The official sources for the RDKit library
This report summarizes scanner evidence for rdkit/rdkit, a HTML project with 3,614 GitHub stars. SynthScan examined 809,601 lines of code across 2568 source files, recording 3667 pattern matches distributed across 22 syntactic categories. The legacy adjusted pattern signal is 6.2 (Moderate pattern signal); it is not an authorship estimate.
Use the findings to ask whether maintainers can explain intent, verify dependencies, simplify unnecessary scaffolding, and focus review effort. Risk Payload v1 adds ownership, supply-chain, over-engineering, and review-effort vectors when available. These are prompts for human verification, not probabilities, security findings, or measured maintenance costs.
Use each vector to guide manual verification of the underlying findings.
Can maintainers explain intent, assumptions, and trade-offs? 2895 finding(s).
Are imports declared and package/API names verified? 263 finding(s).
Are wrappers, guards, and repeated structures necessary? 672 finding(s).
Which changes need focused human review? 3667 finding(s).
This chart tracks the legacy adjusted pattern score across scan runs. Changes can reflect source changes, scan coverage, or detector/scoring versions; they do not measure AI adoption or prove that a team refactored code. Compare runs only when their scoring versions are compatible. The dashed line tracks the raw pattern-hit count.
Groups findings by configured severity weight. Severity is not a confidence estimate, security rating, or proof that a package is missing. Verify imports against the project's manifests and inspect each finding in its local design context.
This horizontal bar chart shows where configured pattern scores accumulate across directories. Treat the bars as locations to inspect, not as evidence of authorship or code quality. Use the file-level findings to decide whether a directory needs a focused ownership, dependency, complexity, or review check.
The scanner identified 3667 distinct pattern matches across 22 syntactic categories. Each entry below represents a discrete location in the source code where the engine recorded a detector match to inspect in context. 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 configured finding weight (CRITICAL / HIGH / MEDIUM / LOW). The Context column identifies whether the match occurred inside executable code, an inline comment, or a string literal — legacy comment-context matches receive a ×1.5 score weight. The ⚡ bolt icon marks clustered matches: three or more patterns within a 10-line window, each receiving an additional ×1.5 density multiplier under the legacy scoring model.
| Severity | File | Line | Snippet | Context |
|---|---|---|---|---|
| LOW | CMakeLists.txt | 861 | # SET(CPACK_NSIS_HELP_LINK "http:\\\\\\\\www.my-project-home-page.org") | 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 |
| 2171 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 |
|---|---|---|---|---|
| HIGH | Web/RDExtras/MolImage.py | 33 | except OSError: | CODE |
| HIGH | Projects/DbCLI/CreateDb.py | 235 | except Exception: | CODE |
| HIGH | Projects/DbCLI/CreateDb.py | 246 | except Exception: | CODE |
| HIGH | Projects/DbCLI/CreateDb.py | 250 | except Exception: | CODE |
| HIGH | Projects/DbCLI/CreateDb.py | 254 | except Exception: | CODE |
| HIGH | Projects/DbCLI/CreateDb.py | 258 | except Exception: | CODE |
| HIGH | Projects/DbCLI/CreateDb.py | 288 | except Exception: | CODE |
| HIGH | Projects/DbCLI/CreateDb.py | 306 | except Exception: | CODE |
| HIGH | Projects/DbCLI/UnitTestDbCLI.py | 369 | except PermissionError: | CODE |
