From 9e8f0cdc86e453ea0013971ea3f1c0dcee4127e2 Mon Sep 17 00:00:00 2001 From: Jeroen Van Goey Date: Fri, 15 Nov 2024 16:13:48 +0200 Subject: [PATCH] Fix typos in various files --- QUICK_START_GUIDE.md | 2 +- README.md | 2 +- docs/download/download.html | 8 ++++---- docs/seq/nucleotide_sequence.html | 2 +- docs/seq/sequence.html | 6 +++--- notebooks/downloading_data.ipynb | 2 +- protkit/download/download.py | 2 +- protkit/seq/sequence.py | 2 +- 8 files changed, 13 insertions(+), 13 deletions(-) diff --git a/QUICK_START_GUIDE.md b/QUICK_START_GUIDE.md index 0511db2..d5cd4fc 100644 --- a/QUICK_START_GUIDE.md +++ b/QUICK_START_GUIDE.md @@ -618,7 +618,7 @@ for residue in protein.residues: #### Accessing Atoms in a Protein -Similary, the atoms that are part of the protein can be accesses through the `atoms` attribute. +Similarly, the atoms that are part of the protein can be accesses through the `atoms` attribute. For example, to access the coordinates of all the atoms in the protein, you can use the following code: ```python diff --git a/README.md b/README.md index b7d9917..cce4a74 100644 --- a/README.md +++ b/README.md @@ -299,7 +299,7 @@ such infrastructure. ## Contributing to Protkit -Protkit is an open source project and we welcome contributions from the community. If you would like to contribute, please see the [Contibuting](CONTRIBUTING.md) file for details. Please also adhere to the [Code of Conduct](CODE_OF_CONDUCT.md). +Protkit is an open source project and we welcome contributions from the community. If you would like to contribute, please see the [Contributing](CONTRIBUTING.md) file for details. Please also adhere to the [Code of Conduct](CODE_OF_CONDUCT.md). --- diff --git a/docs/download/download.html b/docs/download/download.html index bbec2de..5de6b32 100644 --- a/docs/download/download.html +++ b/docs/download/download.html @@ -389,7 +389,7 @@

Module protkit.download.download

directory: str, n_jobs: int = -1) -> None: """ - Downloads multiple Bianry CIF files from the RCSB. + Downloads multiple Binary CIF files from the RCSB. Args: pdb_ids (List[str]): The IDs of the Binary CIF files. @@ -735,7 +735,7 @@

Classes

directory: str, n_jobs: int = -1) -> None: """ - Downloads multiple Bianry CIF files from the RCSB. + Downloads multiple Binary CIF files from the RCSB. Args: pdb_ids (List[str]): The IDs of the Binary CIF files. @@ -794,7 +794,7 @@

Args

def download_binary_cif_files_from_rcsb(pdb_ids: List[str], directory: str, n_jobs: int = -1) ‑> None
-

Downloads multiple Bianry CIF files from the RCSB.

+

Downloads multiple Binary CIF files from the RCSB.

Args

pdb_ids : List[str]
@@ -817,7 +817,7 @@

Returns

directory: str, n_jobs: int = -1) -> None: """ - Downloads multiple Bianry CIF files from the RCSB. + Downloads multiple Binary CIF files from the RCSB. Args: pdb_ids (List[str]): The IDs of the Binary CIF files. diff --git a/docs/seq/nucleotide_sequence.html b/docs/seq/nucleotide_sequence.html index ab527cc..f811016 100644 --- a/docs/seq/nucleotide_sequence.html +++ b/docs/seq/nucleotide_sequence.html @@ -135,7 +135,7 @@

Returns

Notes

The sequence can be provided as a string or a list of strings. If provided as a string, the string will be converted to a list of strings.

-

A sequence can be respresented by a string of single letters, such as "AGILE", +

A sequence can be represented by a string of single letters, such as "AGILE", or a list of three-letter codes such as ["ALA", "GLY", "ILE", "LEU", "GLU"]. For consistency, the sequence is always represented as a list of codes.

diff --git a/docs/seq/sequence.html b/docs/seq/sequence.html index 70429cb..82c8203 100644 --- a/docs/seq/sequence.html +++ b/docs/seq/sequence.html @@ -80,7 +80,7 @@

Module protkit.seq.sequence

The sequence can be provided as a string or a list of strings. If provided as a string, the string will be converted to a list of strings. - A sequence can be respresented by a string of single letters, such as "AGILE", + A sequence can be represented by a string of single letters, such as "AGILE", or a list of three-letter codes such as ["ALA", "GLY", "ILE", "LEU", "GLU"]. For consistency, the sequence is always represented as a list of codes. """ @@ -280,7 +280,7 @@

Returns

Notes

The sequence can be provided as a string or a list of strings. If provided as a string, the string will be converted to a list of strings.

-

A sequence can be respresented by a string of single letters, such as "AGILE", +

A sequence can be represented by a string of single letters, such as "AGILE", or a list of three-letter codes such as ["ALA", "GLY", "ILE", "LEU", "GLU"]. For consistency, the sequence is always represented as a list of codes.

@@ -307,7 +307,7 @@

Notes

The sequence can be provided as a string or a list of strings. If provided as a string, the string will be converted to a list of strings. - A sequence can be respresented by a string of single letters, such as "AGILE", + A sequence can be represented by a string of single letters, such as "AGILE", or a list of three-letter codes such as ["ALA", "GLY", "ILE", "LEU", "GLU"]. For consistency, the sequence is always represented as a list of codes. """ diff --git a/notebooks/downloading_data.ipynb b/notebooks/downloading_data.ipynb index 4fc17a0..c2dfed4 100644 --- a/notebooks/downloading_data.ipynb +++ b/notebooks/downloading_data.ipynb @@ -135,7 +135,7 @@ { "cell_type": "markdown", "source": [ - "Protkit contains a number of modules organised by the functionality they provide. In this demo, we are interested in downloading and file handling capabilties. To use these, we import the relevant modules and classes." + "Protkit contains a number of modules organised by the functionality they provide. In this demo, we are interested in downloading and file handling capabilities. To use these, we import the relevant modules and classes." ], "metadata": { "id": "k87BmqUVbWU9" diff --git a/protkit/download/download.py b/protkit/download/download.py index 8f67a25..7afef75 100644 --- a/protkit/download/download.py +++ b/protkit/download/download.py @@ -343,7 +343,7 @@ def download_binary_cif_files_from_rcsb( directory: str, n_jobs: int = -1) -> None: """ - Downloads multiple Bianry CIF files from the RCSB. + Downloads multiple Binary CIF files from the RCSB. Args: pdb_ids (List[str]): The IDs of the Binary CIF files. diff --git a/protkit/seq/sequence.py b/protkit/seq/sequence.py index 708eb71..8dc52f6 100644 --- a/protkit/seq/sequence.py +++ b/protkit/seq/sequence.py @@ -43,7 +43,7 @@ def __init__(self, The sequence can be provided as a string or a list of strings. If provided as a string, the string will be converted to a list of strings. - A sequence can be respresented by a string of single letters, such as "AGILE", + A sequence can be represented by a string of single letters, such as "AGILE", or a list of three-letter codes such as ["ALA", "GLY", "ILE", "LEU", "GLU"]. For consistency, the sequence is always represented as a list of codes. """