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maclandrol/molecule_alignment.ipynb

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molecule_alignment.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"%load_ext autoreload\n",
"%autoreload 2"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"from typing import List\n",
"from typing import Optional\n",
"\n",
"import datamol as dm\n",
"from rdkit import Chem\n",
"from rdkit.Chem import Draw, rdFMCS, AllChem\n",
"from rdkit.Chem import rdDepictor\n",
"from rdkit.Chem.Scaffolds import MurckoScaffold\n",
"from collections import defaultdict as ddict"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
"def current_alignment(mol, template_smiles:Optional[str]=None):\n",
" if not template_smiles:\n",
" return mol\n",
" rdDepictor.Compute2DCoords(mol)\n",
" template = Chem.MolFromSmiles(template_smiles)\n",
" #rdDepictor.Compute2DCoords(template)\n",
" mcs = rdFMCS.FindMCS([mol, template])\n",
" if mcs.smartsString:\n",
" patt = Chem.MolFromSmarts(mcs.smartsString)\n",
"\n",
" query_match = mol.GetSubstructMatch(patt)\n",
" template_match = template.GetSubstructMatch(patt)\n",
" AllChem.AlignMol(\n",
" mol, template, atomMap=list(zip(query_match, template_match))\n",
" )\n",
" return mol"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
"def check_should_align(mols):\n",
" \"\"\"Check whether we should align the molecules on upload\"\"\"\n",
" # EN: rational is if any of the molecules already have computed conformers\n",
" # then we do not want to align them automatically (unless asked), because of the\n",
" # risk of overwritting the coordinates provided by the user\n",
" return not any(mol.GetNumConformers()> 0 for mol in mols)\n",
" \n",
"def _strip_molecule_to_core(mol, bond_cutter:dm.Mol=None):\n",
" \"\"\"\n",
" Strip a molecule to its core, i.e. remove all atoms not in the core.\n",
" This method 'guess' the molecular core, by finding the ring system\n",
" \"\"\"\n",
" if bond_cutter is None:\n",
" bond_cutter = dm.from_smarts(\"[R;!$(*=,#[!#6])]!@!=!#[*;$([A;!R][A;!R])]\")\n",
" \n",
" with dm.without_rdkit_log():\n",
" scaffold = MurckoScaffold.GetScaffoldForMol(mol)\n",
" out = mol.GetSubstructMatches(bond_cutter)\n",
" bond_inds = [mol.GetBondBetweenAtoms(i, j).GetIdx() for i, j in out]\n",
" if len(bond_inds) > 0:\n",
" fragmented = Chem.FragmentOnBonds(mol, bond_inds)\n",
" fragmented = dm.remove_dummies(fragmented)\n",
" fragmented = MurckoScaffold.GetScaffoldForMol(fragmented)\n",
" scaffold = dm.keep_largest_fragment(fragmented)\n",
" return scaffold\n",
" \n",
" \n",
"def make_scaffold_generic(mol, include_bonds:bool=False):\n",
" \"\"\"Make the atom in a scaffold or molecule generic\n",
" \n",
" Args:\n",
" mol: molecule or scaffold on which we should apply this function\n",
" include_bonds: whether we should also update bond order or keep as is\n",
" \"\"\"\n",
" res = Chem.Mol(mol)\n",
" for atom in res.GetAtoms():\n",
" if atom.GetAtomicNum() != 1:\n",
" atom.SetAtomicNum(0)\n",
" atom.SetFormalCharge(0)\n",
" atom.SetChiralTag(Chem.ChiralType.CHI_UNSPECIFIED)\n",
" atom.SetNoImplicit(0)\n",
" atom.SetNumExplicitHs(0)\n",
" if include_bonds:\n",
" for bond in res.GetBonds():\n",
" bond.SetBondType(Chem.BondType.UNSPECIFIED)\n",
" return dm.from_smarts(dm.to_smiles(res))\n",
"\n",
"def partition_and_align_mols(mols, partition:str=\"scaffold\", copy:bool=True, cutoff:float=0.7, **kwargs):\n",
" \"\"\"\n",
" Partition a list of molecules into clusters sharing common scaffold of common core,\n",
" then align the molecules to that common core. This function will compute the list of \n",
" smiles/smarts representative of each cluster first\n",
"\n",
" !!! note\n",
" Use this function at upload to align molecule when needed\n",
" \n",
" Args:\n",
" mols: list of molecules to partition\n",
" partition (str, optional): Partition method to use. Defaults to \"scaffold\".\n",
" One of ['scaffold', 'strip-scaffold', 'anongraph-scaffold', 'cluster' and 'anon-scaffold']. \n",
" copy: whether to copy the molecules before aligning them. Defaults to True.\n",
" cutoff: Optional cluster cutoff. Defaults to 0.7.\n",
