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ptosco/CrossBonds.ipynb

Last active October 23, 2023 11:16
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CrossBonds
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CrossBonds.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"id": "77f84f35-3f9e-441d-8981-8a838eb9770d",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:56.386686Z",
"iopub.status.busy": "2023-10-23T11:11:56.385482Z",
"iopub.status.idle": "2023-10-23T11:11:56.641106Z",
"shell.execute_reply": "2023-10-23T11:11:56.639817Z",
"shell.execute_reply.started": "2023-10-23T11:11:56.386618Z"
},
"tags": []
},
"outputs": [],
"source": [
"from rdkit import Chem"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "eaa22804-a05b-42b0-83d2-617e90fc7e2e",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:56.644664Z",
"iopub.status.busy": "2023-10-23T11:11:56.644239Z",
"iopub.status.idle": "2023-10-23T11:11:56.651404Z",
"shell.execute_reply": "2023-10-23T11:11:56.650541Z",
"shell.execute_reply.started": "2023-10-23T11:11:56.644639Z"
},
"tags": []
},
"outputs": [],
"source": [
"def print_bond_info(mol):\n",
" for b in mol.GetBonds():\n",
" print(f\"idx {b.GetIdx()+1} bi {b.GetBeginAtomIdx()+1} ei {b.GetEndAtomIdx()+1} \"\n",
" f\"type {b.GetBondType()} stereo {b.GetStereo()} dir {b.GetBondDir()} \"\n",
" f\"prop {list(b.GetPropNames(includePrivate=True, includeComputed=True))} \"\n",
" f\"_MolFileBondType {b.GetProp('_MolFileBondType')} \"\n",
" f\"_UnknownStereo {b.HasProp('_UnknownStereo') and b.GetProp('_UnknownStereo')} \"\n",
" f\"_MolFileBondStereo {b.HasProp('_MolFileBondStereo') and b.GetProp('_MolFileBondStereo')} \"\n",
" f\"_MolFileBondCfg {b.HasProp('_MolFileBondCfg') and b.GetProp('_MolFileBondCfg')}\"\n",
" )"
]
},
{
"cell_type": "markdown",
"id": "1154b58f-5dee-40fa-8bb7-70894464a777",
"metadata": {},
"source": [
"# Example 1"
]
},
{
"attachments": {
"cdfb5fe3-187f-43b1-8b56-1d892d260e1c.png": {
"image/png": "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"
}
},
"cell_type": "markdown",
"id": "52dec482-d1e2-4278-8ac1-0bf6a23acfe1",
"metadata": {},
"source": [
"### ChemDraw\n",
"![image.png](attachment:cdfb5fe3-187f-43b1-8b56-1d892d260e1c.png)"
]
},
{
"cell_type": "markdown",
"id": "503d2c4f-7f90-4c66-8a8f-128849a58e96",
"metadata": {},
"source": [
"### `double-2000.mol`"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "100e4ed0-129a-42c0-bbb9-78dceb293383",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:56.652366Z",
"iopub.status.busy": "2023-10-23T11:11:56.652149Z",
"iopub.status.idle": "2023-10-23T11:11:56.678904Z",
"shell.execute_reply": "2023-10-23T11:11:56.677725Z",
"shell.execute_reply.started": "2023-10-23T11:11:56.652346Z"
},
"tags": []
},
"outputs": [],
"source": [
"mol = Chem.MolFromMolBlock(\"\"\"double-2000.mol\n",
" ChemDraw10192311132D\n",
"\n",
" 4 3 0 0 0 0 0 0 0 0999 V2000\n",
" -0.7145 0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 0.0000 0.6188 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 0.7145 0.2062 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -0.7145 -0.6188 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 1 2 2 0 0\n",
" 2 3 1 4 0\n",
" 1 4 1 4 0\n",
"M END\n",
"\"\"\")"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "a1262a09-5beb-4494-9a68-8d0911d5070d",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:56.682153Z",
"iopub.status.busy": "2023-10-23T11:11:56.681500Z",
"iopub.status.idle": "2023-10-23T11:11:56.773399Z",
"shell.execute_reply": "2023-10-23T11:11:56.772322Z",
"shell.execute_reply.started": "2023-10-23T11:11:56.682107Z"
}
},
"outputs": [
{
"data": {
"image/png": "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\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7f830e716f20>"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mol"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "4148b8f0-0c1e-49a8-aa46-e2fd3dbffd5e",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:56.775148Z",
"iopub.status.busy": "2023-10-23T11:11:56.774710Z",
"iopub.status.idle": "2023-10-23T11:11:56.890477Z",
"shell.execute_reply": "2023-10-23T11:11:56.888643Z",
"shell.execute_reply.started": "2023-10-23T11:11:56.775118Z"
},
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"idx 1 bi 1 ei 2 type DOUBLE stereo STEREOANY dir NONE prop ['_MolFileBondType'] _MolFileBondType 2 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 2 bi 2 ei 3 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType', '_MolFileBondStereo', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 4 _MolFileBondCfg 0\n",
"idx 3 bi 1 ei 4 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType', '_MolFileBondStereo', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 4 _MolFileBondCfg 0\n"
]
}
],
"source": [
"print_bond_info(mol)"
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "c2e89309-b2a7-4cd7-b71d-f32bab7420ef",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:56.894701Z",
"iopub.status.busy": "2023-10-23T11:11:56.893821Z",
"iopub.status.idle": "2023-10-23T11:11:56.935868Z",
"shell.execute_reply": "2023-10-23T11:11:56.934351Z",
"shell.execute_reply.started": "2023-10-23T11:11:56.894640Z"
},
"tags": []
},
"outputs": [
{
"data": {
"image/png": "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\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7f830e716f20>"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"Chem.ReapplyMolBlockWedging(mol)\n",
"mol"
]
},
{
"cell_type": "code",
"execution_count": 7,
"id": "4041c609-7443-4eae-ab75-3f74ba67a35a",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:56.945228Z",
"iopub.status.busy": "2023-10-23T11:11:56.944343Z",
"iopub.status.idle": "2023-10-23T11:11:56.966299Z",
"shell.execute_reply": "2023-10-23T11:11:56.964728Z",
"shell.execute_reply.started": "2023-10-23T11:11:56.945165Z"
},
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"idx 1 bi 1 ei 2 type DOUBLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 2 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 2 bi 2 ei 3 type SINGLE stereo STEREONONE dir UNKNOWN prop ['_MolFileBondType', '_MolFileBondStereo', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 4 _MolFileBondCfg 0\n",
"idx 3 bi 1 ei 4 type SINGLE stereo STEREONONE dir UNKNOWN prop ['_MolFileBondType', '_MolFileBondStereo', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 4 _MolFileBondCfg 0\n"
]
}
],
"source": [
"print_bond_info(mol)"
]
},
{
"cell_type": "markdown",
"id": "347e3afe-3363-49f7-91bd-6c15d5e72e14",
"metadata": {},
"source": [
"### `double-3000.mol`"
]
},
{
"cell_type": "code",
"execution_count": 8,
"id": "3c28306f-4190-45aa-9304-e30363d68819",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:56.970203Z",
"iopub.status.busy": "2023-10-23T11:11:56.969011Z",
"iopub.status.idle": "2023-10-23T11:11:56.994964Z",
"shell.execute_reply": "2023-10-23T11:11:56.993395Z",
"shell.execute_reply.started": "2023-10-23T11:11:56.970141Z"
},
"tags": []
},
"outputs": [],
"source": [
"mol = Chem.MolFromMolBlock(\"\"\"double-3000.mol\n",
" ChemDraw10232310312D\n",
"\n",
" 0 0 0 0 0 0 V3000\n",
"M V30 BEGIN CTAB\n",
"M V30 COUNTS 4 3 0 0 0\n",
"M V30 BEGIN ATOM\n",
"M V30 1 C -0.714435 0.206182 0.000000 0\n",
"M V30 2 C 0.000000 0.618744 0.000000 0\n",
"M V30 3 F 0.714435 0.206182 0.000000 0\n",
"M V30 4 O -0.714435 -0.618744 0.000000 0\n",
"M V30 END ATOM\n",
"M V30 BEGIN BOND\n",
"M V30 1 2 1 2\n",
"M V30 2 1 2 3 CFG=2\n",
"M V30 3 1 1 4 CFG=2\n",
"M V30 END BOND\n",
"M V30 END CTAB\n",
"M END\n",
"\"\"\")"
]
},
{
"cell_type": "code",
"execution_count": 9,
"id": "8f318064-1bad-42ba-bbe2-116a4b12ddbd",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:56.998905Z",
"iopub.status.busy": "2023-10-23T11:11:56.998049Z",
"iopub.status.idle": "2023-10-23T11:11:57.078487Z",
"shell.execute_reply": "2023-10-23T11:11:57.077279Z",
"shell.execute_reply.started": "2023-10-23T11:11:56.998829Z"
}
},
"outputs": [
{
"data": {
"image/png": "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\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7f830e6d6350>"
]
},
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mol"
]
},
{
"cell_type": "code",
"execution_count": 10,
"id": "7d3edea7-d58f-40f3-9c0e-3016e8610d81",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:57.080962Z",
"iopub.status.busy": "2023-10-23T11:11:57.080205Z",
"iopub.status.idle": "2023-10-23T11:11:57.110868Z",
"shell.execute_reply": "2023-10-23T11:11:57.109078Z",
"shell.execute_reply.started": "2023-10-23T11:11:57.080927Z"
},
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"idx 1 bi 1 ei 2 type DOUBLE stereo STEREOANY dir NONE prop ['_MolFileBondType'] _MolFileBondType 2 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 2 bi 2 ei 3 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType', '_MolFileBondCfg', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 0 _MolFileBondCfg 2\n",
"idx 3 bi 1 ei 4 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType', '_MolFileBondCfg', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 0 _MolFileBondCfg 2\n"
]
}
],
"source": [
"print_bond_info(mol)"
]
},
{
"cell_type": "code",
"execution_count": 11,
"id": "07f7b4ca-2720-41b0-9356-6353caa04466",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:57.114555Z",
"iopub.status.busy": "2023-10-23T11:11:57.113863Z",
"iopub.status.idle": "2023-10-23T11:11:57.157964Z",
"shell.execute_reply": "2023-10-23T11:11:57.156766Z",
"shell.execute_reply.started": "2023-10-23T11:11:57.114495Z"
},
"tags": []
},
"outputs": [
{
"data": {
"image/png": "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\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7f830e6d6350>"
]
},
"execution_count": 11,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"Chem.ReapplyMolBlockWedging(mol)\n",
"mol"
]
},
{
"cell_type": "code",
"execution_count": 12,
"id": "ee02cdf7-7c66-4021-876a-50cdd4e8220c",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:57.160361Z",
"iopub.status.busy": "2023-10-23T11:11:57.159724Z",
"iopub.status.idle": "2023-10-23T11:11:57.195259Z",
"shell.execute_reply": "2023-10-23T11:11:57.193447Z",
"shell.execute_reply.started": "2023-10-23T11:11:57.160322Z"
},
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"idx 1 bi 1 ei 2 type DOUBLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 2 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 2 bi 2 ei 3 type SINGLE stereo STEREONONE dir UNKNOWN prop ['_MolFileBondType', '_MolFileBondCfg', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 0 _MolFileBondCfg 2\n",
"idx 3 bi 1 ei 4 type SINGLE stereo STEREONONE dir UNKNOWN prop ['_MolFileBondType', '_MolFileBondCfg', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 0 _MolFileBondCfg 2\n"
]
}
],
"source": [
"print_bond_info(mol)"
]
},
{
"cell_type": "markdown",
"id": "acbbea8f-1f13-4fa8-92be-2dca10f8d3cd",
"metadata": {},
"source": [
"### `double-explicit-crossed-2000.mol`"
]
},
{
"cell_type": "code",
"execution_count": 13,
"id": "eb7398e4-2742-425f-ac64-071c9bacf72d",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:57.199258Z",
"iopub.status.busy": "2023-10-23T11:11:57.198431Z",
"iopub.status.idle": "2023-10-23T11:11:57.227239Z",
"shell.execute_reply": "2023-10-23T11:11:57.225690Z",
"shell.execute_reply.started": "2023-10-23T11:11:57.199197Z"
},
"tags": []
},
"outputs": [],
"source": [
"mol = Chem.MolFromMolBlock(\"\"\"double-explicit-crossed-2000.mol\n",
" ChemDraw10232310432D\n",
"\n",
" 4 3 0 0 0 0 0 0 0 0999 V2000\n",
" -0.7144 0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 0.0000 0.6187 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 0.7144 0.2062 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -0.7144 -0.6187 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 1 2 2 3 \n",
" 2 3 1 4 \n",
" 1 4 1 4 \n",
"M END\n",
"\"\"\")"
]
},
{
"cell_type": "code",
"execution_count": 14,
"id": "dd5eca96-6e91-4799-97b4-579dff04888c",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:57.231334Z",
"iopub.status.busy": "2023-10-23T11:11:57.230490Z",
"iopub.status.idle": "2023-10-23T11:11:57.282585Z",
"shell.execute_reply": "2023-10-23T11:11:57.281261Z",
"shell.execute_reply.started": "2023-10-23T11:11:57.231272Z"
}
},
"outputs": [
{
"data": {
"image/png": "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\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7f830e6d6660>"
]
},
