Repository Analysis

rdkit/rdkit

The official sources for the RDKit library

5.7 Low AI signal View on GitHub

Analysis Overview

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).

5.7
Adjusted Score
5.7
Raw Score
100%
Time Factor
2026-08-28
Last Push
3.6K
Stars
HTML
Language
799.2K
Lines of Code
2.5K
Files
3.6K
Pattern Hits
2026-08-29
Scan Date
0.02
HC Hit Rate

What These Metrics Mean

Adjusted Score
Primary synthetic code indicator. Raw score normalised per 1,000 lines of code and multiplied by the temporal discount factor. This is the definitive comparative metric — use it to rank repositories by AI authorship density.
Raw Score
The unmodified sum of all severity-weighted, context-multiplied pattern match scores before temporal discounting. Reflects the absolute signal strength independent of when the repository was last active.
Time Factor
The temporal discount multiplier (0–100%) applied to the raw score. Repositories last updated before ChatGPT's launch (Nov 2022) receive a 5% factor. Full signal is only assigned to repositories active in the post-adoption era (Jan 2024+).
Pattern Hits
Total count of individual pattern matches across all files and categories. A high hit count with a low score may indicate a very large codebase with isolated AI snippets; a low count with a high score indicates dense, concentrated AI signatures.
HC Hit Rate
High+Critical pattern hits per file, averaged across the repository. This orthogonal signal catches repositories where a few files are densely packed with high-severity AI tells — a strong indicator even when the normalised score appears moderate due to codebase size.
Lines of Code / Files
Total lines and files analysed. The scanner examines 94 file extensions. These denominators are used to normalise the score, enabling fair comparison between repositories of vastly different sizes.

Score History

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.

No multi-scan history yet — run the scanner again to build trend data.

Severity Breakdown

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.

CRITICAL 0HIGH 47MEDIUM 409LOW 3097

Directory Score Breakdown

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.

Pattern Findings

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.

