update docs

chembl · Dec 26, 2024 · 6bc08fd · 6bc08fd
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diff --git a/docs/user_guide/contrib.md b/docs/user_guide/contrib.md
@@ -2,7 +2,7 @@
 
 ## [iSIM](https://pubs.rsc.org/en/content/articlehtml/2024/dd/d4dd00041b) 
 
-iSIM performs comparisons of multiple molecules at the same time and yields the same value as the average pairwise comparisons of molecules represented by binary fingerprints and real-value descriptors.
+iSIM performs comparisons of multiple molecules at the same time and yields the same value as the average pairwise comparisons of molecules represented by binary fingerprints.
 
 ```python
 from FPSim2.contrib.isim.isim_comp import get_sim_dict

diff --git a/docs/user_guide/create_db_file.md b/docs/user_guide/create_db_file.md
@@ -1,6 +1,6 @@
 # Create a fingerprint database file
 
-Use the `FPSim2.io.backends.pytables.create_db_file` function to create the fingerprint database file.
+Use the `FPSim2.io.backends.pytables.create_db_file` function to create the fingerprint database file needed to run the searches.
 
 !!! warning
     FPSim2 only supports integer molecule ids.
@@ -16,7 +16,7 @@ The fingerprints are calculated with [RDKit](https://www.rdkit.org/). Fingerprin
 
 ## From a .sdf file
 ```python
-from FPSim2.io.backends.pytables import create_db_file
+from FPSim2.io import create_db_file
 
 create_db_file(
     mols_source='stuff.sdf',
@@ -30,7 +30,7 @@ create_db_file(
 
 ## From a .smi file
 ```python
-from FPSim2.io.backends.pytables import create_db_file
+from FPSim2.io import create_db_file
 
 create_db_file(
     mols_source='chembl.smi',
@@ -43,7 +43,7 @@ create_db_file(
 
 ## From a Python list
 ```python
-from FPSim2.io.backends.pytables import create_db_file
+from FPSim2.io import create_db_file
 
 mols = [['CC', 1], ['CCC', 2], ['CCCC', 3]]
 create_db_file(
@@ -57,7 +57,7 @@ create_db_file(
 
 ## From any other Python iterable like a SQLAlchemy result proxy
 ```python
-from FPSim2.io.backends.pytables import create_db_file
+from FPSim2.io import create_db_file
 from sqlalchemy.orm import Session
 from sqlalchemy import create_engine
 

diff --git a/docs/user_guide/limitations.md b/docs/user_guide/limitations.md
diff --git a/docs/user_guide/tversky.md b/docs/user_guide/tversky.md
@@ -19,7 +19,7 @@ query = 'CC(=O)Oc1ccccc1C(=O)O'
 results = fpe.tversky(query, 0.7, 0.5, 0.5, n_workers=1)
 ```
 
-> **Tip:** *n_workers* parameter can be used to split a single query into multiple threads to speed up the seach. This is specially useful on big datasets.
+> **Tip:** *n_workers* parameter can be used to split a single query into multiple threads to speed up the seach. This is specially useful when searching big datasets.
 
 ## On disk
 

diff --git a/mkdocs.yml b/mkdocs.yml
@@ -7,7 +7,6 @@ nav:
   - Getting started:
     - Installation: user_guide/install.md
     - Creating FP Database: user_guide/create_db_file.md
-    - Limitations: user_guide/limitations.md
   - CPU searches:
     - Similarity Search: user_guide/similarity.md
     - Tversky Search: user_guide/tversky.md