" kwargs: Additional arguments to pass to clustering method\n",
" \"\"\"\n",
" if copy:\n",
" mols = [dm.copy_mol(mol) for mol in mols]\n",
" mol_groups = ddict(list) # map scaffold index to list of unique molecules\n",
" scaffold_mols = {}\n",
" if \"scaffold\" in partition:\n",
" scaffolds = [MurckoScaffold.GetScaffoldForMol(m) for m in mols]\n",
" scaffolds_ids = [dm.to_smiles(x) for x in scaffolds]\n",
" if partition.startswith(\"strip-\"):\n",
" # with brics scaffold we compute brics bonds, then re-infer and select the biggest\n",
" # fragment as candidate for core\n",
" bond_cutter = dm.from_smarts(\"[R;!$(*=,#[!#6])]!@!=!#[*;$([A;!R][A;!R])]\")\n",
" scaffolds = [_strip_molecule_to_core(x, bond_cutter=bond_cutter) for x in scaffolds]\n",
" scaffolds_ids = [dm.to_smiles(x) for x in scaffolds]\n",
" elif partition.startswith('anongraph-'):\n",
" scaffolds = [make_scaffold_generic(s, include_bonds=True) for s in scaffolds]\n",
" scaffolds_ids = [dm.to_smiles(x) for x in scaffolds]\n",
" elif partition.startswith(\"anon-\"):\n",
" scaffolds = [make_scaffold_generic(s, include_bonds=False) for s in scaffolds]\n",
" scaffolds_ids = [dm.to_smiles(x) for x in scaffolds]\n",
" for i, s in enumerate(scaffolds_ids):\n",
" mol_groups[s].append(i)\n",
" AllChem.Compute2DCoords(scaffolds[i])\n",
" scaffold_mols[s] = scaffolds[i]\n",
" else:\n",
" # partition is cluster, first compute molecule clusters\n",
" clusters, mol_clusters = dm.cluster_mols(mols, cutoff=cutoff, **kwargs)\n",
" # now compute the mcs for each clusters\n",
" cluster_mcs = [(dm.find_mcs(mol_cluster) if len(mol_cluster)>1 else dm.to_smiles(mol_cluster[0])) for mol_cluster in mol_clusters]\n",
" scaffolds_ids = [cluster_mcs[cluster_id] for cluster_id, _ in enumerate(clusters)]\n",
" for i, s in enumerate(scaffolds_ids):\n",
" mol_groups[s].extend(clusters[i])\n",
" for x in scaffolds_ids:\n",
" core = None\n",
" if x is not None:\n",
" core = dm.from_smarts(x)\n",
" AllChem.Compute2DCoords(core)\n",
" scaffold_mols[x] = core\n",
" \n",
" # now we match each molecule to the scaffold and align them\n",
" # note that the molecule object will be modified in place in the list\n",
" for core, mols_ids in mol_groups.items():\n",
" core_mol = scaffold_mols[core]\n",
" if core_mol is None:\n",
" print(core_mol)\n",
" pass\n",
" else:\n",
" for mol_id in mols_ids:\n",
" rdDepictor.GenerateDepictionMatching2DStructure(\n",
" mols[mol_id],\n",
" reference=core_mol,\n",
" acceptFailure=True,\n",
" allowRGroups=True,\n",
" )\n",
"\n",
"\n",
" # EN: you can discard the mol_groups (or keep it and match the values \n",
" # to molecular line notation, so you will not have to reocompute the above)\n",
" # and convert the mols into cxsmiles if you want\n",
" return mols, mol_groups\n",
" \n",
" \n",
"def template_align(mol, template:Optional[str]=None, copy:bool=True, use_depiction:bool=True, remove_confs:bool=True, auto_select_coord_gen:bool=False):\n",
" \"\"\"Align an input molecule to a template\n",
"\n",
" Args:\n",
" mol: input molecule\n",
" template_smiles: template to align to Defaults to None.\n",
" copy: whether to copy the molecule before aligning it. Defaults to True.\n",
" use_depiction: whether to use the depiction API or use MolAlign\n",
" The main difference is around how 3D information is handled, but also, because the depiction API\n",
" will emphasize the atoms that do not match, whereas AlignMol will not.\n",
" remove_confs: Whether to remove all conformation in the input molecule first. Default to True.\n",
" You set this to true when not using depiction\n",
" auto_select_coord_gen: whether to automatically select the coordinate generation method. \n",
"\n",
" Returns:\n",
" mol: aligned molecule to template\n",
" \"\"\"\n",
" # EN: this is for lines: 132-144 in lambda_handler_svg\n",
" # this assumes that whenever template_smiles is None, we should not align\n",
" # the reason being that this needs to be requested by the user\n",
" if isinstance(mol, str):\n",
" mol = dm.to_mol(mol)\n",
" \n",
" elif copy:\n",
" mol = dm.copy_mol(mol)\n",
" \n",
" if isinstance(template, str):\n",
" template = dm.to_mol(template)\n",
" \n",
" if template is None:\n",
" return mol\n",
" \n",