Over-Commented Block2210 hits · 2202 pts
SeverityFileLineSnippetContext
LOWCMakeLists.txt801SET(CPACK_PACKAGE_VERSION_MAJOR ${RDKit_Year})COMMENT
LOWazure-pipelines.yml161# steps:COMMENT
LOWProjects/DbCLI/CreateDb.py1# Copyright (c) 2007, Novartis Institutes for BioMedical Research Inc.COMMENT
LOWProjects/DbCLI/SearchDb.py1# Copyright (c) 2007-2013, Novartis Institutes for BioMedical Research Inc.COMMENT
LOWProjects/DbCLI/SearchDb.py21# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHTCOMMENT
LOWCode/notes.txt21 - when programming the windows, it's useful to use the XXX_API methods thatCOMMENT
LOWCode/DataManip/MetricMatrixCalc/MetricFuncs.h1//COMMENT
LOWCode/DataManip/MetricMatrixCalc/MetricMatrixCalc.h1//COMMENT
LOWCode/DataManip/MetricMatrixCalc/testMatCalc.cpp1//COMMENT
LOW…taManip/MetricMatrixCalc/nbWrap/rdMetricMatrixCalc.cpp1//COMMENT
LOW…taManip/MetricMatrixCalc/nbWrap/rdMetricMatrixCalc.cpp41 private:COMMENT
LOW…taManip/MetricMatrixCalc/nbWrap/rdMetricMatrixCalc.cpp61 // 3. A list (or tuple) of lists (or tuple)COMMENT
LOW…DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp1//COMMENT
LOW…DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp61 // contiguous memory will workCOMMENT
LOWCode/DataStructs/SparseBitVect.cpp1//COMMENT
LOWCode/DataStructs/SparseBitVect.cpp21COMMENT
LOWCode/DataStructs/SparseBitVect.cpp41// """ -------------------------------------------------------COMMENT
LOWCode/DataStructs/SparseBitVect.cpp261 v.resize(nOn);COMMENT
LOWCode/DataStructs/MultiFPBReader.h1//COMMENT
LOWCode/DataStructs/SparseIntVect.h1//COMMENT
LOWCode/DataStructs/SparseIntVect.h61 }COMMENT
LOWCode/DataStructs/Utils.cpp1//COMMENT
LOWCode/DataStructs/testMultiFPB.cpp1//COMMENT
LOWCode/DataStructs/FPBReader.cpp1//COMMENT
LOWCode/DataStructs/BitOps.h1//COMMENT
LOWCode/DataStructs/RealValueVect.h1//COMMENT
LOWCode/DataStructs/DatastructsStreamOps.h1// Copyright (c) 2019, Novartis Institutes for BioMedical Research Inc.COMMENT
LOWCode/DataStructs/DatastructsStreamOps.h21// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FORCOMMENT
LOWCode/DataStructs/base64.h1//COMMENT
LOWCode/DataStructs/testFPB.cpp1//COMMENT
LOWCode/DataStructs/BitVect.cpp1//COMMENT
LOWCode/DataStructs/base64.cpp1//COMMENT
LOWCode/DataStructs/base64.cpp21// 6 G 23 X 40 o 57 5COMMENT
LOWCode/DataStructs/MultiFPBReader.cpp1//COMMENT
LOWCode/DataStructs/DiscreteDistMat.cpp1//COMMENT
LOWCode/DataStructs/BitVect.h1//COMMENT
LOWCode/DataStructs/FPBReader.h1//COMMENT
LOWCode/DataStructs/catch_tests.cpp1//COMMENT
LOWCode/DataStructs/DiscreteValueVect.h1//COMMENT
LOWCode/DataStructs/BitVectUtils.h1//COMMENT
LOWCode/DataStructs/SparseBitVect.h1//COMMENT
LOWCode/DataStructs/RealValueVect.cpp1//COMMENT
LOWCode/DataStructs/BitOps.cpp1//COMMENT
LOWCode/DataStructs/BitOps.cpp461 return 1.0;COMMENT
LOWCode/DataStructs/BitOps.cpp521 static_cast<int>(((*bv1.dp_bits) ^ (*bv2.dp_bits)).count());COMMENT
LOWCode/DataStructs/BitOps.cpp541 throw ValueErrorException("BitVects must be same length");COMMENT
LOWCode/DataStructs/BitOps.cpp601// The on bit projected similarity of T1 onto T2 is theCOMMENT
LOWCode/DataStructs/BitOps.cpp641// percentage of T1's off bits which are off in T2.COMMENT
LOWCode/DataStructs/BitOps.cpp901#include <intrin.h>COMMENT
LOWCode/DataStructs/BitVects.h1//COMMENT
LOWCode/DataStructs/DiscreteDistMat.h1//COMMENT
LOWCode/DataStructs/DatastructsException.h1//COMMENT
LOWCode/DataStructs/ExplicitBitVect.h1//COMMENT
LOWCode/DataStructs/testDatastructs.cpp1//COMMENT
LOWCode/DataStructs/DiscreteValueVect.cpp1//COMMENT
LOWCode/DataStructs/ExplicitBitVect.cpp1//COMMENT
LOWCode/DataStructs/nbWrap/wrap_SparseBV.cpp1//COMMENT
LOWCode/DataStructs/nbWrap/wrap_ExplicitBV.cpp1//COMMENT
LOWCode/DataStructs/nbWrap/wrap_BitOps.cpp1//COMMENT
LOWCode/DataStructs/nbWrap/SparseIntVect.cpp1//COMMENT
2150 more matches not shown…
Self-Referential Comments191 hits · 573 pts
SeverityFileLineSnippetContext
MEDIUMRegress/Scripts/fingerprint_screenout.py5# This file is part of the RDKit.COMMENT
MEDIUMCode/GraphMol/TautomerQuery/Wrap/rough_test.py6# This file is part of the RDKit.COMMENT
MEDIUMCode/GraphMol/DetermineBonds/Wrap/testDetermineBonds.py5# This file is part of the RDKit.COMMENT
MEDIUMCode/GraphMol/MolProcessing/Wrap/testMolProcessing.py5# This file is part of the RDKit.COMMENT
MEDIUM…e/GraphMol/ScaffoldNetwork/Wrap/testScaffoldNetwork.py5# This file is part of the RDKit.COMMENT
MEDIUM…hMol/ScaffoldNetwork/Wrap/testPickleScaffoldNetwork.py5# This file is part of the RDKit.COMMENT
MEDIUMCode/GraphMol/Wrap/testSCSR.py5# This file is part of the RDKit.COMMENT
MEDIUMCode/GraphMol/Wrap/testSubstructureMatch.py5# This file is part of the RDKit.COMMENT
MEDIUMCode/GraphMol/Wrap/testSGroups.py5# This file is part of the RDKit.COMMENT
MEDIUMCode/GraphMol/Descriptors/test_data/pmi.py5# This file is part of the RDKit.COMMENT
MEDIUM…/GeneralizedSubstruct/Wrap/testGeneralizedSubstruct.py5# This file is part of the RDKit.COMMENT
MEDIUMCode/GraphMol/Abbreviations/Wrap/testAbbreviations.py5# This file is part of the RDKit.COMMENT
MEDIUMCode/GraphMol/MolEnumerator/Wrap/rough_test.py5# This file is part of the RDKit.COMMENT
MEDIUMDocs/Book/conf.py6# This file is execfile()d with the current directory set to its containing dir.COMMENT
MEDIUMDocs/Book_jp/conf.py7# This file is execfile()d with the current directory set to itsCOMMENT
MEDIUMContrib/CalcLigRMSD/CalcLigRMSD.py5# This file is part of the RDKit.COMMENT
MEDIUMContrib/Fastcluster/fastcluster.py3# This file is part of the RDKit.COMMENT
MEDIUMContrib/IFG/ifg.py3# This file is part of the RDKit.COMMENT
MEDIUMContrib/efgs/try_efgs.py104 # Create a blank background image for the gridCOMMENT
MEDIUMContrib/efgs/efgs.py371 # Create a copy of the fragment to modifyCOMMENT
MEDIUMContrib/efgs/efgs.py379 # Create a dummy atom with the R group labelCOMMENT
MEDIUMContrib/efgs/efgs.py501 # Define the pattern to matchCOMMENT
MEDIUMContrib/efgs/efgs.py504 # Define the replacement stringCOMMENT
MEDIUMContrib/FreeWilson/freewilson.py4# This file is part of the RDKit.COMMENT
MEDIUMContrib/PBF/pbf.py5# This file is part of the RDKit.COMMENT
MEDIUMScripts/run_python_tests.py5# This file is part of the RDKit.COMMENT
MEDIUMExternal/ChemDraw/Wrap/testChemDraw.py4# This file is part of the RDKit.COMMENT
MEDIUMExternal/CoordGen/Wrap/testCoordGen.py4# This file is part of the RDKit.COMMENT
MEDIUMExternal/YAeHMOP/Wrap/testEHTTools.py4# This file is part of the RDKit.COMMENT
MEDIUMrdkit/RDConfig.py6# This file is part of the RDKit.COMMENT
MEDIUMrdkit/UnitTestLogging.py5# This file is part of the RDKit.COMMENT
MEDIUMrdkit/RDLogger.py4# This file is part of the RDKit.COMMENT
MEDIUMrdkit/TestRunner.py5# This file is part of the RDKit.COMMENT
MEDIUMrdkit/RDRandom.py5# This file is part of the RDKit.COMMENT
MEDIUMrdkit/DataManip/Metric/__init__.py4# This file is part of the RDKit.COMMENT
MEDIUMrdkit/DataStructs/UnitTestTopNContainer.py4# This file is part of the RDKit.COMMENT
