├── .gitattributes ├── .gitignore ├── .travis.yml ├── ANM.cpp ├── ANM.py ├── LICENSE ├── README.md ├── Tutorial ├── Apart_Pentamer.pdb ├── CG3 │ ├── EV71CommonResidues_msf.txt │ ├── EV71_CommonResidues_msfModes9_9.txt │ ├── EV71_msf.txt │ ├── EV71_msfModes9_9.txt │ ├── EVectors9.txt │ ├── ModesOfConformtionalChange.txt │ ├── U_values.txt │ ├── VISUALISE │ │ ├── VISUAL_9.pdb │ │ └── VISUAL_ARROWS_9.txt │ ├── VT_values.txt │ ├── W_values.txt │ └── common_residues_msf ├── EV71CommonResidues_msf.txt ├── EV71_CG3.pdb ├── EV71_CG4.pdb ├── EV71_CommonResidues_msfModes9_9.txt ├── EV71_Pentamer.pdb ├── EV71_msf.txt ├── EV71_msfModes9_9.txt ├── EVectors9.txt ├── ModesOfConformtionalChange.txt ├── U_values.txt ├── VISUALISE │ ├── VISUAL_9.pdb │ └── VISUAL_ARROWS_9.txt ├── VT_values.txt ├── W_values.txt └── common_residues_msf ├── assemblyCovariance.py ├── coarseGrain.py ├── combinationMode.py ├── conformationMode.py ├── cpp ├── gpl2.txt ├── gpl3.txt ├── input │ └── ap.h ├── manual.cpp.html ├── src │ ├── alglibinternal.cpp │ ├── alglibinternal.h │ ├── alglibmisc.cpp │ ├── alglibmisc.h │ ├── ap.cpp │ ├── ap.h │ ├── dataanalysis.cpp │ ├── dataanalysis.h │ ├── diffequations.cpp │ ├── diffequations.h │ ├── fasttransforms.cpp │ ├── fasttransforms.h │ ├── integration.cpp │ ├── integration.h │ ├── interpolation.cpp │ ├── interpolation.h │ ├── linalg.cpp │ ├── linalg.h │ ├── optimization.cpp │ ├── optimization.h │ ├── solvers.cpp │ ├── solvers.h │ ├── specialfunctions.cpp │ ├── specialfunctions.h │ ├── statistics.cpp │ ├── statistics.h │ └── stdafx.h └── tests │ ├── test_c.cpp │ ├── test_i.cpp │ └── test_x.cpp ├── docs ├── Makefile ├── img │ ├── Arrows_Visualisation.png │ ├── Chains_Visualisation.png │ ├── Colours_Visualisation.png │ ├── Covariance_AUnits.png │ ├── Covariance_AUnits1_3.png │ ├── Covariance_Full.png │ ├── Covariance_FullMode7.png │ ├── Covariance_Zoom.png │ ├── Default_Visualisation.png │ ├── Units_Visualisation.png │ ├── logo.png │ ├── mmds1.png │ ├── mmds2.png │ ├── nma_tut0.png │ ├── pca_tut1.png │ ├── pca_tut2.png │ ├── pca_tut3.png │ ├── tsne1.png │ └── tsne2.png ├── make.bat └── source │ ├── conf.py │ ├── index.rst │ ├── installation.rst │ ├── intro.rst │ ├── nma_tut.rst │ ├── nma_use.rst │ ├── pca_tut.rst │ ├── pca_use.rst │ ├── pymol_plugin.rst │ ├── requirements.txt │ └── theory.rst ├── internal_pca.py ├── lib ├── __init__.py ├── sdrms.py ├── traj_info.py ├── utils.py └── write_plot.py ├── mds.py ├── meanSquareFluctuations.py ├── mode-task.yml ├── pca.py ├── tests ├── 3VBSPent.pdb ├── 4hhb.pdb ├── autopilot.sh ├── complex.pdb ├── input_pdb ├── pca_test_trj.xtc ├── test_anm.sh ├── test_anm_wrapper.sh ├── test_cg.sh ├── test_conformation.sh ├── test_internal_pca.sh ├── test_mds.sh ├── test_msf.sh ├── test_pca.sh ├── test_trajectory.sh └── test_tsne.sh ├── tsne.py ├── visualiseVector.py └── welcome_msg.py /.gitattributes: -------------------------------------------------------------------------------- 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