The official sources for the RDKit library
This report presents the forensic synthetic code analysis of rdkit/rdkit, a HTML project with 3,570 GitHub stars. SynthScan v2.0 examined 799,167 lines of code across 2549 source files, recording 3553 pattern matches distributed across 21 syntactic categories. The overall adjusted score of 5.7 places this repository in the Low AI signal band.
The scanner applied 160+ deterministic lexical heuristics, multi-line block detectors, abstract syntax tree depth profilers, and a cross-file Jaccard similarity matrix to construct a statistically normalised synthetic code estimate. All matches are individually weighted by severity coefficient and contextual multiplier before summation, and the resulting headline score is temporally discounted to account for the repository's development history relative to the commercial emergence of large language model coding tooling (November 2022 onward).
Longitudinal tracking requires multiple scan runs. Once this repository is re-scanned after new commits land, this chart will visualise how the synthetic code signal evolves over time — enabling you to detect whether AI authorship is growing, stabilising, or being actively corrected by human engineers.
Classifies detected patterns by their diagnostic confidence and structural impact. CRITICAL patterns (coefficient 10) represent definitive synthetic signatures — hallucinated imports, explicit LLM attribution metadata — virtually never produced by human authors. HIGH (5) indicates strong structural tells such as cross-file repetition or cross-linguistic idioms. MEDIUM (2) covers recognisable conversational padding and AI-specific vocabulary. LOW (1) captures subtle indicators like tautological comments and generic boilerplate that require density to carry independent signal.
This horizontal bar chart decomposes the repository's raw synthetic code score by top-level directory, allowing you to pinpoint precisely which modules or components carry the highest AI authorship density. Directories with disproportionately high scores relative to their size warrant targeted manual review: concentrated AI signatures often trace back to mass-generated configuration layers, auto-ported test suites, LLM-scaffolded boilerplate classes, or entire subsystems authored under heavy copilot assistance. Use this view to prioritise your human code-review effort.
The scanner identified 3553 distinct pattern matches across 21 syntactic categories. Each entry below represents a discrete location in the source code where the engine recorded a statistically significant AI authorship indicator. Expand any category row to inspect the individual file paths, line numbers, code snippets, and the lexical context (CODE, COMMENT, or STRING) in which each match was detected.
Reading the findings table: The Severity column indicates the diagnostic confidence level (CRITICAL / HIGH / MEDIUM / LOW). The Context column identifies whether the match occurred inside executable code, an inline comment, or a string literal — comment-context matches receive a ×1.5 weight because LLMs systematically over-annotate. The ⚡ bolt icon marks clustered matches: three or more patterns within a 10-line window, each receiving an additional ×1.5 density multiplier as dense clusters constitute far stronger evidence of synthetic authorship than isolated hits.
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | CMakeLists.txt | 801 | SET(CPACK_PACKAGE_VERSION_MAJOR ${RDKit_Year}) | COMMENT |
| LOW | azure-pipelines.yml | 161 | # steps: | COMMENT |
| LOW | Projects/DbCLI/CreateDb.py | 1 | # Copyright (c) 2007, Novartis Institutes for BioMedical Research Inc. | COMMENT |
| LOW | Projects/DbCLI/SearchDb.py | 1 | # Copyright (c) 2007-2013, Novartis Institutes for BioMedical Research Inc. | COMMENT |
| LOW | Projects/DbCLI/SearchDb.py | 21 | # A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT | COMMENT |
| LOW | Code/notes.txt | 21 | - when programming the windows, it's useful to use the XXX_API methods that | COMMENT |
| LOW | Code/DataManip/MetricMatrixCalc/MetricFuncs.h | 1 | // | COMMENT |
| LOW | Code/DataManip/MetricMatrixCalc/MetricMatrixCalc.h | 1 | // | COMMENT |
| LOW | Code/DataManip/MetricMatrixCalc/testMatCalc.cpp | 1 | // | COMMENT |
| LOW | …taManip/MetricMatrixCalc/nbWrap/rdMetricMatrixCalc.cpp | 1 | // | COMMENT |
| LOW | …taManip/MetricMatrixCalc/nbWrap/rdMetricMatrixCalc.cpp | 41 | private: | COMMENT |
| LOW | …taManip/MetricMatrixCalc/nbWrap/rdMetricMatrixCalc.cpp | 61 | // 3. A list (or tuple) of lists (or tuple) | COMMENT |
| LOW | …DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp | 1 | // | COMMENT |
| LOW | …DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp | 61 | // contiguous memory will work | COMMENT |
| LOW | Code/DataStructs/SparseBitVect.cpp | 1 | // | COMMENT |
| LOW | Code/DataStructs/SparseBitVect.cpp | 21 | COMMENT | |
| LOW | Code/DataStructs/SparseBitVect.cpp | 41 | // """ ------------------------------------------------------- | COMMENT |
| LOW | Code/DataStructs/SparseBitVect.cpp | 261 | v.resize(nOn); | COMMENT |
| LOW | Code/DataStructs/MultiFPBReader.h | 1 | // | COMMENT |
| LOW | Code/DataStructs/SparseIntVect.h | 1 | // | COMMENT |
| LOW | Code/DataStructs/SparseIntVect.h | 61 | } | COMMENT |
| LOW | Code/DataStructs/Utils.cpp | 1 | // | COMMENT |
| LOW | Code/DataStructs/testMultiFPB.cpp | 1 | // | COMMENT |
| LOW | Code/DataStructs/FPBReader.cpp | 1 | // | COMMENT |
| LOW | Code/DataStructs/BitOps.h | 1 | // | COMMENT |
| LOW | Code/DataStructs/RealValueVect.h | 1 | // | COMMENT |
| LOW | Code/DataStructs/DatastructsStreamOps.h | 1 | // Copyright (c) 2019, Novartis Institutes for BioMedical Research Inc. | COMMENT |
| LOW | Code/DataStructs/DatastructsStreamOps.h | 21 | // LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR | COMMENT |
| LOW | Code/DataStructs/base64.h | 1 | // | COMMENT |
| LOW | Code/DataStructs/testFPB.cpp | 1 | // | COMMENT |
| LOW | Code/DataStructs/BitVect.cpp | 1 | // | COMMENT |
| LOW | Code/DataStructs/base64.cpp | 1 | // | COMMENT |
| LOW | Code/DataStructs/base64.cpp | 21 | // 6 G 23 X 40 o 57 5 | COMMENT |
| LOW | Code/DataStructs/MultiFPBReader.cpp | 1 | // | COMMENT |
| LOW | Code/DataStructs/DiscreteDistMat.cpp | 1 | // | COMMENT |
| LOW | Code/DataStructs/BitVect.h | 1 | // | COMMENT |
| LOW | Code/DataStructs/FPBReader.h | 1 | // | COMMENT |
| LOW | Code/DataStructs/catch_tests.cpp | 1 | // | COMMENT |
| LOW | Code/DataStructs/DiscreteValueVect.h | 1 | // | COMMENT |
| LOW | Code/DataStructs/BitVectUtils.h | 1 | // | COMMENT |
| LOW | Code/DataStructs/SparseBitVect.h | 1 | // | COMMENT |
| LOW | Code/DataStructs/RealValueVect.cpp | 1 | // | COMMENT |
| LOW | Code/DataStructs/BitOps.cpp | 1 | // | COMMENT |
| LOW | Code/DataStructs/BitOps.cpp | 461 | return 1.0; | COMMENT |
| LOW | Code/DataStructs/BitOps.cpp | 521 | static_cast<int>(((*bv1.dp_bits) ^ (*bv2.dp_bits)).count()); | COMMENT |
| LOW | Code/DataStructs/BitOps.cpp | 541 | throw ValueErrorException("BitVects must be same length"); | COMMENT |
| LOW | Code/DataStructs/BitOps.cpp | 601 | // The on bit projected similarity of T1 onto T2 is the | COMMENT |
| LOW | Code/DataStructs/BitOps.cpp | 641 | // percentage of T1's off bits which are off in T2. | COMMENT |
| LOW | Code/DataStructs/BitOps.cpp | 901 | #include <intrin.h> | COMMENT |
| LOW | Code/DataStructs/BitVects.h | 1 | // | COMMENT |
| LOW | Code/DataStructs/DiscreteDistMat.h | 1 | // | COMMENT |
| LOW | Code/DataStructs/DatastructsException.h | 1 | // | COMMENT |
