From cf2e1c1ced933d9a076a2391c884fae978250ee3 Mon Sep 17 00:00:00 2001
From: Ben Webb <ben@salilab.org>
Date: Wed, 20 Nov 2019 09:49:15 -0800
Subject: [PATCH] Hide examples that don't work
---
.../3D-example/input/1WCM.fasta.txt | 0
.../3D-example/input/1WCM.pdb | 0
.../3D-example/input/bayesian_em_restraint/C.mrc | Bin
.../3D-example/input/bayesian_em_restraint/C.txt | 0
.../3D-example/input/bayesian_em_restraint/K.mrc | Bin
.../3D-example/input/bayesian_em_restraint/K.txt | 0
.../input/bayesian_em_restraint/gmm_data/10_2.0.mrc | Bin
.../input/bayesian_em_restraint/gmm_data/10_2.0.txt | 0
.../input/bayesian_em_restraint/gmm_data/15_2.0.mrc | Bin
.../input/bayesian_em_restraint/gmm_data/15_2.0.txt | 0
.../input/bayesian_em_restraint/gmm_data/25_2.0.mrc | Bin
.../input/bayesian_em_restraint/gmm_data/25_2.0.txt | 0
.../input/bayesian_em_restraint/gmm_data/3_2.0.mrc | Bin
.../input/bayesian_em_restraint/gmm_data/3_2.0.txt | 0
.../input/bayesian_em_restraint/gmm_data/5_2.0.mrc | Bin
.../input/bayesian_em_restraint/gmm_data/5_2.0.txt | 0
.../3D-example/input/session.py | 0
.../test_bayesian_gaussian_em_restraint.py | 0
.../3D-example_2/input/1WCM.fasta.txt | 0
.../3D-example_2/input/1WCM.pdb | 0
.../3D-example_2/input/bayesian_em_restraint/C.mrc | Bin
.../3D-example_2/input/bayesian_em_restraint/C.txt | 0
.../3D-example_2/input/bayesian_em_restraint/J.mrc | Bin
.../3D-example_2/input/bayesian_em_restraint/J.txt | 0
.../3D-example_2/input/bayesian_em_restraint/K.mrc | Bin
.../3D-example_2/input/bayesian_em_restraint/K.txt | 0
.../3D-example_2/input/bayesian_em_restraint/L.mrc | Bin
.../3D-example_2/input/bayesian_em_restraint/L.txt | 0
.../analysis/cluster.0/0.1.pdb | 0
.../analysis/cluster.0/0.1.rmf3 | 0
.../bayesian_em_restraint/analysis/clustering.py | 0
.../input/bayesian_em_restraint/gmm_data/10_2.0.mrc | Bin
.../input/bayesian_em_restraint/gmm_data/10_2.0.txt | 0
.../input/bayesian_em_restraint/gmm_data/15_2.0.mrc | Bin
.../input/bayesian_em_restraint/gmm_data/15_2.0.txt | 0
.../input/bayesian_em_restraint/gmm_data/25_2.0.mrc | Bin
.../input/bayesian_em_restraint/gmm_data/25_2.0.txt | 0
.../input/bayesian_em_restraint/gmm_data/30_2.0.mrc | Bin
.../input/bayesian_em_restraint/gmm_data/30_2.0.txt | 0
.../input/bayesian_em_restraint/gmm_data/3_2.0.mrc | Bin
.../input/bayesian_em_restraint/gmm_data/3_2.0.txt | 0
.../input/bayesian_em_restraint/gmm_data/5_2.0.mrc | Bin
.../input/bayesian_em_restraint/gmm_data/5_2.0.txt | 0
.../3D-example_2/input/session.py | 0
.../test_bayesian_gaussian_em_restraint.py | 0
.../exosome/analysis/analysis_xl.py | 0
.../exosome/analysis/clustering.py | 0
.../exosome/analysis/get_data.py | 0
.../exosome/analysis/make_table.py | 0
.../exosome/data/1_imp.gmm | 0
.../exosome/data/2_imp.gmm | 0
.../exosome/data/3_imp.gmm | 0
{examples => broken-examples}/exosome/data/4IFD.pdb | 0
.../exosome/data/4_imp.gmm | 0
.../exosome/data/5_imp.gmm | 0
.../exosome/data/5g06_align_2.pdb | 0
.../exosome/data/6_imp.gmm | 0
.../exosome/data/7_imp.gmm | 0
.../exosome/data/8_imp.gmm | 0
.../exosome/data/9_imp.gmm | 0
.../exosome/data/GFP_1GFL.pdb | 0
.../exosome/data/exosome.fasta | 0
.../exosome/data/exosome_XLMS_column07012014.csv | 0
.../exosome/modeling/get_seeds.py | 0
