├── .gitignore ├── CMakeLists.txt ├── INSTALL ├── LICENSE ├── README ├── README.md ├── cmake └── modules │ ├── FindOpenBabel3.cmake │ └── FindRDKit.cmake ├── example_note └── Align_CDK2_molecule_with_shape-it.ipynb ├── include ├── alignLib.h ├── alignmentInfo.h ├── atomGaussian.h ├── bestResults.h ├── config.h ├── coordinate.h ├── gaussianVolume.h ├── mainErr.h ├── moleculeRotation.h ├── options.h ├── parseCommandLine.h ├── printHeader.h ├── printUsage.h ├── shapeAlignment.h ├── siMath.h └── solutionInfo.h ├── infrastructure ├── docker │ └── Dockerfile └── pyshapeit │ ├── build.sh │ ├── conda_build_config.yaml │ └── meta.yaml ├── pyshapeit ├── __init__.py └── basic_test.py └── src ├── Wrap ├── CMakeLists.txt └── cpyshapeit.cpp ├── alignLib.cpp ├── alignmentInfo.cpp ├── atomGaussian.cpp ├── basic_tests.cpp ├── bestResults.cpp ├── catch_main.cpp ├── coordinate.cpp ├── gaussianVolume.cpp ├── gaussianVolume.cppbk ├── main.cpp ├── mainErr.cpp ├── moleculeRotation.cpp ├── options.cpp ├── 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