| LOW | Code/DataStructs/ExplicitBitVect.h | 1 | // | COMMENT |
| LOW | Code/DataStructs/testDatastructs.cpp | 1 | // | COMMENT |
| LOW | Code/DataStructs/DiscreteValueVect.cpp | 1 | // | COMMENT |
| LOW | Code/DataStructs/ExplicitBitVect.cpp | 1 | // | COMMENT |
| LOW | Code/DataStructs/nbWrap/wrap_SparseBV.cpp | 1 | // | COMMENT |
| LOW | Code/DataStructs/nbWrap/wrap_ExplicitBV.cpp | 1 | // | COMMENT |
| LOW | Code/DataStructs/nbWrap/wrap_BitOps.cpp | 1 | // | COMMENT |
| LOW | Code/DataStructs/nbWrap/SparseIntVect.cpp | 1 | // | COMMENT |
| 2150 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| MEDIUM | Regress/Scripts/fingerprint_screenout.py | 5 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | Code/GraphMol/TautomerQuery/Wrap/rough_test.py | 6 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | Code/GraphMol/DetermineBonds/Wrap/testDetermineBonds.py | 5 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | Code/GraphMol/MolProcessing/Wrap/testMolProcessing.py | 5 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | …e/GraphMol/ScaffoldNetwork/Wrap/testScaffoldNetwork.py | 5 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | …hMol/ScaffoldNetwork/Wrap/testPickleScaffoldNetwork.py | 5 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | Code/GraphMol/Wrap/testSCSR.py | 5 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | Code/GraphMol/Wrap/testSubstructureMatch.py | 5 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | Code/GraphMol/Wrap/testSGroups.py | 5 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | Code/GraphMol/Descriptors/test_data/pmi.py | 5 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | …/GeneralizedSubstruct/Wrap/testGeneralizedSubstruct.py | 5 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | Code/GraphMol/Abbreviations/Wrap/testAbbreviations.py | 5 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | Code/GraphMol/MolEnumerator/Wrap/rough_test.py | 5 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | Docs/Book/conf.py | 6 | # This file is execfile()d with the current directory set to its containing dir. | COMMENT |
| MEDIUM | Docs/Book_jp/conf.py | 7 | # This file is execfile()d with the current directory set to its | COMMENT |
| MEDIUM | Contrib/CalcLigRMSD/CalcLigRMSD.py | 5 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | Contrib/Fastcluster/fastcluster.py | 3 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | Contrib/IFG/ifg.py | 3 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | Contrib/efgs/try_efgs.py | 104 | # Create a blank background image for the grid | COMMENT |
| MEDIUM | Contrib/efgs/efgs.py | 371 | # Create a copy of the fragment to modify | COMMENT |
| MEDIUM | Contrib/efgs/efgs.py | 379 | # Create a dummy atom with the R group label | COMMENT |
| MEDIUM | Contrib/efgs/efgs.py | 501 | # Define the pattern to match | COMMENT |
| MEDIUM | Contrib/efgs/efgs.py | 504 | # Define the replacement string | COMMENT |
| MEDIUM | Contrib/FreeWilson/freewilson.py | 4 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | Contrib/PBF/pbf.py | 5 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | Scripts/run_python_tests.py | 5 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | External/ChemDraw/Wrap/testChemDraw.py | 4 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | External/CoordGen/Wrap/testCoordGen.py | 4 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | External/YAeHMOP/Wrap/testEHTTools.py | 4 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | rdkit/RDConfig.py | 6 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | rdkit/UnitTestLogging.py | 5 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | rdkit/RDLogger.py | 4 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | rdkit/TestRunner.py | 5 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | rdkit/RDRandom.py | 5 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | rdkit/DataManip/Metric/__init__.py | 4 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | rdkit/DataStructs/UnitTestTopNContainer.py | 4 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | rdkit/DataStructs/UnitTestDocTests.py | 4 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | rdkit/DataStructs/BitEnsembleDb.py | 4 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | rdkit/DataStructs/VectCollection.py | 4 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | rdkit/DataStructs/BitUtils.py | 4 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | rdkit/DataStructs/__init__.py | 4 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | rdkit/DataStructs/TopNContainer.py | 4 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | rdkit/DataStructs/UnitTestBitEnsemble.py | 4 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | rdkit/DataStructs/UnitTestFlatMatrix.py | 5 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | rdkit/DataStructs/UnitTestcBitVect.py | 4 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | rdkit/DataStructs/BitEnsemble.py | 4 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | rdkit/DataStructs/HierarchyVis.py | 4 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | rdkit/Dbase/UnitTestDbInfo.py | 5 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | rdkit/Dbase/DbConnection.py | 5 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | rdkit/Dbase/__init__.py | 5 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | rdkit/Dbase/UnitTestDbConnect.py | 4 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | rdkit/Dbase/DbUtils.py | 4 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | rdkit/Dbase/UnitTestDbResultSet.py | 4 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | rdkit/Dbase/StorageUtils.py | 4 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | rdkit/Dbase/UnitTestDbUtils.py | 4 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | rdkit/Dbase/DbInfo.py | 4 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | rdkit/Dbase/UnitTestStorageUtils.py | 4 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | rdkit/Dbase/DbModule.py | 4 | # This file is part of the RDKit. | COMMENT |
| MEDIUM | rdkit/utils/chemdraw_qax.py | 35 | # Create an instance of that class | COMMENT |
| MEDIUM | rdkit/utils/chemdraw.py | 4 | # This file is part of the RDKit. | COMMENT |
| 131 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| MEDIUM | Regress/Data/RLewis_smarts.txt | 6 | #------------------- | COMMENT |
| MEDIUM | Regress/Data/RLewis_smarts.txt | 39 | #------------------- | COMMENT |
| MEDIUM | Regress/Data/RLewis_smarts.txt | 57 | #------------------- | COMMENT |
| MEDIUM | Regress/Data/RLewis_smarts.txt | 67 | #------------------- | COMMENT |
| MEDIUM | Regress/Data/RLewis_smarts.txt | 81 | #------------------- | COMMENT |
| MEDIUM | Regress/Data/RLewis_smarts.txt | 283 | #------------------- | COMMENT |
| MEDIUM | Regress/Data/RLewis_smarts.txt | 336 | #------------------- | COMMENT |
| MEDIUM | Regress/Data/RLewis_smarts.txt | 371 | #------------------- | COMMENT |
| MEDIUM⚡ | Code/GraphMol/Wrap/testGetPropDefault.py | 6 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM⚡ | Code/GraphMol/Wrap/testGetPropDefault.py | 8 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM⚡ | Code/GraphMol/Wrap/testGetPropDefault.py | 76 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM⚡ | Code/GraphMol/Wrap/testGetPropDefault.py | 78 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM⚡ | Code/GraphMol/Wrap/testGetPropDefault.py | 120 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM⚡ | Code/GraphMol/Wrap/testGetPropDefault.py | 122 | # --------------------------------------------------------------------------- | COMMENT |
