Merge pull request #13 from jevandezande/typos

Fixes typos

Author: ntampellini

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

prism_pruner/__init__.py

@@ -1 +1 @@
-"""PRISM - PRuning Interface for Similar Molecules."""
+"""PRISM - Pruning Interface for Similar Molecules."""

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
     """

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
 

prism_pruner/rmsd.py

@@ -1,4 +1,4 @@
-"""PRISM - PRuning Interface for Similar Molecules."""
+"""PRISM - Pruning Interface for Similar Molecules."""
 
 import numpy as np
 

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

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
 

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