residue features centered on CB/CA

deeprank/features/BSA.py

@@ -108,8 +108,13 @@ def get_contact_residue_sasa(self,cutoff=8.5):
 
             # define the xyz key : (chain,x,y,z)
             chain = {'A':0,'B':1}[r[0]]
-            xyz = np.mean(self.sql.get('x,y,z',resSeq=r[1],chainID=r[0]),0)
-            xyzkey = tuple([chain]+xyz.tolist())
+
+            atcenter = 'CB'
+            if r[2] == 'GLY':
+                atcenter = 'CA'
+            xyz = self.sql.get('x,y,z',resSeq=r[1],chainID=r[0],name=atcenter)[0]
+            #xyz = np.mean(self.sql.get('x,y,z',resSeq=r[1],chainID=r[0]),0)
+            xyzkey = tuple([chain]+xyz)
 
             # put the data in dict
             self.bsa_data[r]           =  [bsa]

deeprank/features/FullPSSM.py

@@ -140,7 +140,7 @@ def get_feature_value(self,contact_only=True):
         """get the feature value."""
 
         sql = pdb2sql(self.pdbfile)
-        
+
         xyz_info = sql.get('chainID,resSeq,resName',name='CB')
         xyz_info += sql.get('chainID,resSeq,resName',name='CA',resName='GLY')
 

deeprank/features/PSSM_IC.py

@@ -117,7 +117,10 @@ def get_feature_value(self,contact_only=True):
 
         sql = pdb2sql(self.pdbfile)
         xyz_info = sql.get('chainID,resSeq,resName',name='CB')
+        xyz_info += sql.get('chainID,resSeq,resName',name='CA',resName='GLY')
+
         xyz = sql.get('x,y,z',name='CB')
+        xyz += sql.get('x,y,z',name='CA',resName='GLY')
 
         xyz_dict = {}
         for pos,info in zip(xyz,xyz_info):

deeprank/features/ResidueDensity.py

@@ -92,9 +92,15 @@ def extract_features(self):
             # total density in raw format
             self.feature_data['RCD_total'][key] = [res.density['total']]
 
-            # total density in xyz format
+            # get the type of the center
+            atcenter = 'CB'
+            if key[2] == 'GLY':
+                atcenter = 'CA'
+
+            # get the xyz of the center atom
+            xyz = self.sql.get('x,y,z',resSeq=key[1],chainID=key[0],name=atcenter)[0]
+            #xyz = np.mean(self.sql.get('x,y,z',resSeq=key[1],chainID=key[0]),0).tolist()
 
-            xyz = np.mean(self.sql.get('x,y,z',resSeq=key[1],chainID=key[0]),0).tolist()
             xyz_key = tuple([{'A':0,'B':1}[key[0]]] + xyz)
             self.feature_data_xyz['RCD_total'][xyz_key] = [res.density['total']]