diff --git a/CHANGELOG.md b/CHANGELOG.md index 7398823..d13fd78 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,13 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/). ## [Unreleased] +### Removed +- `geom.is_duplicate_conformer()` and `irmsd` dependency. (Broken `numpy` reference in solved `irmsd` version). +- `Algorithm.IRMSD` conformer-group identity algorithm. + + +### Fixed +- Dependencies listed in `pixi.toml` instead of `pyproject.toml` ## [0.0.22] - 2026-08-28 ### Added diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index b568269..173d51b 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -67,7 +67,7 @@ Conversions are standalone module-level functions, not methods on the Pydantic m ### Current module map -- `automol.geom` — the `Geometry` core model (`core.py`), plus `properties.py` (center of mass, distance matrix/keys, adjacency matrix), `transform.py`, `comparison.py` (e.g. `is_duplicate_conformer`, via `irmsd`), and `view.py` (`View`, 3D visualization, py3Dmol-based). +- `automol.geom` — the `Geometry` core model (`core.py`), plus `properties.py` (center of mass, distance matrix/keys, adjacency matrix), `transform.py`, `comparison.py`, and `view.py` (`View`, 3D visualization, py3Dmol-based). - `automol.rd` — RDKit bridge (`rd/mol.py`) for `Geometry` ↔ RDKit mol conversion. - `automol.ident` — `Algorithm`/`Identity` for InChI/SMILES generation from a `Geometry`. - `automol.utils` — shared low-level helpers: `constants.py`, `types.py`, `exc.py`, `utils/element/`. diff --git a/docs/source/geometry.md b/docs/source/geometry.md index 5b7bc99..295ce77 100644 --- a/docs/source/geometry.md +++ b/docs/source/geometry.md @@ -108,30 +108,6 @@ subset of atoms by index, leaving the rest untouched: geom.transform.translate(water, [1.0, 0.0, 0.0], keys=[0]) # move only atom 0 ``` -## Duplicate conformer detection - -`is_duplicate_conformer` checks whether a `Geometry` is geometrically -identical to any geometry in a list, using -[irmsd](https://pypi.org/project/irmsd/)'s interatomic RMSD after optimal -alignment (translation, rotation, and atom matching) — so a rotated or -translated copy still counts as a match, while a genuinely different -conformer doesn't: - -```python -rotated_water = geom.transform.rotate(water, Rotation.from_euler("z", 60, degrees=True)) -geom.is_duplicate_conformer(water, [rotated_water]) # True - -geom.is_duplicate_conformer(water, []) # False — nothing to compare against -``` - -Candidates with a different atom count are never considered a match. -`rthr` (default `0.125`, matching irmsd's own default) sets the iRMSD -threshold, in Angstroms, below which two geometries count as identical — -lower it for stricter matching: - -```python -geom.is_duplicate_conformer(water, [rotated_water], rthr=1e-6) # stricter -``` ## Next steps diff --git a/pixi.lock b/pixi.lock index ee64a0f..f92179c 100644 --- a/pixi.lock +++ b/pixi.lock @@ -19,100 +19,100 @@ environments: - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-1.2.0-hed03a55_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-bin-1.2.0-hb03c661_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.4-he90730b_1.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.4-h3c89d7e_3.conda - 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shelxfile ; extra == 'all' + requires_python: '>=3.10' - pypi: https://files.pythonhosted.org/packages/dc/76/96b7ffc917962e6f74bff1ec850838796f58bedceac6f610834898af6462/cclib-1.8.1-py3-none-any.whl name: cclib version: 1.8.1 @@ -4673,7 +4918,3 @@ packages: - coverage ; extra == 'test' - pytest-cov ; extra == 'test' requires_python: '>=3.7' -- pypi: https://files.pythonhosted.org/packages/f4/24/2a3e3df732393fed8b3ebf2ec078f05546de641fe1b667ee316ec1dcf3b7/webencodings-0.5.1-py2.py3-none-any.whl - name: webencodings - version: 0.5.1 - sha256: a0af1213f3c2226497a97e2b3aa01a7e4bee4f403f95be16fc9acd2947514a78 diff --git a/pixi.toml b/pixi.toml index f368ea4..2ea717f 100644 --- a/pixi.toml +++ b/pixi.toml @@ -6,8 +6,6 @@ preview = ["pixi-build"] [dependencies] python = ">=3.12,<3.14" automol = { path = "." } -ipython = ">=9.15.0,<10" -pynauty = ">=2.8.8.1,<3" [package] name = "automol" @@ -50,7 +48,6 @@ dev = { features = ["dev", "docs"], solve-group = "default"} [pypi-dependencies] stereomolgraph = ">=0.0.22b0" -irmsd = "==0.1.1" xyzrender = ">=0.3.1, <0.4" [feature.dev.tasks] diff --git a/pyproject.toml b/pyproject.toml index 9b80d9f..b2cf0b9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,15 +7,17 @@ authors = [ ] requires-python = ">= 3.12" dependencies = [ + "ipython>=9.17.1", "numpy>=2.0", "pint>=0.24", "py3dmol>=2.5", "pydantic>=2.5", + "pynauty>=2.8.8.1", "pyparsing>=3.3.2", "rdkit>=2025", "scipy>=1.13", "stereomolgraph>=0.0.22b0", - "irmsd>=0.1.1", + "xyzrender>=0.3.8", ] [build-system] diff --git a/src/automol/geom/__init__.py b/src/automol/geom/__init__.py index c660d56..49fc458 100644 --- a/src/automol/geom/__init__.py +++ b/src/automol/geom/__init__.py @@ -16,7 +16,6 @@ inertia_axes, inertia_moments, inertia_tensor, - is_duplicate_conformer, kabsch_align, mass_weight_vector, normal_mode_projection, @@ -64,7 +63,6 @@ "inertia_moments", "inertia_tensor", "io", - "is_duplicate_conformer", "kabsch_align", "mass_weight_vector", "normal_mode_projection", diff --git a/src/automol/geom/analysis.py b/src/automol/geom/analysis.py index e4760a3..678b1ce 100644 --- a/src/automol/geom/analysis.py +++ b/src/automol/geom/analysis.py @@ -1,11 +1,9 @@ """Geometric, structural, and vibrational analysis of a geometry.""" -from collections.abc import Sequence from itertools import permutations from math import factorial from typing import TYPE_CHECKING, Literal -import irmsd import numpy as np import numpy.typing as npt from pynauty import Graph, autgrp, canon_label @@ -746,50 +744,6 @@ def harmonic_zpv( # Comparison -def is_duplicate_conformer( - geo: "Geometry", - geos: Sequence["Geometry"], - *, - rthr: float = RMSD_THRESHOLD, -) -> list[bool]: - """Check whether a geometry is an identical conformer to one in a list. - - Two geometries are considered identical conformers if, after optimal - alignment (translation, rotation, and atom matching), their interatomic - RMSD is below `rthr`. Candidates with a different atom count are never - considered a match. - - Parameters - ---------- - geo - Geometry to check. - geos - Candidate geometries to compare against. - rthr - iRMSD threshold, in Angstroms, below which two geometries are - considered identical conformers. - - Returns - ------- - List the same length as `geos`, with `True` at each position where `geo` - matches the corresponding candidate, `False` otherwise. - """ - mol = irmsd.Molecule(symbols=geo.symbols, positions=geo.coordinates) - - matches = [] - for candidate in geos: - if len(candidate.symbols) != len(geo.symbols): - matches.append(False) - continue - candidate_mol = irmsd.Molecule( - symbols=candidate.symbols, positions=candidate.coordinates - ) - value, _, _ = irmsd.get_irmsd_molecule(mol, candidate_mol) - matches.append(value <= rthr) - - return matches - - def bond_graph(geo: "Geometry") -> Graph: """Build a pynauty graph representing geo's bond connectivity. diff --git a/tests/test_comparison.py b/tests/test_comparison.py deleted file mode 100644 index 4b844ca..0000000 --- a/tests/test_comparison.py +++ /dev/null @@ -1,56 +0,0 @@ -"""Geometry comparison tests.""" - -from scipy.spatial.transform import Rotation - -from automol import Geometry, geom - - -def test__is_duplicate_conformer_rotated_translated_match(water: Geometry) -> None: - """Test that a rotated and translated copy is recognized as a duplicate.""" - rot = Rotation.from_euler("z", 60, degrees=True) - duplicate = geom.core.rotate(water, rot) - duplicate = geom.core.translate(duplicate, [5.0, 5.0, 5.0]) - - assert all(geom.is_duplicate_conformer(water, [duplicate])) - - -def test__is_duplicate_conformer_different_conformer_no_match(water: Geometry) -> None: - """Test that a geometrically distinct conformer is not a duplicate.""" - stretched = water.model_copy(deep=True) - stretched.coordinates[1] *= 1.5 - - assert not any(geom.is_duplicate_conformer(water, [stretched])) - - -def test__is_duplicate_conformer_different_atom_count_no_match( - water: Geometry, peroxide: Geometry -) -> None: - """Test that a different atom count never counts as a duplicate.""" - assert not any(geom.is_duplicate_conformer(water, [peroxide])) - - -def test__is_duplicate_conformer_mixed_atom_counts_preserves_length( - water: Geometry, peroxide: Geometry -) -> None: - """Test that the result stays aligned with `geos` despite mismatches.""" - rot = Rotation.from_euler("z", 60, degrees=True) - duplicate = geom.core.rotate(water, rot) - duplicate = geom.core.translate(duplicate, [5.0, 5.0, 5.0]) - - matches = geom.is_duplicate_conformer(water, [peroxide, duplicate]) - - assert matches == [False, True] - - -def test__is_duplicate_conformer_empty_list_no_match(water: Geometry) -> None: - """Test that an empty candidate list never matches.""" - assert not any(geom.is_duplicate_conformer(water, [])) - - -def test__is_duplicate_conformer_custom_threshold(water: Geometry) -> None: - """Test that a tighter threshold rejects an otherwise-matching candidate.""" - stretched = water.model_copy(deep=True) - stretched.coordinates[1] *= 1.01 - - assert all(geom.is_duplicate_conformer(water, [stretched], rthr=0.5)) - assert not any(geom.is_duplicate_conformer(water, [stretched], rthr=1e-6))