!pip install nglview --user #установка внешнего пакета nglview
/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
Requirement already satisfied: nglview in /usr/local/lib/python3.7/dist-packages (2.7.7)
Requirement already satisfied: numpy in /usr/local/lib/python3.7/dist-packages (from nglview) (1.20.1)
Requirement already satisfied: ipywidgets>=7 in /usr/local/lib/python3.7/dist-packages (from nglview) (7.5.1)
Requirement already satisfied: ipykernel>=4.5.1 in /usr/local/lib/python3.7/dist-packages (from ipywidgets>=7->nglview) (5.5.0)
Requirement already satisfied: ipython>=4.0.0 in /usr/local/lib/python3.7/dist-packages (from ipywidgets>=7->nglview) (7.21.0)
Requirement already satisfied: widgetsnbextension~=3.5.0 in /usr/local/lib/python3.7/dist-packages (from ipywidgets>=7->nglview) (3.5.1)
Requirement already satisfied: nbformat>=4.2.0 in /usr/local/lib/python3.7/dist-packages (from ipywidgets>=7->nglview) (5.1.2)
Requirement already satisfied: traitlets>=4.3.1 in /usr/local/lib/python3.7/dist-packages (from ipywidgets>=7->nglview) (5.0.5)
Requirement already satisfied: jupyter-client in /usr/local/lib/python3.7/dist-packages (from ipykernel>=4.5.1->ipywidgets>=7->nglview) (6.1.11)
Requirement already satisfied: tornado>=4.2 in /usr/local/lib/python3.7/dist-packages (from ipykernel>=4.5.1->ipywidgets>=7->nglview) (6.1)
Requirement already satisfied: backcall in /usr/local/lib/python3.7/dist-packages (from ipython>=4.0.0->ipywidgets>=7->nglview) (0.2.0)
Requirement already satisfied: pexpect>4.3 in /usr/local/lib/python3.7/dist-packages (from ipython>=4.0.0->ipywidgets>=7->nglview) (4.8.0)
Requirement already satisfied: jedi>=0.16 in /usr/local/lib/python3.7/dist-packages (from ipython>=4.0.0->ipywidgets>=7->nglview) (0.18.0)
Requirement already satisfied: decorator in /usr/local/lib/python3.7/dist-packages (from ipython>=4.0.0->ipywidgets>=7->nglview) (4.4.2)
Requirement already satisfied: pygments in /usr/local/lib/python3.7/dist-packages (from ipython>=4.0.0->ipywidgets>=7->nglview) (2.8.0)
Requirement already satisfied: setuptools>=18.5 in /usr/local/lib/python3.7/dist-packages (from ipython>=4.0.0->ipywidgets>=7->nglview) (54.0.0)
Requirement already satisfied: prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0 in /usr/local/lib/python3.7/dist-packages (from ipython>=4.0.0->ipywidgets>=7->nglview) (3.0.16)
Requirement already satisfied: pickleshare in /usr/local/lib/python3.7/dist-packages (from ipython>=4.0.0->ipywidgets>=7->nglview) (0.7.5)
Requirement already satisfied: parso<0.9.0,>=0.8.0 in /usr/local/lib/python3.7/dist-packages (from jedi>=0.16->ipython>=4.0.0->ipywidgets>=7->nglview) (0.8.1)
Requirement already satisfied: ipython-genutils in /usr/local/lib/python3.7/dist-packages (from nbformat>=4.2.0->ipywidgets>=7->nglview) (0.2.0)
Requirement already satisfied: jupyter-core in /usr/local/lib/python3.7/dist-packages (from nbformat>=4.2.0->ipywidgets>=7->nglview) (4.7.1)
Requirement already satisfied: jsonschema!=2.5.0,>=2.4 in /usr/local/lib/python3.7/dist-packages (from nbformat>=4.2.0->ipywidgets>=7->nglview) (3.2.0)
Requirement already satisfied: attrs>=17.4.0 in /usr/local/lib/python3.7/dist-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets>=7->nglview) (20.3.0)
Requirement already satisfied: importlib-metadata in /usr/local/lib/python3.7/dist-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets>=7->nglview) (3.7.0)
Requirement already satisfied: six>=1.11.0 in /usr/local/lib/python3.7/dist-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets>=7->nglview) (1.15.0)
Requirement already satisfied: pyrsistent>=0.14.0 in /usr/local/lib/python3.7/dist-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets>=7->nglview) (0.17.3)
Requirement already satisfied: ptyprocess>=0.5 in /usr/local/lib/python3.7/dist-packages (from pexpect>4.3->ipython>=4.0.0->ipywidgets>=7->nglview) (0.7.0)
Requirement already satisfied: wcwidth in /usr/local/lib/python3.7/dist-packages (from prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0->ipython>=4.0.0->ipywidgets>=7->nglview) (0.2.5)
Requirement already satisfied: notebook>=4.4.1 in /usr/local/lib/python3.7/dist-packages (from widgetsnbextension~=3.5.0->ipywidgets>=7->nglview) (6.2.0)
Requirement already satisfied: terminado>=0.8.3 in /usr/local/lib/python3.7/dist-packages (from notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets>=7->nglview) (0.9.2)
Requirement already satisfied: pyzmq>=17 in /usr/local/lib/python3.7/dist-packages (from notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets>=7->nglview) (22.0.3)
