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@dprada
dprada committed Feb 14, 2024
1 parent e21354a commit 1bc7664
Showing 1 changed file with 23 additions and 3 deletions.
26 changes: 23 additions & 3 deletions sandbox/Test_2nzt.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -54,12 +54,32 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": 8,
"id": "78decf3e-a27b-4949-ba36-1d022c6aee24",
"metadata": {},
"outputs": [],
"outputs": [
{
"ename": "TypeError",
"evalue": "Structures.append_structures() got an unexpected keyword argument 'coordinates'",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mTypeError\u001b[0m Traceback (most recent call last)",
"Cell \u001b[0;32mIn[8], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m molsys \u001b[38;5;241m=\u001b[39m \u001b[43mmsm\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mconvert\u001b[49m\u001b[43m(\u001b[49m\u001b[43mfile\u001b[49m\u001b[43m)\u001b[49m\n",
"File \u001b[0;32m~/repos@uibcdf/MolSysMT/molsysmt/_private/digestion/digest.py:122\u001b[0m, in \u001b[0;36mdigest.<locals>.digestor.<locals>.wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 120\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m func(all_args[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mself\u001b[39m\u001b[38;5;124m'\u001b[39m], \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mfinal_args)\n\u001b[1;32m 121\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m--> 122\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mfunc\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mfinal_args\u001b[49m\u001b[43m)\u001b[49m\n",
"File \u001b[0;32m~/repos@uibcdf/MolSysMT/molsysmt/basic/convert.py:529\u001b[0m, in \u001b[0;36mconvert\u001b[0;34m(molecular_system, to_form, selection, structure_indices, syntax, verbose, skip_digestion, **kwargs)\u001b[0m\n\u001b[1;32m 526\u001b[0m \u001b[38;5;66;03m# If one to one\u001b[39;00m\n\u001b[1;32m 527\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(from_form, (\u001b[38;5;28mlist\u001b[39m, \u001b[38;5;28mtuple\u001b[39m)):\n\u001b[0;32m--> 529\u001b[0m output \u001b[38;5;241m=\u001b[39m \u001b[43m_convert_one_to_one\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmolecular_system\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mfrom_form\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mto_form\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mto_form\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mselection\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mselection\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mstructure_indices\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mstructure_indices\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 530\u001b[0m \u001b[43m \u001b[49m\u001b[43msyntax\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msyntax\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mverbose\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mverbose\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 532\u001b[0m \u001b[38;5;66;03m# If multiple to one\u001b[39;00m\n\u001b[1;32m 533\u001b[0m \n\u001b[1;32m 534\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 535\u001b[0m \n\u001b[1;32m 536\u001b[0m \u001b[38;5;66;03m# conversions in private shortcuts\u001b[39;00m\n\u001b[1;32m 537\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mtuple\u001b[39m(\u001b[38;5;28msorted\u001b[39m(from_form)) \u001b[38;5;129;01min\u001b[39;00m _multiple_conversion_shortcuts:\n",
"File \u001b[0;32m~/repos@uibcdf/MolSysMT/molsysmt/basic/convert.py:83\u001b[0m, in \u001b[0;36m_convert_one_to_one\u001b[0;34m(molecular_system, from_form, to_form, selection, structure_indices, syntax, verbose, **kwargs)\u001b[0m\n\u001b[1;32m 80\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mlen\u001b[39m(missing_arguments)\u001b[38;5;241m>\u001b[39m\u001b[38;5;241m0\u001b[39m:\n\u001b[1;32m 81\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m NotCompatibleConversionError(from_form, to_form, missing_arguments)\n\u001b[0;32m---> 83\u001b[0m output \u001b[38;5;241m=\u001b[39m \u001b[43mfunction\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmolecular_system\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mconversion_arguments\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 85\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m (\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mmolsysmt.MolSys\u001b[39m\u001b[38;5;124m'\u001b[39m \u001b[38;5;129;01min\u001b[39;00m _dict_modules[from_form]\u001b[38;5;241m.\u001b[39m_convert_to) \u001b[38;5;129;01mand\u001b[39;00m (to_form \u001b[38;5;129;01min\u001b[39;00m _dict_modules[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mmolsysmt.MolSys\u001b[39m\u001b[38;5;124m'\u001b[39m]\u001b[38;5;241m.\u001b[39m_convert_to):\n\u001b[1;32m 87\u001b[0m output \u001b[38;5;241m=\u001b[39m _convert_one_to_one(molecular_system, from_form, to_form\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mmolsysmt.MolSys\u001b[39m\u001b[38;5;124m'\u001b[39m, selection\u001b[38;5;241m=\u001b[39mselection,\n\u001b[1;32m 88\u001b[0m structure_indices\u001b[38;5;241m=\u001b[39mstructure_indices, syntax\u001b[38;5;241m=\u001b[39msyntax, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n",
