Merge pull request #62 from jmp1985/main

Updated links from alan turing institute to ccpem

Author: James Parkhurst

CONTRIBUTING.md

@@ -29,20 +29,20 @@ All types of contributions are encouraged and valued. See the [Table of Contents
 ## Code of Conduct
 
 This project and everyone participating in it is governed by the
-[profet Code of Conduct](https://github.com/alan-turing-institute/profetblob/master/CODE_OF_CONDUCT.md).
+[profet Code of Conduct](https://github.com/ccpem/profetblob/master/CODE_OF_CONDUCT.md).
 By participating, you are expected to uphold this code. Please report unacceptable behavior
 to <>.
 
 
 ## I Have a Question
 
-> If you want to ask a question, we assume that you have read the available [Documentation](https://github.com/alan-turing-institute/profet).
+> If you want to ask a question, we assume that you have read the available [Documentation](https://github.com/ccpem/profet).
 
-Before you ask a question, it is best to search for existing [Issues](https://github.com/alan-turing-institute/profet/issues) that might help you. In case you have found a suitable issue and still need clarification, you can write your question in this issue. It is also advisable to search the internet for answers first.
+Before you ask a question, it is best to search for existing [Issues](https://github.com/ccpem/profet/issues) that might help you. In case you have found a suitable issue and still need clarification, you can write your question in this issue. It is also advisable to search the internet for answers first.
 
 If you then still feel the need to ask a question and need clarification, we recommend the following:
 
-- Open an [Issue](https://github.com/alan-turing-institute/profet/issues/new).
+- Open an [Issue](https://github.com/ccpem/profet/issues/new).
 - Provide as much context as you can about what you're running into.
 - Provide project and platform versions (nodejs, npm, etc), depending on what seems relevant.
 
@@ -61,8 +61,8 @@ We will then take care of the issue as soon as possible.
 A good bug report shouldn't leave others needing to chase you up for more information. Therefore, we ask you to investigate carefully, collect information and describe the issue in detail in your report. Please complete the following steps in advance to help us fix any potential bug as fast as possible.
 
 - Make sure that you are using the latest version.
-- Determine if your bug is really a bug and not an error on your side e.g. using incompatible environment components/versions (Make sure that you have read the [documentation](https://github.com/alan-turing-institute/profet). If you are looking for support, you might want to check [this section](#i-have-a-question)).
-- To see if other users have experienced (and potentially already solved) the same issue you are having, check if there is not already a bug report existing for your bug or error in the [bug tracker](https://github.com/alan-turing-institute/profetissues?q=label%3Abug).
+- Determine if your bug is really a bug and not an error on your side e.g. using incompatible environment components/versions (Make sure that you have read the [documentation](https://github.com/ccpem/profet). If you are looking for support, you might want to check [this section](#i-have-a-question)).
+- To see if other users have experienced (and potentially already solved) the same issue you are having, check if there is not already a bug report existing for your bug or error in the [bug tracker](https://github.com/ccpem/profetissues?q=label%3Abug).
 - Also make sure to search the internet (including Stack Overflow) to see if users outside of the GitHub community have discussed the issue.
 - Collect information about the bug:
   - Stack trace (Traceback)
@@ -76,7 +76,7 @@ A good bug report shouldn't leave others needing to chase you up for more inform
 
 We use GitHub issues to track bugs and errors. If you run into an issue with the project:
 
-- Open an [Issue](https://github.com/alan-turing-institute/profet/issues/new). (Since we can't be sure at this point whether it is a bug or not, we ask you not to talk about a bug yet and not to label the issue.)
+- Open an [Issue](https://github.com/ccpem/profet/issues/new). (Since we can't be sure at this point whether it is a bug or not, we ask you not to talk about a bug yet and not to label the issue.)
 - Explain the behavior you would expect and the actual behavior.
 - Please provide as much context as possible and describe the *reproduction steps* that someone else can follow to recreate the issue on their own. This usually includes your code. For good bug reports you should isolate the problem and create a reduced test case.
 - Provide the information you collected in the previous section.
@@ -95,14 +95,14 @@ This section guides you through submitting an enhancement suggestion for profet,
 #### Before Submitting an Enhancement
 
