change test data files structure

docs/source/CHANGELOG.md

@@ -32,7 +32,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Use `random.random` instead `numpy.random.rand` function for some small cases.
 - `AllChem.MMFFOptimizeMolecule` is only used internally for `moldrug.utils.confgen` and `moldrug.constraintconf.gen_aligned_conf` if `randomseed` is not set and with `maxIters = 500`.
-- `pickle` module is replaced by `dill`. It is better to handle user custom fitness functions.
+- `pickle` module is replaced by `dill`. It is better to handle users' custom fitness functions.
+- Data now is retrieved with `moldrug``.data.get_data` function.
 - Is not needed to input the whole desirability definition if only is intended to change one part of the default desirability used internally by the cost functions of `moldrug.fitness`. For example, if you would like to change the `Target` value of `vina_score` from its default value.
 
   Before:
@@ -101,8 +102,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Fixed
 
 - Small bug when the population has Individuals with the same cost. Better reproducibility.
-- Refactored changes on tutorials.
-- Handled properly in case `receptor_pdbqt_path = None`
+- Refactored changes.
+- Handled properly in case `receptor_pdbqt_path = None`.
 - Convert `self.crem_db_path` to absolute path in `moldrug.utils.Local` and `moldrug.utils.GA`.
 
 ## [3.5.0] - 2023.10.26

pyproject.toml

@@ -82,6 +82,18 @@ include-package-data = true
 [tool.setuptools.packages.find]
 where = ["src"]
 
+[tool.setuptools.package-data]
+moldrug = [
+    "LICENSE",
+    "README.rst",
+    "data/*/*.yml",
+    "data/*/*.mol",
+    "data/*/*.smi",
+    "data/*/*.pdb",
+    "data/*/*.pdbqt",
+
+]
+
 
 [project.scripts]
 moldrug = "moldrug.cli:__moldrug_cmd"

src/moldrug/data/6lu7/box.yml

@@ -0,0 +1,8 @@
+boxcenter:
+  - -13.07
+  - 12.58
+  - 67.15
+boxsize:
+  - 22.5
+  - 23.625
+  - 23.25

src/moldrug/data/6lu7/ligand.smi

@@ -0,0 +1 @@
+CC(C)C[C@H](NC(=O)[C@@H](NC(=O)[C@H](C)NC(O)C1CC(C)ON1)C(C)C)C(=O)N[C@H](CC[C@H](O)OCC1CCCCC1)C[C@@H]1CCNC1O

src/moldrug/data/constraintref.py → src/moldrug/data/6lu7/ligand_3D.mol

@@ -1,9 +1,4 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-"""
-The reference mol blocks ligands for the receptors with PDB id: : 6lu7, x0161.
-"""
-r_6lu7 = """6lu7
+6lu7
      RDKit          3D
 
  23 23  0  0  0  0  0  0  0  0999 V2000
@@ -53,40 +48,4 @@
  10 21  1  0
  13 22  1  0
  14 23  1  0
-M  END
-"""
-
-r_x0161 = """r_x0161
-     RDKit          3D
-
- 14 14  0  0  1  0  0  0  0  0999 V2000
-   13.8921   -2.4077   24.1269 C   0  0  0  0  0  0  0  0  0  0  0  0
-   13.4897   -0.2702   23.1446 C   0  0  0  0  0  0  0  0  0  0  0  0
-   12.8011    1.0351   23.3277 C   0  0  0  0  0  0  0  0  0  0  0  0
-   11.6117    1.1475   24.0810 C   0  0  0  0  0  0  0  0  0  0  0  0
-   10.9808    2.3973   24.2401 C   0  0  0  0  0  0  0  0  0  0  0  0
-   11.5348    3.5418   23.6347 C   0  0  0  0  0  0  0  0  0  0  0  0
-   12.7111    3.4432   22.8672 C   0  0  0  0  0  0  0  0  0  0  0  0
-   13.3408    2.1928   22.7264 C   0  0  0  0  0  0  0  0  0  0  0  0
-    9.4491    5.0959   22.7844 N   0  0  0  0  0  0  0  0  0  0  0  0
-   13.2656   -1.1348   24.1544 O   0  0  0  0  0  0  0  0  0  0  0  0
-   14.2110   -0.5201   22.1789 O   0  0  0  0  0  0  0  0  0  0  0  0
-   11.6894    6.1877   23.4320 O   0  0  0  0  0  0  0  0  0  0  0  0
-   10.1931    5.1760   25.2380 O   0  0  0  0  0  0  0  0  0  0  0  0
-   10.7644    5.1384   23.8833 S   0  0  0  0  0  0  0  0  0  0  0  0
-  1 10  1  0
-  2  3  1  0
-  2 10  1  0
-  2 11  2  0
-  3  4  2  0
-  3  8  1  0
-  4  5  1  0
-  5  6  2  0
-  6  7  1  0
-  6 14  1  0
-  7  8  2  0
-  9 14  1  0
- 12 14  2  0
- 13 14  2  0
-M  END
-"""
+M  END

