From 21cb8d273b7678fe71b16a89b5a815687f077fbc Mon Sep 17 00:00:00 2001
From: Diego Prada-Gracia <prada.gracia@gmail.com>
Date: Wed, 1 May 2024 21:38:30 -0600
Subject: [PATCH] In process

---
 molsysmt/build/add_missing_bonds.py |    4 +-
 molsysmt/build/get_missing_bonds.py |   15 +-
 sandbox/Tests.ipynb                 | 1057 +--------------------------
 3 files changed, 53 insertions(+), 1023 deletions(-)

diff --git a/molsysmt/build/add_missing_bonds.py b/molsysmt/build/add_missing_bonds.py
index b6edbfe31..ddccbc4b7 100644
--- a/molsysmt/build/add_missing_bonds.py
+++ b/molsysmt/build/add_missing_bonds.py
@@ -5,8 +5,7 @@
 @digest()
 def add_missing_bonds(molecular_system, threshold='2 angstroms', selection='all',
                       structure_indices=0, syntax='MolSysMT', engine='MolSysMT',
-                      with_templates=True, with_distances=True, in_place=True,
-                      skip_digestion=False):
+                      in_place=True, skip_digestion=False):
     """
     To be written soon...
     """
@@ -18,7 +17,6 @@ def add_missing_bonds(molecular_system, threshold='2 angstroms', selection='all'
 
         bonds = get_missing_bonds(molecular_system, threshold=threshold, selection=selection,
                                  structure_indices=structure_indices, syntax=syntax,
-                                 with_templates=with_templates, with_distances=with_distances,
                                  skip_digestion=True)
 
         return add_bonds(molecular_system, bonds, in_place=in_place, skip_digestion=True)
diff --git a/molsysmt/build/get_missing_bonds.py b/molsysmt/build/get_missing_bonds.py
index fcab77161..6d277bfd5 100644
--- a/molsysmt/build/get_missing_bonds.py
+++ b/molsysmt/build/get_missing_bonds.py
@@ -44,6 +44,8 @@ def get_missing_bonds(molecular_system, threshold='2 angstroms', selection='all'
         from molsysmt.element.group.small_molecule import get_bonded_atom_pairs as _bonds_in_small_molecule
         from molsysmt.element.group.terminal_capping import is_n_terminal_capping, is_c_terminal_capping
 
+        old_bonds = get(molecular_system, bonded_atom_pairs=True)
+
         aux_lists = get(molecular_system, element='group', selection=selection, group_name=True,
                         group_type=True, atom_index=True, atom_name=True,
                         skip_digestion=True)
@@ -149,6 +151,15 @@ def get_missing_bonds(molecular_system, threshold='2 angstroms', selection='all'
                     tmp_bonds += bond
             bonds = tmp_bonds
 
+
+        if old_bonds:
+
+            tmp_bonds = []
+            for ii in bonds:
+                if ii not in old_bonds:
+                    tmp_bonds.append(ii)
+            bonds = tmp_bonds
+
     elif engine=="pytraj":
 
         from molsysmt.basic import convert, get
@@ -182,8 +193,8 @@ def get_missing_bonds(molecular_system, threshold='2 angstroms', selection='all'
 
         raise NotImplementedMethodError
 
-    #if sorted:
-    #    bonds = _sorted(bonds)
+    if sorted:
+        bonds = _sorted(bonds)
 
