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jbarnoud/issue-RepairGraph-PR2.ipynb

Created April 11, 2018 20:05
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issue-RepairGraph-PR2.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"ExecuteTime": {
"end_time": "2018-04-11T20:03:41.767741Z",
"start_time": "2018-04-11T20:03:41.164828Z"
}
},
"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": "2018-04-11T20:03:41.779488Z",
"start_time": "2018-04-11T20:03:41.769948Z"
}
},
"outputs": [],
"source": [
"nter = nx.Graph()\n",
"nter.add_nodes_from((\n",
" (0, {'atomname': 'CA', 'PTM_atom': False, 'element': 'C'}),\n",
" (1, {'atomname': 'N', 'PTM_atom': False, 'element': 'N'}),\n",
" (2, {'atomname': 'HN', 'PTM_atom': False, 'element': 'H'}),\n",
" (3, {'atomname': 'H', 'PTM_atom': True, 'element': 'H'}),\n",
"))\n",
"nter.add_edges_from([[0, 1], [1, 2], [1, 3]])\n",
"\n",
"gluh = nx.Graph()\n",
"gluh.add_nodes_from((\n",
" (0, {'atomname': 'CD', 'PTM_atom': False, 'element': 'C'}),\n",
" (1, {'atomname': 'OE1', 'PTM_atom': False, 'element': 'O'}),\n",
" (2, {'atomname': 'OE2', 'PTM_atom': False, 'element': 'O'}),\n",
" (3, {'atomname': 'HE1', 'PTM_atom': True, 'element': 'H'}),\n",
"))\n",
"gluh.add_edges_from([[0, 1], [0, 2], [1, 3]])\n",
"martinize2.forcefield.FORCE_FIELDS['universal'].modifications = [nter, gluh]"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"ExecuteTime": {
"end_time": "2018-04-11T20:03:41.805750Z",
"start_time": "2018-04-11T20:03:41.783818Z"
}
},
"outputs": [],
"source": [
"molecule = martinize2.molecule.Molecule()\n",
"molecule.add_nodes_from((\n",
" (0, {'resid': 1, 'resname': 'GLU', 'atomname': 'N', 'chain': 'A', 'element': 'N'}),\n",
" (1, {'resid': 1, 'resname': 'GLU', 'atomname': 'CA', 'chain': 'A', 'element': 'C'}),\n",
" (2, {'resid': 1, 'resname': 'GLU', 'atomname': 'C', 'chain': 'A', 'element': 'C'}),\n",
" (3, {'resid': 1, 'resname': 'GLU', 'atomname': 'O', 'chain': 'A', 'element': 'O'}),\n",
" (4, {'resid': 1, 'resname': 'GLU', 'atomname': 'CB', 'chain': 'A', 'element': 'C'}),\n",
" (5, {'resid': 1, 'resname': 'GLU', 'atomname': 'HB1', 'chain': 'A', 'element': 'H'}),\n",
" (6, {'resid': 1, 'resname': 'GLU', 'atomname': 'HB2', 'chain': 'A', 'element': 'H'}),\n",
" (7, {'resid': 1, 'resname': 'GLU', 'atomname': 'CG', 'chain': 'A', 'element': 'C'}),\n",
" (8, {'resid': 1, 'resname': 'GLU', 'atomname': 'HG1', 'chain': 'A', 'element': 'H'}),\n",
" (9, {'resid': 1, 'resname': 'GLU', 'atomname': 'HG2', 'chain': 'A', 'element': 'H'}),\n",
" (10, {'resid': 1, 'resname': 'GLU', 'atomname': 'CD', 'chain': 'A', 'element': 'C'}),\n",
" (11, {'resid': 1, 'resname': 'GLU', 'atomname': 'OE2', 'chain': 'A', 'element': 'O'}),\n",
" (12, {'resid': 1, 'resname': 'GLU', 'atomname': 'OE1', 'chain': 'A', 'element': 'O'}),\n",
" (13, {'resid': 1, 'resname': 'GLU', 'atomname': 'HE1', 'chain': 'A', 'element': 'H'}),\n",
" (14, {'resid': 1, 'resname': 'GLU', 'atomname': 'H', 'chain': 'A', 'element': 'H'}),\n",
" (15, {'resid': 1, 'resname': 'GLU', 'atomname': 'HA', 'chain': 'A', 'element': 'H'}),\n",
" (16, {'resid': 1, 'resname': 'GLU', 'atomname': 'HN', 'chain': 'A', 'element': 'H'}),\n",
"))\n",
"molecule.add_edges_from([\n",
" [0, 1], [1, 2], [2, 3], [1, 4], [4, 5], [4, 6], [4, 7], [7, 8],\n",
" [7, 9], [7, 10], [10, 11], [10, 12], [12, 13], [14, 0], [15, 1], [16, 0],\n",
"])\n",
"system = martinize2.System()\n",
"system.molecules = [molecule]\n",
"system.force_field = martinize2.forcefield.FORCE_FIELDS['universal']"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {
"ExecuteTime": {
"end_time": "2018-04-11T20:03:41.818947Z",
"start_time": "2018-04-11T20:03:41.807438Z"
}
},
"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": 5,
"metadata": {
"ExecuteTime": {
"end_time": "2018-04-11T20:03:41.840786Z",
"start_time": "2018-04-11T20:03:41.821025Z"
}
},
