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JanCBrammer/molfile_permutation.ipynb

Last active May 20, 2024 18:56
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molfile_permutation.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"import ctypes\n",
"import random\n",
"from rdkit import Chem # RDKit provides a Python wrapper around their C++ library.\n",
"from rdkit.Chem.Draw import IPythonConsole\n",
"from rdkit.Chem.Randomize import RandomizeMolBlock\n",
"from inchi_api import make_inchi_from_molfile_text # Our own Python wrapper around the InChI API.\n",
"from config import INCHI_LIB_PATH, INCHI_API_PARAMETERS\n",
"\n",
"inchi_lib = ctypes.CDLL(str(INCHI_LIB_PATH))\n",
"IPythonConsole.ipython_useSVG=True\n",
"IPythonConsole.drawOptions.addAtomIndices = True\n",
"random.seed(42)\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"We start by generating an InChI string for a structure that's known to fail the shuffle/permutation/invariance test.\n",
"For details have a look at Figure 7 in https://jcheminf.biomedcentral.com/articles/10.1186/s13321-021-00517-z#Sec9."
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"molblock = \"\"\"\n",
" -OEChem-03072403132D\n",
"\n",
" 13 14 0 0 0 0 0 0 0999 V2000\n",
" 2.8660 1.5000 0.0000 O 0 4 0 0 0 0 0 0 0 0 0 0\n",
" 4.6783 0.3047 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n",
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" 2.0000 -1.0000 0.0000 C 0 4 0 0 0 0 0 0 0 0 0 0\n",
" 4.8709 0.8941 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 5.8819 -0.5000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n",
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" 6 7 1 0 0 0 0\n",
" 6 8 1 0 0 0 0\n",
" 9 12 1 0 0 0 0\n",
" 10 13 1 0 0 0 0\n",
"M RAD 7 1 2 4 2 5 2 6 2 7 2 8 2 10 2\n",
"M END\n",
"\"\"\"\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Let's permute the atom indices of the structure and verify the permutation by comparing the structure from before to after the permutation."
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
" -OEChem-03072403132D\n",
"\n",
" 13 14 0 0 0 0 0 0 0999 V2000\n",
" 2.8660 1.5000 0.0000 O 0 4 0 0 0 0 0 0 0 0 0 0\n",
" 4.6783 0.3047 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n",
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" 3.7320 -0.0000 0.0000 C 0 4 0 0 0 0 0 0 0 0 0 0\n",
" 3.7320 -1.0000 0.0000 C 0 4 0 0 0 0 0 0 0 0 0 0\n",
" 2.8660 0.5000 0.0000 C 0 4 0 0 0 0 0 0 0 0 0 0\n",
" 5.2619 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 2.0000 -1.0000 0.0000 C 0 4 0 0 0 0 0 0 0 0 0 0\n",
" 4.8709 0.8941 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 5.8819 -0.5000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 1.4631 -1.3100 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 1 8 1 0 0 0 0\n",
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" 2 9 1 0 0 0 0\n",
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" 6 7 1 0 0 0 0\n",
" 6 8 1 0 0 0 0\n",
" 9 12 1 0 0 0 0\n",
" 10 13 1 0 0 0 0\n",
"M RAD 7 1 2 4 2 5 2 6 2 7 2 8 2 10 2\n",
"M END\n",
"\n",
"\n",
" -OEChem-03072403132D\n",
"\n",
" 13 14 0 0 0 0 0 0 0999 V2000\n",
" 2.0000 -0.0000 0.0000 N 0 4 0 0 0 0 0 0 0 0 0 0\n",
" 4.6783 0.3047 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 4.8709 0.8941 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 2.8660 0.5000 0.0000 C 0 4 0 0 0 0 0 0 0 0 0 0\n",
" 2.0000 -1.0000 0.0000 C 0 4 0 0 0 0 0 0 0 0 0 0\n",
" 5.8819 -0.5000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 1.4631 -1.3100 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 3.7320 -0.0000 0.0000 C 0 4 0 0 0 0 0 0 0 0 0 0\n",
" 3.7320 -1.0000 0.0000 C 0 4 0 0 0 0 0 0 0 0 0 0\n",
" 4.6783 -1.3047 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 2.8660 -1.5000 0.0000 N 0 4 0 0 0 0 0 0 0 0 0 0\n",
" 2.8660 1.5000 0.0000 O 0 4 0 0 0 0 0 0 0 0 0 0\n",
" 5.2619 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 12 4 1 0 0 0 0\n",
" 2 8 1 0 0 0 0\n",
" 2 13 1 0 0 0 0\n",
" 2 3 1 0 0 0 0\n",
" 10 9 1 0 0 0 0\n",
" 10 13 2 0 0 0 0\n",
" 11 9 1 0 0 0 0\n",
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" 1 4 1 0 0 0 0\n",
" 1 5 1 0 0 0 0\n",
" 8 9 1 0 0 0 0\n",
" 8 4 1 0 0 0 0\n",
" 13 6 1 0 0 0 0\n",
" 5 7 1 0 0 0 0\n",
"M END\n"
]
},
{
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"</svg>"
],
"text/plain": [
"<IPython.core.display.SVG object>"
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"molblock_permuted = RandomizeMolBlock(molblock)\n",
"\n",
"print(molblock)\n",
"print(molblock_permuted)\n",
"\n",
"molecule = Chem.MolFromMolBlock(molblock, removeHs=False)\n",
"molecule_permuted = Chem.MolFromMolBlock(molblock_permuted, removeHs=False)\n",
"Chem.Draw.MolsToGridImage([molecule, molecule_permuted])"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Finally, let's compare the InChI strings. As expected, they're different.\n",
"The invariance test fails."
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"InChI=1S/C5H3N4O/c10-5-3-4(7-1-6-3)8-2-9-5/h1-2H,(H,6,7,8,9,10)\n",
"InChI=1S/C5H3N4O/c10-5-3-4(7-1-6-3)8-2-9-5/h1-2H,(H,6,7,8,9)\n"
]
},
{
"ename": "AssertionError",
"evalue": "InChI strings are not the same.",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mAssertionError\u001b[0m Traceback (most recent call last)",
"Cell \u001b[0;32mIn[4], line 10\u001b[0m\n\u001b[1;32m 8\u001b[0m \u001b[38;5;28mprint\u001b[39m(inchi_string)\n\u001b[1;32m 9\u001b[0m \u001b[38;5;28mprint\u001b[39m(inchi_string_permuted)\n\u001b[0;32m---> 10\u001b[0m \u001b[38;5;28;01massert\u001b[39;00m inchi_string \u001b[38;5;241m==\u001b[39m inchi_string_permuted, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mInChI strings are not the same.\u001b[39m\u001b[38;5;124m\"\u001b[39m\n",
"\u001b[0;31mAssertionError\u001b[0m: InChI strings are not the same."
]
}
],
"source": [
"_, inchi_string, _, _, _ = make_inchi_from_molfile_text(\n",
" inchi_lib, molblock, INCHI_API_PARAMETERS\n",
")\n",
"\n",
"_, inchi_string_permuted, _, _, _ = make_inchi_from_molfile_text(\n",
" inchi_lib, molblock_permuted, INCHI_API_PARAMETERS\n",
")\n",
"print(inchi_string)\n",
"print(inchi_string_permuted)\n",
"assert inchi_string == inchi_string_permuted, \"InChI strings are not the same.\""
]
}
],
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"language": "python",
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},
"language_info": {
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"file_extension": ".py",
"mimetype": "text/x-python",
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"pygments_lexer": "ipython3",
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