Практикум 1. Поиск в PDB и основы визуализации

!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.

import nglview as nv
import requests  
import json

Задание 1

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

#Ключевое слово
keyword_clause = {
    "type": "terminal",
    "service": "full_text",
                           
    "parameters": {
        "value": "androgen"
    }
}

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

#Разрешение
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)

#Лиганды
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)

#Дата
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)

#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]>

#Распаковка
search_result = search.json() 
search_result

{'query_id': '277fd3de-470d-4819-a03e-88eb6dd25426',
 'result_type': 'entry',
 'total_count': 42,
 'result_set': [{'identifier': '1GS4',
   'score': 1.0,
   'services': [{'service_type': 'full_text',
     'nodes': [{'node_id': 12350,
       'original_score': 9.654606819152832,
       'norm_score': 1.0}]},
    {'service_type': 'text',
     'nodes': [{'node_id': 15870, 'original_score': 1.0, 'norm_score': 1.0},
      {'node_id': 6213, 'original_score': 1.0, 'norm_score': 1.0},
      {'node_id': 3507, 'original_score': 1.0, 'norm_score': 1.0}]}]},
  {'identifier': '1T73',
   'score': 0.9984281452306885,
   'services': [{'service_type': 'full_text',
     'nodes': [{'node_id': 12350,
       'original_score': 9.604939460754395,
       'norm_score': 0.9937125809227536}]},
    {'service_type': 'text',
     'nodes': [{'node_id': 15870, 'original_score': 1.0, 'norm_score': 1.0},
      {'node_id': 6213, 'original_score': 1.0, 'norm_score': 1.0},
      {'node_id': 3507, 'original_score': 1.0, 'norm_score': 1.0}]}]},
  {'identifier': '1T74',
   'score': 0.9984281452306885,
   'services': [{'service_type': 'full_text',
     'nodes': [{'node_id': 12350,
       'original_score': 9.604939460754395,
       'norm_score': 0.9937125809227536}]},
    {'service_type': 'text',
     'nodes': [{'node_id': 15870, 'original_score': 1.0, 'norm_score': 1.0},
      {'node_id': 6213, 'original_score': 1.0, 'norm_score': 1.0},
      {'node_id': 3507, 'original_score': 1.0, 'norm_score': 1.0}]}]},
  {'identifier': '1T76',
   'score': 0.9984281452306885,
   'services': [{'service_type': 'full_text',
     'nodes': [{'node_id': 12350,
       'original_score': 9.604939460754395,
       'norm_score': 0.9937125809227536}]},
    {'service_type': 'text',
     'nodes': [{'node_id': 15870, 'original_score': 1.0, 'norm_score': 1.0},
      {'node_id': 6213, 'original_score': 1.0, 'norm_score': 1.0},
      {'node_id': 3507, 'original_score': 1.0, 'norm_score': 1.0}]}]},
  {'identifier': '1T7M',
   'score': 0.9984281452306885,
   'services': [{'service_type': 'full_text',
     'nodes': [{'node_id': 12350,
       'original_score': 9.604939460754395,
       'norm_score': 0.9937125809227536}]},
    {'service_type': 'text',
     'nodes': [{'node_id': 15870, 'original_score': 1.0, 'norm_score': 1.0},
      {'node_id': 6213, 'original_score': 1.0, 'norm_score': 1.0},
      {'node_id': 3507, 'original_score': 1.0, 'norm_score': 1.0}]}]},
  {'identifier': '1LHN',
   'score': 0.9499101072917643,
   'services': [{'service_type': 'full_text',
     'nodes': [{'node_id': 12350,
       'original_score': 8.071869850158691,
       'norm_score': 0.799640429167057}]},
    {'service_type': 'text',
     'nodes': [{'node_id': 15870, 'original_score': 1.0, 'norm_score': 1.0},
      {'node_id': 6213, 'original_score': 1.0, 'norm_score': 1.0},
      {'node_id': 3507, 'original_score': 1.0, 'norm_score': 1.0}]}]},
  {'identifier': '1LHO',
   'score': 0.9499101072917643,
   'services': [{'service_type': 'full_text',
     'nodes': [{'node_id': 12350,
       'original_score': 8.071869850158691,
       'norm_score': 0.799640429167057}]},
    {'service_type': 'text',
     'nodes': [{'node_id': 15870, 'original_score': 1.0, 'norm_score': 1.0},
      {'node_id': 6213, 'original_score': 1.0, 'norm_score': 1.0},
      {'node_id': 3507, 'original_score': 1.0, 'norm_score': 1.0}]}]},
  {'identifier': '1D2S',
   'score': 0.946142288712296,
   'services': [{'service_type': 'full_text',
     'nodes': [{'node_id': 12350,
       'original_score': 7.95281457901001,
       'norm_score': 0.784569154849184}]},
    {'service_type': 'text',
     'nodes': [{'node_id': 15870, 'original_score': 1.0, 'norm_score': 1.0},
      {'node_id': 6213, 'original_score': 1.0, 'norm_score': 1.0},
      {'node_id': 3507, 'original_score': 1.0, 'norm_score': 1.0}]}]},
  {'identifier': '1LHU',
   'score': 0.9354774442462389,
   'services': [{'service_type': 'full_text',
     'nodes': [{'node_id': 12350,
       'original_score': 7.615827560424805,
       'norm_score': 0.7419097769849556}]},
    {'service_type': 'text',
     'nodes': [{'node_id': 15870, 'original_score': 1.0, 'norm_score': 1.0},
      {'node_id': 6213, 'original_score': 1.0, 'norm_score': 1.0},
      {'node_id': 3507, 'original_score': 1.0, 'norm_score': 1.0}]}]},
  {'identifier': '1LHV',
   'score': 0.9219846948187225,
   'services': [{'service_type': 'full_text',
     'nodes': [{'node_id': 12350,
       'original_score': 7.189484596252441,
       'norm_score': 0.6879387792748897}]},
    {'service_type': 'text',
     'nodes': [{'node_id': 15870, 'original_score': 1.0, 'norm_score': 1.0},
      {'node_id': 6213, 'original_score': 1.0, 'norm_score': 1.0},
      {'node_id': 3507, 'original_score': 1.0, 'norm_score': 1.0}]}]}]}