| MEDIUM | Contrib/ChiralPairs/ChiralDescriptors.py | 404 | #------------------------------------ | COMMENT |
| MEDIUM | Contrib/SA_Score/sascorer.py | 86 | # --------------------------------------- | COMMENT |
| MEDIUM | rdkit/RDConfig.py | 47 | # --------------------- | COMMENT |
| MEDIUM | rdkit/RDConfig.py | 52 | # --------------------- | COMMENT |
| MEDIUM | rdkit/RDConfig.py | 85 | # --------------------- | COMMENT |
| MEDIUM | rdkit/DataStructs/LazySignature.py | 69 | # ------------------------------------ | COMMENT |
| MEDIUM | rdkit/DataStructs/VectCollection.py | 270 | # ------------------------------------ | COMMENT |
| MEDIUM | rdkit/DataStructs/BitUtils.py | 39 | # ------------------------------------ | COMMENT |
| MEDIUM | rdkit/Dbase/StorageUtils.py | 264 | # ------------------------------------ | COMMENT |
| MEDIUM | rdkit/utils/chemdraw_qax.py | 22 | #---------------------------------------------------------------------- | COMMENT |
| MEDIUM | rdkit/utils/chemdraw.py | 85 | # ------------------------------------------------------------------ | COMMENT |
| MEDIUM | rdkit/utils/chemdraw.py | 87 | # ------------------------------------------------------------------ | COMMENT |
| MEDIUM | rdkit/utils/chemdraw.py | 275 | # ------------------------------------------------------------------ | COMMENT |
| MEDIUM | rdkit/utils/chemdraw.py | 277 | # ------------------------------------------------------------------ | COMMENT |
| MEDIUM | rdkit/utils/listutils.py | 52 | # ------------------------------------ | COMMENT |
| MEDIUM | rdkit/ML/Descriptors/CompoundDescriptors.py | 100 | # ------------ | COMMENT |
| MEDIUM | rdkit/ML/Descriptors/CompoundDescriptors.py | 102 | # ------------ | COMMENT |
| MEDIUM | rdkit/ML/Descriptors/CompoundDescriptors.py | 208 | # ------------ | COMMENT |
| MEDIUM | rdkit/ML/Descriptors/CompoundDescriptors.py | 210 | # ------------ | COMMENT |
| MEDIUM | rdkit/ML/Descriptors/Parser.py | 56 | # ---------------------- | COMMENT |
| MEDIUM | rdkit/ML/Descriptors/Parser.py | 58 | # ---------------------- | COMMENT |
| MEDIUM | rdkit/ML/Descriptors/Parser.py | 227 | # ------------------ | COMMENT |
| MEDIUM | rdkit/ML/Descriptors/Parser.py | 230 | # ------------------ | COMMENT |
| MEDIUM⚡ | rdkit/ML/Descriptors/Parser.py | 430 | # ------------ | COMMENT |
| MEDIUM⚡ | rdkit/ML/Descriptors/Parser.py | 432 | # ------------ | COMMENT |
| MEDIUM | rdkit/ML/Descriptors/Descriptors.py | 24 | # ------------ | COMMENT |
| MEDIUM | rdkit/ML/Descriptors/Descriptors.py | 26 | # ------------ | COMMENT |
| MEDIUM | rdkit/ML/Data/SplitData.py | 295 | # ------------------------------------ | COMMENT |
| MEDIUM | rdkit/ML/Data/Quantize.py | 237 | # -------------------------------- | COMMENT |
| MEDIUM | rdkit/ML/Data/Quantize.py | 248 | # -------------------------------- | COMMENT |
| MEDIUM | rdkit/ML/Data/DataUtils.py | 669 | # ------------------------------------ | COMMENT |
| MEDIUM | rdkit/sping/stringformat.py | 44 | #------------------------------------------------------------------------ | COMMENT |
| MEDIUM | rdkit/sping/stringformat.py | 50 | #------------------------------------------------------------------------ | COMMENT |
| MEDIUM | rdkit/sping/stringformat.py | 97 | #------------------------------------------------------------------------ | COMMENT |
| MEDIUM | rdkit/sping/stringformat.py | 152 | #------------------------------------------------------------------ | COMMENT |
| MEDIUM | rdkit/sping/stringformat.py | 165 | #------------------------------------------------------------------ | COMMENT |
| MEDIUM | rdkit/sping/stringformat.py | 168 | #---------------------------------------------------------- | COMMENT |
| MEDIUM | rdkit/sping/stringformat.py | 180 | #---------------------------------------------------------- | COMMENT |
| MEDIUM | rdkit/sping/stringformat.py | 226 | #---------------------------------------------------------------- | COMMENT |
| MEDIUM | rdkit/sping/stringformat.py | 286 | #---------------------------------------------------------------- | COMMENT |
| MEDIUM | rdkit/sping/stringformat.py | 290 | #---------------------------------------------------------------- | COMMENT |
| MEDIUM | rdkit/sping/stringformat.py | 317 | #---------------------------------------------------------------- | COMMENT |
| MEDIUM | rdkit/sping/stringformat.py | 332 | #------------------------------------------------------------------------ | COMMENT |
| MEDIUM | rdkit/sping/stringformat.py | 351 | #------------------------------------------------------------------------ | COMMENT |
| MEDIUM | rdkit/sping/stringformat.py | 355 | #------------------------------------------------------------------------ | COMMENT |
| MEDIUM | rdkit/sping/stringformat.py | 413 | #------------------------------------------------------------------------ | COMMENT |
| 81 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | Regress/Scripts/fingerprint_screenout.py | 16 | CODE | |
| LOW | Regress/Scripts/timings.py | 2 | CODE | |
| LOW | Web/RDExtras/MolImage.py | 5 | CODE | |
| LOW | Web/RDExtras/MolImage.py | 11 | CODE | |
| LOW | Web/RDExtras/MolDepict.py | 1 | CODE | |
| LOW | Web/RDExtras/MolDepict.py | 2 | CODE | |
| LOW | Web/RDExtras/MolDepict.py | 3 | CODE | |
| LOW | Web/RDExtras/MolDepict.py | 6 | CODE | |
| LOW | Projects/DbCLI/CreateDb.py | 277 | CODE | |
| LOW | Projects/DbCLI/UnitTestDbCLI.py | 10 | CODE | |
| LOW | Code/DataStructs/Wrap/testBV.py | 3 | CODE | |
| LOW | Code/DataStructs/Wrap/testRealValueVect.py | 5 | CODE | |
| LOW | Code/DataStructs/Wrap/testRealValueVect.py | 5 | CODE | |
| LOW | Code/JavaWrappers/parse_doxy_html.py | 15 | CODE | |
| LOW | Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelWrapTest.py | 3 | CODE | |
| LOW | Code/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py | 5 | CODE | |
| LOW | Code/GraphMol/Wrap/test_cdxml.py | 306 | CODE | |
| LOW | Code/GraphMol/Wrap/test_cdxml.py | 347 | CODE | |
| LOW | Code/GraphMol/MolInteractionFields/Wrap/testMIF.py | 1 | CODE | |
| LOW | Code/GraphMol/Descriptors/test_data/pmi.py | 14 | CODE | |
| LOW | Code/GraphMol/Descriptors/Wrap/test3D.py | 2 | CODE | |
| LOW | Code/GraphMol/MolDraw2D/update_hash_codes.py | 11 | CODE | |
| LOW | Code/GraphMol/MolDraw2D/Qt/Wrap/testMolDraw2DQt.py | 10 | CODE | |
| LOW | Code/GraphMol/MolDraw2D/Qt/Wrap/testMolDraw2DQt.py | 13 | CODE | |
| LOW | …hMol/SynthonSpaceSearch/Wrap/testSynthonSpaceSearch.py | 43 | CODE | |
| LOW | Code/Demos/boost/numpy/test.py | 2 | CODE | |
| LOW | Code/Demos/boost/smartPtrsAndIters/setup.py | 5 | CODE | |
| LOW | Docs/Book/data/test_multi_colours.py | 3 | CODE | |
| LOW | Docs/Book/data/test_multi_colours.py | 5 | CODE | |
| LOW | Docs/Book/data/test_multi_colours.py | 6 | CODE | |
| LOW | Contrib/RxnRoleAssignment/identifyReactants.py | 34 | CODE | |
| LOW | Contrib/RxnRoleAssignment/utils.py | 37 | CODE | |
| LOW | Contrib/Fastcluster/fastcluster.py | 18 | CODE | |
| LOW | Contrib/Fastcluster/fastcluster.py | 19 | CODE | |
| LOW | Contrib/M_Kossner/Frames.py | 21 | CODE | |
| LOW | Contrib/pzc/p_con.py | 17 | CODE | |
| LOW | Contrib/pzc/p_con.py | 18 | CODE | |
| LOW | Contrib/pzc/p_con.py | 19 | CODE | |
| LOW | Contrib/pzc/p_con.py | 22 | CODE | |
| LOW | Contrib/pzc/p_con.py | 22 | CODE | |
| LOW | Contrib/pzc/p_con.py | 22 | CODE | |
| LOW | Contrib/efgs/try_efgs.py | 16 | CODE | |
| LOW | Contrib/efgs/try_efgs.py | 19 | CODE | |
| LOW | Contrib/FreeWilson/freewilson.py | 138 | CODE | |