| HIGH | Projects/DbCLI/UnitTestDbCLI.py | 398 | except PermissionError: | CODE |
| HIGH | Projects/DbCLI/UnitTestDbCLI.py | 488 | except PermissionError: | CODE |
| HIGH | Projects/DbCLI/SearchDb.py | 320 | except Exception: | CODE |
| HIGH | Code/ForceField/Wrap/testConstraints.py | 36 | except RuntimeError: | CODE |
| HIGH | Code/ForceField/Wrap/testConstraints.py | 46 | except RuntimeError: | CODE |
| HIGH | Code/GraphMol/nbWrap/rough_test.py | 589 | except ValueError: | CODE |
| HIGH | Code/GraphMol/nbWrap/rough_test.py | 595 | except ValueError: | CODE |
| HIGH | Code/GraphMol/nbWrap/rough_test.py | 606 | except TypeError: | CODE |
| HIGH | Code/GraphMol/nbWrap/rough_test.py | 2371 | except Exception: | CODE |
| HIGH | Code/GraphMol/nbWrap/rough_test.py | 2379 | except Exception: | CODE |
| HIGH | Code/GraphMol/nbWrap/rough_test.py | 5189 | except RuntimeError: | CODE |
| HIGH | Code/GraphMol/nbWrap/rough_test.py | 7327 | except Exception: | CODE |
| HIGH | Code/GraphMol/Wrap/rough_test.py | 576 | except ValueError: | CODE |
| HIGH | Code/GraphMol/Wrap/rough_test.py | 582 | except ValueError: | CODE |
| HIGH | Code/GraphMol/Wrap/rough_test.py | 593 | except OverflowError: | CODE |
| HIGH | Code/GraphMol/Wrap/rough_test.py | 2348 | except Exception: | CODE |
| HIGH | Code/GraphMol/Wrap/rough_test.py | 2356 | except Exception: | CODE |
| HIGH | Code/GraphMol/Wrap/rough_test.py | 5124 | except RuntimeError: | CODE |
| HIGH | Code/GraphMol/Wrap/rough_test.py | 7240 | except Exception: | CODE |
| HIGH | Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py | 518 | except TypeError: | CODE |
| HIGH | Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py | 524 | except KeyError: | CODE |
| HIGH | …hMol/SynthonSpaceSearch/Wrap/testSynthonSpaceSearch.py | 111 | except StopIteration: | CODE |
| HIGH | Code/Demos/boost/python_objs/test.py | 10 | except TypeError: | CODE |
| HIGH | Code/Demos/boost/python_objs/test.py | 23 | except TypeError: | CODE |
| HIGH | Code/Demos/boost/python_objs/test.py | 31 | except TypeError: | CODE |
| HIGH | Code/Demos/boost/python_objs/test.py | 39 | except TypeError: | CODE |
| HIGH | Scripts/gen_rdkit_stubs/__init__.py | 63 | except ValueError: | CODE |
| HIGH | Scripts/patch_rdkit_docstrings/__init__.py | 1538 | except Exception: | CODE |
| HIGH | Scripts/patch_rdkit_docstrings/__init__.py | 1496 | except Exception as e: | CODE |
| HIGH | rdkit/__init__.py | 25 | except Exception: | CODE |
| HIGH | rdkit/RDConfig.py | 72 | except ImportError: | CODE |
| HIGH | rdkit/Dbase/DbConnection.py | 227 | except Exception: | CODE |
| HIGH | rdkit/Dbase/UnitTestDbConnect.py | 62 | except Exception: | CODE |
| HIGH | rdkit/Dbase/UnitTestDbConnect.py | 83 | except Exception: | CODE |
| HIGH | rdkit/Dbase/UnitTestDbConnect.py | 198 | except Exception: | CODE |
| HIGH | rdkit/Dbase/UnitTestDbConnect.py | 233 | except Exception: | CODE |
| HIGH | rdkit/utils/chemdraw.py | 187 | except Exception: | CODE |
| HIGH | rdkit/utils/cactvs.py | 55 | except Exception: | CODE |
| HIGH | rdkit/ML/Cluster/Clusters.py | 237 | except Exception: | CODE |
| HIGH | rdkit/ML/Data/DataUtils.py | 206 | except ValueError: | CODE |
| HIGH | rdkit/sping/PDF/pdfdoc.py | 188 | except Exception: | CODE |
| HIGH | rdkit/sping/PIL/pidPIL.py | 462 | except Exception: | CODE |
| HIGH | rdkit/sping/PIL/pidPIL.py | 137 | except Exception: | CODE |
| HIGH | rdkit/Chem/MolSurf.py | 45 | except AttributeError: | CODE |
| HIGH | rdkit/Chem/MolSurf.py | 69 | except AttributeError: | CODE |
| HIGH | rdkit/Chem/MolSurf.py | 130 | except AttributeError: | CODE |
| HIGH | rdkit/Chem/MolSurf.py | 169 | except AttributeError: | CODE |
