Merge 60d4197 into 4026caf

deeprank/features/FullPSSM.py

@@ -140,8 +140,12 @@ 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')
+
         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/tools/pdb2sql.py

@@ -381,6 +381,10 @@ def get(self,atnames,**kwargs):
 
             # check that all the keys exists
             for k in keys:
+
+                if k.startswith('no_'):
+                    k = k[3:]
+
                 try:
                     self.c.execute("SELECT EXISTS(SELECT {an} FROM ATOM)".format(an=k))
                 except:
@@ -396,6 +400,14 @@ def get(self,atnames,**kwargs):
             # iterate through the kwargs
             for ik,(k,v) in enumerate(kwargs.items()):
 
+
+                # deals with negative conditions
+                if k.startswith('no_'):
+                    k = k[3:]
+                    neg = ' NOT'
+                else:
+                    neg = ''
+
                 # get if we have an array or a scalar
                 # and build the value tuple for the sql query
                 # deal with the indexing issue if rowID is required
@@ -438,7 +450,7 @@ def get(self,atnames,**kwargs):
                         vals = vals + (v,)
 
                 # create the condition for that key
-                conditions.append(k + ' in (' + ','.join('?'*nv) + ')')
+                conditions.append(k + neg + ' in (' + ','.join('?'*nv) + ')')
 
             # stitch the conditions and append to the query
             query += ' AND '.join(conditions)

test/test_generate.py

@@ -98,7 +98,7 @@ def test_4_add_feature(self):
         for h5 in self.h5file:
 
             #init the data assembler
-            database = DataGenerator(pdb_source=None,pdb_native=None,data_augmentation=None,
+            database = DataGenerator(pdb_source=None, pdb_native=None, data_augmentation=None,
                                      pssm_source='./1AK4/pssm_new/',
                                      compute_features  = ['deeprank.features.FullPSSM'], hdf5=h5)
 

test/test_learn.py

@@ -177,7 +177,8 @@ def test_learn_2d_reg():
               select_feature={'AtomicDensities_ind' : 'all',
                               'Feature_ind' : ['coulomb','vdwaals','charge','PSSM_*'] },
                               select_target='DOCKQ',tqdm=True,
-                              normalize_features = True, normalize_targets=True,
+                              normalize_features = True, 
+                              normalize_targets=True,
                               clip_features=False,
                               pair_chain_feature=np.add,
                               dict_filter={'IRMSD':'<4. or >10.'})
@@ -222,7 +223,7 @@ def test_transfer():
 
 if __name__ == "__main__":
 
-  TestLearn.test_learn_3d_reg_mapfly()
+  #TestLearn.test_learn_3d_reg_mapfly()
   #TestLearn.test_learn_3d_reg()
   TestLearn.test_learn_3d_class()
   #TestLearn.test_learn_2d_reg()