src/moldrug/data/__init__.py

@@ -0,0 +1,6 @@
+from moldrug.data._get import get_data
+import json
+
+if __name__ == "__main__":
+
+    print(json.dumps(get_data('6lu7'), indent=3))

src/moldrug/data/_get.py

@@ -0,0 +1,57 @@
+import yaml
+from moldrug import home
+import os
+
+_AVAILABLE_DATA = ['6lu7', 'x0161']
+
+
+class DataNotFound(Exception):
+    pass
+
+
+def get_data(name: str) -> dict:
+    """Retrieve MolDrug data
+
+    Parameters
+    ----------
+    name : str
+        Name of the data directory of MolDrug
+
+    Returns
+    -------
+    dict
+        A dictionary with keys:
+
+        * box: boxcenter, boxsize
+        * ligand_3D: absolute path
+        * smiles: the ligans's SMILES
+        * protein: pdb, pdbqt
+
+    Raises
+    ------
+    DataNotFound
+        MolDrug does not contains the data.
+    """
+
+    root_data = home.home(dataDir=name)
+
+    if not os.path.exists(root_data) or not name:
+        raise DataNotFound(f"MolDrug data does not have '{name}' data set. "
+                           f"Choose from: {_AVAILABLE_DATA}")
+
+    with open(os.path.join(root_data, 'box.yml'), 'r') as f:
+        box = yaml.safe_load(f)
+
+    with open(os.path.join(root_data, 'ligand.smi'), 'r') as f:
+        smiles = f.readline()
+
+    data = {
+        'box': box,
+        'ligand_3D': os.path.join(root_data, 'ligand_3D.mol'),
+        'smiles': smiles,
+        'protein': {
+            'pdb': os.path.join(root_data, 'protein.pdb'),
+            'pdbqt': os.path.join(root_data, 'protein.pdbqt'),
+        }
+    }
+    return data

src/moldrug/data/x0161/box.yml

@@ -0,0 +1,8 @@
+boxcenter:
+  - 12.11
+  - 1.84
+  - 23.56
+boxsize:
+  - 22.5
+  - 22.5
+  - 22.5

src/moldrug/data/x0161/ligand.smi

@@ -0,0 +1 @@
+COC(=O)C=1C=CC(=CC1)S(=O)(=O)N

src/moldrug/data/x0161/ligand_3D.mol

@@ -0,0 +1,33 @@
+x0161
+     RDKit          3D
+
+ 14 14  0  0  1  0  0  0  0  0999 V2000
+   13.8921   -2.4077   24.1269 C   0  0  0  0  0  0  0  0  0  0  0  0
+   13.4897   -0.2702   23.1446 C   0  0  0  0  0  0  0  0  0  0  0  0
+   12.8011    1.0351   23.3277 C   0  0  0  0  0  0  0  0  0  0  0  0
+   11.6117    1.1475   24.0810 C   0  0  0  0  0  0  0  0  0  0  0  0
+   10.9808    2.3973   24.2401 C   0  0  0  0  0  0  0  0  0  0  0  0
+   11.5348    3.5418   23.6347 C   0  0  0  0  0  0  0  0  0  0  0  0
+   12.7111    3.4432   22.8672 C   0  0  0  0  0  0  0  0  0  0  0  0
+   13.3408    2.1928   22.7264 C   0  0  0  0  0  0  0  0  0  0  0  0
+    9.4491    5.0959   22.7844 N   0  0  0  0  0  0  0  0  0  0  0  0
+   13.2656   -1.1348   24.1544 O   0  0  0  0  0  0  0  0  0  0  0  0
+   14.2110   -0.5201   22.1789 O   0  0  0  0  0  0  0  0  0  0  0  0
+   11.6894    6.1877   23.4320 O   0  0  0  0  0  0  0  0  0  0  0  0
+   10.1931    5.1760   25.2380 O   0  0  0  0  0  0  0  0  0  0  0  0
+   10.7644    5.1384   23.8833 S   0  0  0  0  0  0  0  0  0  0  0  0
+  1 10  1  0
+  2  3  1  0
+  2 10  1  0
+  2 11  2  0
+  3  4  2  0
+  3  8  1  0
+  4  5  1  0
+  5  6  2  0
+  6  7  1  0
+  6 14  1  0
+  7  8  2  0
+  9 14  1  0
+ 12 14  2  0
+ 13 14  2  0
+M  END