 4 | 3 2 0 0 0 0 0 0 0 0999 V2000 5 | -0.8675 0.0000 0.0000 Fe 0 5 0 0 0 0 0 0 0 0 0 0 6 | 0.0425 0.0000 0.0000 C 0 3 0 0 0 4 1 0 0 0 0 0 7 | 0.8675 0.0000 0.0000 O 0 0 0 0 0 3 1 0 0 0 0 0 8 | 2 3 3 0 9 | 2 1 1 0 10 | M CHG 2 1 -1 2 1 11 | M END 12 | -------------------------------------------------------------------------------- /rdkit/sping/utils.py: -------------------------------------------------------------------------------- 1 | # 2 | # Copyright (C) 2003 Rational Discovery LLC 3 | # All Rights Reserved 4 | # 5 | 6 | availableCanvases={'pdf':('PDF.pidPDF','PDFCanvas','PDF'), 7 | 'ps':('PS.pidPS','PSCanvas','PS'), 8 | 'svg':('SVG.pidSVG','SVGCanvas','SVG'), 9 | 'jpg':('PIL.pidPIL','PILCanvas','JPEG'), 10 | 'png':('PIL.pidPIL','PILCanvas','PNG')} 11 | 12 | -------------------------------------------------------------------------------- /Code/GraphMol/MolTransforms/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | rdkit_library(MolTransforms MolTransforms.cpp 2 | LINK_LIBRARIES GraphMol EigenSolvers) 3 | 4 | rdkit_headers(MolTransforms.h DEST GraphMol/MolTransforms) 5 | 6 | rdkit_test(testMolTransforms test1.cpp 7 | LINK_LIBRARIES MolTransforms 8 | FileParsers SmilesParse 9 | EigenSolvers 10 | GraphMol RDGeometryLib RDGeneral 11 | ) 12 | 13 | add_subdirectory(Wrap) 14 | -------------------------------------------------------------------------------- /rdkit/Dbase/Pubmed/test_data/haslinks.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | PubMed 6 | 7 | 11960484 8 | 10893315 9 | 10 | 11 | 12 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/D_in_CTAB.mol: -------------------------------------------------------------------------------- 1 | D isotope problem.mol 2 | ChemDraw08141214462D 3 | 4 | 3 2 0 0 0 0 0 0 0 0999 V2000 5 | -0.7143 -0.2063 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | 0.0002 0.2063 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 0.7143 -0.2061 0.0000 D 0 0 0 0 0 0 0 0 0 0 0 0 8 | 1 2 1 0 9 | 2 3 1 0 10 | M END 11 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/T_in_CTAB.mol: -------------------------------------------------------------------------------- 1 | T isotope problem.mol 2 | ChemDraw08141214462D 3 | 4 | 3 2 0 0 0 0 0 0 0 0999 V2000 5 | -0.7143 -0.2063 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | 0.0002 0.2063 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 0.7143 -0.2061 0.0000 T 0 0 0 0 0 0 0 0 0 0 0 0 8 | 1 2 1 0 9 | 2 3 1 0 10 | M END 11 | -------------------------------------------------------------------------------- /Code/Numerics/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","test_list.py",{'dir':'Optimizer'}), 4 | ("python","test_list.py",{'dir':'EigenSolvers'}), 5 | ("python","test_list.py",{'dir':'Alignment'}), 6 | ("testExecs/main.exe","",{}), 7 | 8 | ] 9 | 10 | 11 | if __name__=='__main__': 12 | import sys 13 | from rdkit import TestRunner 14 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 15 | sys.exit(len(failed)) 16 | -------------------------------------------------------------------------------- /Web/RDExtras/.htaccess: -------------------------------------------------------------------------------- 1 | # Note: setting environment variables here does no good at all 2 | SetEnv RDBASE /home2/glandrum/RD/trunk 3 | SetEnv BOOSTBASE boost_1_31 4 | SetEnv LD_LIBRARY_PATH "/home2/glandrum/RD/trunk/bin:/usr/local/lib" 5 | SetEnv GDFONTPATH "/usr/local/share/fonts/truetype" 6 | PythonPath "sys.path+['/home2/glandrum/RD/trunk/Python']" 7 | AddHandler mod_python .py 8 | PythonHandler mod_python.publisher 9 | PythonDebug On 10 | -------------------------------------------------------------------------------- /Code/GraphMol/ChemReactions/Wrap/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | rdkit_python_extension(rdChemReactions 2 | rdChemReactions.cpp 3 | DEST Chem 4 | LINK_LIBRARIES 5 | ChemReactions ChemTransforms Depictor FileParsers SmilesParse SubstructMatch GraphMol RDGeneral RDGeometryLib RDBoost) 6 | 7 | add_pytest(pyChemReactions 8 | ${CMAKE_CURRENT_SOURCE_DIR}/testReactionWrapper.py) 9 | 10 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/subst3.mol: -------------------------------------------------------------------------------- 1 | 2 | -ISIS- 08070713512D 3 | 4 | 3 2 0 0 0 0 0 0 0 0999 V2000 5 | -0.2208 -2.3125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | 0.4936 -1.9000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 0.4936 -1.0750 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8 | 1 2 1 0 0 0 0 9 | 2 3 2 0 0 0 0 10 | M SUB 1 2 3 11 | M END 12 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/subst4.mol: -------------------------------------------------------------------------------- 1 | 2 | -ISIS- 08070713512D 3 | 4 | 3 2 0 0 0 0 0 0 0 0999 V2000 5 | -0.2208 -2.3125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | 0.4936 -1.9000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 0.4936 -1.0750 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8 | 1 2 1 0 0 0 0 9 | 2 3 2 0 0 0 0 10 | M SUB 1 2 4 11 | M END 12 | -------------------------------------------------------------------------------- /Code/GraphMol/MolAlign/Wrap/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | rdkit_python_extension(rdMolAlign rdMolAlign.cpp 2 | DEST Chem 3 | LINK_LIBRARIES 4 | MolAlign MolTransforms 5 | EigenSolvers Alignment Optimizer SubstructMatch 6 | GraphMol RDGeneral RDGeometryLib DataStructs 7 | RDBoost) 8 | 9 | add_pytest(pyMolAlign ${CMAKE_CURRENT_SOURCE_DIR}/testMolAlign.py) 10 | 11 | 12 | 13 | 14 | 15 | -------------------------------------------------------------------------------- /Code/SimDivPickers/MaxMinPicker.cpp: -------------------------------------------------------------------------------- 1 | // $Id$ 2 | // 3 | // Copyright (C) 2003-2007 Rational Discovery LLC 4 | // 5 | // @@ All Rights Reserved @@ 6 | // This file is part of the RDKit. 7 | // The contents are covered by the terms of the BSD license 8 | // which is included in the file license.txt, found at the root 9 | // of the RDKit source tree. 10 | // 11 | 12 | #include "MaxMinPicker.h" 13 | 14 | namespace RDPickers { 15 | } 16 | -------------------------------------------------------------------------------- /rdkit/Chem/EState/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","UnitTestEState.py",{}), 4 | ("python","UnitTestFingerprints.py",{}), 5 | ("python","UnitTestTypes.py",{}), 6 | ("python","UnitTestVSA.py",{}), 7 | ] 8 | 9 | 10 | 11 | longTests=[ 12 | ] 13 | 14 | if __name__=='__main__': 15 | import sys 16 | from rdkit import TestRunner 17 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 18 | sys.exit(len(failed)) 19 | -------------------------------------------------------------------------------- /Code/Demos/RDKit/GettingStarted/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | cmake_minimum_required (VERSION 2.6) 2 | project (GettingStartedDemo) 3 | 4 | find_package (RDKit 1.2011.09 REQUIRED) 5 | 6 | include_directories (${RDKit_INCLUDE_DIRS}) 7 | 8 | add_executable (sample sample.cpp) 9 | target_link_libraries (sample ChemReactions FileParsers 10 | SmilesParse Depictor SubstructMatch GraphMol 11 | DataStructs RDGeometryLib RDGeneral 12 | ) 13 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/SkipLines.sdf: -------------------------------------------------------------------------------- 1 | 2 | -ABC123-10021209442D 3 | 4 | 1 0 0 0 0 0 0 0 0999 V2000 5 | 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | S SKP007 7 | M END 8 | $$$$ 9 | 10 | -ABC123-10021209442D 11 | 12 | 1 0 0 0 0 0 0 0 0999 V2000 13 | 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 14 | M END 15 | > 16 | value 17 | 18 | $$$$ 19 | -------------------------------------------------------------------------------- /rdkit/Chem/FeatMaps/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","FeatMapPoint.py",{}), 4 | ("python","UnitTestFeatMap.py",{}), 5 | ("python","UnitTestFeatMapParser.py",{}), 6 | ("python","UnitTestFeatMapUtils.py",{}), 7 | ] 8 | 9 | 10 | 11 | longTests=[] 12 | 13 | if __name__=='__main__': 14 | import sys 15 | from rdkit import TestRunner 16 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 17 | sys.exit(len(failed)) 18 | -------------------------------------------------------------------------------- /Code/Catalogs/Catalog.cpp: -------------------------------------------------------------------------------- 1 | // $Id$ 2 | // 3 | // Copyright (C) 2003-2006 Rational Discovery LLC 4 | // 5 | // @@ All Rights Reserved @@ 6 | // This file is part of the RDKit. 