| LOW | Contrib/FreeWilson/freewilson.py | 142 | CODE | |
| LOW | Contrib/mmpa/test_rfrag.py | 6 | CODE | |
| LOW | Contrib/mmpa/test_rfrag.py | 10 | CODE | |
| LOW | Contrib/AtomAtomSimilarity/AtomAtomPathSimilarity.py | 13 | CODE | |
| LOW | Contrib/LEF/AddLabels.py | 33 | CODE | |
| LOW | Contrib/LEF/CreateFps.py | 38 | CODE | |
| LOW | Contrib/LEF/DistancePredict.py | 39 | CODE | |
| LOW | Contrib/SA_Score/UnitTestSAScore.py | 1 | CODE | |
| LOW | Contrib/SA_Score/UnitTestSAScore.py | 6 | CODE | |
| LOW | …b/NIBRSubstructureFilters/assignSubstructureFilters.py | 2 | CODE | |
| LOW | …b/NIBRSubstructureFilters/assignSubstructureFilters.py | 4 | CODE | |
| LOW | …b/NIBRSubstructureFilters/assignSubstructureFilters.py | 4 | CODE | |
| LOW | …b/NIBRSubstructureFilters/assignSubstructureFilters.py | 10 | CODE | |
| LOW | Contrib/PBF/pbf.py | 14 | CODE | |
| LOW | Contrib/fraggle/atomcontrib.py | 37 | CODE | |
| LOW | build_support/pkg_version.py | 1 | CODE | |
| 187 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | Regress/Scripts/chiral_embed.py | 10 | except Exception: | CODE |
| LOW | Web/RDExtras/MolImage.py | 58 | except Exception: | CODE |
| LOW | Projects/DbCLI/CreateDb.py | 231 | except Exception: | CODE |
| LOW⚡ | Projects/DbCLI/CreateDb.py | 242 | except Exception: | CODE |
| LOW⚡ | Projects/DbCLI/CreateDb.py | 246 | except Exception: | CODE |
| LOW⚡ | Projects/DbCLI/CreateDb.py | 250 | except Exception: | CODE |
| LOW⚡ | Projects/DbCLI/CreateDb.py | 254 | except Exception: | CODE |
| LOW | Projects/DbCLI/CreateDb.py | 284 | except Exception: | CODE |
| LOW | Projects/DbCLI/CreateDb.py | 302 | except Exception: | CODE |
| LOW | Projects/DbCLI/CreateDb.py | 330 | except Exception: | CODE |
| LOW | Projects/DbCLI/CreateDb.py | 469 | except Exception: | CODE |
| LOW | Projects/DbCLI/SearchDb.py | 318 | except Exception: | STRING |
| LOW | Code/ML/InfoTheory/Wrap/testRanker.py | 149 | except Exception: | CODE |
| LOW | Code/GraphMol/TautomerQuery/Wrap/rough_test.py | 84 | except Exception: | CODE |
| LOW | Code/GraphMol/nbWrap/rough_test.py | 523 | except Exception: | STRING |
| LOW | Code/GraphMol/nbWrap/rough_test.py | 2359 | except Exception: | CODE |
| LOW | Code/GraphMol/nbWrap/rough_test.py | 2367 | except Exception: | CODE |
| LOW | Code/GraphMol/nbWrap/rough_test.py | 5633 | except Exception: | STRING |
| LOW | Code/GraphMol/nbWrap/rough_test.py | 7315 | except Exception: | CODE |
| LOW | Code/GraphMol/nbWrap/rough_test.py | 8531 | except Exception as e: | STRING |
| LOW | Code/GraphMol/nbWrap/rough_test.py | 8537 | except Exception as e: | STRING |
| MEDIUM | Code/GraphMol/nbWrap/rough_test.py | 6256 | def testSanitizationExceptionBasics(self): | CODE |
| LOW | Code/GraphMol/PartialCharges/Wrap/testPartialCharges.py | 118 | except Exception: | CODE |
| LOW | Code/GraphMol/MolTransforms/Wrap/testMolTransforms.py | 99 | except Exception: | STRING |
| LOW | Code/GraphMol/MolTransforms/Wrap/testMolTransforms.py | 145 | except Exception: | STRING |
| LOW | Code/GraphMol/Wrap/testTrajectory.py | 24 | except Exception: | CODE |
| LOW | Code/GraphMol/Wrap/testTrajectory.py | 31 | except Exception: | CODE |
| LOW⚡ | Code/GraphMol/Wrap/testTrajectory.py | 51 | except Exception: | CODE |
| LOW⚡ | Code/GraphMol/Wrap/testTrajectory.py | 57 | except Exception: | CODE |
| LOW⚡ | Code/GraphMol/Wrap/testTrajectory.py | 66 | except Exception: | CODE |
| LOW | Code/GraphMol/Wrap/testTrajectory.py | 102 | except Exception: | CODE |
| LOW | Code/GraphMol/Wrap/testTrajectory.py | 108 | except Exception: | CODE |
| LOW | Code/GraphMol/Wrap/testTrajectory.py | 119 | except Exception: | CODE |
| LOW⚡ | Code/GraphMol/Wrap/testTrajectory.py | 146 | except Exception: | CODE |
| LOW⚡ | Code/GraphMol/Wrap/testTrajectory.py | 153 | except Exception: | CODE |
| LOW⚡ | Code/GraphMol/Wrap/testTrajectory.py | 161 | except Exception: | CODE |
| LOW⚡ | Code/GraphMol/Wrap/testTrajectory.py | 228 | except Exception: | CODE |
| LOW⚡ | Code/GraphMol/Wrap/testTrajectory.py | 235 | except Exception: | CODE |
| LOW⚡ | Code/GraphMol/Wrap/testTrajectory.py | 243 | except Exception: | CODE |
| LOW | Code/GraphMol/Wrap/testTrajectory.py | 436 | except Exception: | CODE |
| LOW | Code/GraphMol/Wrap/testTrajectory.py | 457 | except Exception: | CODE |
| LOW | Code/GraphMol/Wrap/testTrajectory.py | 490 | except Exception: | CODE |
| LOW | Code/GraphMol/Wrap/rough_test.py | 522 | except Exception: | STRING |
| LOW | Code/GraphMol/Wrap/rough_test.py | 828 | except Exception: | STRING |
| LOW | Code/GraphMol/Wrap/rough_test.py | 2348 | except Exception: | CODE |
| LOW | Code/GraphMol/Wrap/rough_test.py | 2356 | except Exception: | CODE |
| LOW | Code/GraphMol/Wrap/rough_test.py | 5580 | except Exception: | STRING |
| LOW | Code/GraphMol/Wrap/rough_test.py | 7238 | except Exception: | CODE |
| LOW | Code/GraphMol/Wrap/rough_test.py | 8649 | except Exception as e: | STRING |
| LOW | Code/GraphMol/Wrap/rough_test.py | 8655 | except Exception as e: | STRING |
| MEDIUM | Code/GraphMol/Wrap/rough_test.py | 6198 | def testSanitizationExceptionBasics(self): | CODE |
| LOW⚡ | Code/GraphMol/ChemReactions/Wrap/testSanitize.py | 294 | except Exception: | STRING |
| LOW | Code/GraphMol/SubstructLibrary/Wrap/rough_test.py | 530 | except Exception: | CODE |
| LOW | Code/Demos/boost/python_objs/test.py | 12 | except Exception: | CODE |
| LOW⚡ | Code/Demos/boost/python_objs/test.py | 25 | except Exception: | CODE |
| LOW⚡ | Code/Demos/boost/python_objs/test.py | 33 | except Exception: | CODE |
| LOW⚡ | Code/Demos/boost/python_objs/test.py | 41 | except Exception: | CODE |
| LOW⚡ | Contrib/pzc/p_con.py | 491 | except Exception: | STRING |
| LOW⚡ | Contrib/pzc/p_con.py | 501 | except Exception: | STRING |
| LOW | Contrib/pzc/p_con.py | 520 | except Exception: | STRING |
| 169 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | Projects/DbCLI/CreateDb.py | 168 | CODE | |
| LOW | Projects/DbCLI/SearchDb.py | 76 | CODE | |
| LOW | Projects/DbCLI/SearchDb.py | 134 | CODE | |
| LOW | Projects/DbCLI/SearchDb.py | 156 | CODE | |
| LOW | Code/JavaWrappers/parse_doxy_html.py | 359 | CODE | |
| LOW | Code/JavaWrappers/parse_doxy_html.py | 423 | CODE | |
| LOW | Code/JavaWrappers/parse_doxy_html.py | 447 | CODE | |
| LOW | Code/GraphMol/nbWrap/rough_test.py | 1943 | CODE | |
| LOW | Code/GraphMol/nbWrap/rough_test.py | 7516 | CODE | |
| LOW | Code/GraphMol/DetermineBonds/Wrap/testDetermineBonds.py | 20 | CODE | |
| LOW | Code/GraphMol/DetermineBonds/Wrap/testDetermineBonds.py | 39 | CODE | |
| LOW | Code/GraphMol/DetermineBonds/Wrap/testDetermineBonds.py | 59 | CODE | |
| LOW | Code/GraphMol/DetermineBonds/Wrap/testDetermineBonds.py | 79 | CODE | |
| LOW | Code/GraphMol/MolTransforms/Wrap/testMolTransforms.py | 239 | CODE | |
| LOW | Code/GraphMol/Wrap/test_cdxml.py | 345 | CODE | |
| LOW | Code/GraphMol/Wrap/rough_test.py | 1933 | CODE | |
| LOW | Code/GraphMol/Wrap/rough_test.py | 7439 | CODE | |
| LOW | Code/GraphMol/ChemReactions/Wrap/testEnumerations.py | 223 | CODE | |
| LOW | Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py | 579 | CODE | |
| LOW | Code/GraphMol/SubstructLibrary/Wrap/rough_test.py | 59 | CODE | |
| LOW | Code/GraphMol/SubstructLibrary/Wrap/rough_test.py | 82 | CODE | |
| LOW | Code/GraphMol/SubstructLibrary/Wrap/rough_test.py | 135 | CODE | |
| LOW | Code/GraphMol/MolDraw2D/Wrap/testMolDraw2D.py | 448 | CODE | |
| LOW | Code/GraphMol/MolDraw2D/Wrap/testMolDraw2D.py | 577 | CODE | |
| LOW | Code/GraphMol/MolDraw2D/Wrap/testMolDraw2D.py | 580 | CODE | |
