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github.com/bioinf-jku/FCD @v1.2.1

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repository ↗ · DeepWiki ↗ · release v1.2.1 ↗ · + Follow
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README

Fréchet ChemNet Distance

PyPI Tests (master) Tests (dev) PyPI - Downloads GitHub release (latest by date) GitHub release date GitHub

Code for the paper "Fréchet ChemNet Distance: A Metric for Generative Models for Molecules in Drug Discovery" JCIM / ArXiv

Installation

You can install the FCD using

pip install fcd

Requirements

numpy
torch
scipy
rdkit

Updates

Version 1.1 changes

  • Got rid of unneeded imports
  • load_ref_model doesn't need an argument any more to load a model.
  • canonical and canonical_smiles now return None for invalid smiles.
  • Added get_fcd as a quick way to get a the fcd score from two lists of smiles.

Version 1.2 changes

  • Ported the package to pytorch with the help of https://github.com/insilicomedicine/fcd_torch
  • pytorch allows a lighter package and is more popular than Tensorflow which saves an additional install

Core symbols most depended-on inside this repo

get_fcd
called by 4
fcd/fcd.py
get_one_hot
called by 3
fcd/utils.py
get_predictions
called by 2
fcd/fcd.py
tokenize
called by 1
fcd/utils.py
load_imported_model
called by 1
fcd/utils.py
calculate_frechet_distance
called by 1
fcd/utils.py
todevice
called by 1
fcd/utils.py
load_ref_model
called by 1
fcd/fcd.py

Shape

Method 21
Function 10
Class 8

Languages

Python100%

Modules by API surface

fcd/torch_layers.py13 symbols
test/test_fcd.py12 symbols
fcd/utils.py11 symbols
fcd/fcd.py3 symbols

For agents

$ claude mcp add FCD \
  -- python -m otcore.mcp_server <graph>

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