Renaming

.conda-noarch/meta.yaml

@@ -32,6 +32,6 @@ about:
   license:  {{ data['license'] }}
   dev_url: {{ data['url'] }}
   doc_url: {{ data['project_urls']['Documentation'] }}
-  doc_source_url: https://github.com/ale94mleon/MolDrug/tree/main/docs/source
+  doc_source_url: https://github.com/ale94mleon/moldrug/tree/main/docs/source
   summary: {{ data['description'] }}
 

.gitignore

@@ -6,7 +6,7 @@ __pycache__
 .ipynb_checkpoints
 jupyter_execute
 error
-*.costfunc_MolDrug*
+*.costfunc_moldrug*
 .coverage*
 coverage.xml
 interesting_struct.txt

Contrib/MolSkill/fitness_molskill.py

@@ -1,11 +1,13 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
-from moldrug import utils
-from moldrug.fitness import _vinadock
-from rdkit import Chem
 from typing import Dict, List
-from rdkit import RDLogger
+
 from molskill.scorer import MolSkillScorer
+from rdkit import Chem, RDLogger
+
+from moldrug import utils
+from moldrug.fitness import _vinadock
+
 RDLogger.DisableLog('rdApp.*')
 
 
@@ -74,7 +76,7 @@ def Cost(
     constraint_receptor_pdb_path : str, optional
         The same as constraint_receptor_pdbqt_path but in pdb format, by default None
     constraint_num_conf : int, optional
-        Maximum number of conformer to be generated internally by MolDrug , by default 100
+        Maximum number of conformer to be generated internally by moldrug , by default 100
     constraint_minimum_conf_rms : int, optional
         RMS to filter duplicate conformers, by default 0.01
     desirability : dict, optional

Contrib/using_models/README.md

@@ -18,7 +18,7 @@ Install dependencies:
 pip install sklearn
 ```
 
-The other dependencies are already inside **MolDrug**. You must have in the same folder the scripts: `train_models.py`, `featurize.py` and then just:
+The other dependencies are already inside **moldrug**. You must have in the same folder the scripts: `train_models.py`, `featurize.py` and then just:
 
 ```bash
 python train_models.py
@@ -32,9 +32,9 @@ Here is a detailed list of public databases to construct ADME models: [adme](htt
 
 ## EGFR data set
 
-This data was retrieved using this [EGFR-kinase tutorial](https://projects.volkamerlab.org/teachopencadd/talktorials/T001_query_chembl.html#Get-target-data-(EGFR-kinase)). The mentioned tutorial should encourage the user to retrieve data for proteins for which the 3D structure is not available and use ML/AI methods like the ones presented in this example and design molecules with MolDrug using those models as fitness functions.
+This data was retrieved using this [EGFR-kinase tutorial](https://projects.volkamerlab.org/teachopencadd/talktorials/T001_query_chembl.html#Get-target-data-(EGFR-kinase)). The mentioned tutorial should encourage the user to retrieve data for proteins for which the 3D structure is not available and use ML/AI methods like the ones presented in this example and design molecules with moldrug using those models as fitness functions.
 