MEDIUMrdkit/DataStructs/UnitTestDocTests.py4# This file is part of the RDKit.COMMENT
MEDIUMrdkit/DataStructs/BitEnsembleDb.py4# This file is part of the RDKit.COMMENT
MEDIUMrdkit/DataStructs/VectCollection.py4# This file is part of the RDKit.COMMENT
MEDIUMrdkit/DataStructs/BitUtils.py4# This file is part of the RDKit.COMMENT
MEDIUMrdkit/DataStructs/__init__.py4# This file is part of the RDKit.COMMENT
MEDIUMrdkit/DataStructs/TopNContainer.py4# This file is part of the RDKit.COMMENT
MEDIUMrdkit/DataStructs/UnitTestBitEnsemble.py4# This file is part of the RDKit.COMMENT
MEDIUMrdkit/DataStructs/UnitTestFlatMatrix.py5# This file is part of the RDKit.COMMENT
MEDIUMrdkit/DataStructs/UnitTestcBitVect.py4# This file is part of the RDKit.COMMENT
MEDIUMrdkit/DataStructs/BitEnsemble.py4# This file is part of the RDKit.COMMENT
MEDIUMrdkit/DataStructs/HierarchyVis.py4# This file is part of the RDKit.COMMENT
MEDIUMrdkit/Dbase/UnitTestDbInfo.py5# This file is part of the RDKit.COMMENT
MEDIUMrdkit/Dbase/DbConnection.py5# This file is part of the RDKit.COMMENT
MEDIUMrdkit/Dbase/__init__.py5# This file is part of the RDKit.COMMENT
MEDIUMrdkit/Dbase/UnitTestDbConnect.py4# This file is part of the RDKit.COMMENT
MEDIUMrdkit/Dbase/DbUtils.py4# This file is part of the RDKit.COMMENT
MEDIUMrdkit/Dbase/UnitTestDbResultSet.py4# This file is part of the RDKit.COMMENT
MEDIUMrdkit/Dbase/StorageUtils.py4# This file is part of the RDKit.COMMENT
MEDIUMrdkit/Dbase/UnitTestDbUtils.py4# This file is part of the RDKit.COMMENT
MEDIUMrdkit/Dbase/DbInfo.py4# This file is part of the RDKit.COMMENT
MEDIUMrdkit/Dbase/UnitTestStorageUtils.py4# This file is part of the RDKit.COMMENT
MEDIUMrdkit/Dbase/DbModule.py4# This file is part of the RDKit.COMMENT
MEDIUMrdkit/utils/chemdraw_qax.py35 # Create an instance of that classCOMMENT
MEDIUMrdkit/utils/chemdraw.py4# This file is part of the RDKit.COMMENT
131 more matches not shown…
Decorative Section Separators141 hits · 438 pts
SeverityFileLineSnippetContext
MEDIUMRegress/Data/RLewis_smarts.txt6#-------------------COMMENT
MEDIUMRegress/Data/RLewis_smarts.txt39#-------------------COMMENT
MEDIUMRegress/Data/RLewis_smarts.txt57#-------------------COMMENT
MEDIUMRegress/Data/RLewis_smarts.txt67#-------------------COMMENT
MEDIUMRegress/Data/RLewis_smarts.txt81#-------------------COMMENT
MEDIUMRegress/Data/RLewis_smarts.txt283#-------------------COMMENT
MEDIUMRegress/Data/RLewis_smarts.txt336#-------------------COMMENT
MEDIUMRegress/Data/RLewis_smarts.txt371#-------------------COMMENT
MEDIUMCode/GraphMol/Wrap/testGetPropDefault.py6# ---------------------------------------------------------------------------COMMENT
MEDIUMCode/GraphMol/Wrap/testGetPropDefault.py8# ---------------------------------------------------------------------------COMMENT
MEDIUMCode/GraphMol/Wrap/testGetPropDefault.py76# ---------------------------------------------------------------------------COMMENT
MEDIUMCode/GraphMol/Wrap/testGetPropDefault.py78# ---------------------------------------------------------------------------COMMENT
MEDIUMCode/GraphMol/Wrap/testGetPropDefault.py120# ---------------------------------------------------------------------------COMMENT
MEDIUMCode/GraphMol/Wrap/testGetPropDefault.py122# ---------------------------------------------------------------------------COMMENT
MEDIUMContrib/ChiralPairs/ChiralDescriptors.py404#------------------------------------COMMENT
MEDIUMContrib/SA_Score/sascorer.py86 # ---------------------------------------COMMENT
MEDIUMrdkit/RDConfig.py47# ---------------------COMMENT
MEDIUMrdkit/RDConfig.py52# ---------------------COMMENT
MEDIUMrdkit/RDConfig.py85# ---------------------COMMENT
MEDIUMrdkit/DataStructs/LazySignature.py69# ------------------------------------COMMENT
MEDIUMrdkit/DataStructs/VectCollection.py270# ------------------------------------COMMENT
MEDIUMrdkit/DataStructs/BitUtils.py39# ------------------------------------COMMENT
MEDIUMrdkit/Dbase/StorageUtils.py264# ------------------------------------COMMENT
MEDIUMrdkit/utils/chemdraw_qax.py22#----------------------------------------------------------------------COMMENT
MEDIUMrdkit/utils/chemdraw.py85# ------------------------------------------------------------------COMMENT
MEDIUMrdkit/utils/chemdraw.py87# ------------------------------------------------------------------COMMENT
MEDIUMrdkit/utils/chemdraw.py275# ------------------------------------------------------------------COMMENT
MEDIUMrdkit/utils/chemdraw.py277# ------------------------------------------------------------------COMMENT
MEDIUMrdkit/utils/listutils.py52# ------------------------------------COMMENT
MEDIUMrdkit/ML/Descriptors/CompoundDescriptors.py100 # ------------COMMENT
MEDIUMrdkit/ML/Descriptors/CompoundDescriptors.py102 # ------------COMMENT
MEDIUMrdkit/ML/Descriptors/CompoundDescriptors.py208 # ------------COMMENT
MEDIUMrdkit/ML/Descriptors/CompoundDescriptors.py210 # ------------COMMENT
MEDIUMrdkit/ML/Descriptors/Parser.py56# ----------------------COMMENT
MEDIUMrdkit/ML/Descriptors/Parser.py58# ----------------------COMMENT
MEDIUMrdkit/ML/Descriptors/Parser.py227# ------------------COMMENT
MEDIUMrdkit/ML/Descriptors/Parser.py230# ------------------COMMENT
MEDIUMrdkit/ML/Descriptors/Parser.py430# ------------COMMENT
MEDIUMrdkit/ML/Descriptors/Parser.py432# ------------COMMENT
MEDIUMrdkit/ML/Descriptors/Descriptors.py24 # ------------COMMENT
MEDIUMrdkit/ML/Descriptors/Descriptors.py26 # ------------COMMENT
MEDIUMrdkit/ML/Data/SplitData.py295# ------------------------------------COMMENT
MEDIUMrdkit/ML/Data/Quantize.py237 # --------------------------------COMMENT
MEDIUMrdkit/ML/Data/Quantize.py248 # --------------------------------COMMENT
MEDIUMrdkit/ML/Data/DataUtils.py669# ------------------------------------COMMENT
MEDIUMrdkit/sping/stringformat.py44#------------------------------------------------------------------------COMMENT
MEDIUMrdkit/sping/stringformat.py50#------------------------------------------------------------------------COMMENT
MEDIUMrdkit/sping/stringformat.py97#------------------------------------------------------------------------COMMENT
MEDIUMrdkit/sping/stringformat.py152#------------------------------------------------------------------COMMENT
MEDIUMrdkit/sping/stringformat.py165#------------------------------------------------------------------COMMENT
MEDIUMrdkit/sping/stringformat.py168 #----------------------------------------------------------COMMENT
MEDIUMrdkit/sping/stringformat.py180 #----------------------------------------------------------COMMENT
MEDIUMrdkit/sping/stringformat.py226 #----------------------------------------------------------------COMMENT
MEDIUMrdkit/sping/stringformat.py286 #----------------------------------------------------------------COMMENT
MEDIUMrdkit/sping/stringformat.py290 #----------------------------------------------------------------COMMENT
MEDIUMrdkit/sping/stringformat.py317 #----------------------------------------------------------------COMMENT