" if remove_confs:\n",
" mol.RemoveAllConformers()\n",
" \n",
" # EN: to make this more general and robust, we need to first check whether the template\n",
" # has 2D coordinates or not. If it does not, we need to compute them.\n",
" # This is a very rare edge case if requests are comming from the UI, but better to check than not xD\n",
" if template.GetNumConformers() == 0:\n",
" AllChem.Compute2DCoords(template)\n",
" # EN: now we can align the molecule to the template\n",
" # but first, we should avoid MCS as much as possible, because it's expensive\n",
" # so if the template is a subgraph of the molecule, no need to perform any MCS\n",
" # Another reason for this, is to avoid inconsistency in alignment between molecules that are\n",
" # supergraph of the template vs molecules that are subgraph of the template.\n",
" pattern = template\n",
" if not mol.HasSubstructMatch(template):\n",
" pattern = None\n",
" mcs_smarts = dm.find_mcs([mol, template]) \n",
" if mcs_smarts is not None:\n",
" pattern = dm.from_smarts(mcs_smarts)\n",
" \n",
" if pattern is not None:\n",
" if auto_select_coord_gen:\n",
" rdDepictor.SetPreferCoordGen(use_depiction)\n",
" # we would need to compute 2d coordinates for the molecules if it doesn't have any\n",
" if mol.GetNumConformers() == 0:\n",
" AllChem.Compute2DCoords(mol)\n",
" if use_depiction:\n",
" rdDepictor.GenerateDepictionMatching2DStructure(\n",
" mol,\n",
" reference=template,\n",
" refPatt=pattern,\n",
" acceptFailure=True,\n",
" allowRGroups=True,\n",
" )\n",
" else:\n",
" query_match = mol.GetSubstructMatch(pattern)\n",
" template_match = template.GetSubstructMatch(pattern)\n",
" AllChem.AlignMol(mol, template, atomMap=list(zip(query_match, template_match)))\n",
" return mol"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Scenario:\n",
"\n",
"1. On upload check whether the molecules have coordinate already with `check_should_align`\n",
" - If yes, do nothing\n",
" - Otherwise, attemp to partition and align then store the new coordinate\n",
"2. When the user perfom alignment again a template\n",
" - Call `template_align` with the input template"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Test obvious failure cases"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"1. Test coordinate presence"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
"# use the volkamer data\n",
"import pandas as pd\n",
"data = pd.read_csv(\"~/Desktop/chem-series.csv\")\n",
"# prioritize the smaller molecules xD"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [],
"source": [
"molecules = data.SMILES.apply(dm.to_mol).values"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [],
"source": [
"# we compute random coordinates for the molecules\n",
"molecules_with_confs = [dm.conformers.generate(mol, n_confs=2, align_conformers=False) for mol in molecules]"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [],
"source": [
"# if we convert to cx smiles and reload, we should still have the coordinates\n",
"molecules_cx_smiles = [dm.to_smiles(x, cxsmiles=True) for x in molecules_with_confs]\n",
"molecules_cx = [dm.to_mol(x) for x in molecules_cx_smiles]"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [],
"source": [
"# we expect no alignment on input for the molecules with conformers\n",
"assert check_should_align(molecules_with_confs) == False\n",
"assert check_should_align(molecules_cx) == False\n",
"assert check_should_align(molecules) == True"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"2. Test partition and align on full dataset effect"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
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}
],
"source": [
"# Test partition and alignment on auto core generation based on ring system linker cut\n",
"\n",
"aligned_mols, mol_groups = partition_and_align_mols(molecules_with_confs, partition='strip-scaffold')\n",
"display(dm.to_image(molecules[:16], mol_size=(200, 150)))\n",
"display(dm.to_image(aligned_mols[:16], mol_size=(200, 150)))"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [
{
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}
],
"source": [
"# Test partition and alignment on raw murko scaffold generation\n",
