Fix protein.pdb files; remove GROMACS-specific files; drop LFS usage (#…

…52) * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Dropping all LFS filters to avoid LFS handling of all files * Updated PDB files and docked ligands Updated PDB files with alt loc commits and docked ligands * Added pde10 protein.pdb as non-LFS file * Remove MacOS .DS_Store files * Add .DS_Store to gitignore * Update incorrect fiels Updated ligands.sdf for BACE. Replaced TYK2 with correct protein.pdb * Add PDE10 data Add prepped PDE10 structure (from 4BBX) and docked ligands. * Replace TNKS2 protein.pdb Replace TNK2 protein.pdb with re-prepped structure. * PDE10 ligand fix Upload re-docked PDE10 ligands . Manually defined common core substructure. * Remove DS_Store OSX files; add proper gitignore for these * Accepting redocked ligands for pde10 * Added separated ligand SDFs for all targets * Cleanup for #52; almost complete - [x] delete [2019-09-23_jnk1/04_schrodinger](https://github.com/openforcefield/protein-ligand-benchmark/tree/fix_data/data/2019-09-23_jnk1/04_schrodinger) since we have to drop JNK1 - [x] remove all `04_schrodinger/` directories - [x] move `protein.pdb` into `01_protein/` - [x] remove all old stuff :`01_protein/top`, `02_ligands/lig_*`, `03_hybrid/` - [x] get rid of the dates in target name directories--they are meaningless and belong in the metadata if anything (e.g. [2019-12-13_mcl1](https://github.com/openforcefield/protein-ligand-benchmark/tree/fix_data/data/2019-12-13_mcl1)) and update `targets.yml` - [ ] update edges for all targets using newest lomap (with @IAlibay) - [x] eliminate redundant and inhomogeneously named `.smi` files like [ligands_mcl1.smi](https://github.com/openforcefield/protein-ligand-benchmark/blob/fix_data/data/2019-12-13_mcl1/00_data/ligands_mcl1.smi) Also need to: - [ ] update each `ligands.yml` file to include only ligands that could be docked - [x] remove jnk1 and galectin * Update each `ligands.yml` file to include only ligands that could be docked * Update protein.pdb * Push CLI-prepped protein structures, split non-metal cofactors, include prep documentation * Remove large files from preparation folder Removed large files from prep folder -- input and setup scripts still available. Co-authored-by: David Dotson <[email protected]>
openforcefield · Oct 7, 2022 · 262633b · 262633b
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diff --git a/.gitattributes b/.gitattributes
@@ -1,6 +0,0 @@
-data/**/*.dat filter=lfs diff=lfs merge=lfs -text
-data/**/*.pdb filter=lfs diff=lfs merge=lfs -text
-data/**/*.gro filter=lfs diff=lfs merge=lfs -text
-data/**/*.top filter=lfs diff=lfs merge=lfs -text
-data/**/*.itp filter=lfs diff=lfs merge=lfs -text
-data/**/*.sdf filter=lfs diff=lfs merge=lfs -text

diff --git a/.gitignore b/.gitignore
@@ -101,10 +101,12 @@ ENV/
 # mypy
 .mypy_cache/
 
+# MacOS
+*.DS_Store
 
 #*#
 *~
 *#
 
 mdout.mdp
-tpr.tpr
+tpr.tpr
diff --git a/data/2019-09-23_jnk1/00_data/edges.yml b/data/2019-09-23_jnk1/00_data/edges.yml
diff --git a/data/2019-09-23_jnk1/00_data/ligands.yml b/data/2019-09-23_jnk1/00_data/ligands.yml
diff --git a/data/2019-09-23_jnk1/00_data/target.yml b/data/2019-09-23_jnk1/00_data/target.yml
diff --git a/data/2019-09-23_jnk1/01_protein/crd/cofactors_crystalwater.pdb b/data/2019-09-23_jnk1/01_protein/crd/cofactors_crystalwater.pdb
diff --git a/data/2019-09-23_jnk1/01_protein/crd/protein.pdb b/data/2019-09-23_jnk1/01_protein/crd/protein.pdb
diff --git a/data/2019-09-23_jnk1/01_protein/top/amber99sb-star-ildn-mut.ff/cofactors_crystalwater.top b/data/2019-09-23_jnk1/01_protein/top/amber99sb-star-ildn-mut.ff/cofactors_crystalwater.top
diff --git a/data/2019-09-23_jnk1/01_protein/top/amber99sb-star-ildn-mut.ff/protein.top b/data/2019-09-23_jnk1/01_protein/top/amber99sb-star-ildn-mut.ff/protein.top
diff --git a/data/2019-09-23_jnk1/01_protein/top/amber99sb-star-ildn-mut.ff/topol_Protein_chain_A.itp b/data/2019-09-23_jnk1/01_protein/top/amber99sb-star-ildn-mut.ff/topol_Protein_chain_A.itp