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jbarnoud/issue-RepairGraph-PR2.ipynb

Created April 11, 2018 11:32
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Demonstration of a RepairGraph issue
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issue-RepairGraph-PR2.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"ExecuteTime": {
"end_time": "2018-04-11T11:28:33.646002Z",
"start_time": "2018-04-11T11:28:32.770834Z"
}
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Using redistributed KDTree\n"
]
}
],
"source": [
"import networkx as nx\n",
"import martinize2\n",
"import martinize2.forcefield\n",
"import collections"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"ExecuteTime": {
"end_time": "2018-04-11T11:28:52.581835Z",
"start_time": "2018-04-11T11:28:52.533163Z"
}
},
"outputs": [],
"source": [
"molecule = martinize2.molecule.Molecule()\n",
"molecule.add_nodes_from((\n",
" (0, {'resid': 1, 'resname': 'GLU', 'atomname': 'N', 'chain': 'A'}),\n",
" (1, {'resid': 1, 'resname': 'GLU', 'atomname': 'CA', 'chain': 'A'}),\n",
" (2, {'resid': 1, 'resname': 'GLU', 'atomname': 'C', 'chain': 'A'}),\n",
" (3, {'resid': 1, 'resname': 'GLU', 'atomname': 'O', 'chain': 'A'}),\n",
" (4, {'resid': 1, 'resname': 'GLU', 'atomname': 'CB', 'chain': 'A'}),\n",
" (5, {'resid': 1, 'resname': 'GLU', 'atomname': 'HB1', 'chain': 'A'}),\n",
" (6, {'resid': 1, 'resname': 'GLU', 'atomname': 'HB2', 'chain': 'A'}),\n",
" (7, {'resid': 1, 'resname': 'GLU', 'atomname': 'CG', 'chain': 'A'}),\n",
" (8, {'resid': 1, 'resname': 'GLU', 'atomname': 'HG1', 'chain': 'A'}),\n",
" (9, {'resid': 1, 'resname': 'GLU', 'atomname': 'HG2', 'chain': 'A'}),\n",
" (10, {'resid': 1, 'resname': 'GLU', 'atomname': 'CD', 'chain': 'A'}),\n",
" (11, {'resid': 1, 'resname': 'GLU', 'atomname': 'OE2', 'chain': 'A'}),\n",
" (12, {'resid': 1, 'resname': 'GLU', 'atomname': 'OE1', 'chain': 'A'}),\n",
" (13, {'resid': 1, 'resname': 'GLU', 'atomname': 'HE1', 'chain': 'A'}),\n",
" (14, {'resid': 1, 'resname': 'GLU', 'atomname': 'H', 'chain': 'A'}),\n",
" (15, {'resid': 1, 'resname': 'GLU', 'atomname': 'HA', 'chain': 'A'}),\n",
" (16, {'resid': 1, 'resname': 'GLU', 'atomname': 'HN', 'chain': 'A'}),\n",
"))\n",
"system = martinize2.System()\n",
"system.molecules = [molecule]\n",
"system.force_field = martinize2.forcefield.FORCE_FIELDS['universal']"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"ExecuteTime": {
"end_time": "2018-04-11T11:28:56.892534Z",
"start_time": "2018-04-11T11:28:56.881647Z"
}
},
"outputs": [],
"source": [
"name_count_before = collections.Counter(\n",
" node['atomname']\n",
" for molecule in system.molecules\n",
" for node in molecule.nodes.values()\n",
")"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {
"ExecuteTime": {
"end_time": "2018-04-11T11:28:57.741969Z",
"start_time": "2018-04-11T11:28:57.727303Z"
}
},
"outputs": [
{
"data": {
"text/plain": [
"Counter({'N': 1,\n",
" 'CA': 1,\n",
" 'C': 1,\n",
" 'O': 1,\n",
" 'CB': 1,\n",
" 'HB1': 1,\n",
" 'HB2': 1,\n",
" 'CG': 1,\n",
" 'HG1': 1,\n",
" 'HG2': 1,\n",
" 'CD': 1,\n",
" 'OE2': 1,\n",
" 'OE1': 1,\n",
" 'HE1': 1,\n",
" 'H': 1,\n",
" 'HA': 1,\n",
" 'HN': 1})"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"name_count_before"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"ExecuteTime": {
"end_time": "2018-04-11T11:28:59.722354Z",
"start_time": "2018-04-11T11:28:59.710564Z"
}
},
"outputs": [
{
"data": {
"text/plain": [
"17"
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"sum(name_count_before.values())"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {
"ExecuteTime": {
"end_time": "2018-04-11T11:29:06.318762Z",
"start_time": "2018-04-11T11:29:05.592325Z"
}
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Doing MCS matching for residue GLU1\n",
"{'N': 0, 'C': 2, 'CB': 4, 'HG1': 8, 'HG2': 9, 'CD': 10, 'HA': 15}\n",
"Missing atom GLU1:HN\n",
"{'N': 0, 'C': 2, 'CB': 4, 'HG1': 8, 'HG2': 9, 'CD': 10, 'HA': 15}\n",