-## Run MolDrug from the command line
+## Run moldrug from the command line
 
 ```bash
 moldrug config.yml --fitness /the/path/for/fitness_plus_admes.py

Contrib/using_models/fitness_plus_models.py

@@ -1,15 +1,16 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
-from moldrug import utils
-from moldrug.fitness import _vinadock
-from rdkit import Chem
-import numpy as np
+from copy import deepcopy
 from typing import Dict, List
+
 import joblib
-from rdkit.Chem import AllChem
-from rdkit.Chem import Descriptors
-from rdkit import RDLogger
-from copy import deepcopy
+import numpy as np
+from rdkit import Chem, RDLogger
+from rdkit.Chem import AllChem, Descriptors
+
+from moldrug import utils
+from moldrug.fitness import _vinadock
+
 RDLogger.DisableLog('rdApp.*')
 
 
@@ -182,7 +183,7 @@ def Cost(
     constraint_receptor_pdb_path : str, optional
         The same as constraint_receptor_pdbqt_path but in pdb format, by default None
     constraint_num_conf : int, optional
-        Maximum number of conformer to be generated internally by MolDrug , by default 100
+        Maximum number of conformer to be generated internally by moldrug , by default 100
     constraint_minimum_conf_rms : int, optional
         RMS to filter duplicate conformers, by default 0.01
     models : dict = None,

Contrib/using_models/train_models.py

@@ -1,16 +1,18 @@
+import os
 import urllib.request
 from io import StringIO
-import pandas as pd
-from scipy.stats import pearsonr
+from urllib.parse import urlparse
+
+import joblib
 import numpy as np
+import pandas as pd
+from featurize import Featurizer
 from rdkit import Chem
+from scipy.stats import pearsonr
 from sklearn.ensemble import RandomForestRegressor
-from sklearn.preprocessing import StandardScaler
 from sklearn.model_selection import train_test_split
-from featurize import Featurizer
-import joblib
-from urllib.parse import urlparse
-import os
+from sklearn.preprocessing import StandardScaler
+
 
 def is_url(string:str) -> bool:
     """Check if the string is a valid URL
@@ -85,7 +87,7 @@ def prepare_model(name, source, y_transform = None, scaler = None):
     y_pred = model.predict(X_te)
     print("Pearson Correlation: {:.3f}".format(pearsonr(y_pred, y_te)[0]))
 
-    # Change n_jobs to 1 in order to avoid warnings during MolDrug run.
+    # Change n_jobs to 1 in order to avoid warnings during moldrug run.
     model.n_jobs = 1
 
     joblib.dump(

README.rst

@@ -1,4 +1,4 @@
-MolDrug
+moldrug
 =======
 
 |logo|
@@ -29,13 +29,13 @@ MolDrug
 Description
 -----------
 
-**MolDrug** is a Python package for drug-oriented optimization in the chemical space. It uses a Genetic Algorithm (GA) as a search engine in the chemical space and
+**moldrug** is a Python package for drug-oriented optimization in the chemical space. It uses a Genetic Algorithm (GA) as a search engine in the chemical space and
 `CReM <https://github.com/DrrDom/crem>`__ library as chemical structure generator.
 
 
 You can try it out before any installation on `Binder <https://mybinder.org/v2/gh/ale94mleon/moldrug/HEAD?labpath=%2Fdocs%2Fnotebooks%2F>`__.
 
-You can use `MolDrug-Dashboard <https://moldrug-dashboard.streamlit.app/>`__ to process the results.
+You can use `moldrug-Dashboard <https://moldrug-dashboard.streamlit.app/>`__ to process the results.
 
 Documentation
 -------------
@@ -50,9 +50,9 @@ If you have found a bug, please open an issue on the `GitHub Issues <https://git
 Discussion
 ----------
 
-If you have questions on how to use **MolDrug**, or if you want to give feedback or share ideas and new features, please head to the `GitHub Discussions <https://github.com/ale94mleon/moldrug/discussions>`_.
+If you have questions on how to use **moldrug**, or if you want to give feedback or share ideas and new features, please head to the `GitHub Discussions <https://github.com/ale94mleon/moldrug/discussions>`_.
 
-Citing **MolDrug**
+Citing **moldrug**
 ------------------
 
 Please refer to the `citation page <https://moldrug.readthedocs.io/en/latest/source/citations.html>`__ on the documentation.
@@ -65,7 +65,7 @@ This project received funding from `Marie Skłodowska-Curie Actions <https://cor
 with the pharmaceutical company `Boehringer Ingelheim <https://www.boehringer-ingelheim.com/de/>`__.
 
 
-..  |logo|  image:: https://github.com/ale94mleon/MolDrug/blob/main/docs/source/_static/MolDrug-logo-full.svg?raw=true
+..  |logo|  image:: https://github.com/ale94mleon/moldrug/blob/main/docs/source/_static/moldrug-logo-full.svg?raw=true
     :target: https://github.com/ale94mleon/moldrug/
     :alt: logo
 ..  |docs|  image:: https://readthedocs.org/projects/moldrug/badge/?version=latest
@@ -74,17 +74,17 @@ with the pharmaceutical company `Boehringer Ingelheim <https://www.boehringer-in
 ..  |binder| image:: https://mybinder.org/badge_logo.svg
     :target: https://mybinder.org/v2/gh/ale94mleon/moldrug/HEAD?labpath=%2Fdocs%2Fnotebooks%2F
     :alt: binder
-..  |tests| image:: https://github.com/ale94mleon/MolDrug/actions/workflows/tests.yml/badge.svg
-    :target: https://github.com/ale94mleon/MolDrug/actions/workflows/tests.yml
+..  |tests| image:: https://github.com/ale94mleon/moldrug/actions/workflows/tests.yml/badge.svg
+    :target: https://github.com/ale94mleon/moldrug/actions/workflows/tests.yml
     :alt: tests
 ..  |codacy-codecove| image:: https://app.codacy.com/project/badge/Coverage/08a3ac7c13df4339b8a1da0e8d31810e
-    :target: https://app.codacy.com/gh/ale94mleon/MolDrug/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_coverage
+    :target: https://app.codacy.com/gh/ale94mleon/moldrug/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_coverage
     :alt: codacy-codecove
 ..  |codacy-grade| image:: https://app.codacy.com/project/badge/Grade/08a3ac7c13df4339b8a1da0e8d31810e
-    :target: https://app.codacy.com/gh/ale94mleon/MolDrug/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade
+    :target: https://app.codacy.com/gh/ale94mleon/moldrug/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade
     :alt: codacy-grade
-..  |CodeQL| image:: https://github.com/ale94mleon/MolDrug/actions/workflows/codeql-analysis.yml/badge.svg
-    :target: https://github.com/ale94mleon/MolDrug/actions/workflows/codeql-analysis.yml
+..  |CodeQL| image:: https://github.com/ale94mleon/moldrug/actions/workflows/codeql-analysis.yml/badge.svg
+    :target: https://github.com/ale94mleon/moldrug/actions/workflows/codeql-analysis.yml
     :alt: CodeQL
 ..  |pypi-version|  image:: https://img.shields.io/pypi/v/moldrug.svg
     :target: https://pypi.python.org/pypi/moldrug/

conda/meta.yaml

@@ -31,6 +31,6 @@ about:
   license:  {{ data['license'] }}
   dev_url: {{ data['url'] }}
   doc_url: {{ data['project_urls']['Documentation'] }}
-  doc_source_url: https://github.com/ale94mleon/MolDrug/tree/main/docs/source
+  doc_source_url: https://github.com/ale94mleon/moldrug/tree/main/docs/source
   summary: {{ data['description'] }}
 

docs/conf.py

@@ -21,7 +21,7 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'MolDrug'
+project = 'moldrug'
 copyright = f"2022-{datetime.now().year}, Alejandro Martínez León"
 author = 'Alejandro Martínez León'
 
@@ -110,7 +110,7 @@
         }
     ],
 }
-html_logo = "source/_static/MolDrug-logo.svg"
+html_logo = "source/_static/moldrug-logo.svg"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,