From 6d1490bdc8878ff6342a5581c8bbe1984ff2153b Mon Sep 17 00:00:00 2001 From: Jonathon Vandezande Date: Fri, 14 Nov 2025 07:26:12 -0500 Subject: [PATCH] Fixes typos --- README.md | 4 ++-- prism_pruner/__init__.py | 2 +- prism_pruner/graph_manipulations.py | 4 ++-- prism_pruner/pruner.py | 4 ++-- prism_pruner/rmsd.py | 2 +- prism_pruner/torsion_module.py | 4 ++-- prism_pruner/typing.py | 2 +- prism_pruner/utils.py | 2 +- 8 files changed, 12 insertions(+), 12 deletions(-) diff --git a/README.md b/README.md index 9869834..faa787a 100644 --- a/README.md +++ b/README.md @@ -7,9 +7,9 @@ [![Codecov](https://img.shields.io/codecov/c/github/ntampellini/prism_pruner)](https://codecov.io/gh/ntampellini/prism_pruner) [![PyPI - Version](https://img.shields.io/pypi/v/prism_pruner)](https://pypi.org/project/prism-pruner/) -PRISM (PRuning Interface for Similar Molecules) is the modular similarity pruning code originally from [FIRECODE](https://github.com/ntampellini/FIRECODE/tree/main), in a polished standalone package. It filters out duplicate structures from conformational ensembles, leaving behind non-redundant states. +PRISM (Pruning Interface for Similar Molecules) is the modular similarity pruning code originally from [FIRECODE](https://github.com/ntampellini/FIRECODE/tree/main), in a polished standalone package. It filters out duplicate structures from conformational ensembles, leaving behind non-redundant states. -The code implements a cached, iterative, divide-and conquer approach on increasingly large subsets of the ensemble and removes duplicates as assessed by one of three metrics: +The code implements a cached, iterative, divide-and-conquer approach on increasingly large subsets of the ensemble and removes duplicates as assessed by one of three metrics: - Relative deviation of the moments of inertia on the principal axes - Heavy-atom RMSD and maximum deviation - Rotamer-corrected heavy-atom RMSD and maximum deviation diff --git a/prism_pruner/__init__.py b/prism_pruner/__init__.py index dc65487..319f144 100644 --- a/prism_pruner/__init__.py +++ b/prism_pruner/__init__.py @@ -1 +1 @@ -"""PRISM - PRuning Interface for Similar Molecules.""" +"""PRISM - Pruning Interface for Similar Molecules.""" diff --git a/prism_pruner/graph_manipulations.py b/prism_pruner/graph_manipulations.py index ca50a03..86bac9d 100644 --- a/prism_pruner/graph_manipulations.py +++ b/prism_pruner/graph_manipulations.py @@ -60,7 +60,7 @@ def get_sp_n(index: int, graph: Graph) -> int | None: This is just an assimilation to the carbon geometry in relation to sp^n: - sp¹ is linear - sp² is planar - - sp³ is tetraedral + - sp³ is tetrahedral This is mainly used to understand if a torsion is to be rotated or not. """ atom = graph.nodes[index]["atoms"] @@ -139,7 +139,7 @@ def is_phenyl(coords: Array2D_float) -> bool: Note: quinones evaluate to True - :params coords: six coordinates of C/N atoms + :param coords: six coordinates of C/N atoms :return: bool indicating if the six atoms look like part of a phenyl/naphtyl/pyridine system, coordinates for the center of that ring """ diff --git a/prism_pruner/pruner.py b/prism_pruner/pruner.py index 4a9e235..1978d75 100644 --- a/prism_pruner/pruner.py +++ b/prism_pruner/pruner.py @@ -1,4 +1,4 @@ -"""PRISM - PRuning Interface for Similar Molecules.""" +"""PRISM - Pruning Interface for Similar Molecules.""" from dataclasses import dataclass, field from time import perf_counter @@ -206,7 +206,7 @@ def _main_compute_subrow( Ignores structures that are False (0) in in_mask and does not perform the comparison if the energy difference between the structures is less than self.max_dE. Saves dissimilar structural pairs (i.e. that evaluate to - False (0)) by adding them to self.cache, avoiding redundant calcaulations. + False (0)) by adding them to self.cache, avoiding redundant calculations. """ i1 = first_abs_index diff --git a/prism_pruner/rmsd.py b/prism_pruner/rmsd.py index eca74a7..60fe5b6 100644 --- a/prism_pruner/rmsd.py +++ b/prism_pruner/rmsd.py @@ -1,4 +1,4 @@ -"""PRISM - PRuning Interface for Similar Molecules.""" +"""PRISM - Pruning Interface for Similar Molecules.""" import numpy as np diff --git a/prism_pruner/torsion_module.py b/prism_pruner/torsion_module.py index 88c1bb6..53afdf4 100644 --- a/prism_pruner/torsion_module.py +++ b/prism_pruner/torsion_module.py @@ -1,4 +1,4 @@ -"""PRISM - PRuning Interface for Similar Molecules.""" +"""PRISM - Pruning Interface for Similar Molecules.""" from copy import deepcopy from dataclasses import dataclass @@ -436,7 +436,7 @@ def rotationally_corrected_rmsd_and_max( best_rmsd = locally_corrected_rmsd torsion_corrections[i] = angle - # it is faster to undo the rotation rather than working with a copy of coordss + # it is faster to undo the rotation rather than working with a copy of coords coord = rotate_dihedral(coord, torsion, -angle, indices_to_be_moved=[torsion[3]]) # now rotate that angle to the desired orientation before going to the next angle diff --git a/prism_pruner/typing.py b/prism_pruner/typing.py index efeeea5..8d336ca 100644 --- a/prism_pruner/typing.py +++ b/prism_pruner/typing.py @@ -1,4 +1,4 @@ -"""PRISM - PRuning Interface for Similar Molecules.""" +"""PRISM - Pruning Interface for Similar Molecules.""" from typing import Annotated, Any, Union diff --git a/prism_pruner/utils.py b/prism_pruner/utils.py index 75b8f04..567d573 100644 --- a/prism_pruner/utils.py +++ b/prism_pruner/utils.py @@ -1,4 +1,4 @@ -"""PRISM - PRuning Interface for Similar Molecules.""" +"""PRISM - Pruning Interface for Similar Molecules.""" from typing import Any, Sequence