"execution_count": 14,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mol"
]
},
{
"cell_type": "code",
"execution_count": 15,
"id": "2644b546-e143-4463-b163-238eba2bc7d4",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:57.285472Z",
"iopub.status.busy": "2023-10-23T11:11:57.284809Z",
"iopub.status.idle": "2023-10-23T11:11:57.311104Z",
"shell.execute_reply": "2023-10-23T11:11:57.309513Z",
"shell.execute_reply.started": "2023-10-23T11:11:57.285430Z"
},
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"idx 1 bi 1 ei 2 type DOUBLE stereo STEREOANY dir NONE prop ['_MolFileBondType', '_MolFileBondStereo'] _MolFileBondType 2 _UnknownStereo 0 _MolFileBondStereo 3 _MolFileBondCfg 0\n",
"idx 2 bi 2 ei 3 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType', '_MolFileBondStereo', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 4 _MolFileBondCfg 0\n",
"idx 3 bi 1 ei 4 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType', '_MolFileBondStereo', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 4 _MolFileBondCfg 0\n"
]
}
],
"source": [
"print_bond_info(mol)"
]
},
{
"cell_type": "code",
"execution_count": 16,
"id": "222aa460-8e88-4df9-9de8-c83d2298fce3",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:57.315012Z",
"iopub.status.busy": "2023-10-23T11:11:57.314151Z",
"iopub.status.idle": "2023-10-23T11:11:57.391272Z",
"shell.execute_reply": "2023-10-23T11:11:57.390053Z",
"shell.execute_reply.started": "2023-10-23T11:11:57.314950Z"
},
"tags": []
},
"outputs": [
{
"data": {
"image/png": "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\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7f830e6d6660>"
]
},
"execution_count": 16,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"Chem.ReapplyMolBlockWedging(mol)\n",
"mol"
]
},
{
"cell_type": "code",
"execution_count": 17,
"id": "8dee994b-f848-4cd8-ad18-891ec79d44e8",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:57.394045Z",
"iopub.status.busy": "2023-10-23T11:11:57.393474Z",
"iopub.status.idle": "2023-10-23T11:11:57.420267Z",
"shell.execute_reply": "2023-10-23T11:11:57.418684Z",
"shell.execute_reply.started": "2023-10-23T11:11:57.394010Z"
},
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"idx 1 bi 1 ei 2 type DOUBLE stereo STEREOANY dir EITHERDOUBLE prop ['_MolFileBondType', '_MolFileBondStereo'] _MolFileBondType 2 _UnknownStereo 0 _MolFileBondStereo 3 _MolFileBondCfg 0\n",
"idx 2 bi 2 ei 3 type SINGLE stereo STEREONONE dir UNKNOWN prop ['_MolFileBondType', '_MolFileBondStereo', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 4 _MolFileBondCfg 0\n",
"idx 3 bi 1 ei 4 type SINGLE stereo STEREONONE dir UNKNOWN prop ['_MolFileBondType', '_MolFileBondStereo', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 4 _MolFileBondCfg 0\n"
]
}
],
"source": [
"print_bond_info(mol)"
]
},
{
"cell_type": "markdown",
"id": "397a746b-fa3a-4450-99db-ffa2d0614ebf",
"metadata": {},
"source": [
"### `double-explicit-crossed-3000.mol`"
]
},
{
"cell_type": "code",
"execution_count": 18,
"id": "ad84db21-d9e9-4dcd-adf4-2b66f09e611b",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:57.424114Z",
"iopub.status.busy": "2023-10-23T11:11:57.423284Z",
"iopub.status.idle": "2023-10-23T11:11:57.447535Z",
"shell.execute_reply": "2023-10-23T11:11:57.445811Z",
"shell.execute_reply.started": "2023-10-23T11:11:57.424054Z"
},
"tags": []
},
"outputs": [],
"source": [
"mol = Chem.MolFromMolBlock(\"\"\"double-explicit-crossed-3000.mol\n",
" ChemDraw10232310422D\n",
"\n",
" 0 0 0 0 0 0 V3000\n",
"M V30 BEGIN CTAB\n",
"M V30 COUNTS 4 3 0 0 0\n",
"M V30 BEGIN ATOM\n",
"M V30 1 C -0.714435 0.206182 0.000000 0\n",
"M V30 2 C 0.000000 0.618744 0.000000 0\n",
"M V30 3 F 0.714435 0.206182 0.000000 0\n",
"M V30 4 O -0.714435 -0.618744 0.000000 0\n",
"M V30 END ATOM\n",
"M V30 BEGIN BOND\n",
"M V30 1 2 1 2 CFG=2\n",
"M V30 2 1 2 3 CFG=2\n",
"M V30 3 1 1 4 CFG=2\n",
"M V30 END BOND\n",
"M V30 END CTAB\n",
"M END\n",
"\"\"\")"
]
},
{
"cell_type": "code",
"execution_count": 19,
"id": "b0d90afe-d487-42da-96c9-89bc0107d50a",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:57.451525Z",
"iopub.status.busy": "2023-10-23T11:11:57.450708Z",
"iopub.status.idle": "2023-10-23T11:11:57.495425Z",
"shell.execute_reply": "2023-10-23T11:11:57.494216Z",
"shell.execute_reply.started": "2023-10-23T11:11:57.451465Z"
}
},
"outputs": [
{
"data": {
"image/png": "iVBORw0KGgoAAAANSUhEUgAAAcIAAACWCAIAAADCEh9HAAAABmJLR0QA/wD/AP+gvaeTAAARKElEQVR4nO3da1RTZ74G8H/CxYBgwAjKTbwBQo911KktKqejotWKoIIXwADWVahX6rEW63KVGdtxQC2u6miVcVBAEAEVsNYeWmHsUGVab4UjqFVRbkK5yZ0Qkn0+hBJUxMAOCUme36c38d07z2pZz9o7efOGwzAMAQBAf3HVHQAAQLOhRgEAWEGNAgCwghoFAGAFNQoAwApqFACAFdQoAAArqFEAAFZQo6ABYmNjt27dmpOTo+4gAD3g4FtMMMh5enqeP39eNl6/fn1ERISpqal6IwF0hxqFwau1tfW1114rKioiIhMTk+bmZoZhbGxsIiIi/P39ORyOugMCEOGmHgat8vLy2bNnFxUVcTicsLCwxsbGn376acaMGWVlZUKhcPr06VeuXFF3RgAiXI3C4HTz5k0vL6+SkpJx48YdOnRowYIFsucZhklNTf3oo4+Ki4s5HI6Pj8++fftGjx6t3rSg41CjMOicOnVq7dq1ra2tbm5uqamplpaWz01obm7eu3dvZGRkW1ubsbHxtm3btm/fzuPx1JIWgBiAQaOjoyMsLEz2lxkcHNze3t7L5OLiYqFQKJtsZ2cXGxurspwA3eFqFAaLxsbG1atXZ2Rk6OvrR0VFbdq0SZGjsrOzP/zww7y8PCKaPXv2/v37J0+ePMBJAZ6BGoVB4f79+56enoWFhQKBICUlZfbs2YofK5VKT548uW3btt9++43L5fr7++/bt+/FtwIABghqFNQvMzNz1apVdXV1r7/+enp6+pgxY/pxkrq6usjIyP3797e3t5uZmW3fvn3Lli2GhobKDgvwPNQoqFl0dPSGDRs6Ojo8PDwSEhKGDRvG5mx3797dunXrhQsXiMjR0TEqKmrRokVKSgrQM6wbBbURiUTvvfdeSEiIRCIJCwtLT09n2aFE5OTk9PXXX3/33XcuLi737t3z8PCYN29eQUGBUgID9AhXo6AeT548WbZsWW5u7tChQ2NjY729vZV7frFYfPjw4fDw8Pr6egMDg3Xr1u3atYvP5yv3VQAIV6OgFrdu3Xrrrbdyc3NtbW0vX778yg7Ny8uTSqV9egkDA4PQ0NAHDx5s3rxZKpUeOHBg/PjxX375pUQiYREcoCdqXW4FuigpKcnY2JiIZs6cWVFR0cvM2trao0ePzpw5k4iysrL6/Yo3btxwc3OT/cFPmTLl8uXL/T4VwItQo6A6Uqk0PDxctqVIcHCwSCTqcZpYLD5//vyyZcu6PmcfPnx4fHw8y1fPyMjoWgPg4eFRVFTE8oQAMqhRUJGGhgYvLy8i0tfXj4iI6HFOYWFhWFjYqFGjZGXH5XLd3d1jY2Nlezux19zcHB4eLrsWNjY2jsnPb5VIlHJm0GX4iAlU4cGDB15eXrdv3xYIBMnJyXPmzOn+r/X19adPn46Li/vxxx9lzzg5Oa1atWrNmjX29vZKD1NWVvbJJ588IGoPDbUwMNhgY/OuQIBN96DfUKMw4H744QcfH5+qqqpJkyalp6ePHTtW9rxUKs3KyoqLiztz5kxLSwsR8fl8T0/PgICAuXPnDvR2orfq6r6oqChsaSGiySYmH9nZORsbD+grgrZCjcLAio6O3rhxo1gsXrRoUWJiomxl6L179xITE2NjYx89ekREXC7X1dU1ICDA399/6NChKsvGEH1TU3OgrKxGLOYQLRQIQm1sBAYGKgsA2gE1CgOlvb193bp1MTExHA7n448/3r17d1NTU1paWnx8/KVLl2R/eKNHj/b19Q0JCem6RFW9Vqk0vqLiREVFO8MYcbnCkSODRo0y5GItICgKNQoDorq62sfH5/LlyzweLzo6euzYsfHx8YmJiU1NTURkZGTk4eERHBysgpt3BZWIRIfKyr6vqyMiuyFDNtjYuJubqzsUaAbUKCjfL7/84uXl9fjxYysrK29v72+++ebhw4eyf5o2bVpwcLCfn5+JiYl6Q/bo58bGL0pK7re2EtEbpqZb7ewmGBmpOxQMdqhRULKUlJSgoKCWlhY+n9/Q0CD7A7O1tfX393///ffHjx+v7oCvIGGY9Jqar8rK6jo69DgcL4FgnY2Nub6+unPB4IUaBaVhGCY0NPTgwYNdz/B4vMWLFwuFwnfffVdPT0+N2fqqQSKJLi9PqaqSMMwwPb33ra1XWFjoDY73H2CwQY2CEpSVlcXExOzZs0f21icRTZs2TSgUCoXC4cOHqzcbG4/a2qJKS6/U1xPRGB7vf2xtZyiwuYmUYT57/LhPLzTS0PADa+t+pgR1Q41C/4lEooyMjLi4uIsXL8q2/OByucuXL//ss88cHBzUnU5pfqivjyopKRWJiMiNz99qZ2c7ZEgv8zsY5q0bN/r0EhOMjJJcXFilBPXBOz7QH9evX4+Li0tISKipqSEi2aftNjY2mZmZLlpXB//N588YNiylqupIefm/6+uvNjT4WFiss7YeqlFvU8DAwdUo9MGTJ0+Sk5NjYmJkPyFHRPb29qWlpRKJZOHChadOndLuDT2rxeLo8vK0mhopw4wwMAi2tl4iEHBfeMO0+9Woub7+LAX+m+CmXqOhRuHVRCJRZmZmfHz8uXPnOjo6iGjUqFE+Pj7V1dVJSUldq+u5urFkvbCl5YuSkltNTUTkbGy81c7uD88u3upeo/81dOiJiRPVkBJUCDUKvbl9+3Z8fHxMTExVVRURGRoazp8/PyAgwM3Nzc/PLzs7W7a6vuv34nUEQ3Spru7L0tIn7e0cornm5qG2tla/b+uHGtU1eG8UelBbW5uamnrkyJGbN2/KnnFxcQkICFizZo2lpWVeXp6rq+ujR49sbGzOnTv3xhtvqDet6nGI3M3NZ/H5cRUVsZWV39fV5dTXr7S0XGtlZawbl+TQHWoU5CQSSXZ2dnR0dFpamlgsJiJzc/Ply5eHhIRMnTpVNic1NTUoKKi5udnV1fXs2bNde4PqIB6XG2xt7TFixIHS0u/r6mIrKgpbWg5r0RIFUBBqFIiICgoK4uLiTpw4UVlZSUR6enru7u7BwcFeXl5dW9AzDLNnz54dO3ZIpVI/P79jx44Z4YuSRNaGhhHjxt1obNxXWupraanuOKAGqFGd9vTp0+Tk5O77JTs7OwcGBgYFBY0cObL7zKampsDAwLNnz+rp6UVERISFhakj7+A11dT0pLMz7ud1E2pUF3Xtl5yamtra2kpEZmZmK1asEAqFs2bNenF+aWnpkiVLrl+/PmzYsISEBA8PD5VH1gDoUJ2FGtUtd+7cSUpKOn78eHFxMf3+Y0dCodDHx8f4JXu/5+Tk+Pj4VFZWOjg4ZGRkTMTnzgDPQo3qhOLi4k8//fTevXu5ubmyJW4K/thRdHT0pk2b2tvbFyxYcOrUKTMzM1VF1hIPW1uD7tzpfc5aKys3rf7agtZDjWq527dvL1q06PHvO2Xw+fyVK1cGBQW5urr2fmBHR8fOnTsjIyOJaPPmzVFRUZq1RdMg0SKV/l9zc+9z6sRi1YSBAYIa1XK+vr6yDjUzM/P19d27d68iP3ZUU1OzYsWKrKysIUOGHD16NDAwcOCTAmgq1KiW+/XXX4loz54927ZtU/CQ/Px8Ly+voqIia2vrc+fOTZ8+fSADajlLA4MlI0b0PscJv0iq4VCjWs7BwSE/P/+dd95RcP6FCxf8/PwaGhqmTp2alpZmZ2c3oPG0nqWhYTD2HNF2WKQBnRiGiYyM9PT0bGho8PX1zcnJQYcCKAI1CkREbW1tAQEB27dv53A4ERERiYmJ+IYSgIJwUw9UWlq6dOnSa9eumZqanjx50tPTU92JADQJahTIz8/v2rVrTk5O6enpTk5O6o4DoGFwUw907NixlStX5ubmokMB+gFXo0COjo5JSUnqTgGgqXA1CgDACmoUAIAV1CgAACuoUQAAVlCjAACs4JN6ACXjEnXtHzqGx1NvGFAB1CiAknE5nP0TJqg7BagObuoBAFhBjQIAsIIaBQBgBTUKAMAKahQAgBXUKAAAK6hRAABWUKMAAKygRgEAWEGNAgCwghoFAGAFNQoAwApqFACAFdQoAAAr2ChPy/3vhAn6Q4YY6+mpOwiA1kKNajmr+/cpP58kEnUHAdBauKkHAGAFNQoAwApqFACAFdQoAAArqFEAAFZQowAArKBGAQBYQY0CALCCGgUAYAU1CgDACmoUAIAV1CgAACuoUQAAVlCjAACsoEYBAFhBjQIAsIIaBQBgBTUKAMAKahQAgBXUKAAAK6hRAABWUKMAAKygRgEAWEGNAgCwghoFAGAFNQoAwApqFACAFdQoAAArHIZh1J0BBpJIRFIp8XjE4ag7CoB2Qo0CALCir+4AMDBaWujmTaqupupqamsjgYAsLcnJiWxsFDq8sZFqajrHAgGZmip0lERCJSWdYyMjGjmy77kBNA9qVLu0t9M//0lnzlBODolEPUxwcaEFCygkhBwdeztPfDxt2NA5PnCANm1S6NWrqmjs2M7xn/5E2dmKBwfQXPiISYskJ5OTE61fT5cu9dyhRFRQQFFR5OxM69dTS4tq8wFoJ9SotggPp5Ur6dGjZ560tqbJk+nNN2nMGDIwkD8vldJXX9HcuVRdrdqUAFoINaoVwsJo1y75Q1tbOniQiouprIxu3aLcXCoqotpaOnuW3n5bPi03l9zcqKFB9XkBtAlqVPNlZtLevfKHa9fS3bu0cSPZ2T0zzcSEli6lf/2Ljh+XX5neuUOhoaqLCqCNUKMarrWV1qyhrlVrISH0j3+QsXFvhwQF0enT8mWkJ07Qt98ObEgArYYa1XAJCVRe3jl2dKT9+xVaZr90KX3wgfzhvn0Dkg1AN6BGNdyhQ/Lxrl1kZKTogbt3yydnZVFBgZKDAegM1Kgme/yYbt3qHPP55OnZh2PNzMjbu3PMMJSRoeRsADoDNarJcnPl43nz+nApKtO9dq9eVU4kAN2DGtVk3Wt0ypQ+Hz51qnz8n/8oIQ+ATsKXQTVZWZl87Ozc58PHjSMej9raiIgqK0ksfmaJfpemJqqqUuiEXV/DB9AlqFFNVlcnH5uZ9flwDof4/M4aJaKnT8nCoodpO3bQjh39ygegE3BTr8nq6+VjBTdhek738u1eygCgMNSoJuN2+9/Xv31jpVL5WE+PbR4AnYSbek3W/VqysbE/Z+j+hXpz857n/OUvFBSk0NmqquiPf+xPDABNhhrVZHy+fPz0aZ8PZxj52wKy90l7ZG5Oo0crdEJDwz5nANB8uKnXZLa28nFhYZ8Pf/BA/vmStTVu6gH6BzWqyd58Uz7u+jqT4rof0v1UANAXqFFN1r37srJeuuP9y1y4IB+7uionEoDuQY1qMnt7mjSpc1xb+0wtvlJzM5050znmcMjDQ8nZAHQGalTDrV8vH//5zyQWK3rg3/4m/3Df3Z0mTlRyMACdgRrVcKtX04gRneP8fPr8c4WO+vnnZzbM37JF+cEAdAZqVMOZmNDhw/KHu3bRX//6iqX4V6/S/PnU3t750M+PFi4cwIQA2g41qvmWL6fAQPnDnTtp1izKziaJ5PmZDx/Sxo3k5iZfZGpvT3//u4pyAmgpLL/XCseOEYdDJ050PrxyhebMIYGApk8nS0vi8aiyku7efX5tqbMzffvtS7+8BACKQY1qBX19iomhiRPp88+pqanzyZoaunix5/kcDnl705EjJBCoLCOAtsJNvbbgcCgsjO7fp82bycrqpdOMjGjxYrpyhVJS0KEASsFh+rczEAxmDEN5eXT1KlVWUnU1iURkYUEWFuTsTG+/TTzeq89QXU3FxZ1jO7ue9yF9UUcH5eV1jk1NycGhX+kBNAxqFACAFdzUAwCwghoFAGAFNQoAwApqFACAFdQoAAArqFEAAFZQowAArKBGAQBYQY0CALDy//HlzBXptDd0AAAAeXpUWHRyZGtpdFBLTCByZGtpdCAyMDI0LjAzLjFwcmUAAHice79v7T0GIOBnQAAWIGYG4gZGNoYMEJsZweBkUAAyGDkgfEZGbgZGLSZGBkYmIE9BBKRb3AqkAG6W2VOz/QmKwXYwAaY0OXsQDRS3h4mD1ADF94PYYgDt9xAWcMNXkgAAAN96VFh0TU9MIHJka2l0IDIwMjQuMDMuMXByZQAAeJyNUEEOgjAQvPOK/UCbpa0iBw9AgRhDSRR9gMCBBIMRTHy+LQYLiTHudpPpZHa626p7XNqa1M9b25TNQMp71/d1RTgi0mvXOmDiIPfNAJ9g0tE8/ji+78PZeDgZGABhnO4UREUQTkyUn1RxBAFcd+hcKoMizybGhQgIUs8Vgq8AKcO1u2Ea4Bi2lWmhZalWeUJ80XFI4B8/AfnsYfLDMVZyMfJ7iTBX0i7BxoqSdMvswIbidi5Xp5ibzi3MffpBjZ0Xt9xads01tmEAAABfelRYdFNNSUxFUyByZGtpdCAyMDI0LjAzLjFwcmUAAHic83e2dXZTqNHQNdAzNzQxMTbVAbLMDC3MTUx0rBGCBnpGBkBRIx1rAx2EPKa0pk65laGegY6hnqGOkZ5RDQCwgBOMcEZ4bwAAAABJRU5ErkJggg==\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7f830e6d6900>"
]
},
"execution_count": 19,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mol"
]
},
{
"cell_type": "code",
"execution_count": 20,
"id": "28ce7645-8132-4579-bf87-8ee3448af9c5",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:57.498849Z",
"iopub.status.busy": "2023-10-23T11:11:57.497515Z",
"iopub.status.idle": "2023-10-23T11:11:57.521147Z",
"shell.execute_reply": "2023-10-23T11:11:57.519545Z",
"shell.execute_reply.started": "2023-10-23T11:11:57.498808Z"
},
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"idx 1 bi 1 ei 2 type DOUBLE stereo STEREOANY dir NONE prop ['_MolFileBondType', '_MolFileBondCfg'] _MolFileBondType 2 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 2\n",
"idx 2 bi 2 ei 3 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType', '_MolFileBondCfg', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 0 _MolFileBondCfg 2\n",
"idx 3 bi 1 ei 4 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType', '_MolFileBondCfg', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 0 _MolFileBondCfg 2\n"
]
}
],
"source": [
"print_bond_info(mol)"
]
},
{
"cell_type": "code",
"execution_count": 21,
"id": "80bc6d82-6b36-41ea-aa7a-033067470f15",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:57.525088Z",
"iopub.status.busy": "2023-10-23T11:11:57.524252Z",
"iopub.status.idle": "2023-10-23T11:11:57.682075Z",
"shell.execute_reply": "2023-10-23T11:11:57.680854Z",
