Практикум №3.

Задание 1

Скачивание ПО.

!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 22.0.3 is available.
You should consider upgrading via the '/usr/bin/python3 -m pip install --upgrade pip' command.

Импорт модулей.

import nglview as nv
import requests
import json

Создание заготовки.

my_query = {
    "query": {
        "type": "group",
        "logical_operator": "and",
        "nodes": []
    },
    "return_type": "entry"
}

Задаём искомое вещество и место, где искать (заголовок).

keyword_clause = {
    "type": "terminal",
    "service": "text",
    "parameters": {
        "value": "ampicillin",
        "attribute": "struct.title",
        "operator": "contains_words"
    }
}

my_query["query"]["nodes"].append(keyword_clause)

Задаём разрешение (не более 2,7 ангстрем)

resolution_clause = {
    "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)

Задаём число лигандов (не менее 2, то есть более 1)

has_ligand_clause = {
    "type": "terminal",
    "service": "text",
    "parameters": {
        "attribute": "rcsb_entry_info.nonpolymer_entity_count",
        "value": 1,
        "operator": "greater"
    }
}

my_query["query"]["nodes"].append(has_ligand_clause)

Задаём искомые даты.

date_range_clause = {
    "type": "terminal",
    "service": "text",
    "parameters": {
        "attribute": "rcsb_accession_info.initial_release_date",
        "value": {
            "from": "2000-01-01",
            "to": "2005-01-01",
        },
        "operator": "range"
    }
}

my_query["query"]["nodes"].append(date_range_clause)

Создаём json-строку и отсылаем запрос.

rcsb = 'https://search.rcsb.org/rcsbsearch/v1/query'

json_query = json.dumps(my_query)

search = requests.post(f'{rcsb}', data=json_query)

search

<Response [200]>

Переводим результат в словарь.

search_result = search.json()
search_result

{'query_id': '6957f80d-eccb-4b9b-ae7f-61533ffc16eb',
 'result_type': 'entry',
 'total_count': 5,
 'result_set': [{'identifier': '1UNB',
   'score': 1.0,
   'services': [{'service_type': 'text',
     'nodes': [{'node_id': 9588,
       'original_score': 194.04849243164062,
       'norm_score': 1.0}]}]},
  {'identifier': '1NX9',
   'score': 0.5130061954191562,
   'services': [{'service_type': 'text',
     'nodes': [{'node_id': 9588,
       'original_score': 174.515869140625,
       'norm_score': 0.5130061954191562}]}]},
  {'identifier': '1H8S',
   'score': 0.24013573997880966,
   'services': [{'service_type': 'text',
     'nodes': [{'node_id': 9588,
       'original_score': 163.57142639160156,
       'norm_score': 0.24013573997880966}]}]},
  {'identifier': '1H8N',
   'score': 0.0,
   'services': [{'service_type': 'text',
     'nodes': [{'node_id': 9588,
       'original_score': 153.93992614746094,
       'norm_score': 0.0}]}]},
  {'identifier': '1W2N',
   'score': 0.0,
   'services': [{'service_type': 'text',
     'nodes': [{'node_id': 9588,
       'original_score': 153.93992614746094,
       'norm_score': 0.0}]}]}]}

Отбираем "лучший" результат.

best_hit = search_result["result_set"][0]
best_hit

{'identifier': '1UNB',
 'score': 1.0,
 'services': [{'service_type': 'text',
   'nodes': [{'node_id': 9588,
     'original_score': 194.04849243164062,
     'norm_score': 1.0}]}]}

Задание 2

Белок, найденный по заданным параметрам - деацетоксицефалоспорин-С-синтаза, фермент превращающий пенициллины в цефалоспорины (ОВР с участием иона железа(II), меняющего в ходе реакции свою степень окисления) путём встраивания атома углерода в пенициллиновое ядро. Параллельно происходит окисление 2-оксоглутарата до сукцината с выделением молекулы углекислого газа. Ампициллин, который мы указали как искомую "малую молекулу", относится к пенициллинам и тоже может быть связан в качестве субстрата деацетоксицефалоспорин-С-синтазой.

Задание 3

Просматриваем результат.

view = nv.show_pdbid('1UNB') 
view

from ipywidgets import interact, fixed

my_examples = {
    'Example 1': {
        'description': '''
Вариант 4.

    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': 'backbone',                      
                'params': {
                    'sele': 'sidestrainAttached',                
                    'color': 'element',
                 }
                
            },
            { 
                'type': 'spacefill',                      
                'params': {
                    'sele': 'ligand',                
                    'color': 'hydrophobicity',
                 }
                
            },
            {
                'type': 'licorice',                      
                'params': {
                    'sele': 'sidestrainAttached' and 'aromatic',                  
                 }
            },
        ],
    },
    'Example 2': {
        'description': '''
Вариант 9.
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': 'protein',               
                    'color': 'element'  
                 }
            },
            {
                'type': 'ball+stick',                      
                'params': {
                    'sele': 'protein and :A and 30-70 and _C',               
                    'color': 'lightblue'  
                 }
            },
            {
                'type': 'licorice',                      
                'params': {
                    'sele': 'sidechainAttached',                     
                    'color': 'element'  
                 }
            },
            {
                'type': 'line',                      
                'params': {
                    'sele': 'ligand',                     
                    'color': 'orange'  
                 }
            },
                 
        ],
    },
    'Example 3': {
        'description': '''
Вариант 7.

    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': 'sidechainAttached and hydrophobic and _C',                     
                    'color': '#FFFACD'  
                 }
            },
            {
                'type': 'liocorice',
                'params': {
                    'sele': 'sidechainAttached and polar 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("1UNB", default_representation=False)
interact(show_examples, view=fixed(view), example_name=list(my_examples.keys()))
view

view = nv.show_pdbid("1UNB", default_representation=False)
interact(show_examples, view=fixed(view), example_name=list(my_examples.keys()))
view

view = nv.show_pdbid("1UNB", default_representation=False)
interact(show_examples, view=fixed(view), example_name=list(my_examples.keys()))
view