Instruction:
Here you have a function in Python 3, explain what it does
def course_key_is_valid(course_key):
    if course_key is None:
        return False
    try:
        CourseKey.from_string(text_type(course_key))
    except (InvalidKeyError, UnicodeDecodeError):
        return False
    return True

Response: Checks if the given course key is valid.


Instruction:
Can you tell what is the following Python 3 function doing
def organization_data_is_valid(organization_data):
    if organization_data is None:
        return False
    if 'id' in organization_data and not organization_data.get('id'):
        return False
    if 'name' in organization_data and not organization_data.get('name'):
        return False
    return True

Response: Checks if organization data is valid.


Instruction:
How would you explain what the following Python 3 function does
def _activate_organization(organization):
    [_activate_organization_course_relationship(record) for record
     in internal.OrganizationCourse.objects.filter(organization_id=organization.id, active=False)]

    [_activate_record(record) for record
     in internal.Organization.objects.filter(id=organization.id, active=False)]

Response: Activates an inactivated organization as well as any inactive relationships


Instruction:
Given the following Python 3 function, write the documentation
def _inactivate_organization(organization):
    [_inactivate_organization_course_relationship(record) for record
     in internal.OrganizationCourse.objects.filter(organization_id=organization.id, active=True)]

    [_inactivate_record(record) for record
     in internal.Organization.objects.filter(id=organization.id, active=True)]

Response: Inactivates an activated organization as well as any active relationships


Instruction:
Can you implement a function in Python 3 that
activates an inactive organization - course relationship

Response:
def _activate_organization_course_relationship(relationship):  # pylint: disable=invalid-name
    """
    Activates an inactive organization-course relationship
    """
    # If the relationship doesn't exist or the organization isn't active we'll want to raise an error
    relationship = internal.OrganizationCourse.objects.get(
        id=relationship.id,
        active=False,
        organization__active=True
    )
    _activate_record(relationship)


Instruction:
Can you generate the documentation for the following Python 3 function
def _inactivate_organization_course_relationship(relationship):  # pylint: disable=invalid-name
    relationship = internal.OrganizationCourse.objects.get(
        id=relationship.id,
        active=True
    )
    _inactivate_record(relationship)

Response: Inactivates an active organization - course relationship


Instruction:
Given the following Python 3 function, write the documentation
def create_organization(organization):
    # Trust, but verify...
    if not organization.get('name'):
        exceptions.raise_exception("organization", organization, exceptions.InvalidOrganizationException)
    organization_obj = serializers.deserialize_organization(organization)
    try:
        organization = internal.Organization.objects.get(
            name=organization_obj.name,
        )
        # If the organization exists, but was inactivated, we can simply turn it back on
        if not organization.active:
            _activate_organization(organization_obj)
    except internal.Organization.DoesNotExist:
        organization = internal.Organization.objects.create(
            name=organization_obj.name,
            short_name=organization_obj.short_name,
            description=organization_obj.description,
            logo=organization_obj.logo,
            active=True
        )
    return serializers.serialize_organization(organization)

Response: Creates a new organization into app / local state given the following dictionary


Instruction:
How would you implement a function in Python 3 that
updates an existing organization in app / local state Returns a dictionary representation of the organization

Response:
def update_organization(organization):
    """
    Updates an existing organization in app/local state
    Returns a dictionary representation of the object
    """
    organization_obj = serializers.deserialize_organization(organization)
    try:
        organization = internal.Organization.objects.get(id=organization_obj.id)
        organization.name = organization_obj.name
        organization.short_name = organization_obj.short_name
        organization.description = organization_obj.description
        organization.logo = organization_obj.logo
        organization.active = organization_obj.active
    except internal.Organization.DoesNotExist:
        exceptions.raise_exception("organization", organization, exceptions.InvalidOrganizationException)
    return serializers.serialize_organization(organization)


Instruction:
Write a Python 3 script for
returning a specific organization from app / local state

Response:
def fetch_organization(organization_id):
    """
    Retrieves a specific organization from app/local state
    Returns a dictionary representation of the object
    """
    organization = {'id': organization_id}
    if not organization_id:
        exceptions.raise_exception("organization", organization, exceptions.InvalidOrganizationException)
    organizations = serializers.serialize_organizations(
        internal.Organization.objects.filter(id=organization_id, active=True)
    )
    if not organizations:
        exceptions.raise_exception("organization", organization, exceptions.InvalidOrganizationException)
    return organizations[0]


