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provide a light update of the README.md #42

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provide a light update of the README.md #42

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e9711ce
docs(README.md): ammend appetizing code snippet
nbehrnd Mar 26, 2024
7d65c13
docs(README.md): add cross link to RDKit blog post
nbehrnd Mar 26, 2024
81c3afb
style(README.md): lint lightly the syntax
nbehrnd Mar 26, 2024
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13 changes: 10 additions & 3 deletions README.md
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Original file line number Diff line number Diff line change
@@ -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
Expand All @@ -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`

Expand All @@ -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.
Expand All @@ -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
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