MEDIUMrdkit/sping/stringformat.py332 #------------------------------------------------------------------------COMMENT
MEDIUMrdkit/sping/stringformat.py351#------------------------------------------------------------------------COMMENT
MEDIUMrdkit/sping/stringformat.py355#------------------------------------------------------------------------COMMENT
MEDIUMrdkit/sping/stringformat.py413 #------------------------------------------------------------------------COMMENT
81 more matches not shown…
Unused Imports247 hits · 244 pts
SeverityFileLineSnippetContext
LOWRegress/Scripts/fingerprint_screenout.py16CODE
LOWRegress/Scripts/timings.py2CODE
LOWWeb/RDExtras/MolImage.py5CODE
LOWWeb/RDExtras/MolImage.py11CODE
LOWWeb/RDExtras/MolDepict.py1CODE
LOWWeb/RDExtras/MolDepict.py2CODE
LOWWeb/RDExtras/MolDepict.py3CODE
LOWWeb/RDExtras/MolDepict.py6CODE
LOWProjects/DbCLI/CreateDb.py277CODE
LOWProjects/DbCLI/UnitTestDbCLI.py10CODE
LOWCode/DataStructs/Wrap/testBV.py3CODE
LOWCode/DataStructs/Wrap/testRealValueVect.py5CODE
LOWCode/DataStructs/Wrap/testRealValueVect.py5CODE
LOWCode/JavaWrappers/parse_doxy_html.py15CODE
LOWCode/GraphMol/CIPLabeler/Wrap/pyCIPLabelWrapTest.py3CODE
LOWCode/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py5CODE
LOWCode/GraphMol/Wrap/test_cdxml.py306CODE
LOWCode/GraphMol/Wrap/test_cdxml.py347CODE
LOWCode/GraphMol/MolInteractionFields/Wrap/testMIF.py1CODE
LOWCode/GraphMol/Descriptors/test_data/pmi.py14CODE
LOWCode/GraphMol/Descriptors/Wrap/test3D.py2CODE
LOWCode/GraphMol/MolDraw2D/update_hash_codes.py11CODE
LOWCode/GraphMol/MolDraw2D/Qt/Wrap/testMolDraw2DQt.py10CODE
LOWCode/GraphMol/MolDraw2D/Qt/Wrap/testMolDraw2DQt.py13CODE
LOW…hMol/SynthonSpaceSearch/Wrap/testSynthonSpaceSearch.py43CODE
LOWCode/Demos/boost/numpy/test.py2CODE
LOWCode/Demos/boost/smartPtrsAndIters/setup.py5CODE
LOWDocs/Book/data/test_multi_colours.py3CODE
LOWDocs/Book/data/test_multi_colours.py5CODE
LOWDocs/Book/data/test_multi_colours.py6CODE
LOWContrib/RxnRoleAssignment/identifyReactants.py34CODE
LOWContrib/RxnRoleAssignment/utils.py37CODE
LOWContrib/Fastcluster/fastcluster.py18CODE
LOWContrib/Fastcluster/fastcluster.py19CODE
LOWContrib/M_Kossner/Frames.py21CODE
LOWContrib/pzc/p_con.py17CODE
LOWContrib/pzc/p_con.py18CODE
LOWContrib/pzc/p_con.py19CODE
LOWContrib/pzc/p_con.py22CODE
LOWContrib/pzc/p_con.py22CODE
LOWContrib/pzc/p_con.py22CODE
LOWContrib/efgs/try_efgs.py16CODE
LOWContrib/efgs/try_efgs.py19CODE
LOWContrib/FreeWilson/freewilson.py138CODE
LOWContrib/FreeWilson/freewilson.py142CODE
LOWContrib/mmpa/test_rfrag.py6CODE
LOWContrib/mmpa/test_rfrag.py10CODE
LOWContrib/AtomAtomSimilarity/AtomAtomPathSimilarity.py13CODE
LOWContrib/LEF/AddLabels.py33CODE
LOWContrib/LEF/CreateFps.py38CODE
LOWContrib/LEF/DistancePredict.py39CODE
LOWContrib/SA_Score/UnitTestSAScore.py1CODE
LOWContrib/SA_Score/UnitTestSAScore.py6CODE
LOW…b/NIBRSubstructureFilters/assignSubstructureFilters.py2CODE
LOW…b/NIBRSubstructureFilters/assignSubstructureFilters.py4CODE
LOW…b/NIBRSubstructureFilters/assignSubstructureFilters.py4CODE
LOW…b/NIBRSubstructureFilters/assignSubstructureFilters.py10CODE
LOWContrib/PBF/pbf.py14CODE
LOWContrib/fraggle/atomcontrib.py37CODE
LOWbuild_support/pkg_version.py1CODE
187 more matches not shown…
Excessive Try-Catch Wrapping229 hits · 240 pts
SeverityFileLineSnippetContext
LOWRegress/Scripts/chiral_embed.py10except Exception:CODE
LOWWeb/RDExtras/MolImage.py58 except Exception:CODE
LOWProjects/DbCLI/CreateDb.py231 except Exception:CODE
LOWProjects/DbCLI/CreateDb.py242 except Exception:CODE
LOWProjects/DbCLI/CreateDb.py246 except Exception:CODE
LOWProjects/DbCLI/CreateDb.py250 except Exception:CODE
LOWProjects/DbCLI/CreateDb.py254 except Exception:CODE
LOWProjects/DbCLI/CreateDb.py284 except Exception:CODE
LOWProjects/DbCLI/CreateDb.py302 except Exception:CODE
LOWProjects/DbCLI/CreateDb.py330 except Exception:CODE
LOWProjects/DbCLI/CreateDb.py469 except Exception:CODE
LOWProjects/DbCLI/SearchDb.py318 except Exception:STRING
LOWCode/ML/InfoTheory/Wrap/testRanker.py149 except Exception:CODE
LOWCode/GraphMol/TautomerQuery/Wrap/rough_test.py84 except Exception:CODE
LOWCode/GraphMol/nbWrap/rough_test.py523 except Exception:STRING
LOWCode/GraphMol/nbWrap/rough_test.py2359 except Exception:CODE
LOWCode/GraphMol/nbWrap/rough_test.py2367 except Exception:CODE
LOWCode/GraphMol/nbWrap/rough_test.py5633 except Exception:STRING
LOWCode/GraphMol/nbWrap/rough_test.py7315 except Exception:CODE
LOWCode/GraphMol/nbWrap/rough_test.py8531 except Exception as e:STRING
LOWCode/GraphMol/nbWrap/rough_test.py8537 except Exception as e:STRING
MEDIUMCode/GraphMol/nbWrap/rough_test.py6256def testSanitizationExceptionBasics(self):CODE
LOWCode/GraphMol/PartialCharges/Wrap/testPartialCharges.py118 except Exception:CODE
LOWCode/GraphMol/MolTransforms/Wrap/testMolTransforms.py99 except Exception:STRING
LOWCode/GraphMol/MolTransforms/Wrap/testMolTransforms.py145 except Exception:STRING
LOWCode/GraphMol/Wrap/testTrajectory.py24 except Exception:CODE
LOWCode/GraphMol/Wrap/testTrajectory.py31 except Exception:CODE
LOWCode/GraphMol/Wrap/testTrajectory.py51 except Exception:CODE
LOWCode/GraphMol/Wrap/testTrajectory.py57 except Exception:CODE
LOWCode/GraphMol/Wrap/testTrajectory.py66 except Exception:CODE
LOWCode/GraphMol/Wrap/testTrajectory.py102 except Exception:CODE
LOWCode/GraphMol/Wrap/testTrajectory.py108 except Exception:CODE
LOWCode/GraphMol/Wrap/testTrajectory.py119 except Exception:CODE
LOWCode/GraphMol/Wrap/testTrajectory.py146 except Exception:CODE
LOWCode/GraphMol/Wrap/testTrajectory.py153 except Exception:CODE
LOWCode/GraphMol/Wrap/testTrajectory.py161 except Exception:CODE
LOWCode/GraphMol/Wrap/testTrajectory.py228 except Exception:CODE
LOWCode/GraphMol/Wrap/testTrajectory.py235 except Exception:CODE
LOWCode/GraphMol/Wrap/testTrajectory.py243 except Exception:CODE
LOWCode/GraphMol/Wrap/testTrajectory.py436 except Exception:CODE
LOWCode/GraphMol/Wrap/testTrajectory.py457 except Exception:CODE
LOWCode/GraphMol/Wrap/testTrajectory.py490 except Exception:CODE
LOWCode/GraphMol/Wrap/rough_test.py522 except Exception:STRING
LOWCode/GraphMol/Wrap/rough_test.py828 except Exception:STRING
LOWCode/GraphMol/Wrap/rough_test.py2348 except Exception:CODE
LOWCode/GraphMol/Wrap/rough_test.py2356 except Exception:CODE
LOWCode/GraphMol/Wrap/rough_test.py5580 except Exception:STRING
LOWCode/GraphMol/Wrap/rough_test.py7238 except Exception:CODE
LOWCode/GraphMol/Wrap/rough_test.py8649 except Exception as e:STRING
LOWCode/GraphMol/Wrap/rough_test.py8655 except Exception as e:STRING
MEDIUMCode/GraphMol/Wrap/rough_test.py6198def testSanitizationExceptionBasics(self):CODE
LOWCode/GraphMol/ChemReactions/Wrap/testSanitize.py294 except Exception:STRING
LOWCode/GraphMol/SubstructLibrary/Wrap/rough_test.py530 except Exception:CODE
LOWCode/Demos/boost/python_objs/test.py12 except Exception:CODE
LOWCode/Demos/boost/python_objs/test.py25 except Exception:CODE
LOWCode/Demos/boost/python_objs/test.py33 except Exception:CODE
LOWCode/Demos/boost/python_objs/test.py41 except Exception:CODE