Instruction:
Here you have a function in Python 3, explain what it does
def fetch_organization_by_short_name(organization_short_name):
    organization = {'short_name': organization_short_name}
    if not organization_short_name:
        exceptions.raise_exception("organization", organization, exceptions.InvalidOrganizationException)
    organizations = serializers.serialize_organizations(internal.Organization.objects.filter(
        active=True, short_name=organization_short_name
    ))
    if not organizations:
        exceptions.raise_exception("organization", organization, exceptions.InvalidOrganizationException)
    return organizations[0]

Response: Returns a specific organization from app state by short name


Instruction:
Can you generate the documentation for the following Python 3 function
def create_organization_course(organization, course_key):
    organization_obj = serializers.deserialize_organization(organization)
    try:
        relationship = internal.OrganizationCourse.objects.get(
            organization=organization_obj,
            course_id=text_type(course_key)
        )
        # If the relationship exists, but was inactivated, we can simply turn it back on
        if not relationship.active:
            _activate_organization_course_relationship(relationship)
    except internal.OrganizationCourse.DoesNotExist:
        relationship = internal.OrganizationCourse.objects.create(
            organization=organization_obj,
            course_id=text_type(course_key),
            active=True
        )

Response: Creates a new organization - course relationship into app - local state


Instruction:
Can you implement a function in Python 3 that
removes an existing organization - course relationship from app / local state

Response:
def delete_organization_course(organization, course_key):
    """
    Removes an existing organization-course relationship from app/local state
    No response currently defined for this operation
    """
    try:
        relationship = internal.OrganizationCourse.objects.get(
            organization=organization['id'],
            course_id=text_type(course_key),
            active=True,
        )
        _inactivate_organization_course_relationship(relationship)
    except internal.OrganizationCourse.DoesNotExist:
        # If we're being asked to delete an organization-course link
        # that does not exist in the database then our work is done
        pass


Instruction:
Can you generate the documentation for the following Python 3 function
def fetch_organization_courses(organization):
    organization_obj = serializers.deserialize_organization(organization)
    queryset = internal.OrganizationCourse.objects.filter(
        organization=organization_obj,
        active=True
    ).select_related('organization')
    return [serializers.serialize_organization_with_course(organization) for organization in queryset]

Response: Returns the set of courses currently linked to the organization


Instruction:
Can you write a function in Python 3 where it
retrieves the organizations linked to the specified course

Response:
def fetch_course_organizations(course_key):
    """
    Retrieves the organizations linked to the specified course
    """
    queryset = internal.OrganizationCourse.objects.filter(
        course_id=text_type(course_key),
        active=True
    ).select_related('organization')
    return [serializers.serialize_organization_with_course(organization) for organization in queryset]


Instruction:
Can you generate a brief explanation for the following Python 3 code
def delete_course_references(course_key):
    [_inactivate_record(record) for record in internal.OrganizationCourse.objects.filter(
        course_id=text_type(course_key),
        active=True
    )]

Response: Delete all references to the given course key within this app.


Instruction:
Write a Python 3 script to
serialize an organization object to a dictionary.

Response:
def serialize_organization(organization):
    """
    Organization object-to-dict serialization
    """
    return {
        'id': organization.id,
        'name': organization.name,
        'short_name': organization.short_name,
        'description': organization.description,
        'logo': organization.logo
    }


Instruction:
Here you have a function in Python 3, explain what it does
def serialize_organization_with_course(organization_course):
    return {
        'id': organization_course.organization.id,
        'name': organization_course.organization.name,
        'short_name': organization_course.organization.short_name,
        'description': organization_course.organization.description,
        'logo': organization_course.organization.logo,
        'course_id': organization_course.course_id
    }

Response: Serialize organization_course object into a composite object.


Instruction:
Given the following Python 3 function, write the documentation
def deserialize_organization(organization_dict):
    return models.Organization(
        id=organization_dict.get('id'),
        name=organization_dict.get('name', ''),
        short_name=organization_dict.get('short_name', ''),
        description=organization_dict.get('description', ''),
        logo=organization_dict.get('logo', '')
    )

Response: Deserialize an organization dict - to - object serialization


Instruction:
Can you tell what is the following Python 3 function doing
def check_large_images(self, node, parent_depth_level, sibling_depth_level):
        good_images = self.get_image_candidates(node)

        if good_images:
            scored_images = self.fetch_images(good_images, parent_depth_level)
            if scored_images:
                highscore_image = sorted(list(scored_images.items()),
                                         key=lambda x: x[1], reverse=True)[0][0]
                main_image = Image()
                main_image._src = highscore_image.src
                main_image._width = highscore_image.width
                main_image._height = highscore_image.height
                main_image._extraction_type = "bigimage"
                score_len = len(scored_images)
                main_image._confidence_score = 100 / score_len if score_len > 0 else 0
                return main_image

        depth_obj = self.get_depth_level(node, parent_depth_level, sibling_depth_level)
        if depth_obj:
            return self.check_large_images(depth_obj.node, depth_obj.parent_depth,
                                           depth_obj.sibling_depth)

        return None

Response: This method checks if the node has any images that are too large and returns the Image object that is the same as the parent.


