!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 22.1 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": "full_text", 
    "parameters": {
        "value": "testosterone" 
    }
}
my_query["query"]["nodes"].append(keyword_clause)
resolution_clause = {
    "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 = {
    "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 = {
    "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)

search

<Response [200]>

search_result = search.json()
best_hit = search_result["result_set"][0]

best_hit

{'identifier': '6MDQ',
 'score': 0.997126609757752,
 'services': [{'service_type': 'full_text',
   'nodes': [{'node_id': 15462,
     'original_score': 10.789904594421387,
     'norm_score': 0.9885064390310079}]},
  {'service_type': 'text',
   'nodes': [{'node_id': 17812, 'original_score': 1.0, 'norm_score': 1.0},
    {'node_id': 28200, 'original_score': 1.0, 'norm_score': 1.0},
    {'node_id': 28001, 'original_score': 1.0, 'norm_score': 1.0}]}]}

from ipywidgets import interact, fixed

representations = [
  'ball+stick',
  'backbone',
  'cartoon',
  'helixorient',
  'hyperball',
  'licorice',
  'line',
  'point',
  'ribbon',
  'rocket',
  'rope',
  'spacefill',
  'surface',
  'trace',
  'tube'             ]
colors = [
  'random',
  'uniform',
  'atomindex',
  'residueindex',
  'chainindex',
  'sstruc',
  'element',
  'resname',
  'bfactor',
  'hydrophobicity', ]

my_examples = {
'отображение 1': {
        'description': '''
Белок в виде cartoon, покраска по типу вторичной структуры
Показана поверхность, с непрозрачностью 0.1
Лиганды в виде hyperball, покрашены в оттенок желтого на ваш выбор
''','representations':
        [ 
            {
                                "type": "cartoon", 
                           "params" : {"color":"sstruc", 
                                 "sele":"protein"} 
            },
                         {"type":"hyperball",
                         "params": {"color":"yellow",
                                  "sele":"ligand"
                                   }
                          },
                          {"type":"surface",
                           "params":{
                                    "sele":"protein",
                                    'opacity': 0.1}
                          } 
        ],
    },
'отображение 2': {
        '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":{"color":"atomindex",
                           "sele":"protein"}
                },

               {"type":"ball+stick",
                "params":{"color":"element",
                         "sele":"sidechainAttached"}
               },

               {"type":"ball+stick",
                "params":{"color":"#FFF700",
                         "sele":"_C and hydrophobic"}
                },
                {"type":"ball+stick",
                "params":{"color":"#40cfff",
                         "sele":"_C and charged"}
                },

                {"type":"none",
                 "params":{"sele":"ligand"}}
         ],
    },
'отображение 3': {
        'description': '''
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': 'backbone',
                    'color': 'element'
                }
            },
            {
                'type': 'licorice',
                'params': {
                    'sele': 'sidechain',
                    'color': 'element'
                 }
            },
            {
                'type': 'ball+stick',
                'params': 
                {
                    'sele': 'protein and :A and 1030-1070 and _C',
                    'color': 'lightblue'
                }
            },
            {
                'type': 'line',
                'params': 
                {
                    'sele': 'ligand',
                    'color': 'orange'
                }
            },
        ],
},
}
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("6MDQ", default_representation=False)
interact(show_examples, view=fixed(view), example_name=list(my_examples.keys()))
view

Запись, найденная по идентификатору 6MDQ, содержит информацию о белке альбумине. Сывороточный альбумин является наиболее распространенным белком в плазме крови млекопитающих и отвечает за транспорт металлов, лекарств и различных метаболитов, включая гормоны. Альбумин может связываться с тестостероном в двух местах. Определить константу связывания можно двумя способами: тушение флуоресценции триптофана и сверхбыстрая аффинная экстракция. Это позволяет сделать вывод о влиянии ряда соединений в крови на транспорт тестостерона альбумином. Например, обсуждается связь о низком уровне тестостерона у пациентов с диабетом.