"shell.execute_reply.started": "2023-10-23T11:11:57.525027Z"
},
"tags": []
},
"outputs": [
{
"data": {
"image/png": "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\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7f830e6d6900>"
]
},
"execution_count": 21,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"Chem.ReapplyMolBlockWedging(mol)\n",
"mol"
]
},
{
"cell_type": "code",
"execution_count": 22,
"id": "87f8ff9d-2fb9-4643-ab9a-90a26bbe38bc",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:57.694234Z",
"iopub.status.busy": "2023-10-23T11:11:57.693642Z",
"iopub.status.idle": "2023-10-23T11:11:57.707774Z",
"shell.execute_reply": "2023-10-23T11:11:57.706730Z",
"shell.execute_reply.started": "2023-10-23T11:11:57.694199Z"
},
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"idx 1 bi 1 ei 2 type DOUBLE stereo STEREOANY dir EITHERDOUBLE prop ['_MolFileBondType', '_MolFileBondCfg'] _MolFileBondType 2 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 2\n",
"idx 2 bi 2 ei 3 type SINGLE stereo STEREONONE dir UNKNOWN prop ['_MolFileBondType', '_MolFileBondCfg', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 0 _MolFileBondCfg 2\n",
"idx 3 bi 1 ei 4 type SINGLE stereo STEREONONE dir UNKNOWN prop ['_MolFileBondType', '_MolFileBondCfg', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 0 _MolFileBondCfg 2\n"
]
}
],
"source": [
"print_bond_info(mol)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "a2e5f17e-7a5d-414c-933f-7941d367418a",
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "markdown",
"id": "d7225ab8-7061-42d7-a6d9-e4036f8ba4ff",
"metadata": {},
"source": [
"# Example 2"
]
},
{
"attachments": {
"88b054a0-d11e-4493-9466-c668aa4f4896.png": {
"image/png": "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"
}
},
"cell_type": "markdown",
"id": "e441fa11-0d9a-47af-9cc1-95002979410b",
"metadata": {},
"source": [
"### ChemDraw\n",
"![image.png](attachment:88b054a0-d11e-4493-9466-c668aa4f4896.png)"
]
},
{
"cell_type": "markdown",
"id": "d2d88ef2-54cc-40dc-88a0-c95ccf0c827d",
"metadata": {
"tags": []
},
"source": [
"### `double-2-2000.mol`"
]
},
{
"cell_type": "code",
"execution_count": 23,
"id": "cddafc08-fe93-43a5-8e4c-f9e22a294028",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:57.709804Z",
"iopub.status.busy": "2023-10-23T11:11:57.709240Z",
"iopub.status.idle": "2023-10-23T11:11:57.781803Z",
"shell.execute_reply": "2023-10-23T11:11:57.780041Z",
"shell.execute_reply.started": "2023-10-23T11:11:57.709770Z"
},
"tags": []
},
"outputs": [],
"source": [
"mol = Chem.MolFromMolBlock(\"\"\"double-2-2000.mol\n",
" ChemDraw10192311332D\n",
"\n",
" 4 3 0 0 0 0 0 0 0 0999 V2000\n",
" -0.3572 -0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 0.3572 0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 1.0717 0.6188 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -1.0717 -0.6188 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 1 2 2 0 0\n",
" 2 3 1 4 0\n",
" 1 4 1 4 0\n",
"M END\n",
"\"\"\")"
]
},
{
"cell_type": "code",
"execution_count": 24,
"id": "83cd8879-6734-4fed-9346-86fcbd8f2d3e",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:57.786107Z",
"iopub.status.busy": "2023-10-23T11:11:57.785148Z",
"iopub.status.idle": "2023-10-23T11:11:57.835985Z",
"shell.execute_reply": "2023-10-23T11:11:57.834662Z",
"shell.execute_reply.started": "2023-10-23T11:11:57.786045Z"
}
},
"outputs": [
{
"data": {
"image/png": 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+XN8D3dxo+3bdy6HTowBgMNQoe/z737rtjRtHd+xf/qJ7EP7yZWpvN1oqAJuHGmUP7aOZWoO39+vJ05PCwwe21WoqLjZaKgCbhxplidZWun17YJvPp+DgUX9DSIhuWy43TioAwJV6k1MoBu5s10df37AfNTbS4GO7U6eO5c6k6dN12/X1oz4cAIaBGjWx/HzKzzfC9zQ367bH9ozm0F88bm01NA8A/AdO6lli6EUhV9exfANqFMA0MBo1MScncnHRd+fmZhpuwS1HR912b+9Ykgw++6RNBQBGgho1sb/+dSwL5T32o0EdHWNJMvSbx48fyzcAwOPgpJ4lhtZoU9NYvmHoUUO/DQAMgxplCT8/4vMHtn/5ZdhB6wi0P4ys9dRTxkkFAKhR1nBwoNDQgW2N5qFO1NP167rtqCjjpAIA1CibDO2+f/1rdMeWl+uWhvLwwHIkAEaEGmWP1at12ydPDvz4nZ7++c+Hvgc/UQdgPPjnxB4REbrn4uvrae9efQ+sqnpoVaehCzkDgMFQo6ySmKjb/vhjksmefMiDB7RxI6lUAy+XL6d580ySDcBWoUZZZfVq3al9VxctW0Z5eSPtX1tLy5bploby9KTDh02bEMD2oEbZJjtbd7tSZyetXEkrVlBBgW68qXXjBqWk0MyZJJUOvGNnR0eO0KRJZk0LYAPwFBPbeHmRVDrwc3Va2tVPHB0pIIC8venBA6qre/QWfWdn+vJLevll8+cFsHoYjbKQjw8VFdFbbz10wb27m6qrqbiYysoe7VCBgCQSdCiAiaBG2cnNjQ4fprIyevddmjXr8ft4eNCqVfT11ySV0oIF5s0HYEM4muGWFAIWUSjo9m2qq6OWFuLzydub/P3p6afJHpM2ACaHGgUAMAhO6gEADIIaBQAwCGoUAMAgqFEAAIOgRgEADIIaBQAwCGoUAMAgqFEAAIOgRgEADPL/ucPcaWzAFxUAAAB/elRYdHJka2l0UEtMIHJka2l0IDIwMjQuMDMuMXByZQAAeJx7v2/tPQYg4GdAABYgZgbiBkY2hgwQmxnB4GRQADIYOSB8RkZuBkYtJkYGRiYgT0EEpFvcCqQAbtbrR9v2SagF7wNxgGw7INsOxC7X7bRfmylnD2XvB7L3g9hiAJ2cFRaI9w/nAAAA1HpUWHRNT0wgcmRraXQgMjAyNC4wMy4xcHJlAAB4nH1QSwrCMBDd5xRzgYRJUvtZuGjTDyJNQKsHEF0IlW70/k4qbVqQziTw8ubN8Cb34XPrH1xxhYjiNfQMfJzK4/MNc6iSEY8bJ8syuGqawVrwAIqqOVgwXV5MjHEX250hAk0dlGtl3rl2YiQY4Cj0LiFXHimMPUKBY4ReRcpZuKHTUIMUmMhkLMcyTf/qInDAZyHfUFa2XHn+bVE4W4Yt1HhN3exVMOwpHXxJymg5dDnCv6cvJMy+JshULJZNQowAAABTelRYdFNNSUxFUyByZGtpdCAyMDI0LjAzLjFwcmUAAHic83e2dXZTqNHQNdQzMDc019E10DMztLDQsQYyjE3NjUACRgZmRjrWUD6MC1UPVa5ZAwAyAg77JwlO7QAAAABJRU5ErkJggg==\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7f830e6d65f0>"
]
},
"execution_count": 24,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mol"
]
},
{
"cell_type": "code",
"execution_count": 25,
"id": "39d0c7e3-deed-4262-9249-6218c3a2769b",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:57.838415Z",
"iopub.status.busy": "2023-10-23T11:11:57.837978Z",
"iopub.status.idle": "2023-10-23T11:11:57.867054Z",
"shell.execute_reply": "2023-10-23T11:11:57.865222Z",
"shell.execute_reply.started": "2023-10-23T11:11:57.838376Z"
},
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"idx 1 bi 1 ei 2 type DOUBLE stereo STEREOANY dir NONE prop ['_MolFileBondType'] _MolFileBondType 2 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 2 bi 2 ei 3 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType', '_MolFileBondStereo', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 4 _MolFileBondCfg 0\n",
"idx 3 bi 1 ei 4 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType', '_MolFileBondStereo', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 4 _MolFileBondCfg 0\n"
]
}
],
"source": [
"print_bond_info(mol)"
]
},
{
"cell_type": "code",
"execution_count": 26,
"id": "6e692bc9-bf7d-4bc4-a78a-074cdcc67f80",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:57.870845Z",
"iopub.status.busy": "2023-10-23T11:11:57.870162Z",
"iopub.status.idle": "2023-10-23T11:11:57.912216Z",
"shell.execute_reply": "2023-10-23T11:11:57.911001Z",
"shell.execute_reply.started": "2023-10-23T11:11:57.870785Z"
},
"tags": []
},
"outputs": [
{
"data": {
"image/png": "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\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7f830e6d65f0>"
]
},
"execution_count": 26,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"Chem.ReapplyMolBlockWedging(mol)\n",
"mol"
]
},
{
"cell_type": "code",
"execution_count": 27,
"id": "3c6b7ecd-861d-4513-8dad-27c65a72cefe",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:57.915005Z",
"iopub.status.busy": "2023-10-23T11:11:57.914526Z",
"iopub.status.idle": "2023-10-23T11:11:58.027684Z",
"shell.execute_reply": "2023-10-23T11:11:58.026087Z",
"shell.execute_reply.started": "2023-10-23T11:11:57.914964Z"
},
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"idx 1 bi 1 ei 2 type DOUBLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 2 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 2 bi 2 ei 3 type SINGLE stereo STEREONONE dir UNKNOWN prop ['_MolFileBondType', '_MolFileBondStereo', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 4 _MolFileBondCfg 0\n",
"idx 3 bi 1 ei 4 type SINGLE stereo STEREONONE dir UNKNOWN prop ['_MolFileBondType', '_MolFileBondStereo', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 4 _MolFileBondCfg 0\n"
]
}
],
"source": [
"print_bond_info(mol)"
]
},
{
"cell_type": "markdown",
"id": "0a1d2c2c-e1f8-4848-8dd6-9f0ade22eaf4",
"metadata": {},
"source": [
"### `double-2-3000.mol`"
]
},
{
"cell_type": "code",
"execution_count": 28,
"id": "ef4bcf86-ecbb-4a9c-a23b-790e6e1cab7a",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:58.031815Z",
"iopub.status.busy": "2023-10-23T11:11:58.030572Z",
"iopub.status.idle": "2023-10-23T11:11:58.055009Z",
"shell.execute_reply": "2023-10-23T11:11:58.053015Z",
"shell.execute_reply.started": "2023-10-23T11:11:58.031754Z"
},
"tags": []
},
"outputs": [],
"source": [
"mol = Chem.MolFromMolBlock(\"\"\"double-2-3000.mol\n",
" ChemDraw10232310312D\n",
"\n",
" 0 0 0 0 0 0 V3000\n",
"M V30 BEGIN CTAB\n",
"M V30 COUNTS 4 3 0 0 0\n",
"M V30 BEGIN ATOM\n",
"M V30 1 C -0.357168 -0.206181 0.000000 0\n",
"M V30 2 C 0.357167 0.206182 0.000000 0\n",
"M V30 3 F 1.071603 0.618744 0.000000 0\n",
"M V30 4 O -1.071603 -0.618744 0.000000 0\n",
"M V30 END ATOM\n",
"M V30 BEGIN BOND\n",
"M V30 1 2 1 2\n",
"M V30 2 1 2 3 CFG=2\n",
"M V30 3 1 1 4 CFG=2\n",
"M V30 END BOND\n",
"M V30 END CTAB\n",
"M END\n",
"\"\"\")"
]
},
{
"cell_type": "code",
"execution_count": 29,
"id": "429d8006-ca7c-45fa-8c56-3923c725337b",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:58.059098Z",
"iopub.status.busy": "2023-10-23T11:11:58.058210Z",
"iopub.status.idle": "2023-10-23T11:11:58.094616Z",
"shell.execute_reply": "2023-10-23T11:11:58.093390Z",
"shell.execute_reply.started": "2023-10-23T11:11:58.059036Z"
}
},
"outputs": [
{
"data": {
"image/png": "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\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7f830e6d6c10>"
]
},
"execution_count": 29,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mol"
]
},
{
"cell_type": "code",
"execution_count": 30,
"id": "1af1d0d4-593c-471c-bbc3-3ed8f355e25c",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:58.097232Z",
"iopub.status.busy": "2023-10-23T11:11:58.096492Z",
"iopub.status.idle": "2023-10-23T11:11:58.119477Z",
"shell.execute_reply": "2023-10-23T11:11:58.117978Z",
"shell.execute_reply.started": "2023-10-23T11:11:58.097193Z"
},
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"idx 1 bi 1 ei 2 type DOUBLE stereo STEREOANY dir NONE prop ['_MolFileBondType'] _MolFileBondType 2 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 2 bi 2 ei 3 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType', '_MolFileBondCfg', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 0 _MolFileBondCfg 2\n",
"idx 3 bi 1 ei 4 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType', '_MolFileBondCfg', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 0 _MolFileBondCfg 2\n"
]
}
],
"source": [
"print_bond_info(mol)"
]
},
{
"cell_type": "code",
"execution_count": 31,
"id": "24a31b1b-ac77-4c1d-966a-5a15a41efade",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:58.123580Z",
"iopub.status.busy": "2023-10-23T11:11:58.122703Z",
"iopub.status.idle": "2023-10-23T11:11:58.161350Z",
"shell.execute_reply": "2023-10-23T11:11:58.160139Z",
"shell.execute_reply.started": "2023-10-23T11:11:58.123519Z"
},
"tags": []
},
"outputs": [
{
"data": {
"image/png": "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\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7f830e6d6c10>"
]
},
"execution_count": 31,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"Chem.ReapplyMolBlockWedging(mol)\n",
"mol"
]
},
{
"cell_type": "code",
"execution_count": 32,
"id": "9e61f9d7-0bbd-4c71-abb5-412f3b7c8745",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:58.163717Z",
"iopub.status.busy": "2023-10-23T11:11:58.163061Z",
"iopub.status.idle": "2023-10-23T11:11:58.188260Z",
"shell.execute_reply": "2023-10-23T11:11:58.186477Z",
"shell.execute_reply.started": "2023-10-23T11:11:58.163678Z"
},
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"idx 1 bi 1 ei 2 type DOUBLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 2 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 2 bi 2 ei 3 type SINGLE stereo STEREONONE dir UNKNOWN prop ['_MolFileBondType', '_MolFileBondCfg', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 0 _MolFileBondCfg 2\n",
"idx 3 bi 1 ei 4 type SINGLE stereo STEREONONE dir UNKNOWN prop ['_MolFileBondType', '_MolFileBondCfg', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 0 _MolFileBondCfg 2\n"
]
}
],
"source": [
"print_bond_info(mol)"
]
},
{
"cell_type": "markdown",
"id": "df71a331-fa3a-440d-8b1d-099904e6ade1",
"metadata": {
"tags": []
},
"source": [
"### `double-2-explicit-crossed-2000.mol`"
