In process to write more tests

.coveragerc

@@ -16,4 +16,6 @@ omit =
     molsysmt/element/atom/names.py
     molsysmt/element/atom/names_cg.py
     molsysmt/element/chain/chain_names.py
+    molsysmt/native/file_tng.py
+    molsysmt/native/file_xtc.py
 

molsysmt/native/pdb_file_handler.py

@@ -184,7 +184,7 @@ def parse_format33(file):
                 elif aux.startswith('EC:'): ### EC
                     compnd.ec = aux[3:].strip()[:-1]
                 elif aux.startswith('SYNONYM:'): ### SYNONYM
-                    compnd.synonym += [ii.strip() for ii in aux[8:].strip()[:-1].split(',')]
+                    compnd.synonym = [ii.strip() for ii in aux[8:].strip()[:-1].split(',')]
                 elif aux.startswith('ENGINEERED:'): ### ENGINEERED
                     compnd.engineered = aux[11:].strip()[:-1]
                 elif aux.startswith('MUTATION:'): ### MUTATION
@@ -561,7 +561,10 @@ def parse_format33(file):
                 seqadv.database = _dict_database_name[line[24:28].strip()]
                 seqadv.dbAccesion = line[29:38].strip()
                 seqadv.dbRes = line[39:42].strip()
-                seqadv.dbSeq = int(line[43:48])
+                try:
+                    seqadv.dbSeq = int(line[43:48])
+                except:
+                    seqadv.dbSeq = None
                 seqadv.conflict = line[49:70].strip()
 
                 counter += 1
@@ -1092,8 +1095,8 @@ def parse_format33(file):
 
                 elif record == 'ANISOU':
 
-                    record_element = AtomRecord()
-                    model.record.append(record_element)
+                    #record_element = AtomRecord()
+                    #model.record.append(record_element)
 
                     if record_element.serial!=int(line[6:11]):
                         raise ValueError("ANISOU record not referring previous atom record.")

molsysmt/systems.py

@@ -58,6 +58,7 @@ def path(package, file):
 systems['chicken villin HP35']['chicken_villin_HP35_solvated.h5msm'] = path('molsysmt.data.h5msm', 'chicken_villin_HP35_solvated.h5msm')
 systems['chicken villin HP35']['traj_chicken_villin_HP35_solvated.dcd'] = path('molsysmt.data.dcd', 'traj_chicken_villin_HP35_solvated.dcd')
 systems['chicken villin HP35']['traj_chicken_villin_HP35_solvated.h5'] = path('molsysmt.data.h5', 'traj_chicken_villin_HP35_solvated.h5')
+systems['chicken villin HP35']['traj_chicken_villin_HP35_solvated.h5msm'] = path('molsysmt.data.h5msm', 'traj_chicken_villin_HP35_solvated.h5msm')
 