7 | // The contents are covered by the terms of the BSD license 8 | // which is included in the file license.txt, found at the root 9 | // of the RDKit source tree. 10 | // 11 | // 12 | 13 | #include "Catalog.h" 14 | 15 | namespace RDCatalog { 16 | 17 | 18 | } 19 | 20 | -------------------------------------------------------------------------------- /Code/Demos/boost/cross_mod_err/moduleB.cpp: -------------------------------------------------------------------------------- 1 | #include 2 | #include "classA.h" 3 | #include "classC.h" 4 | 5 | namespace python = boost::python; 6 | 7 | void testCrossA(classA *A) { 8 | A->printA(); 9 | }; 10 | 11 | void testCrossC(classC *C) { 12 | C->printC(); 13 | }; 14 | 15 | 16 | BOOST_PYTHON_MODULE(moduleB) 17 | { 18 | python::def("testCrossA", testCrossA); 19 | python::def("testCrossC", testCrossC); 20 | 21 | } 22 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/v3k.rbc.mol: -------------------------------------------------------------------------------- 1 | 2 | Marvin 06021017292D 3 | 4 | 0 0 0 0 0 999 V3000 5 | M V30 BEGIN CTAB 6 | M V30 COUNTS 3 2 0 0 0 7 | M V30 BEGIN ATOM 8 | M V30 1 C -2.915 0.495 0 0 RBCNT=2 9 | M V30 2 C -1.5813 1.265 0 0 10 | M V30 3 C -4.2487 1.265 0 0 11 | M V30 END ATOM 12 | M V30 BEGIN BOND 13 | M V30 1 1 1 2 14 | M V30 2 1 1 3 15 | M V30 END BOND 16 | M V30 END CTAB 17 | M END 18 | -------------------------------------------------------------------------------- /rdkit/Chem/ChemicalForceFields.py: -------------------------------------------------------------------------------- 1 | # $Id$ 2 | # 3 | # Copyright (C) 2006 greg Landrum and Rational Discovery LLC 4 | # 5 | # @@ All Rights Reserved @@ 6 | # This file is part of the RDKit. 7 | # The contents are covered by the terms of the BSD license 8 | # which is included in the file license.txt, found at the root 9 | # of the RDKit source tree. 10 | # 11 | from rdkit.ForceField import * 12 | from rdkit.Chem.rdForceFieldHelpers import * 13 | -------------------------------------------------------------------------------- /rdkit/DataStructs/test_list.py: -------------------------------------------------------------------------------- 1 | tests=[ 2 | ("python","UnitTestBitVect.py",{}), 3 | ("python","UnitTestcBitVect.py",{}), 4 | ("python","UnitTestcBitVect2.py",{}), 5 | ("python","UnitTestBitEnsemble.py",{}), 6 | ("python","UnitTestTopNContainer.py",{}), 7 | ("python","BitUtils.py",{}), 8 | ("python","VectCollection.py",{}), 9 | ("python","LazySignature.py",{}), 10 | ("python","SparseIntVect.py",{}), 11 | ] 12 | longTests=[ 13 | ] 14 | -------------------------------------------------------------------------------- /Code/GraphMol/ForceFieldHelpers/Wrap/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | rdkit_python_extension(rdForceFieldHelpers rdForceFields.cpp 2 | DEST Chem 3 | LINK_LIBRARIES 4 | ForceFieldHelpers 5 | SmilesParse SubstructMatch GraphMol ForceField Optimizer RDGeometryLib RDGeneral DataStructs 6 | RDBoost) 7 | 8 | add_pytest(pyForceFieldHelpers ${CMAKE_CURRENT_SOURCE_DIR}/testHelpers.py) 9 | 10 | 11 | 12 | 13 | -------------------------------------------------------------------------------- /Code/GraphMol/GraphMol.cpp: -------------------------------------------------------------------------------- 1 | // 2 | // Copyright (C) 2001-2006 Greg Landrum and Rational Discovery LLC 3 | // 4 | // @@ All Rights Reserved @@ 5 | // This file is part of the RDKit. 6 | // The contents are covered by the terms of the BSD license 7 | // which is included in the file license.txt, found at the root 8 | // of the RDKit source tree. 9 | // 10 | #include "GraphMol.h" 11 | 12 | namespace RDKit{ 13 | 14 | 15 | 16 | } // end o' namespace 17 | -------------------------------------------------------------------------------- /Code/Numerics/Optimizer/BFGSOpt.cpp: -------------------------------------------------------------------------------- 1 | // $Id$ 2 | // 3 | // Copyright (C) 2004-2008 Greg Landrum and Rational Discovery LLC 4 | // 5 | // @@ All Rights Reserved @@ 6 | // This file is part of the RDKit. 7 | // The contents are covered by the terms of the BSD license 8 | // which is included in the file license.txt, found at the root 9 | // of the RDKit source tree. 10 | // 11 | 12 | #include "BFGSOpt.h" 13 | 14 | namespace BFGSOpt { 15 | 16 | } 17 | -------------------------------------------------------------------------------- /Code/Numerics/Optimizer/LinearSearch.cpp: -------------------------------------------------------------------------------- 1 | // $Id$ 2 | // 3 | // Copyright (C) 2005-2008 Greg Landrum and Rational Discovery LLC 4 | // 5 | // @@ All Rights Reserved @@ 6 | // This file is part of the RDKit. 7 | // The contents are covered by the terms of the BSD license 8 | // which is included in the file license.txt, found at the root 9 | // of the RDKit source tree. 10 | // 11 | #include "BFGSOpt.h" 12 | 13 | namespace BFGSOpt { 14 | 15 | } 16 | -------------------------------------------------------------------------------- /Code/GraphMol/Descriptors/Wrap/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | rdkit_python_extension(rdMolDescriptors rdMolDescriptors.cpp 2 | DEST Chem 3 | LINK_LIBRARIES 4 | LINK_LIBRARIES Descriptors PartialCharges Fingerprints FileParsers SmilesParse Subgraphs SubstructMatch GraphMol DataStructs RDGeneral RDGeometryLib RDBoost ) 5 | 6 | add_pytest(pyMolDescriptors ${CMAKE_CURRENT_SOURCE_DIR}/testMolDescriptors.py) 7 | 8 | 9 | 10 | 11 | 12 | -------------------------------------------------------------------------------- /rdkit/Chem/MolDb/Loader.py: -------------------------------------------------------------------------------- 1 | # $Id$ 2 | # 3 | # Copyright (C) 2007-2009 Greg Landrum 4 | # @@ All Rights Reserved @@ 5 | # This file is part of the RDKit. 6 | # The contents are covered by the terms of the BSD license 7 | # which is included in the file license.txt, found at the root 8 | # of the RDKit source tree. 9 | # 10 | try: 11 | import sqlalchemy 12 | except ImportError: 13 | from Loader_orig import * 14 | else: 15 | from Loader_sa import * 16 | -------------------------------------------------------------------------------- /Code/GraphMol/ForceFieldHelpers/test_data/Issue2378119.mol: -------------------------------------------------------------------------------- 1 | 2 | RDKit 3D 3 | 4 | 4 1 0 0 0 0 0 0 0 0999 V2000 5 | 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 0.7520 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8 | -0.7520 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | 3 4 1 0 10 | M END 11 | 12 | -------------------------------------------------------------------------------- /Contrib/mmpa/sample.smi: -------------------------------------------------------------------------------- 1 | Cc1cc(C)n(Cc2ccc(C(=O)O)o2)n1 658387 2 | Cc1cc(C)n(Cc2ccc(C(=O)O)cc2)n1 615212 3 | Nc1ccc(-c2cc3ccccc3oc2=O)cc1 310860 4 | O=c1oc2ccccc2cc1-c1ccc(O)cc1 4055843 5 | Cc1cccn2cc(-c3cccc(S(=O)(=O)N4CCCCC4)c3)nc12 2963575 6 | O=C(O)c1ccc(NC(=O)C2COc3ccccc3O2)cc1 2881039 7 | NC(=O)c1ccc(NC(=O)C2COc3ccccc3O2)cc1 2787356 8 | c1cc2c(ncnc2NCc2cccnc2)s1 2531831 9 | c1cc2c(ncnc2NCc2ccccc2)s1 2139597 10 | Cc1cccn2cc(-c3ccc(S(=O)(=O)N4CCCCC4)cc3)nc12 1156028 11 | -------------------------------------------------------------------------------- /External/AvalonTools/Wrap/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | include_directories( ${RDKit_ExternalDir}/AvalonTools ) 2 | rdkit_python_extension(pyAvalonTools 3 | pyAvalonTools.cpp 4 | DEST Avalon 5 | LINK_LIBRARIES 6 | AvalonLib avalon_clib SmilesParse FileParsers GraphMol DataStructs RDGeometryLib RDGeneral RDBoost) 7 | add_pytest(pyAvalonTools 8 | ${CMAKE_CURRENT_SOURCE_DIR}/testAvalonTools.py) 9 | -------------------------------------------------------------------------------- /rdkit/Chem/EState/__init__.py: -------------------------------------------------------------------------------- 1 | # 2 | # Copyright (C) 2002 greg Landrum and Rational Discovery LLC 3 | # 4 | """ A module for Kier and Hall's EState Descriptors 5 | 6 | Unless otherwise noted, all definitions here can be found in: 7 | 8 | L.B. Kier and L.H. Hall _Molecular Structure Description: 9 | The Electrotopological State"_ Academic Press (1999) 10 | 11 | """ 12 | 13 | from rdkit.Chem.EState.EState import * 14 | from rdkit.Chem.EState.AtomTypes import * 15 | -------------------------------------------------------------------------------- /Code/Catalogs/CatalogParams.cpp: -------------------------------------------------------------------------------- 1 | // $Id$ 2 | // 3 | // Copyright (C) 2003-2006 Rational Discovery LLC 4 | // 5 | // @@ All Rights Reserved @@ 6 | // This file is part of the RDKit. 