| LOW | Code/GraphMol/FilterCatalog/Wrap/rough_test.py | 122 | CODE | |
| LOW | Code/GraphMol/MolStandardize/Wrap/testMolStandardize.py | 532 | CODE | |
| LOW | Docs/Book/data/test_multi_colours.py | 12 | CODE | |
| LOW | Contrib/RxnRoleAssignment/identifyReactants.py | 205 | CODE | |
| LOW | Contrib/RxnRoleAssignment/identifyReactants.py | 317 | CODE | |
| LOW | Contrib/RxnRoleAssignment/identifyReactants.py | 95 | CODE | |
| LOW | Contrib/M_Kossner/Frames.py | 45 | CODE | |
| LOW | Contrib/pzc/p_con.py | 113 | CODE | |
| LOW | Contrib/pzc/p_con.py | 357 | CODE | |
| LOW | Contrib/pzc/p_con.py | 480 | CODE | |
| LOW | Contrib/pzc/p_con.py | 602 | CODE | |
| LOW | Contrib/pzc/p_con.py | 746 | CODE | |
| LOW | Contrib/IFG/ifg.py | 48 | CODE | |
| LOW | Contrib/efgs/efgs.py | 33 | CODE | |
| LOW | Contrib/efgs/efgs.py | 69 | CODE | |
| LOW | Contrib/efgs/efgs.py | 141 | CODE | |
| LOW | Contrib/efgs/efgs.py | 175 | CODE | |
| LOW | Contrib/efgs/efgs.py | 207 | CODE | |
| LOW | Contrib/efgs/efgs.py | 272 | CODE | |
| LOW | Contrib/FreeWilson/freewilson.py | 163 | CODE | |
| LOW | Contrib/FreeWilson/freewilson.py | 213 | CODE | |
| LOW | Contrib/FreeWilson/freewilson.py | 276 | CODE | |
| LOW | Contrib/mmpa/search_mmp_db.py | 91 | CODE | |
| LOW | Contrib/mmpa/create_mmp_db.py | 75 | CODE | |
| LOW | Contrib/mmpa/rfrag.py | 68 | CODE | |
| LOW | Contrib/mmpa/indexing.py | 78 | CODE | |
| LOW | Contrib/mmpa/indexing.py | 350 | CODE | |
| LOW | Contrib/AtomAtomSimilarity/AtomAtomPathSimilarity.py | 31 | CODE | |
| LOW | Contrib/AtomAtomSimilarity/AtomAtomPathSimilarity.py | 55 | CODE | |
| LOW | Contrib/AtomAtomSimilarity/AtomAtomPathSimilarity.py | 77 | CODE | |
| LOW | Contrib/ChiralPairs/ChiralDescriptors.py | 94 | CODE | |
| LOW | …b/NIBRSubstructureFilters/assignSubstructureFilters.py | 41 | CODE | |
| LOW | Contrib/Glare/glare.py | 319 | CODE | |
| LOW | Scripts/gen_rdkit_stubs/__init__.py | 191 | CODE | |
| LOW | Scripts/gen_rdkit_stubs/__init__.py | 379 | CODE | |
| 166 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| MEDIUM | Code/MinimalLib/cffi_test.c | 1715 | // bridged system is entirely rebuilt since it is not part of the scaffold | COMMENT |
| MEDIUM | Code/MinimalLib/cffi_test.c | 1742 | // Additionally, CoordGen also rebuilds the scaffold, therefore original | COMMENT |
| MEDIUM | Code/MinimalLib/cffi_test.c | 1846 | // bridged system is entirely rebuilt since it is not part of the scaffold | COMMENT |
| MEDIUM | Code/MinimalLib/cffi_test.c | 1873 | // Additionally, CoordGen also rebuilds the scaffold, therefore original | COMMENT |
| MEDIUM | Code/MinimalLib/tests/tests.js | 1653 | // bridged system is entirely rebuilt since it is not part of the scaffold | COMMENT |
| MEDIUM | Code/MinimalLib/tests/tests.js | 1673 | // Additionally, CoordGen also rebuilds the scaffold, therefore original wedging | COMMENT |
| MEDIUM | Code/MinimalLib/tests/tests.js | 1743 | // bridged system is entirely rebuilt since it is not part of the scaffold | COMMENT |
| MEDIUM | Code/MinimalLib/tests/tests.js | 1763 | // Additionally, CoordGen also rebuilds the scaffold, therefore original wedging | COMMENT |
| MEDIUM | Code/GraphMol/RGroupDecomposition/RGroupDecompData.cpp | 571 | // the scaffold | COMMENT |
| MEDIUM⚡ | Code/GraphMol/ChemTransforms/testChemTransforms.cpp | 1070 | {"C1CC1C(=O)OC", "C1CC1"}, // Carbonyl outside scaffold | CODE |
| MEDIUM⚡ | Code/GraphMol/ChemTransforms/testChemTransforms.cpp | 1071 | {"C1CC1C=C", "C1CC1"}, // Double bond outside scaffold | CODE |
| MEDIUM⚡ | Code/GraphMol/ChemTransforms/testChemTransforms.cpp | 1072 | {"C1CC1C=CC1CC1C=CNNCO", "C1CC1C=CC1CC1"}, // Double bond in scaffold | CODE |
| MEDIUM⚡ | Code/GraphMol/ChemTransforms/testChemTransforms.cpp | 1074 | {"C1CC1S(=O)C1CC1C=CNNCO", "C1CC1S(=O)C1CC1"}, // S=O group in scaffold | CODE |
| MEDIUM⚡ | Code/GraphMol/ChemTransforms/testChemTransforms.cpp | 1076 | "C1CC1S(=O)C1CC1"}, // S=O group outside scaffold | CODE |
| MEDIUM⚡ | Code/GraphMol/ChemTransforms/testChemTransforms.cpp | 1078 | "C1CC1S(=O)(=O)C1CC1"}, // SO2 group in scaffold | CODE |
| MEDIUM⚡ | Code/GraphMol/ChemTransforms/testChemTransforms.cpp | 1080 | "C1CC1S(=O)(=O)C1CC1"}, // SO2 group outside scaffold | CODE |
| MEDIUM | Code/GraphMol/ScaffoldNetwork/catch_tests.cpp | 459 | // this tests a very particular case where the generic bond scaffold is the | COMMENT |
| MEDIUM | Code/GraphMol/ScaffoldNetwork/catch_tests.cpp | 460 | // same as the generic scaffold that leads to it. Make sure we do not end up | COMMENT |
| MEDIUM | Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h | 45 | true; ///< Include the version of the scaffold with attachment points | CODE |
| MEDIUM | Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h | 58 | ///< scaffold was reached from | COMMENT |
| MEDIUM | Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h | 105 | counts; ///< number of times each scaffold was encountered | CODE |
| MEDIUM | Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h | 107 | molCounts; ///< number of molecules each scaffold was found in | CODE |
| MEDIUM | Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h | 178 | //! returns parameters for constructing scaffold networks using BRICS | COMMENT |
| MEDIUM | Code/GraphMol/ChemReactions/ReactionRunner.cpp | 2047 | // add dummy atom where the reaction scaffold would have been | COMMENT |
| MEDIUM | Code/GraphMol/Depictor/catch_tests.cpp | 897 | // bridged system is entirely rebuilt since it is not part of the scaffold | COMMENT |
| MEDIUM | Code/GraphMol/Depictor/catch_tests.cpp | 915 | // bridged system is entirely rebuilt since it is not part of the scaffold | COMMENT |
| MEDIUM | Code/GraphMol/Depictor/catch_tests.cpp | 936 | // also rebuilds the scaffold, therefore original wedging should be cleared | COMMENT |
| MEDIUM | Code/GraphMol/Depictor/catch_tests.cpp | 1045 | // bridged system is entirely rebuilt since it is not part of the scaffold | COMMENT |
| MEDIUM | Code/GraphMol/Depictor/catch_tests.cpp | 1063 | // bridged system is entirely rebuilt since it is not part of the scaffold | COMMENT |
| MEDIUM | Code/GraphMol/Depictor/catch_tests.cpp | 1084 | // also rebuilds the scaffold, therefore original wedging should be cleared | COMMENT |
| MEDIUM | Code/GraphMol/Depictor/RDDepictor.cpp | 804 | // 2. there is a match and wedges are outside the constrained scaffold | COMMENT |
| MEDIUM | Code/GraphMol/Depictor/RDDepictor.cpp | 813 | // has at least one atom which is not part of the scaffold, we cannot | COMMENT |
| MEDIUM | Code/GraphMol/Depictor/RDDepictor.cpp | 827 | // check that scaffold coordinates have not changed, which may | COMMENT |
| MEDIUM | Code/GraphMol/Depictor/RDDepictor.cpp | 839 | // has flipped to match the scaffold | COMMENT |
| MEDIUM | Contrib/RxnRoleAssignment/identifyReactants.py | 292 | # atoms based on the scaffold FP, the number of unmapped scaffoldFP bits, and the unmapped scaffoldFP bits | COMMENT |
| MEDIUM⚡ | rdkit/Chem/Scaffolds/UnitTestMurckoScaffold.py | 83 | # Carbonyl outside scaffold | COMMENT |
| MEDIUM⚡ | rdkit/Chem/Scaffolds/UnitTestMurckoScaffold.py | 85 | # Double bond outside scaffold | COMMENT |
| MEDIUM⚡ | rdkit/Chem/Scaffolds/UnitTestMurckoScaffold.py | 87 | # Double bond in scaffold | COMMENT |
| MEDIUM⚡ | rdkit/Chem/Scaffolds/UnitTestMurckoScaffold.py | 92 | # S=O group in scaffold | COMMENT |
| MEDIUM⚡ | rdkit/Chem/Scaffolds/UnitTestMurckoScaffold.py | 94 | # S=O group outside scaffold | COMMENT |
| MEDIUM⚡ | rdkit/Chem/Scaffolds/UnitTestMurckoScaffold.py | 96 | # SO2 group in scaffold | COMMENT |