LOWContrib/pzc/p_con.py491 except Exception:STRING
LOWContrib/pzc/p_con.py501 except Exception:STRING
LOWContrib/pzc/p_con.py520 except Exception:STRING
169 more matches not shown…
Deep Nesting226 hits · 222 pts
SeverityFileLineSnippetContext
LOWProjects/DbCLI/CreateDb.py168CODE
LOWProjects/DbCLI/SearchDb.py76CODE
LOWProjects/DbCLI/SearchDb.py134CODE
LOWProjects/DbCLI/SearchDb.py156CODE
LOWCode/JavaWrappers/parse_doxy_html.py359CODE
LOWCode/JavaWrappers/parse_doxy_html.py423CODE
LOWCode/JavaWrappers/parse_doxy_html.py447CODE
LOWCode/GraphMol/nbWrap/rough_test.py1943CODE
LOWCode/GraphMol/nbWrap/rough_test.py7516CODE
LOWCode/GraphMol/DetermineBonds/Wrap/testDetermineBonds.py20CODE
LOWCode/GraphMol/DetermineBonds/Wrap/testDetermineBonds.py39CODE
LOWCode/GraphMol/DetermineBonds/Wrap/testDetermineBonds.py59CODE
LOWCode/GraphMol/DetermineBonds/Wrap/testDetermineBonds.py79CODE
LOWCode/GraphMol/MolTransforms/Wrap/testMolTransforms.py239CODE
LOWCode/GraphMol/Wrap/test_cdxml.py345CODE
LOWCode/GraphMol/Wrap/rough_test.py1933CODE
LOWCode/GraphMol/Wrap/rough_test.py7439CODE
LOWCode/GraphMol/ChemReactions/Wrap/testEnumerations.py223CODE
LOWCode/GraphMol/ChemReactions/Wrap/testReactionWrapper.py579CODE
LOWCode/GraphMol/SubstructLibrary/Wrap/rough_test.py59CODE
LOWCode/GraphMol/SubstructLibrary/Wrap/rough_test.py82CODE
LOWCode/GraphMol/SubstructLibrary/Wrap/rough_test.py135CODE
LOWCode/GraphMol/MolDraw2D/Wrap/testMolDraw2D.py448CODE
LOWCode/GraphMol/MolDraw2D/Wrap/testMolDraw2D.py577CODE
LOWCode/GraphMol/MolDraw2D/Wrap/testMolDraw2D.py580CODE
LOWCode/GraphMol/FilterCatalog/Wrap/rough_test.py122CODE
LOWCode/GraphMol/MolStandardize/Wrap/testMolStandardize.py532CODE
LOWDocs/Book/data/test_multi_colours.py12CODE
LOWContrib/RxnRoleAssignment/identifyReactants.py205CODE
LOWContrib/RxnRoleAssignment/identifyReactants.py317CODE
LOWContrib/RxnRoleAssignment/identifyReactants.py95CODE
LOWContrib/M_Kossner/Frames.py45CODE
LOWContrib/pzc/p_con.py113CODE
LOWContrib/pzc/p_con.py357CODE
LOWContrib/pzc/p_con.py480CODE
LOWContrib/pzc/p_con.py602CODE
LOWContrib/pzc/p_con.py746CODE
LOWContrib/IFG/ifg.py48CODE
LOWContrib/efgs/efgs.py33CODE
LOWContrib/efgs/efgs.py69CODE
LOWContrib/efgs/efgs.py141CODE
LOWContrib/efgs/efgs.py175CODE
LOWContrib/efgs/efgs.py207CODE
LOWContrib/efgs/efgs.py272CODE
LOWContrib/FreeWilson/freewilson.py163CODE
LOWContrib/FreeWilson/freewilson.py213CODE
LOWContrib/FreeWilson/freewilson.py276CODE
LOWContrib/mmpa/search_mmp_db.py91CODE
LOWContrib/mmpa/create_mmp_db.py75CODE
LOWContrib/mmpa/rfrag.py68CODE
LOWContrib/mmpa/indexing.py78CODE
LOWContrib/mmpa/indexing.py350CODE
LOWContrib/AtomAtomSimilarity/AtomAtomPathSimilarity.py31CODE
LOWContrib/AtomAtomSimilarity/AtomAtomPathSimilarity.py55CODE
LOWContrib/AtomAtomSimilarity/AtomAtomPathSimilarity.py77CODE
LOWContrib/ChiralPairs/ChiralDescriptors.py94CODE
LOW…b/NIBRSubstructureFilters/assignSubstructureFilters.py41CODE
LOWContrib/Glare/glare.py319CODE
LOWScripts/gen_rdkit_stubs/__init__.py191CODE
LOWScripts/gen_rdkit_stubs/__init__.py379CODE
166 more matches not shown…
Modern AI Meta-Vocabulary46 hits · 146 pts
SeverityFileLineSnippetContext
MEDIUMCode/MinimalLib/cffi_test.c1715 // bridged system is entirely rebuilt since it is not part of the scaffoldCOMMENT
MEDIUMCode/MinimalLib/cffi_test.c1742 // Additionally, CoordGen also rebuilds the scaffold, therefore originalCOMMENT
MEDIUMCode/MinimalLib/cffi_test.c1846 // bridged system is entirely rebuilt since it is not part of the scaffoldCOMMENT
MEDIUMCode/MinimalLib/cffi_test.c1873 // Additionally, CoordGen also rebuilds the scaffold, therefore originalCOMMENT
MEDIUMCode/MinimalLib/tests/tests.js1653 // bridged system is entirely rebuilt since it is not part of the scaffoldCOMMENT
MEDIUMCode/MinimalLib/tests/tests.js1673 // Additionally, CoordGen also rebuilds the scaffold, therefore original wedgingCOMMENT
MEDIUMCode/MinimalLib/tests/tests.js1743 // bridged system is entirely rebuilt since it is not part of the scaffoldCOMMENT
MEDIUMCode/MinimalLib/tests/tests.js1763 // Additionally, CoordGen also rebuilds the scaffold, therefore original wedgingCOMMENT
MEDIUMCode/GraphMol/RGroupDecomposition/RGroupDecompData.cpp571 // the scaffoldCOMMENT
MEDIUMCode/GraphMol/ChemTransforms/testChemTransforms.cpp1070 {"C1CC1C(=O)OC", "C1CC1"}, // Carbonyl outside scaffoldCODE
MEDIUMCode/GraphMol/ChemTransforms/testChemTransforms.cpp1071 {"C1CC1C=C", "C1CC1"}, // Double bond outside scaffoldCODE
MEDIUMCode/GraphMol/ChemTransforms/testChemTransforms.cpp1072 {"C1CC1C=CC1CC1C=CNNCO", "C1CC1C=CC1CC1"}, // Double bond in scaffoldCODE
MEDIUMCode/GraphMol/ChemTransforms/testChemTransforms.cpp1074 {"C1CC1S(=O)C1CC1C=CNNCO", "C1CC1S(=O)C1CC1"}, // S=O group in scaffoldCODE
MEDIUMCode/GraphMol/ChemTransforms/testChemTransforms.cpp1076 "C1CC1S(=O)C1CC1"}, // S=O group outside scaffoldCODE
MEDIUMCode/GraphMol/ChemTransforms/testChemTransforms.cpp1078 "C1CC1S(=O)(=O)C1CC1"}, // SO2 group in scaffoldCODE
MEDIUMCode/GraphMol/ChemTransforms/testChemTransforms.cpp1080 "C1CC1S(=O)(=O)C1CC1"}, // SO2 group outside scaffoldCODE
MEDIUMCode/GraphMol/ScaffoldNetwork/catch_tests.cpp459 // this tests a very particular case where the generic bond scaffold is theCOMMENT
MEDIUMCode/GraphMol/ScaffoldNetwork/catch_tests.cpp460 // same as the generic scaffold that leads to it. Make sure we do not end upCOMMENT
MEDIUMCode/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h45 true; ///< Include the version of the scaffold with attachment pointsCODE
MEDIUMCode/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h58 ///< scaffold was reached fromCOMMENT
MEDIUMCode/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h105 counts; ///< number of times each scaffold was encounteredCODE
MEDIUMCode/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h107 molCounts; ///< number of molecules each scaffold was found inCODE
MEDIUMCode/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h178//! returns parameters for constructing scaffold networks using BRICSCOMMENT
MEDIUMCode/GraphMol/ChemReactions/ReactionRunner.cpp2047 // add dummy atom where the reaction scaffold would have beenCOMMENT
MEDIUMCode/GraphMol/Depictor/catch_tests.cpp897 // bridged system is entirely rebuilt since it is not part of the scaffoldCOMMENT
MEDIUMCode/GraphMol/Depictor/catch_tests.cpp915 // bridged system is entirely rebuilt since it is not part of the scaffoldCOMMENT
MEDIUMCode/GraphMol/Depictor/catch_tests.cpp936 // also rebuilds the scaffold, therefore original wedging should be clearedCOMMENT
MEDIUMCode/GraphMol/Depictor/catch_tests.cpp1045 // bridged system is entirely rebuilt since it is not part of the scaffoldCOMMENT
MEDIUMCode/GraphMol/Depictor/catch_tests.cpp1063 // bridged system is entirely rebuilt since it is not part of the scaffoldCOMMENT
MEDIUMCode/GraphMol/Depictor/catch_tests.cpp1084 // also rebuilds the scaffold, therefore original wedging should be clearedCOMMENT
