move urls to dedicated module

haddocking · May 22, 2024 · 66e6948 · 66e6948
1 parent a7454db
commit 66e6948
Show file tree

Hide file tree

Showing 5 changed files with 18 additions and 15 deletions.
diff --git a/src/arctic3d/cli_localise.py b/src/arctic3d/cli_localise.py
@@ -41,27 +41,25 @@
     arctic3d-localise ./example/clustered_interfaces.out \
         --scale=2.0
 """
+
 import argparse
 import os
 import sys
 import time
 from pathlib import Path
 
 from arctic3d import log
-
 from arctic3d.functions import make_request
 from arctic3d.modules.interface import parse_out_partner
 from arctic3d.modules.log import add_log_for_CLI
-from arctic3d.modules.output import (
-    #    create_barplot,
+from arctic3d.modules.output import (  # create_barplot,
     create_barplotly,
     create_output_folder,
     parse_clusters,
     setup_output_folder,
     write_dict,
 )
-
-UNIPROT_API_URL = "https://www.ebi.ac.uk/proteins/api/proteins"
+from arctic3d.modules.url import UNIPROT_API_URL
 
 argument_parser = argparse.ArgumentParser()
 argument_parser.add_argument(

diff --git a/src/arctic3d/modules/interface.py b/src/arctic3d/modules/interface.py
@@ -5,13 +5,10 @@
 import jsonpickle
 
 from arctic3d.functions import make_request
+from arctic3d.modules.url import INTERFACE_URL, LIGAND_URL
 
 log = logging.getLogger("arctic3d.log")
 
-INTERFACE_URL = (
-    "https://www.ebi.ac.uk/pdbe/graph-api/uniprot/interface_residues"
-)
-LIGAND_URL = "https://www.ebi.ac.uk/pdbe/graph-api/uniprot/ligand_sites/"
 # maximum number of interfaces in interface file
 MAX_INTERFACES = 10000
 

diff --git a/src/arctic3d/modules/pdb.py b/src/arctic3d/modules/pdb.py
@@ -15,12 +15,10 @@
 
 from arctic3d.functions import make_request
 from arctic3d.modules.interface_matrix import filter_interfaces
+from arctic3d.modules.url import BESTPDB_URL, PDBE_URL
 
 log = logging.getLogger("arctic3d.log")
 
-BESTPDB_URL = "https://www.ebi.ac.uk/pdbe/graph-api/mappings/best_structures"
-PDBE_URL = "https://www.ebi.ac.uk/pdbe/entry-files/download"
-
 
 def _remove_altloc(lines):
     # the altloc ID is removed in processed altloc lines

diff --git a/src/arctic3d/modules/url.py b/src/arctic3d/modules/url.py
@@ -0,0 +1,7 @@
+UNIPROT_API_URL = "https://www.ebi.ac.uk/proteins/api/proteins"
+INTERFACE_URL = (
+    "https://www.ebi.ac.uk/pdbe/graph-api/uniprot/interface_residues"
+)
+LIGAND_URL = "https://www.ebi.ac.uk/pdbe/graph-api/uniprot/ligand_sites/"
+BESTPDB_URL = "https://www.ebi.ac.uk/pdbe/graph-api/mappings/best_structures"
+PDBE_URL = "https://www.ebi.ac.uk/pdbe/entry-files/download"
diff --git a/tests/test_apis.py b/tests/test_apis.py
@@ -3,9 +3,12 @@
 import pytest
 import requests
 
-from arctic3d.cli_localise import UNIPROT_API_URL
-from arctic3d.modules.interface import LIGAND_URL
-from arctic3d.modules.pdb import BESTPDB_URL, PDBE_URL
+from arctic3d.modules.url import (  # noqa
+    BESTPDB_URL,
+    LIGAND_URL,
+    PDBE_URL,
+    UNIPROT_API_URL,
+)
 
 TARGET_UNIPROT = "P07550"
 TARGET_PDB = "1crn"