support mmcif with no b fac and occ

.github/workflows/main.yml

@@ -30,7 +30,7 @@ jobs:
         source activate test
         conda config --add channels conda-forge
         conda install --yes numpy scipy nose requests
-        conda install --yes pdbfixer mdtraj
+        conda install --yes pdbfixer mdtraj openmm
         pip install mmtf-python scikit-learn
         pip install .
         python setup.py build_ext --inplace --force

prody/proteins/ciffile.py

@@ -478,8 +478,10 @@ def _parseMMCIFLines(atomgroup, lines, model, chain, subset,
 
         serials[acount] = line.split()[fields['id']]
         elements[acount] = line.split()[fields['type_symbol']]
-        bfactors[acount] = line.split()[fields['B_iso_or_equiv']]
-        occupancies[acount] = line.split()[fields['occupancy']]
+        if 'B_iso_or_equiv' in fields.keys():
+            bfactors[acount] = line.split()[fields['B_iso_or_equiv']]
+        if 'occupancy' in fields.keys():
+            occupancies[acount] = line.split()[fields['occupancy']]
 
         acount += 1
 

prody/proteins/interactions.py

@@ -13,8 +13,8 @@
 """
 
 __author__ = 'Karolina Mikulska-Ruminska'
-__credits__ = ['James Krieger', 'Karolina Mikulska-Ruminska']
-__email__ = ['[email protected]', '[email protected]']
+__credits__ = ['James Krieger', 'Karolina Mikulska-Ruminska', 'Anupam Banerjee']
+__email__ = ['[email protected]', '[email protected]', '[email protected]']
 
 
 import numpy as np
@@ -4545,7 +4545,14 @@ def buildInteractionMatrixEnergy(self, **kwargs):
         O Keskin, I Bahar and colleagues from [OK98]_ and have RT units.
 
         'CS' is from MD simulations of amino acid pairs from Carlos Simmerling
-        and Gary Wu in the InSty paper (under preparation) and have units of kcal/mol. """
+        and Gary Wu in the [MR25]_ and have units of kcal/mol. 
+
+        .. [MR25] Mikulska-Ruminska K, Krieger JM, Cao X, Banerjee A, Wu G, 
+        Bogetti AT, Zhang F, Simmerling C, Coutsias EA, Bahar I
+        InSty: a new module in ProDy for evaluating the interactions 
+        and stability of proteins
+        *Bioinformatics* **2025** 169009
+        """
 
         import numpy as np
         import matplotlib
@@ -4898,7 +4905,7 @@ def showCumulativeInteractionTypes(self, **kwargs):
         O Keskin, I Bahar and colleagues from [OK98]_ and have RT units.
 
         'CS' is from MD simulations of amino acid pairs from Carlos Simmerling
-        and Gary Wu for the InSty paper (under preparation) and have units kcal/mol.
+        and Gary Wu for [MR25]_ and have units kcal/mol.
         """
 
         import numpy as np