Merge pull request #22 from volkamerlab/polish

Polish READMEs

README.md

@@ -13,15 +13,12 @@
 
 ## Repository content
 
-This repository holds 
-(i) fragment library data, 
-(ii) a *quick start* notebook explaining how to load and use the library, alongside 
-(iii) notebooks covering the full analyses regarding the fragment library and the combinatorial library as described in 
-the corresponding paper.
-
-    data/
-    notebooks/
-    environment.yml
+This repository holds the following resources:  
+
+1. Fragment library data and a link to the combinatorial library data.
+2. *Quick start* notebook explaining how to load and use the fragment library.  
+3. Notebooks covering the full analyses regarding the fragment and combinatorial libraries as described in 
+the corresponding paper.  
 
 Please find detailed description of files in `data/` and `notebooks/` in the folders' `README` files.
 

data/README.md

@@ -1,9 +1,9 @@
 # Data
 
-Overview on data content:
+Overview on data content.
 
-- `fragment_library/`: Fullfragment library resulting from the KinFragLib fragmentation procedure comprises of about 3,000 fragments, which are the basis for exploring the subpocket-based chemical space of ligands co-crystallized with kinases.
-- `fragment_library_filtered/`: Filtered fragment library: Select fragments meaningful for the recombination (remove pool X, deduplicate per subpocket, remove unfragmented ligands, remove all fragments that connect only to pool X, keep only fragment-like fragments, and filter for hinge-like AP fragments).
+- `fragment_library/`: Full fragment library resulting from the KinFragLib fragmentation procedure comprises of about 3000 fragments, which are the basis for exploring the subpocket-based chemical space of ligands co-crystallized with kinases.
+- `fragment_library_filtered/`: Filtered fragment library: Select fragments tailored for the recombination (remove pool X, deduplicate per subpocket, remove unfragmented ligands, remove all fragments that connect only to pool X, keep only fragment-like fragments, and filter for hinge-like AP fragments).
 - `fragment_library_reduced/`: Reduced fragment library: Select a diverse set of fragments (per subpocket) for recombination starting from the filtered fragment library.
 - `combinatorial_library/`: Combinatorial library based on the reduced fragment library.
 - `external/`: Data from external resources.

data/fragment_library/README.md

@@ -17,15 +17,15 @@ Fragments are organized by the subpockets they occupy. Each fragment subpocket p
 
 Each fragment contains the following information:
 
-- 3D coordinates of the fragment's atoms as reported in the corresponding KLIFS complex structure file
+- 3D coordinates of the fragment's atoms as reported in the corresponding KLIFS complex structure file.
 - `kinase`, `family`, and `group`: 
 *Kinase* name, *family* and *group* of the kinase that the ligand (from which the fragment originates) was 
-co-crystallized with
+co-crystallized with.
 - `complex_pdb`, `ligand_pdb`, `alt`, and `chain`: 
 *PDB complex* and *ligand ID*, *alternate model* and *chain* for the KLIFS structure that the ligand 
-(from which the fragment originates) was co-crystallized with
-- `atom.prop.subpocket`: Subpocket assignment for each of the fragment's atoms
-- `atom.prop.environment`: BRICS environment IDs for each of the fragment's atoms
+(from which the fragment originates) was co-crystallized with.
+- `atom.prop.subpocket`: Subpocket assignment for each of the fragment's atoms.
+- `atom.prop.environment`: BRICS environment IDs for each of the fragment's atoms.
 
 Please refer to `notebooks/1_1_quick_start.ipynb` on how to load and work with this dataset.
 
@@ -38,14 +38,14 @@ Original ligands that are composed of the fragments in the full fragment library
 Each ligand contains the following information:
 
 - `kinase`, `family`, and `group`: 
-*Kinase* name, *family* and *group* of the kinase that the ligand was co-crystallized with
+*Kinase* name, *family* and *group* of the kinase that the ligand was co-crystallized with.
 - `complex_pdb`, `ligand_pdb`, `alt`, and `chain`: 
-*PDB complex* and *ligand ID*, *alternate model* and *chain* for the KLIFS structure that the ligand was co-crystallized with
+*PDB complex* and *ligand ID*, *alternate model* and *chain* for the KLIFS structure that the ligand was co-crystallized with.
 - `subpocket`: 
-Subpockets that the ligand occupies
+Subpockets that the ligand occupies.
 - `ac_helix`:
-aC-helix conformation for the KLIFS structure that the ligand was co-crystallized with
+aC-helix conformation for the KLIFS structure that the ligand was co-crystallized with.
 - `smiles`:
-Ligand's SMILES string
+Ligand's SMILES string.
 
 Please refer to `notebooks/2_1_fragment_analysis_original_ligands.ipynb` where this data is generated.

data/fragment_library_filtered/README.md

@@ -2,7 +2,7 @@
 
 The (full) fragment library resulting from the KinFragLib fragmentation procedure comprises of 7486 fragments, which are the basis for exploring the subpocket-based chemical space of ligands co-crystallized with kinases (see `data/fragment_library/`).
 
