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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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