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[examples/notebooks] update notebooks to work with latest version
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gph82 committed Jun 13, 2024
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25 changes: 16 additions & 9 deletions mdciao/examples/Comparing_CGs_Bars.ipynb
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Expand Up @@ -594,7 +594,7 @@
" sort_by=\"std\",\n",
" lower_cutoff_val=.25,\n",
" defrag=None,\n",
" legend_rows=2\n",
" legend_rows=2,\n",
" );"
]
},
Expand Down Expand Up @@ -694,9 +694,23 @@
" lower_cutoff_val=.25,\n",
" per_residue=True,\n",
" defrag=None,\n",
" colors=\"Set2\"\n",
" colors=\"Set2\",\n",
" );"
]
},
{
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"metadata": {
Expand All @@ -716,13 +730,6 @@
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.12"
},
"widgets": {
"application/vnd.jupyter.widget-state+json": {
"state": {},
"version_major": 2,
"version_minor": 0
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"nbformat": 4,
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4 changes: 2 additions & 2 deletions mdciao/examples/EGFR_Kinase_Inhibitors.ipynb
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Expand Up @@ -59,7 +59,7 @@
"metadata": {},
"outputs": [],
"source": [
"KLIFS = mdciao.nomenclature.LabelerKLIFS(\"P00533\")"
"KLIFS = mdciao.nomenclature.LabelerKLIFS(\"UniProtAC:P00533\")"
]
},
{
Expand Down Expand Up @@ -163,7 +163,7 @@
" binding_pocket[key]=mdciao.cli.interface(xtc, \n",
" pdb, \n",
" fragment_names=[\"EGFR\", \"ligand\"],\n",
" KLIFS_UniProtAC=KLIFS, \n",
" KLIFS_string=KLIFS, \n",
" ctc_control=1.0, \n",
" frag_idxs_group_1=[0],\n",
" frag_idxs_group_2=[1],\n",
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49 changes: 21 additions & 28 deletions mdciao/examples/Flareplot_Schemes.ipynb
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Expand Up @@ -371,27 +371,27 @@
"If the interface is plotted using the same ```ctc_cutoff_Ang```, these residues will be those listed in the initial output, on top of the notebook:\n",
"\n",
"```\n",
" freq label residue idxs sum\n",
"0 1.0 [email protected] - [email protected] 335 1105 1.0\n",
"1 1.0 [email protected] - [email protected] 334 1015 2.0\n",
"2 1.0 [email protected] - R239@ICL3 304 1112 3.0\n",
"3 1.0 [email protected] - [email protected] 312 1106 4.0\n",
"4 1.0 [email protected] - [email protected] 346 1118 5.0\n",
"5 1.0 [email protected] - [email protected] 346 1122 6.0\n",
"6 1.0 [email protected] - [email protected] 330 1015 7.0\n",
"7 1.0 [email protected] - [email protected] 88 1185 8.0\n",
"8 1.0 [email protected] - [email protected] 334 1012 9.0\n",
"9 1.0 [email protected] - [email protected] 85 1185 10.0\n",
"10 1.0 [email protected] - [email protected] 347 1122 11.0\n",
"11 1.0 [email protected] - [email protected] 341 1010 12.0\n",
"12 1.0 [email protected] - [email protected] 347 1119 13.0\n",
"13 1.0 [email protected] - [email protected] 338 1098 14.0\n",
"14 1.0 [email protected] - [email protected] 338 1014 15.0\n",
"15 1.0 [email protected] - [email protected] 339 1102 16.0\n",
"16 1.0 [email protected] - [email protected] 338 1102 17.0\n",
"17 1.0 [email protected] - [email protected] 337 1014 18.0\n",
"18 1.0 [email protected] - [email protected] 338 1011 19.0\n",
"19 1.0 [email protected] - [email protected] 339 1106 20.0\n",
" freq label residues fragments sum\n",
"1 1.0 [email protected] - [email protected] 335 - 1105 0 - 4 1.0\n",
"2 1.0 [email protected] - [email protected] 334 - 1015 0 - 4 2.0\n",
"3 1.0 [email protected] - R239@ICL3 304 - 1112 0 - 4 3.0\n",
"4 1.0 [email protected] - [email protected] 312 - 1106 0 - 4 4.0\n",
"5 1.0 [email protected] - [email protected] 346 - 1118 0 - 4 5.0\n",
"6 1.0 [email protected] - [email protected] 346 - 1122 0 - 4 6.0\n",
"7 1.0 [email protected] - [email protected] 330 - 1015 0 - 4 7.0\n",
"8 1.0 [email protected] - [email protected] 88 - 1185 0 - 4 8.0\n",
"9 1.0 [email protected] - [email protected] 334 - 1012 0 - 4 9.0\n",
"10 1.0 [email protected] - [email protected] 85 - 1185 0 - 4 10.0\n",
"11 1.0 [email protected] - [email protected] 347 - 1122 0 - 4 11.0\n",
"12 1.0 [email protected] - [email protected] 341 - 1010 0 - 4 12.0\n",
"13 1.0 [email protected] - [email protected] 347 - 1119 0 - 4 13.0\n",