-In order to prepare a library with fragments meaningful for recombination, we offer heare a filtered fragment library (2009 fragments) based on the following filters:
+In order to prepare a library with fragments tailored for recombination, we offer heare a filtered fragment library (2009 fragments) based on the following filters:
 
 1. Remove pool X
 2. Deduplicate fragment library (per subpocket)
@@ -11,4 +11,4 @@ In order to prepare a library with fragments meaningful for recombination, we of
 5. Keep "Rule of Three (Ro3)" compliant fragments (fragment-likeness)
 6. Filter AP subpocket fragments (typical hinge-like)
 
-Please refer to the notebook `notebooks/3_1_fragment_library_reduced.ipynb` to check how the data was generated and/or use it as a starting point for customized protocols.
+Please refer to the notebook `notebooks/3_1_fragment_library_reduced.ipynb` to check how the data was generated and/or use it as a starting point for customized protocols.

data/fragment_library_reduced/README.md

@@ -1,13 +1,13 @@
 # Reduced fragment library
 
-The (full) fragment library resulting from the KinFragLib fragmentation procedure comprises of 7486 fragments, which are the basis for exploring the subpocket-based chemical space of ligands co-crystallized with kinases (see `data/fragment_library/`).
+The (full) fragment library resulting from the KinFragLib fragmentation procedure comprises of 7,486 fragments, which are the basis for exploring the subpocket-based chemical space of ligands co-crystallized with kinases (see `data/fragment_library/`).
 
 In order to demonstrate how this library can be used for recombining ligands, we offer here a reduced fragment library (624 fragments) based on the following filters:
 
 1. Remove all fragments that are not useful in a recombination. Check `data/fragment_library_filtered/`.
 2. Select a diverse set of fragments (per subpocket) for recombination to (i) save computational cost and (ii) avoid recombination of highly similar fragments.
 
-Step 1 is necessary to focus on fragments meaningful for the recombination, whereas step 2 mainly aims to reduce computational costs during recombination.
+Step 1 is necessary to focus on fragments tailored for the recombination, whereas step 2 mainly aims to reduce computational costs during recombination.
 
 ## Reduction steps
 
@@ -23,4 +23,4 @@ Step 1 is necessary to focus on fragments meaningful for the recombination, wher
 - `N_REPRESENTED_FRAGMENTS` = 10
 - `INCLUDE_SINGLETONS` = True
 
-Please refer to the notebook `notebooks/3_1_fragment_library_reduced.ipynb` to check how the data was generated and/or use it as a starting point for customized protocols.
+Please refer to the notebook `notebooks/3_1_fragment_library_reduced.ipynb` to check how the data was generated and/or use it as a starting point for customized protocols.

notebooks/3_1_fragment_library_reduced.ipynb

@@ -1060,7 +1060,7 @@
     "        f'The (full) fragment library resulting from the KinFragLib fragmentation procedure comprises of {fragment_library_concat.shape[0]} fragments, '\n",
     "        f'which are the basis for exploring the subpocket-based chemical space of ligands co-crystallized with kinases '\n",
     "        f'(see `data/fragment_library/`).\\n\\n'\n",
-    "        f'In order to prepare a library with fragments meaningful for recombination, '\n",
+    "        f'In order to prepare a library with fragments tailored for recombination, '\n",
     "        f'we offer heare a filtered fragment library ({fragment_library_concat_filtered.shape[0]} fragments) based on the following filters:\\n\\n'\n",
     "        f'1. Remove pool X\\n'\n",
     "        f'2. Deduplicate fragment library (per subpocket)\\n'\n",
@@ -16550,7 +16550,7 @@
     "        f'(i) save computational cost and '\n",
     "        f'(ii) avoid recombination of highly similar fragments.'\n",
     "        f'\\n\\n'\n",
-    "        f'Step 1 is necessary to focus on fragments meaningful for the recombination, whereas step 2 mainly aims to reduce computational costs during recombination.'\n",
+    "        f'Step 1 is necessary to focus on fragments tailored for the recombination, whereas step 2 mainly aims to reduce computational costs during recombination.'\n",
     "        f'\\n\\n'\n",
     "        f'## Reduction steps'\n",
     "        f'\\n\\n'\n",

notebooks/README.md

@@ -1,6 +1,6 @@
 # Notebooks
 
-Overview on notebook content:
+Overview on notebook content.
 
 ## 1. Quick start
 
@@ -50,12 +50,12 @@ The aim of this notebook is to extract information from the combinatorial librar
 
 ### `4_2_combinatorial_library_properties.ipynb`
 
-In this notebook we want to analyze properties of the combinatorial library, such as the ligand size and Lipinski's rule of five criteria.
+In this notebook, we want to analyze properties of the combinatorial library, such as the ligand size and Lipinski's rule of five criteria.
 
 ### `4_3_combinatorial_library_comparison_klifs.ipynb`
 
-In this notebook we want to compare the combinatorial library to the original KLIFS ligands, i.e. the ligands from which the fragment library originates from. We consider exact and substructure matches.
+In this notebook, we want to compare the combinatorial library to the original KLIFS ligands, i.e. the ligands from which the fragment library originates from. We consider exact and substructure matches.
 
 ### `4_4_combinatorial_library_comparison_chembl.ipynb`
 
-In this notebook we want to compare the combinatorial library to the ChEMBL 25 dataset in order to find exact matches and the most similar ChEMBL ligand per recombined ligand.
+In this notebook, we want to compare the combinatorial library to the ChEMBL 25 dataset in order to find exact matches and the most similar ChEMBL molecule per recombined ligand.