 
 # T4 Lysozyme L99A

sandbox/Tests.ipynb

@@ -18,7 +18,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "ea2e8c1e89bc4d219d42d82c9108c88f",
+       "model_id": "95de59dde5df459d82c20bbf895a5d69",
        "version_major": 2,
        "version_minor": 0
       },
@@ -36,158 +36,71 @@
   {
    "cell_type": "code",
    "execution_count": 2,
-   "id": "e4442462-d13a-4102-831e-53432b0b04de",
+   "id": "a16f2547-2fb8-4db4-9016-9dec5ea6f43e",
    "metadata": {},
    "outputs": [],
    "source": [
-    "molsys_1 = msm.convert(systems['alanine dipeptide']['alanine_dipeptide.h5msm'], to_form='molsysmt.MolSys')"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 3,
-   "id": "48649be7-9724-48f0-9f73-1c8ad9f577d2",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "molsys_2 = msm.structure.translate(molsys_1, translation='[0.5, 0.0, 0.0] nm')"
+    "from molsysmt.native import H5MSMFileHandler"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 4,
-   "id": "588d98cf-50f6-4a99-a562-d207ffb7e869",
+   "id": "dd50ad05-29ea-40f0-9559-e0879608c639",
    "metadata": {},
    "outputs": [],
    "source": [
-    "molsys_merged = msm.merge([molsys_1, molsys_2], keep_ids=False)"
+    "molsys = msm.systems['chicken villin HP35']['traj_chicken_villin_HP35_solvated.h5msm']"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 5,
-   "id": "038cd459-facb-47d5-ae4f-26deefc4a9e1",
+   "id": "77f6def6-7552-42fd-ba30-e0bdc269a5f3",
    "metadata": {},
    "outputs": [],
    "source": [
-    "msm.build.define_new_chain(molsys_merged)"
+    "handler = H5MSMFileHandler(molsys)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
-   "id": "8aa9e648-9c87-4701-bba5-3bf2d5aff9d9",
+   "execution_count": 25,
+   "id": "765f4408-8691-4868-9e0f-fbcd00d9b526",
    "metadata": {},
    "outputs": [
     {
      "data": {
-      "text/html": [
-       "<div>\n",
-       "<style scoped>\n",
-       "    .dataframe tbody tr th:only-of-type {\n",
-       "        vertical-align: middle;\n",
-       "    }\n",
-       "\n",
-       "    .dataframe tbody tr th {\n",
-       "        vertical-align: top;\n",
-       "    }\n",
-       "\n",
-       "    .dataframe thead th {\n",
-       "        text-align: right;\n",
-       "    }\n",
-       "</style>\n",
-       "<table border=\"1\" class=\"dataframe\">\n",
-       "  <thead>\n",
-       "    <tr style=\"text-align: right;\">\n",
-       "      <th></th>\n",
-       "      <th>chain_id</th>\n",
-       "      <th>chain_name</th>\n",
-       "      <th>chain_type</th>\n",
-       "    </tr>\n",
-       "  </thead>\n",
-       "  <tbody>\n",
-       "    <tr>\n",
-       "      <th>0</th>\n",
-       "      <td>0</td>\n",
-       "      <td>A</td>\n",
-       "      <td>system</td>\n",
-       "    </tr>\n",
-       "  </tbody>\n",
-       "</table>\n",
-       "</div>"
-      ],
       "text/plain": [
-       "   chain_id chain_name chain_type\n",
-       "0         0          A     system"
+       "4456"
       ]
      },
-     "execution_count": 6,
+     "execution_count": 25,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
-    "molsys_merged.topology.chains"
+    "handler.file['topology']['atoms']['name'].shape[0]"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
-   "id": "0d985652-a9f6-4617-b92e-c7fef89f24f6",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "view = msm.view(molsys_merged, viewer='NGLView')"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 10,
-   "id": "4eff5af0-50ea-4c4a-a6b9-73c21170159e",
+   "execution_count": null,
+   "id": "985a9ddf-8653-4212-8d69-319d9c439840",
    "metadata": {},
    "outputs": [],
    "source": [
-    "comparison = msm.compare(view, molsys_merged, attribute_type='topological',\n",
-    "             coordinates=True)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 11,
-   "id": "ddbf7195-e17f-43b4-a70a-8074f72d7ee5",
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "True"
-      ]
-     },
-     "execution_count": 11,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "comparison"
+    "pdb_file_handler.entry.crystallographic_and_coordinate_transformation.scale.u2"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9c305a1e-1f6c-4ecf-8138-0f55ade00df8",
+   "id": "1d7e2708-12cf-4bfe-8ed4-5f88c37430e7",
    "metadata": {},
    "outputs": [],
-   "source": [
-    "    molsys_1 = msm.convert(systems['alanine dipeptide']['alanine_dipeptide.h5msm'], to_form='molsysmt.MolSys')\n",
-    "    molsys_2 = msm.structure.translate(molsys_1, translation='[0.5, 0.0, 0.0] nm')\n",
-    "    molsys_merged = msm.merge([molsys_1, molsys_2], keep_ids=False)\n",
-    "    msm.build.define_new_chain(molsys_merged, selection='all', chain_id=0, chain_name='A')\n",
-    "    view = msm.view(molsys_merged, viewer='NGLView')\n",
-    "    comparison = msm.compare(view, molsys_merged, attribute_type='topological',\n",
-    "            coordinates=True)\n",
-    "    assert comparison\n"
-   ]
+   "source": []
   }
  ],
  "metadata": {