"aligned_mols, mol_groups = partition_and_align_mols(molecules_with_confs, partition='scaffold')\n",
"display(dm.to_image(aligned_mols[:16], mol_size=(200, 150)))"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [
{
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],
"source": [
"# Test with anonymous graph generation\n",
"# with the anonymous scaffold, bond order are discarded, meaning that we expected confusion between \n",
"# aromatic and aliphatic rings sometimes, but it does not seem to happen\n",
"aligned_mols, mol_groups = partition_and_align_mols(molecules_with_confs, partition='anongraph-scaffold')\n",
"display(dm.to_image(aligned_mols[:16], mol_size=(200, 150)))"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [
{
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654.2,493.1 L 654.7,499.5\" style=\"fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-2 atom-2 atom-3\" d=\"M 652.9,503.8 L 648.1,508.0\" style=\"fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-2 atom-2 atom-3\" d=\"M 648.1,508.0 L 643.2,512.1\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-18 atom-18 atom-2\" d=\"M 668.1,510.1 L 662.5,506.7\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-18 atom-18 atom-2\" d=\"M 662.5,506.7 L 657.0,503.3\" style=\"fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-3 atom-3 atom-4\" d=\"M 643.2,512.1 L 649.2,526.3\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-4 atom-4 atom-5\" d=\"M 649.2,526.3 L 664.5,525.1\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-5 atom-5 atom-6\" d=\"M 664.5,525.1 L 674.6,536.8\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-17 atom-5 atom-18\" d=\"M 664.5,525.1 L 668.1,510.1\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-6 atom-6 atom-7\" d=\"M 674.6,536.8 L 681.2,535.5\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-6 atom-6 atom-7\" d=\"M 681.2,535.5 L 687.7,534.3\" style=\"fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-7 atom-7 atom-8\" d=\"M 691.8,536.3 L 695.8,540.9\" style=\"fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-7 atom-7 atom-8\" d=\"M 695.8,540.9 L 699.8,545.6\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-8 atom-8 atom-9\" d=\"M 698.3,545.1 L 696.2,551.0\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-8 atom-8 atom-9\" d=\"M 696.2,551.0 L 694.2,557.0\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-8 atom-8 atom-9\" d=\"M 701.3,546.1 L 699.2,552.1\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-8 atom-8 atom-9\" d=\"M 699.2,552.1 L 697.1,558.0\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-9 atom-8 atom-10\" d=\"M 699.8,545.6 L 706.3,544.3\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-9 atom-8 atom-10\" d=\"M 706.3,544.3 L 712.9,543.1\" style=\"fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-10 atom-10 atom-11\" d=\"M 715.8,540.1 L 717.9,534.2\" style=\"fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-10 atom-10 atom-11\" d=\"M 717.9,534.2 L 720.0,528.2\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-11 atom-11 atom-12\" d=\"M 720.0,528.2 L 735.2,525.3\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-11 atom-11 atom-12\" d=\"M 721.7,524.7 L 732.3,522.7\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-19 atom-17 atom-11\" d=\"M 710.0,516.5 L 720.0,528.2\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-12 atom-12 atom-13\" d=\"M 735.2,525.3 L 740.3,510.8\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-13 atom-13 atom-14\" d=\"M 740.3,510.8 L 730.2,499.1\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-13 atom-13 atom-14\" d=\"M 736.4,511.0 L 729.4,502.8\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-14 atom-14 atom-15\" d=\"M 730.2,499.1 L 732.3,493.2\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-14 atom-14 atom-15\" d=\"M 732.3,493.2 L 734.3,487.3\" style=\"fill:none;fill-rule:evenodd;stroke:#00CC00;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-15 atom-14 atom-16\" d=\"M 730.2,499.1 L 715.1,501.9\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-16 atom-16 atom-17\" d=\"M 715.1,501.9 L 710.0,516.5\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"bond-16 atom-16 atom-17\" d=\"M 717.2,505.1 L 713.7,515.3\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n<path class=\"atom-2\" d=\"M 654.0 499.9 L 655.4 502.2 Q 655.5 502.4, 655.8 502.8 Q 656.0 503.2, 656.0 503.3 L 656.0 499.9 L 656.6 499.9 L 656.6 504.2 L 656.0 504.2 L 654.4 501.7 Q 654.3 501.4, 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"text/plain": [
