Fix

lcmd-epfl · Jun 2, 2024 · d05e956 · d05e956
1 parent 42c39d3
commit d05e956
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Showing 3 changed files with 14 additions and 33 deletions.
diff --git a/cell2mol/new_cell_reconstruction.py b/cell2mol/new_cell_reconstruction.py
@@ -595,29 +595,27 @@ def reconstuct (refcell, newcell, sym_ops, debug: int=0):
     print("reconstructed_molecules", len(reconstructed_molecules), [mol.formula for mol in reconstructed_molecules])
 
     if len(all_found) == len(cell_pos):
+        newcell.error_get_fragments = False
         num_rem_frags = 0
         for rem_frag_list in remaining_fragments:
             num_rem_frags += len(rem_frag_list) 
 
         if num_rem_frags == 0 :
             print("All fragments are reconstructed successfully")
-            newcell.is_fragmented = False
             newcell.error_reconstruction = False
         else:
             print(f"There are {num_rem_frags} remaining fragments.")
             final_remaining_fragments, reconstructed_molecules = final_remaining_reconstruction(remaining_fragments, newcell, cell_vector, reconstructed_molecules, debug=0)
             if len(final_remaining_fragments) == 0:
                 print("All fragments are reconstructed successfully")
-                newcell.is_fragmented = False
                 newcell.error_reconstruction = False
             else :
                 print("Error in reconstruction!!")
-                newcell.is_fragmented = True
                 newcell.error_reconstruction = True
                 print("final remaining fragments", len(final_remaining_fragments), [mol.formula for mol in final_remaining_fragments])    
     else:
-        print("Error in reconstruction!!")
-        newcell.is_fragmented = True
+        print("Error in getting fragments and reconstruction!!")
+        newcell.error_get_fragments = True
         newcell.error_reconstruction = True          
         for i, pos in enumerate(cell_pos):
             if i not in all_found:

diff --git a/cell2mol/read_write.py b/cell2mol/read_write.py
@@ -379,7 +379,7 @@ def parse_formula_with_quantity(formula: str):
 ######################################################
 def print_output(moleclist):
 
-    print(moleclist[0].refcode)
+    print(moleclist[0].get_parent("reference").name)
     for idx, mol in enumerate(moleclist):
         if mol.iscomplex:
             if hasattr(mol, "totcharge") and hasattr(mol, "spin"):

diff --git a/cell2mol/test/check_Cell_object.ipynb b/cell2mol/test/check_Cell_object.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 30,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [
     {
@@ -11,7 +11,7 @@
        "'2023.09.6'"
       ]
      },
-     "execution_count": 30,
+     "execution_count": 1,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -31,7 +31,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [
     {
@@ -48,50 +48,33 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 42,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
-    "name = \"ZURVIR\"\n",
+    "name = \"ACEYOW\"\n",
     "refcell = np.load(f\"{name}/Ref_Cell_{name}.cell\", allow_pickle=True)\n",
-    "# cell = np.load(f\"{name}/Cell_{name}.cell\", allow_pickle=True)"
+    "cell = np.load(f\"{name}/Cell_{name}.cell\", allow_pickle=True)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 45,
+   "execution_count": 17,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "------------- Cell2mol CELL Object ----------------\n",
-       " Version               = 2.0\n",
-       " Type                  = cell\n",
-       " Sub-Type              = reference\n",
-       " Name (Refcode)        = ZURVIR\n",
-       " Num Atoms             = 167\n",
-       " Cell Parameters a:c   = [20.504, 12.347, 22.524]\n",
-       " Cell Parameters al:ga = [90.0, 94.56, 90.0]\n",
-       "---------------------------------------------------\n",
-       " # of Ref Molecules:   = 7\n",
-       " With Formulae:                                  \n",
-       "    0: H8-C4-O \n",
-       "    1: H8-C4-O \n",
-       "    2: H8-C4-O \n",
-       "    3: H8-C4-O \n",
-       "    4: H64-C44-N4-Cr \n",
-       "    5: Li \n",
-       "    6: Li "
+       "'ACEYOW'"
       ]
      },
-     "execution_count": 45,
+     "execution_count": 17,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
-    "refcell"
+    "refcell.refmoleclist[0].get_parent(\"reference\").name"
    ]
   },
   {