.../exosome/modeling/get_seeds.sh | 0
.../exosome/modeling/init.py | 0
.../exosome/modeling/job.sh | 0
.../exosome/modeling/model.py | 0
.../exosome/modeling/submit.sh | 0
{examples => broken-examples}/modeling.py | 0
.../rnapolii/analysis/Makefile | 0
.../rnapolii/analysis/analysis_xl.py | 0
.../rnapolii/analysis/clustering_new.py | 0
.../rnapolii/analysis/get_data.py | 0
.../rnapolii/analysis/get_stat_or_rmf3.sh | 0
.../rnapolii/analysis/make_table_new.py | 0
.../rnapolii/data/1WCM.fasta.txt | 0
.../rnapolii/data/1WCM.pdb | 0
.../rnapolii/data/1WCM_map_fitted.pdb | 0
.../rnapolii/data/1WCM_new.fasta.txt | 0
.../rnapolii/data/1_imp.gmm | 0
.../rnapolii/data/2_imp.gmm | 0
.../rnapolii/data/3_imp.gmm | 0
.../rnapolii/data/4_imp.gmm | 0
.../rnapolii/data/5_imp.gmm | 0
.../rnapolii/data/6_imp.gmm | 0
.../rnapolii/data/7_imp.gmm | 0
.../rnapolii/data/8_imp.gmm | 0
.../rnapolii/data/9_imp.gmm | 0
.../rnapolii/data/native.rmf3 | 0
.../rnapolii/data/polii_juri.csv | 0
.../rnapolii/data/polii_xlinks.csv | 0
.../rnapolii/data/topology.txt | 0
.../rnapolii/modeling/get_seeds.py | 0
.../rnapolii/modeling/get_seeds.sh | 0
.../rnapolii/modeling/job.sh | 0
.../rnapolii/modeling/modeling.py | 0
.../rnapolii/modeling/submit.sh | 0
98 files changed, 0 insertions(+), 0 deletions(-)
rename {examples => broken-examples}/3D-example/input/1WCM.fasta.txt (100%)
rename {examples => broken-examples}/3D-example/input/1WCM.pdb (100%)
rename {examples => broken-examples}/3D-example/input/bayesian_em_restraint/C.mrc (100%)
rename {examples => broken-examples}/3D-example/input/bayesian_em_restraint/C.txt (100%)
rename {examples => broken-examples}/3D-example/input/bayesian_em_restraint/K.mrc (100%)
rename {examples => broken-examples}/3D-example/input/bayesian_em_restraint/K.txt (100%)
rename {examples => broken-examples}/3D-example/input/bayesian_em_restraint/gmm_data/10_2.0.mrc (100%)
rename {examples => broken-examples}/3D-example/input/bayesian_em_restraint/gmm_data/10_2.0.txt (100%)
rename {examples => broken-examples}/3D-example/input/bayesian_em_restraint/gmm_data/15_2.0.mrc (100%)
rename {examples => broken-examples}/3D-example/input/bayesian_em_restraint/gmm_data/15_2.0.txt (100%)
rename {examples => broken-examples}/3D-example/input/bayesian_em_restraint/gmm_data/25_2.0.mrc (100%)
rename {examples => broken-examples}/3D-example/input/bayesian_em_restraint/gmm_data/25_2.0.txt (100%)
rename {examples => broken-examples}/3D-example/input/bayesian_em_restraint/gmm_data/3_2.0.mrc (100%)
rename {examples => broken-examples}/3D-example/input/bayesian_em_restraint/gmm_data/3_2.0.txt (100%)
rename {examples => broken-examples}/3D-example/input/bayesian_em_restraint/gmm_data/5_2.0.mrc (100%)
rename {examples => broken-examples}/3D-example/input/bayesian_em_restraint/gmm_data/5_2.0.txt (100%)
rename {examples => broken-examples}/3D-example/input/session.py (100%)
rename {examples => broken-examples}/3D-example/test_bayesian_gaussian_em_restraint.py (100%)
rename {examples => broken-examples}/3D-example_2/input/1WCM.fasta.txt (100%)
rename {examples => broken-examples}/3D-example_2/input/1WCM.pdb (100%)
rename {examples => broken-examples}/3D-example_2/input/bayesian_em_restraint/C.mrc (100%)