"<IPython.core.display.SVG object>"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"aligned_mols, mol_groups = partition_and_align_mols(molecules_with_confs, partition='anon-scaffold')\n",
"display(dm.to_image(aligned_mols[:16], mol_size=(200, 150)))"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Note here how molecule 12 is different in the `anon*-scaffold`. Because it actually belong to a separate cluster. "
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"3. Test align with custom template"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [],
"source": [
"template_with_2d_coords_mdl = \"\"\"\n",
" MJ220600 \n",
"\n",
" 22 24 0 0 0 0 0 0 0 0999 V2000\n",
" -2.3616 -3.3697 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -1.6472 -2.9572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -0.9327 -3.3697 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -0.9327 -4.1947 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -0.2183 -4.6072 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -0.2183 -5.4322 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -0.9327 -5.8447 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -1.6472 -5.4322 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -1.6472 -4.6072 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -1.6472 -2.1322 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -2.3616 -1.7197 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -2.3616 -0.8947 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -1.6472 -0.4822 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -1.6472 0.3427 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -0.9327 0.7552 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -0.9327 1.5802 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -0.2183 1.9927 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 0.4961 1.5802 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 0.4961 0.7552 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -0.2183 0.3427 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -0.9327 -0.8947 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -0.9327 -1.7197 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 1 2 2 0 0 0 0\n",
" 2 3 1 0 0 0 0\n",
" 3 4 1 0 0 0 0\n",
" 4 5 4 0 0 0 0\n",
" 5 6 4 0 0 0 0\n",
" 6 7 4 0 0 0 0\n",
" 7 8 4 0 0 0 0\n",
" 8 9 4 0 0 0 0\n",
" 4 9 4 0 0 0 0\n",
" 2 10 1 0 0 0 0\n",
" 10 11 1 0 0 0 0\n",
" 11 12 1 0 0 0 0\n",
" 12 13 1 0 0 0 0\n",
" 13 14 1 0 0 0 0\n",
" 14 15 1 0 0 0 0\n",
" 15 16 1 0 0 0 0\n",
" 16 17 1 0 0 0 0\n",
" 17 18 1 0 0 0 0\n",
" 18 19 1 0 0 0 0\n",
" 19 20 1 0 0 0 0\n",
" 15 20 1 0 0 0 0\n",
" 13 21 1 0 0 0 0\n",
" 21 22 1 0 0 0 0\n",
" 10 22 1 0 0 0 0\n",
"M END\n",
"\"\"\"\n",
"\n",
"template_with_3d_coords_mdl = \"\"\"\n",
" MJ220600 \n",
"\n",
" 22 24 0 0 0 0 0 0 0 0999 V2000\n",
" -3.0912 -2.6881 0.7272 O 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -2.4306 -2.7347 0.8385 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -2.2114 -3.4239 0.9549 N 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -1.6047 -3.6636 1.2823 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -1.2964 -4.3094 1.0362 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -0.6845 -4.5957 1.3717 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -0.3805 -4.2432 1.9643 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -0.6874 -3.6030 2.2173 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -1.2985 -3.3161 1.8823 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -2.0101 -2.1210 0.8350 N 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -1.2626 -2.1319 0.6182 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -1.0952 -1.5604 0.0358 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -1.342
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