"14 1.0 [email protected] - [email protected] 338 - 1098 0 - 4 14.0\n",
"15 1.0 [email protected] - [email protected] 338 - 1014 0 - 4 15.0\n",
"16 1.0 [email protected] - [email protected] 339 - 1102 0 - 4 16.0\n",
"17 1.0 [email protected] - [email protected] 338 - 1102 0 - 4 17.0\n",
"18 1.0 [email protected] - [email protected] 337 - 1014 0 - 4 18.0\n",
"19 1.0 [email protected] - [email protected] 338 - 1011 0 - 4 19.0\n",
"20 1.0 [email protected] - [email protected] 339 - 1106 0 - 4 20.0\n",
"````"
]
},
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"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.12"
},
"widgets": {
"application/vnd.jupyter.widget-state+json": {
"state": {},
"version_major": 2,
"version_minor": 0
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"nbformat": 4,
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7 changes: 0 additions & 7 deletions mdciao/examples/MSA_via_Consensus_Labels.ipynb
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Expand Up @@ -249,13 +249,6 @@
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.12"
},
"widgets": {
"application/vnd.jupyter.widget-state+json": {
"state": {},
"version_major": 2,
"version_minor": 0
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"nbformat": 4,
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7 changes: 0 additions & 7 deletions mdciao/examples/Manuscript.ipynb
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Expand Up @@ -259,13 +259,6 @@
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.12"
},
"widgets": {
"application/vnd.jupyter.widget-state+json": {
"state": {},
"version_major": 2,
"version_minor": 0
}
}
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"nbformat": 4,
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19 changes: 6 additions & 13 deletions mdciao/examples/Missing_Contacts.ipynb
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Expand Up @@ -351,11 +351,11 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"In the graph (double click to enlarge), we note the *long tail* of the bar-plot as we move to the right. *Where exactly* should one stop to pay attention can't be really answered numercally alone. `mdciao` tries to provide cues as to what might be sane values, e.g, the log reports:\n",
"In the graph (double click to enlarge), we note the *long tail* of the bar-plot as we move to the right. *Where exactly* should one stop to pay attention can't be really answered numercally alone. `mdciao` tries to provide hints as to what might be sane values, e.g, the log reports:\n",
"```\n",
" The following 117 contacts capture 57.11 (~100%) of the total frequency 57.11 (over 117 contacts with nonzero frequency).\n",
" As orientation value, the first 60 ctcs already capture 90.0% of 57.11.\n",
" The 60-th contact has a frequency of 0.53.\n",
" The following 103 contacts capture 57.05 (~100%) of the total frequency 57.11 (over 117 contacts with nonzero frequency at 4.00 Angstrom).\n",
" As orientation value, the first 60 ctcs already capture 90.0% of 57.11.\n",
" The 60-th contact has a frequency of 0.53.\n",
" ```\n",
"which means:\n",
"1. the reported contacts, which have resulted from using `ctc_control=1.0, min_freq=0.0`, are capturing **100%** of anything there is to report. \n",
Expand Down Expand Up @@ -391,7 +391,7 @@
"As orientation value, the first 60 ctcs already capture 90.0% of 57.11.\n",
"The 60-th contact has a frequency of 0.53.\n",
"```\n",
"let's us know that ignoring frequencies < .1 reduces the full list from 117 to 80 entries while keeping ca 98% of $\\Sigma_t$."
"let's us know that ignoring frequencies < .1 reduces the full list from 117 to 80 entries while keeping ca 98% of $\\Sigma_t$. In this case, even if we have `ctc_control=1.0` we don't get 100% of the freqs reported (only 98%) because the `min_freq=0.1` (default value) is causing the loss of %2 of contacts all of which have frequencies below 10%."
]
},
{
Expand Down Expand Up @@ -488,14 +488,7 @@
"pygments_lexer": "ipython3",
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"toc-autonumbering": true,
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"nbformat_minor": 4
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542 changes: 1 addition & 541 deletions mdciao/examples/Tutorial.ipynb
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