 - Make sure that you are using the latest version.
-- Read the [documentation](https://github.com/alan-turing-institute/profet) carefully and find out if the functionality is already covered.
-- Perform a [search](https://github.com/alan-turing-institute/profet/issues) to see if the enhancement has already been suggested. If it has, add a comment to the existing issue instead of opening a new one.
+- Read the [documentation](https://github.com/ccpem/profet) carefully and find out if the functionality is already covered.
+- Perform a [search](https://github.com/ccpem/profet/issues) to see if the enhancement has already been suggested. If it has, add a comment to the existing issue instead of opening a new one.
 - Find out whether your idea fits with the scope and aims of the project. It's up to you to make a strong case to convince the project's developers of the merits of this feature. Keep in mind that we want features that will be useful to the majority of our users and not just a small subset. If you're just targeting a minority of users, consider writing an add-on/plugin library.
 
 <!-- omit in toc -->
 #### How Do I Submit a Good Enhancement Suggestion?
 
-Enhancement suggestions are tracked as [GitHub issues](https://github.com/alan-turing-institute/profet/issues).
+Enhancement suggestions are tracked as [GitHub issues](https://github.com/ccpem/profet/issues).
 
 - Use a **clear and descriptive title** for the issue to identify the suggestion.
 - Provide a **step-by-step description of the suggested enhancement** in as many details as possible.

README.md

@@ -5,9 +5,9 @@ A Python 3  **pro**tein structure **fet**cher. Retrieves the cif or pdb files fr
 [![PyPI version shields.io](https://img.shields.io/pypi/v/profet.svg)](https://pypi.python.org/pypi/profet/)
 [![PyPI pyversions](https://img.shields.io/pypi/pyversions/profet.svg)](https://pypi.python.org/pypi/profet/)
 
-[![Building](https://github.com/alan-turing-institute/profet/actions/workflows/python-package.yml/badge.svg)](https://github.com/alan-turing-institute/profet/actions/workflows/python-package.yml)
-[![Publishing](https://github.com/alan-turing-institute/profet/actions/workflows/python-publish.yml/badge.svg)](https://github.com/alan-turing-institute/profet/actions/workflows/python-publish.yml)
-[![Documentation](https://github.com/alan-turing-institute/profet/actions/workflows/sphinx.yml/badge.svg)](https://github.com/alan-turing-institute/profet/actions/workflows/sphinx.yml)
+[![Building](https://github.com/ccpem/profet/actions/workflows/python-package.yml/badge.svg)](https://github.com/ccpem/profet/actions/workflows/python-package.yml)
+[![Publishing](https://github.com/ccpem/profet/actions/workflows/python-publish.yml/badge.svg)](https://github.com/ccpem/profet/actions/workflows/python-publish.yml)
+[![Documentation](https://github.com/ccpem/profet/actions/workflows/sphinx.yml/badge.svg)](https://github.com/ccpem/profet/actions/workflows/sphinx.yml)
 
 ## Dependencies
 
@@ -38,7 +38,7 @@ pip install profet
 To install the development version, which contains the latest features and fixes, install directly from GitHub using:
 
 ```sh
-pip install git+git://github.com/alan-turing-institute/profet
+pip install git+git://github.com/ccpem/profet
 ```
 
 To test the installation, you need to have pytest and pytest-cov packagages installed which can be done as follows.
@@ -128,11 +128,11 @@ a .pdb file. The file will be cached in the "~/.pdb" directory for future use.
 
 ## Documentation
 
-You can find more documentation including a description of the python api [here](https://alan-turing-institute.github.io/profet/).
+You can find more documentation including a description of the python api [here](https://ccpem.github.io/profet/).
 
 ## Issues and Feature Requests
 
-If you run into an issue, or if you find a workaround for an existing issue, we would very much appreciate it if you could post your question or code as a [GitHub issue](https://github.com/alan-turing-institute/profet/issues). 
+If you run into an issue, or if you find a workaround for an existing issue, we would very much appreciate it if you could post your question or code as a [GitHub issue](https://github.com/ccpem/profet/issues). 
 