]
},
{
"cell_type": "code",
"execution_count": 33,
"id": "49ae2129-85f6-42dc-8aef-f0dd351c6ed6",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:58.192309Z",
"iopub.status.busy": "2023-10-23T11:11:58.191451Z",
"iopub.status.idle": "2023-10-23T11:11:58.219769Z",
"shell.execute_reply": "2023-10-23T11:11:58.218227Z",
"shell.execute_reply.started": "2023-10-23T11:11:58.192249Z"
},
"tags": []
},
"outputs": [],
"source": [
"mol = Chem.MolFromMolBlock(\"\"\"double-2-explicit-crossed-2000.mol\n",
" ChemDraw10232310432D\n",
"\n",
" 4 3 0 0 0 0 0 0 0 0999 V2000\n",
" -0.3572 -0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 0.3572 0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 1.0716 0.6187 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -1.0716 -0.6187 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 1 2 2 3 \n",
" 2 3 1 4 \n",
" 1 4 1 4 \n",
"M END\n",
"\"\"\")"
]
},
{
"cell_type": "code",
"execution_count": 34,
"id": "52a2ecef-0f77-4b67-9d56-6ce18efd5790",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:58.223703Z",
"iopub.status.busy": "2023-10-23T11:11:58.222844Z",
"iopub.status.idle": "2023-10-23T11:11:58.297576Z",
"shell.execute_reply": "2023-10-23T11:11:58.296383Z",
"shell.execute_reply.started": "2023-10-23T11:11:58.223642Z"
}
},
"outputs": [
{
"data": {
"image/png": "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\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7f830e6df0b0>"
]
},
"execution_count": 34,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mol"
]
},
{
"cell_type": "code",
"execution_count": 35,
"id": "8906cd4b-071b-410c-bcd0-84ec01726a94",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:58.299744Z",
"iopub.status.busy": "2023-10-23T11:11:58.299299Z",
"iopub.status.idle": "2023-10-23T11:11:58.323687Z",
"shell.execute_reply": "2023-10-23T11:11:58.321967Z",
"shell.execute_reply.started": "2023-10-23T11:11:58.299711Z"
},
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"idx 1 bi 1 ei 2 type DOUBLE stereo STEREOANY dir NONE prop ['_MolFileBondType', '_MolFileBondStereo'] _MolFileBondType 2 _UnknownStereo 0 _MolFileBondStereo 3 _MolFileBondCfg 0\n",
"idx 2 bi 2 ei 3 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType', '_MolFileBondStereo', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 4 _MolFileBondCfg 0\n",
"idx 3 bi 1 ei 4 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType', '_MolFileBondStereo', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 4 _MolFileBondCfg 0\n"
]
}
],
"source": [
"print_bond_info(mol)"
]
},
{
"cell_type": "code",
"execution_count": 36,
"id": "01b6d3dd-472f-4f3c-9c6a-0e91ef4ba362",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:58.327786Z",
"iopub.status.busy": "2023-10-23T11:11:58.326938Z",
"iopub.status.idle": "2023-10-23T11:11:58.365705Z",
"shell.execute_reply": "2023-10-23T11:11:58.364516Z",
"shell.execute_reply.started": "2023-10-23T11:11:58.327725Z"
},
"tags": []
},
"outputs": [
{
"data": {
"image/png": "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\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7f830e6df0b0>"
]
},
"execution_count": 36,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"Chem.ReapplyMolBlockWedging(mol)\n",
"mol"
]
},
{
"cell_type": "code",
"execution_count": 37,
"id": "f89bdb7f-b794-445b-877f-9456209ade2d",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:58.368249Z",
"iopub.status.busy": "2023-10-23T11:11:58.367500Z",
"iopub.status.idle": "2023-10-23T11:11:58.391935Z",
"shell.execute_reply": "2023-10-23T11:11:58.390263Z",
"shell.execute_reply.started": "2023-10-23T11:11:58.368211Z"
},
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"idx 1 bi 1 ei 2 type DOUBLE stereo STEREOANY dir EITHERDOUBLE prop ['_MolFileBondType', '_MolFileBondStereo'] _MolFileBondType 2 _UnknownStereo 0 _MolFileBondStereo 3 _MolFileBondCfg 0\n",
"idx 2 bi 2 ei 3 type SINGLE stereo STEREONONE dir UNKNOWN prop ['_MolFileBondType', '_MolFileBondStereo', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 4 _MolFileBondCfg 0\n",
"idx 3 bi 1 ei 4 type SINGLE stereo STEREONONE dir UNKNOWN prop ['_MolFileBondType', '_MolFileBondStereo', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 4 _MolFileBondCfg 0\n"
]
}
],
"source": [
"print_bond_info(mol)"
]
},
{
"cell_type": "markdown",
"id": "9dabd8e1-29f4-4949-ae85-d90d8caf7160",
"metadata": {
"tags": []
},
"source": [
"### `double-2-explicit-crossed-3000.mol`"
]
},
{
"cell_type": "code",
"execution_count": 38,
"id": "965f25ae-581c-4b9b-aebe-bb58182713b8",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:58.395875Z",
"iopub.status.busy": "2023-10-23T11:11:58.395025Z",
"iopub.status.idle": "2023-10-23T11:11:58.439319Z",
"shell.execute_reply": "2023-10-23T11:11:58.437745Z",
"shell.execute_reply.started": "2023-10-23T11:11:58.395814Z"
},
"tags": []
},
"outputs": [],
"source": [
"mol = Chem.MolFromMolBlock(\"\"\"double-2-explicit-crossed-3000.mol\n",
" ChemDraw10232310422D\n",
"\n",
" 0 0 0 0 0 0 V3000\n",
"M V30 BEGIN CTAB\n",
"M V30 COUNTS 4 3 0 0 0\n",
"M V30 BEGIN ATOM\n",
"M V30 1 C -0.357168 -0.206181 0.000000 0\n",
"M V30 2 C 0.357167 0.206182 0.000000 0\n",
"M V30 3 F 1.071603 0.618744 0.000000 0\n",
"M V30 4 O -1.071603 -0.618744 0.000000 0\n",
"M V30 END ATOM\n",
"M V30 BEGIN BOND\n",
"M V30 1 2 1 2 CFG=2\n",
"M V30 2 1 2 3 CFG=2\n",
"M V30 3 1 1 4 CFG=2\n",
"M V30 END BOND\n",
"M V30 END CTAB\n",
"M END\n",
"\"\"\")"
]
},
{
"cell_type": "code",
"execution_count": 39,
"id": "a6029e6c-d221-45e3-9ed5-c659703d7271",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:58.443240Z",
"iopub.status.busy": "2023-10-23T11:11:58.442537Z",
"iopub.status.idle": "2023-10-23T11:11:58.559808Z",
"shell.execute_reply": "2023-10-23T11:11:58.557984Z",
"shell.execute_reply.started": "2023-10-23T11:11:58.443179Z"
}
},
"outputs": [
{
"data": {
"image/png": "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\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7f830e6df430>"
]
},
"execution_count": 39,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mol"
]
},
{
"cell_type": "code",
"execution_count": 40,
"id": "39eaf8a3-2c3b-41aa-b744-c1a17b1397a6",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:58.563448Z",
"iopub.status.busy": "2023-10-23T11:11:58.562705Z",
"iopub.status.idle": "2023-10-23T11:11:58.653611Z",
"shell.execute_reply": "2023-10-23T11:11:58.652057Z",
"shell.execute_reply.started": "2023-10-23T11:11:58.563386Z"
},
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"idx 1 bi 1 ei 2 type DOUBLE stereo STEREOANY dir NONE prop ['_MolFileBondType', '_MolFileBondCfg'] _MolFileBondType 2 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 2\n",
"idx 2 bi 2 ei 3 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType', '_MolFileBondCfg', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 0 _MolFileBondCfg 2\n",
"idx 3 bi 1 ei 4 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType', '_MolFileBondCfg', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 0 _MolFileBondCfg 2\n"
]
}
],
"source": [
"print_bond_info(mol)"
]
},
{
"cell_type": "code",
"execution_count": 41,
"id": "6bd67b86-4377-4ed5-b32f-7186473b6145",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:58.657679Z",
"iopub.status.busy": "2023-10-23T11:11:58.656791Z",
"iopub.status.idle": "2023-10-23T11:11:58.738652Z",
"shell.execute_reply": "2023-10-23T11:11:58.737358Z",
"shell.execute_reply.started": "2023-10-23T11:11:58.657616Z"
},
"tags": []
},
"outputs": [
{
"data": {
"image/png": "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\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7f830e6df430>"
]
},
"execution_count": 41,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"Chem.ReapplyMolBlockWedging(mol)\n",
"mol"
]
},
{
"cell_type": "code",
"execution_count": 42,
"id": "d6f54aeb-1201-4586-925e-2a4a065a7032",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:58.742181Z",
"iopub.status.busy": "2023-10-23T11:11:58.741453Z",
"iopub.status.idle": "2023-10-23T11:11:58.773358Z",
"shell.execute_reply": "2023-10-23T11:11:58.771579Z",
"shell.execute_reply.started": "2023-10-23T11:11:58.742118Z"
},
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"idx 1 bi 1 ei 2 type DOUBLE stereo STEREOANY dir EITHERDOUBLE prop ['_MolFileBondType', '_MolFileBondCfg'] _MolFileBondType 2 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 2\n",
"idx 2 bi 2 ei 3 type SINGLE stereo STEREONONE dir UNKNOWN prop ['_MolFileBondType', '_MolFileBondCfg', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 0 _MolFileBondCfg 2\n",
"idx 3 bi 1 ei 4 type SINGLE stereo STEREONONE dir UNKNOWN prop ['_MolFileBondType', '_MolFileBondCfg', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 0 _MolFileBondCfg 2\n"
]
}
],
"source": [
"print_bond_info(mol)"
]
},
{
"cell_type": "markdown",
"id": "5fc19ec3-3777-4018-ae71-273eec6c4607",
"metadata": {},
"source": [
"# Example 3"
]
},
{
"attachments": {
"d9dfad51-071c-4cc6-aadb-88f45bacceee.png": {
"image/png": "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"
}
},
"cell_type": "markdown",
"id": "218c9376-8b40-44e1-b1c7-570139aad529",
"metadata": {},
"source": [
"### ChemDraw\n",
"![image.png](attachment:d9dfad51-071c-4cc6-aadb-88f45bacceee.png)"
]
},
{
"cell_type": "markdown",
"id": "af716449-6b40-4977-9d4c-e5ab49af8e84",
"metadata": {},
"source": [
"### `di-imine-2-2000.mol`"
]
},
{
"cell_type": "code",
"execution_count": 43,
"id": "d9292541-7d44-4628-9394-2e90738384b3",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:58.777203Z",
"iopub.status.busy": "2023-10-23T11:11:58.776502Z",
"iopub.status.idle": "2023-10-23T11:11:58.805616Z",
"shell.execute_reply": "2023-10-23T11:11:58.803825Z",
"shell.execute_reply.started": "2023-10-23T11:11:58.777142Z"
},
"tags": []
},
"outputs": [],
"source": [
"mol = Chem.MolFromMolBlock(\"\"\"di-imine-2-2000.mol\n",
" ChemDraw10192311522D\n",
"\n",
" 8 7 0 0 0 0 0 0 0 0999 V2000\n",
" -0.9959 -1.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -0.4125 -0.4767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 0.4125 -0.4767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 0.9959 -1.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -0.7282 0.2855 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -0.9971 1.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 0.7282 0.2855 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 0.9971 1.0270 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 1 2 1 0 0\n",
" 2 3 1 0 0\n",
" 3 4 1 0 0\n",
" 2 5 2 0 0\n",
" 5 6 1 4 0\n",
" 3 7 2 0 0\n",
" 7 8 1 4 0\n",
"M END\n",
"\"\"\")"
]
},
{
"cell_type": "code",
"execution_count": 44,
"id": "5b1fa427-bed0-4430-ae53-f2652660f731",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:58.809343Z",
"iopub.status.busy": "2023-10-23T11:11:58.808646Z",
"iopub.status.idle": "2023-10-23T11:11:58.849627Z",
"shell.execute_reply": "2023-10-23T11:11:58.848403Z",
"shell.execute_reply.started": "2023-10-23T11:11:58.809282Z"
}
},
"outputs": [
{
"data": {
"image/png": "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\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7f830e6df740>"
]
},
"execution_count": 44,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mol"
]
},
{
"cell_type": "code",
"execution_count": 45,
"id": "d7660376-b798-4199-ac32-2b5a78f9b490",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:58.851823Z",
"iopub.status.busy": "2023-10-23T11:11:58.851288Z",
"iopub.status.idle": "2023-10-23T11:11:59.023055Z",
"shell.execute_reply": "2023-10-23T11:11:59.021280Z",
"shell.execute_reply.started": "2023-10-23T11:11:58.851785Z"
},
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"idx 1 bi 1 ei 2 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 2 bi 2 ei 3 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 3 bi 3 ei 4 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 4 bi 2 ei 5 type DOUBLE stereo STEREOANY dir NONE prop ['_MolFileBondType'] _MolFileBondType 2 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 5 bi 5 ei 6 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType', '_MolFileBondStereo', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 4 _MolFileBondCfg 0\n",
"idx 6 bi 3 ei 7 type DOUBLE stereo STEREOANY dir NONE prop ['_MolFileBondType'] _MolFileBondType 2 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 7 bi 7 ei 8 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType', '_MolFileBondStereo', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 4 _MolFileBondCfg 0\n"