"File \u001b[0;32m~/repos@uibcdf/MolSysMT/molsysmt/_private/digestion/digest.py:52\u001b[0m, in \u001b[0;36mdigest.<locals>.digestor.<locals>.wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 48\u001b[0m \u001b[38;5;129m@functools\u001b[39m\u001b[38;5;241m.\u001b[39mwraps(func)\n\u001b[1;32m 49\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mwrapper\u001b[39m(\u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs):\n\u001b[1;32m 51\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m kwargs\u001b[38;5;241m.\u001b[39mget(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mskip_digestion\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;28;01mFalse\u001b[39;00m):\n\u001b[0;32m---> 52\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mfunc\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 54\u001b[0m \u001b[38;5;66;03m# Define caller\u001b[39;00m\n\u001b[1;32m 56\u001b[0m caller \u001b[38;5;241m=\u001b[39m func\u001b[38;5;241m.\u001b[39m\u001b[38;5;18m__module__\u001b[39m\u001b[38;5;241m+\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m.\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;241m+\u001b[39mfunc\u001b[38;5;241m.\u001b[39m\u001b[38;5;18m__name__\u001b[39m\n",
"File \u001b[0;32m~/repos@uibcdf/MolSysMT/molsysmt/form/file_pdb/to_molsysmt_MolSys.py:12\u001b[0m, in \u001b[0;36mto_molsysmt_MolSys\u001b[0;34m(item, atom_indices, structure_indices, skip_digestion)\u001b[0m\n\u001b[1;32m 10\u001b[0m tmp_item \u001b[38;5;241m=\u001b[39m MolSys()\n\u001b[1;32m 11\u001b[0m tmp_item\u001b[38;5;241m.\u001b[39mtopology \u001b[38;5;241m=\u001b[39m to_molsysmt_Topology(item, atom_indices\u001b[38;5;241m=\u001b[39matom_indices, skip_digestion\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m)\n\u001b[0;32m---> 12\u001b[0m tmp_item\u001b[38;5;241m.\u001b[39mstructures \u001b[38;5;241m=\u001b[39m \u001b[43mto_molsysmt_Structures\u001b[49m\u001b[43m(\u001b[49m\u001b[43mitem\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43matom_indices\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43matom_indices\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 13\u001b[0m \u001b[43m \u001b[49m\u001b[43mstructure_indices\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mstructure_indices\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mskip_digestion\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m)\u001b[49m\n\u001b[1;32m 15\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m tmp_item\n",
"File \u001b[0;32m~/repos@uibcdf/MolSysMT/molsysmt/_private/digestion/digest.py:52\u001b[0m, in \u001b[0;36mdigest.<locals>.digestor.<locals>.wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 48\u001b[0m \u001b[38;5;129m@functools\u001b[39m\u001b[38;5;241m.\u001b[39mwraps(func)\n\u001b[1;32m 49\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mwrapper\u001b[39m(\u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs):\n\u001b[1;32m 51\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m kwargs\u001b[38;5;241m.\u001b[39mget(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mskip_digestion\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;28;01mFalse\u001b[39;00m):\n\u001b[0;32m---> 52\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mfunc\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 54\u001b[0m \u001b[38;5;66;03m# Define caller\u001b[39;00m\n\u001b[1;32m 56\u001b[0m caller \u001b[38;5;241m=\u001b[39m func\u001b[38;5;241m.\u001b[39m\u001b[38;5;18m__module__\u001b[39m\u001b[38;5;241m+\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m.\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;241m+\u001b[39mfunc\u001b[38;5;241m.\u001b[39m\u001b[38;5;18m__name__\u001b[39m\n",
"File \u001b[0;32m~/repos@uibcdf/MolSysMT/molsysmt/form/file_pdb/to_molsysmt_Structures.py:15\u001b[0m, in \u001b[0;36mto_molsysmt_Structures\u001b[0;34m(item, atom_indices, structure_indices, skip_digestion)\u001b[0m\n\u001b[1;32m 11\u001b[0m coordinates \u001b[38;5;241m=\u001b[39m get_coordinates_from_atom(item, indices\u001b[38;5;241m=\u001b[39matom_indices, structure_indices\u001b[38;5;241m=\u001b[39mstructure_indices,\n\u001b[1;32m 12\u001b[0m skip_digestion\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m)\n\u001b[1;32m 13\u001b[0m box \u001b[38;5;241m=\u001b[39m get_box_from_system(item, structure_indices\u001b[38;5;241m=\u001b[39mstructure_indices, skip_digestion\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m)\n\u001b[0;32m---> 15\u001b[0m \u001b[43mtmp_item\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mappend_structures\u001b[49m\u001b[43m(\u001b[49m\u001b[43mcoordinates\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcoordinates\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mbox\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mbox\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 17\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m tmp_item\n",
"File \u001b[0;32m~/repos@uibcdf/MolSysMT/molsysmt/_private/digestion/digest.py:120\u001b[0m, in \u001b[0;36mdigest.<locals>.digestor.<locals>.wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 117\u001b[0m final_args \u001b[38;5;241m=\u001b[39m digested_args\n\u001b[1;32m 119\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mself\u001b[39m\u001b[38;5;124m'\u001b[39m \u001b[38;5;129;01min\u001b[39;00m all_args:\n\u001b[0;32m--> 120\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mfunc\u001b[49m\u001b[43m(\u001b[49m\u001b[43mall_args\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mself\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mfinal_args\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 121\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 122\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m func(\u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mfinal_args)\n",
"\u001b[0;31mTypeError\u001b[0m: Structures.append_structures() got an unexpected keyword argument 'coordinates'"
]
}
],
"source": [
"molsys = msm.convert(file, 'molsysmt.Topology')"
"molsys = msm.convert(file)"
]
},
{
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