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Adding seach API and fixing typos
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Mihaly Varadi committed Aug 24, 2018
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22 changes: 11 additions & 11 deletions API workshop #1 - Basics.ipynb
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"cell_type": "code",
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{
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},
{
"cell_type": "code",
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{
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{
"cell_type": "code",
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"execution_count": 5,
"metadata": {},
"outputs": [
{
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"simple_dictionary = {\"key\": \"value\"}\n",
"\n",
"# Getting value directly from a dictionary using its key\n",
"simple_dictionary[]\n",
"simple_dictionary[\"key\"]\n",
"\n",
"# Basic example of a dictionary with two keys and two\n",
"# corresponding values\n",
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},
{
"cell_type": "code",
"execution_count": 53,
"execution_count": 6,
"metadata": {},
"outputs": [],
"source": [
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},
{
"cell_type": "code",
"execution_count": 54,
"execution_count": 7,
"metadata": {},
"outputs": [
{
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},
{
"cell_type": "code",
"execution_count": 55,
"execution_count": 8,
"metadata": {},
"outputs": [
{
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},
{
"cell_type": "code",
"execution_count": 56,
"execution_count": 9,
"metadata": {},
"outputs": [
{
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},
{
"cell_type": "code",
"execution_count": 57,
"execution_count": 10,
"metadata": {},
"outputs": [
{
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"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.4"
"version": "3.6.3"
}
},
"nbformat": 4,
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21 changes: 4 additions & 17 deletions API workshop #2 - Secondary structure mapping.ipynb
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},
{
"cell_type": "code",
"execution_count": 22,
"execution_count": 2,
"metadata": {},
"outputs": [],
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},
{
"cell_type": "code",
"execution_count": 48,
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
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},
{
"cell_type": "code",
"execution_count": 49,
"execution_count": null,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Example of a single PDB entry\n",
"1cbs chain A has helices at residue ranges ['14-22', '25-37'] and strands at ['5-13', '40-46', '49-55', '60-66', '71-74', '80-89', '92-99', '107-113', '119-125', '128-136']\n",
"\n",
"Example of multiple PDB entries\n",
"2klm chain A has helices at residue ranges ['24-29', '33-49', '74-83', '100-110', '119-135'] and strands at ['4-14', '51-60', '64-66', '98-99', '137-138']\n",
"2aqa chain A has helices at residue ranges ['41-46'] and strands at ['5-6', '12-13']\n"
]
}
],
"outputs": [],
"source": [
"print(\"Example of a single PDB entry\")\n",
"get_secondary_structure_ranges(pdb_id=\"1cbs\")\n",
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44 changes: 22 additions & 22 deletions API workshop #3 - Citations of PDB entries.ipynb
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},
{
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},
{
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},
{
"cell_type": "code",
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},
{
"cell_type": "code",
"execution_count": 20,
"execution_count": 5,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"{'3bow': {'appears_without_citation': {'Articles': [], 'Reviews': []},\n",
" 'cited_by': {'Articles': [],\n",
" 'Reviews': [{'authors': 'Moretti D, Del Bello B, Allavena G, Maellaro E.',\n",
" 'citation_type': 'Review',\n",
" 'cited_by_count': 12,\n",
"{'3bow': {'appears_without_citation': {'Reviews': [], 'Articles': []},\n",
" 'cited_by': {'Reviews': [{'title': 'Calpains and cancer: friends or enemies?',\n",
" 'journal': 'Arch. Biochem. Biophys.',\n",
" 'pages': '26-36',\n",
" 'pubmed_id': '25305531',\n",
" 'title': 'Calpains and cancer: friends or enemies?',\n",
" 'citation_type': 'Review',\n",
" 'year': '2014',\n",
" 'volume': '564',\n",
" 'year': '2014'}]},\n",
" 'uniprot_publications': {'Articles': [], 'Reviews': []}}}"
" 'pubmed_id': '25305531',\n",
" 'authors': 'Moretti D, Del Bello B, Allavena G, Maellaro E.',\n",
" 'cited_by_count': 12,\n",
" 'pages': '26-36'}],\n",
" 'Articles': []},\n",
" 'uniprot_publications': {'Reviews': [], 'Articles': []}}}"
]
},
"execution_count": 20,
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
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},
{
"cell_type": "code",
"execution_count": 18,
"execution_count": 6,
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"outputs": [],
"source": [
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},
{
"cell_type": "code",
"execution_count": 19,
"execution_count": 7,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Getting citation counts:\n",
"{'2klm': {'reviews': 11, 'articles': 10}, '3bow': {'reviews': 24, 'articles': 73}, '2aqa': {'reviews': 0, 'articles': 0}, '5tok': {'reviews': 1, 'articles': 0}, '1cbs': {'reviews': 0, 'articles': 0}}\n",
"{'2klm': {'reviews': 11, 'articles': 10}, '1cbs': {'reviews': 16, 'articles': 80}, '2aqa': {'reviews': 22, 'articles': 42}, '5tok': {'reviews': 3, 'articles': 1}, '3bow': {'reviews': 25, 'articles': 86}}\n",
"\n",
"pdb id\tarticles\treviews\n",
"2klm\t10\t11\n",
"3bow\t73\t24\n",
"2aqa\t0\t0\n",
"5tok\t0\t1\n",
"1cbs\t0\t0\n"
"1cbs\t80\t16\n",
"2aqa\t42\t22\n",
"5tok\t1\t3\n",
"3bow\t86\t25\n"
]
}
],
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},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": 2,
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{
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},
{
"cell_type": "code",
"execution_count": 19,
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},
{
"cell_type": "code",
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{
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{
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{
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12 changes: 6 additions & 6 deletions API workshop #5 - PDB to UniProt mappings with SIFTS.ipynb
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},
{
"cell_type": "code",
"execution_count": 30,
"execution_count": 1,
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"outputs": [],
"source": [
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},
{
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"source": [
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"\n",
"The situation is further complicated when you try to find out how a certain residue in the PDB entry relates to the same residue numbered in UniProt (i.e. the main protein sequence database).\n",
"\n",
"We have developed SIFTS to address this issue. SIFTS is an up-to-date resource for residue-level mapping between UniProt and PDB entries. The resource also provides residue-level annotation from the IntEnz, GO, Pfam, InterPro, SCOP, CATH and PubMed resources. The information is updated and released every week at the same time as the release of new PDB entries and is widely used by resources such as RCSB, PDBsum, Pfam, SCOP, InterPro, and DAS server providers.\n",
"We have developed SIFTS to address this issue. SIFTS is an up-to-date resource for residue-level mapping between UniProt and PDB entries. The resource also provides residue-level annotation from the IntEnz, GO, Pfam, InterPro, SCOP, CATH and PubMed resources. The information is updated and released every week at the same time as the release of new PDB entries and is widely used by resources such as RCSB, PDBsum, Pfam, SCOP, InterPro.\n",
"\n",
"In this example we will look at how to map PDB residues to UniProt residues."
]
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},
{
"cell_type": "code",
"execution_count": 32,
"execution_count": 3,
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"outputs": [],
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},
{
"cell_type": "code",
"execution_count": 33,
"execution_count": 4,
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"outputs": [
{
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},
{
"cell_type": "code",
"execution_count": 34,
"execution_count": 5,
"metadata": {},
"outputs": [
{
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