]
}
],
"source": [
"print_bond_info(mol)"
]
},
{
"cell_type": "code",
"execution_count": 46,
"id": "cbc069d8-0066-43fb-beb0-c80921d0ae7b",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:59.027673Z",
"iopub.status.busy": "2023-10-23T11:11:59.026781Z",
"iopub.status.idle": "2023-10-23T11:11:59.091320Z",
"shell.execute_reply": "2023-10-23T11:11:59.090094Z",
"shell.execute_reply.started": "2023-10-23T11:11:59.027610Z"
},
"tags": []
},
"outputs": [
{
"data": {
"image/png": "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\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7f830e6df740>"
]
},
"execution_count": 46,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"Chem.ReapplyMolBlockWedging(mol)\n",
"mol"
]
},
{
"cell_type": "code",
"execution_count": 47,
"id": "9e4a0ca3-7d8e-4da3-82e5-f98a53de38e8",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:59.093611Z",
"iopub.status.busy": "2023-10-23T11:11:59.093075Z",
"iopub.status.idle": "2023-10-23T11:11:59.120773Z",
"shell.execute_reply": "2023-10-23T11:11:59.118989Z",
"shell.execute_reply.started": "2023-10-23T11:11:59.093573Z"
},
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"idx 1 bi 1 ei 2 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 2 bi 2 ei 3 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 3 bi 3 ei 4 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 4 bi 2 ei 5 type DOUBLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 2 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 5 bi 5 ei 6 type SINGLE stereo STEREONONE dir UNKNOWN prop ['_MolFileBondType', '_MolFileBondStereo', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 4 _MolFileBondCfg 0\n",
"idx 6 bi 3 ei 7 type DOUBLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 2 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 7 bi 7 ei 8 type SINGLE stereo STEREONONE dir UNKNOWN prop ['_MolFileBondType', '_MolFileBondStereo', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 4 _MolFileBondCfg 0\n"
]
}
],
"source": [
"print_bond_info(mol)"
]
},
{
"cell_type": "markdown",
"id": "2bff392a-f7d3-4f7c-af80-75234654b0eb",
"metadata": {},
"source": [
"### `di-imine-2-3000.mol`"
]
},
{
"cell_type": "code",
"execution_count": 48,
"id": "e1338522-eec7-4755-a564-ed691cd83794",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:59.124772Z",
"iopub.status.busy": "2023-10-23T11:11:59.123920Z",
"iopub.status.idle": "2023-10-23T11:11:59.169085Z",
"shell.execute_reply": "2023-10-23T11:11:59.167297Z",
"shell.execute_reply.started": "2023-10-23T11:11:59.124711Z"
},
"tags": []
},
"outputs": [],
"source": [
"mol = Chem.MolFromMolBlock(\"\"\"di-imine-2-3000.mol\n",
" ChemDraw10232310302D\n",
"\n",
" 0 0 0 0 0 0 V3000\n",
"M V30 BEGIN CTAB\n",
"M V30 COUNTS 8 7 0 0 0\n",
"M V30 BEGIN ATOM\n",
"M V30 1 C -0.995922 -1.060024 0.000000 0\n",
"M V30 2 C -0.412509 -0.476711 0.000000 0\n",
"M V30 3 C 0.412509 -0.476711 0.000000 0\n",
"M V30 4 C 0.995923 -1.060024 0.000000 0\n",
"M V30 5 N -0.728217 0.285506 0.000000 0\n",
"M V30 6 C -0.997122 1.060024 0.000000 0\n",
"M V30 7 N 0.728216 0.285506 0.000000 0\n",
"M V30 8 C 0.997122 1.027023 0.000000 0\n",
"M V30 END ATOM\n",
"M V30 BEGIN BOND\n",
"M V30 1 1 1 2\n",
"M V30 2 1 2 3\n",
"M V30 3 1 3 4\n",
"M V30 4 2 2 5\n",
"M V30 5 1 5 6 CFG=2\n",
"M V30 6 2 3 7\n",
"M V30 7 1 7 8 CFG=2\n",
"M V30 END BOND\n",
"M V30 END CTAB\n",
"M END\n",
"\"\"\")"
]
},
{
"cell_type": "code",
"execution_count": 49,
"id": "9a10ff4b-e764-4b6a-ab30-16e448b051eb",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:59.172912Z",
"iopub.status.busy": "2023-10-23T11:11:59.172217Z",
"iopub.status.idle": "2023-10-23T11:11:59.232674Z",
"shell.execute_reply": "2023-10-23T11:11:59.231473Z",
"shell.execute_reply.started": "2023-10-23T11:11:59.172837Z"
}
},
"outputs": [
{
"data": {
"image/png": "iVBORw0KGgoAAAANSUhEUgAAAcIAAACWCAIAAADCEh9HAAAABmJLR0QA/wD/AP+gvaeTAAAQUElEQVR4nO3de1BU1wEG8G+XJQgIQQFFRcAH9UEAqzU+4lSsUvFdJ4gIYmy1Ipg4SdWmptG2hsaM1qqJ1kaxf+CT2CiOyUikg2gdNWOYMUiMFkUjqETRVeoij81u/7hXQIrCPuDcu/f7/XVcvTPf6Phxzt5zz9VZrVYQEZG99KIDEBGpG2uUiMghrFEiIoewRomIHMIaJSJyCGuUiMghBtEBqH3dvHkzMzPT29t7+fLlorMQuSYd9426tnPnzr388stBQUHl5eVubm6i4xC5IC7qXdzw4cPDw8MrKipOnDghOovmZGZm7tix4+HDh6KDUPtijbq+2bNnA9i/f7/oINpisVjWrFmzaNGi4uJi0VmofXFR7/ouXbo0aNCgLl26VFRUvPDCC6LjaEV+fv748ePDwsJKS0t1Op3oONSOOBt1fQMHDoyKijIajceOHROdRUN27doFYN68eexQl8ca1YQ5c+YA2Ldvn+ggWlFTU3Po0CEASUlJorNQu2ONakJSUpJOpzt8+LDJZBKdRRNycnIePnw4YsSIAQMGiM5C7Y41qgkhISEjR440mUyfffaZ6CyaIK3oU1JSRAehjsAa1Qqu6zvMnTt38vLy3N3dpT0S5PJYo1oxe/Zsg8Fw9OjR+/fvi87i4vbt21dfXz9p0qSAgADRWagjsEa1olu3bjExMXV1dTk5OaKzuDiu6LWGNaohiYmJ4Lq+nV26dKmwsNDX13fKlCmis1AHYY1qyKuvvurh4ZGfn3/r1i3RWVyWNBVNSEjw9PQUnYU6CGtUQ/z8/CZOnGixWD799FPRWVyT1WqVJvtc0WsKa1RbeL++XZ08efLatWuhoaFjxowRnYU6DmtUW6ZPn965c+ezZ89eu3ZNdBYXJK3o586dq9fzf5aG8B9bW7y8vFJSlowdu+rIES/RWVxNTU2N9G2JNOUn7eDp95ozadIH27bBaMTSpaKjuJajR2uHDHnd0/PbiIgI0VmoQ/GgPM2pr0ePHrh3D8XF4P93J5o+HUeOYPNm/nzSHC7qNcfdHTNnAkB2tugoLuTePXzxBQwG8PlPDWKNapH03d3eveBSxFn27UNdHSZORPfuoqNQh2ONalFMDHr2xNWrKCwUHcVV7NoFANwtqk2sUS3S6xEfDwDcP+oUJSU4dw6+vpg2TXQUEoE1qlHSun7/flgsoqOoX1YWrFbEx8OLu8g0iTWqUSNHon9/3LqFU6dER1E5qxV79wJc0WsYa1S7Zs0CuK532KlTKC1Fr1746U9FRyFBWKPaJa3r//lP1NeLjqJmu3cDQEoK+PynZvFfXrsiI/HSS6isxL/+JTqKatXVQTotKzlZdBQShzWqadJeca7r7XbkCO7dw9CheOkl0VFIHNaops2ZA50OOTl4/Fh0FHXidlECa1Tj+vXDT36C//4Xn38uOooK3b+P3FwYDEhMFB2FhGKNal3DBlKy1f79qK1FbCyCgkRHIaFYo1qXmAg3N3z+OR4+FB1FbbiiJwnPG9W6Hj0wdy6Cg2E2i46iKlYrkpLQqRNmzBAdhUTjeaNERA7hbFSj1q1DXp48Dg7Gzp2t7x5ftQpnzwJAYKD8+KPrSUrC3bvyeMoUvPlm65dMnYraWgCIjcVvf9uO2UixWKMadfHiU7vuX3kFCxe2csn58/IlvXu3YzCxTp1CWZk8PnkSP/85Bg9u5ZLjx1FdDQC9erVvNlIs3mIiAHj7bdy5IzqEwtTVYfFinmxNrWONEgDcv48VK0SHUJ5//xtZWaJDkOKxRkmWlYX8fNEhlGfZMlRWig5BysYa1bpevRAdLY/T0uS7JTR2LDw8AODePaxcKToNKRtrVOv0emRkyOP//Afr1wtNoxhhYUhPl8c7d6KgQGQYUjjWKGHq1MYjh//8Z1y5IjSNYvz+9/DzAwCrFW+8wVNZ6ZlYowQAmzbBzQ0AamqwZInoNMrg74/Vq+VxcTH++lehaUjBWKMEAD/+MX71K3l87Biys4WmUYw33mg8SHTNGpSWCk1DSsUaJdnatfD3l8dvvokHD4SmUQaDARs3yuPqas7TqWWsUZL5+2PVKnlcUYF33xWaRjEmTMD06fI4NxcHDwpNQ4rEGqVGS5ZgyBB5vG2b/AQ9ffQRvL3l8euv80RBao41So0MBmzZAp0OACwWpKby9DwACAnB734nj2/fxp/+JDQNKQ9rlJ7yyiuYP18eFxVh61aRYZRjxQr86Efy+KOPcP680DSkMKxRam79egQEyOPVq1FRITSNMnh4NP5EMZuxZAmPLKFGrFFqzt8f770nj6uq8Mc/igyjHBMmICFBHp8+jU8+EZqGlIQ1Si1YtAgjR8rjHTtQWCg0jWJs3owXX5THy5fLx4wSsUapBXo9tmyRn2uyWLB8uehAyhAU1PhcU3k5NmwQmoYUgzVKLRs2DKmp8rigAEeOCE2jGEuXNh6ItW4dbt8WmoaUgTVKz7R2LXr0kMcrVvBsDuDpPWGPHnHzEwGsUXoOX1988IE8vnyZh8XJxozBvHnyeOdOntBKrFF6rpQUxMTIY/ZFgw0b5PMHzGb88IPoNCQaa5SeR6fDli1wdxedQ2H8/bFmjegQpBisUWpFRASWLhUdQnkWL8aIEaJDkDKwRql1f/gDgoNb/i2zWaPP3ev12LpV3hNGGscapdb5+LR89vuCBejcWd23ni5fRteuGDXKnmuHDcOvf+3sQKRCBtEBSIwlSzBlCgB4ebXpz8+ahZwc1NU9dUmnTqitRVERJkxon5TtT6eD0Yj79+VfbtsmP5sUFtamy9euxc9+Jo/beAm5HtaoRg0fjuHDbbvExwcxMdA3WcBERgJAUZEzg3UwgwFA4/cS0o8WoK3v9fPzw6xZ7RCLVIWLemqTt9/G+PH4y1+e+lB6nscFarTZkwXnziE8HPHxQhKR+rBGqU0mTIBOh9Wr8fXXjR9GRUGvx8WLKn7ASdrL1ewumXQmXt++AvKQGrFGqU1iY5GejtpaJCWhpkb+0NsbffqgthaXLwsN54Bmi3oARiMOHIBOx9tH1FasUWqrdeswYAAuXmw85QhAVBSg5nX9/y/qMzNRXY24OISHiwpFKsMapbby8sKePXB3x4YNjZucpBq9cEFcLMc0W9RbrdixAwDS04VFItVhjZINhg3DO+/AYkFKCoxG4EmNNv3CVF2aLepzc1FSgpAQTJokMBSpDGuUbPPuuxgxAuXl+M1vAJdb1G/bBgBpaXw8iWygs/LVXGSjq1cxZAgePcInnyA+Hn5+qKrC3buNL8JTF70eVissFpSVoW9fuLmhrAzduomORerB2SjZrF8/+RzS9HR8/z0iIgA1fz3asK7/+9/xww9ISGCHkm1Yo2SP9HRMnozKSsyf7yJfj1ZX4x//AIC0NLFxSH1Yo2QPnQ47dsDfH198gaoqQP2z0QMH8P33iI7G6NGiA5HasEbJTj17Yvt2ADh0CFDzXSZpz1NmJsB9TmQX3mIihyQnY+9eAPD0RFWVPLNTl+7dcecOAPj44OZN+PiIDkRqw9koOeRvf0NICAA8foySEtFp7NJQ/b/8JTuU7MEaJYe8+KJ8ZwYwZmWdFxvGPg1bRBctEpqDVIuLenKCqKiVFy6s69TJy2i826lTJ9FxbBMYiMpKjBqF06dFRyF14myUnCA1NRiw1NQ8WrlypegstrFYLI8fv2YwrP3FL26JzkJqxRolJ4iNjQWg0+k2b96cm5srOo4Njh8/bjJlmc3vREUVi85CasUaJSfo37+/t7e31Wq1Wq0LFy40SseWqMHHH38sDYKC+OgS2Yk1Sk6g1+sjIiIAREVF3bx5c6lKXmx/+/btnJwcnU4HoF69J/iTaKxRco6oqCgAM2fO9PHx2b17d3Z2tuhErdu+fXt9fX3Xrl0BmJu9SISozVij5BxSjd66dWv9+vUAFi9eXFZWJjrU85jN5szMTAA9e/YEa5QcwBol55BqtKioKDU1derUqQ8ePFiwYIGSt9MdPny4vLx84MCBgYGB4KKeHMAaJeeIjo7W6XTFxcUWi2Xnzp3du3fPy8vbJh2DrEhStrS0NIPBAM5GyQGsUXIOPz+/4OBgk8l05cqVbt26SXfAV6xYcVmRbw0tKSnJz8/38vJKSUlhjZKDWKPkNA3regAzZsx47bXXqqurk5OTFbhe3rp1q9VqnTt3bpcuXdzd3cFFPTmANUpOEx0dDeDCk5NHP/zww9DQ0MLCwvfff19oruaqq6uzsrIApKamAuBslBzEGiWniYyMBPD1k3PwfX19d+/e7ebmlpGR8eWXXwqN9pQ9e/YYjcbRo0cPHToUT2qUs1GyG2uUnKbpol4yZsyYt956y2w2JycnP3r0SFy0p0jf26Y9eVuItKjnbJTsxholpxkwYICnp+f169erpPeKAAAyMjIiIyOvXr2akZEhMFuDM2fOFBYWBgQExMfHS59wUU8OYo2S07i5uQ0aNMhqtV5o8mImDw+PXbt2JSQkLFu2TGC2BtI+p4ULFzYc6MdbTOQg1ig5k3SXqejpFzNFR0dnZ2dLu9zFqqysPHDggF6vX9TkiGbORslBKnx1DilYeHg4gI0bN546dUp0lhZcvHixpqYmLi6uT58+DR/yFhM5iDVKTmMymQ4ePBgYGFhSUlKi1BczBQYGlpWVVVVV+fr6Sp/wFhM5iDVKzlFVVRUXF/fVV1/17t1706ZNAQEBohO1oLKycsOGDd98801cXFxubq7UpFzUk4NYo+QEJpNp2rRpZ86cCQkJOX78eN++fUUneqaZM2eOGzfuzJkzDU3KW0zkIL7SjhxlMpkmT5588uRJ5Xeo5MaNG+PGjSstLR01alRubu6NGze+/fbbiIiIwYMHi45GqsQaJYeorkMlzZq04XtSIjtwwxPZT6UdCqAhsLS6b/q8AJGtWKNkJ/V2qIRNSs7CGiV7qL1DJWxScgrWKNnMNTpUwiYlx7FGyTau1KESNik5iDVKNnC9DpWwSckRrFFqK1ftUAmblOzGGqU2ce0OlbBJyT6sUWqdFjpUwiYlO7BGqRXa6VAJm5RsxRql59Fah0rYpGQT1ig9kzY7VMImpbZjjVLLtNyhEjYptRFrlFrADpWwSaktWKPUHDu0KTYptYrnjdJTmnZoQUFB01e/aRnPJ6Xn4GyUGrFDn4VzUnoO1ijJ2KHPxyalZ2GNEsAObRs2KbWINUrsUBuwSen/sUa1jh1qKzYpNcMa1TR2qH3YpNQUa1S72KGOYJNSA9aoRrFDHccmJQlrVIvYoc7CJiXwKSYNqqqqmjhx4tmzZ9mhztLwjNOwYcPy8vK6dOkiOhF1KM5GtYUd2h4a5qSFhYWxsbFGo1F0IupQrFENYYe2HzaplrFGtYId2t7YpJrFGtUEdmjHYJNqE2vU9bFDOxKbVIN4p97Fmc3msWPHnj59OiwsrKCgIDQ0VHQiTfjuu+9iYmKuX78+evToEydOGAwG0YmoHXE26uIMBsP8+fPDwsLy8/PZoR0mNDT0xIkT/fr1S0xMZIe6PM5GNcFkMnl7e4tOoTn8a9cI1igRkUO4qCcicghrlIjIIaxRIiKHsEaJiBzCGiUicsj/AJvvw+fksbSeAAAArHpUWHRyZGtpdFBLTCByZGtpdCAyMDI0LjAzLjFwcmUAAHice79v7T0GIOBnQAAOIGYH4gZGNoYEIM3IzMagAaSZWRA0RJwdwmfGxedmYGRgZFJgYmZgZNFiYmRgYWVgYgMx2NgZREBWiWeB1MEt3v+lbv+9de37QZxEk8v7yoW/7IOy7WDs81/q7GFq8nKs9t/QnWQHYic714P02oPYsTlW9kji9rWlzWBxMQAscCkeSM+ZSwAAARZ6VFh0TU9MIHJka2l0IDIwMjQuMDMuMXByZQAAeJyNUsFqwzAMvecr9AM2shJb9mGHJmlLGXWgzfYF2yGwbpf9P5PTem5YCZNikMXTs94jb5OaLtPnuyJVI6K+fH1UkOLUP0/f8BvUV9LHlS+EAK+JozpCKqDd7g8RunHT5k43vMTxDB5YJiSXyM04HHPHQAcKdQg2EIEyGh0iNYAa5yizdEU2hiyGuWLHxjxA1oL8F7CZgfPb9erbFmIiYvJkRJImby26B0CX5bAROSuMLIw3QrdG6G8rZj5ilF3/4raxX/h6dbodYl+cTknFTrlAXTwzcpriDEla6Hb7JyouGDmuaJV5EbLAsGAY/P1a90uke/5RpK5+AP5EfzRecTomAAAAhnpUWHRTTUlMRVMgcmRraXQgMjAyNC4wMy4xcHJlAAB4nG2OQQqAMAwEv+KxQlqSaBOj9NR7v+Olj7ctIgoeAsswyyaXlF2e+6WSp+o8BjMlZqCAgshwNKS8MSlg4C1GlMFW4ogGPako0YBm0VrXP+U/79aWjzYm5DXxfoS1STOce8sgQeoFhKElPhOUJuwAAAAASUVORK5CYII=\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7f830e6dfac0>"
]
},
"execution_count": 49,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mol"
]
},
{
"cell_type": "code",
"execution_count": 50,
"id": "2660f68c-6520-45ab-aa0b-5ca7174e54d2",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:59.234938Z",
"iopub.status.busy": "2023-10-23T11:11:59.234355Z",
"iopub.status.idle": "2023-10-23T11:11:59.259847Z",
"shell.execute_reply": "2023-10-23T11:11:59.258312Z",
"shell.execute_reply.started": "2023-10-23T11:11:59.234887Z"
},
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"idx 1 bi 1 ei 2 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 2 bi 2 ei 3 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 3 bi 3 ei 4 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 4 bi 2 ei 5 type DOUBLE stereo STEREOANY dir NONE prop ['_MolFileBondType'] _MolFileBondType 2 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 5 bi 5 ei 6 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType', '_MolFileBondCfg', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 0 _MolFileBondCfg 2\n",
"idx 6 bi 3 ei 7 type DOUBLE stereo STEREOANY dir NONE prop ['_MolFileBondType'] _MolFileBondType 2 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 7 bi 7 ei 8 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType', '_MolFileBondCfg', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 0 _MolFileBondCfg 2\n"
]
}
],
"source": [
"print_bond_info(mol)"
]
},
{
"cell_type": "code",
"execution_count": 51,
"id": "7321f052-87d1-4dce-8489-c174f24f54bd",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:59.263714Z",
"iopub.status.busy": "2023-10-23T11:11:59.262867Z",
"iopub.status.idle": "2023-10-23T11:11:59.302595Z",
"shell.execute_reply": "2023-10-23T11:11:59.301401Z",
"shell.execute_reply.started": "2023-10-23T11:11:59.263653Z"
},
"tags": []
},
"outputs": [
{
"data": {
"image/png": "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\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7f830e6dfac0>"
