[](https://opensource.org/licenses/MIT)
 
# Mold² Python wrapper
Python wrapper to ease the calculation of Mold2 molecular descriptors.
## Copyright notice
Mold2 is a product designed and produced by the National Center for Toxicological
Research (NCTR).<br/>FDA and NCTR retain ownership of this product.
Olivier J. M. Béquignon is **neither** the copyright holder of Mold2 **nor** responsible for it.
Only the Python wrapper is the work of Olivier J. M. Béquignon.
## Installation
From source:
git clone https://github.com/OlivierBeq/Mold2_pywrapper.git
pip install ./Mold2_pywrapper
with pip:
```bash
pip install mold2-pywrapper
```
### Get started
```python
from Mold2_pywrapper import Mold2
smiles_list = [
# erlotinib
"n1cnc(c2cc(c(cc12)OCCOC)OCCOC)Nc1cc(ccc1)C#C",
# midecamycin
"CCC(=O)O[C@@H]1CC(=O)O[C@@H](C/C=C/C=C/[C@@H]([C@@H](C[C@@H]([C@@H]([C@H]1OC)O[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)C)O[C@H]3C[C@@]([C@H]([C@@H](O3)C)OC(=O)CC)(C)O)N(C)C)O)CC=O)C)O)C",
# selenofolate
"C1=CC(=CC=C1C(=O)NC(CCC(=O)OCC[Se]C#N)C(=O)O)NCC2=CN=C3C(=N2)C(=O)NC(=N3)N",
# cisplatin
"N.N.Cl[Pt]Cl"
]
mols = [Chem.MolFromSmiles(smiles) for smiles in smiles_list]
mold2 = Mold2()
print(mold2.calculate(mols))
```
Instantiating a Mold2 object ensures that the executables for your platform are accessible.
If this is not the case, an attempt to download them from the
[website of the FDA](https://www.fda.gov/science-research/bioinformatics-tools/mold2) is made.
Should one have downloaded the original ZIP file available from the
[website of the FDA](https://www.fda.gov/science-research/bioinformatics-tools/mold2), the executables can be installed
using the following:
```python
path_to_zipfile = '...' # Replace by the path to the ZIP file on your machine
mold2 = Mold2.from_executable(path_to_zipfile)
print(mold2.calculate(mols))
```
Executables will be installed for future use. From then on, default instanciation may be carried out:
```python
mold2 = Mold2()
print(mold2.calculate(mols))
```
### Details about descriptors
Any detail about the 777 Mold2 descriptors can be obtained either for a single descriptor, by providing its index:
```python
print(mold2.descriptor_detail(15))
# rotatable bond fraction
```
Or for all at once:
```python
print(mold2.descriptor_details())
# {"D001": "number of 6-membered aromatic rings (only carbon atoms)",
# "D002": "number of 03-membered rings",
# ...
# }
```
## Documentation
```python
def calculate(mols, show_banner=True, njobs=1, chunksize=100):
```
Default method to calculate #### Parameters
- ***mols : Iterable[Chem.Mol]***
RDKit molecule objects for which to obtain Mold2 descriptors.
- ***show_banner : bool***
Displays default notice about Mold2 descriptors.
- ***njobs : int***
Maximum number of simultaneous processes.
- ***chunksize : int***
Maximum number of molecules each process is charged of.
- ***return_type : pd.DataFramce***
Pandas DataFrame containing Mold2 molecular descriptors.Mold2 descriptors.
If executables have not previously been downloaded, attempts to download and install them.
________________
```python
def descriptor_detail(index):
```
Obtain detils about one descriptor.
#### Parameters
- ***index : int***
Index of the descriptor.
- ***return_type : str***
Description of the descriptor.
________________
```python
def descriptor_details():
```
Obtain details about all descriptors.
#### Parameters
- ***return_type : dict***
Mapping of molecular descriptors with their details.
________________
```python
def from_executable(zipfile_path):
```
Install executables and instantiate a Mold2 calculator.
#### Parameters
- ***zipfile_path : str***
Path to the user-downloaded ZIP file containing Mold2 executables.
Raw data
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