| MEDIUM⚡ | rdkit/Chem/Scaffolds/UnitTestMurckoScaffold.py | 98 | # SO2 group outside scaffold | COMMENT |
| MEDIUM | rdkit/Chem/Pharm2D/SigFactory.py | 297 | # and which scaffold: | COMMENT |
| MEDIUM | rdkit/Chem/Pharm2D/Utils.py | 78 | # number of points in a scaffold -> sequence of distances (p1, p2) in | COMMENT |
| MEDIUM | rdkit/Chem/Pharm2D/Utils.py | 79 | # the scaffold | COMMENT |
| MEDIUM | rdkit/Chem/Pharm2D/Utils.py | 97 | # number of distances in a scaffold -> number of points in the scaffold | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| HIGH | Code/GraphMol/nbWrap/rough_test.py | 0 | this is a rough coverage test of the python wrapper it's intended to be shallow, but broad | STRING |
| HIGH | Code/GraphMol/FragCatalog/Wrap/rough_test.py | 0 | this is a rough coverage test of the python wrapper it's intended to be shallow, but broad | STRING |
| HIGH | Code/GraphMol/Wrap/test_cdxml.py | 0 | this is a rough coverage test of the python wrapper it's intended to be shallow, but broad | STRING |
| HIGH | Code/GraphMol/Wrap/rough_test.py | 0 | this is a rough coverage test of the python wrapper it's intended to be shallow, but broad | STRING |
| HIGH | Code/GraphMol/nbWrap/rough_test.py | 0 | rdkit 2d 6 6 0 0 0 0 0 0 0 0999 v2000 1.5000 0.0000 0.0000 c 0 0 0 0 0 0 0 0 0 0 0 0 0.7500 -1.2990 0.0000 c 0 0 0 0 0 0 | STRING |
| HIGH | Code/GraphMol/Wrap/rough_test.py | 0 | rdkit 2d 6 6 0 0 0 0 0 0 0 0999 v2000 1.5000 0.0000 0.0000 c 0 0 0 0 0 0 0 0 0 0 0 0 0.7500 -1.2990 0.0000 c 0 0 0 0 0 0 | STRING |
| HIGH | rdkit/Chem/UnitTestRandomize.py | 0 | rdkit 2d 6 6 0 0 0 0 0 0 0 0999 v2000 1.5000 0.0000 0.0000 c 0 0 0 0 0 0 0 0 0 0 0 0 0.7500 -1.2990 0.0000 c 0 0 0 0 0 0 | STRING |
| HIGH | rdkit/sping/pid.py | 0 | draw a pil image into the specified rectangle. if x2 and y2 are omitted, they are calculated from the image size. jjk 11 | STRING |
| HIGH | rdkit/sping/PIL/pidPIL.py | 0 | draw a pil image into the specified rectangle. if x2 and y2 are omitted, they are calculated from the image size. jjk 11 | STRING |
| HIGH | rdkit/sping/PDF/pidPDF.py | 0 | draw a pil image into the specified rectangle. if x2 and y2 are omitted, they are calculated from the image size. jjk 11 | STRING |
| HIGH | rdkit/sping/WX/pidWxDc.py | 0 | draw a pil image into the specified rectangle. if x2 and y2 are omitted, they are calculated from the image size. jjk 11 | STRING |
| HIGH | rdkit/sping/SVG/pidSVG.py | 0 | attempts to return proper font name. pdf uses a standard 14 fonts referred to by name. default to self.defaultfont('helv | STRING |
| HIGH | rdkit/sping/PS/pidPS.py | 0 | attempts to return proper font name. pdf uses a standard 14 fonts referred to by name. default to self.defaultfont('helv | STRING |
| HIGH | rdkit/sping/Pyart/pidPyart.py | 0 | attempts to return proper font name. pdf uses a standard 14 fonts referred to by name. default to self.defaultfont('helv | STRING |
| HIGH | rdkit/sping/SVG/pidSVG.py | 0 | drawpolygon(pointlist) -- draws a polygon pointlist: a list of (x,y) tuples defining vertices | STRING |
| HIGH | rdkit/sping/Qt/pidQt4.py | 0 | drawpolygon(pointlist) -- draws a polygon pointlist: a list of (x,y) tuples defining vertices | STRING |
| HIGH | rdkit/sping/Qt/pidQt.py | 0 | drawpolygon(pointlist) -- draws a polygon pointlist: a list of (x,y) tuples defining vertices | STRING |
| HIGH | rdkit/sping/PIL/pidPIL.py | 0 | drawpolygon(pointlist) -- draws a polygon pointlist: a list of (x,y) tuples defining vertices | STRING |
| HIGH | rdkit/sping/ReportLab/pidReportLab.py | 0 | drawpolygon(pointlist) -- draws a polygon pointlist: a list of (x,y) tuples defining vertices | STRING |
| HIGH | rdkit/sping/PDF/pidPDF.py | 0 | pdf escapes are almost like python ones, but brackets need slashes before them too. use python's repr function and chop | STRING |
| HIGH | rdkit/sping/PDF/pdfgen.py | 0 | pdf escapes are almost like python ones, but brackets need slashes before them too. use python's repr function and chop | STRING |
| HIGH | rdkit/sping/PDF/pdfutils.py | 0 | pdf escapes are almost like python ones, but brackets need slashes before them too. use python's repr function and chop | STRING |
| HIGH | rdkit/Chem/UnitTestLipinski.py | 0 | return entries form regression dataset. returns the line number, smiles, molecule, and the value found in column col | STRING |
| HIGH | rdkit/Chem/UnitTestSurf.py | 0 | return entries form regression dataset. returns the line number, smiles, molecule, and the value found in column col | STRING |
| HIGH | rdkit/Chem/UnitTestGraphDescriptors_2.py | 0 | return entries form regression dataset. returns the line number, smiles, molecule, and the value found in column col | STRING |
| HIGH | rdkit/Chem/UnitTestFeatFinderCLI.py | 0 | redirect standard output and error to string io and return | STRING |
| HIGH | rdkit/Chem/ChemUtils/UnitTestSDFToCSV.py | 0 | redirect standard output and error to string io and return | STRING |
| HIGH | rdkit/Chem/ChemUtils/UnitTestAlignDepict.py | 0 | redirect standard output and error to string io and return | STRING |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | ReleaseNotes.md | 8573 | - The function getHashedMorganFingerprint (GetHashedMorganFingerprint | CODE |
| LOW | Code/MinimalLib/tests/tests.js | 1486 | function getWedgedMolAndInvertedWedges() { | CODE |
| LOW | Code/GraphMol/RGroupDecomposition/Wrap/test_rgroups.py | 209 | def test_match_only_at_rgroups(self): | STRING |
| LOW | Code/GraphMol/RGroupDecomposition/Wrap/test_rgroups.py | 220 | def test_incorrect_multiple_rlabels(self): | STRING |
| LOW | Code/GraphMol/RGroupDecomposition/Wrap/test_rgroups.py | 411 | def test_multicore_prelabelled(self): | STRING |
| LOW | Code/GraphMol/nbWrap/rough_test.py | 1819 | def recursive_enumerate_stereo_bonds(self, mol, done_bonds, bonds): | STRING |
| LOW | Code/GraphMol/nbWrap/rough_test.py | 7096 | def test_get_set_positions_stride(self): | STRING |
| LOW | Code/GraphMol/Wrap/test_lazy_numpy.py | 29 | def test_chem_import_does_not_load_numpy(self): | CODE |
| LOW | Code/GraphMol/Wrap/test_lazy_numpy.py | 40 | def test_basic_smiles_roundtrip_without_numpy(self): | STRING |
| LOW | Code/GraphMol/Wrap/test_lazy_numpy.py | 56 | def test_mol_operations_without_numpy(self): | STRING |
| LOW | Code/GraphMol/Wrap/test_lazy_numpy.py | 89 | def test_numpy_loads_on_demand(self): | STRING |
| LOW | Code/GraphMol/Wrap/test_lazy_numpy.py | 106 | def test_conformer_positions_loads_numpy(self): | STRING |
| LOW | Code/GraphMol/Wrap/test_lazy_numpy.py | 127 | def test_datastructs_convert_loads_numpy(self): | STRING |
| LOW | Code/GraphMol/Wrap/test_lazy_numpy.py | 144 | def test_adjacency_matrix_loads_numpy(self): | STRING |
| LOW⚡ | Code/GraphMol/Wrap/testGetPropDefault.py | 12 | def test_get_prop_with_default_missing(auto_convert, default): | CODE |
| LOW | Code/GraphMol/Wrap/testGetPropDefault.py | 26 | def test_get_prop_with_default_present(auto_convert, prop_value, default, unconverted_value): | CODE |
| LOW | Code/GraphMol/Wrap/testGetPropDefault.py | 41 | def test_get_prop_no_default_not_set(auto_convert): | CODE |
| LOW | Code/GraphMol/Wrap/testGetPropDefault.py | 54 | def test_get_prop_no_default_set(auto_convert, prop_value, unconverted_value): | CODE |
| LOW⚡ | Code/GraphMol/Wrap/testGetPropDefault.py | 67 | def test_get_prop_default_positional(): | CODE |
| LOW⚡ | Code/GraphMol/Wrap/testGetPropDefault.py | 80 | def test_get_prop_default_on_atom(): | CODE |
| LOW⚡ | Code/GraphMol/Wrap/testGetPropDefault.py | 90 | def test_get_prop_default_on_bond(): | CODE |