"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": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"name_count_before"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {
"ExecuteTime": {
"end_time": "2018-04-11T20:03:41.847993Z",
"start_time": "2018-04-11T20:03:41.843615Z"
}
},
"outputs": [
{
"data": {
"text/plain": [
"17"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"sum(name_count_before.values())"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {
"ExecuteTime": {
"end_time": "2018-04-11T20:03:41.876396Z",
"start_time": "2018-04-11T20:03:41.850605Z"
}
},
"outputs": [],
"source": [
"martinize2.RepairGraph().run_system(system)"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {
"ExecuteTime": {
"end_time": "2018-04-11T20:03:41.886258Z",
"start_time": "2018-04-11T20:03:41.879735Z"
}
},
"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": "2018-04-11T20:03:41.900032Z",
"start_time": "2018-04-11T20:03:41.888643Z"
}
},
"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",
" 'OE1': 1,\n",
" 'OE2': 1,\n",
" 'HE1': 1,\n",
" 'HN': 2,\n",
" 'HA': 1})"
]
},
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"name_count_after"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {
"ExecuteTime": {
"end_time": "2018-04-11T20:03:41.910968Z",
"start_time": "2018-04-11T20:03:41.902614Z"
}
},
"outputs": [
{
"data": {
"text/plain": [
"17"
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"sum(name_count_after.values())"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {
"ExecuteTime": {
"end_time": "2018-04-11T20:03:41.919526Z",
"start_time": "2018-04-11T20:03:41.913014Z"
}
},
"outputs": [],
"source": [
"name_count_block = collections.Counter(\n",
" martinize2.forcefield.FORCE_FIELDS['universal'].blocks['GLU'].nodes.keys()\n",
")"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {
"ExecuteTime": {
"end_time": "2018-04-11T20:03:41.933827Z",
"start_time": "2018-04-11T20:03:41.921245Z"
}
},
"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": 12,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"name_count_block"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {
"ExecuteTime": {
"end_time": "2018-04-11T20:03:41.944965Z",
"start_time": "2018-04-11T20:03:41.936403Z"
}
},
"outputs": [
{
"data": {
"text/plain": [
"15"
]
},
"execution_count": 13,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"sum(name_count_block.values())"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {
"ExecuteTime": {
"end_time": "2018-04-11T20:03:41.967892Z",
"start_time": "2018-04-11T20:03:41.948353Z"
},
"scrolled": false
},
"outputs": [
{
"data": {
"text/plain": [
"[{'resid': 1,\n",
" 'resname': 'GLU',\n",
" 'atomname': 'N',\n",
" 'chain': 'A',\n",
" 'element': 'N',\n",
" 'graph': <martinize2.molecule.Molecule at 0x7f2613836358>,\n",
" 'atype': 'NH1',\n",
" 'charge': -0.47,\n",
" 'charge_group': 0},\n",
" {'resid': 1,\n",
" 'resname': 'GLU',\n",
" 'atomname': 'CA',\n",
" 'chain': 'A',\n",
" 'element': 'C',\n",
" 'graph': <martinize2.molecule.Molecule at 0x7f26138361d0>,\n",
" 'atype': 'CT1',\n",
" 'charge': 0.07,\n",
" 'charge_group': 2},\n",
" {'resid': 1,\n",
" 'resname': 'GLU',\n",
" 'atomname': 'C',\n",
" 'chain': 'A',\n",
" 'element': 'C',\n",
" 'graph': <martinize2.molecule.Molecule at 0x7f2613836320>,\n",
" 'atype': 'C',\n",
" 'charge': 0.51,\n",
" 'charge_group': 13},\n",
" {'resid': 1,\n",
" 'resname': 'GLU',\n",
" 'atomname': 'O',\n",
" 'chain': 'A',\n",
" 'element': 'O',\n",
" 'graph': <martinize2.molecule.Molecule at 0x7f26137ef438>,\n",
" 'atype': 'O',\n",
" 'charge': -0.51,\n",
" 'charge_group': 14},\n",
" {'resid': 1,\n",
" 'resname': 'GLU',\n",
" 'atomname': 'CB',\n",
" 'chain': 'A',\n",
" 'element': 'C',\n",
" 'graph': <martinize2.molecule.Molecule at 0x7f2613836a20>,\n",
" 'atype': 'CT2',\n",
" 'charge': -0.18,\n",
" 'charge_group': 4},\n",
" {'resid': 1,\n",
" 'resname': 'GLU',\n",
" 'atomname': 'HB1',\n",
" 'chain': 'A',\n",
" 'element': 'H',\n",