| HIGH | rdkit/Chem/MolSurf.py | 204 | except AttributeError: | CODE |
| HIGH | rdkit/Chem/UnitTestMCS.py | 327 | except OverflowError: | CODE |
| HIGH | rdkit/Chem/UnitTestMCS.py | 329 | except TypeError: | CODE |
| HIGH | rdkit/Chem/Lipinski.py | 95 | except AttributeError: | CODE |
| 24 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 | 281 | 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/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/Descriptors/Wrap/testMolDescriptors.py | 7 | CODE | |
| LOW | Code/GraphMol/MolDraw2D/Qt/Wrap/testMolDraw2DQt.py | 10 | CODE | |
| LOW | Code/GraphMol/MolDraw2D/Qt/Wrap/testMolDraw2DQt.py | 13 | CODE | |
| LOW | Code/GraphMol/MolAlign/Wrap/testMolAlign.py | 14 | CODE | |
| LOW | Code/GraphMol/MolAlign/Wrap/testMolAlign.py | 15 | CODE | |
| LOW | …hMol/SynthonSpaceSearch/Wrap/testSynthonSpaceSearch.py | 44 | 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 | |
| 188 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 | 235 | 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 | 258 | except Exception: | CODE |
| LOW | Projects/DbCLI/CreateDb.py | 288 | except Exception: | CODE |
| LOW | Projects/DbCLI/CreateDb.py | 306 | except Exception: | CODE |
| LOW | Projects/DbCLI/CreateDb.py | 334 | except Exception: | CODE |
| LOW | Projects/DbCLI/CreateDb.py | 473 | except Exception: | CODE |
| LOW | Projects/DbCLI/SearchDb.py | 320 | 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 |
| MEDIUM | Code/GraphMol/nbWrap/rough_test.py | 6268 | def testSanitizationExceptionBasics(self): | CODE |
| LOW | Code/GraphMol/nbWrap/rough_test.py | 2371 | except Exception: | CODE |
| LOW | Code/GraphMol/nbWrap/rough_test.py | 2379 | except Exception: | CODE |
| LOW | Code/GraphMol/nbWrap/rough_test.py | 7327 | except Exception: | CODE |
| LOW | Code/GraphMol/nbWrap/rough_test.py | 535 | except Exception: | STRING |
| LOW | Code/GraphMol/nbWrap/rough_test.py | 5645 | except Exception: | STRING |
| LOW | Code/GraphMol/nbWrap/rough_test.py | 8543 | except Exception as e: | STRING |
| LOW | Code/GraphMol/nbWrap/rough_test.py | 8549 | except Exception as e: | STRING |
| 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 |
| MEDIUM | Code/GraphMol/Wrap/rough_test.py | 6199 | def testSanitizationExceptionBasics(self): | CODE |
| 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 | 7240 | 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 | 5580 | except Exception: | STRING |
| LOW | Code/GraphMol/Wrap/rough_test.py | 8672 | except Exception as e: | STRING |
| LOW | Code/GraphMol/Wrap/rough_test.py | 8678 | except Exception as e: | STRING |
| 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 | 172 | CODE | |
| LOW | Projects/DbCLI/SearchDb.py | 78 | CODE | |
| LOW | Projects/DbCLI/SearchDb.py | 136 | CODE | |
| LOW | Projects/DbCLI/SearchDb.py | 158 | 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 | 1955 | CODE | |
| LOW | Code/GraphMol/nbWrap/rough_test.py | 7528 | 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 | 7441 | 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 | |
| 167 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 | 1647 | // bridged system is entirely rebuilt since it is not part of the scaffold | COMMENT |
| MEDIUM | Code/MinimalLib/tests/tests.js | 1667 | // Additionally, CoordGen also rebuilds the scaffold, therefore original wedging | COMMENT |
| MEDIUM | Code/MinimalLib/tests/tests.js | 1737 | // bridged system is entirely rebuilt since it is not part of the scaffold | COMMENT |