 ## Contributions
 

docs/source/installation.rst

@@ -12,7 +12,7 @@ fixes, install directly from GitHub using:
 
 .. code-block:: bash
 
-  pip install git+git://github.com/alan-turing-institute/profet`
+  pip install git+git://github.com/ccpem/profet`
 
 Test the installation, navigate to the root directory and run
 

profet/alphafold.py

@@ -9,6 +9,7 @@
 from requests_html import HTMLSession
 import requests
 from bs4 import BeautifulSoup
+from .enums import FileType
 
 
 class Alphafold_DB:
@@ -40,11 +41,13 @@ def check_structure(self, uniprot_id: str) -> bool:
 
         """
         uniprot_id = uniprot_id.upper()
-        url = self.make_url(uniprot_id, "pdb")
+        url = self.make_url(uniprot_id, FileType.pdb)
         r = requests.get(url)
         return r.status_code != 404
 
-    def get_file_url(self, uniprot_id: str, filetype: str = "cif") -> str:
+    def get_file_url(
+        self, uniprot_id: str, filetype: FileType = FileType.cif
+    ) -> str:
         """
         Get file url relative to an id from the the Alphafold entry page
 
@@ -56,6 +59,7 @@ def get_file_url(self, uniprot_id: str, filetype: str = "cif") -> str:
             The URL of the file to download
 
         """
+        filetype = FileType(filetype)
 
         # Do we recognise the filetpye, otherwise raise an exception.
         if filetype in ["pdb", "cif"]:
@@ -77,7 +81,9 @@ def get_file_url(self, uniprot_id: str, filetype: str = "cif") -> str:
         # Return the URL
         return url["href"]
 
-    def make_url(self, uniprot_id: str, filetype: str = "cif") -> str:
+    def make_url(
+        self, uniprot_id: str, filetype: FileType = FileType.cif
+    ) -> str:
         """
         Make the URL for the protein
 
@@ -89,6 +95,7 @@ def make_url(self, uniprot_id: str, filetype: str = "cif") -> str:
             The URL of the file to download
 
         """
+        filetype = FileType(filetype)
 
         uniprot_id = uniprot_id.upper()
         af_id = "AF-" + uniprot_id + "-F1"
@@ -101,15 +108,15 @@ def make_url(self, uniprot_id: str, filetype: str = "cif") -> str:
             + "-model_v"
             + str(version)
             + "."
-            + filetype
+            + filetype.name
         )
 
         return url
 
     def get_pdb(
         self,
         uniprot_id: str,
-        filetype: str = "cif",
+        filetype: FileType = FileType.cif,
     ) -> tuple:
         """
         Returns pdb/cif as strings, saves to file if requested.
@@ -123,6 +130,7 @@ def get_pdb(
             Tuple containing the filename and file from the database
 
         """
+        filetype = FileType(filetype)
         # af_id = self.df.loc[self.df['Uniprot_ID'] == uniprot_id.upper()]["AF_ID"].to_numpy()[0]
         # version = self.df.loc[self.df['Uniprot_ID'] == uniprot_id.upper()]["version"].to_numpy()[0]
         # af_id = "AF-"+uniprot_id+"-F1"

profet/cache.py

@@ -1,5 +1,6 @@
 import json
 import os
+from .enums import FileType
 
 
 class PDBFileCache(object):
@@ -35,7 +36,7 @@ def __init__(self, directory: str = None):
         # The manifest filename
         self.manifest = os.path.join(self.directory, "manifest.txt")
 
-    def path(self, uniprot_id: str, filetype: str = "cif") -> str:
+    def path(self, uniprot_id: str, filetype: FileType = FileType.cif) -> str:
         """
         Get the proposed path
 
@@ -47,6 +48,7 @@ def path(self, uniprot_id: str, filetype: str = "cif") -> str:
             The absolute path
 
         """
+        filetype = FileType(filetype)
         assert filetype in ["pdb", "cif"]
         return os.path.join(self.directory, uniprot_id.lower()) + "." + filetype
 
@@ -64,7 +66,7 @@ def find(self, uniprot_id: str) -> list:
         return [
             filename
             for filename in [
-                self.path(uniprot_id, filetype) for filetype in ["pdb", "cif"]
+                self.path(uniprot_id, filetype) for filetype in FileType
             ]
             if os.path.exists(filename)
         ]
@@ -137,7 +139,11 @@ def items(self):
                 yield uniprot_id, self.path(uniprot_id, filetype[1:])
 
     def _update_manifest(
-        self, uniprot_id: str, fileorigin: str, filetype: str, filename: str
+        self,
+        uniprot_id: str,
+        fileorigin: str,
+        filetype: FileType,
+        filename: str,
     ):
         """
         Update the manifest file
@@ -149,6 +155,7 @@ def _update_manifest(
             filename: The filename
 
