使用Python从蛋白质数据库下载特定的.pdb文件

我一直在尝试从蛋白质数据库下载.pdb文件。我已经编写了下面的代码块来提取这些文件，但是我发现正在下载的文件包含网页

#Sector C - Processing block:
RefinedPDBCodeList = [] #C1
with open('RefinedPDBCodeList') as inputfile:
    for line in inputfile:
         RefinedPDBCodeList.append(line.strip().split(','))

print(RefinedPDBCodeList[0])
['101m.pdb']

import urllib.request      
for i in range(0, 1): #S2 - range(0, len(RefinedPDBCodeList)):
    path=urllib.request.urlretrieve('http://www.rcsb.org/pdb/explore/explore.do?structureId=101m', '101m.pdb')

---

看起来你的基本url搞错了。请尝试：

urllib.request.urlretrieve('http://files.rcsb.org/download/101M.pdb', '101m.pdb')

---

看起来你的基本url搞错了。请尝试：

urllib.request.urlretrieve('http://files.rcsb.org/download/101M.pdb', '101m.pdb')

---

虽然旧URL重定向到新URL，但该URL已更新，目前：

urllib.request.urlretrieve('https://files.rcsb.org/download/101M.pdb', '101m.pdb')

---

有关RCSB PDB提供的不同下载的完整URL列表，请参阅

虽然旧URL重定向到新URL，但URL已经更新，目前：

urllib.request.urlretrieve('https://files.rcsb.org/download/101M.pdb', '101m.pdb')

---

有关RCSB PDB提供的不同下载的完整URL列表，请参阅

BioPython提供了一种检索方法。但是，这依赖于PDB FTP服务。如果由于防火墙等原因FTP端口未打开，则可以使用此功能：

def download_pdb(pdbcode, datadir, downloadurl="https://files.rcsb.org/download/"):
    """
    Downloads a PDB file from the Internet and saves it in a data directory.
    :param pdbcode: The standard PDB ID e.g. '3ICB' or '3icb'
    :param datadir: The directory where the downloaded file will be saved
    :param downloadurl: The base PDB download URL, cf.
        `https://www.rcsb.org/pages/download/http#structures` for details
    :return: the full path to the downloaded PDB file or None if something went wrong
    """
    pdbfn = pdbcode + ".pdb"
    url = downloadurl + pdbfn
    outfnm = os.path.join(datadir, pdbfn)
    try:
        urllib.request.urlretrieve(url, outfnm)
        return outfnm
    except Exception as err:
        print(str(err), file=sys.stderr)
        return None

---

BioPython提供了一种检索方法。但是，这依赖于PDB FTP服务。如果由于防火墙等原因FTP端口未打开，则可以使用此功能：

def download_pdb(pdbcode, datadir, downloadurl="https://files.rcsb.org/download/"):
    """
    Downloads a PDB file from the Internet and saves it in a data directory.
    :param pdbcode: The standard PDB ID e.g. '3ICB' or '3icb'
    :param datadir: The directory where the downloaded file will be saved
    :param downloadurl: The base PDB download URL, cf.
        `https://www.rcsb.org/pages/download/http#structures` for details
    :return: the full path to the downloaded PDB file or None if something went wrong
    """
    pdbfn = pdbcode + ".pdb"
    url = downloadurl + pdbfn
    outfnm = os.path.join(datadir, pdbfn)
    try:
        urllib.request.urlretrieve(url, outfnm)
        return outfnm
    except Exception as err:
        print(str(err), file=sys.stderr)
        return None