Help with KeyError for Custom Scoring Plugin

[xjtx21]

Hello,

Firstly, I just want to say I love REINVENT and am having a lot of fun with the program.

I am an amateur with computational chemistry, and I'm trying to figure out how to create a custom scoring plugin but am running into some trouble. I would really appreciate some guidance.

1. I tried to copy the general structure of the comp_group_count.py file and adjusted it to calculate the distance between 2 substructures. I called it comp_closeness.py (file at the bottom of the post).
2. I placed comp_closeness.py in the /top/dir/somewhere/reinvent/reinvent_plugins/components directory.
3. I added /top/dir/somewhere/reinvent to the python path with sys.path.insert (I am a little confused why I had to do this because all the other components work).
4. I then added the following block to my config file:

# Closeness between 2 specified SMARTS
[[stage.scoring.component]]
[stage.scoring.component.Closeness]
[[stage.scoring.component.Closeness.endpoint]]
name = "Closeness Distance"
weight = 0.5
params.smarts = "[Cl,n;H1]"

5. I ran reinvent and get the follow error:

Traceback (most recent call last):
  File "/home/jt/anaconda3/envs/reinvent4/bin/reinvent", line 8, in <module>
    sys.exit(main_script())
  File "/home/jt/anaconda3/envs/reinvent4/lib/python3.10/site-packages/reinvent/Reinvent.py", line 195, in main_script
    main(args)
  File "/home/jt/anaconda3/envs/reinvent4/lib/python3.10/site-packages/reinvent/Reinvent.py", line 164, in main
    runner(
  File "/home/jt/anaconda3/envs/reinvent4/lib/python3.10/site-packages/reinvent/runmodes/RL/run_staged_learning.py", line 296, in run_staged_learning
    packages = create_packages(reward_strategy, stages, rdkit_smiles_flags2)
  File "/home/jt/anaconda3/envs/reinvent4/lib/python3.10/site-packages/reinvent/runmodes/RL/run_staged_learning.py", line 157, in create_packages
    scoring_function = Scorer(stage.scoring)
  File "/home/jt/anaconda3/envs/reinvent4/lib/python3.10/site-packages/reinvent/scoring/scorer.py", line 80, in __init__
    self.components = get_components(config.component)
  File "/home/jt/anaconda3/envs/reinvent4/lib/python3.10/site-packages/reinvent/scoring/config.py", line 53, in get_components
    Component, ComponentParams = component_registry[component_type_lookup]
KeyError: 'closeness'
CPU times: user 21.6 ms, sys: 34.2 ms, total: 55.7 ms
Wall time: 4.06 s

Please note, I haven't fully worked out the scoring function, transforms or using molcache in comp_closeness.py yet. I'll get to that once REINVENT can find the component.

Any help is appreciated!

Thanks,
JT

"""
Score the distance between 2 SMARTS patterns
"""

__all__ = ["Closeness"]

from typing import List

from rdkit import Chem
from rdkit.Chem import AllChem
import numpy as np
from pydantic.dataclasses import dataclass

from .component_results import ComponentResults
from reinvent_plugins.mol_cache import molcache
from .add_tag import add_tag

@add_tag("__parameters")
@dataclass
class Parameters:
    """Parameters for the scoring component

    Note that all parameters are always lists because components can have
    multiple endpoints and so all the parameters from each endpoint is
    collected into a list.  This is also true in cases where there is only one
    endpoint.
    """

    smarts: List[str]


@add_tag("__component")
class Closeness:
    def __init__(self, params: Parameters):
        # Parameters could include SMARTS patterns or other settings
        self.patterns = []

        for smarts in params.smarts:
            pattern = Chem.MolFromSmarts(smarts)

            if pattern:
                self.patterns.append(pattern)

        if not self.patterns:
            raise ValueError(f"{__name__}: no valid SMARTS patterns found")
        
        self.number_of_endpoints = len(params.smarts)
    
    @molcache
    def __call__(self, smiles):
        mol = Chem.MolFromSmiles(smiles)
        if mol is None:
            return 0.0, {"error": "Invalid SMILES"}

        mol = Chem.AddHs(mol)  # Add hydrogens if not present
        AllChem.EmbedMolecule(mol)  # Generate 3D conformer

        if mol.HasSubstructMatch(self.pattern1) and mol.HasSubstructMatch(self.pattern2):
            matches1 = mol.GetSubstructMatches(self.pattern1)
            matches2 = mol.GetSubstructMatches(self.pattern2)
            
            min_distance = float('inf')
            for match1 in matches1:
                for match2 in matches2:
                    distance = mol.GetConformer().GetAtomPosition(match1[0]).Distance(mol.GetConformer().GetAtomPosition(match2[0]))
                    min_distance = min(min_distance, distance)
            
            # return min_distance, {"distance": min_distance}
            return ComponentResults(min_distance)
        else:
            return 0.0, {"message": "Molecule does not contain both specified atom types."}