rename {examples => broken-examples}/3D-example_2/input/bayesian_em_restraint/C.txt (100%)
rename {examples => broken-examples}/3D-example_2/input/bayesian_em_restraint/J.mrc (100%)
rename {examples => broken-examples}/3D-example_2/input/bayesian_em_restraint/J.txt (100%)
rename {examples => broken-examples}/3D-example_2/input/bayesian_em_restraint/K.mrc (100%)
rename {examples => broken-examples}/3D-example_2/input/bayesian_em_restraint/K.txt (100%)
rename {examples => broken-examples}/3D-example_2/input/bayesian_em_restraint/L.mrc (100%)
rename {examples => broken-examples}/3D-example_2/input/bayesian_em_restraint/L.txt (100%)
rename {examples => broken-examples}/3D-example_2/input/bayesian_em_restraint/analysis/cluster.0/0.1.pdb (100%)
rename {examples => broken-examples}/3D-example_2/input/bayesian_em_restraint/analysis/cluster.0/0.1.rmf3 (100%)
rename {examples => broken-examples}/3D-example_2/input/bayesian_em_restraint/analysis/clustering.py (100%)
rename {examples => broken-examples}/3D-example_2/input/bayesian_em_restraint/gmm_data/10_2.0.mrc (100%)
rename {examples => broken-examples}/3D-example_2/input/bayesian_em_restraint/gmm_data/10_2.0.txt (100%)
rename {examples => broken-examples}/3D-example_2/input/bayesian_em_restraint/gmm_data/15_2.0.mrc (100%)
rename {examples => broken-examples}/3D-example_2/input/bayesian_em_restraint/gmm_data/15_2.0.txt (100%)
rename {examples => broken-examples}/3D-example_2/input/bayesian_em_restraint/gmm_data/25_2.0.mrc (100%)
rename {examples => broken-examples}/3D-example_2/input/bayesian_em_restraint/gmm_data/25_2.0.txt (100%)
rename {examples => broken-examples}/3D-example_2/input/bayesian_em_restraint/gmm_data/30_2.0.mrc (100%)
rename {examples => broken-examples}/3D-example_2/input/bayesian_em_restraint/gmm_data/30_2.0.txt (100%)
rename {examples => broken-examples}/3D-example_2/input/bayesian_em_restraint/gmm_data/3_2.0.mrc (100%)
rename {examples => broken-examples}/3D-example_2/input/bayesian_em_restraint/gmm_data/3_2.0.txt (100%)
rename {examples => broken-examples}/3D-example_2/input/bayesian_em_restraint/gmm_data/5_2.0.mrc (100%)
rename {examples => broken-examples}/3D-example_2/input/bayesian_em_restraint/gmm_data/5_2.0.txt (100%)
rename {examples => broken-examples}/3D-example_2/input/session.py (100%)
rename {examples => broken-examples}/3D-example_2/test_bayesian_gaussian_em_restraint.py (100%)
rename {examples => broken-examples}/exosome/analysis/analysis_xl.py (100%)
rename {examples => broken-examples}/exosome/analysis/clustering.py (100%)
rename {examples => broken-examples}/exosome/analysis/get_data.py (100%)
rename {examples => broken-examples}/exosome/analysis/make_table.py (100%)
rename {examples => broken-examples}/exosome/data/1_imp.gmm (100%)
rename {examples => broken-examples}/exosome/data/2_imp.gmm (100%)
rename {examples => broken-examples}/exosome/data/3_imp.gmm (100%)
rename {examples => broken-examples}/exosome/data/4IFD.pdb (100%)
rename {examples => broken-examples}/exosome/data/4_imp.gmm (100%)
rename {examples => broken-examples}/exosome/data/5_imp.gmm (100%)
rename {examples => broken-examples}/exosome/data/5g06_align_2.pdb (100%)
rename {examples => broken-examples}/exosome/data/6_imp.gmm (100%)
rename {examples => broken-examples}/exosome/data/7_imp.gmm (100%)