Requirement already satisfied: argon2-cffi in /usr/local/lib/python3.7/dist-packages (from notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets>=7->nglview) (20.1.0)
Requirement already satisfied: prometheus-client in /usr/local/lib/python3.7/dist-packages (from notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets>=7->nglview) (0.9.0)
Requirement already satisfied: nbconvert in /usr/local/lib/python3.7/dist-packages (from notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets>=7->nglview) (6.0.7)
Requirement already satisfied: Send2Trash>=1.5.0 in /usr/local/lib/python3.7/dist-packages (from notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets>=7->nglview) (1.5.0)
Requirement already satisfied: jinja2 in /usr/local/lib/python3.7/dist-packages (from notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets>=7->nglview) (2.11.3)
Requirement already satisfied: python-dateutil>=2.1 in /usr/local/lib/python3.7/dist-packages (from jupyter-client->ipykernel>=4.5.1->ipywidgets>=7->nglview) (2.8.1)
Requirement already satisfied: cffi>=1.0.0 in /usr/local/lib/python3.7/dist-packages (from argon2-cffi->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets>=7->nglview) (1.14.5)
Requirement already satisfied: pycparser in /usr/local/lib/python3.7/dist-packages (from cffi>=1.0.0->argon2-cffi->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets>=7->nglview) (2.20)
Requirement already satisfied: typing-extensions>=3.6.4 in /usr/local/lib/python3.7/dist-packages (from importlib-metadata->jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets>=7->nglview) (3.7.4.3)
Requirement already satisfied: zipp>=0.5 in /usr/local/lib/python3.7/dist-packages (from importlib-metadata->jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets>=7->nglview) (3.4.0)
Requirement already satisfied: MarkupSafe>=0.23 in /usr/local/lib/python3.7/dist-packages (from jinja2->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets>=7->nglview) (1.1.1)
Requirement already satisfied: jupyterlab-pygments in /usr/local/lib/python3.7/dist-packages (from nbconvert->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets>=7->nglview) (0.1.2)
Requirement already satisfied: testpath in /usr/local/lib/python3.7/dist-packages (from nbconvert->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets>=7->nglview) (0.4.4)
Requirement already satisfied: mistune<2,>=0.8.1 in /usr/local/lib/python3.7/dist-packages (from nbconvert->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets>=7->nglview) (0.8.4)
Requirement already satisfied: pandocfilters>=1.4.1 in /usr/local/lib/python3.7/dist-packages (from nbconvert->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets>=7->nglview) (1.4.3)
Requirement already satisfied: nbclient<0.6.0,>=0.5.0 in /usr/local/lib/python3.7/dist-packages (from nbconvert->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets>=7->nglview) (0.5.3)
Requirement already satisfied: defusedxml in /usr/local/lib/python3.7/dist-packages (from nbconvert->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets>=7->nglview) (0.7.0)
Requirement already satisfied: entrypoints>=0.2.2 in /usr/lib/python3/dist-packages (from nbconvert->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets>=7->nglview) (0.3)
Requirement already satisfied: bleach in /usr/local/lib/python3.7/dist-packages (from nbconvert->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets>=7->nglview) (3.3.0)
Requirement already satisfied: nest-asyncio in /usr/local/lib/python3.7/dist-packages (from nbclient<0.6.0,>=0.5.0->nbconvert->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets>=7->nglview) (1.5.1)
Requirement already satisfied: async-generator in /usr/local/lib/python3.7/dist-packages (from nbclient<0.6.0,>=0.5.0->nbconvert->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets>=7->nglview) (1.10)
Requirement already satisfied: webencodings in /usr/local/lib/python3.7/dist-packages (from bleach->nbconvert->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets>=7->nglview) (0.5.1)
Requirement already satisfied: packaging in /usr/local/lib/python3.7/dist-packages (from bleach->nbconvert->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets>=7->nglview) (20.9)
Requirement already satisfied: pyparsing>=2.0.2 in /usr/local/lib/python3.7/dist-packages (from packaging->bleach->nbconvert->notebook>=4.4.1->widgetsnbextension~=3.5.0->ipywidgets>=7->nglview) (2.4.7)
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 # модуль, который позволяет посылать запросы к веб-ресурсам