| LOW⚡ | Code/GraphMol/Wrap/testGetPropDefault.py | 100 | def test_get_prop_default_on_conformer(): | CODE |
| LOW⚡ | Code/GraphMol/Wrap/testGetPropDefault.py | 110 | def test_get_prop_default_on_substance_group(): | CODE |
| LOW⚡ | Code/GraphMol/Wrap/testGetPropDefault.py | 130 | def test_typed_getter_with_default_present(set_fn, get_fn, val, default): | CODE |
| LOW⚡ | Code/GraphMol/Wrap/testGetPropDefault.py | 143 | def test_typed_getter_with_default_missing(get_fn, default): | CODE |
| LOW⚡ | Code/GraphMol/Wrap/testGetPropDefault.py | 150 | def test_typed_getter_no_default_raises(get_fn): | CODE |
| LOW⚡ | Code/GraphMol/Wrap/testGetPropDefault.py | 157 | def test_typed_getter_default_wrong_type_raises_value_error(): | CODE |
| LOW | Code/GraphMol/Wrap/rough_test.py | 1809 | def recursive_enumerate_stereo_bonds(self, mol, done_bonds, bonds): | STRING |
| LOW | Code/GraphMol/Wrap/rough_test.py | 7019 | def test_get_set_positions_stride(self): | STRING |
| LOW | Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py | 824 | def test_reaction_preserves_stereo(self): | STRING |
| LOW | Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py | 836 | def test_reaction_ignores_stereo(self): | STRING |
| LOW | Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py | 848 | def test_reaction_inverts_stereo(self): | STRING |
| LOW | Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py | 863 | def test_reaction_destroys_stereo(self): | STRING |
| LOW | Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py | 886 | def test_reaction_defines_stereo(self): | STRING |
| LOW | Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py | 908 | def test_stereogroup_is_spectator_to_reaction(self): | STRING |
| LOW | Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py | 929 | def test_reaction_splits_stereogroup(self): | STRING |
| LOW | Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py | 939 | def test_reaction_copies_stereogroup(self): | STRING |
| LOW⚡ | Code/GraphMol/ChemReactions/Wrap/testSanitize.py | 300 | def test_unused_rlabel_in_product(self): | STRING |
| LOW⚡ | Code/GraphMol/ChemReactions/Wrap/testSanitize.py | 305 | def test_only_aromatize_if_possible(self): | STRING |
| LOW | Code/GraphMol/ForceFieldHelpers/Wrap/testHelpers.py | 419 | def test_uff_get_forcefield_runs(self): | CODE |
| LOW | Code/GraphMol/SubstructLibrary/Wrap/rough_test.py | 382 | def test_init_from_and_to_stream(self): | CODE |
| LOW | Contrib/IFG/ifg.py | 48 | def identify_functional_groups(mol): | CODE |
| LOW | Contrib/mmpa/search_mmp_db.py | 91 | def print_smallest_change_mmp(db_results, cmpd_id, query_size): | CODE |
| LOW | Contrib/mmpa/indexing.py | 271 | def switch_specific_labels_on_symmetry(smi, symmetry_class, a, b): | CODE |
| LOW | Contrib/mmpa/indexing.py | 294 | def switch_labels_on_position(smi): | CODE |
| LOW | Scripts/gen_rdkit_stubs/worker.py | 45 | def parse_function_docstring_patched(self, func_name, doc_lines, **kwargs): | CODE |
| LOW | Scripts/gen_rdkit_stubs/worker.py | 54 | def print_submodule_import_patched(self, name): | CODE |
| LOW | Scripts/gen_rdkit_stubs/__init__.py | 38 | def purge_rdkit_source_dir_from_sys_path(): | CODE |
| LOW | Scripts/gen_rdkit_stubs/__init__.py | 46 | def find_rdkit_site_packages_path(): | CODE |
| LOW | Scripts/gen_rdkit_stubs/__init__.py | 156 | def concat_parent_child_module(parent_module, child_module): | CODE |
| LOW | Scripts/gen_rdkit_stubs/__init__.py | 379 | def protect_quoted_square_brackets_and_equals(cls, arg): | CODE |
| LOW | Scripts/gen_rdkit_stubs/__init__.py | 402 | def deprotect_quoted_square_brackets_and_equals(cls, arg): | CODE |
| LOW | Scripts/patch_rdkit_docstrings/__init__.py | 778 | def find_def_init_nodes_in_class_r(self, cursor, func_names, func_name_to_hash, def_init_nodes): | CODE |
| LOW | Scripts/patch_rdkit_docstrings/__init__.py | 798 | def is_class_hash_among_node_children_r(self, class_hash, node): | CODE |
| LOW | Scripts/patch_rdkit_docstrings/__init__.py | 1397 | def get_include_flags_from_include_path(include_path): | CODE |
| LOW | External/INCHI-API/python/inchi.py | 56 | def _parse_auxinfo_coordinates(auxinfo): | CODE |
| LOW | External/INCHI-API/python/inchi.py | 93 | def _parse_auxinfo_atom_order(auxinfo): | CODE |
| LOW | External/INCHI-API/python/inchi.py | 125 | def _build_inverse_permutation(atom_order, size): | CODE |
| LOW | rdkit/Chem/UnitTestRandomize.py | 64 | def test_smiles_canonicalization(self): | CODE |
| LOW | rdkit/Chem/UnitTestMCS.py | 93 | def test_atom_compare_default(self): | STRING |
| 55 more matches not shown… | ||||
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| HIGH⚡ | Contrib/pzc/p_con.py | 482 | min(IC50) => IC50_avg-3*IC50_stddev && max(IC50) <= IC50_avg+3*IC50_stddev && IC50_stddev <= IC50_avg""" | STRING |
| HIGH | Contrib/Glare/glare.py | 210 | # would be needed, and the net speedup would be null, hence, the decision to | COMMENT |
| HIGH | rdkit/Dbase/DbConnection.py | 56 | - includeViews: if this is non-null, the views in the db will | STRING |
| HIGH | rdkit/Dbase/DbInfo.py | 69 | - includeViews: if this is non-null, the views in the db will | STRING |
| HIGH | rdkit/ML/Cluster/Resemblance.py | 17 | || - || 0 || 1 || 3 | STRING |
| HIGH | rdkit/ML/Cluster/Resemblance.py | 18 | || - || - || 2 || 4 | STRING |
| HIGH⚡ | rdkit/Chem/MolKey/MolKey.py | 329 | elif n_udf == 1: # one undefined, no defined | CODE |
| HIGH⚡ | rdkit/Chem/MolKey/MolKey.py | 331 | else: # several undefined, no defined | CODE |
| HIGH⚡ | rdkit/Chem/Draw/InteractiveRenderer.py | 101 | const rdkStrRnr = window.rdkStrRnr || Promise.resolve(null); | CODE |
| HIGH⚡ | rdkit/Chem/Draw/InteractiveRenderer.py | 101 | const rdkStrRnr = window.rdkStrRnr || Promise.resolve(null); | CODE |
| HIGH⚡ | rdkit/Chem/Draw/InteractiveRenderer.py | 105 | if (Renderer && Renderer.updateMolDrawDivs) {{ | CODE |
| HIGH⚡ | rdkit/Chem/Draw/InteractiveRenderer.py | 111 | window.rdkStrRnr = null; | CODE |
| HIGH⚡ | rdkit/Chem/Draw/InteractiveRenderer.py | 115 | console.error(e.toString()); | CODE |
| HIGH | rdkit/Chem/Draw/InteractiveRenderer.py | 132 | e.toString() + '<br>' + | CODE |
| HIGH | rdkit/Chem/Draw/InteractiveRenderer.py | 135 | window.rdkStrRnr = null; | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | Code/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py | 90 | CODE | |
| LOW | Contrib/efgs/try_efgs.py | 79 | CODE | |
| LOW | Contrib/AtomAtomSimilarity/AtomAtomPathSimilarity.py | 183 | CODE | |
| LOW | Contrib/ChiralPairs/ChiralDescriptors.py | 91 | CODE | |
| LOW | Contrib/Glare/glare.py | 217 | CODE | |
| LOW | rdkit/Dbase/DbUtils.py | 62 | CODE | |
| LOW | rdkit/Dbase/DbInfo.py | 207 | CODE | |
| LOW | rdkit/utils/chemdraw_qax.py | 59 | CODE | |
| LOW | rdkit/ML/Data/SplitData.py | 165 | CODE | |
| LOW | rdkit/ML/Data/DataUtils.py | 230 | CODE | |
| LOW | rdkit/ML/Data/DataUtils.py | 249 | CODE | |
| LOW | rdkit/ML/Data/DataUtils.py | 405 | CODE | |
| LOW | rdkit/ML/Data/DataUtils.py | 352 | CODE | |
| LOW | rdkit/ML/Data/DataUtils.py | 456 | CODE | |
| LOW | rdkit/ML/Data/MLData.py | 129 | CODE | |
| LOW | rdkit/sping/PS/pidPS.py | 166 | CODE | |
| LOW | rdkit/Chem/RegistrationHash.py | 280 | CODE | |
| LOW | rdkit/Chem/RegistrationHash.py | 352 | CODE | |
| LOW | rdkit/Chem/__init__.py | 125 | CODE | |
| LOW | rdkit/Chem/MCS.py | 266 | CODE | |
| LOW | rdkit/Chem/GraphDescriptors.py | 46 | CODE | |
| LOW | rdkit/Chem/GraphDescriptors.py | 232 | CODE | |
| LOW | rdkit/Chem/GraphDescriptors.py | 247 | CODE | |