rename {examples => broken-examples}/exosome/data/8_imp.gmm (100%)
rename {examples => broken-examples}/exosome/data/9_imp.gmm (100%)
rename {examples => broken-examples}/exosome/data/GFP_1GFL.pdb (100%)
rename {examples => broken-examples}/exosome/data/exosome.fasta (100%)
rename {examples => broken-examples}/exosome/data/exosome_XLMS_column07012014.csv (100%)
rename {examples => broken-examples}/exosome/modeling/get_seeds.py (100%)
rename {examples => broken-examples}/exosome/modeling/get_seeds.sh (100%)
rename {examples => broken-examples}/exosome/modeling/init.py (100%)
rename {examples => broken-examples}/exosome/modeling/job.sh (100%)
rename {examples => broken-examples}/exosome/modeling/model.py (100%)
rename {examples => broken-examples}/exosome/modeling/submit.sh (100%)
rename {examples => broken-examples}/modeling.py (100%)
rename {examples => broken-examples}/rnapolii/analysis/Makefile (100%)
rename {examples => broken-examples}/rnapolii/analysis/analysis_xl.py (100%)
rename {examples => broken-examples}/rnapolii/analysis/clustering_new.py (100%)
rename {examples => broken-examples}/rnapolii/analysis/get_data.py (100%)
rename {examples => broken-examples}/rnapolii/analysis/get_stat_or_rmf3.sh (100%)
rename {examples => broken-examples}/rnapolii/analysis/make_table_new.py (100%)
rename {examples => broken-examples}/rnapolii/data/1WCM.fasta.txt (100%)
rename {examples => broken-examples}/rnapolii/data/1WCM.pdb (100%)
rename {examples => broken-examples}/rnapolii/data/1WCM_map_fitted.pdb (100%)
rename {examples => broken-examples}/rnapolii/data/1WCM_new.fasta.txt (100%)
rename {examples => broken-examples}/rnapolii/data/1_imp.gmm (100%)
rename {examples => broken-examples}/rnapolii/data/2_imp.gmm (100%)
rename {examples => broken-examples}/rnapolii/data/3_imp.gmm (100%)
rename {examples => broken-examples}/rnapolii/data/4_imp.gmm (100%)
rename {examples => broken-examples}/rnapolii/data/5_imp.gmm (100%)
rename {examples => broken-examples}/rnapolii/data/6_imp.gmm (100%)
rename {examples => broken-examples}/rnapolii/data/7_imp.gmm (100%)
rename {examples => broken-examples}/rnapolii/data/8_imp.gmm (100%)
rename {examples => broken-examples}/rnapolii/data/9_imp.gmm (100%)
rename {examples => broken-examples}/rnapolii/data/native.rmf3 (100%)
rename {examples => broken-examples}/rnapolii/data/polii_juri.csv (100%)
rename {examples => broken-examples}/rnapolii/data/polii_xlinks.csv (100%)
rename {examples => broken-examples}/rnapolii/data/topology.txt (100%)
rename {examples => broken-examples}/rnapolii/modeling/get_seeds.py (100%)
rename {examples => broken-examples}/rnapolii/modeling/get_seeds.sh (100%)
rename {examples => broken-examples}/rnapolii/modeling/job.sh (100%)
rename {examples => broken-examples}/rnapolii/modeling/modeling.py (100%)
rename {examples => broken-examples}/rnapolii/modeling/submit.sh (100%)
diff --git a/examples/3D-example/input/1WCM.fasta.txt b/broken-examples/3D-example/input/1WCM.fasta.txt
similarity index 100%
rename from examples/3D-example/input/1WCM.fasta.txt
rename to broken-examples/3D-example/input/1WCM.fasta.txt
diff --git a/examples/3D-example/input/1WCM.pdb b/broken-examples/3D-example/input/1WCM.pdb
similarity index 100%
