PDBe Basic¶

def get_entry(pdb_id):
    """
    This function tries to get the data that corresponds to
    a PDB id

    If the entry id is not found, it print an error message
    and returns None

    :param pdb_id: String
    :return: Dict or None
    """
    try:
        # This next line will use our previously written
        # get_value() function
        return {pdb_id: get_value(pdb_id, mock_entry_summary)}
    except KeyError as error:
        print("Key error: %s" % error)
        return None

# Try to get PDB entry "3bow"
print("Trying with PDB id which is not in the dictionary:")
print(get_entry("3bow"))
print()

# Try to get PDB entry "1cbs"
print("Trying with PDB id which is in the dictionary:")
print(get_entry("1cbs"))

def make_summary(data):
    """
    This function creates a summary for a PDB entry
    by getting data for an entry, and extracting
    pieces of information

    :param data: Dict
    :return: String
    """

    pdb_id = ""
    # Certain calls could return multiple PDB entries,
    # but the GET summary call we use in this exercise
    # will always return only one PDB entry
    for key in data.keys():
        pdb_id = key

    # The data is a list of dictionaries, and for the summary information,
    # it is always the first element of the list
    entry = get_item(0, data[pdb_id])

    # Getting the title of the entry
    title = get_value("title", entry)

    # Getting the release date of the entry
    release_date = get_value("release_date", entry)
    # Formatting the entry to make it more user-friendly
    formatted_release_date = "%s/%s/%s" % (
        release_date[:4],
        release_date[4:6],
        release_date[6:])

    # Getting the experimental methods
    # Note that there can be multiple methods, so this is a list that
    # needs to be iterated
    experimental_methods = ""
    for experimental_method in get_value("experimental_method", entry):
        if experimental_methods:
            experimental_methods += " and "
        experimental_methods += experimental_method

    # Creating the summary text using all the extracted
    # information
    summary = "Entry is titled \"%s\" and was released on %s." % (
        title,
        formatted_release_date)
    summary += " This entry was determined using %s." % experimental_methods
    return summary

print(make_summary(get_entry("1cbs")))

def get_entry_from_api(pdb_id, api_url):
    """
    This function will make a call to the PDBe API using
    the PDB id and API url provided as arguments

    :param pdb_id: String,
    :param api_url: String
    :return: Dict or None
    """
    if not re.match("[0-9][A-Za-z][A-Za-z0-9]{2}", pdb_id):
        print("Invalid PDB id")
        return None

    # Make a GET call to the API URL
    get_request = requests.get(url=api_url+pdb_id)

    if get_request.status_code == 200:
        # If there is data returned (with HTML status code 200)
        # then return the data in JSON format
        return get_request.json()
    else:
        # If there is no data, print status code and response
        print(get_request.status_code, get_request.text)
        return None

# Try our GET function with an invalid PDB id
print("Trying to GET data with invalid PDB id:")
print(get_entry_from_api("whatever", summary_url))
print()

print("Trying to GET data with valid PDB id:")
print(get_entry_from_api("1cbs", summary_url))

# As you can hopefully see, the data displayed is very similar to
# what we had in the mock data in previous sections - however,
# this is actual data coming from the PDBe API

print("Example #1")
print(make_summary(get_entry_from_api("3bow", summary_url)))
print()
print("Example #2")
print(make_summary(get_entry_from_api("2klm", summary_url)))