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我有许多微笑格式的分子，我想从分子的微笑格式中获取分子名称，我想使用 python 进行转换。

例如 ： 

CN1CCC[C@H]1c2cccnc2 - Nicotine  
OCCc1c(C)[n+](=cs1)Cc2cnc(C)nc(N)2 - Thiamin

哪个 python 模块将帮助我进行此类转换？
请告诉我。

4

4 回答 4

1

我不知道有哪个模块可以让你做到这一点，我不得不在 data wrangler 上玩，试图得到一个满意的答案。

我使用 Wikipedia 解决了这个问题，该 Wikipedia 越来越多地用于结构化生物信息学/化学信息学数据，但事实证明我的程序显示很多数据是不正确的。

我使用 urllib 向 dbpedia 提交了一个 SPARQL 查询，首先搜索微笑字符串，然后搜索化合物的分子量失败。

import sys
import urllib
import urllib2
import traceback
import pybel
import json

def query(q,epr,f='application/json'):
    try:
        params = {'query': q}
        params = urllib.urlencode(params)
        opener = urllib2.build_opener(urllib2.HTTPHandler)
        request = urllib2.Request(epr+'?'+params)
        request.add_header('Accept', f)
        request.get_method = lambda: 'GET'
        url = opener.open(request)
        return url.read()
    except Exception, e:
        traceback.print_exc(file=sys.stdout)
        raise e 

url = 'http://dbpedia.org/sparql'

q1 = '''
select ?name where {
    ?s <http://dbpedia.org/property/smiles> "%s"@en.
    ?s rdfs:label ?name.
    FILTER(LANG(?name) = "" || LANGMATCHES(LANG(?name), "en"))
}
limit 10
'''
q2 = '''
select ?name where {
    ?s <http://dbpedia.org/property/molecularWeight> '%s'^^xsd:double.
    ?s rdfs:label ?name.
    FILTER(LANG(?name) = "" || LANGMATCHES(LANG(?name), "en"))
}
limit 10
'''

smiles = filter(None, '''

CN1CCC[C@H]1c2cccnc2
CN(CCC1)[C@@H]1C2=CC=CN=C2

OCCc1c(C)[n+](=cs1)Cc2cnc(C)nc(N)2

Cc1nnc2CN=C(c3ccccc3)c4cc(Cl)ccc4-n12

CN1C(=O)CN=C(c2ccccc2)c3cc(Cl)ccc13

CCc1nn(C)c2c(=O)[nH]c(nc12)c3cc(ccc3OCC)S(=O)(=O)N4CCN(C)CC4

CC(C)(N)Cc1ccccc1

CN(C)C(=O)Cc1c(nc2ccc(C)cn12)c3ccc(C)cc3

COc1ccc2[nH]c(nc2c1)S(=O)Cc3ncc(C)c(OC)c3C

CCN(CC)C(=O)[C@H]1CN(C)[C@@H]2Cc3c[nH]c4cccc(C2=C1)c34
'''.splitlines())

OBMolecules = {}
for smile in smiles:
    try:
        OBMolecules[smile] = pybel.readstring('smi', smile)
    except Exception as e:
        print e

for smi in smiles:
    print '--------------'
    print smi
    try:
        print "searching by smiles string.."
        results = json.loads(query(q1 % smi, url))
        if len(results['results']['bindings']) == 0:
            raise Exception('no results from smiles')
        else:
            print 'NAME: ', results['results']['bindings'][0]['name']['value']

    except Exception as e:
        print e

        try:
            mol_weight = round(OBMolecules[smi].molwt, 2)
            print "search ing by molecular weight %s" % mol_weight
            results = json.loads(query(q2 % mol_weight, url))
            if len(results['results']['bindings']) == 0:
                raise Exception('no results from molecular weight')
            else:
                print 'NAME: ', results['results']['bindings'][0]['name']['value']
        except Exception as e:
            print e

输出...

--------------
CN1CCC[C@H]1c2cccnc2
searching by smiles string..
no results from smiles
search ing by molecular weight 162.23
NAME:  Anabasine
--------------
CN(CCC1)[C@@H]1C2=CC=CN=C2
searching by smiles string..
no results from smiles
search ing by molecular weight 162.23
NAME:  Anabasine
--------------
OCCc1c(C)[n+](=cs1)Cc2cnc(C)nc(N)2
searching by smiles string..
no results from smiles
search ing by molecular weight 267.37
NAME:  Pipradrol
--------------
Cc1nnc2CN=C(c3ccccc3)c4cc(Cl)ccc4-n12
searching by smiles string..
no results from smiles
search ing by molecular weight 308.76
no results from molecular weight
--------------
CN1C(=O)CN=C(c2ccccc2)c3cc(Cl)ccc13
searching by smiles string..
no results from smiles
search ing by molecular weight 284.74
NAME:  Mazindol
--------------
CCc1nn(C)c2c(=O)[nH]c(nc12)c3cc(ccc3OCC)S(=O)(=O)N4CCN(C)CC4
searching by smiles string..
no results from smiles
search ing by molecular weight 460.55
no results from molecular weight
--------------
CC(C)(N)Cc1ccccc1
searching by smiles string..
no results from smiles
search ing by molecular weight 149.23
NAME:  Phenpromethamine
--------------
CN(C)C(=O)Cc1c(nc2ccc(C)cn12)c3ccc(C)cc3
searching by smiles string..
no results from smiles
search ing by molecular weight 307.39
NAME:  Talastine
--------------
COc1ccc2[nH]c(nc2c1)S(=O)Cc3ncc(C)c(OC)c3C
searching by smiles string..
no results from smiles
search ing by molecular weight 345.42
no results from molecular weight
--------------
CCN(CC)C(=O)[C@H]1CN(C)[C@@H]2Cc3c[nH]c4cccc(C2=C1)c34
searching by smiles string..
no results from smiles
search ing by molecular weight 323.43
NAME:  Lysergic acid diethylamide

如您所见，应该是尼古丁的前两个结果是错误的，这是因为尼古丁的维基百科条目报告了分子量字段中的分子量。

于 2014-01-20T19:25:18.963 回答
1

在打开的 babel 文档中有一个关于相似性搜索的部分您可能想要查看，您可以将其与从Chembl派生的 sdl 文件结合使用。

我稍后会试一试，因为它比我之前的回答更有成效！

于 2014-01-20T19:52:45.273 回答
0

参考：NCI/CADD from urllib.request import urlopen

def CIRconvert(smi):
    try:
        url ="https://cactus.nci.nih.gov/chemical/structure/" + smi+"/iupac_name" 
        ans = urlopen(url).read().decode('utf8')
        return ans
    except:
        return 'Name Not Available'

smiles  = 'CCCCC(C)CC'
print(smiles, CIRconvert(smiles))

输出：CCCCC(C)CC - 3-甲基庚烷

于 2020-02-05T12:05:47.463 回答
0

下载 RDkit 模块并使用如下内容：

ms_smis = [["CN1CCC[C@H]1c2cccnc2", "Nicotine"],
           ["OCCc1c(C)[n+](=cs1)Cc2cnc(C)nc(N)2", "Thiamin"]]
ms = [[Chem.MolFromSmiles(x[0]), x[1]] for x in ms_smis]

for m in ms: Draw.MolToFile(m[0], m[1] + ".png", size=(800, 800))

这是文档： https ://www.rdkit.org/docs/GettingStartedInPython.html

于 2021-09-15T22:52:52.923 回答