7 | // The contents are covered by the terms of the BSD license 8 | // which is included in the file license.txt, found at the root 9 | // of the RDKit source tree. 10 | // 11 | 12 | #include "CatalogParams.h" 13 | 14 | namespace RDCatalog { 15 | CatalogParams::~CatalogParams() {}; 16 | } 17 | -------------------------------------------------------------------------------- /Code/Catalogs/CatalogEntry.cpp: -------------------------------------------------------------------------------- 1 | // $Id$ 2 | // 3 | // Copyright (C) 2004-2006 Rational Discovery LLC 4 | // 5 | // @@ All Rights Reserved @@ 6 | // This file is part of the RDKit. 7 | // The contents are covered by the terms of the BSD license 8 | // which is included in the file license.txt, found at the root 9 | // of the RDKit source tree. 10 | // 11 | 12 | #include "CatalogEntry.h" 13 | 14 | namespace RDCatalog { 15 | CatalogEntry::~CatalogEntry() {} 16 | 17 | } 18 | -------------------------------------------------------------------------------- /Code/GraphMol/Substruct/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | rdkit_library(SubstructMatch 2 | SubstructMatch.cpp SubstructUtils.cpp 3 | LINK_LIBRARIES GraphMol 4 | ${RDKit_THREAD_LIBS} ) 5 | 6 | rdkit_headers(SubstructMatch.h 7 | SubstructUtils.h DEST GraphMol/Substruct) 8 | 9 | rdkit_test(testSubstructMatch test1.cpp LINK_LIBRARIES FileParsers SmilesParse SubstructMatch 10 | GraphMol RDGeometryLib RDGeneral ${RDKit_THREAD_LIBS} ) 11 | 12 | -------------------------------------------------------------------------------- /Code/Query/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | rdkit_headers(AndQuery.h 2 | EqualityQuery.h 3 | GreaterEqualQuery.h 4 | GreaterQuery.h 5 | LessEqualQuery.h 6 | LessQuery.h 7 | OrQuery.h 8 | Query.h 9 | QueryObjects.h 10 | RangeQuery.h 11 | SetQuery.h 12 | XOrQuery.h DEST Query) 13 | 14 | rdkit_test(testQuery test.cpp LINK_LIBRARIES RDGeneral) 15 | 16 | -------------------------------------------------------------------------------- /Code/Demos/boost/cross_module/modb.cpp: -------------------------------------------------------------------------------- 1 | // 2 | // Copyright (C) 2003 Rational Discovery LLC 3 | // 4 | 5 | #include "mods.h" 6 | 7 | namespace python = boost::python; 8 | 9 | BOOST_PYTHON_MODULE(modb) 10 | { 11 | python::class_("ClassB") 12 | .def("Get3",&ClassB::get3) 13 | .def("ReturnOther",&ClassB::returnOther, 14 | python::return_value_policy()) 15 | .def("AcceptOther",&ClassB::acceptOther) 16 | ; 17 | 18 | } 19 | -------------------------------------------------------------------------------- /Code/GraphMol/Wrap/rdmolops.h: -------------------------------------------------------------------------------- 1 | // 2 | // Copyright (C) 2003-2006 Rational Discovery LLC 3 | // 4 | // @@ All Rights Reserved @@ 5 | // This file is part of the RDKit. 6 | // The contents are covered by the terms of the BSD license 7 | // which is included in the file license.txt, found at the root 8 | // of the RDKit source tree. 9 | // 10 | #ifndef _RDMOLOPS_INCL_ 11 | #define _RDMOLOPS_INCL_ 12 | 13 | #define PY_ARRAY_UNIQUE_SYMBOL rdmolops_array_API 14 | 15 | #endif 16 | 17 | -------------------------------------------------------------------------------- /rdkit/Chem/Pharm3D/test_data/mol-r.mol: -------------------------------------------------------------------------------- 1 | mol-r.mol 2 | 3 | 4 | 5 4 0 0 0 1 V2000 5 | -0.7657 1.1135 1.2900 F 0 0 0 0 0 6 | -0.1332 0.6558 0.1671 C 0 0 0 0 0 7 | -0.9081 1.2867 -1.2835 Cl 0 0 0 0 0 8 | -0.1304 -1.2874 0.1637 Br 0 0 0 0 0 9 | 0.9133 0.9789 0.1461 H 0 0 0 0 0 10 | 1 2 1 6 0 0 11 | 2 3 1 6 0 0 12 | 2 4 1 0 0 0 13 | 2 5 1 0 0 0 14 | M END 15 | -------------------------------------------------------------------------------- /rdkit/Chem/Pharm3D/test_data/mol-s.mol: -------------------------------------------------------------------------------- 1 | mol-s.mol 2 | 3 | 4 | 5 4 0 0 0 1 V2000 5 | -0.7375 1.0123 1.3585 F 0 0 0 0 0 6 | -0.0942 0.5332 0.2506 C 0 0 0 0 0 7 | -0.9459 1.2280 -1.3520 Br 0 0 0 0 0 8 | -0.0907 -1.2282 0.2487 Cl 0 0 0 0 0 9 | 0.9503 0.8624 0.2300 H 0 0 0 0 0 10 | 1 2 1 6 0 0 11 | 2 3 1 6 0 0 12 | 2 4 1 0 0 0 13 | 2 5 1 0 0 0 14 | M END 15 | -------------------------------------------------------------------------------- /rdkit/utils/GUIDs.py: -------------------------------------------------------------------------------- 1 | # 2 | # Copyright (C) 2003 Greg Landrum and Rational Discovery LLC 3 | # All Rights Reserved 4 | # 5 | import time,random 6 | 7 | def get12DigitString(): 8 | """ returns a basic 12-digit GUID as a string 9 | """ 10 | # 9 digits of time: 11 | t = '%9.0f'%(100*time.time()) 12 | # 3 random digits 13 | digits = '%03d'%(random.randrange(1000)) 14 | return '%s-%s-%s-%s'%(t[-9:-6],t[-6:-3],t[-3:],digits) 15 | 16 | 17 | getGUID = get12DigitString 18 | -------------------------------------------------------------------------------- /Code/GraphMol/Wrap/rdmolfiles.h: -------------------------------------------------------------------------------- 1 | // 2 | // Copyright (C) 2005-2006 Rational Discovery LLC 3 | // 4 | // @@ All Rights Reserved @@ 5 | // This file is part of the RDKit. 6 | // The contents are covered by the terms of the BSD license 7 | // which is included in the file license.txt, found at the root 8 | // of the RDKit source tree. 9 | // 10 | #ifndef _RDMOLFILES_INCL_ 11 | #define _RDMOLFILES_INCL_ 12 | 13 | #define PY_ARRAY_UNIQUE_SYMBOL rdmolfile_array_API 14 | 15 | #endif 16 | 17 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/v3k.6a.mol: -------------------------------------------------------------------------------- 1 | 2 | Marvin 06110906262D 3 | 4 | 0 0 0 0 0 999 V3000 5 | M V30 BEGIN CTAB 6 | M V30 COUNTS 4 3 0 0 0 7 | M V30 BEGIN ATOM 8 | M V30 1 C -5.7751 6.325 0 0 9 | M V30 2 C -4.4414 7.095 0 0 10 | M V30 3 C -3.1076 6.325 0 0 11 | M V30 4 C -7.1086 7.095 0 0 12 | M V30 END ATOM 13 | M V30 BEGIN BOND 14 | M V30 1 2 1 2 15 | M V30 2 1 2 3 16 | M V30 3 1 1 4 17 | M V30 END BOND 18 | M V30 END CTAB 19 | M END 20 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("testExecs/test1.exe","",{}), 4 | ("testExecs/testMolSupplier.exe","",{}), 5 | ("testExecs/testMolWriter.exe","",{}), 6 | ("testExecs/testTplParser.exe","",{}), 7 | ("testExecs/testMol2ToMol.exe","",{}), 8 | ] 9 | 10 | 11 | 12 | longTests=[] 13 | 14 | if __name__=='__main__': 15 | import sys 16 | from rdkit import TestRunner 17 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 18 | sys.exit(len(failed)) 19 | -------------------------------------------------------------------------------- /Docs/Programs/RDPharm3D/index.htm: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 7 | RDPharm3D 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | -------------------------------------------------------------------------------- /Code/Demos/RDKit/Draw/qtDemo/qtdraw_demo.pro: -------------------------------------------------------------------------------- 1 | SOURCES += qtdraw_demo.cc RDKitMolToQPainter.cc 2 | 3 | HEADERS += ../../../../GraphMol/MolDrawing/MolDrawing.h 4 | 5 | TARGET = qtdraw_demo 6 | 7 | CONFIG += qt 8 | 9 | INCLUDEPATH += ${RDBASE}/Code 10 | 11 | RD_STATIC_LIBS = -lSmilesParse_static -lDepictor_static -lGraphMol_static \ 12 | -lRDGeometryLib_static -lRDGeneral_static 13 | 14 | LIBS += -L${RDBASE}/lib $${RD_STATIC_LIBS} 15 | 16 | LIBS += -L${BOOST}/lib -lboost_regex -lboost_system 17 | -------------------------------------------------------------------------------- /Code/GraphMol/DistGeomHelpers/Wrap/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | rdkit_python_extension(rdDistGeom rdDistGeom.cpp 2 | DEST Chem 3 | LINK_LIBRARIES 4 | LINK_LIBRARIES 5 | DistGeomHelpers DistGeometry FileParsers MolTransforms SmilesParse SubstructMatch ForceFieldHelpers ForceField MolAlign Optimizer EigenSolvers Alignment GraphMol DataStructs RDGeometryLib RDGeneral RDBoost) 6 | 7 | add_pytest(pyDistGeom ${CMAKE_CURRENT_SOURCE_DIR}/testDistGeom.py) 8 | 9 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/v3k.6b.mol: -------------------------------------------------------------------------------- 1 | 2 | Marvin 06110906262D 3 | 4 | 0 0 0 0 0 999 V3000 5 | M V30 BEGIN CTAB 6 | M V30 COUNTS 4 3 0 0 0 7 | M V30 BEGIN ATOM 8 | M V30 1 C -5.775 6.325 0 0 9 | M V30 2 C -4.4413 7.095 0 0 10 | M V30 3 C -3.1076 6.325 0 0 11 | M V30 4 C -7.1087 7.095 0 0 12 | M V30 END ATOM 13 | M V30 BEGIN BOND 14 | M V30 1 2 1 2 CFG=2 15 | M V30 2 1 2 3 16 | M V30 3 1 1 4 17 | M V30 END BOND 18 | M V30 END CTAB 19 | M END 20 | -------------------------------------------------------------------------------- /Code/GraphMol/MolCatalog/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | rdkit_library(MolCatalog MolCatalogEntry.cpp MolCatalogParams.cpp 2 | LINK_LIBRARIES GraphMol Catalogs) 3 | 4 | rdkit_headers(MolCatalogEntry.h 5 | MolCatalog.h 6 | MolCatalogParams.h DEST GraphMol/MolCatalog) 7 | 8 | rdkit_test(testMolCatalog test1.cpp LINK_LIBRARIES 9 | MolCatalog FileParsers Catalogs SmilesParse GraphMol DataStructs RDGeneral RDGeometryLib ) 10 | 11 | add_subdirectory(Wrap) 12 | 13 | 14 | 15 | -------------------------------------------------------------------------------- /rdkit/ML/Data/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","UnitTestFilter.py",{}), 4 | ("python","UnitTestMLData.py",{}), 5 | ("python","UnitTestQuantize.py",{}), 6 | ("python","UnitTestStats.py",{}), 7 | ("python","SplitData.py",{}), 8 | ("python","DataUtils.py",{}), 9 | ] 10 | 11 | 12 | 13 | longTests=[ 14 | ] 15 | if __name__=='__main__': 16 | import sys 17 | from rdkit import TestRunner 18 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 19 | sys.exit(len(failed)) 20 | -------------------------------------------------------------------------------- /Code/GraphMol/MolCatalog/MolCatalog.h: -------------------------------------------------------------------------------- 1 | // 2 | // Copyright (C) 2006 Greg Landrum 3 | // 4 | // 5 | #ifndef _RD_MOL_CATALOG_H_ 6 | #define _RD_MOL_CATALOG_H_ 7 | 8 | #include 9 | #include 10 | #include 11 | 12 | namespace RDKit { 13 | 14 | //! a hierarchical catalog for holding molecules 15 | typedef RDCatalog::HierarchCatalog MolCatalog; 16 | } 17 | 18 | #endif 19 | -------------------------------------------------------------------------------- /Code/GraphMol/test_data/Issue2951221.2.mol: -------------------------------------------------------------------------------- 1 | 2 | Marvin 02141007002D 3 | 4 | 4 3 0 0 0 0 999 V2000 5 | -2.8580 1.6795 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 6 | -2.0330 1.6795 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 7 | -1.6205 0.9650 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 8 | -1.3186 2.0920 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 9 | 2 1 1 1 0 0 0 10 | 2 3 1 0 0 0 0 11 | 2 4 1 0 0 0 0 12 | M END 13 | -------------------------------------------------------------------------------- /Code/GraphMol/test_data/Issue2951221.3.mol: -------------------------------------------------------------------------------- 1 | 2 | Marvin 02141007012D 3 | 4 | 4 3 0 0 0 0 999 V2000 5 | -2.8580 1.6795 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 6 | -2.0330 1.6795 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 7 | -1.6205 0.9650 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 8 | -1.3186 2.0920 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 9 | 2 1 1 6 0 0 0 10 | 2 3 1 0 0 0 0 11 | 2 4 1 0 0 0 0 12 | M END 13 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/Issue142d.mol: -------------------------------------------------------------------------------- 1 | Issue142d.mol 2 | I[C@H](O)S 3 | 4 | 4 3 0 0 0 0 0 0 0 0999 V2000 5 | -0.6675 -0.6843 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6 | -0.0196 -0.1648 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 0.6675 -0.6517 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 8 | -0.0948 0.6843 0.0000 I 0 0 0 0 0 0 0 0 0 0 0 0 9 | 2 1 1 0 10 | 3 2 1 0 11 | 2 4 1 1 12 | M END 13 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/simple_e.mol: -------------------------------------------------------------------------------- 1 | 2 | Marvin 08270812032D 3 | 4 | 4 3 0 0 0 0 999 V2000 5 | -2.5929 1.4143 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | -1.7679 1.4143 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | -1.3554 2.1288 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8 | -3.0054 0.6998 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | 1 2 2 0 0 0 0 10 | 2 3 1 0 0 0 0 11 | 1 4 1 0 0 0 0 12 | M END 13 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/simple_z.mol: -------------------------------------------------------------------------------- 1 | 2 | Marvin 08270812032D 3 | 4 | 4 3 0 0 0 0 999 V2000 5 | -2.5929 1.4143 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | -1.7679 1.4143 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | -1.3554 2.1288 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8 | -2.9759 2.2025 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | 1 2 2 0 0 0 0 10 | 2 3 1 0 0 0 0 11 | 1 4 1 0 0 0 0 12 | M END 13 | -------------------------------------------------------------------------------- /Code/RDGeneral/versions.h.cmake: -------------------------------------------------------------------------------- 1 | // $Id: versions.h 1443 2010-07-01 03:55:11Z glandrum $ 2 | // 3 | // Copyright (c) 2010 greg Landrum 4 | // 5 | // @@ All Rights Reserved @@ 6 | // 7 | namespace RDKit { 8 | const char *rdkitVersion="@RDKit_RELEASENAME@"; 9 | 10 | // The Boost version as detected at build time. 11 | // CMake's Boost_LIB_VERSION is defined by the FindBoost.cmake module 12 | // to be the same as the value from 13 | const char *boostVersion="@Boost_LIB_VERSION@"; 14 | } 15 | -------------------------------------------------------------------------------- /Code/Demos/RDKit/Basement/xpcom/RDMolImpl.h: -------------------------------------------------------------------------------- 1 | #ifndef _RDMOLIMPL_H_ 2 | #define _RDMOLIMPL_H_ 3 | #include "IRDKit.h" 4 | 5 | namespace RDKit { 6 | class ROMol; 7 | } 8 | 9 | class RDMolecule : public IRDMolecule 10 | { 11 | public: 12 | NS_DECL_ISUPPORTS 13 | NS_DECL_IRDMOLECULE 14 | 15 | RDMolecule() : dp_mol(0) {}; 16 | RDMolecule(RDKit::ROMol *mol) : dp_mol(mol) {}; 17 | RDKit::ROMol *dp_mol; 18 | private: 19 | ~RDMolecule(); 20 | 21 | protected: 22 | /* additional members */ 23 | }; 24 | 25 | #endif 26 | -------------------------------------------------------------------------------- /Code/Demos/boost/smartPtrsAndIters/setup.py: -------------------------------------------------------------------------------- 1 | # Run this with: 2 | # python setup.py install --install-lib=. 