Instruction:
How would you explain what the following Python 3 function does
def is_banner_dimensions(width, height):
        if width == height:
            return False

        if width > height:
            diff = float(width / height)
            if diff > 5:
                return True

        if height > width:
            diff = float(height / width)
            if diff > 5:
                return True

        return False

Response: \ Returns True if we think this is a bannery dimension.


Instruction:
Here you have a function in Python 3, explain what it does
def is_valid_filename(self, image_node):
        src = self.parser.getAttribute(image_node, attr='src')

        if not src:
            return False

        if self.badimages_names_re.search(src):
            return False

        return True

Response: \ This method checks if the image src attribute is a valid filename.


Instruction:
Implement a function in Python 3 to
loop through all the images and find the ones that have the best bytez to even make them a candidate

Response:
def get_images_bytesize_match(self, images):
        """\
        loop through all the images and find the ones
        that have the best bytez to even make them a candidate
        """
        cnt = 0
        max_bytes_size = 15728640
        good_images = []
        for image in images:
            if cnt > 30:
                return good_images
            src = self.parser.getAttribute(image, attr='src')
            src = self.build_image_path(src)
            src = self.add_schema_if_none(src)
            local_image = self.get_local_image(src)
            if local_image:
                filesize = local_image.bytes
                if (filesize == 0 or filesize > self.images_min_bytes) and filesize < max_bytes_size:
                    good_images.append(image)
                else:
                    images.remove(image)
            cnt += 1
        return good_images if len(good_images) > 0 else None


Instruction:
Implement a Python 3 function for
checking if the image is in the known schemas and returns the image object.

Response:
def check_known_schemas(self):
        """\
        checks to see if we were able to find the image via known schemas:

        Supported Schemas
         - Open Graph
         - schema.org
        """
        if 'image' in self.article.opengraph:
            return self.get_image(self.article.opengraph["image"],
                                  extraction_type='opengraph')
        elif (self.article.schema and 'image' in self.article.schema and
              "url" in self.article.schema["image"]):
            return self.get_image(self.article.schema["image"]["url"],
                                  extraction_type='schema.org')
        return None


Instruction:
Can you generate the documentation for the following Python 3 function
def get_local_image(self, src):
        return ImageUtils.store_image(self.fetcher, self.article.link_hash, src, self.config)

Response: \ Returns the bytes of the image on disk


Instruction:
Can you generate the documentation for the following Python 3 function
def get_video(self, node):
        video = Video()
        video._embed_code = self.get_embed_code(node)
        video._embed_type = self.get_embed_type(node)
        video._width = self.get_width(node)
        video._height = self.get_height(node)
        video._src = self.get_src(node)
        video._provider = self.get_provider(video.src)
        return video

Response: Create a video object from a video embed node


Instruction:
Can you tell what is the following Python 3 function doing
def get_encodings_from_content(content):
    if isinstance(content, bytes):
        find_charset = re.compile(
            br'<meta.*?charset=["\']*([a-z0-9\-_]+?) *?["\'>]', flags=re.I
        ).findall

        find_xml = re.compile(
            br'^<\?xml.*?encoding=["\']*([a-z0-9\-_]+?) *?["\'>]'
        ).findall
        return [encoding.decode('utf-8') for encoding in
                find_charset(content) + find_xml(content)]
    else:
        find_charset = re.compile(
            r'<meta.*?charset=["\']*([a-z0-9\-_]+?) *?["\'>]', flags=re.I
        ).findall

        find_xml = re.compile(
            r'^<\?xml.*?encoding=["\']*([a-z0-9\-_]+?) *?["\'>]'
        ).findall
        return find_charset(content) + find_xml(content)

Response: Return encodings from given content string.