rename from examples/3D-example/input/1WCM.pdb
rename to broken-examples/3D-example/input/1WCM.pdb
diff --git a/examples/3D-example/input/bayesian_em_restraint/C.mrc b/broken-examples/3D-example/input/bayesian_em_restraint/C.mrc
similarity index 100%
rename from examples/3D-example/input/bayesian_em_restraint/C.mrc
rename to broken-examples/3D-example/input/bayesian_em_restraint/C.mrc
diff --git a/examples/3D-example/input/bayesian_em_restraint/C.txt b/broken-examples/3D-example/input/bayesian_em_restraint/C.txt
similarity index 100%
rename from examples/3D-example/input/bayesian_em_restraint/C.txt
rename to broken-examples/3D-example/input/bayesian_em_restraint/C.txt
diff --git a/examples/3D-example/input/bayesian_em_restraint/K.mrc b/broken-examples/3D-example/input/bayesian_em_restraint/K.mrc
similarity index 100%
rename from examples/3D-example/input/bayesian_em_restraint/K.mrc
rename to broken-examples/3D-example/input/bayesian_em_restraint/K.mrc
diff --git a/examples/3D-example/input/bayesian_em_restraint/K.txt b/broken-examples/3D-example/input/bayesian_em_restraint/K.txt
similarity index 100%
rename from examples/3D-example/input/bayesian_em_restraint/K.txt
rename to broken-examples/3D-example/input/bayesian_em_restraint/K.txt
diff --git a/examples/3D-example/input/bayesian_em_restraint/gmm_data/10_2.0.mrc b/broken-examples/3D-example/input/bayesian_em_restraint/gmm_data/10_2.0.mrc
similarity index 100%
rename from examples/3D-example/input/bayesian_em_restraint/gmm_data/10_2.0.mrc
rename to broken-examples/3D-example/input/bayesian_em_restraint/gmm_data/10_2.0.mrc
diff --git a/examples/3D-example/input/bayesian_em_restraint/gmm_data/10_2.0.txt b/broken-examples/3D-example/input/bayesian_em_restraint/gmm_data/10_2.0.txt
similarity index 100%
rename from examples/3D-example/input/bayesian_em_restraint/gmm_data/10_2.0.txt
rename to broken-examples/3D-example/input/bayesian_em_restraint/gmm_data/10_2.0.txt
diff --git a/examples/3D-example/input/bayesian_em_restraint/gmm_data/15_2.0.mrc b/broken-examples/3D-example/input/bayesian_em_restraint/gmm_data/15_2.0.mrc
similarity index 100%
rename from examples/3D-example/input/bayesian_em_restraint/gmm_data/15_2.0.mrc
rename to broken-examples/3D-example/input/bayesian_em_restraint/gmm_data/15_2.0.mrc
diff --git a/examples/3D-example/input/bayesian_em_restraint/gmm_data/15_2.0.txt b/broken-examples/3D-example/input/bayesian_em_restraint/gmm_data/15_2.0.txt
similarity index 100%
rename from examples/3D-example/input/bayesian_em_restraint/gmm_data/15_2.0.txt
rename to broken-examples/3D-example/input/bayesian_em_restraint/gmm_data/15_2.0.txt
diff --git a/examples/3D-example/input/bayesian_em_restraint/gmm_data/25_2.0.mrc b/broken-examples/3D-example/input/bayesian_em_restraint/gmm_data/25_2.0.mrc
similarity index 100%
rename from examples/3D-example/input/bayesian_em_restraint/gmm_data/25_2.0.mrc
rename to broken-examples/3D-example/input/bayesian_em_restraint/gmm_data/25_2.0.mrc
diff --git a/examples/3D-example/input/bayesian_em_restraint/gmm_data/25_2.0.txt b/broken-examples/3D-example/input/bayesian_em_restraint/gmm_data/25_2.0.txt
similarity index 100%
rename from examples/3D-example/input/bayesian_em_restraint/gmm_data/25_2.0.txt