| LOW | rdkit/Chem/GraphDescriptors.py | 291 | CODE | |
| LOW | rdkit/Chem/GraphDescriptors.py | 361 | CODE | |
| LOW | rdkit/Chem/PandasTools.py | 241 | CODE | |
| LOW | rdkit/Chem/PyMol.py | 75 | CODE | |
| LOW | rdkit/Chem/fmcs/fmcs.py | 2196 | CODE | |
| LOW | rdkit/Chem/Pharm3D/EmbedLib.py | 321 | CODE | |
| LOW | rdkit/Chem/Features/ShowFeats.py | 155 | CODE | |
| LOW | rdkit/Chem/Subshape/SubshapeAligner.py | 80 | CODE | |
| LOW | rdkit/Chem/Subshape/BuilderUtils.py | 180 | CODE | |
| LOW | rdkit/Chem/MolDb/Loader_sa.py | 91 | CODE | |
| LOW | rdkit/Chem/MolDb/Loader_orig.py | 21 | CODE | |
| LOW | rdkit/Chem/MolDb/Loader_orig.py | 92 | CODE | |
| LOW | rdkit/Chem/Draw/MolDrawing.py | 333 | CODE | |
| LOW | rdkit/Chem/Draw/__init__.py | 581 | CODE | |
| LOW | rdkit/Chem/Draw/__init__.py | 758 | CODE | |
| LOW | rdkit/Chem/Draw/__init__.py | 804 | CODE | |
| LOW | rdkit/Chem/Draw/__init__.py | 901 | CODE | |
| LOW | rdkit/Chem/Draw/__init__.py | 993 | CODE | |
| LOW | rdkit/Chem/Draw/SimilarityMaps.py | 131 | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| MEDIUM | Code/DistGeom/Wrap/rough_test.py | 93 | CODE | |
| MEDIUM | Code/DistGeom/Wrap/rough_test.py | 99 | CODE | |
| MEDIUM | Code/DistGeom/Wrap/rough_test.py | 100 | CODE | |
| MEDIUM | Code/DistGeom/Wrap/rough_test.py | 101 | CODE | |
| MEDIUM | Code/DistGeom/Wrap/rough_test.py | 102 | CODE | |
| MEDIUM | Code/DistGeom/Wrap/rough_test.py | 103 | CODE | |
| MEDIUM | Code/DistGeom/Wrap/rough_test.py | 104 | CODE | |
| MEDIUM | Code/DistGeom/Wrap/rough_test.py | 105 | CODE | |
| MEDIUM | Code/DistGeom/Wrap/rough_test.py | 106 | CODE | |
| MEDIUM | Code/GraphMol/Wrap/rough_test.py | 5709 | CODE | |
| MEDIUM | Code/GraphMol/Wrap/rough_test.py | 5713 | CODE | |
| MEDIUM | Code/GraphMol/Wrap/rough_test.py | 5714 | CODE | |
| MEDIUM | rdkit/Chem/fmcs/fmcs.py | 628 | CODE | |
| MEDIUM | rdkit/Chem/fmcs/fmcs.py | 630 | CODE | |
| MEDIUM | rdkit/Chem/fmcs/fmcs.py | 631 | CODE | |
| MEDIUM | rdkit/Chem/fmcs/fmcs.py | 632 | CODE | |
| MEDIUM | rdkit/Chem/fmcs/fmcs.py | 643 | CODE | |
| MEDIUM | rdkit/Chem/fmcs/fmcs.py | 644 | CODE | |
| MEDIUM | rdkit/Chem/fmcs/fmcs.py | 645 | CODE | |
| MEDIUM | rdkit/Chem/fmcs/fmcs.py | 647 | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | Code/GraphMol/nbWrap/rough_test.py | 3437 | for n in atom.GetNeighbors(): # Check if neighbor is from the same residue | CODE |
| LOW | …e/GraphMol/GaussianShape/Wrap/test_rdgaussian_shape.py | 195 | # Set the to default values, just to show that they can be set. | COMMENT |
| LOW | Code/GraphMol/Wrap/rough_test.py | 3387 | for n in atom.GetNeighbors(): # Check if neighbor is from the same residue | CODE |
| LOW | Contrib/efgs/efgs.py | 401 | if map_idx in neigh_atoms: # Check if that position is an environment atom in original molecule | CODE |
| LOW⚡ | rdkit/ML/Cluster/Butina.py | 66 | # Check if data is a supported type | COMMENT |
| LOW⚡ | rdkit/ML/Cluster/Butina.py | 70 | # Check if data is a 1D array or list | COMMENT |
| LOW⚡ | rdkit/ML/Cluster/Butina.py | 72 | # Check if data length matches the required number of points | COMMENT |
| LOW⚡ | rdkit/ML/Cluster/Butina.py | 82 | # Check if data is a matrix of the correct shape and use it as distance matrix | COMMENT |
| LOW | rdkit/Chem/fmcs/fmcs.py | 1538 | # Check if a SMARTS is in all targets. | COMMENT |
| LOW | rdkit/Chem/fmcs/fmcs.py | 1753 | ### Check if there are any ring atoms; used in --complete-rings-only | COMMENT |
| LOW | rdkit/Chem/fmcs/fmcs.py | 2500 | # Check if this is the end of string or a ',' | COMMENT |
| LOW | rdkit/Chem/Features/UnitTestFeatDirUtilsRD.py | 44 | #Check if there are two vectors | COMMENT |
| LOW | rdkit/Chem/Features/UnitTestFeatDirUtilsRD.py | 78 | #Check if there is one vector | COMMENT |
| LOW | rdkit/Chem/Features/UnitTestFeatDirUtilsRD.py | 101 | #Check if there are two vectors | COMMENT |
| LOW | rdkit/Chem/Features/UnitTestFeatDirUtilsRD.py | 140 | #Check if there is one vector | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| HIGH | Code/JavaWrappers/parse_doxy_html.py | 31 | int RDKit::Atom::getPerturbationOrder ( INT_LIST probe ) const returns the perturbation order for a list of int | STRING |
| HIGH | Code/JavaWrappers/parse_doxy_html.py | 69 | Detailed Description The class for representing atoms. Notes: * many of the methods of Atom require that the Atom | STRING |
| HIGH | Scripts/patch_rdkit_docstrings/__init__.py | 928 | Insert the appropriate python::args where needed based on the C++ method parameter names. Args: | STRING |
| HIGH | rdkit/Chem/Draw/__init__.py | 455 | Creates a mol grid image from a nested data structure (where each data substructure represents a row), padding rows as | STRING |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | Code/GraphMol/PartialCharges/Wrap/testPartialCharges.py | 119 | # can't set the required locale, might as well just return | COMMENT |
| LOW | rdkit/sping/TK/pidTK.py | 47 | # removed reference to "BaseTKCanvas" (should just use TKCanvas as default) | COMMENT |
| LOW | rdkit/sping/TK/pidTK.py | 112 | # XXX: should just return the internal tk font name? | COMMENT |
| LOW | rdkit/sping/PS/pidPS.py | 27 | # _ Base85 encoding just use hex encoding involves 1:2 expansion of image data vs 4:5 | COMMENT |
| LOW | rdkit/sping/PS/pidPS.py | 677 | # should fix this so it doesn't define path twice, just use gsave if need | COMMENT |
| LOW | rdkit/Chem/TorsionFingerprints.py | 135 | # sort by atom inv and simply use the first neighbor | COMMENT |
| LOW | rdkit/Chem/TorsionFingerprints.py | 144 | # sort by atom inv and simply use the first neighbor | COMMENT |
| MEDIUM | rdkit/Chem/PandasPatcher.py | 220 | """ Disable escaping of HTML in order to render img / svg tags """ | STRING |
| LOW | rdkit/Chem/Pharm3D/EmbedLib.py | 970 | # we ignore the point locations here and just use their definitions: | STRING |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | Scripts/gen_rdkit_stubs/__init__.py | 14 | logger = logging.getLogger(__name__) | CODE |
| LOW | External/INCHI-API/python/inchi.py | 393 | __all__ = [ | CODE |
| LOW | rdkit/DataManip/__init__.py | 1 | __all__ = ['Metric'] | CODE |
| LOW | rdkit/Chem/RegistrationHash.py | 36 | logger = logging.getLogger(__name__) | CODE |
| LOW | rdkit/Chem/MCS.py | 239 | __all__ = ["FindMCS"] | CODE |
| LOW | rdkit/VLib/__init__.py | 1 | __all__ = [] | CODE |
| LOW | rdkit/VLib/NodeLib/__init__.py | 1 | __all__ = ['SmartsMolFilter', 'SDSupply', 'SmartsRemover', 'SmilesDupeFilter', 'SmilesOutput'] | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | …/MinimalLib/docker/docker_compose_build_minimallib.yml | 13 | # Example usage: | COMMENT |
| LOW | Code/RDBoost/list_indexing_suite.hpp | 37 | // Example usage: | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.cpp | 80 | // don't forget to set the H count on that atom: | COMMENT |
| LOW | rdkit/Chem/PandasPatcher.py | 196 | # in pandas 0.25 we need to make sure to update buf as return value will be ignored | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | Code/GraphMol/Wrap/testMultithreadedMolSupplier.py | 141 | def helper(smiSup): | CODE |
| LOW | Code/GraphMol/Wrap/testMultithreadedMolSupplier.py | 158 | def helper(sdSup): | CODE |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | Code/GraphMol/Canon.cpp | 244 | // the double bond's stereo label. Now we need to check if we can | COMMENT |
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | Code/GraphMol/SmilesParse/SmilesParse.cpp | 87 | // NOTE: This variable will be used to point to the location of the | COMMENT |