         """
+        filetype = FileType(filetype)
 
         # Read the current manifest
         if os.path.exists(self.manifest):

profet/enums.py

@@ -0,0 +1,6 @@
+from enum import Enum
+
+
+class FileType(str, Enum):
+    pdb = "pdb"
+    cif = "cif"

profet/pdb.py

@@ -1,5 +1,6 @@
 from urllib.request import urlretrieve
 from rcsbapi.search import TextQuery
+from .enums import FileType
 
 
 class PDB_DB:
@@ -50,7 +51,9 @@ def check_structure(self, uniprot_id: str) -> bool:
             return True
         return False
 
-    def make_url(self, uniprot_id: str, filetype: str = "pdb") -> str:
+    def make_url(
+        self, uniprot_id: str, filetype: FileType = FileType.pdb
+    ) -> str:
         """
         Make the URL for the protein
 
@@ -63,14 +66,15 @@ def make_url(self, uniprot_id: str, filetype: str = "pdb") -> str:
 
         """
 
+        filetype = FileType(filetype)
         uniprot_id = uniprot_id.upper()
-        url = f"https://files.rcsb.org/download/{uniprot_id}.{filetype}"
+        url = f"https://files.rcsb.org/download/{uniprot_id}.{filetype.name}"
         return url
 
     def get_pdb(
         self,
         uniprot_id: str,
-        filetype: str = "cif",
+        filetype: FileType = FileType.cif,
     ) -> tuple:
         """
         Returns pdb/cif as strings, saves to file if requested
@@ -84,6 +88,7 @@ def get_pdb(
 
         """
 
+        filetype = FileType(filetype)
         if not self.results:
             self.results = [self.uniprot_id_to_pdb_id(uniprot_id)]
 
@@ -97,9 +102,9 @@ def get_pdb(
                 filedata = file.read()
         except Exception:
             if filetype == "pdb":
-                filetype = "cif"
+                filetype = FileType.cif
             else:
-                filetype = "pdb"
+                filetype = FileType.pdb
             url = self.make_url(pdb_id, filetype)
             filename, result = urlretrieve(url)
             with open(filename) as file:

profet/profet.py

@@ -2,6 +2,7 @@
 from .pdb import PDB_DB
 from .cache import PDBFileCache
 from .cleaver import Cleaver
+from .enums import FileType
 import os
 
 
@@ -54,7 +55,7 @@ def cache(self) -> PDBFileCache:
     def file_from_db(
         self,
         prot_id: str,
-        filetype: str = "cif",
+        filetype: FileType = FileType.cif,
         db: str = "pdb",
     ) -> tuple:
         """
@@ -69,14 +70,15 @@ def file_from_db(
             Tuple containing the filename and file from the database
 
         """
+        filetype = FileType(filetype)
         return {"pdb": self.pdb.get_pdb, "alphafold": self.alpha.get_pdb}[db](
             prot_id, filetype=filetype
         )
 
     def get_file(
         self,
         uniprot_id: str,
-        filetype: str = "cif",
+        filetype: FileType = FileType.cif,
         filesave: bool = False,
         db: str = "pdb",
     ) -> tuple:
@@ -96,6 +98,7 @@ def get_file(
             2. File from the database, or None if it is not available in any database.
 
         """
+        filetype = FileType(filetype)
 
         # Get the PDB cache
         cache = PDBFileCache(directory=self.save_directory)
@@ -211,7 +214,7 @@ def remove(
         """
         # Get the PDB cache
         cache = PDBFileCache(directory=self.save_directory)
-        identifier, _, _ = self.pdb.get_pdb(uniprot_id, filetype="cif")
+        identifier, _, _ = self.pdb.get_pdb(uniprot_id, filetype=FileType.cif)
         if uniprot_id in cache:
             filename = cache[uniprot_id]
             signal_list = self.Cleaver.signal_residuenumbers_requester(