     return bonds
 
diff --git a/sandbox/Tests.ipynb b/sandbox/Tests.ipynb
index ae3a9ed51..23af50901 100644
--- a/sandbox/Tests.ipynb
+++ b/sandbox/Tests.ipynb
@@ -28,7 +28,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "926c78f156bf4fd4b078c84b1c7466ba",
+       "model_id": "ee91a13b16be4b1b84d6f8951102a2c7",
        "version_major": 2,
        "version_minor": 0
       },
@@ -76,26 +76,16 @@
   {
    "cell_type": "code",
    "execution_count": 6,
-   "id": "9dc3125c-8c88-458a-839d-8e1fb5f08a94",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "msm.build.remove_bonds(molsys)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 7,
-   "id": "0f2e011a-e04a-4eab-98f1-df632c2cc111",
+   "id": "b0c4ea1d-d076-42e1-8259-5c22d52bf775",
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "0"
+       "2645"
       ]
      },
-     "execution_count": 7,
+     "execution_count": 6,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -104,14 +94,34 @@
     "msm.get(molsys, n_bonds=True)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "id": "9dc3125c-8c88-458a-839d-8e1fb5f08a94",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "msm.build.remove_bonds(molsys)"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 8,
    "id": "2bfbe476-e055-4ba0-aaf4-7acefa3af748",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "CPU times: user 2.34 s, sys: 47.4 ms, total: 2.38 s\n",
+      "Wall time: 2.38 s\n"
+     ]
+    }
+   ],
    "source": [
-    "aa = msm.build.get_missing_bonds(molsys)"
+    "%%time\n",
+    "msm.build.add_missing_bonds(molsys)"
    ]
   },
   {
@@ -123,1007 +133,7 @@
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-       " [851, 852],\n",
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-       " [853, 854],\n",
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-       " [856, 857],\n",
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-       " [858, 859],\n",
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-       " [863, 865],\n",
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-       " [863, 864],\n",
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-       " [867, 868],\n",
-       " [869, 870],\n",
-       " [871, 872],\n",
-       " [871, 873],\n",
-       " [871, 874],\n",
-       " [875, 877],\n",
-       " [875, 876],\n",
-       " [877, 879],\n",
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-       " [877, 878],\n",
-       " [879, 880],\n",
-       " [881, 884],\n",
-       " [881, 882],\n",
-       " [881, 883],\n",
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-       " [891, 893],\n",
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-       " [902, 908],\n",
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-       " [904, 905],\n",
-       " [904, 906],\n",
-       " [904, 907],\n",
-       " [908, 909],\n",
-       " [908, 910],\n",
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-       " [912, 914],\n",
-       " [912, 913],\n",
-       " [914, 916],\n",
-       " [914, 918],\n",
-       " [914, 915],\n",
-       " [916, 917],\n",
-       " [918, 920],\n",
-       " [918, 923],\n",
-       " [918, 919],\n",
-       " [920, 927],\n",
-       " [920, 921],\n",
-       " [920, 922],\n",
-       " [923, 924],\n",
-       " [923, 925],\n",
-       " [923, 926],\n",
-       " [927, 928],\n",
-       " [927, 929],\n",
-       " [927, 930],\n",
-       " [931, 933],\n",
-       " [931, 932],\n",
-       " [933, 935],\n",
-       " [933, 937],\n",
-       " [933, 934],\n",
-       " [935, 936],\n",
-       " [937, 939],\n",
-       " [937, 941],\n",
-       " [937, 938],\n",
-       " [939, 940],\n",
-       " [941, 942],\n",
-       " [941, 943],\n",
-       " [941, 944],\n",
-       " [945, 947],\n",
-       " [945, 946],\n",
-       " [947, 949],\n",
-       " [947, 951],\n",
-       " [947, 948],\n",
-       " [949, 950],\n",
-       " [951, 954],\n",
-       " [951, 952],\n",
-       " [951, 953],\n",
-       " [954, 957],\n",
-       " [954, 955],\n",
-       " [954, 956],\n",
-       " [957, 960],\n",
-       " [957, 958],\n",
-       " [957, 959],\n",
-       " [960, 963],\n",
-       " [960, 961],\n",
-       " [960, 962],\n",
-       " [963, 964],\n",
-       " [963, 965],\n",
-       " [963, 966],\n",
-       " [967, 969],\n",
-       " [967, 968],\n",
-       " [969, 971],\n",
-       " [969, 973],\n",
-       " [969, 970],\n",
-       " [971, 972],\n",
-       " [973, 976],\n",
-       " [973, 974],\n",
-       " [973, 975],\n",
-       " [976, 977],\n",
-       " [976, 978],\n",
-       " [979, 981],\n",
-       " [979, 980],\n",
-       " [981, 983],\n",
-       " [981, 985],\n",
-       " [981, 982],\n",
-       " [983, 984],\n",
-       " [985, 988],\n",
-       " [985, 986],\n",
-       " [985, 987],\n",
-       " [988, 991],\n",
-       " [988, 989],\n",
-       " [988, 990],\n",
-       " [991, 992],\n",
-       " [991, 993],\n",
-       " [994, 996],\n",
-       " [994, 995],\n",
-       " [996, 998],\n",
-       " [996, 1000],\n",
-       " [996, 997],\n",
-       " [998, 999],\n",
-       " [1000, 1001],\n",
-       " [1000, 1002],\n",
-       " [1000, 1003],\n",
-       " [1004, 1006],\n",
-       " [1004, 1005],\n",
-       " [1006, 1008],\n",
-       " [1006, 1010],\n",
-       " [1006, 1007],\n",
-       " [1008, 1009],\n",
-       " [1010, 1013],\n",
-       " [1010, 1011],\n",
-       " [1010, 1012],\n",
-       " [1013, 1016],\n",
-       " [1013, 1014],\n",
-       " [1013, 1015],\n",
-       " [1016, 1017],\n",
-       " [1016, 1018],\n",
-       " [1019, 1021],\n",
-       " [1019, 1020],\n",
-       " [1021, 1023],\n",
-       " [1021, 1025],\n",
-       " [1021, 1022],\n",
-       " [1023, 1024],\n",
-       " [1025, 1028],\n",
-       " [1025, 1026],\n",
-       " [1025, 1027],\n",
-       " [1028, 1031],\n",
-       " [1028, 1029],\n",
-       " [1028, 1030],\n",
-       " [1031, 1034],\n",
-       " [1031, 1032],\n",
-       " [1031, 1033],\n",
-       " [1034, 1037],\n",
-       " [1034, 1035],\n",
-       " [1034, 1036],\n",
-       " [1037, 1038],\n",
-       " [1037, 1039],\n",
-       " [1037, 1040],\n",
-       " [1041, 1043],\n",
-       " [1041, 1042],\n",
-       " [1043, 1045],\n",
-       " [1043, 1047],\n",
-       " [1043, 1044],\n",
-       " [1045, 1046],\n",
-       " [1047, 1050],\n",
-       " [1047, 1048],\n",
-       " [1047, 1049],\n",
-       " [1050, 1052],\n",
-       " [1050, 1056],\n",
-       " [1050, 1051],\n",
-       " [1052, 1053],\n",
-       " [1052, 1054],\n",
-       " [1052, 1055],\n",
-       " [1056, 1057],\n",
-       " [1056, 1058],\n",
-       " [1056, 1059],\n",
-       " [1060, 1062],\n",
-       " ...]"
+       "2645"
       ]
      },
      "execution_count": 9,
@@ -1132,7 +142,7 @@
     }
    ],
    "source": [
-    "aa"
+    "msm.get(molsys, n_bonds=True)"
    ]
   },
   {
@@ -1223,6 +233,17 @@
    "id": "0a294fc7-05e2-4a73-b6e7-b4cfd181a4bb",
    "metadata": {},
    "outputs": [],
+   "source": [
+    "if []:\n",
+    "    print('si')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8343990e-0e26-4afe-b110-78d915015a51",
+   "metadata": {},
+   "outputs": [],
    "source": []
   }
  ],