"Missing atom GLU1:CA\n",
"{'N': 0, 'C': 2, 'CB': 4, 'HG1': 8, 'HG2': 9, 'CD': 10, 'HA': 15}\n",
"Missing atom GLU1:HB1\n",
"{'N': 0, 'C': 2, 'CB': 4, 'HG1': 8, 'HG2': 9, 'CD': 10, 'HA': 15}\n",
"Missing atom GLU1:HB2\n",
"{'N': 0, 'C': 2, 'CB': 4, 'HG1': 8, 'HG2': 9, 'CD': 10, 'HA': 15}\n",
"Missing atom GLU1:CG\n",
"{'N': 0, 'C': 2, 'CB': 4, 'HG1': 8, 'HG2': 9, 'CD': 10, 'HA': 15}\n",
"Missing atom GLU1:OE1\n",
"{'N': 0, 'C': 2, 'CB': 4, 'HG1': 8, 'HG2': 9, 'CD': 10, 'HA': 15}\n",
"Missing atom GLU1:OE2\n",
"{'N': 0, 'C': 2, 'CB': 4, 'HG1': 8, 'HG2': 9, 'CD': 10, 'HA': 15}\n",
"Missing atom GLU1:O\n"
]
}
],
"source": [
"martinize2.RepairGraph().run_system(system)"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {
"ExecuteTime": {
"end_time": "2018-04-11T11:29:14.816305Z",
"start_time": "2018-04-11T11:29:14.810185Z"
}
},
"outputs": [],
"source": [
"name_count_after = collections.Counter(\n",
" node['atomname']\n",
" for molecule in system.molecules\n",
" for node in molecule.nodes.values()\n",
")"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {
"ExecuteTime": {
"end_time": "2018-04-11T11:29:17.037531Z",
"start_time": "2018-04-11T11:29:17.031088Z"
}
},
"outputs": [
{
"data": {
"text/plain": [
"Counter({'N': 1,\n",
" 'CA': 2,\n",
" 'C': 1,\n",
" 'O': 2,\n",
" 'CB': 1,\n",
" 'HB1': 2,\n",
" 'HB2': 2,\n",
" 'CG': 2,\n",
" 'HG1': 1,\n",
" 'HG2': 1,\n",
" 'CD': 1,\n",
" 'OE2': 2,\n",
" 'OE1': 2,\n",
" 'HE1': 1,\n",
" 'H': 1,\n",
" 'HA': 1,\n",
" 'HN': 2})"
]
},
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"name_count_after"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {
"ExecuteTime": {
"end_time": "2018-04-11T11:29:18.777363Z",
"start_time": "2018-04-11T11:29:18.770732Z"
}
},
"outputs": [
{
"data": {
"text/plain": [
"25"
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"sum(name_count_after.values())"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {
"ExecuteTime": {
"end_time": "2018-04-11T11:29:30.385291Z",
"start_time": "2018-04-11T11:29:30.370776Z"
}
},
"outputs": [],
"source": [
"name_count_block = collections.Counter(\n",
" martinize2.forcefield.FORCE_FIELDS['universal'].blocks['GLU'].nodes.keys()\n",
")"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {
"ExecuteTime": {
"end_time": "2018-04-11T11:29:31.594095Z",
"start_time": "2018-04-11T11:29:31.579554Z"
}
},
"outputs": [
{
"data": {
"text/plain": [
"Counter({'N': 1,\n",
" 'HN': 1,\n",
" 'CA': 1,\n",
" 'HA': 1,\n",
" 'CB': 1,\n",
" 'HB1': 1,\n",
" 'HB2': 1,\n",
" 'CG': 1,\n",
" 'HG1': 1,\n",
" 'HG2': 1,\n",
" 'CD': 1,\n",
" 'OE1': 1,\n",
" 'OE2': 1,\n",
" 'C': 1,\n",
" 'O': 1})"
]
},
"execution_count": 13,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"name_count_block"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {
"ExecuteTime": {
"end_time": "2018-04-11T11:29:33.542096Z",
"start_time": "2018-04-11T11:29:33.524953Z"
}
},
"outputs": [
{
"data": {
"text/plain": [
"15"
]
},
"execution_count": 14,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"sum(name_count_block.values())"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {
"ExecuteTime": {
"end_time": "2018-04-11T11:29:34.832519Z",
"start_time": "2018-04-11T11:29:34.824189Z"
}
},
"outputs": [
{
"data": {
"text/plain": [
"[<martinize2.molecule.Molecule at 0x7f9d94e213c8>]"
]
},
"execution_count": 15,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"system.molecules"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"hide_input": false,
"kernelspec": {
"display_name": "Python 3 (oldm2)",
"language": "python",
"name": "oldm2"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.5"
},
"toc": {
"nav_menu": {},
"number_sections": true,
"sideBar": true,
"skip_h1_title": false,
"toc_cell": false,
"toc_position": {},
"toc_section_display": "block",
"toc_window_display": false
}
},
"nbformat": 4,
"nbformat_minor": 2
}
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