cgbind automates the process of generating and analysing metallocage structures from just SMILES strings of the corresponding linkers. Binding affinity calculations can be performed with SMILES or 3D structures of linkers and the guest(s). A graphical user interface (GUI) is available at cgbind.chem.ox.ac.uk.
Install with:
conda install numpy autode rdkit scipy networkx Cython -c conda-forge
pip install cgbind
For detailed instructions see the installation instructions
- Python > v. 3.6
- All Python packages listed in requirements.txt
- ORCA >v. 4.0 (optional)
- XTB >v. 6.2 (optional)
cgbind constructs cages from SMILES strings, which can be generated directly from ChemDraw, as
To generate a simple Pd2L4 construct and print the geometry
from cgbind import Linker, Cage
linker = Linker(smiles='C1(C#CC2=CC=CC(C#CC3=CC=CN=C3)=C2)=CC=CN=C1', arch_name='m2l4')
cage = Cage(linker, metal='Pd')
cage.print_xyz_file()See examples/ and the documentation for further examples.
If you find cgbind useful in your research please consider citing the paper:
T. A. Young, R. Gheorghe and F. Duarte, cgbind: A Python Module and Web App for Automated Metallocage Construction and Host–Guest Characterization. J. Chem. Inf. Model. 2020, 60, 7, 3546–3557. DOI