!pip install nglview --user # устанавливаю внешний пакет nglview для визуализации структуры биомакромолекул
/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
import requests
import json
my_query = {
"query": {
"type": "group",
"logical_operator": "and",
"nodes": []
},
"return_type": "entry"
}
keyword_clause = {
"type": "terminal",
"service": "text",
"parameters": {
"value": "streptomycin",
"attribute": "struct.title",
"operator": "contains_words"
}
}
my_query["query"]["nodes"].append(keyword_clause)
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)
has_ligand_clause = {
"type": "terminal",
"service": "text",
"parameters": {
"attribute": "rcsb_entry_info.nonpolymer_entity_count",
"value": 2,
"operator": "greater_or_equal"
}
}
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": "2015-01-01",
"to": "2020-01-01",
},
"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) # отправляю запрос на сервер RCSB
search # проверяю корректность запроса. Получено число 200 - всё прошло правильно
<Response [200]>
search_result = search.json() # просматриваю результаты поиска
search_result
{'query_id': 'dc169ece-0271-455c-8bc6-c9b7dee3bfde',
'result_type': 'entry',
'total_count': 3,
'result_set': [{'identifier': '6FZB',
'score': 1.0,
'services': [{'service_type': 'text',
'nodes': [{'node_id': 27064,
'original_score': 213.1577606201172,
'norm_score': 1.0}]}]},
{'identifier': '5LUH',
'score': 0.8551485224229958,
'services': [{'service_type': 'text',
'nodes': [{'node_id': 27064,
'original_score': 205.18060302734375,
'norm_score': 0.8551485224229958}]}]},
{'identifier': '6FUX',
'score': 0.0,
'services': [{'service_type': 'text',
'nodes': [{'node_id': 27064,
'original_score': 158.0864715576172,
'norm_score': 0.0}]}]}]}
best_hit = search_result["result_set"][0] # выявляю лучшее совпадение
best_hit
{'identifier': '6FZB',
'score': 1.0,
'services': [{'service_type': 'text',
'nodes': [{'node_id': 27064,
'original_score': 213.1577606201172,
'norm_score': 1.0}]}]}
Поиск по идентификатору 6FZB выдаёт запись, соответствующую белку AadA - аминогликозид-аденилилтрансферазе, связанной с АТФ, ионами магния и молекулой стрептомицина. Стрептомицин является антибиотиком, связывающимся с бактериальной рибосомой и препятствующим синтезу белка. Для воспрепятствования действию стрептомицина, бактерии используют аминогликозид-модифицирующие ферменты, одним из которых является AadA.
representations = [ # задаю типы отображения белка
'ball+stick', # шаростержневая модель
'backbone', # прямые линии, соединяющие С-альфа атомы
'cartoon', # условное отображение вторичной структуры
'helixorient', # упрощенное отображение
'hyperball', # сглаженная шаростержневая модель
'licorice', # стержневая модель (без шаров)
'line', # очень тонкая стержневая модель
'point', # атомы в виде плоских точек
'ribbon', # отображение остова в виде ленты
'rocket', # отображение альфа-спиралей как цилиндров
'rope', # отображение остова в виде колбасы
'spacefill', # атомы в виде шаров соотв. Ван-дер-Ваальсова радиуса
'surface', # поверхность
'trace', # сглаженная линия, соединяющая С-альфа атомы
'tube' # более сдержанный rope
]
colors = [ # задаю типы окраски молекул
'random',
'uniform',
'atomindex', # от синего к красному с ростом номера атома
'residueindex', # от синего к красному с ростом номера остатка
'chainindex', # каждой цепи свой цвет
'sstruc', # стандартные цвета для типа вторичной структуры
'element', # стандартные цвета для химических элементов
'resname', # свой цвет каждому из 20 остатков
'bfactor', # чем темнее, тем подвижнее
'hydrophobicity', # чем темнее, тем гидрофобнее
]
from ipywidgets import interact, fixed # импортирую функции interact и fixed
my_examples = {
'Тип отображения 1': {
'description': '''
Белок в виде cartoon, покраска по типу вторичной структуры
Показана поверхность, с непрозрачностью 0.1
Лиганды в виде hyperball, покрашены в оттенок Gold
''',
'representations': [
{
'type': 'cartoon',
'params': {
'sele': 'protein',
'color': 'sstruc'
}
},
{
'type': 'surface',
'params': {
'sele': 'protein',
'color': 'white',
'opacity': 0.1
}
},
{
'type': 'hyperball',
'params': {
'sele': 'ligand',
'color': '#FFD700'
}
},
],
},
'Тип отображения 2': {
'description': '''
Белок в виде tube, покраска по типу вторичной структуры
Боковые радикалы в стержневой модели, покрашены по гидрофобности
Лиганды показаны линиями, покрашены по элементам
Вода и ионы показаны в виде Ван-дер-Ваальсовых сфер
''',
'representations': [
{
'type': 'tube',
'params': {
'sele': 'protein',
'color': 'sstruc'
}
},
{
'type': 'licorice',
'params': {
'sele': 'sidechain',
'color': 'hydrophobicity'
}
},
{
'type': 'line',
'params': {
'sele': 'ligand C',
'color': 'element'
}
},
{
'type': 'spacefill',
'params': {
'sele': 'water',
'color': 'element'
}
},
{
'type': 'spacefill',
'params': {
'sele': 'ion',
'color': 'element',
}
},
],
},
'Тип отображения 3': {
'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': '#ffff7a'
}
},
{
'type': 'licorice',
'params': {
'sele': 'charged and _C',
'color': '#87cefa'
}
},
{
'type': 'licorice',
'params': {
'sele': 'ligand',
'color': 'white',
'opacity': 0
}
},
],
},
}
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("6FZB", default_representation=False)
interact(show_examples, view=fixed(view), example_name=list(my_examples.keys()))
view