!pip install nglview --user #скачиваю внешний пакет 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
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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.

import nglview as nv
import requests         # Этот стандартный модуль позволяет посылать запросы к веб-ресурсам
import json             # Этот стандартный модуль позволяет легко работать с текстовым форматом json

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

keyword_example = { #ключевое слово 
    "type": "terminal",
    "service": "full_text",
    "parameters": {
        "value": "thiamine"
    }
}

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

resolution_clause = { #разрешение
    "type": "terminal",
    "service": "text",
    "parameters": {
        "value": 2.5,
        "attribute": "rcsb_entry_info.resolution_combined",
        "operator": "less_or_equal"
    }
}

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

has_ligand_clause = { #число лигандов
    "type": "terminal",
    "service": "text",
    "parameters": {
        "attribute": "rcsb_entry_info.nonpolymer_entity_count",
        "value": 0,
        "operator": "greater"
    }
}

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

date_range_clause = {  #дата публикации 
    "type": "terminal",
    "service": "text",
    "parameters": {
        "attribute": "rcsb_accession_info.initial_release_date",
        "value": {
            "from": "2000-01-01", # год-месяц-день
            "to": "2005-01-01",
        },
        "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 #проверяем правильность запроса

<Response [200]>

search_result = search.json() #распаковка ответа сервера в словарь
best_hit = search_result["result_set"][0] # лучший результат
best_hit

{'identifier': '1IG0',
 'score': 0.9950491934781867,
 'services': [{'service_type': 'text',
   'nodes': [{'node_id': 18046, 'original_score': 1.0, 'norm_score': 1.0},
    {'node_id': 4060, 'original_score': 1.0, 'norm_score': 1.0},
    {'node_id': 29765, 'original_score': 1.0, 'norm_score': 1.0}]},
  {'service_type': 'full_text',
   'nodes': [{'node_id': 5763,
     'original_score': 11.850417137145996,
     'norm_score': 0.9801967739127464}]}]}

view = nv.show_pdbid('1IG3')
view

from ipywidgets import interact, fixed

Использовав идентификатор 1IG3 , в PDB я нашел статью о тиаминпирофосфокиназе в комплексе с тиамином ( поэтому ключевое слово - тиамин ) . Тиаминпирофосфокиназа способна катализировать перенос пирофосфатной группы с АТФ к тиамину , что необходимо для получения тиаминпирофосфата.

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 = [
  '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 = {
    'Example 1': {
        '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': 'licorice',                      
                'params': {
                    'sele': 'sidechainAttached and charged',                  
                 }
            },
            {
                'type': 'line',                      
                'params': {
                    'sele': 'sidechainAttached',                
                    'color': 'lightgrey'  
                 }
            },
            {
                'type': 'ball+stick',                      
                'params': {
                    'sele': 'ligand',               
                    'color': 'element'  
                 }
            },
            {
                'type': 'ball+stick',                      
                'params': {
                    'sele': 'ligand AND _C',               
                    'color': '#FFF0F5'  
                 }
            }
        ],
    },
    'Example 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': 'sidechainAttached',                     
                    'color': 'hydrophobicity'  
                 }
            },
            {
                'type': 'line',                      
                'params': {
                    'sele': 'ligand',                     
                    'color': 'element'  
                 }
            },
            {
                'type': 'spacefill',
                'params': {
                    'sele': 'water',
                    'color': 'element'
                }
            },
            {
                'type': 'spacefill',
                'params': {
                    'sele': 'ion',
                    'color': 'element'
                }
            }
        ],
    },
    'Example 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("1IG3", default_representation=False)
interact(show_examples, view=fixed(view), example_name=list(my_examples.keys()))
view