3 | from RDBuild import * 4 | from distutils.core import setup,Extension 5 | 6 | setup(name="SPtrTestModule",version="1.0", 7 | ext_modules=[Extension("SPtrTestModule",["module.cpp"], 8 | library_dirs=libDirs, 9 | libraries=libraries, 10 | extra_link_args=linkArgs, 11 | extra_compile_args=compileArgs)]) 12 | 13 | 14 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/chiral3.mol: -------------------------------------------------------------------------------- 1 | chiral3.mol 2 | ChemDraw04210412502D 3 | 4 | 4 3 0 0 0 0 0 0 0 0999 V2000 5 | -0.0141 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | 0.8109 0.4125 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 7 | -0.0141 -0.4125 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 8 | -0.8109 0.1989 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | 1 2 1 0 10 | 1 3 1 1 11 | 1 4 1 0 12 | M END 13 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/chiral3a.mol: -------------------------------------------------------------------------------- 1 | chiral3.mol 2 | ChemDraw04210412502D 3 | 4 | 4 3 0 0 0 0 0 0 0 0999 V2000 5 | -0.0141 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | 0.8109 0.4125 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 7 | -0.0141 -0.4125 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 8 | -0.8109 0.1989 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | 1 2 1 6 10 | 1 3 1 0 11 | 1 4 1 0 12 | M END 13 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/chiral4.mol: -------------------------------------------------------------------------------- 1 | chiral4.mol 2 | ChemDraw04210412512D 3 | 4 | 4 3 0 0 0 0 0 0 0 0999 V2000 5 | -0.0141 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | 0.8109 0.4125 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 7 | -0.0141 -0.4125 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 8 | -0.8109 0.1989 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | 1 2 1 0 10 | 1 3 1 6 11 | 1 4 1 0 12 | M END 13 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/chiral4a.mol: -------------------------------------------------------------------------------- 1 | chiral4.mol 2 | ChemDraw04210412512D 3 | 4 | 4 3 0 0 0 0 0 0 0 0999 V2000 5 | -0.0141 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | 0.8109 0.4125 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 7 | -0.0141 -0.4125 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 8 | -0.8109 0.1989 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | 1 2 1 1 10 | 1 3 1 0 11 | 1 4 1 0 12 | M END 13 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/cistrans.1.mol: -------------------------------------------------------------------------------- 1 | 2 | Marvin 05140717372D 3 | 4 | 4 3 0 0 0 0 999 V2000 5 | -1.3750 1.2812 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | -0.6605 1.6937 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | -2.0895 1.6937 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8 | 0.0539 1.2812 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | 1 2 2 0 0 0 0 10 | 1 3 1 0 0 0 0 11 | 2 4 1 0 0 0 0 12 | M END 13 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/cistrans.1a.mol: -------------------------------------------------------------------------------- 1 | 2 | -ISIS- 05140717422D 3 | 4 | 4 3 0 0 0 0 0 0 0 0999 V2000 5 | 4.2458 -5.7126 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | 5.5796 -4.9426 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 2.9121 -4.9426 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8 | 6.9132 -5.7127 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 9 | 1 2 2 0 0 0 0 10 | 1 3 1 0 0 0 0 11 | 2 4 1 0 0 0 0 12 | M END 13 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/cistrans.2.mol: -------------------------------------------------------------------------------- 1 | 2 | Marvin 05140717372D 3 | 4 | 4 3 0 0 0 0 999 V2000 5 | -1.3750 1.2812 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | -0.6605 1.6937 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | -2.0895 1.6937 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8 | -0.6605 2.5187 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | 1 2 2 0 0 0 0 10 | 1 3 1 0 0 0 0 11 | 2 4 1 0 0 0 0 12 | M END 13 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/cistrans.2a.mol: -------------------------------------------------------------------------------- 1 | 2 | -ISIS- 05140717422D 3 | 4 | 4 3 0 0 0 0 0 0 0 0999 V2000 5 | 4.9125 -6.5917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | 6.2463 -5.8217 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 3.5788 -5.8217 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8 | 6.2463 -4.2849 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 9 | 1 2 2 0 0 0 0 10 | 1 3 1 0 0 0 0 11 | 2 4 1 0 0 0 0 12 | M END 13 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/cistrans.3.mol: -------------------------------------------------------------------------------- 1 | 2 | Marvin 05140717372D 3 | 4 | 4 3 0 0 0 0 999 V2000 5 | -1.3750 1.2812 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | -0.6605 1.6937 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | -2.0895 1.6937 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8 | -0.6605 2.5187 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | 1 2 2 3 0 0 0 10 | 1 3 1 0 0 0 0 11 | 2 4 1 0 0 0 0 12 | M END 13 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/simple_either.mol: -------------------------------------------------------------------------------- 1 | 2 | Marvin 08270811582D 3 | 4 | 4 3 0 0 0 0 999 V2000 5 | -2.5929 1.4143 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | -1.7679 1.4143 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | -1.3554 2.1288 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8 | -3.0054 0.6998 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | 1 2 2 3 0 0 0 10 | 2 3 1 0 0 0 0 11 | 1 4 1 0 0 0 0 12 | M END 13 | -------------------------------------------------------------------------------- /rdkit/Chem/Pharm2D/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","UnitTestMatcher.py",{}), 4 | ("python","UnitTestSignature.py",{}), 5 | #("python","UnitTestLazyGenerator.py",{}), 6 | ("python","UnitTestUtils.py",{}), 7 | ("python","UnitTestGobbi.py",{}), 8 | ("python","Utils.py",{}), 9 | 10 | ] 11 | 12 | 13 | 14 | longTests=[ 15 | ] 16 | 17 | if __name__=='__main__': 18 | import sys 19 | from rdkit import TestRunner 20 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 21 | sys.exit(len(failed)) 22 | -------------------------------------------------------------------------------- /rdkit/epydoc.config: -------------------------------------------------------------------------------- 1 | [epydoc] 2 | 3 | modules: Chem,DataManip, DataStructs, Dbase, DistanceGeometry, ForceField, Geometry, Logger, ML, Numerics, rdBase, RDConfig, RDLogger, RDRandom, SimDivFilters, VLib, Avalon 4 | output: html 5 | target: docs/ 6 | 7 | docformat: plaintext 8 | parse: yes 9 | introspect: yes 10 | exclude: UnitTest.*|test* 11 | inheritance: listed 12 | private: yes 13 | imports: yes 14 | sourcecode: yes 15 | name: RDPython 16 | url: http://www.rdkit.org 17 | link: RDKit 18 | 19 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/ChiralityAndBondDir1b.mol: -------------------------------------------------------------------------------- 1 | 2 | Marvin 01040817562D 3 | 4 | 4 3 0 0 0 0 999 V2000 5 | -0.6250 -0.8438 0.0000 I 0 0 0 0 0 0 0 0 0 0 0 0 6 | 0.0895 -0.4313 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 7 | 0.8039 -0.8438 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8 | -0.4939 0.1521 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 9 | 1 2 1 0 0 0 0 10 | 2 3 1 0 0 0 0 11 | 2 4 1 6 0 0 0 12 | M END 13 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/ChiralityAndBondDir2b.mol: -------------------------------------------------------------------------------- 1 | 2 | Marvin 01040817562D 3 | 4 | 4 3 0 0 0 0 999 V2000 5 | -0.6250 -0.8438 0.0000 I 0 0 0 0 0 0 0 0 0 0 0 0 6 | 0.0895 -0.4313 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 7 | 0.8039 -0.8438 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8 | -0.4939 0.1521 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 9 | 2 1 1 0 0 0 0 10 | 2 3 1 0 0 0 0 11 | 2 4 1 6 0 0 0 12 | M END 13 | -------------------------------------------------------------------------------- /Code/GraphMol/ShapeHelpers/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | rdkit_library(ShapeHelpers ShapeEncoder.cpp ShapeUtils.cpp 2 | LINK_LIBRARIES MolTransforms) 3 | 4 | rdkit_headers(ShapeEncoder.h 5 | ShapeUtils.h DEST GraphMol/ShapeHelpers) 6 | 7 | rdkit_test(testShapeHelpers testShapeHelpers.cpp 8 | LINK_LIBRARIES ShapeHelpers FileParsers MolAlign 9 | SmilesParse FileParsers MolTransforms SubstructMatch EigenSolvers Alignment DataStructs 10 | GraphMol RDGeneral RDGeometryLib ) 11 | 12 | add_subdirectory(Wrap) 13 | 14 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/AtomProps1.mol: -------------------------------------------------------------------------------- 1 | 2 | -ISIS- 05110910502D 3 | 4 | 4 3 0 0 0 0 0 0 0 0999 V2000 5 | -3.0000 -7.8750 0.0000 C 0 0 0 0 0 0 0 0 0 1 0 0 6 | -2.2855 -7.4625 0.0000 C 0 0 0 0 0 0 0 0 0 2 0 0 7 | -2.2855 -6.6375 0.0000 O 0 0 