Instruction:
Make a summary of the following Python 3 code
def store_image(cls, http_client, link_hash, src, config):
        # check for a cache hit already on disk
        image = cls.read_localfile(link_hash, src, config)
        if image:
            return image

        # no cache found; do something else

        # parse base64 image
        if src.startswith('data:image'):
            image = cls.write_localfile_base64(link_hash, src, config)
            return image

        # download the image
        data = http_client.fetch(src)
        if data:
            image = cls.write_localfile(data, link_hash, src, config)
            if image:
                return image

        return None

Response:
\ Writes an image src http string to disk as a temporary file
        and returns the LocallyStoredImage object that has the info you need on the image.


Instruction:
Create a Python 3 function for
setting the list of known context patterns.

Response:
def known_context_patterns(self, val):
        ''' val must be an ArticleContextPattern, a dictionary, or list of \
            dictionaries
            e.g., {'attr': 'class', 'value': 'my-article-class'}
                or [{'attr': 'class', 'value': 'my-article-class'},
                    {'attr': 'id', 'value': 'my-article-id'}]
        '''
        def create_pat_from_dict(val):
            '''Helper function used to create an ArticleContextPattern from a dictionary
            '''
            if "tag" in val:
                pat = ArticleContextPattern(tag=val["tag"])
                if "attr" in val:
                    pat.attr = val["attr"]
                    pat.value = val["value"]
            elif "attr" in val:
                pat = ArticleContextPattern(attr=val["attr"], value=val["value"])

            if "domain" in val:
                pat.domain = val["domain"]

            return pat

        if isinstance(val, list):
            self._known_context_patterns = [
                x if isinstance(x, ArticleContextPattern) else create_pat_from_dict(x)
                for x in val
            ] + self.known_context_patterns
        elif isinstance(val, ArticleContextPattern):
            self._known_context_patterns.insert(0, val)
        elif isinstance(val, dict):
            self._known_context_patterns.insert(0, create_pat_from_dict(val))
        else:
            raise Exception("Unknown type: {}. Use a ArticleContextPattern.".format(type(val)))


Instruction:
How would you explain what the following Python 3 function does
def known_publish_date_tags(self, val):
        ''' val must be a dictionary or list of dictionaries
            e.g., {'attrribute': 'name', 'value': 'my-pubdate', 'content': 'datetime'}
                or [{'attrribute': 'name', 'value': 'my-pubdate', 'content': 'datetime'},
                    {'attrribute': 'property', 'value': 'pub_time', 'content': 'content'}]
        '''
        def create_pat_from_dict(val):
            '''Helper function used to create an PublishDatePattern from a dictionary
            '''
            if "tag" in val:
                pat = PublishDatePattern(tag=val["tag"])
                if "attribute" in val:
                    pat.attr = val["attribute"]
                    pat.value = val["value"]
            elif "attribute" in val:
                pat = PublishDatePattern(attr=val["attribute"], value=val["value"],
                                         content=val["content"])
                if "subcontent" in val:
                    pat.subcontent = val["subcontent"]

            if "domain" in val:
                pat.domain = val["domain"]

            return pat

        if isinstance(val, list):
            self._known_publish_date_tags = [
                x if isinstance(x, PublishDatePattern) else create_pat_from_dict(x)
                for x in val
            ] + self.known_publish_date_tags
        elif isinstance(val, PublishDatePattern):
            self._known_publish_date_tags.insert(0, val)
        elif isinstance(val, dict):
            self._known_publish_date_tags.insert(0, create_pat_from_dict(val))
        else:
            raise Exception("Unknown type: {}. Use a PublishDatePattern.".format(type(val)))

Response: Set self. _known_publish_date_tags based on a dictionary or list of dictionaries.


Instruction:
Create a Python 3 function for
setting self. _known_author_patterns based on a dictionary or list of dictionaries.

Response:
def known_author_patterns(self, val):
        ''' val must be a dictionary or list of dictionaries
            e.g., {'attrribute': 'name', 'value': 'my-pubdate', 'content': 'datetime'}
                or [{'attrribute': 'name', 'value': 'my-pubdate', 'content': 'datetime'},
                    {'attrribute': 'property', 'value': 'pub_time', 'content': 'content'}]
        '''

        def create_pat_from_dict(val):
            '''Helper function used to create an AuthorPatterns from a dictionary
            '''
            if "tag" in val:
                pat = AuthorPattern(tag=val["tag"])
                if "attribute" in val:
                    pat.attr = val["attribute"]
                    pat.value = val["value"]
            elif "attribute" in val:
                pat = AuthorPattern(attr=val["attribute"], value=val["value"],
                                    content=val["content"])
            if "subpattern" in val:
                pat.subpattern = create_pat_from_dict(val["subpattern"])

            return pat

        if isinstance(val, list):
            self._known_author_patterns = [
                x if isinstance(x, AuthorPattern) else create_pat_from_dict(x)
                for x in val
            ] + self.known_author_patterns
        elif isinstance(val, AuthorPattern):
            self._known_author_patterns.insert(0, val)
        elif isinstance(val, dict):
            self._known_author_patterns.insert(0, create_pat_from_dict(val))
        else:
            raise Exception("Unknown type: {}. Use an AuthorPattern.".format(type(val)))


