Name		Name	Last commit message	Last commit date
%s		%s
instcheck-vsp-compute-33-diagnostics		instcheck-vsp-compute-33-diagnostics
Hypothetical_CB_Ligand_generator.ipynb		Hypothetical_CB_Ligand_generator.ipynb
LandmarkNystroem.py		LandmarkNystroem.py
PDB_Order_Fixer.py		PDB_Order_Fixer.py
PDB_Order_Fixer2.py		PDB_Order_Fixer2.py
README.md		README.md
ROC_curve.R		ROC_curve.R
Rplots.pdf		Rplots.pdf
TLR8.ipynb		TLR8.ipynb
Untitled.ipynb		Untitled.ipynb
Untitled1.ipynb		Untitled1.ipynb
align_in_directory.py		align_in_directory.py
amir_experiment.ipynb		amir_experiment.ipynb
analysis.R		analysis.R
analysis.py		analysis.py
analyze_tica_performance.R		analyze_tica_performance.R
aromatic_featurizer.py		aromatic_featurizer.py
auto_reimage.in		auto_reimage.in
b1ar_analysis-sparse.ipynb		b1ar_analysis-sparse.ipynb
b1ar_bias_analysis-tICs_3_5.ipynb		b1ar_bias_analysis-tICs_3_5.ipynb
b1ar_feature_types		b1ar_feature_types
b1ar_feature_types.py		b1ar_feature_types.py
b1ar_tica_config.py		b1ar_tica_config.py
b2ar_analysis.R		b2ar_analysis.R
b2ar_analysis.py		b2ar_analysis.py
b2ar_anton.py		b2ar_anton.py
b2ar_bias_analysis-Copy1.ipynb		b2ar_bias_analysis-Copy1.ipynb
b2ar_bias_analysis-Copy2.ipynb		b2ar_bias_analysis-Copy2.ipynb
b2ar_bias_analysis-Copy3.ipynb		b2ar_bias_analysis-Copy3.ipynb
b2ar_bias_analysis-Copy4.ipynb		b2ar_bias_analysis-Copy4.ipynb
b2ar_bias_analysis-HTBC-Analysis.ipynb		b2ar_bias_analysis-HTBC-Analysis.ipynb
b2ar_bias_analysis-HTBC.ipynb		b2ar_bias_analysis-HTBC.ipynb
b2ar_bias_analysis-all_tICs.ipynb		b2ar_bias_analysis-all_tICs.ipynb
b2ar_bias_analysis-tICs_10.ipynb		b2ar_bias_analysis-tICs_10.ipynb
b2ar_bias_analysis-tICs_1_2.ipynb		b2ar_bias_analysis-tICs_1_2.ipynb
b2ar_bias_analysis-tICs_1_2_3-Copy1.ipynb		b2ar_bias_analysis-tICs_1_2_3-Copy1.ipynb
b2ar_bias_analysis-tICs_1_2_3-r2.ipynb		b2ar_bias_analysis-tICs_1_2_3-r2.ipynb
b2ar_bias_analysis-tICs_1_2_3.ipynb		b2ar_bias_analysis-tICs_1_2_3.ipynb
b2ar_bias_analysis-tICs_1_2_3_4.ipynb		b2ar_bias_analysis-tICs_1_2_3_4.ipynb
b2ar_bias_analysis.ipynb		b2ar_bias_analysis.ipynb
b2ar_exacycle.py		b2ar_exacycle.py
b2ar_feature_types.py		b2ar_feature_types.py
b2ar_gprot_analysis.py		b2ar_gprot_analysis.py
b2ar_gprot_feature_types.py		b2ar_gprot_feature_types.py
b2ar_gprot_ktica_config.py		b2ar_gprot_ktica_config.py
b2ar_gprot_tica_config.py		b2ar_gprot_tica_config.py
b2ar_ktica_config.py		b2ar_ktica_config.py
b2ar_salmeterol-analysis.ipynb		b2ar_salmeterol-analysis.ipynb
b2ar_salmeterol-analysis2.ipynb		b2ar_salmeterol-analysis2.ipynb
b2ar_tica_config.py		b2ar_tica_config.py
backup_subsample3.py		backup_subsample3.py
cb2_ligands - Sheet1.csv		cb2_ligands - Sheet1.csv
check_docking_results.R		check_docking_results.R
check_pkg.py		check_pkg.py
cluster.py		cluster.py
color_obj.py		color_obj.py
colormap_docking.R		colormap_docking.R
conversions.py		conversions.py
convert_mae.py		convert_mae.py
cpptraj.log		cpptraj.log
custom_clusterer.py		custom_clusterer.py
custom_featurizer.py		custom_featurizer.py
custom_featurizer_anton.py		custom_featurizer_anton.py
custom_msm.py		custom_msm.py
custom_tica.py		custom_tica.py
detect_intermediates.py		detect_intermediates.py
docking_analysis.py		docking_analysis.py
dt.dot		dt.dot
efficacy_analysis.py		efficacy_analysis.py
efficacy_scripts.py		efficacy_scripts.py
enrichment_clusters_vs_samples.R		enrichment_clusters_vs_samples.R
enrichment_vs_n.R		enrichment_vs_n.R
enrichment_vs_n_anton_data_exacycle_criteria.R		enrichment_vs_n_anton_data_exacycle_criteria.R
enrichment_vs_n_anton_data_exacycle_criteria_clusters.R		enrichment_vs_n_anton_data_exacycle_criteria_clusters.R
enrichment_vs_n_anton_data_exacycle_criteria_samples.R		enrichment_vs_n_anton_data_exacycle_criteria_samples.R
enrichment_vs_n_anton_data_exacycle_criteria_samples2.R		enrichment_vs_n_anton_data_exacycle_criteria_samples2.R
enrichment_vs_n_exacycle_data_exacycle_criteria_samples2.R		enrichment_vs_n_exacycle_data_exacycle_criteria_samples2.R
entropy_estimators.py		entropy_estimators.py
extra_code.txt		extra_code.txt
feature_types.py		feature_types.py
find_states.py		find_states.py
general_reimage.py		general_reimage.py
generate_grids.py		generate_grids.py
get_variable_names.py		get_variable_names.py
glide_test.py		glide_test.py
grids.py		grids.py
hypotheticalprods.csv		hypotheticalprods.csv
instcheck-vsp-compute-33-diagnostics.summary		instcheck-vsp-compute-33-diagnostics.summary
instcheck-vsp-compute-33-diagnostics.zip		instcheck-vsp-compute-33-diagnostics.zip
instcheck_results.json		instcheck_results.json
interpret_tICs.py		interpret_tICs.py
io_functions.py		io_functions.py
jointplot-d3.py		jointplot-d3.py
jointplot_d3.py		jointplot_d3.py
ktica_config.py		ktica_config.py
ktica_variables.py		ktica_variables.py
landmark_kernel_tica.py		landmark_kernel_tica.py
ligand_protein_contact_tica.ipynb		ligand_protein_contact_tica.ipynb
ligand_protein_contact_tica_hyperparam.ipynb		ligand_protein_contact_tica_hyperparam.ipynb

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Utilities for connecting molecular dynamics and experimental datasets with the power of machine learning.

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