0 0 0 0 0 0 0 3 0 0 8 | -1.5711 -7.8750 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 9 | 2 3 2 0 0 0 0 10 | 1 2 1 0 0 0 0 11 | 2 4 1 0 0 0 0 12 | V 2 acidchloride 13 | M END 14 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/three_coordinate_chirality.1.mol: -------------------------------------------------------------------------------- 1 | 2 | Mrv0540 07221113152D 3 | 4 | 4 3 0 0 0 0 999 V2000 5 | -0.2121 0.4950 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6 | 0.6129 0.4950 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 7 | 0.6129 1.3200 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 8 | 1.1962 -0.0884 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | 1 2 1 0 0 0 0 10 | 2 3 1 0 0 0 0 11 | 2 4 1 1 0 0 0 12 | M END 13 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/three_coordinate_chirality.2.mol: -------------------------------------------------------------------------------- 1 | 2 | Mrv0540 07221113182D 3 | 4 | 4 3 0 0 0 0 999 V2000 5 | -0.2121 0.4950 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6 | 0.6129 0.4950 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 7 | 0.6129 1.3200 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 8 | 1.1962 -0.0884 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | 1 2 1 0 0 0 0 10 | 2 3 1 1 0 0 0 11 | 2 4 1 1 0 0 0 12 | M END 13 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/three_coordinate_chirality.3.mol: -------------------------------------------------------------------------------- 1 | 2 | Mrv0540 07221113182D 3 | 4 | 4 3 0 0 0 0 999 V2000 5 | -0.2121 0.4950 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6 | 0.6129 0.4950 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 0.6129 1.3200 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 8 | 1.1962 -0.0884 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | 1 2 1 0 0 0 0 10 | 2 3 1 6 0 0 0 11 | 2 4 1 1 0 0 0 12 | M END 13 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/three_coordinate_chirality.4.mol: -------------------------------------------------------------------------------- 1 | 2 | Mrv0540 07221114242D 3 | 4 | 4 3 0 0 0 0 999 V2000 5 | -0.2121 0.4950 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6 | 0.6129 0.4950 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 0.6129 1.3200 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 8 | 1.1962 0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | 2 1 1 0 0 0 0 10 | 2 3 1 6 0 0 0 11 | 2 4 1 1 0 0 0 12 | M END 13 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/three_coordinate_chirality.5.mol: -------------------------------------------------------------------------------- 1 | 2 | Mrv0540 07221114392D 3 | 4 | 4 3 0 0 0 0 999 V2000 5 | -0.2121 0.4950 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6 | 0.6129 0.4950 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 7 | 0.6129 1.3200 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 8 | 1.1962 0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | 2 1 1 1 0 0 0 10 | 2 3 1 1 0 0 0 11 | 2 4 1 1 0 0 0 12 | M END 13 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/three_coordinate_chirality.6.mol: -------------------------------------------------------------------------------- 1 | 2 | Mrv0540 07221114422D 3 | 4 | 4 3 0 0 0 0 999 V2000 5 | -0.2121 0.4950 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6 | 0.6129 0.4950 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 7 | 0.6129 1.3200 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 8 | 1.3730 1.0312 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | 2 1 1 1 0 0 0 10 | 2 3 1 6 0 0 0 11 | 2 4 1 1 0 0 0 12 | M END 13 | -------------------------------------------------------------------------------- /Code/GraphMol/ForceFieldHelpers/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | # moved library build directives to UFF (actual location of ForceFieldHelpers 2 | # modules.. might have been a bad idea). 3 | add_subdirectory(UFF) 4 | 5 | rdkit_test(testForceFieldHelpers testHelpers.cpp 6 | LINK_LIBRARIES 7 | ForceFieldHelpers 8 | DistGeomHelpers DistGeometry FileParsers MolTransforms SmilesParse SubstructMatch ForceField MolAlign Optimizer EigenSolvers Alignment GraphMol RDGeometryLib RDGeneral ) 9 | 10 | add_subdirectory(Wrap) 11 | 12 | -------------------------------------------------------------------------------- /Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.h: -------------------------------------------------------------------------------- 1 | // 2 | // Copyright (C) 2006 Greg Landrum 3 | // 4 | // @@ All Rights Reserved @@ 5 | // This file is part of the RDKit. 6 | // The contents are covered by the terms of the BSD license 7 | // which is included in the file license.txt, found at the root 8 | // of the RDKit source tree. 9 | // 10 | #ifndef _RDMOLCATALOG_WRAP_INCL_ 11 | #define _RDMOLCATALOG_WRAP_INCL_ 12 | 13 | #define PY_ARRAY_UNIQUE_SYMBOL rdmolcat_array_API 14 | #include 15 | 16 | 17 | 18 | #endif 19 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/radical.mol: -------------------------------------------------------------------------------- 1 | 2 | Marvin 09040818012D 3 | 4 | 4 3 0 0 0 0 999 V2000 5 | -3.0348 0.7071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | -2.3204 1.1196 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | -1.6059 0.7071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8 | -2.5339 0.3228 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | 1 2 1 0 0 0 0 10 | 2 3 1 0 0 0 0 11 | 2 4 1 0 0 0 0 12 | M RAD 1 2 2 13 | M END 14 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/subst1.mol: -------------------------------------------------------------------------------- 1 | 2 | -ISIS- 08070713502D 3 | 4 | 4 3 0 0 0 0 0 0 0 0999 V2000 5 | -0.2208 -2.3125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | 0.4936 -1.9000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 1.2081 -2.3125 0.0000 * 0 0 0 0 0 0 0 0 0 0 0 0 8 | 0.4936 -1.0750 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9 | 2 3 1 0 0 0 0 10 | 1 2 1 0 0 0 0 11 | 2 4 2 0 0 0 0 12 | M SUB 1 2 3 13 | M END 14 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/subst2.mol: -------------------------------------------------------------------------------- 1 | 2 | -ISIS- 08070714512D 3 | 4 | 4 3 0 0 0 0 0 0 0 0999 V2000 5 | -3.0208 -7.6167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | -2.3064 -7.2042 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 7 | -1.5919 -7.6167 0.0000 * 0 0 0 0 0 0 0 0 0 0 0 0 8 | -2.3064 -6.3792 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9 | 2 3 1 0 0 0 0 10 | 1 2 1 0 0 0 0 11 | 2 4 5 0 0 0 0 12 | M SUB 1 2 -2 13 | M END 14 | -------------------------------------------------------------------------------- /Code/GraphMol/FragCatalog/Wrap/rdfragcatalog.h: -------------------------------------------------------------------------------- 1 | // 2 | // Copyright (C) 2003-2006 Rational Discovery LLC 3 | // 4 | // @@ All Rights Reserved @@ 5 | // This file is part of the RDKit. 