MEDIUMCode/GraphMol/Depictor/RDDepictor.cpp804 // 2. there is a match and wedges are outside the constrained scaffoldCOMMENT
MEDIUMCode/GraphMol/Depictor/RDDepictor.cpp813 // has at least one atom which is not part of the scaffold, we cannotCOMMENT
MEDIUMCode/GraphMol/Depictor/RDDepictor.cpp827 // check that scaffold coordinates have not changed, which mayCOMMENT
MEDIUMCode/GraphMol/Depictor/RDDepictor.cpp839 // has flipped to match the scaffoldCOMMENT
MEDIUMContrib/RxnRoleAssignment/identifyReactants.py292 # atoms based on the scaffold FP, the number of unmapped scaffoldFP bits, and the unmapped scaffoldFP bitsCOMMENT
MEDIUMrdkit/Chem/Scaffolds/UnitTestMurckoScaffold.py83 # Carbonyl outside scaffoldCOMMENT
MEDIUMrdkit/Chem/Scaffolds/UnitTestMurckoScaffold.py85 # Double bond outside scaffoldCOMMENT
MEDIUMrdkit/Chem/Scaffolds/UnitTestMurckoScaffold.py87 # Double bond in scaffoldCOMMENT
MEDIUMrdkit/Chem/Scaffolds/UnitTestMurckoScaffold.py92 # S=O group in scaffoldCOMMENT
MEDIUMrdkit/Chem/Scaffolds/UnitTestMurckoScaffold.py94 # S=O group outside scaffoldCOMMENT
MEDIUMrdkit/Chem/Scaffolds/UnitTestMurckoScaffold.py96 # SO2 group in scaffoldCOMMENT
MEDIUMrdkit/Chem/Scaffolds/UnitTestMurckoScaffold.py98 # SO2 group outside scaffoldCOMMENT
MEDIUMrdkit/Chem/Pharm2D/SigFactory.py297 # and which scaffold:COMMENT
MEDIUMrdkit/Chem/Pharm2D/Utils.py78# number of points in a scaffold -> sequence of distances (p1, p2) inCOMMENT
MEDIUMrdkit/Chem/Pharm2D/Utils.py79# the scaffoldCOMMENT
MEDIUMrdkit/Chem/Pharm2D/Utils.py97# number of distances in a scaffold -> number of points in the scaffoldCOMMENT
Cross-File Repetition28 hits · 140 pts
SeverityFileLineSnippetContext
HIGHCode/GraphMol/nbWrap/rough_test.py0this is a rough coverage test of the python wrapper it's intended to be shallow, but broadSTRING
HIGHCode/GraphMol/FragCatalog/Wrap/rough_test.py0this is a rough coverage test of the python wrapper it's intended to be shallow, but broadSTRING
HIGHCode/GraphMol/Wrap/test_cdxml.py0this is a rough coverage test of the python wrapper it's intended to be shallow, but broadSTRING
HIGHCode/GraphMol/Wrap/rough_test.py0this is a rough coverage test of the python wrapper it's intended to be shallow, but broadSTRING
HIGHCode/GraphMol/nbWrap/rough_test.py0rdkit 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 0STRING
HIGHCode/GraphMol/Wrap/rough_test.py0rdkit 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 0STRING
HIGHrdkit/Chem/UnitTestRandomize.py0rdkit 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 0STRING
HIGHrdkit/sping/pid.py0draw a pil image into the specified rectangle. if x2 and y2 are omitted, they are calculated from the image size. jjk 11STRING
HIGHrdkit/sping/PIL/pidPIL.py0draw a pil image into the specified rectangle. if x2 and y2 are omitted, they are calculated from the image size. jjk 11STRING
HIGHrdkit/sping/PDF/pidPDF.py0draw a pil image into the specified rectangle. if x2 and y2 are omitted, they are calculated from the image size. jjk 11STRING
HIGHrdkit/sping/WX/pidWxDc.py0draw a pil image into the specified rectangle. if x2 and y2 are omitted, they are calculated from the image size. jjk 11STRING
HIGHrdkit/sping/SVG/pidSVG.py0attempts to return proper font name. pdf uses a standard 14 fonts referred to by name. default to self.defaultfont('helvSTRING
HIGHrdkit/sping/PS/pidPS.py0attempts to return proper font name. pdf uses a standard 14 fonts referred to by name. default to self.defaultfont('helvSTRING
HIGHrdkit/sping/Pyart/pidPyart.py0attempts to return proper font name. pdf uses a standard 14 fonts referred to by name. default to self.defaultfont('helvSTRING
HIGHrdkit/sping/SVG/pidSVG.py0drawpolygon(pointlist) -- draws a polygon pointlist: a list of (x,y) tuples defining verticesSTRING
HIGHrdkit/sping/Qt/pidQt4.py0drawpolygon(pointlist) -- draws a polygon pointlist: a list of (x,y) tuples defining verticesSTRING
HIGHrdkit/sping/Qt/pidQt.py0drawpolygon(pointlist) -- draws a polygon pointlist: a list of (x,y) tuples defining verticesSTRING
HIGHrdkit/sping/PIL/pidPIL.py0drawpolygon(pointlist) -- draws a polygon pointlist: a list of (x,y) tuples defining verticesSTRING
HIGHrdkit/sping/ReportLab/pidReportLab.py0drawpolygon(pointlist) -- draws a polygon pointlist: a list of (x,y) tuples defining verticesSTRING
HIGHrdkit/sping/PDF/pidPDF.py0pdf escapes are almost like python ones, but brackets need slashes before them too. use python's repr function and chop STRING
HIGHrdkit/sping/PDF/pdfgen.py0pdf escapes are almost like python ones, but brackets need slashes before them too. use python's repr function and chop STRING
HIGHrdkit/sping/PDF/pdfutils.py0pdf escapes are almost like python ones, but brackets need slashes before them too. use python's repr function and chop STRING
HIGHrdkit/Chem/UnitTestLipinski.py0return entries form regression dataset. returns the line number, smiles, molecule, and the value found in column colSTRING
HIGHrdkit/Chem/UnitTestSurf.py0return entries form regression dataset. returns the line number, smiles, molecule, and the value found in column colSTRING
HIGHrdkit/Chem/UnitTestGraphDescriptors_2.py0return entries form regression dataset. returns the line number, smiles, molecule, and the value found in column colSTRING
HIGHrdkit/Chem/UnitTestFeatFinderCLI.py0redirect standard output and error to string io and returnSTRING
HIGHrdkit/Chem/ChemUtils/UnitTestSDFToCSV.py0redirect standard output and error to string io and returnSTRING
HIGHrdkit/Chem/ChemUtils/UnitTestAlignDepict.py0redirect standard output and error to string io and returnSTRING
Hyper-Verbose Identifiers115 hits · 102 pts
SeverityFileLineSnippetContext
LOWReleaseNotes.md8573 - The function getHashedMorganFingerprint (GetHashedMorganFingerprintCODE
LOWCode/MinimalLib/tests/tests.js1486function getWedgedMolAndInvertedWedges() {CODE
LOWCode/GraphMol/RGroupDecomposition/Wrap/test_rgroups.py209 def test_match_only_at_rgroups(self):STRING
LOWCode/GraphMol/RGroupDecomposition/Wrap/test_rgroups.py220 def test_incorrect_multiple_rlabels(self):STRING
LOWCode/GraphMol/RGroupDecomposition/Wrap/test_rgroups.py411 def test_multicore_prelabelled(self):STRING
LOWCode/GraphMol/nbWrap/rough_test.py1819 def recursive_enumerate_stereo_bonds(self, mol, done_bonds, bonds):STRING
LOWCode/GraphMol/nbWrap/rough_test.py7096 def test_get_set_positions_stride(self):STRING
LOWCode/GraphMol/Wrap/test_lazy_numpy.py29 def test_chem_import_does_not_load_numpy(self):CODE
LOWCode/GraphMol/Wrap/test_lazy_numpy.py40 def test_basic_smiles_roundtrip_without_numpy(self):STRING
LOWCode/GraphMol/Wrap/test_lazy_numpy.py56 def test_mol_operations_without_numpy(self):STRING
LOWCode/GraphMol/Wrap/test_lazy_numpy.py89 def test_numpy_loads_on_demand(self):STRING
LOWCode/GraphMol/Wrap/test_lazy_numpy.py106 def test_conformer_positions_loads_numpy(self):STRING
LOWCode/GraphMol/Wrap/test_lazy_numpy.py127 def test_datastructs_convert_loads_numpy(self):STRING
LOWCode/GraphMol/Wrap/test_lazy_numpy.py144 def test_adjacency_matrix_loads_numpy(self):STRING