rename to broken-examples/3D-example/input/bayesian_em_restraint/gmm_data/25_2.0.txt
diff --git a/examples/3D-example/input/bayesian_em_restraint/gmm_data/3_2.0.mrc b/broken-examples/3D-example/input/bayesian_em_restraint/gmm_data/3_2.0.mrc
similarity index 100%
rename from examples/3D-example/input/bayesian_em_restraint/gmm_data/3_2.0.mrc
rename to broken-examples/3D-example/input/bayesian_em_restraint/gmm_data/3_2.0.mrc
diff --git a/examples/3D-example/input/bayesian_em_restraint/gmm_data/3_2.0.txt b/broken-examples/3D-example/input/bayesian_em_restraint/gmm_data/3_2.0.txt
similarity index 100%
rename from examples/3D-example/input/bayesian_em_restraint/gmm_data/3_2.0.txt
rename to broken-examples/3D-example/input/bayesian_em_restraint/gmm_data/3_2.0.txt
diff --git a/examples/3D-example/input/bayesian_em_restraint/gmm_data/5_2.0.mrc b/broken-examples/3D-example/input/bayesian_em_restraint/gmm_data/5_2.0.mrc
similarity index 100%
rename from examples/3D-example/input/bayesian_em_restraint/gmm_data/5_2.0.mrc
rename to broken-examples/3D-example/input/bayesian_em_restraint/gmm_data/5_2.0.mrc
diff --git a/examples/3D-example/input/bayesian_em_restraint/gmm_data/5_2.0.txt b/broken-examples/3D-example/input/bayesian_em_restraint/gmm_data/5_2.0.txt
similarity index 100%
rename from examples/3D-example/input/bayesian_em_restraint/gmm_data/5_2.0.txt
rename to broken-examples/3D-example/input/bayesian_em_restraint/gmm_data/5_2.0.txt
diff --git a/examples/3D-example/input/session.py b/broken-examples/3D-example/input/session.py
similarity index 100%
rename from examples/3D-example/input/session.py
rename to broken-examples/3D-example/input/session.py
diff --git a/examples/3D-example/test_bayesian_gaussian_em_restraint.py b/broken-examples/3D-example/test_bayesian_gaussian_em_restraint.py
similarity index 100%
rename from examples/3D-example/test_bayesian_gaussian_em_restraint.py
rename to broken-examples/3D-example/test_bayesian_gaussian_em_restraint.py
diff --git a/examples/3D-example_2/input/1WCM.fasta.txt b/broken-examples/3D-example_2/input/1WCM.fasta.txt
similarity index 100%
rename from examples/3D-example_2/input/1WCM.fasta.txt
rename to broken-examples/3D-example_2/input/1WCM.fasta.txt
diff --git a/examples/3D-example_2/input/1WCM.pdb b/broken-examples/3D-example_2/input/1WCM.pdb
similarity index 100%
rename from examples/3D-example_2/input/1WCM.pdb
rename to broken-examples/3D-example_2/input/1WCM.pdb
diff --git a/examples/3D-example_2/input/bayesian_em_restraint/C.mrc b/broken-examples/3D-example_2/input/bayesian_em_restraint/C.mrc
similarity index 100%
rename from examples/3D-example_2/input/bayesian_em_restraint/C.mrc
rename to broken-examples/3D-example_2/input/bayesian_em_restraint/C.mrc
diff --git a/examples/3D-example_2/input/bayesian_em_restraint/C.txt b/broken-examples/3D-example_2/input/bayesian_em_restraint/C.txt
similarity index 100%
rename from examples/3D-example_2/input/bayesian_em_restraint/C.txt
rename to broken-examples/3D-example_2/input/bayesian_em_restraint/C.txt
diff --git a/examples/3D-example_2/input/bayesian_em_restraint/J.mrc b/broken-examples/3D-example_2/input/bayesian_em_restraint/J.mrc
similarity index 100%
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