import json # модуль, который позволяет работать с текстовым форматом json
my_query = {
"query": {
"type": "group",
"logical_operator": "and",
"nodes": []
},
"return_type": "entry"
}
example_field_search = { #ключевое слово во всех полях
"type": "terminal",
"service": "full_text",
"parameters": {
"value": "ampicillin"
}
}
my_query["query"]["nodes"].append(example_field_search)
resolution_clause = { #разрешение
"type": "terminal",
"service": "text",
"parameters": {
"value": 2.7,
"attribute": "rcsb_entry_info.resolution_combined",
"operator": "less_or_equal"
}
}
my_query["query"]["nodes"].append(resolution_clause)
has_ligand_clause = { #сколько лигандов
"type": "terminal",
"service": "text",
"parameters": {
"attribute": "rcsb_entry_info.nonpolymer_entity_count",
"value": 1,
"operator": "greater"
}
}
my_query["query"]["nodes"].append(has_ligand_clause)
date_range_clause = { # год-месяц-день
"type": "terminal",
"service": "text",
"parameters": {
"attribute": "rcsb_accession_info.initial_release_date",
"value": {
"from": "2005-01-01",
"to": "2010-01-01",
},
"operator": "range"
}
}
my_query["query"]["nodes"].append(date_range_clause)
rcsb = 'https://search.rcsb.org/rcsbsearch/v1/query' #отправка запроса
json_query = json.dumps(my_query)
search = requests.post(f'{rcsb}', data=json_query)
search # проверка правильности запроса (200 - все хорошо)
<Response [200]>
search_result = search.json() # распаковка ответа сервера в словарь
best_hit = search_result["result_set"][0] # лучший результат
best_hit
{'identifier': '3ITA',
'score': 0.997848728737562,
'services': [{'service_type': 'text',
'nodes': [{'node_id': 4228, 'original_score': 1.0, 'norm_score': 1.0},
{'node_id': 3629, 'original_score': 1.0, 'norm_score': 1.0},
{'node_id': 31359, 'original_score': 1.0, 'norm_score': 1.0}]},
{'service_type': 'full_text',
'nodes': [{'node_id': 29602,
'original_score': 15.640780448913574,
'norm_score': 0.9913949149502481}]}]}
Пенициллин-связывающий белок 6 из E. coli в комплексе с ампициллином (Penicillin-Binding Protein 6 (PBP6) from E. coli in acyl-enzyme complex with ampicillin).
Запись была опубликована 2009-10-20, разрешение 1.80 Å, 3 лиганда.
PBP6 является одной из основных DD-карбоксипептидаз Escherichia coli. Она участвует в синтезе клеточной стенки бактерий. Ампициллин относится к бета-лактамным антибиотикам. Их принцип действия - ингибирование транспептидаз, которые участвуют в синтезе клеточной стенки.
Построение отображений записи 3ITA (варинаты 1, 4, 7)
from ipywidgets import interact, fixed
representations = [
'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 = [
'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
]
my_examples = {
'пример 1': {
'description': '''
Поверхность белка покрашена в белый, с непрозрачностью 0.1
Белок в виде rope красного цвета
Боковые радикалы в стержневой модели, покрашенные согласно элементу
Лиганды в виде Ван-дер-Ваальсовых сфер, покрашены по элементам
''',
'representations': [
{
'type': 'surface',
'params': {
'sele': 'protein',
'opacity': 0.1 ,
'color': 'white'
}
},
{
'type': 'rope',
'params': {
'sele': 'protein',
'color': 'red'
}
},
{
'type': 'licorice',
'params': {
'sele': 'sidechainAttached',
'color': 'element'
}
},
{
'type': 'spacefill',
'params': {
'sele': 'ligand',
'color': 'element',
}
},
],
},
'пример 4': {
'description': '''
Белок в виде cartoon, покраска по типу вторичной структуры
Боковые радикалы покрашены по элементу, показаны линиями
Боковые радикалы ароматических аминокислот показаны в стержневой модели
Лиганды показаны в виде Ван-дер-Ваальсовых сфер, покрашены по гидрофобности
''',
'representations': [
{
'type': 'cartoon',
'params': {
'sele': 'protein',
'color': 'sstruc'
}
},
{
'type': 'line',
'params': {
'sele': 'sidechainAttached and not aromatic',
'color': 'element'
}
},
{
'type': 'licorice',
'params': {
'sele': 'sidechainAttached and aromatic',
'color': 'element'
}
},
{
'type': 'spacefill',
'params': {
'sele': 'ligand',
'color': 'hydrophobicity'
}
},
],
},
'пример 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': 'all',
'color': 'residueindex'
}
},
{
'type': 'licorice',
'params': {
'sele': 'sidechainAttached',
'color': 'element'
}
},
{
'type': 'licorice',
'params': {
'sele': 'sidechainAttached and hydrophobic and _C',
'color': 'lightyellow'
}
},
{
'type': 'licorice',
'params': {
'sele': 'sidechainAttached and charged and _C',
'color': 'lightblue'
}
},
],
},
}
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("3ita", default_representation=False)
interact(show_examples, view=fixed(view), example_name=list(my_examples.keys()))
view