diff --git a/docs/user_guide/contrib.md b/docs/user_guide/contrib.md index 63083e14..24d76ae4 100644 --- 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 index 31a39cc3..21fa139f 100644 --- 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 deleted file mode 100644 index 40de9a0d..00000000 --- a/docs/user_guide/limitations.md +++ /dev/null @@ -1,9 +0,0 @@ -# Limitations - -Due to it's simplicity FPSim2 can only use integer ids to store the fingerprints, however it can generate new ids for the provided molecules using gen_ids flag. - -```python -create_db_file('mols.smi', 'mols.h5', mol_format=None, fp_type='Morgan', fp_params={'radius': 2, 'fpSize': 2048}) -``` - -In case RDKit is not able to load a molecule, the id assigned to the molecule will be also skipped so the nth molecule in the input file will have id=n. diff --git a/docs/user_guide/tversky.md b/docs/user_guide/tversky.md index 299c0832..cfec265f 100644 --- 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 index 006a4fa4..d41eb999 100644 --- 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