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

{'identifier': '1GS4',
 'score': 1.0,
 'services': [{'service_type': 'full_text',
   'nodes': [{'node_id': 12350,
     'original_score': 9.654606819152832,
     'norm_score': 1.0}]},
  {'service_type': 'text',
   'nodes': [{'node_id': 15870, 'original_score': 1.0, 'norm_score': 1.0},
    {'node_id': 6213, 'original_score': 1.0, 'norm_score': 1.0},
    {'node_id': 3507, 'original_score': 1.0, 'norm_score': 1.0}]}]}

Задание 2

В первом задании был получен ID '1GS4'- это структурная основа глюкокортикоидного ответа в мутантном рецепторе андрогенов человека (ARccr), полученном из андроген-независимого рака предстательной железы. Определена кристаллическая структура лиганд-связывающего домена (LBD) мутантного рецептора андрогенов (AR) в комплексе с агонистом 9альфа-фторкортизола с разрешением 1,95 A. Имеет два лиганда 9ALPHA-FLUOROCORTISOL и PHOSPHATE ION. Обнаружена 27 декабря 2001 г.

Задание 3

view = nv.show_pdbid('1GS4') 
view

from ipywidgets import interact, fixed

my_examples = {
    'Example 1': {
        'description': '''
Вариант 2
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': 'line',
                'params': {
                    'sele': 'sidechainAttached',                 
                    'color': 'lightgray'  
                 }
            },
{
                'type': 'licorice',                      
                'params': {
                    'sele': 'sidechainAttached and charged',                  
                 }
            },
            {
                'type': 'ball+stick',                      
                'params': {
                    'sele': 'ligand',               
                    'color': 'element'  
                 }
            },
            {
                'type': 'ball+stick',                      
                'params': {
                    'sele': 'ligand AND _C',               
                    'color': '#FFF0F5'  
                 }
            }
        ],
    },
    'Example 2': {
        '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 and not ( hydrophobic and _C )',              
                    '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 polar and _C',               
                    'color': 'lightskyblue'  
                 }
            }
        ],
    },
    'Example 3': {
        'description': '''
Вариант 8.
Поверхность белка покрашена в белый, с непрозрачностью 0.1
Белок в виде cartoon темно-серого цвета
Боковые радикалы в стержневой модели, покрашены по гидрофобности
Лиганды в виде Ван-дер-Ваальсовых сфер, покрашены по элементам
''',
        'representations': [
             {
                'type': 'surface',                      
                'params': {
                    'sele': 'protein',               
                    'color': 'white',  
                    'opacity': 0.1
                 }
            },
            {
                'type': 'cartoon',                      
                'params': {
                    'sele': 'protein',                     
                    'color': 'darkgray'  
                 }
            },
            {
                'type': 'licorice',                      
                'params': {
                    'sele': 'sidechain',                     
                    'color': 'hydrophobicity'  
                 }
            },
            {
                'type': 'spacefill',
                'params': {
                    'sele': 'ligand',                     
                    'color': 'element'  
                 }
            },
        ],
    },
}

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("1gs4", default_representation=False)
interact(show_examples, view=fixed(view), example_name=list(my_examples.keys()))
view