tests/native/test_h5msm_file_handler.py

@@ -0,0 +1,27 @@
+"""
+Unit and regression test for the get_form module of the molsysmt package.
+"""
+
+# Import package, test suite, and other packages as needed
+import molsysmt as msm
+from molsysmt.native import H5MSMFileHandler
+from molsysmt._private.files_and_directories import temp_filename
+
+def test_pdb_file_handler_1():
+
+    molsys = msm.systems['chicken villin HP35']['traj_chicken_villin_HP35_solvated.h5msm']
+    handler = H5MSMFileHandler(molsys)
+    assert 4456==handler.file['topology']['atoms']['name'].shape[0]
+
+def test_pdb_file_handler_2():
+
+    topology = msm.convert(msm.systems['chicken villin HP35']['traj_chicken_villin_HP35_solvated.h5msm'],
+                           'molsysmt.Topology')
+    tmpfile = str(temp_filename(extension='h5msm'))
+    molsys = H5MSMFileHandler(tmpfile, 'w')
+    molsys.write_topology(topology)
+    molsys.close()
+
+    handler = H5MSMFileHandler(tmpfile)
+    assert 4456==handler.file['topology']['atoms']['name'].shape[0]
+

tests/native/test_pdb_file_handler.py

@@ -0,0 +1,58 @@
+"""
+Unit and regression test for the get_form module of the molsysmt package.
+"""
+
+# Import package, test suite, and other packages as needed
+import molsysmt as msm
+from molsysmt.native import PDBFileHandler
+
+import sys
+
+if sys.version_info[1] in (10,11):
+    from importlib.resources import files
+    def path(package, file):
+        return files(package).joinpath(file)
+elif sys.version_info[1] in (8,9):
+    from pathlib import PurePath
+    parent = PurePath(__file__).parent
+    def path(package, file):
+        data_dir = package.split('.')[-1]
+        return parent.joinpath('data/'+data_dir+'/'+file).__str__()
+
+systems = {}
+
+systems['3c0f.pdb'] = str(path('molsysmt.data.pdb', '3c0f.pdb'))
+systems['1bnf.pdb'] = str(path('molsysmt.data.pdb', '1bnf.pdb'))
+systems['3c8h.pdb'] = str(path('molsysmt.data.pdb', '3c8h.pdb'))
+systems['2vgy.pdb'] = str(path('molsysmt.data.pdb', '2vgy.pdb'))
+systems['5ip4.pdb'] = str(path('molsysmt.data.pdb', '5ip4.pdb'))
+
+def test_pdb_file_handler_1():
+
+    pdb_file_handler = PDBFileHandler(systems['3c0f.pdb'])
+    pdb_file_handler.load()
+    assert pdb_file_handler.entry.title.source[0].organism_scientific == 'ARCHAEOGLOBUS FULGIDUS DSM 4304'
+
+def test_pdb_file_handler_2():
+
+    pdb_file_handler = PDBFileHandler(systems['1bnf.pdb'])
+    pdb_file_handler.load()
+    assert pdb_file_handler.entry.connectivity.conect[4].atomSerNum == 1339
+
+def test_pdb_file_handler_3():
+
+    pdb_file_handler = PDBFileHandler(systems['3c8h.pdb'])
+    pdb_file_handler.load()
+    assert pdb_file_handler.entry.coordinate.model[0].record[0].anisou11 == 9993
+
+def test_pdb_file_handler_4():
+
+    pdb_file_handler = PDBFileHandler(systems['2vgy.pdb'])
+    pdb_file_handler.load()
+    assert pdb_file_handler.entry.coordinate.model[0].record[0].anisou11 == 10496
+
+def test_pdb_file_handler_5():
+
+    pdb_file_handler = PDBFileHandler(systems['5ip4.pdb'])
+    pdb_file_handler.load()
+    assert pdb_file_handler.entry.crystallographic_and_coordinate_transformation.scale.u2 == 0.0