| MEDIUM | Code/MinimalLib/tests/tests.js | 1757 | // 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 | 905 | // bridged system is entirely rebuilt since it is not part of the scaffold | COMMENT |
| MEDIUM | Code/GraphMol/Depictor/catch_tests.cpp | 923 | // bridged system is entirely rebuilt since it is not part of the scaffold | COMMENT |
| MEDIUM | Code/GraphMol/Depictor/catch_tests.cpp | 944 | // also rebuilds the scaffold, therefore original wedging should be cleared | COMMENT |
| MEDIUM | Code/GraphMol/Depictor/catch_tests.cpp | 1053 | // bridged system is entirely rebuilt since it is not part of the scaffold | COMMENT |
| MEDIUM | Code/GraphMol/Depictor/catch_tests.cpp | 1071 | // bridged system is entirely rebuilt since it is not part of the scaffold | COMMENT |
| MEDIUM | Code/GraphMol/Depictor/catch_tests.cpp | 1092 | // also rebuilds the scaffold, therefore original wedging should be cleared | COMMENT |
| MEDIUM | Code/GraphMol/Depictor/RDDepictor.cpp | 809 | // 2. there is a match and wedges are outside the constrained scaffold | COMMENT |
| MEDIUM | Code/GraphMol/Depictor/RDDepictor.cpp | 818 | // has at least one atom which is not part of the scaffold, we cannot | COMMENT |
| MEDIUM | Code/GraphMol/Depictor/RDDepictor.cpp | 832 | // check that scaffold coordinates have not changed, which may | COMMENT |
| MEDIUM | Code/GraphMol/Depictor/RDDepictor.cpp | 844 | // 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 | 9024 | - The function getHashedMorganFingerprint (GetHashedMorganFingerprint | CODE |
| LOW | Code/MinimalLib/tests/tests.js | 1480 | 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 | 1831 | def recursive_enumerate_stereo_bonds(self, mol, done_bonds, bonds): | STRING |
| LOW | Code/GraphMol/nbWrap/rough_test.py | 7108 | 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/test_cdxml.py | 436 | def test_cdxml_hydrogen_bond_query(self): | CODE |
| LOW | Code/GraphMol/Wrap/test_cdxml.py | 450 | def test_cdxml_multiattachment_query(self): | CODE |
| LOW | Code/GraphMol/Wrap/test_cdxml.py | 473 | def test_cdxml_external_connection_fragment_query(self): | CODE |
| LOW | Code/GraphMol/Wrap/test_cdxml.py | 483 | def test_cdxml_spiro_ring_bond_count_query(self): | CODE |
| LOW | Code/GraphMol/Wrap/test_cdxml.py | 499 | def test_cdxml_explicit_hydrogen_minimum_queries(self): | CODE |
| LOW | Code/GraphMol/Wrap/test_cdxml.py | 519 | def test_cdxml_atom_restriction_queries(self): | 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 | 7021 | 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 |
| 61 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 | 92 | 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 | 130 | 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 | 579 | CODE | |
| LOW | rdkit/Chem/Draw/__init__.py | 756 | CODE | |
| LOW | rdkit/Chem/Draw/__init__.py | 802 | CODE | |
| LOW | rdkit/Chem/Draw/__init__.py | 899 | CODE | |
| LOW | rdkit/Chem/Draw/__init__.py | 991 | 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 | 5710 | CODE | |
| MEDIUM | Code/GraphMol/Wrap/rough_test.py | 5714 | CODE | |
| MEDIUM | Code/GraphMol/Wrap/rough_test.py | 5715 | 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/MinimalLib/scripts/build_rdkitjs.sh | 8 | # Set buildkit to false to force sequential docker compilation | COMMENT |
| LOW | Code/GraphMol/nbWrap/rough_test.py | 3449 | 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 | 222 | """ 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 | 15 | # 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 | 198 | # 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 | 85 | // NOTE: This variable will be used to point to the location of the | COMMENT |