diff --git a/README.md b/README.md index 965e0ad..b585a8c 100644 --- a/README.md +++ b/README.md @@ -1,9 +1,14 @@ # xyz2mol has now been implented in RDKit ``` +from rdkit import Chem +from rdkit.Chem import rdDetermineBonds + raw_mol = Chem.MolFromXYZFile('acetate.xyz') mol = Chem.Mol(raw_mol) rdDetermineBonds.DetermineBonds(mol,charge=-1) + +print(Chem.MolToMolBlock(mol)) ``` # Convert Cartesian coordinates to one or more molecular graphs @@ -21,7 +26,7 @@ DOI: [10.1002/bkcs.10334](http://dx.doi.org/10.1002/bkcs.10334) ## Setup -Depends on `rdkit`, `numpy`, and `networkx`. Easiest to setup via anaconda/conda: +Depends on `rdkit`, `numpy`, and `networkx`. Easiest to setup via anaconda/conda: `conda install -c conda-forge xyz2mol` @@ -36,7 +41,6 @@ and then run the following the the `xyz2mol` folder Note, it is also possible to run the code without the `networkx` dependencies, but is slower. - ## Example usage Read in xyz file and print out the SMILES, but don't incode the chirality. @@ -51,7 +55,10 @@ Read in xyz file with a charge and print out the SMILES xyz2mol.py examples/acetate.xyz --charge -1 -## Dependencies: +For additional examples of application, visit the corresponding post on the +[RDKit blog](https://greglandrum.github.io/rdkit-blog/posts/2022-12-18-introducing-rdDetermineBonds.html) + +## Dependencies rdkit # (version 2019.9.1 or later needed for huckel option) networkx