Merge branch 'patch'

.gitignore

@@ -4,3 +4,4 @@ examples/*
 .vscode/*
 .pytest_cache/*
 .mypy_cache
+arpeggio.egg-info

arpeggio/core/interactions.py

@@ -1226,9 +1226,6 @@ def __calculate_group_group_contacts(self):
                 if amide_key == amide_key2:
                     continue
 
-                if amide_key == 441 and amide2 == 442:
-                    print('foo')
-
                 # CHECK RING IS INVOLVED WITH THE SELECTION OR BINDING SITE
                 if amide_key2 not in self.selection_plus_amide_ids:
                     continue

arpeggio/core/protein_reader.py

@@ -8,7 +8,7 @@
 import numpy
 from Bio import PDB
 from Bio.PDB.StructureBuilder import StructureBuilder
-from mmCif.mmcifIO import MMCIF2Dict
+from pdbecif.mmcif_io import MMCIF2Dict
 import openbabel as ob
 
 

arpeggio/scripts/process_protein_cli.py

@@ -144,3 +144,7 @@ def _parse_selection(args):
     else:
         logger.warning(f'No selection was perceived. Defaults into full structure!!')
     return selection
+
+
+if __name__ == "__main__":
+    main()

setup.py

@@ -31,8 +31,10 @@
     ],
     zip_safe=False,
     include_package_data=True,
-    install_requires=["pdbecif", "numpy", "biopython"],
-    tests_require=["pytest"],
+    install_requires=["pdbecif>=1.5", "numpy", "biopython"],
+    extras_require={
+        "tests": ["pytest", "pytest-cov"]
+    },
     entry_points={
         "console_scripts": ["arpeggio=arpeggio.scripts.process_protein_cli:main"]
     },