Fix for Ryan upload_2

xchem · Dec 4, 2024 · 0a979c1 · 0a979c1
1 parent 0f81ea3
commit 0a979c1
Showing 1 changed file with 6 additions and 8 deletions.
diff --git a/src/xchemalign/utils.py b/src/xchemalign/utils.py
@@ -360,7 +360,6 @@ def gen_mols_from_cif(cif_file):
     :param cif_file: The CIF file to read
     :return: A list of molecules found in the CIF
     """
-    print(cif_file)
     doc = cif.read(str(cif_file))
 
     ligand_blocks = []
@@ -386,14 +385,14 @@ def gen_mols_from_cif(cif_file):
         atom_symbols = block.find_loop('_chem_comp_atom.type_symbol')
         # coordinates are sometimes called "x" and sometimes "model_Cartn_x" etc.
         x = block.find_loop('_chem_comp_atom.x')
-        # if not x:
-        #     x = block.find_loop('_chem_comp_atom.model_Cartn_x')
+        if not x:
+            x = block.find_loop('_chem_comp_atom.model_Cartn_x')
         y = block.find_loop('_chem_comp_atom.y')
-        # if not y:
-        #     y = block.find_loop('_chem_comp_atom.model_Cartn_y')
+        if not y:
+            y = block.find_loop('_chem_comp_atom.model_Cartn_y')
         z = block.find_loop('_chem_comp_atom.z')
-        # if not z:
-        #     z = block.find_loop('_chem_comp_atom.model_Cartn_z')
+        if not z:
+            z = block.find_loop('_chem_comp_atom.model_Cartn_z')
         charges = [0] * len(atom_ids)
         if block.find_loop('_chem_comp_atom.charge'):
             charges = list(block.find_loop('_chem_comp_atom.charge'))
@@ -434,7 +433,6 @@ def gen_mols_from_cif(cif_file):
 
         try:
             for a1, a2, bt in zip(atom1, atom2, bond_type):
-                print([a1, a2, bt])
                 mol.AddBond(
                     atoms[strip_quotes(a1)].GetIntProp('idx'), atoms[strip_quotes(a2)].GetIntProp('idx'), BOND_TYPES[bt]
                 )