#устанавливаю необходимые модули
!pip install nglview --user
/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 22.0.4 is available.
You should consider upgrading via the '/usr/bin/python3 -m pip install --upgrade pip' command.
#импортирую необходимые модули
import nglview as nv
import requests
import json
#создаю запрос
my_query = {
"query": {
"type": "group",
"logical_operator": "and",
"nodes": []
},
"return_type": "entry"
}
#ищу термин в заголовке
keyword_clause = {
"type": "terminal",
"service": "text",
"parameters": {
"value": "ampicillin",
"attribute": "struct.title",
"operator": "contains_words"
}
}
my_query["query"]["nodes"].append(keyword_clause)
#разрешение не больше 2.6
resolution_clause = {
"type": "terminal",
"service": "text",
"parameters": {
"value": 2.6,
"attribute": "rcsb_entry_info.resolution_combined",
"operator": "less_or_equal"
}
}
my_query["query"]["nodes"].append(resolution_clause)
#число лигандов больше 0
has_ligand_clause = {
"type": "terminal",
"service": "text",
"parameters": {
"attribute": "rcsb_entry_info.nonpolymer_entity_count",
"value": 0,
"operator": "greater"
}
}
my_query["query"]["nodes"].append(has_ligand_clause)
#задаю дату публикации
date_range_clause = {
"type": "terminal",
"service": "text",
"parameters": {
"attribute": "rcsb_accession_info.initial_release_date",
"value": {
"from": "2020-01-01", # год-месяц-день
"to": "2023-01-01",
},
"operator": "range"
}
}
my_query["query"]["nodes"].append(date_range_clause)
#форматирую и отправляю запрос на сервер RCSB
rcsb = 'https://search.rcsb.org/rcsbsearch/v1/query'
json_query = json.dumps(my_query)
search = requests.post(f'{rcsb}', data=json_query)
search_result = search.json() # Распаковываю ответ сервера в словарь
search_result
{'query_id': 'ce84fa92-8a90-4a3d-a54a-bda921694e53',
'result_type': 'entry',
'total_count': 5,
'result_set': [{'identifier': '6XD7',
'score': 1.0,
'services': [{'service_type': 'text',
'nodes': [{'node_id': 11626,
'original_score': 180.64039611816406,
'norm_score': 1.0}]}]},
{'identifier': '6JKB',
'score': 0.4670456337175098,
'services': [{'service_type': 'text',
'nodes': [{'node_id': 11626,
'original_score': 168.93238830566406,
'norm_score': 0.4670456337175098}]}]},
{'identifier': '6OL8',
'score': 0.4670456337175098,
'services': [{'service_type': 'text',
'nodes': [{'node_id': 11626,
'original_score': 168.93238830566406,
'norm_score': 0.4670456337175098}]}]},
{'identifier': '6KGW',
'score': 0.22607371103623455,
'services': [{'service_type': 'text',
'nodes': [{'node_id': 11626,
'original_score': 163.63868713378906,
'norm_score': 0.22607371103623455}]}]},
{'identifier': '7K2Y',
'score': 0.0,
'services': [{'service_type': 'text',
'nodes': [{'node_id': 11626,
'original_score': 158.67227172851562,
'norm_score': 0.0}]}]}]}
best_hit = search_result["result_set"][0] # Лучшая находка
best_hit
{'identifier': '6XD7',
'score': 1.0,
'services': [{'service_type': 'text',
'nodes': [{'node_id': 11626,
'original_score': 180.64039611816406,
'norm_score': 1.0}]}]}
KPC-2 N170A мутант связанный с гидролизированным ампициллином. Данный фермент является мутантным по отношению к обычным β-лактамазам и в 20000 раз ускоряет процесс деацитилирования бета-лактамных антибиотиков (в т.ч. ампициллина). Появление KPC-2 привело к широкому распространению устойчивости к антибиотикам этого типа.
Фермент пренадлежит Klebsiella pneumoniae и получен из Escherichia coli BL21(DE3). Представлен в разрешении 1.65 A.
#смотрю, что нашлось
#красивое
view = nv.show_pdbid('6XD7')
view
#формирую запросы для 3х типов отображений
my_examples = {
'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': 'indigo'
}
}
],
},
'Example 7': {
'description': '''
Белок в виде ribbon, покрашенной градиентом от N к C концу
Боковые радикалы в стержневой модели, покрашенные по элементам
Углероды гидрофобных аминокислот покрашены в светло-желтый
Углероды полярных заряженных аминокислот покрашены в светло-голубой
Лиганды не показаны никак''',
'representations': [
{
'type': 'ribbon',
'params': {
'sele': 'protein',
'color': 'residueindex'
}
},
{
'type': 'licorice',
'params': {
'sele': 'sidechainAttached',
'color': 'element'
}
},
{
'type': 'licorice',
'params': {
'sele': 'hydrophobic and _C',
'color': 'lightyellow'
}
},
{
'type': 'licorice',
'params': {
'sele': 'charged and _C',
'color': 'lightblue'
}
},
],
},
'Example 8': {
'description': '''
Поверхность белка покрашена в белый, с непрозрачностью 0.1
Белок в виде cartoon темно-серого цвета
Боковые радикалы в стержневой модели, покрашены по гидрофобности
Лиганды в виде Ван-дер-Ваальсовых сфер, покрашены по элементам''',
'representations': [
{
'type': 'surface',
'params': {
'sele': 'prtein',
'color': 'white',
'opacity': 0.1
}
},
{
'type': 'cartoon',
'params': {
'sele': 'protein',
'color': 'darkblue'
}
},
{
'type': 'licorice',
'params': {
'sele': 'sidechainAttached',
'color': 'hydrophobicity'
}
},
{
'type': 'spacefill',
'params': {
'sele': 'ligand',
'color': 'element'
}
},
],
},
}
from ipywidgets import interact, fixed
#формирую интерактивную ячейку
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("3uc8", default_representation=False)
interact(show_examples, view=fixed(view), example_name=list(my_examples.keys()))
view