]
},
"execution_count": 51,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"Chem.ReapplyMolBlockWedging(mol)\n",
"mol"
]
},
{
"cell_type": "code",
"execution_count": 52,
"id": "576434c4-246d-44c6-83a6-8b48cabadb34",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:59.304781Z",
"iopub.status.busy": "2023-10-23T11:11:59.304249Z",
"iopub.status.idle": "2023-10-23T11:11:59.330154Z",
"shell.execute_reply": "2023-10-23T11:11:59.328423Z",
"shell.execute_reply.started": "2023-10-23T11:11:59.304742Z"
},
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"idx 1 bi 1 ei 2 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 2 bi 2 ei 3 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 3 bi 3 ei 4 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 4 bi 2 ei 5 type DOUBLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 2 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 5 bi 5 ei 6 type SINGLE stereo STEREONONE dir UNKNOWN prop ['_MolFileBondType', '_MolFileBondCfg', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 0 _MolFileBondCfg 2\n",
"idx 6 bi 3 ei 7 type DOUBLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 2 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 7 bi 7 ei 8 type SINGLE stereo STEREONONE dir UNKNOWN prop ['_MolFileBondType', '_MolFileBondCfg', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 0 _MolFileBondCfg 2\n"
]
}
],
"source": [
"print_bond_info(mol)"
]
},
{
"cell_type": "markdown",
"id": "00ee6963-bee7-43a2-9e01-b09a66aeaa32",
"metadata": {},
"source": [
"### `di-imine-2-explicit-crossed-2000.mol`"
]
},
{
"cell_type": "code",
"execution_count": 53,
"id": "2f9d3fd2-76b5-40e1-aa3e-507913b61970",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:59.333941Z",
"iopub.status.busy": "2023-10-23T11:11:59.333242Z",
"iopub.status.idle": "2023-10-23T11:11:59.357389Z",
"shell.execute_reply": "2023-10-23T11:11:59.355785Z",
"shell.execute_reply.started": "2023-10-23T11:11:59.333866Z"
},
"tags": []
},
"outputs": [],
"source": [
"mol = Chem.MolFromMolBlock(\"\"\"di-imine-2-explicit-crossed-2000.mol\n",
" ChemDraw10232310432D\n",
"\n",
" 8 7 0 0 0 0 0 0 0 0999 V2000\n",
" -0.9959 -1.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -0.4125 -0.4767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 0.4125 -0.4767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 0.9959 -1.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -0.7282 0.2855 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -0.9971 1.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 0.7282 0.2855 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 0.9971 1.0270 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 1 2 1 0 \n",
" 2 3 1 0 \n",
" 3 4 1 0 \n",
" 2 5 2 3 \n",
" 5 6 1 4 \n",
" 3 7 2 0 \n",
" 7 8 1 4 \n",
"M END\n",
"\"\"\")"
]
},
{
"cell_type": "code",
"execution_count": 54,
"id": "a2cba633-b34f-4a34-be83-88a994b9bb2b",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:59.361559Z",
"iopub.status.busy": "2023-10-23T11:11:59.360671Z",
"iopub.status.idle": "2023-10-23T11:11:59.421121Z",
"shell.execute_reply": "2023-10-23T11:11:59.419885Z",
"shell.execute_reply.started": "2023-10-23T11:11:59.361497Z"
},
"tags": []
},
"outputs": [
{
"data": {
"image/png": "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\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7f830e6dff20>"
]
},
"execution_count": 54,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mol"
]
},
{
"cell_type": "code",
"execution_count": 55,
"id": "aa65244b-1029-40a9-9408-5bfa60cdd57a",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:59.424074Z",
"iopub.status.busy": "2023-10-23T11:11:59.423087Z",
"iopub.status.idle": "2023-10-23T11:11:59.509404Z",
"shell.execute_reply": "2023-10-23T11:11:59.507827Z",
"shell.execute_reply.started": "2023-10-23T11:11:59.424033Z"
},
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"idx 1 bi 1 ei 2 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 2 bi 2 ei 3 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 3 bi 3 ei 4 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 4 bi 2 ei 5 type DOUBLE stereo STEREOANY dir NONE prop ['_MolFileBondType', '_MolFileBondStereo'] _MolFileBondType 2 _UnknownStereo 0 _MolFileBondStereo 3 _MolFileBondCfg 0\n",
"idx 5 bi 5 ei 6 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType', '_MolFileBondStereo', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 4 _MolFileBondCfg 0\n",
"idx 6 bi 3 ei 7 type DOUBLE stereo STEREOANY dir NONE prop ['_MolFileBondType'] _MolFileBondType 2 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 7 bi 7 ei 8 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType', '_MolFileBondStereo', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 4 _MolFileBondCfg 0\n"
]
}
],
"source": [
"print_bond_info(mol)"
]
},
{
"cell_type": "code",
"execution_count": 56,
"id": "62c8f0f3-9c1c-436f-a522-2a1adbc455c4",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:59.513534Z",
"iopub.status.busy": "2023-10-23T11:11:59.512643Z",
"iopub.status.idle": "2023-10-23T11:11:59.571105Z",
"shell.execute_reply": "2023-10-23T11:11:59.569925Z",
"shell.execute_reply.started": "2023-10-23T11:11:59.513471Z"
},
"tags": []
},
"outputs": [
{
"data": {
"image/png": "iVBORw0KGgoAAAANSUhEUgAAAcIAAACWCAIAAADCEh9HAAAABmJLR0QA/wD/AP+gvaeTAAARg0lEQVR4nO3de1BU58EG8GdhURRBEdRYEVBjEBGxGi+JELFIpF5rOjGJjoZEjRYTk3ipiRoUQ9TBUtGYOjbFJl4ykraTtHG+YGwVqFUTIQKLUEUsiBcSQRBZkdvu98c5cssiy+7Cu7vn+f31enRnHnR89j2X9z0qvV4PIiIylYPoAEREto01SkRkFtYoEZFZWKNERGZhjRIRmYU1SkRkFtYoEZFZWKNERGZhjRIRmUUtOgB1hTt38M03uH0bY8di8mTRaYjsi4qLQZWguBi+vtDpAGDhQhw6BJVKdCYie8EaVYqNG1FVhSNHUFaGpCTMny86kAJcvYqhQ0WHoM7Ha6NK8cEH2L0b69YBQEaG6DQK0NCAyZMRFoa7d0VHoU7GGlWQK1dw8CAA+PuLjqIAxcXQ63HyJBYtEh2FOhlP6hWhpARbtuDAAdTVYfx4pKSgZ0/RmRSgpAQjRuDePZSUoF8/0Wmo0/BOvf2rqEBYGHJz4eSEqChs3coO7Sznz+PoUZSVYcwYTJgArRY6HXQ6qPn/zK7xn9f+/elPyM3Fk08iKYl3PDrR55/jpZfkxyE+/bTp+MKFcHcXFYq6AmvU/l28CABRUezQzhUdDZ0Oa9di5EikpyM9Hc7OiIjA6tWik1En47VR+7dnD958E4MH46WXcP06MjNRUYEnn0RcHPz8RIezI56eKCtDQQG/rhSHNWr/amsxYwb+9a/Wx/v2RV4e+vcXkckeLV2KxEQMGYJt2/DCC1zgoCCsUUXQ63H8ODQaDByIoCB4emLJEnz9NRIS8OabosPZi8pKTJ+Oc+cAYOxY/OMfGDRIdCbqErw2qggqFSIiEBHRdGTwYACorhaVyA65ueE//8GRI9i8Gd9/jzlzuMxBKTgbVZzCQsTE4NNPoVYjK4uP4lvevXsIDERREbKzERgoOg11Ps5GlSU+Hhs2oLYWzs7Yv58dahm5ufjzn1FSglGjMGECHB1RVwcAjo6ik1GX4GxUQY4fxy9/CUdHREYiOlo+ryczpaTg2Wfl3mwuLAwnTvBGkyJwNqogn30GvR7btskblJBFxMSgrg7LliEkBBcuID0dej1CQ7F+PTtUKVijCuLkBAB37qCuDsXFuHABd+9i0iSMHCk6mS27cwcAFi9GcDB3IVEontQryJkzCAmRVys2Uqmwfj22bxeUyfZFR+P99zFgAGJi8Oqr8ncVKQprVFmOHcOmTcjNhZcXgoLg7o6jR1FdjbQ0hISIDmebamvx61/j2DEAGD4cX37J2b3isEaVbvVq7NqF+Hgu/TbLV19h40ZoNPD2xuXL6N5ddCDqQty2WdHy8/H3vwPA8OGio9i42bORno6xY3HtGlJSRKehrsVbTAp18ya2bMEnn6CuDiEhmD5ddCAb9L//Yf9+FBfjiScwYQJ698b9+wAfF1UentQr0Y8/4umnUVCAbt2wbBliY9Gnj+hMtkajwcSJBlbTBgXh/HneaFIWzkaVKCEBBQUIDsahQ/D1FZ3GNu3YgepqzJ+PuXORk4Pz53H/PiZNwsaN7FDFYY0qUXY2ALzzDjvUdNLjos89hxdeEB2FROMtJiUaPRoA1q9HTAwiIzFmDIYPxyuv4NYt0clsx9y5APDaa4iLky+JkmLx2qgS3b2LZ56R56TNDR0KjYYvvDOKXo9ly5CYCACDBuHoUQQHi85EgrBGFaq2Fl98gbw8eHtjzBi4uWHBAvnFljxLNV5qKjZswJkzcHfHpUt8i7JC8dqoQnXr1roufXxw/jyqqgQFsk1TpuD0acycia+/xrFjeOUV0YFIBNYoAcDSpfjrX+U3WZLx0tLg5ITycgB8Gb1y8V+eAKC0FD164NAhvj6oA374AWFhqK8HAB8f/OpXogORILw2SgBw4QL69YOXl+gcNiUjA5s3o7wcY8Zg0yYMHCg6EAnCGlWouDicOCGPvbyQmAiH9h5+e+89+bWX/frhs886N54oCxbg9m15PHMm3nqr/Y/MmoWaGgAID8dvf9uJ2chq8aReoXJz8c9/Nv1y8mQsXdrORzIz5Y/Y8dtHTp9GcbE8TkvDs8+2v+vdqVPyc6O8HqJYfPyeAGD9evz4o+gQVqa2FitWgGdr1C7WKAHAnTt8QZMB//43Dh4UHYKsHmuUZAcP4uRJ0SGsz5o1KC0VHYKsG2tU6QYNQlCQPP7Nb+S7JTRliryDfVkZ3nlHdBqybqxRpXNwQGysPL58GTt3Ck1jNXx9ERUljw8c4Ib29CisUcKsWXjmGXn8wQe4ckVoGquxcaO8m7Vej9dfR12d6EBkrVijBAAJCfKrLx48wMqVotNYBw8PREfL44sXER8vNA1ZMdYoAcDPf45XX5XH33yDpCShaazGG29g1Ch5vHUrrl4VmoasFWuUZNu3w8NDHr/1FioqhKaxDmo1du2Sx9XVnKeTYaxRknl44L335HFJCTZtEprGakybhjlz5HFyMv72N6FpyCqxRqnJypUYM0Ye79snr6CnDz+Ei4s8fuMN3L0rNA1ZH9YoNVGrsXcvVCoA0OmwfLm8C5zCeXs3PTp66xa2bBEZhqwQa5RamDwZkZHyODsbH30kMoz1WLcOTzwhjz/8EBcuCE1DVoY1Sq3t3AlPT3kcHY2SEqFprEP37k3fKA0NeP11bllCTVij1JqHB95/Xx5XVvIcVjZtGubPl8dnzuDzz4WmIWvCGiUDXnsNkybJ448/RkaG0DRWY/du9O4tj9eu5evpScYaJQMcHLB3r7yuSafD2rWiA1mHxx5rWtd0/TrXNZGMNUqGjRuH5cvlcUoKvvpKaBqrsWpV04ZYcXG4dUtoGrIOrFFq0/btTa9pW7eOe3MALZ8Jq6pCTIzoQGQFWKPUJjc37Nghjy9d4mZxsuBgLF4sjxMTuUMrsUbpkRYtQmioPGZfNIqPl/cfqK9HQ4PoNCQaa5QeRaXC3r1wchKdw8p4eGDrVtEhyGqwRqkdAQFYtUp0COuzYgUmThQdgqwDa5Tat3kzvLwM/5atn9U2NJi4b4CDAz76SH4mjBSONUrtc3XF739v4PiSJejVC6dOdXkgyzl1Cr16YckSUz47bhyWLbN0ILJBatEBSIyVKzFzJgD07GnUn3/+eXz5JWprW3zE2Rk1NcjOxrRpnZOy82VloaYGPXrIv9y3T16b5Otr1Me3b8cvfiGPjfwI2R/WqEKNH4/x4zv2EVdXhIbCodkJTGAgAGRnWzJYF5PCSz8IIH+1AKiuNurjffrg+ec7IRbZFJ7Uk1HWr0dYGH73uxYHR48G7KJGpR+kUVUV3NwQGMhtnMgorFEyyrRpUKkQHY2srKaDgYFwcEBurq0ucKqvR14eVCoEBLQ4rtGgvh5OTvJqJaJHY42SUcLDERWFmhosWIAHD+SDrq4YMgQ1Nbh8WWg4U/33v6ipwbBhcHNrcVz6qmg1RSVqC2uUjBUXBz8/5OY27XKEh13TfIpqQ9qqS43G8HEig1ijZKyePXHkCJycEB/ftL5e6hqpd2xOW3Vp8IIpUVtYo9QB48ZhwwbodFi0COXlgD3ORvV65OQYOE7UFtYodcymTZg4EdevY/VqwMZv1hucdRYWoqICjz2G/v2FhCLbwxqljlGrceQIevXCJ5/gL3+R78/cuIHSUtHJOqisDDdvynfJmuMZPXUUa5Q6bNgweR/SqCj88IP8tJDNXR6VzuilZ7aak2q0cYt7onaxRskUUVGYMQOlpYiMtNXLo23dpm+1romoXaxRMoVKhY8/hocHjh9HZSVgg7NR3qYnS2GNkol+9jP88Y8A8MUXgA3eZTJYl9XVKCiAkxP8/YWEIpvEGiXTPfdc06KmixdN3LhTiIYG5OZCpWp98q7RoKEB/v7o1k1QMrJBrFEyyx/+AG9vAKiuRn6+6DRGu3QJ1dXw9W29DJRn9GQC1iiZpXdvHDggDcsPHswUG8Z4bdUl7y+RCVijZK6wMAQGvgt4JiSEPGjctsS65eXt8PdfHBKS0uo4n3YiE7BGyQKWL/cCdA8eVL377ruisxglI+N0Xt4hH5/Wawa4DJRMwBolCwgPDwegUql2796dnJwsOk77srOzAQS1nHYWF6OsDJ6eGDhQUCyyTaxRsoDHH3/cxcVFr9fr9fqlS5eWS9uWWKuKiorr16+7uLgMGzas+XGN5vjQoTPnzDksKhjZKNYoWYCDg0NAQACA0aNH37hxY5V1v9g+KytLr9ePGjXKoeU60MzMjKtX/6937+9FBSMbxRolyxg9ejSAefPmubq6Hj58OCkpSXSiNmVlZeFh4OakM/2fHid6NNYoWYbUPjdv3ty5cyeAFStWFBcXiw5lmEajAWuULIc1SpYhtU92dvby5ctnzZpVUVGxZMkSvVW+WtNgXdbU1OTn56vV6pEjRwrKRbaKNUqWERQUpFKpcnJydDpdYmLigAEDTpw4sW/fPtG5WtPpdBcvXgQQ2PIh+5ycnPr6ej8/P2dnZ0HRyFaxRsky+vTp4+XlpdVqr1y50r9///379wNYt27dpUuXREdrIT8/X6vVent7u7u7Nz/e1gVTonaxRsliGs/rAcydO/fll1++f//+woUL66zpNfZtXQCVLpgGch0odRxrlCxGeppd83Dn0T179vj4+GRkZGzbtk1orhakeEE/We9p8IF8ImOwRslipKlc1sN98N3c3A4fPuzo6BgbG/vtt98KjdZEivfTWSdv05PJWKNkMc1P6iXBwcFvv/12fX39woULq6qqxEVrYrAub9y4UVpa2rdvXy8vL0G5yIaxRsli/Pz8evToUVhYWCm9VwQAEBsbGxgYWFBQEBsbKzCbpLKysqioyNnZefjw4c2PcypK5mCNksU4Ojr6+/vr9XpNsxczde/e/dChQ/Pnz1+zZo3AbJLs7Gy9Xh8QEKBWq1sdBy+MkqlYo2RJUhNlt3wxU1BQUFJSUr9+/QSFatJWXUrHeZueTKNu/48QGU06Wd61a9fp06dFZzHgu+++w8OQzXE2SuZQWedyPbJFWq02NDS0qKjo9u3borO0acCAAQMHDkxNTXV7+BqmmpoaV1dXnU5XWVnZs2dPsfHIFnE2SpZRWVkZERGRnp4+ePDghIQET09P0YkMKC0tjY+Pz8zMjIiISE5Olpo0Ly+vrq5uxIgR7FAyDWuULECr1c6ePfvs2bPe3t6nTp0aOnSo6ERtmjdv3tSpU8+ePdvYpFwGSmbiST2ZS6vVzpgxIy0tzfo7VHLt2rWpU6devXr1qaeeSk5OvnfvXlpaWv/+/cPCwkRHI5vEGiWz2FyHSlo1qVur19UTdQQfeCLT2WiHAmgMLJ3dN18vQNRRrFEyke12qIRNSpbCGiVT2HqHStikZBGsUeow++hQCZuUzMcapY6xpw6VsEnJTKxR6gD761AJm5TMwRolY9lrh0rYpGQy1igZxb47VMImJdOwRql9SuhQCZuUTMAapXYop0MlbFLqKNYoPYrSOlTCJqUOYY1Sm5TZoRI2KRmPNUqGKblDJWxSMhJrlAxgh0rYpGQM1ii1xg5tjk1K7eJ+o9RC8w5NSUkZMmSI6ERWgfuT0iNwNkpN2KFt4ZyUHoE1SjJ26KOxSaktrFEC2KHGYZOSQaxRYod2AJuUfoo1qnTs0I5ik1IrrFFFY4eahk1KzbFGlYsdag42KTVijSoUO9R8bFKSsEaViB1qKWxSAlcxKVBlZeX06dPPnTvHDrWUxjVO48aNO3HihLu7u+hE1KU4G1UWdmhnaJyTZmRkhIeHl5eXi05EXYo1qiDs0M7DJlUy1qhSsEM7G5tUsVijisAO7RpsUmVijdo/dmhXYpMqEO/U27n6+vopU6acOXPG19c3JSXFx8dHdCJFKCoqCg0NLSwsfPrpp1NTU9VqtehE1Ik4G7VzarU6MjLS19f35MmT7NAu4+Pjk5qaOmzYsBdffJEdavc4G1UErVbr4uIiOoXi8K9dIVijRERm4Uk9EZFZWKNERGZhjRIRmYU1SkRkFtYoEZFZ/h/bwlP3+rwtQQAAAKt6VFh0cmRraXRQS0wgcmRraXQgMjAyNC4wMy4xcHJlAAB4nHu/b+09BiDgZ0AADiBmB+IGRjaGBCDNyMzGoAGkmVkQNEScHcJnxsXnZmBkYGRSYGJmYGTRY2JlZGBhZWFjYtNgYmNnYRMB2SWeBVIIt9n3c91+kXXt+0EcY+PL+9iEvuyDsu1gbKAae5iawGyr/Xy6k+xA7E+O9SC99lBxeyRx+z0lzWBxMQDnYCQ7CtQemAAAASB6VFh0TU9MIHJka2l0IDIwMjQuMDMuMXByZQAAeJyNkkFugzAQRfecYi5gNB6wjRddBEijqoqRWpoLJCwsJU3VZNHjdxzqOkgowsbS+PP8GX9x8MKf/OcgSAw/X0e/91ex/z5fLsNBECLmp/MxgzDe2ld/hf9BbcY6PnistbAr2CPbQiigXm9eHDT9qo5K0324/h0qMHyC55Rc9d02KhIaEJhbqywiCJmjZmc+kiOORSRpJEtJKpBcGW1myYLJRWB5Axd8W4ELRoYqur2nSqlZUMfrGMnyA0fDjksMq78Wox+Zeb+1aye5jknXnWtT0mFSipM3UKTMJK8yJUM8FTTPmydKKUheeirq4MLXmYiGSRN6vxdDi/cNhX38abjOfgFi4YhHyIJ0swAAAHl6VFh0U01JTEVTIHJka2l0IDIwMjQuMDMuMXByZQAAeJxljTEOgDAMA7/CWCQnaiOaEqpO2fsdFh5PYUHAYDnWWbH35sHnS637dITIZiUhcZSCGrnIKogsa85XXJJk0PCiNzbLBhptRaUvph9/faNnSzFj38YBZT1O93oeZGvv588AAAAASUVORK5CYII=\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7f830e6dff20>"
]
},
"execution_count": 56,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"Chem.ReapplyMolBlockWedging(mol)\n",