LOWCode/GraphMol/Wrap/testGetPropDefault.py12def test_get_prop_with_default_missing(auto_convert, default):CODE
LOWCode/GraphMol/Wrap/testGetPropDefault.py26def test_get_prop_with_default_present(auto_convert, prop_value, default, unconverted_value):CODE
LOWCode/GraphMol/Wrap/testGetPropDefault.py41def test_get_prop_no_default_not_set(auto_convert):CODE
LOWCode/GraphMol/Wrap/testGetPropDefault.py54def test_get_prop_no_default_set(auto_convert, prop_value, unconverted_value):CODE
LOWCode/GraphMol/Wrap/testGetPropDefault.py67def test_get_prop_default_positional():CODE
LOWCode/GraphMol/Wrap/testGetPropDefault.py80def test_get_prop_default_on_atom():CODE
LOWCode/GraphMol/Wrap/testGetPropDefault.py90def test_get_prop_default_on_bond():CODE
LOWCode/GraphMol/Wrap/testGetPropDefault.py100def test_get_prop_default_on_conformer():CODE
LOWCode/GraphMol/Wrap/testGetPropDefault.py110def test_get_prop_default_on_substance_group():CODE
LOWCode/GraphMol/Wrap/testGetPropDefault.py130def test_typed_getter_with_default_present(set_fn, get_fn, val, default):CODE
LOWCode/GraphMol/Wrap/testGetPropDefault.py143def test_typed_getter_with_default_missing(get_fn, default):CODE
LOWCode/GraphMol/Wrap/testGetPropDefault.py150def test_typed_getter_no_default_raises(get_fn):CODE
LOWCode/GraphMol/Wrap/testGetPropDefault.py157def test_typed_getter_default_wrong_type_raises_value_error():CODE
LOWCode/GraphMol/Wrap/rough_test.py1809 def recursive_enumerate_stereo_bonds(self, mol, done_bonds, bonds):STRING
LOWCode/GraphMol/Wrap/rough_test.py7019 def test_get_set_positions_stride(self):STRING
LOWCode/GraphMol/ChemReactions/Wrap/testReactionWrapper.py824 def test_reaction_preserves_stereo(self):STRING
LOWCode/GraphMol/ChemReactions/Wrap/testReactionWrapper.py836 def test_reaction_ignores_stereo(self):STRING
LOWCode/GraphMol/ChemReactions/Wrap/testReactionWrapper.py848 def test_reaction_inverts_stereo(self):STRING
LOWCode/GraphMol/ChemReactions/Wrap/testReactionWrapper.py863 def test_reaction_destroys_stereo(self):STRING
LOWCode/GraphMol/ChemReactions/Wrap/testReactionWrapper.py886 def test_reaction_defines_stereo(self):STRING
LOWCode/GraphMol/ChemReactions/Wrap/testReactionWrapper.py908 def test_stereogroup_is_spectator_to_reaction(self):STRING
LOWCode/GraphMol/ChemReactions/Wrap/testReactionWrapper.py929 def test_reaction_splits_stereogroup(self):STRING
LOWCode/GraphMol/ChemReactions/Wrap/testReactionWrapper.py939 def test_reaction_copies_stereogroup(self):STRING
LOWCode/GraphMol/ChemReactions/Wrap/testSanitize.py300 def test_unused_rlabel_in_product(self):STRING
LOWCode/GraphMol/ChemReactions/Wrap/testSanitize.py305 def test_only_aromatize_if_possible(self):STRING
LOWCode/GraphMol/ForceFieldHelpers/Wrap/testHelpers.py419 def test_uff_get_forcefield_runs(self):CODE
LOWCode/GraphMol/SubstructLibrary/Wrap/rough_test.py382 def test_init_from_and_to_stream(self):CODE
LOWContrib/IFG/ifg.py48def identify_functional_groups(mol):CODE
LOWContrib/mmpa/search_mmp_db.py91def print_smallest_change_mmp(db_results, cmpd_id, query_size):CODE
LOWContrib/mmpa/indexing.py271def switch_specific_labels_on_symmetry(smi, symmetry_class, a, b):CODE
LOWContrib/mmpa/indexing.py294def switch_labels_on_position(smi):CODE
LOWScripts/gen_rdkit_stubs/worker.py45 def parse_function_docstring_patched(self, func_name, doc_lines, **kwargs):CODE
LOWScripts/gen_rdkit_stubs/worker.py54 def print_submodule_import_patched(self, name):CODE
LOWScripts/gen_rdkit_stubs/__init__.py38def purge_rdkit_source_dir_from_sys_path():CODE
LOWScripts/gen_rdkit_stubs/__init__.py46def find_rdkit_site_packages_path():CODE
LOWScripts/gen_rdkit_stubs/__init__.py156def concat_parent_child_module(parent_module, child_module):CODE
LOWScripts/gen_rdkit_stubs/__init__.py379 def protect_quoted_square_brackets_and_equals(cls, arg):CODE
LOWScripts/gen_rdkit_stubs/__init__.py402 def deprotect_quoted_square_brackets_and_equals(cls, arg):CODE
LOWScripts/patch_rdkit_docstrings/__init__.py778 def find_def_init_nodes_in_class_r(self, cursor, func_names, func_name_to_hash, def_init_nodes):CODE
LOWScripts/patch_rdkit_docstrings/__init__.py798 def is_class_hash_among_node_children_r(self, class_hash, node):CODE
LOWScripts/patch_rdkit_docstrings/__init__.py1397 def get_include_flags_from_include_path(include_path):CODE
LOWExternal/INCHI-API/python/inchi.py56def _parse_auxinfo_coordinates(auxinfo):CODE
LOWExternal/INCHI-API/python/inchi.py93def _parse_auxinfo_atom_order(auxinfo):CODE
LOWExternal/INCHI-API/python/inchi.py125def _build_inverse_permutation(atom_order, size):CODE
LOWrdkit/Chem/UnitTestRandomize.py64 def test_smiles_canonicalization(self):CODE
LOWrdkit/Chem/UnitTestMCS.py93 def test_atom_compare_default(self):STRING
55 more matches not shown…
Cross-Language Confusion15 hits · 84 pts
SeverityFileLineSnippetContext
HIGHContrib/pzc/p_con.py482 min(IC50) => IC50_avg-3*IC50_stddev && max(IC50) <= IC50_avg+3*IC50_stddev && IC50_stddev <= IC50_avg"""STRING
HIGHContrib/Glare/glare.py210 # would be needed, and the net speedup would be null, hence, the decision toCOMMENT
HIGHrdkit/Dbase/DbConnection.py56 - includeViews: if this is non-null, the views in the db willSTRING
HIGHrdkit/Dbase/DbInfo.py69 - includeViews: if this is non-null, the views in the db willSTRING
HIGHrdkit/ML/Cluster/Resemblance.py17 || - || 0 || 1 || 3STRING
HIGHrdkit/ML/Cluster/Resemblance.py18 || - || - || 2 || 4STRING
HIGHrdkit/Chem/MolKey/MolKey.py329 elif n_udf == 1: # one undefined, no definedCODE
HIGHrdkit/Chem/MolKey/MolKey.py331 else: # several undefined, no definedCODE
HIGHrdkit/Chem/Draw/InteractiveRenderer.py101 const rdkStrRnr = window.rdkStrRnr || Promise.resolve(null);CODE
HIGHrdkit/Chem/Draw/InteractiveRenderer.py101 const rdkStrRnr = window.rdkStrRnr || Promise.resolve(null);CODE
HIGHrdkit/Chem/Draw/InteractiveRenderer.py105 if (Renderer && Renderer.updateMolDrawDivs) {{CODE
HIGHrdkit/Chem/Draw/InteractiveRenderer.py111 window.rdkStrRnr = null;CODE
HIGHrdkit/Chem/Draw/InteractiveRenderer.py115 console.error(e.toString());CODE
HIGHrdkit/Chem/Draw/InteractiveRenderer.py132 e.toString() + '<br>' +CODE
HIGHrdkit/Chem/Draw/InteractiveRenderer.py135 window.rdkStrRnr = null;CODE
AI Structural Patterns42 hits · 42 pts
SeverityFileLineSnippetContext
LOWCode/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py90CODE
LOWContrib/efgs/try_efgs.py79CODE
LOWContrib/AtomAtomSimilarity/AtomAtomPathSimilarity.py183CODE
LOWContrib/ChiralPairs/ChiralDescriptors.py91CODE
LOWContrib/Glare/glare.py217CODE
LOWrdkit/Dbase/DbUtils.py62CODE
LOWrdkit/Dbase/DbInfo.py207CODE
LOWrdkit/utils/chemdraw_qax.py59CODE
LOWrdkit/ML/Data/SplitData.py165CODE
LOWrdkit/ML/Data/DataUtils.py230CODE
LOWrdkit/ML/Data/DataUtils.py249CODE
LOWrdkit/ML/Data/DataUtils.py405CODE
LOWrdkit/ML/Data/DataUtils.py352CODE
LOWrdkit/ML/Data/DataUtils.py456CODE
LOWrdkit/ML/Data/MLData.py129CODE
LOWrdkit/sping/PS/pidPS.py166CODE
LOWrdkit/Chem/RegistrationHash.py280CODE
LOWrdkit/Chem/RegistrationHash.py352CODE
LOWrdkit/Chem/__init__.py125CODE
LOWrdkit/Chem/MCS.py266CODE
