Ниже приведен запрос для условий: pantothenic acid, искать во всех текстовых полях, с 2000-01-01 по 2005-01-01, разрешение не хуже 2.8, число лигандов не меньше 1.
!pip install nglview --user # установка всего необходимого
/usr/lib/python3/dist-packages/secretstorage/dhcrypto.py:15: CryptographyDeprecationWarning: int_from_bytes is deprecated, use int.from_bytes instead
from cryptography.utils import int_from_bytes
/usr/lib/python3/dist-packages/secretstorage/util.py:19: CryptographyDeprecationWarning: int_from_bytes is deprecated, use int.from_bytes instead
from cryptography.utils import int_from_bytes
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WARNING: You are using pip version 21.0.1; however, version 22.0.3 is available.
You should consider upgrading via the '/usr/bin/python3 -m pip install --upgrade pip' command.
import nglview as nv # импорт всего необходимого
import requests
import json
my_query = {
"query": {
"type": "group",
"logical_operator": "and",
"nodes": []
},
"return_type": "entry"
}
keyword_clause = {
"type": "terminal",
"service": "full_text", # искать во всех текстовых полях
"parameters": {
"value": "pantothenic acid" # ключевые слова
}
}
my_query["query"]["nodes"].append(keyword_clause)
resolution_clause = {
"type": "terminal",
"service": "text",
"parameters": {
"value": 2.8, # разрешение не хуже 2.8 ангстрем
"attribute": "rcsb_entry_info.resolution_combined",
"operator": "less_or_equal"
}
}
my_query["query"]["nodes"].append(resolution_clause)
has_ligand_clause = {
"type": "terminal",
"service": "text",
"parameters": {
"attribute": "rcsb_entry_info.nonpolymer_entity_count",
"value": 0, # больше нуля лигандов,
"operator": "greater" # то есть не меньше 1
}
}
my_query["query"]["nodes"].append(has_ligand_clause)
date_range_clause = {
"type": "terminal",
"service": "text",
"parameters": {
"attribute": "rcsb_accession_info.initial_release_date",
"value": {
"from": "2000-01-01", # дата с 2000-01-01
"to": "2005-01-01", # по 2005-01-01
},
"operator": "range"
}
}
my_query["query"]["nodes"].append(date_range_clause)
rcsb = 'https://search.rcsb.org/rcsbsearch/v1/query'
json_query = json.dumps(my_query)
search = requests.post(f'{rcsb}', data=json_query) # отправляем запрос
search # убеждаемся, что все прошло хорошо
<Response [200]>
search_result = search.json() # распаковываем результат в словарь
best_hit = search_result["result_set"][0] # выделяем лучшую находку
best_hit
{'identifier': '1SQ5',
'score': 1.0,
'services': [{'service_type': 'text',
'nodes': [{'node_id': 14194, 'original_score': 1.0, 'norm_score': 1.0},
{'node_id': 9865, 'original_score': 1.0, 'norm_score': 1.0},
{'node_id': 25961, 'original_score': 1.0, 'norm_score': 1.0}]},
{'service_type': 'full_text',
'nodes': [{'node_id': 23002,
'original_score': 15.249217987060547,
'norm_score': 1.0}]}]}
Таким образом, я далее буду работать с PDB ID 1SQ5
По идентификатору 1SQ5 был найден фермент E. coli пантотенат киназа. Этот фермент катализирует реакцию фосфорилирования пантотеновой кислоты (ключевое слово запроса) за счет молекулы АТФ. Эта реакция - первая и лимитирующая стадия биосинтеза кофермента А.
Ниже приведен код интерактивной ячейки для вариантов 2, 6 и 9.
from ipywidgets import interact, fixed
my_examples = {
'Example 2': {
'description': '''
Белок в виде cartoon, покраска от N к C концу
Боковые радикалы покрашены в светло-серый, показаны линиями
Боковые радикалы заряженных аминокислот показаны в стержневой модели
Лиганды показаны в шаростержневой модели, покрашены по элементам, углерод покрашен в любой цвет, кроме стандартного
''',
'representations': [
{
'type': 'cartoon',
'params': {
'sele': 'protein',
'color': 'residueindex'
}
},
{
'type': 'line',
'params': {
'sele': 'sidechain',
'color': 'lightgray'
}
},
{
'type': 'licorice',
'params': {
'sele': 'charged',
'color': 'lightgray'
}
},
{
'type': 'ball+stick',
'params': {
'sele': 'ligand',
'color': 'element'
}
},
{
'type': 'ball+stick',
'params': {
'sele': 'ligand and _C',
'color': 'indigo',
}
},
],
},
'Example 6': {
'description': '''
Белок в виде cartoon темно-серого цвета
Боковые радикалы в виде линий светло-серого цвета
Боковые радикалы полярных аминокислот в виде hyperball, покрашены по элементам
Лиганды в шаростержневой модели, покрашены по элементам, углероды покрашены в темно-синий
''',
'representations': [
{
'type': 'cartoon',
'params': {
'sele': 'protein',
'color': 'darkgray'
}
},
{
'type': 'line',
'params': {
'sele': 'sidechain',
'color': 'lightgray'
}
},
{
'type': 'hyperball',
'params': {
'sele': 'polar',
'color': 'element'
}
},
{
'type': 'ball+stick',
'params': {
'sele': 'ligand',
'color': 'element'
}
},
{
'type': 'ball+stick',
'params': {
'sele': 'ligand and _C',
'color': 'darkblue'
}
},
],
},
'Example 9': {
'description': '''
Остов белка в шаростержневой модели, покрашен по элементам
Боковые радикалы в стержневой модели, покрашены по элементам
Углероды остатков с 30 по 70-й покрашены в светло-голубой
Лиганды показаны в виде линий, покрашены в любой оттенок оранжевого
''',
'representations': [
{
'type': 'ball+stick',
'params': {
'sele': 'backbone',
'color': 'element'
}
},
{
'type': 'licorice',
'params': {
'sele': 'sidechain',
'color': 'element'
}
},
{
'type': 'ball+stick',
'params': {
'sele': 'protein and :A and 1030-1070 and _C',
'color': 'lightblue'
}
},
{
'type': 'line',
'params': {
'sele': 'ligand',
'color': 'orange'
}
},
],
},
}
def show_examples(view, example_name):
view.clear()
example = my_examples[example_name]
print(example['description'])
view.set_representations(example['representations'])
view.center()
view = nv.show_pdbid("1SQ5", default_representation=False)
interact(show_examples, view=fixed(view), example_name=list(my_examples.keys()))
view