"mol"
]
},
{
"cell_type": "code",
"execution_count": 57,
"id": "15da7421-c78c-426f-9e8f-ed37adaf4f00",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:59.573451Z",
"iopub.status.busy": "2023-10-23T11:11:59.573022Z",
"iopub.status.idle": "2023-10-23T11:11:59.607966Z",
"shell.execute_reply": "2023-10-23T11:11:59.606248Z",
"shell.execute_reply.started": "2023-10-23T11:11:59.573413Z"
},
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"idx 1 bi 1 ei 2 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 2 bi 2 ei 3 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 3 bi 3 ei 4 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 4 bi 2 ei 5 type DOUBLE stereo STEREOANY dir EITHERDOUBLE prop ['_MolFileBondType', '_MolFileBondStereo'] _MolFileBondType 2 _UnknownStereo 0 _MolFileBondStereo 3 _MolFileBondCfg 0\n",
"idx 5 bi 5 ei 6 type SINGLE stereo STEREONONE dir UNKNOWN prop ['_MolFileBondType', '_MolFileBondStereo', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 4 _MolFileBondCfg 0\n",
"idx 6 bi 3 ei 7 type DOUBLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 2 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 7 bi 7 ei 8 type SINGLE stereo STEREONONE dir UNKNOWN prop ['_MolFileBondType', '_MolFileBondStereo', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 4 _MolFileBondCfg 0\n"
]
}
],
"source": [
"print_bond_info(mol)"
]
},
{
"cell_type": "markdown",
"id": "408687a1-fc7b-4812-bf0e-ec548b03ee34",
"metadata": {},
"source": [
"### `di-imine-2-explicit-crossed-3000.mol`"
]
},
{
"cell_type": "code",
"execution_count": 58,
"id": "0d7ec364-f387-4c8e-a82e-3dedb84039f9",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:59.612067Z",
"iopub.status.busy": "2023-10-23T11:11:59.611162Z",
"iopub.status.idle": "2023-10-23T11:11:59.639714Z",
"shell.execute_reply": "2023-10-23T11:11:59.637954Z",
"shell.execute_reply.started": "2023-10-23T11:11:59.612005Z"
},
"tags": []
},
"outputs": [],
"source": [
"mol = Chem.MolFromMolBlock(\"\"\"di-imine-2-explicit-crossed-3000.mol\n",
" ChemDraw10232310432D\n",
"\n",
" 0 0 0 0 0 0 V3000\n",
"M V30 BEGIN CTAB\n",
"M V30 COUNTS 8 7 0 0 0\n",
"M V30 BEGIN ATOM\n",
"M V30 1 C -0.995922 -1.060024 0.000000 0\n",
"M V30 2 C -0.412509 -0.476711 0.000000 0\n",
"M V30 3 C 0.412509 -0.476711 0.000000 0\n",
"M V30 4 C 0.995923 -1.060024 0.000000 0\n",
"M V30 5 N -0.728217 0.285506 0.000000 0\n",
"M V30 6 C -0.997122 1.060024 0.000000 0\n",
"M V30 7 N 0.728216 0.285506 0.000000 0\n",
"M V30 8 C 0.997122 1.027023 0.000000 0\n",
"M V30 END ATOM\n",
"M V30 BEGIN BOND\n",
"M V30 1 1 1 2\n",
"M V30 2 1 2 3\n",
"M V30 3 1 3 4\n",
"M V30 4 2 2 5 CFG=2\n",
"M V30 5 1 5 6 CFG=2\n",
"M V30 6 2 3 7\n",
"M V30 7 1 7 8 CFG=2\n",
"M V30 END BOND\n",
"M V30 END CTAB\n",
"M END\n",
"\"\"\")"
]
},
{
"cell_type": "code",
"execution_count": 59,
"id": "0e372ff1-82ca-4099-be3d-872276d0cf57",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:59.643701Z",
"iopub.status.busy": "2023-10-23T11:11:59.642831Z",
"iopub.status.idle": "2023-10-23T11:11:59.730147Z",
"shell.execute_reply": "2023-10-23T11:11:59.728908Z",
"shell.execute_reply.started": "2023-10-23T11:11:59.643639Z"
},
"tags": []
},
"outputs": [
{
"data": {
"image/png": "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\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7f830e69d040>"
]
},
"execution_count": 59,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mol"
]
},
{
"cell_type": "code",
"execution_count": 60,
"id": "c1f4352f-5168-4caf-990b-1bffbcb389d3",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:59.732363Z",
"iopub.status.busy": "2023-10-23T11:11:59.731943Z",
"iopub.status.idle": "2023-10-23T11:11:59.757352Z",
"shell.execute_reply": "2023-10-23T11:11:59.755811Z",
"shell.execute_reply.started": "2023-10-23T11:11:59.732326Z"
},
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"idx 1 bi 1 ei 2 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 2 bi 2 ei 3 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 3 bi 3 ei 4 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 4 bi 2 ei 5 type DOUBLE stereo STEREOANY dir NONE prop ['_MolFileBondType', '_MolFileBondCfg'] _MolFileBondType 2 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 2\n",
"idx 5 bi 5 ei 6 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType', '_MolFileBondCfg', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 0 _MolFileBondCfg 2\n",
"idx 6 bi 3 ei 7 type DOUBLE stereo STEREOANY dir NONE prop ['_MolFileBondType'] _MolFileBondType 2 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 7 bi 7 ei 8 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType', '_MolFileBondCfg', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 0 _MolFileBondCfg 2\n"
]
}
],
"source": [
"print_bond_info(mol)"
]
},
{
"cell_type": "code",
"execution_count": 61,
"id": "ede118f2-751d-4f19-8c70-19c93efb2a7f",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:59.761432Z",
"iopub.status.busy": "2023-10-23T11:11:59.760568Z",
"iopub.status.idle": "2023-10-23T11:11:59.796874Z",
"shell.execute_reply": "2023-10-23T11:11:59.795321Z",
"shell.execute_reply.started": "2023-10-23T11:11:59.761370Z"
},
"tags": []
},
"outputs": [
{
"data": {
"image/png": "iVBORw0KGgoAAAANSUhEUgAAAcIAAACWCAIAAADCEh9HAAAABmJLR0QA/wD/AP+gvaeTAAARiElEQVR4nO3de1BU58EG8GdhURRBEdRYERBjFBWhXhITJWLRSL3WZmKMjoZEjAYbk3ipGg1KJOpoqWhMrU1JEy+ZkHbStHG+YmwVqFETIQIrUKM4IHiLoIhcBNbd749zlIsLLLsL7549z++v16M78yjjs+f2vq/GaDSCiIgs5SQ6ABGRsrFGiYiswholIrIKa5SIyCqsUSIiq7BGiYiswholIrIKa5SIyCqsUSIiq2hFB6COcOsWvvkGN29i5EiMGyc6DZFj0XAyqBoUFcHfHwYDAMyfjwMHoNGIzkTkKFijarF+PSoqcOgQSkuRlIQ5c0QHUoFLlxAQIDoEtT/eG1WL99/Hrl1YvRoAMjJEp1GB+/cxbhzCw3Hnjugo1M5YoyqSn4/9+wEgMFB0FBUoKoLRiGPHsGCB6CjUznhRrwo3bmDTJiQmoq4Oo0cjNRVdu4rOpALXr2PIENy9i+vX0auX6DTUbvik3vGVlSE8HDk5cHHB669j82Z2aHs5cwaff47SUoSE4MknUVkJgwEGA7T8f+bQ+ON1fH/+M3JyMHo0kpL4xKMdffEFXnpJfh3i00/rj8+fD09PUaGoI7BGHV9ODgBER7ND21dMDAwGrFqFoUORno70dLi6IiICK1aITkbtjPdGHd/u3XjzTfTvj5deQnExMjNRVobRo7F9OwYPFh3OgXh7o7QU+fn8ulId1qjjq63F1Kn4z3+aHu/ZE3l56N1bRCZHFBWFxEQMGIAtW/Dii5zgoCKsUVUwGnHkCHQ69O2L4GB4e2PRIvzrX0hIwJtvig7nKMrLMWUKTp8GgJEj8c9/ol8/0ZmoQ/DeqCpoNIiIQERE/ZH+/QGgulpUIgfk4YFvv8WhQ9i4ET/8gJkzOc1BLXg2qjoFBYiNxaefQqtFVhZfxbe9u3cRFITCQmRnIyhIdBpqfzwbVZf4eLzzDmpr4eqKffvYobaRm4u//AXXr2P4cDz5JJydUVcHAM7OopNRh+DZqIocOYJf/hLOzoiMREyMfF1PVkpJwXPPyb3ZUHg4jh7lgyZV4Nmoinz2GYxGbNkiL1BCNhEbi7o6LF6M0FCcPYv0dBiNCAvDmjXsULVgjaqIiwsA3LqFujoUFeHsWdy5g7FjMXSo6GRKdusWACxciPHjuQqJSvGiXkVOnkRoqDxb8SGNBmvWYOtWQZmULyYGmzejTx/ExuLVV+XvKlIV1qi6HD6MDRuQmwsfHwQHw9MTn3+O6mqkpSE0VHQ4ZaqtxfPP4/BhABg0CF99xbN71WGNqt2KFdi5E/HxnPptla+/xvr10Ong64sff0TnzqIDUQfiss2qduEC/vEPABg0SHQUhZsxA+npGDkSly8jJUV0GupYfMSkUlevYtMmfPIJ6uoQGoopU0QHUqCCAvzxjyguxhNPYMwYdO+OqiqAr4uqDy/q1einn/DMM8jPR6dOWLwYcXHo0UN0JqXR6TB2rNybDQUH48wZPmhSF56NqlFCAvLzMX48DhyAv7/oNMq0bRuqqjBnDmbNgk6H9HRUVWHsWKxfzw5VHdaoGmVlAcDatexQy5WWAsDzz3OrauIjJlUKDgaAtWsRG4vISISEYNAgvPIKrl0TnUw5Zs0CgNdew/btXChL7XhvVI3KyvDss9Dpmh4PCIBOxw3vzGI0IioKH38MAP36ISkJ48aJzkSCsEZVqrYWX36J//0Pvr4ICYGHB+bNkze2fPFF0eGUIzUV69bh1Cl4euL8ee6irFK8N6pSnTph7txGR/z8cOYMKioEBVKmCRPw7beYOhXJyTh8GK+8IjoQicAaJQCIisLf/ibvZEnmS0uDiwvKygBwM3r14k+eAKCkBF264MABbh/UBjduIDwcej0A+PnhV78SHYgE4b1RAoCzZ9GrF3x8ROdQlIwMbNyI27cREoING9C3r+hAJAhrVKW2b8fRo/LYxweJiXBq7eW3d9+Vt73s1Quffda+8USZNw83b8rjadPw1lutf2T6dNTUAMDkyfjtb9sxG9ktXtSrVG4u/v3v+l+OG4eoqFY+kpkpf8SBdx85cQJFRfI4LQ3PPdf6qnfHj8tTQnk/RLX4+j0BwJo1+Okn0SHsTG0tli4Fr9aoVaxRAoBbt7hBkwn//S/27xcdguwea5Rk+/fj2DHRIezPypUoKREdguwba1Tt+vWTp9gDeP11+WkJTZggr2BfWop160SnIfvGGlU7JyfExcnjH3/Ejh1C09gNf39ER8vjxEQuaE8tYY0Spk/Hs8/K4/ffx8WLQtPYjfXr5dWsjUa88Qbq6kQHInvFGiUASEiQt764dw/LlolOYx+8vBATI4/PncPvfy80Ddkx1igBwM9/jldflcfffIOkJKFp7MYbb2D4cHn83nu4dEloGrJXrFGSbd0KLy95/NZb8nIbKqfVYudOeVxVxfN0Mo01SjIvL7z7rjy+fh0bNghNYzcmTcLMmfI4ORlffik0Ddkl1ijVW7YMISHyeO9eeQY9ffAB3Nzk8W9+gzt3hKYh+8MapXpaLfbsgUYDAAYDliyRV4FTOV9frF0rj69dQ2ys0DRkf1ij1Mi4cYiMlMfZ2fjwQ5Fh7Mfq1XjiCXn8wQfIzBSahuwMa5Sa2rED3t7yOCYG168LTWMfOneu/0bR67FsGZcsoXqsUWrKywubN8vj8nJs2iQyjP2YNKl+S/qTJ/HFF0LTkD1hjZIJr72GsWPl8UcfISNDaBq7sWsXuneXx6tWycuMErFGyQQnJ+zZI89rMhiwapXoQPbhscfq5zUVFyM+XmgashusUTJt1CgsWSKPU1Lw9ddC09iN5cvrF8Tavh3XrglNQ/aBNUrN2rq1fpu21au5NgfQ+J2wigq+/EQAa5Ra4OGBbdvk8fnzXCxONn48Fi6Ux4mJXKGVWKPUogULEBYmj9kXD8XHy+sP6PW4f190GhKNNUot0WiwZw9cXETnsDNeXnjvPdEhyG6wRqkVw4Zh+XLRIezP0qV46inRIcg+sEapdRs3wsfH9G/p9cqed29xficnfPih/E4YqRxrlFrn7m567fdFi9Ctm7IfPaWkoFs3LFpkyWdHjcLixbYORAqkFR2AxFi2DNOmAUDXrmb9+RdewFdfoba20UdcXVFTg+xsTJrUPinbX1YWamrQpYv8y7175blJ/v5mfXzrVvziF/LYzI+Q42GNqtSYMRgzpm0fcXdHWBicGlzABAUBQHa2LYN1MCm89BcB5K8WANXVZn28Rw+88EI7xCJF4UU9mWXNGoSH43e/a3RQms/jADX6cGKSpKICHh4ICuIyTmQW1iiZZdIkaDSIiUFWVv3BESPg5ITcXKVOcNLrkZcHJ6f6feskOh30eri4yLOViFrGGiWzTJ6M6GjU1GDePNy7Jx90c8OAAaipwfnzQsNZKi8PNTUICEC3bo2OS18VI0YICUXKwxolc23fjsGDkZtbv8oRHnSNQq/rpdiP1qVOZ/o4kUmsUTJX1644dAguLoiPr3/JSeoaqXcUp7m6bK5eiUxijVIbjBqFd96BwYAFC3D7NvCgaxreMFUQkxfvRiPOnTNxnKg5rFFqmw0b8NRTKC7GihWAI17UFxSgrAyPPYbevYWEIuVhjVLbaLU4dAjduuGTT/DXv2LgQHh44MoVlJSITtZGpaW4ehXu7hgwoNFxXtFTW7FGqc0GDpTXIY2Oxo0bGDYMUODtUemKPiio0YQCNPMmKVELWKNkiehoTJ2KkhJERir19mhzbzU1mddE1CrWKFlCo8FHH8HLC0eOoLwcUODZKB/Tk62wRslCP/sZ/vQnAPj73wEFPmUyWZfV1cjPh4sLAgOFhCJFYo2S5X796/pJTTk5Slp49P595OZCo2l68a7T4f59BAaiUydByUiBWKNklT/8Ab6+AFBdjQsXRKcx2/nzqK6Gvz88PBod5xU9WYA1Slbp3h0ffywNb+/fnyk2jPmaq0s+XyILsEbJWuHhCApaB3gnJITee7hsiX3Ly9sWGLgwNDSlyXG+7UQWYI2SDSxZ4gMY7t2rWLdunegsZsnIOJGXd8DPr+mcAU4DJQuwRskGJk+eDECj0ezatSs5OVl0nNZlZ2cDCG582llUhNJSeHujb19BsUiZWKNkA48//ribm5vRaDQajVFRUbelZUvsVVlZWXFxsZub28CBAxse1+mOBARMmznzoKhgpFCsUbIBJyenYcOGARgxYsSVK1eW2/fG9llZWUajcfjw4U6N54FmZmZcuvR/3bv/ICoYKRRrlGxjxIgRAGbPnu3u7n7w4MGkpCTRiZqVlZWFB4Ebkq70Hz1O1DLWKNmG1D5Xr17dsWMHgKVLlxYVFYkOZZpOpwNrlGyHNUq2IbVPdnb2kiVLpk+fXlZWtmjRIqNdbq1psi5ramouXLig1WqHDh0qKBcpFWuUbCM4OFij0Zw7d85gMCQmJvbp0+fo0aN79+4Vnaspg8GQk5MDIKjxS/bnzp3T6/WDBw92dXUVFI2UijVKttGjRw8fH5/KysqLFy/27t173759AFavXn3eznYNvXDhQmVlpa+vr6enZ8Pjzd0wJWoVa5Rs5uF1PYBZs2a9/PLLVVVV8+fPr7OnbeybuwEq3TAN4jxQajvWKNmM9Da77sHKo7t37/bz88vIyNiyZYvQXI1I8YIfme9p8oV8InOwRslmpFO5rAfr4Ht4eBw8eNDZ2TkuLu67774TGq2eFO/Rs04+pieLsUbJZhpe1EvGjx//9ttv6/X6+fPnV1RUiItWz2RdXrlypaSkpGfPnj4+PoJykYKxRslmBg8e3KVLl4KCgnJpXxEAQFxcXFBQUH5+flxcnMBskvLy8sLCQldX10GDBjU8zlNRsgZrlGzG2dk5MDDQaDTqGmzM1Llz5wMHDsyZM2flypUCs0mys7ONRuOwYcO0Wm2T4+CNUbIUa5RsSWqi7MYbMwUHByclJfXq1UtQqHrN1aV0nI/pyTLa1v8Ikdmki+WdO3eeOHFCdBYTvv/+ezwI2RDPRskaGvucrkdKVFlZGRYWVlhYePPmTdFZmtWnT5++ffumpqZ6PNiGqaamxt3d3WAwlJeXd+3aVWw8UiKejZJtlJeXR0REpKen9+/fPyEhwdvbW3QiE0pKSuLj4zMzMyMiIpKTk6UmzcvLq6urGzJkCDuULMMaJRuorKycMWPGqVOnfH19jx8/HhAQIDpRs2bPnj1x4sRTp049bFJOAyUr8aKerFVZWTl16tS0tDT771DJ5cuXJ06ceOnSpaeffjo5Ofnu3btpaWm9e/cODw8XHY0UiTVKVlFch0qaNKlHk+3qidqCLzyR5RTaoQAeBpau7hvOFyBqK9YoWUi5HSphk5KtsEbJEkrvUAmblGyCNUpt5hgdKmGTkvVYo9Q2jtShEjYpWYk1Sm3geB0qYZOSNVijZC5H7VAJm5Qsxholszh2h0rYpGQZ1ii1Tg0dKmGTkgVYo9QK9XSohE1KbcUapZaorUMlbFJqE9YoNUudHSphk5L5WKNkmpo7VMImJTOxRskEdqiETUrmYI1SU+zQhtik1CquN0qNNOzQlJSUAQMGiE5kF7g+KbWAZ6NUjx3aHJ6TUgtYoyRjh7aMTUrNYY0SwA41D5uUTGKNEju0Ddik9CjWqNqxQ9uKTUpNsEZVjR1qGTYpNcQaVS92qDXYpPQQa1Sl2KHWY5OShDWqRuxQW2GTEjiLSYXKy8unTJly+vRpdqitPJzjNGrUqKNHj3p6eopORB2KZ6Pqwg5tDw/PSTMyMiZPnnz79m3RiahDsUZVhB3aftikasYaVQt2aHtjk6oWa1QV2KEdg02qTqxRx8cO7UhsUhXik3oHp9frJ0yYcPLkSX9//5SUFD8/P9GJVKGwsDAsLKygoOCZZ55JTU3VarWiE1E74tmog9NqtZGRkf7+/seOHWOHdhg/P7/U1NSBAwfOnTuXHerweDaqCpWVlW5ubqJTqA7/2VWCNUpEZBVe1BMRWYU1SkRkFdYoEZFVWKNERFZhjRIRWeX/AWTJU/tZjqOBAAAAr3pUWHRyZGtpdFBLTCByZGtpdCAyMDI0LjAzLjFwcmUAAHice79v7T0GIOBnQAAOIGYH4gZGNoYEIM3IzMagAaSZWRA0RJwdwmfGxedmYGRgZFJgYmZgZNFjYmVkYGFlYWNi02BiY2dhEwHZJZ4FUgi3ef+Xuv331rXvB3ESTS7vKxf+sg/KtoOxz3+ps4epycux2n9Dd5IdiJ3sXA/Saw9ix+ZY2SOJ29eWNoPFxQA/zik4JUnM1AAAASl6VFh0TU9MIHJka2l0IDIwMjQuMDMuMXByZQAAeJyNUsFuwyAMvecr/AMg4wQIhx2apKumqYm0ZfuBNgekdq3aHvb5M2kZjVZFs0EyT4+H/cTWC7/3X4MgMXwfd37jL2JzOpzPw1bkiCj3h10GId6aV3+B36AmYxxnlnMOPoNGtoZQQLVcvbRQ94sqInX30fbvUILlG5xT5qLv1hFRUINA6Zx2RCCURINIBaDEMdJdujILRRrdWFljlXrAzJn5L2IxEse389m3NbRByFJJikeSVGqN5gHRxHGs4nFmFC0r3gTNnGB5azHqkUXu9S9v2TYTX69OV13bJKdDUrKTD5AnzxTvIjlDnBrq59UTJRcUbzMFTVDhcSagZaYNvd+DocX7hsI5fhqusx/jRYihcTVgUQAAAIx6VFh0U01JTEVTIHJka2l0IDIwMjQuMDMuMXByZQAAeJxtjjEKw1AMQ6/SMQHb2GpsxymZ/p7rdMnh+3/okEIHgRBPSO3Y29Tmof1oj3NSqUoDyESRCnqpJFZYkApWd40RLQbXIu4uI81GVuWFJ3Fvho4m/+P4C+IXvDbytsH3Jxc203vrnhZxConzAyIJJgEiCE8xAAAAAElFTkSuQmCC\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7f830e69d040>"
]
},
"execution_count": 61,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"Chem.ReapplyMolBlockWedging(mol)\n",
"mol"
]
},
{
"cell_type": "code",
"execution_count": 62,