LOWrdkit/Chem/GraphDescriptors.py46CODE
LOWrdkit/Chem/GraphDescriptors.py232CODE
LOWrdkit/Chem/GraphDescriptors.py247CODE
LOWrdkit/Chem/GraphDescriptors.py291CODE
LOWrdkit/Chem/GraphDescriptors.py361CODE
LOWrdkit/Chem/PandasTools.py241CODE
LOWrdkit/Chem/PyMol.py75CODE
LOWrdkit/Chem/fmcs/fmcs.py2196CODE
LOWrdkit/Chem/Pharm3D/EmbedLib.py321CODE
LOWrdkit/Chem/Features/ShowFeats.py155CODE
LOWrdkit/Chem/Subshape/SubshapeAligner.py80CODE
LOWrdkit/Chem/Subshape/BuilderUtils.py180CODE
LOWrdkit/Chem/MolDb/Loader_sa.py91CODE
LOWrdkit/Chem/MolDb/Loader_orig.py21CODE
LOWrdkit/Chem/MolDb/Loader_orig.py92CODE
LOWrdkit/Chem/Draw/MolDrawing.py333CODE
LOWrdkit/Chem/Draw/__init__.py581CODE
LOWrdkit/Chem/Draw/__init__.py758CODE
LOWrdkit/Chem/Draw/__init__.py804CODE
LOWrdkit/Chem/Draw/__init__.py901CODE
LOWrdkit/Chem/Draw/__init__.py993CODE
LOWrdkit/Chem/Draw/SimilarityMaps.py131CODE
Dead Code20 hits · 40 pts
SeverityFileLineSnippetContext
MEDIUMCode/DistGeom/Wrap/rough_test.py93CODE
MEDIUMCode/DistGeom/Wrap/rough_test.py99CODE
MEDIUMCode/DistGeom/Wrap/rough_test.py100CODE
MEDIUMCode/DistGeom/Wrap/rough_test.py101CODE
MEDIUMCode/DistGeom/Wrap/rough_test.py102CODE
MEDIUMCode/DistGeom/Wrap/rough_test.py103CODE
MEDIUMCode/DistGeom/Wrap/rough_test.py104CODE
MEDIUMCode/DistGeom/Wrap/rough_test.py105CODE
MEDIUMCode/DistGeom/Wrap/rough_test.py106CODE
MEDIUMCode/GraphMol/Wrap/rough_test.py5709CODE
MEDIUMCode/GraphMol/Wrap/rough_test.py5713CODE
MEDIUMCode/GraphMol/Wrap/rough_test.py5714CODE
MEDIUMrdkit/Chem/fmcs/fmcs.py628CODE
MEDIUMrdkit/Chem/fmcs/fmcs.py630CODE
MEDIUMrdkit/Chem/fmcs/fmcs.py631CODE
MEDIUMrdkit/Chem/fmcs/fmcs.py632CODE
MEDIUMrdkit/Chem/fmcs/fmcs.py643CODE
MEDIUMrdkit/Chem/fmcs/fmcs.py644CODE
MEDIUMrdkit/Chem/fmcs/fmcs.py645CODE
MEDIUMrdkit/Chem/fmcs/fmcs.py647CODE
Redundant / Tautological Comments15 hits · 24 pts
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LOWCode/GraphMol/nbWrap/rough_test.py3437 for n in atom.GetNeighbors(): # Check if neighbor is from the same residueCODE
LOW…e/GraphMol/GaussianShape/Wrap/test_rdgaussian_shape.py195 # Set the to default values, just to show that they can be set.COMMENT
LOWCode/GraphMol/Wrap/rough_test.py3387 for n in atom.GetNeighbors(): # Check if neighbor is from the same residueCODE
LOWContrib/efgs/efgs.py401 if map_idx in neigh_atoms: # Check if that position is an environment atom in original moleculeCODE
LOWrdkit/ML/Cluster/Butina.py66 # Check if data is a supported typeCOMMENT
LOWrdkit/ML/Cluster/Butina.py70 # Check if data is a 1D array or listCOMMENT
LOWrdkit/ML/Cluster/Butina.py72 # Check if data length matches the required number of pointsCOMMENT
LOWrdkit/ML/Cluster/Butina.py82 # Check if data is a matrix of the correct shape and use it as distance matrixCOMMENT
LOWrdkit/Chem/fmcs/fmcs.py1538# Check if a SMARTS is in all targets.COMMENT
LOWrdkit/Chem/fmcs/fmcs.py1753### Check if there are any ring atoms; used in --complete-rings-onlyCOMMENT
LOWrdkit/Chem/fmcs/fmcs.py2500 # Check if this is the end of string or a ','COMMENT
LOWrdkit/Chem/Features/UnitTestFeatDirUtilsRD.py44 #Check if there are two vectorsCOMMENT
LOWrdkit/Chem/Features/UnitTestFeatDirUtilsRD.py78 #Check if there is one vectorCOMMENT
LOWrdkit/Chem/Features/UnitTestFeatDirUtilsRD.py101 #Check if there are two vectorsCOMMENT
LOWrdkit/Chem/Features/UnitTestFeatDirUtilsRD.py140 #Check if there is one vectorCOMMENT
Docstring Block Structure4 hits · 20 pts
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HIGHCode/JavaWrappers/parse_doxy_html.py31int RDKit::Atom::getPerturbationOrder ( INT_LIST probe ) const returns the perturbation order for a list of intSTRING
HIGHCode/JavaWrappers/parse_doxy_html.py69Detailed Description The class for representing atoms. Notes: * many of the methods of Atom require that the AtomSTRING
HIGHScripts/patch_rdkit_docstrings/__init__.py928Insert the appropriate python::args where needed based on the C++ method parameter names. Args: STRING
HIGHrdkit/Chem/Draw/__init__.py455Creates a mol grid image from a nested data structure (where each data substructure represents a row), padding rows asSTRING
AI Slop Vocabulary9 hits · 12 pts
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LOWCode/GraphMol/PartialCharges/Wrap/testPartialCharges.py119 # can't set the required locale, might as well just returnCOMMENT
LOWrdkit/sping/TK/pidTK.py47# removed reference to "BaseTKCanvas" (should just use TKCanvas as default)COMMENT
LOWrdkit/sping/TK/pidTK.py112 # XXX: should just return the internal tk font name?COMMENT
LOWrdkit/sping/PS/pidPS.py27# _ Base85 encoding just use hex encoding involves 1:2 expansion of image data vs 4:5COMMENT
LOWrdkit/sping/PS/pidPS.py677 # should fix this so it doesn't define path twice, just use gsave if needCOMMENT
LOWrdkit/Chem/TorsionFingerprints.py135 # sort by atom inv and simply use the first neighborCOMMENT
LOWrdkit/Chem/TorsionFingerprints.py144 # sort by atom inv and simply use the first neighborCOMMENT
MEDIUMrdkit/Chem/PandasPatcher.py220 """ Disable escaping of HTML in order to render img / svg tags """STRING
LOWrdkit/Chem/Pharm3D/EmbedLib.py970 # we ignore the point locations here and just use their definitions:STRING
Modern Structural Boilerplate7 hits · 7 pts
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LOWScripts/gen_rdkit_stubs/__init__.py14logger = logging.getLogger(__name__)CODE
LOWExternal/INCHI-API/python/inchi.py393__all__ = [CODE
LOWrdkit/DataManip/__init__.py1__all__ = ['Metric']CODE
LOWrdkit/Chem/RegistrationHash.py36logger = logging.getLogger(__name__)CODE
LOWrdkit/Chem/MCS.py239__all__ = ["FindMCS"]CODE
LOWrdkit/VLib/__init__.py1__all__ = []CODE
LOWrdkit/VLib/NodeLib/__init__.py1__all__ = ['SmartsMolFilter', 'SDSupply', 'SmartsRemover', 'SmilesDupeFilter', 'SmilesOutput']CODE
Example Usage Blocks2 hits · 3 pts
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LOW…/MinimalLib/docker/docker_compose_build_minimallib.yml13# Example usage:COMMENT
LOWCode/RDBoost/list_indexing_suite.hpp37// Example usage:COMMENT
Slop Phrases2 hits · 3 pts
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LOWCode/GraphMol/ScaffoldNetwork/ScaffoldNetwork.cpp80 // don't forget to set the H count on that atom:COMMENT
LOWrdkit/Chem/PandasPatcher.py196 # in pandas 0.25 we need to make sure to update buf as return value will be ignoredCOMMENT
Overly Generic Function Names2 hits · 2 pts
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LOWCode/GraphMol/Wrap/testMultithreadedMolSupplier.py141 def helper(smiSup):CODE
LOWCode/GraphMol/Wrap/testMultithreadedMolSupplier.py158 def helper(sdSup):CODE
Verbosity Indicators1 hit · 2 pts
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LOWCode/GraphMol/Canon.cpp244 // the double bond's stereo label. Now we need to check if we canCOMMENT
Structural Annotation Overuse1 hit · 2 pts
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LOWCode/GraphMol/SmilesParse/SmilesParse.cpp87 // NOTE: This variable will be used to point to the location of theCOMMENT