---
name: conformer-filtering-threshold-selection
description: Use when after RDKit has generated a large ensemble of 3D conformers for a molecule (typically hundreds to thousands), you need to reduce computational burden before quantum-chemical single-point energy evaluation.
license: CC-BY-4.0
metadata:
  edam_operation: http://edamontology.org/operation_3802
  edam_topics:
  - http://edamontology.org/topic_3047
  - http://edamontology.org/topic_0176
  tools:
  - ASE-ANI
  - RDKit
  - QUICK
  - Snakemake
  techniques:
  - ion-mobility-MS
derived_from:
- doi: 10.1021/jasms.1c00315
  title: POMICS
evidence_spans:
- 'ASE-ANI: For conformation filtering'
claims: []
provenance:
  collection: https://w3id.org/holobiomicslab/asb-skill/collection/metabolomics/v2
  assembled_by: scripts/collect_metabolomics_collection.py
  sources:
  - build: coll_pomics_cq
    doi: 10.1021/jasms.1c00315
    title: POMICS
  dedup_kept_from: coll_pomics_cq
schema_version: 0.2.0
attribution:
  generator: AgenticScienceBuilder
  original_doi: 10.1021/jasms.1c00315
  all_source_dois:
  - 10.1021/jasms.1c00315
  zenodo_doi: 10.5281/zenodo.20794027
  curators: []
  promoter: Louis-Félix Nothias
  sponsor: CNRS & Université Côte d'Azur
---

# conformer-filtering-threshold-selection

## Summary

Select energy thresholds and ranking criteria to filter conformer ensembles generated by RDKit, retaining the lowest-energy subset for downstream quantum-chemical calculations in CCS prediction workflows. This skill bridges conformation generation and expensive quantum chemistry by eliminating high-energy states early.

## When to use

After RDKit has generated a large ensemble of 3D conformers for a molecule (typically hundreds to thousands), you need to reduce computational burden before quantum-chemical single-point energy evaluation. Use this skill when the full conformer set exceeds practical limits for QUICK or similar QM software, or when you want to prioritize geometries most likely to contribute to the Boltzmann ensemble at experimental conditions.

## When NOT to use

- The conformer ensemble is already small (< 10–20 geometries) or already filtered by another validated method; neural-network filtering adds overhead without benefit.
- Your molecule contains elements outside CHNO (e.g., halogens, metals); ASE-ANI was trained only on CHNO and will produce unreliable energies.
- Downstream QM calculations are not the bottleneck; if conformer count is manageable, skip filtering to avoid discarding rare but important geometries.

## Inputs

- Conformer ensemble in SDF or XYZ format (generated by RDKit)
- ASE-ANI neural-network potential (pre-trained CHNO model or equivalent)
- Filtering parameters: either target count N or energy window ΔE

## Outputs

- Filtered conformer subset in SDF or XYZ format
- Energy-ranked conformer list (text file with conformer ID, energy, rank)
- Filtered conformer set compatible with downstream quantum-chemical software (QUICK)

## How to apply

Compute single-point energies for all RDKit-generated conformers using a fast neural-network potential (ASE-ANI). Rank conformers by total energy in ascending order. Apply a filtering criterion: either retain the top N lowest-energy conformers (e.g., best 10–50 geometries) or apply an absolute energy threshold (e.g., within ΔE = 10 kcal/mol of the global minimum). The choice between N-based and threshold-based filtering should account for downstream QM budget and the expected energy distribution of your compound class. Export the filtered subset in a format compatible with your quantum-chemistry code (e.g., XYZ or SDF). Verify that retained conformers span diverse geometries (not just minor rotations of one core structure) to capture relevant conformational space.

## Related tools

- **ASE-ANI** (Compute single-point energies for conformer ranking and filtering) — https://github.com/isayev/ASE_ANI
- **RDKit** (Generate initial conformer ensemble before filtering) — https://www.rdkit.org
- **QUICK** (Downstream quantum-chemistry software that receives filtered conformer subset)
- **Snakemake** (Workflow orchestration for automated conformer filtering pipeline) — https://github.com/DasSusanta/snakemake_ccs

## Evaluation signals

- Retained conformer count matches the specified threshold (N or ΔE window); no conformers above the threshold remain.
- Energy distribution of filtered set is monotonically ranked; each retained conformer has lower or equal energy than the next.
- Geometric diversity check: retained conformers represent distinct 3D arrangements (e.g., different rotamer or stereoisomer states), not micro-variations of a single structure.
- File format validation: output XYZ or SDF conforms to specification expected by QUICK or downstream tool; atom count and bond topology are preserved.
- Computational efficiency gain: filtered set size is reduced by at least 50–90% compared to input, demonstrating practical filtering; downstream QM runtime is proportionally reduced.

## Limitations

- ASE-ANI is deprecated and no longer supported; users are advised to migrate to TorchANI (PyTorch implementation) for long-term compatibility and better performance.
- ASE-ANI relies on NVIDIA GPU and CUDA 9.2; older GPUs with compute capability < 5.0 or different CUDA versions are incompatible.
- Element scope: ASE-ANI is trained on CHNO only; conformers containing S, F, Cl, P, or other elements will have unreliable energies and should not be filtered with this tool.
- Neural-network predictions may miss rare, high-energy conformers relevant to specialized applications (e.g., transition states, highly strained intermediates); validation against quantum-chemistry benchmarks is recommended for novel compound classes.
- Threshold selection (N or ΔE) is user-dependent and not automatic; inappropriate choices can either over-filter (eliminating valid geometries) or under-filter (retaining too many for tractable QM).

## Evidence

- [other] Rank conformers by energy and select the lowest-energy subset (retain top N conformers or apply an energy threshold).: "Rank conformers by energy and select the lowest-energy subset (retain top N conformers or apply an energy threshold)."
- [other] Initialize ASE-ANI potential and compute single-point energy for each conformer.: "Initialize ASE-ANI potential and compute single-point energy for each conformer."
- [other] Load conformer structures generated by RDKit in a standard molecular format (e.g., SDF or XYZ).: "Load conformer structures generated by RDKit in a standard molecular format (e.g., SDF or XYZ)."
- [other] Export filtered conformer set in a format compatible with downstream quantum-chemical software (QUICK).: "Export filtered conformer set in a format compatible with downstream quantum-chemical software (QUICK)."
- [readme] DEPRECATED and no longer supported, please use TorchANI implementation: "DEPRECATED and no longer supported, please use TorchANI implementation"
- [readme] Modern NVIDIA GPU, compute capability 5.0 of newer. CUDA 9.2: "Modern NVIDIA GPU, compute capability 5.0 of newer. CUDA 9.2"
- [readme] Current ANI-1x and ANI-1ccx potentials provide predictions for the CHNO elements.: "Current ANI-1x and ANI-1ccx potentials provide predictions for the CHNO elements."