6 | // The contents are covered by the terms of the BSD license 7 | // which is included in the file license.txt, found at the root 8 | // of the RDKit source tree. 9 | // 10 | #ifndef _RDFRAGCAT_INCL_ 11 | #define _RDFRAGCAT_INCL_ 12 | 13 | #define PY_ARRAY_UNIQUE_SYMBOL rdfragcat_array_API 14 | #include 15 | 16 | 17 | 18 | #endif 19 | -------------------------------------------------------------------------------- /Code/GraphMol/Subgraphs/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | include_directories(${CMAKE_SOURCE_DIR}/External/boost-numeric-bindings) 2 | 3 | rdkit_library(Subgraphs Subgraphs.cpp SubgraphUtils.cpp 4 | LINK_LIBRARIES GraphMol ) 5 | 6 | rdkit_headers(Subgraphs.h 7 | SubgraphUtils.h DEST GraphMol/Subgraphs) 8 | 9 | rdkit_test(testSubgraphs1 test1.cpp LINK_LIBRARIES Subgraphs SmilesParse GraphMol RDGeometryLib RDGeneral ) 10 | rdkit_test(testSubgraphs2 test2.cpp LINK_LIBRARIES SmilesParse Subgraphs GraphMol RDGeometryLib RDGeneral ) 11 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/v3k.5b.mol: -------------------------------------------------------------------------------- 1 | 2 | Marvin 06110906172D 3 | 4 | 0 0 0 0 0 999 V3000 5 | M V30 BEGIN CTAB 6 | M V30 COUNTS 5 4 0 0 0 7 | M V30 BEGIN ATOM 8 | M V30 1 C -4.73 3.41 0 0 CFG=1 9 | M V30 2 C -3.3963 4.18 0 0 10 | M V30 3 F -6.0637 4.18 0 0 11 | M V30 4 C -4.73 1.87 0 0 12 | M V30 5 O -6.0637 2.64 0 0 13 | M V30 END ATOM 14 | M V30 BEGIN BOND 15 | M V30 1 1 1 2 CFG=1 16 | M V30 2 1 1 3 17 | M V30 3 1 1 4 18 | M V30 4 1 1 5 19 | M V30 END BOND 20 | M V30 END CTAB 21 | M END 22 | -------------------------------------------------------------------------------- /Code/GraphMol/FragCatalog/Wrap/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | rdkit_python_extension(rdfragcatalog 2 | rdfragcatalog.cpp FragCatalog.cpp FragCatParams.cpp 3 | FragCatGenerator.cpp FragFPGenerator.cpp 4 | DEST Chem 5 | LINK_LIBRARIES 6 | FragCatalog 7 | Subgraphs SubstructMatch SmilesParse Catalogs FileParsers GraphMol DataStructs RDGeometryLib RDGeneral 8 | RDBoost) 9 | 10 | add_pytest(pyFragCatalog ${CMAKE_CURRENT_SOURCE_DIR}/rough_test.py) 11 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/AtomProps2.mol: -------------------------------------------------------------------------------- 1 | 2 | -ISIS- 05110910502D 3 | 4 | 4 2 0 0 0 0 0 0 0 0999 V2000 5 | -3.0000 -7.8750 0.0000 C 0 0 0 0 0 0 0 0 0 1 0 0 6 | -2.2855 -7.4625 0.0000 C 0 0 0 0 0 0 0 0 0 2 0 0 7 | -2.2855 -6.6375 0.0000 O 0 0 0 0 0 0 0 0 0 3 0 0 8 | -1.5711 -7.8750 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 9 | 2 3 2 0 0 0 0 10 | 1 2 1 0 0 0 0 11 | V 2 acidchloride 12 | M CHG 1 4 -1 13 | V 3 testing 14 | M END 15 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/Issue399a.mol: -------------------------------------------------------------------------------- 1 | Issue399a.mol 2 | ChemDraw04050615582D 3 | 4 | 4 4 0 0 0 0 0 0 0 0999 V2000 5 | -0.7697 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | 0.0553 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 0.7697 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8 | 0.7697 -0.4125 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9 | 2 1 1 1 10 | 2 3 1 0 11 | 3 4 1 0 12 | 2 4 1 0 13 | M END 14 | -------------------------------------------------------------------------------- /Code/GraphMol/MolAlign/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | rdkit_library(MolAlign AlignMolecules.cpp 2 | LINK_LIBRARIES MolTransforms SubstructMatch Alignment) 3 | 4 | rdkit_headers(AlignMolecules.h DEST GraphMol/MolAlign) 5 | 6 | rdkit_test(testMolAlign testMolAlign.cpp 7 | LINK_LIBRARIES MolAlign 8 | FileParsers DistGeomHelpers MolTransforms ForceFieldHelpers 9 | SmilesParse DistGeometry ForceField Optimizer EigenSolvers Alignment SubstructMatch 10 | GraphMol RDGeneral RDGeometryLib ) 11 | 12 | add_subdirectory(Wrap) 13 | 14 | 15 | 16 | 17 | -------------------------------------------------------------------------------- /Code/GraphMol/Wrap/rdchem.h: -------------------------------------------------------------------------------- 1 | // 2 | // Copyright (C) 2003-2006 Rational Discovery LLC 3 | // 4 | // @@ All Rights Reserved @@ 5 | // This file is part of the RDKit. 6 | // The contents are covered by the terms of the BSD license 7 | // which is included in the file license.txt, found at the root 8 | // of the RDKit source tree. 9 | // 10 | #ifndef _RDCHEM_INCL_ 11 | #define _RDCHEM_INCL_ 12 | 13 | namespace RDKit { 14 | class ConformerException; 15 | } 16 | void rdExceptionTranslator(RDKit::ConformerException const& x); 17 | 18 | #endif 19 | 20 | -------------------------------------------------------------------------------- /Contrib/PBF/Makefile: -------------------------------------------------------------------------------- 1 | 2 | LDFLAGS = -L${RDBASE}/lib -lFileParsers_static \ 3 | -lGraphMol_static -lDataStructs_static -lEigenSolvers_static -lRDGeometryLib_static -lRDGeneral_static \ 4 | -lboost_thread -lboost_system 5 | 6 | ifndef BOOSTHOME 7 | BOOSTHOME=/usr/local/include 8 | endif 9 | CPPFLAGS = -O2 -I${BOOSTHOME} -I${RDBASE}/Code -Wno-deprecated -I/usr/local/include/eigen3 -DUSE_EIGEN2 10 | 11 | %.o : %.cpp PBFRDKit.h 12 | $(CXX) $(CPPFLAGS) -c -o $@ $< 13 | 14 | demo.exe: demo.o PBFRDKit.o 15 | $(CXX) -o $@ $< PBFRDKit.o $(LDFLAGS) 16 | -------------------------------------------------------------------------------- /rdkit/ML/DecTree/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","TreeUtils.py",{}), 4 | ("python","UnitTestTree.py",{}), 5 | ("python","UnitTestXVal.py",{}), 6 | ("python","UnitTestID3.py",{}), 7 | ("python","UnitTestPrune.py",{}), 8 | ("python","UnitTestQuantTree.py",{}), 9 | ("python","UnitTestSigTree.py",{}), 10 | 11 | ] 12 | 13 | 14 | 15 | longTests=[ 16 | ] 17 | if __name__=='__main__': 18 | import sys 19 | from rdkit import TestRunner 20 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 21 | sys.exit(len(failed)) 22 | -------------------------------------------------------------------------------- /Code/Geometry/Transform.h: -------------------------------------------------------------------------------- 1 | // 2 | // Copyright (C) 2003-2006 Rational Discovery LLC 3 | // 4 | // @@ All Rights Reserved @@ 5 | // This file is part of the RDKit. 6 | // The contents are covered by the terms of the BSD license 7 | // which is included in the file license.txt, found at the root 8 | // of the RDKit source tree. 9 | // 10 | #ifndef __RD_TRANSFORM_H__ 11 | #define __RD_TRANSFORM_H__ 12 | 13 | namespace RDGeom { 14 | 15 | typedef enum { 16 | X_Axis, 17 | Y_Axis, 18 | Z_Axis 19 | } AxisType; 20 | } 21 | 22 | #endif 23 | -------------------------------------------------------------------------------- /Code/GraphMol/SmilesParse/primes.h: -------------------------------------------------------------------------------- 1 | // 2 | // Copyright (C) 2002-2006 Greg Landrum and Rational Discovery LLC 3 | // 4 | // @@ All Rights Reserved @@ 5 | // This file is part of the RDKit. 6 | // The contents are covered by the terms of the BSD license 7 | // which is included in the file license.txt, found at the root 8 | // of the RDKit source tree. 9 | // 10 | #ifndef _RD_PRIMES_H 11 | #define _RD_PRIMES_H 12 | 13 | namespace RDKit{ 14 | const int NUM_PRIMES_AVAIL = 1000; 15 | extern int firstThousandPrimes[NUM_PRIMES_AVAIL]; 16 | } 17 | #endif 18 | -------------------------------------------------------------------------------- /Code/doxygen/rdkdocs_header.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | $title 6 | 7 | 8 | 9 | 10 | 11 | -------------------------------------------------------------------------------- /Code/GraphMol/ChemTransforms/testData/oldcrash.mol: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 4 0 0 0 0 0 0 0 0999 V2000 5 | 0.0000 0.2833 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 6 | -1.2417 -0.4208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 1.2375 -0.4208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8 | -2.4917 0.2833 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | 2.4875 0.2833 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10 | 2 1 1 0 11 | 3 1 1 0 12 | 4 2 1 0 13 | 5 3 1 0 14 | M END 15 | 16 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/v3k.5a.mol: -------------------------------------------------------------------------------- 1 | 2 | Marvin 06110906172D 3 | 4 | 0 0 0 0 0 999 V3000 5 | M V30 BEGIN CTAB 6 | M V30 COUNTS 5 4 0 0 0 7 | M V30 BEGIN ATOM 8 | M V30 1 C -4.7303 3.4103 0 0 CFG=1 9 | M V30 2 C -3.3967 4.1803 0 0 10 | M V30 3 F -6.0641 4.1803 0 0 11 | M V30 4 Cl -4.7303 1.8702 0 0 12 | M V30 5 O -6.0641 2.6402 0 0 13 | M V30 END ATOM 14 | M V30 BEGIN BOND 15 | M V30 1 1 1 2 CFG=1 16 | M V30 2 1 1 3 17 | M V30 3 1 1 4 18 | M V30 4 1 1 5 19 | M V30 END BOND 20 | M V30 END CTAB 21 | M END 22 | -------------------------------------------------------------------------------- /Code/GraphMol/MolChemicalFeatures/Wrap/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | rdkit_python_extension(rdMolChemicalFeatures 2 | rdMolChemicalFeatures.cpp MolChemicalFeature.cpp 3 | MolChemicalFeatureFactory.cpp ChemicalFeatureUtils.cpp 4 | DEST Chem 5 | LINK_LIBRARIES MolChemicalFeatures 6 | Catalogs 7 | SmilesParse SubstructMatch DataStructs 8 | GraphMol RDGeometryLib RDGeneral 9 | RDBoost) 10 | 11 | add_pytest(pyChemicalFeatures 12 | ${CMAKE_CURRENT_SOURCE_DIR}/testChemicalFeatures.py) 13 | 14 | 15 | 16 | 17 | -------------------------------------------------------------------------------- /Code/Demos/RDKit/Basement/TemplEnum/Makefile: -------------------------------------------------------------------------------- 1 | include $(RDBASE)/Code/rdvars.make 2 | CXXFLAGS=$(BASECXXFLAGS) 3 | 4 | LDFLAGS= $(RDFILEPARSE) $(RDSMILES) $(RDSUBSTRUCT) $(VFLIB) $(RDKIT) $(RDBITVECS) \ 5 | $(RDMOLTRANSFORMS) $(RDGENERAL) $(RDGEOMETRY) 6 | 7 | OBJS=main.o TemplEnumTools.o 8 | 9 | main.exe: $(OBJS) 10 | g++ -o main.exe $(CXXFLAGS) $(OBJS) $(LDFLAGS) 11 | 12 | SIMPLEOBJS=simple.o TemplEnumTools.o 13 | simple.exe: $(SIMPLEOBJS) 14 | g++ -o simple.exe $(CXXFLAGS) $(SIMPLEOBJS) $(LDFLAGS) 15 | 16 | clean: 17 | rm -f main.exe $(OBJS) 18 | 19 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/not-list-query.mol: -------------------------------------------------------------------------------- 1 | 2 | -ISIS- 07190711082D 3 | 4 | 4 3 1 0 0 0 0 0 0 0999 V2000 5 | 1.5250 -2.2500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | 2.2395 -1.8375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 2.9539 -2.2500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8 | 2.2395 -1.0125 0.0000 L 0 0 0 0 0 0 0 0 0 0 0 0 9 | 2 3 1 0 0 0 0 10 | 1 2 1 0 0 0 0 11 | 2 4 2 0 0 0 0 12 | 4 T 2 7 8 13 | M ALS 4 2 T N O 14 | M END 15 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/ringcount_star2.mol: -------------------------------------------------------------------------------- 1 | 2 | -ISIS- 02260813412D 3 | 4 | 4 4 0 0 0 0 0 0 0 0999 V2000 5 | 2.9666 -3.9416 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | 2.9666 -4.7666 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 3.7916 -4.7666 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8 | 3.7916 -3.9416 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | 1 2 1 0 0 0 0 10 | 2 3 1 0 0 0 0 11 | 3 4 1 0 0 0 0 12 | 4 1 1 0 0 0 0 13 | M RBC 1 3 -2 14 | M END 15 | -------------------------------------------------------------------------------- /Code/GraphMol/GraphMol.h: -------------------------------------------------------------------------------- 1 | // 2 | // Copyright (C) 2001-2006 Greg Landrum and Rational Discovery LLC 3 | // 4 | // @@ All Rights Reserved @@ 5 | // This file is part of the RDKit. 6 | // The contents are covered by the terms of the BSD license 7 | // which is included in the file license.txt, found at the root 8 | // of the RDKit source tree. 9 | // 10 | /*! \file GraphMol.h 11 | 12 | \brief pulls in RWMol and ROMol 13 | 14 | */ 15 | #ifndef _GRAPH_MOL_H 16 | #define _GRAPH_MOL_H 17 | 18 | 19 | #include "ROMol.h" 20 | #include "RWMol.h" 21 | 22 | #endif 23 | -------------------------------------------------------------------------------- /rdkit/test_list.py: -------------------------------------------------------------------------------- 1 | 2 | tests=[ 3 | ("python","test_list.py",{'dir':'ML'}), 4 | ("python","test_list.py",{'dir':'Chem'}), 5 | ("python","test_list.py",{'dir':'DataStructs'}), 6 | ("python","test_list.py",{'dir':'Dbase'}), 7 | ("python","test_list.py",{'dir':'SimDivFilters'}), 8 | ("python","test_list.py",{'dir':'VLib'}), 9 | 10 | ] 11 | 12 | 13 | 14 | longTests=[ 15 | ] 16 | 17 | if __name__=='__main__': 18 | import sys 19 | from rdkit import TestRunner 20 | failed,tests = TestRunner.RunScript('test_list.py',0,1) 21 | sys.exit(len(failed)) 22 | -------------------------------------------------------------------------------- /Code/Demos/RDKit/Basement/BinaryIO/Makefile: -------------------------------------------------------------------------------- 1 | include $(RDBASE)/Code/rdvars.make 2 | include $(RDBASE)/Code/rdrules.make 3 | CXXFLAGS=$(BASECXXFLAGS) -DSUPPORT_COMPRESSED_IO 4 | LDFLAGS= $(RDFILEPARSE) $(RDSMILES) $(RDSUBSTRUCT) $(VFLIB) $(RDKIT) $(RDBITVECS) \ 5 | $(RDGENERAL) $(RDGEOMETRY) $(RDDEPICTOR) 6 | 7 | SOURCES=iotest.cpp 8 | 9 | testExecs/iotest.exe: iotest.o $(RDFILEPARSELIB) 10 | $(CXX) -o $@ $(CXXFLAGS) $< $(LDFLAGS) -L$(BOOSTHOME)/lib -lboost_iostreams-gcc-mt 11 | 12 | clean: 13 | rm -f iotest.o testExecs/iotest.exe 14 | 15 | include $(DEPENDS) 16 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/combined.mol: -------------------------------------------------------------------------------- 1 | 2 | Marvin 06021016032D 3 | 4 | 4 3 0 0 0 0 999 V2000 5 | -0.2208 -2.3127 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | 0.4936 -1.9001 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 1.2082 -2.3127 0.0000 C 0 5 0 0 0 0 0 0 0 0 0 0 8 | 0.4936 -1.0751 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9 | 2 3 1 0 0 0 0 10 | 1 2 1 0 0 0 0 11 | 2 4 2 0 0 0 0 12 | M CHG 1 3 -1 13 | M SUB 1 3 2 14 | M END 15 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/conflicting-list-query.mol: -------------------------------------------------------------------------------- 1 | 2 | -ISIS- 07190711082D 3 | 4 | 4 3 1 0 0 0 0 0 0 0999 V2000 5 | 1.5250 -2.2500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | 2.2395 -1.8375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 2.9539 -2.2500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8 | 2.2395 -1.0125 0.0000 L 0 0 0 0 0 0 0 0 0 0 0 0 9 | 2 3 1 0 0 0 0 10 | 1 2 1 0 0 0 0 11 | 2 4 2 0 0 0 0 12 | 4 F 2 7 8 13 | M ALS 4 2 T N O 14 | M END 15 | -------------------------------------------------------------------------------- /Code/GraphMol/PartialCharges/Wrap/test_data/halgren.smi: -------------------------------------------------------------------------------- 1 | Smiles Name 2 | CO Methanol 3 | CN Methylamine 4 | CC#N Acetonitrile 5 | COC Dimethyl_Ether 6 | CS Methanethiol 7 | C[Cl] Chloromethane 8 | CC Ethane 9 | CC(=O)N Acetamide 10 | CC(=O)O Acetic_Acid_prot 11 | CC(=O)C Acetone 12 | CC(=O)OC Methyl_Acetate 13 | c1ccccc1 Benzene 14 | c1ccncc1 Pyridine 15 | c1ccccc1N Aniline 16 | C1=CNC=N1 Imidazole 17 | O Water 18 | CC(=O)[O-] Acetic_Acid(-) 19 | C[NH3+] Methylamonium 20 | C1=C[NH+]=CN1 Imidazolium(+) 21 | [NH3+]CCCCCCC(=O)[O-] 7-Aminoheptanoic_Acid 22 | 23 | -------------------------------------------------------------------------------- /Docs/Book/data/bzr.smi: -------------------------------------------------------------------------------- 1 | CN(C)Cc1n-2c(nn1)CN=C(c1ccccc1)c1cc(Cl)ccc12 Adinazolam 2 | Cc1n-2c(nn1)CN=C(c1ccccc1)c1cc(Cl)ccc12 Alprazolam 3 | Brc1cc2c(cc1)NC(=O)CN=C2c1ncccc1 Bromazepam 4 | CNC1=Nc2c(cc(Cl)cc2)C(c2ccccc2)=[N+]([O-])C1 Chlordiazepoxide 5 | CN1c2ccc(Cl)cc2N(c2ccccc2)C(=O)CC1=O Clobazam 6 | [O-][N+](=O)c1cc2c(cc1)NC(=O)CN=C2c1c(Cl)cccc1 Clonazepam 7 | OC(=O)C1N=C(c2ccccc2)c2cc(Cl)ccc2NC1=O Clorazepate 8 | Clc1cc2c(cc1)NC(=O)CN=C2c1c(Cl)cccc1 Delorazepam 9 | [O-][N+]1=C(c2ccccc2)c2cc(Cl)ccc2NC(=O)C1 Demoxepam 10 | Clc1cc2c(cc1)NC(=O)CC(=O)N2c1ccccc1 Desmethylclobazam 11 | -------------------------------------------------------------------------------- /Contrib/mmpa/sample_mmps_sym_maxheavy.csv: -------------------------------------------------------------------------------- 1 | Nc1ccc(-c2cc3ccccc3oc2=O)cc1,O=c1oc2ccccc2cc1-c1ccc(O)cc1,310860,4055843,[*:1]N>>[*:1]O,[*:1]c1ccc(-c2cc3ccccc3oc2=O)cc1 2 | O=c1oc2ccccc2cc1-c1ccc(O)cc1,Nc1ccc(-c2cc3ccccc3oc2=O)cc1,4055843,310860,[*:1]O>>[*:1]N,[*:1]c1ccc(-c2cc3ccccc3oc2=O)cc1 3 | O=C(O)c1ccc(NC(=O)C2COc3ccccc3O2)cc1,NC(=O)c1ccc(NC(=O)C2COc3ccccc3O2)cc1,2881039,2787356,[*:1]C(=O)O>>[*:1]C(N)=O,[*:1]c1ccc(NC(=O)C2COc3ccccc3O2)cc1 4 | NC(=O)c1ccc(NC(=O)C2COc3ccccc3O2)cc1,O=C(O)c1ccc(NC(=O)C2COc3ccccc3O2)cc1,2787356,2881039,[*:1]C(N)=O>>[*:1]C(=O)O,[*:1]c1ccc(NC(=O)C2COc3ccccc3O2)cc1 5 | -------------------------------------------------------------------------------- /Code/GraphMol/FileParsers/test_data/ringcount_star3.mol: -------------------------------------------------------------------------------- 1 | 2 | -ISIS- 02260816512D 3 | 4 | 4 4 0 0 0 0 0 0 0 0999 V2000 5 | 2.9666 -3.9416 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6 | 2.9666 -4.7666 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7 | 3.7916 -4.7666 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8 | 3.7916 -3.9416 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9 | 1 2 1 0 0 0 0 10 | 2 3 1 0 0 0 0 11 | 3 4 1 0 0 0 0 12 | 4 1 1 0 0 0 0 13 | M RBC 4 1 -2 2 -2 3 -2 4 -2 14 | M END 15 | --------------------------------------------------------------------------------