"id": "224f8542-e60a-4f4a-bee8-138fbd08d481",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:59.800269Z",
"iopub.status.busy": "2023-10-23T11:11:59.799588Z",
"iopub.status.idle": "2023-10-23T11:11:59.824849Z",
"shell.execute_reply": "2023-10-23T11:11:59.822904Z",
"shell.execute_reply.started": "2023-10-23T11:11:59.800226Z"
},
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"idx 1 bi 1 ei 2 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 2 bi 2 ei 3 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 3 bi 3 ei 4 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 4 bi 2 ei 5 type DOUBLE stereo STEREOANY dir EITHERDOUBLE prop ['_MolFileBondType', '_MolFileBondCfg'] _MolFileBondType 2 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 2\n",
"idx 5 bi 5 ei 6 type SINGLE stereo STEREONONE dir UNKNOWN prop ['_MolFileBondType', '_MolFileBondCfg', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 0 _MolFileBondCfg 2\n",
"idx 6 bi 3 ei 7 type DOUBLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 2 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 7 bi 7 ei 8 type SINGLE stereo STEREONONE dir UNKNOWN prop ['_MolFileBondType', '_MolFileBondCfg', '_UnknownStereo'] _MolFileBondType 1 _UnknownStereo 1 _MolFileBondStereo 0 _MolFileBondCfg 2\n"
]
}
],
"source": [
"print_bond_info(mol)"
]
},
{
"cell_type": "markdown",
"id": "67bc1ce7-2b8d-4b0d-8154-42ec4a3bc4ca",
"metadata": {},
"source": [
"# Example 4"
]
},
{
"attachments": {
"be0fbfed-0050-407c-832d-da445c09e998.png": {
"image/png": "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"
}
},
"cell_type": "markdown",
"id": "115a9110-ea81-46a3-94d1-fd471a0600db",
"metadata": {},
"source": [
"### ChemDraw\n",
"![image.png](attachment:be0fbfed-0050-407c-832d-da445c09e998.png)"
]
},
{
"cell_type": "markdown",
"id": "5d41c2c6-b2bf-40cd-a057-225c809aa4c1",
"metadata": {},
"source": [
"### `di-imine-cross-2000.mol`"
]
},
{
"cell_type": "code",
"execution_count": 63,
"id": "bfea8de4-93f5-4efc-8383-2b5d3c6c16b4",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:59.829316Z",
"iopub.status.busy": "2023-10-23T11:11:59.828296Z",
"iopub.status.idle": "2023-10-23T11:11:59.854817Z",
"shell.execute_reply": "2023-10-23T11:11:59.853117Z",
"shell.execute_reply.started": "2023-10-23T11:11:59.829247Z"
},
"tags": []
},
"outputs": [],
"source": [
"mol = Chem.MolFromMolBlock(\"\"\"di-imine-cross-2000.mol\n",
" ChemDraw10192311582D\n",
"\n",
" 8 7 0 0 0 0 0 0 0 0999 V2000\n",
" -1.0099 -1.1129 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -0.5974 -0.3984 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 0.2276 -0.3984 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 0.6401 -1.1129 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -0.8109 0.3984 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 0.6401 0.3160 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n",
" -1.2234 1.1129 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 1.2234 0.8994 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 1 2 1 0 0\n",
" 2 3 1 0 0\n",
" 3 4 1 0 0\n",
" 2 5 2 3 0\n",
" 3 6 2 3 0\n",
" 5 7 1 0 0\n",
" 6 8 1 0 0\n",
"M END\n",
"\"\"\")"
]
},
{
"cell_type": "code",
"execution_count": 64,
"id": "4087158a-8d69-4620-9df1-29d25d2a0389",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:59.859629Z",
"iopub.status.busy": "2023-10-23T11:11:59.858512Z",
"iopub.status.idle": "2023-10-23T11:11:59.900209Z",
"shell.execute_reply": "2023-10-23T11:11:59.898844Z",
"shell.execute_reply.started": "2023-10-23T11:11:59.859557Z"
}
},
"outputs": [
{
"data": {
"image/png": "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\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7f830e69d2e0>"
]
},
"execution_count": 64,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mol"
]
},
{
"cell_type": "code",
"execution_count": 65,
"id": "014d4032-c4aa-427b-a7b5-5f51be8ffa0e",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:59.903472Z",
"iopub.status.busy": "2023-10-23T11:11:59.902403Z",
"iopub.status.idle": "2023-10-23T11:11:59.933344Z",
"shell.execute_reply": "2023-10-23T11:11:59.931230Z",
"shell.execute_reply.started": "2023-10-23T11:11:59.903427Z"
},
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"idx 1 bi 1 ei 2 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 2 bi 2 ei 3 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 3 bi 3 ei 4 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 4 bi 2 ei 5 type DOUBLE stereo STEREOANY dir NONE prop ['_MolFileBondType', '_MolFileBondStereo'] _MolFileBondType 2 _UnknownStereo 0 _MolFileBondStereo 3 _MolFileBondCfg 0\n",
"idx 5 bi 3 ei 6 type DOUBLE stereo STEREOANY dir NONE prop ['_MolFileBondType', '_MolFileBondStereo'] _MolFileBondType 2 _UnknownStereo 0 _MolFileBondStereo 3 _MolFileBondCfg 0\n",
"idx 6 bi 5 ei 7 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 7 bi 6 ei 8 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n"
]
}
],
"source": [
"print_bond_info(mol)"
]
},
{
"cell_type": "code",
"execution_count": 66,
"id": "829f03ee-dd0b-458b-9f2a-905d9fda29df",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:11:59.937394Z",
"iopub.status.busy": "2023-10-23T11:11:59.936488Z",
"iopub.status.idle": "2023-10-23T11:12:00.036569Z",
"shell.execute_reply": "2023-10-23T11:12:00.035331Z",
"shell.execute_reply.started": "2023-10-23T11:11:59.937331Z"
},
"tags": []
},
"outputs": [
{
"data": {
"image/png": "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\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7f830e69d2e0>"
]
},
"execution_count": 66,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"Chem.ReapplyMolBlockWedging(mol)\n",
"mol"
]
},
{
"cell_type": "code",
"execution_count": 67,
"id": "21d4d359-0f60-4484-b44f-2ef905d2a2c7",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:12:00.051850Z",
"iopub.status.busy": "2023-10-23T11:12:00.051251Z",
"iopub.status.idle": "2023-10-23T11:12:00.089848Z",
"shell.execute_reply": "2023-10-23T11:12:00.088053Z",
"shell.execute_reply.started": "2023-10-23T11:12:00.051816Z"
},
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"idx 1 bi 1 ei 2 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 2 bi 2 ei 3 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 3 bi 3 ei 4 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 4 bi 2 ei 5 type DOUBLE stereo STEREOANY dir EITHERDOUBLE prop ['_MolFileBondType', '_MolFileBondStereo'] _MolFileBondType 2 _UnknownStereo 0 _MolFileBondStereo 3 _MolFileBondCfg 0\n",
"idx 5 bi 3 ei 6 type DOUBLE stereo STEREOANY dir EITHERDOUBLE prop ['_MolFileBondType', '_MolFileBondStereo'] _MolFileBondType 2 _UnknownStereo 0 _MolFileBondStereo 3 _MolFileBondCfg 0\n",
"idx 6 bi 5 ei 7 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 7 bi 6 ei 8 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n"
]
}
],
"source": [
"print_bond_info(mol)"
]
},
{
"cell_type": "markdown",
"id": "ec74d489-345a-45da-826c-84f43231cffd",
"metadata": {},
"source": [
"### `di-imine-cross-3000.mol`"
]
},
{
"cell_type": "code",
"execution_count": 68,
"id": "8eca2093-6344-4c43-9e2b-689993726245",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:12:00.094013Z",
"iopub.status.busy": "2023-10-23T11:12:00.093021Z",
"iopub.status.idle": "2023-10-23T11:12:00.122238Z",
"shell.execute_reply": "2023-10-23T11:12:00.120073Z",
"shell.execute_reply.started": "2023-10-23T11:12:00.093945Z"
},
"tags": []
},
"outputs": [],
"source": [
"mol = Chem.MolFromMolBlock(\"\"\"di-imine-cross-3000.mol\n",
" ChemDraw10232310302D\n",
"\n",
" 0 0 0 0 0 0 V3000\n",
"M V30 BEGIN CTAB\n",
"M V30 COUNTS 8 7 0 0 0\n",
"M V30 BEGIN ATOM\n",
"M V30 1 C -1.009900 -1.112900 0.000000 0\n",
"M V30 2 C -0.597400 -0.398400 0.000000 0\n",
"M V30 3 C 0.227600 -0.398400 0.000000 0\n",
"M V30 4 C 0.640100 -1.112900 0.000000 0\n",
"M V30 5 N -0.810900 0.398400 0.000000 0\n",
"M V30 6 N 0.640100 0.316000 0.000000 0\n",
"M V30 7 C -1.223400 1.112900 0.000000 0\n",
"M V30 8 C 1.223400 0.899400 0.000000 0\n",
"M V30 END ATOM\n",
"M V30 BEGIN BOND\n",
"M V30 1 1 1 2\n",
"M V30 2 1 2 3\n",
"M V30 3 1 3 4\n",
"M V30 4 2 2 5 CFG=2\n",
"M V30 5 2 3 6 CFG=2\n",
"M V30 6 1 5 7\n",
"M V30 7 1 6 8\n",
"M V30 END BOND\n",
"M V30 END CTAB\n",
"M END\n",
"\"\"\")"
]
},
{
"cell_type": "code",
"execution_count": 69,
"id": "09625f1d-9e38-41f0-9656-42a0a58ec476",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:12:00.126464Z",
"iopub.status.busy": "2023-10-23T11:12:00.125619Z",
"iopub.status.idle": "2023-10-23T11:12:00.171187Z",
"shell.execute_reply": "2023-10-23T11:12:00.169775Z",
"shell.execute_reply.started": "2023-10-23T11:12:00.126395Z"
}
},
"outputs": [
{
"data": {
"image/png": "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\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7f830e69d740>"
]
},
"execution_count": 69,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mol"
]
},
{
"cell_type": "code",
"execution_count": 70,
"id": "6d1f8827-53cf-4864-a3b9-ce593be69488",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:12:00.174378Z",
"iopub.status.busy": "2023-10-23T11:12:00.173281Z",
"iopub.status.idle": "2023-10-23T11:12:00.200065Z",
"shell.execute_reply": "2023-10-23T11:12:00.198321Z",
"shell.execute_reply.started": "2023-10-23T11:12:00.174332Z"
},
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"idx 1 bi 1 ei 2 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 2 bi 2 ei 3 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 3 bi 3 ei 4 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 4 bi 2 ei 5 type DOUBLE stereo STEREOANY dir NONE prop ['_MolFileBondType', '_MolFileBondCfg'] _MolFileBondType 2 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 2\n",
"idx 5 bi 3 ei 6 type DOUBLE stereo STEREOANY dir NONE prop ['_MolFileBondType', '_MolFileBondCfg'] _MolFileBondType 2 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 2\n",
"idx 6 bi 5 ei 7 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 7 bi 6 ei 8 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n"
]
}
],
"source": [
"print_bond_info(mol)"
]
},
{
"cell_type": "code",
"execution_count": 71,
"id": "6cb4448a-df32-4ffa-9b7b-c78c98da03ac",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:12:00.204499Z",
"iopub.status.busy": "2023-10-23T11:12:00.203100Z",
"iopub.status.idle": "2023-10-23T11:12:00.243636Z",
"shell.execute_reply": "2023-10-23T11:12:00.242198Z",
"shell.execute_reply.started": "2023-10-23T11:12:00.204427Z"
},
"tags": []
},
"outputs": [
{
"data": {
"image/png": 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\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7f830e69d740>"
]
},
"execution_count": 71,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"Chem.ReapplyMolBlockWedging(mol)\n",
"mol"
]
},
{
"cell_type": "code",
"execution_count": 72,
"id": "fe78e370-dbac-4711-a418-ff42c59d768e",
"metadata": {
"execution": {
"iopub.execute_input": "2023-10-23T11:12:00.246874Z",
"iopub.status.busy": "2023-10-23T11:12:00.245758Z",
"iopub.status.idle": "2023-10-23T11:12:00.293409Z",
"shell.execute_reply": "2023-10-23T11:12:00.291605Z",
"shell.execute_reply.started": "2023-10-23T11:12:00.246834Z"
},
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"idx 1 bi 1 ei 2 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 2 bi 2 ei 3 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 3 bi 3 ei 4 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 4 bi 2 ei 5 type DOUBLE stereo STEREOANY dir EITHERDOUBLE prop ['_MolFileBondType', '_MolFileBondCfg'] _MolFileBondType 2 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 2\n",
"idx 5 bi 3 ei 6 type DOUBLE stereo STEREOANY dir EITHERDOUBLE prop ['_MolFileBondType', '_MolFileBondCfg'] _MolFileBondType 2 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 2\n",
"idx 6 bi 5 ei 7 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n",
"idx 7 bi 6 ei 8 type SINGLE stereo STEREONONE dir NONE prop ['_MolFileBondType'] _MolFileBondType 1 _UnknownStereo 0 _MolFileBondStereo 0 _MolFileBondCfg 0\n"
]
}
],
"source": [
"print_bond_info(mol)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "16db24d0-3bdf-474e-bb8c-eb53b0db43a4",
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "rdkit_master",
"language": "python",
"name": "rdkit_master"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.15"
}
},
"nbformat": 4,
"nbformat_minor": 5
}
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