" 'graph': <martinize2.molecule.Molecule at 0x7f2613836a58>,\n",
" 'atype': 'HA',\n",
" 'charge': 0.09,\n",
" 'charge_group': 5},\n",
" {'resid': 1,\n",
" 'resname': 'GLU',\n",
" 'atomname': 'HB2',\n",
" 'chain': 'A',\n",
" 'element': 'H',\n",
" 'graph': <martinize2.molecule.Molecule at 0x7f26138367f0>,\n",
" 'atype': 'HA',\n",
" 'charge': 0.09,\n",
" 'charge_group': 6},\n",
" {'resid': 1,\n",
" 'resname': 'GLU',\n",
" 'atomname': 'CG',\n",
" 'chain': 'A',\n",
" 'element': 'C',\n",
" 'graph': <martinize2.molecule.Molecule at 0x7f26138366d8>,\n",
" 'atype': 'CT2',\n",
" 'charge': -0.28,\n",
" 'charge_group': 7},\n",
" {'resid': 1,\n",
" 'resname': 'GLU',\n",
" 'atomname': 'HG1',\n",
" 'chain': 'A',\n",
" 'element': 'H',\n",
" 'graph': <martinize2.molecule.Molecule at 0x7f2613836da0>,\n",
" 'atype': 'HA',\n",
" 'charge': 0.09,\n",
" 'charge_group': 8},\n",
" {'resid': 1,\n",
" 'resname': 'GLU',\n",
" 'atomname': 'HG2',\n",
" 'chain': 'A',\n",
" 'element': 'H',\n",
" 'graph': <martinize2.molecule.Molecule at 0x7f2613836d68>,\n",
" 'atype': 'HA',\n",
" 'charge': 0.09,\n",
" 'charge_group': 9},\n",
" {'resid': 1,\n",
" 'resname': 'GLU',\n",
" 'atomname': 'CD',\n",
" 'chain': 'A',\n",
" 'element': 'C',\n",
" 'graph': <martinize2.molecule.Molecule at 0x7f2613836ef0>,\n",
" 'atype': 'CC',\n",
" 'charge': 0.62,\n",
" 'charge_group': 10},\n",
" {'resid': 1,\n",
" 'resname': 'GLU',\n",
" 'atomname': 'OE1',\n",
" 'chain': 'A',\n",
" 'element': 'O',\n",
" 'graph': <martinize2.molecule.Molecule at 0x7f2613836eb8>,\n",
" 'atype': 'OC',\n",
" 'charge': -0.76,\n",
" 'charge_group': 11},\n",
" {'resid': 1,\n",
" 'resname': 'GLU',\n",
" 'atomname': 'OE2',\n",
" 'chain': 'A',\n",
" 'element': 'O',\n",
" 'graph': <martinize2.molecule.Molecule at 0x7f2613836f98>,\n",
" 'atype': 'OC',\n",
" 'charge': -0.76,\n",
" 'charge_group': 12},\n",
" {'resid': 1,\n",
" 'resname': 'GLU',\n",
" 'atomname': 'HE1',\n",
" 'chain': 'A',\n",
" 'element': 'H',\n",
" 'PTM_atom': True},\n",
" {'resid': 1,\n",
" 'resname': 'GLU',\n",
" 'atomname': 'HN',\n",
" 'chain': 'A',\n",
" 'element': 'H',\n",
" 'graph': <martinize2.molecule.Molecule at 0x7f26138360f0>,\n",
" 'atype': 'H',\n",
" 'charge': 0.31,\n",
" 'charge_group': 1},\n",
" {'resid': 1,\n",
" 'resname': 'GLU',\n",
" 'atomname': 'HA',\n",
" 'chain': 'A',\n",
" 'element': 'H',\n",
" 'graph': <martinize2.molecule.Molecule at 0x7f2613836b38>,\n",
" 'atype': 'HB',\n",
" 'charge': 0.09,\n",
" 'charge_group': 3},\n",
" {'resid': 1,\n",
" 'resname': 'GLU',\n",
" 'atomname': 'HN',\n",
" 'chain': 'A',\n",
" 'element': 'H',\n",
" 'PTM_atom': True}]"
]
},
"execution_count": 14,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"list(system.molecules[0].nodes.values())"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {
"ExecuteTime": {
"end_time": "2018-04-11T20:03:42.087028Z",
"start_time": "2018-04-11T20:03:41.971193Z"
}
},
"outputs": [
{
"ename": "KeyError",
"evalue": "'Could not identify PTM'",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mKeyError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-15-a0d2d8d78673>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mmartinize2\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mCanonicalizeModifications\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun_system\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0msystem\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;32m~/dev/old/vermouth-martinize/martinize2/processors/processor.py\u001b[0m in \u001b[0;36mrun_system\u001b[0;34m(self, system)\u001b[0m\n\u001b[1;32m 11\u001b[0m \u001b[0mmols\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 12\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mmolecule\u001b[0m \u001b[0;32min\u001b[0m \u001b[0msystem\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmolecules\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 13\u001b[0;31m \u001b[0mmols\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun_molecule\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmolecule\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 14\u001b[0m \u001b[0msystem\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmolecules\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mmols\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/dev/old/vermouth-martinize/martinize2/processors/canonicalize_modifications.py\u001b[0m in \u001b[0;36mrun_molecule\u001b[0;34m(self, molecule)\u001b[0m\n\u001b[1;32m 275\u001b[0m \u001b[0;32mclass\u001b[0m \u001b[0mCanonicalizeModifications\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mProcessor\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 276\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mrun_molecule\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmolecule\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 277\u001b[0;31m \u001b[0mfix_ptm\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmolecule\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 278\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mmolecule\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/dev/old/vermouth-martinize/martinize2/processors/canonicalize_modifications.py\u001b[0m in \u001b[0;36mfix_ptm\u001b[0;34m(molecule)\u001b[0m\n\u001b[1;32m 244\u001b[0m \u001b[0;31m# TODO/FIXME: This includes anchors in sorting by size.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 245\u001b[0m \u001b[0moptions\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msorted\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0moptions\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mkey\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mlambda\u001b[0m \u001b[0mopt\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mopt\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mreverse\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mTrue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 246\u001b[0;31m \u001b[0midentified\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0midentify_ptms\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mresidue\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mres_ptms\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0moptions\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 247\u001b[0m \u001b[0;31m# INFO output: Identified modification X.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 248\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'Today your answer is: {}!'\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mout\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mgraph\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'name'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mout\u001b[0m \u001b[0;32min\u001b[0m \u001b[0midentified\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/dev/old/vermouth-martinize/martinize2/processors/canonicalize_modifications.py\u001b[0m in \u001b[0;36midentify_ptms\u001b[0;34m(residue, residue_ptms, known_PTMs)\u001b[0m\n\u001b[1;32m 155\u001b[0m \u001b[0;32mexcept\u001b[0m \u001b[0mKeyError\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 156\u001b[0m \u001b[0;32mcontinue\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 157\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mKeyError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'Could not identify PTM'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 158\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 159\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mKeyError\u001b[0m: 'Could not identify PTM'"
]
}
],
"source": [
"martinize2.CanonicalizeModifications().run_system(system)"
]
},
{
"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
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"nbformat": 4,
"nbformat_minor": 2
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