Instruction:
Explain what the following Python 3 code does
def get_siblings_content(self, current_sibling, baselinescore_siblings_para):
        if current_sibling.tag == 'p' and self.parser.getText(current_sibling):
            tmp = current_sibling
            if tmp.tail:
                tmp = deepcopy(tmp)
                tmp.tail = ''
            return [tmp]
        else:
            potential_paragraphs = self.parser.getElementsByTag(current_sibling, tag='p')
            if potential_paragraphs is None:
                return None

            paragraphs = list()
            for first_paragraph in potential_paragraphs:
                text = self.parser.getText(first_paragraph)
                if text:  # no len(text) > 0
                    word_stats = self.stopwords_class(language=self.get_language()).get_stopword_count(text)
                    paragraph_score = word_stats.get_stopword_count()
                    sibling_baseline_score = float(.30)
                    high_link_density = self.is_highlink_density(first_paragraph)
                    score = float(baselinescore_siblings_para * sibling_baseline_score)
                    if score < paragraph_score and not high_link_density:
                        para = self.parser.createElement(tag='p', text=text, tail=None)
                        paragraphs.append(para)
            return paragraphs

Response: returns a list of paragraphs that are more than baselinescore_siblings_para


Instruction:
Make a summary of the following Python 3 code
def is_highlink_density(self, element):
        links = self.parser.getElementsByTag(element, tag='a')
        if not links:
            return False

        text = self.parser.getText(element)
        words = text.split(' ')
        words_number = float(len(words))
        link_text_parts = []
        for link in links:
            link_text_parts.append(self.parser.getText(link))

        link_text = ''.join(link_text_parts)
        link_words = link_text.split(' ')
        number_of_link_words = float(len(link_words))
        number_of_links = float(len(links))
        link_divisor = float(number_of_link_words / words_number)
        score = float(link_divisor * number_of_links)
        if score >= 1.0:
            return True
        return False

Response: Checks the density of links within a node


Instruction:
Can you generate the documentation for the following Python 3 function
def post_cleanup(self):
        parse_tags = ['p']
        if self.config.parse_lists:
            parse_tags.extend(['ul', 'ol'])
        if self.config.parse_headers:
            parse_tags.extend(['h1', 'h2', 'h3', 'h4', 'h5', 'h6'])

        target_node = self.article.top_node
        node = self.add_siblings(target_node)
        for elm in self.parser.getChildren(node):
            e_tag = self.parser.getTag(elm)
            if e_tag not in parse_tags:
                if (self.is_highlink_density(elm) or self.is_table_and_no_para_exist(elm) or
                        not self.is_nodescore_threshold_met(node, elm)):
                    self.parser.remove(elm)
        return node

Response: \ Removes any divs that looks like non - content links or paras with no gusto ArcGIS or no gusto ArcGIS.


Instruction:
Write a Python 3 function for
cleaning the title with the use of og : site_name and use TITLE_SPLITTERS to reformat it

Response:
def clean_title(self, title):
        """Clean title with the use of og:site_name
        in this case try to get rid of site name
        and use TITLE_SPLITTERS to reformat title
        """
        # check if we have the site name in opengraph data
        if "site_name" in list(self.article.opengraph.keys()):
            site_name = self.article.opengraph['site_name']
            # remove the site name from title
            title = title.replace(site_name, '').strip()
        elif (self.article.schema and "publisher" in self.article.schema and
              "name" in self.article.schema["publisher"]):
            site_name = self.article.schema["publisher"]["name"]
            # remove the site name from title
            title = title.replace(site_name, '').strip()

        # try to remove the domain from url
        if self.article.domain:
            pattern = re.compile(self.article.domain, re.IGNORECASE)
            title = pattern.sub("", title).strip()

        # split the title in words
        # TechCrunch | my wonderfull article
        # my wonderfull article | TechCrunch
        title_words = title.split()

        # check if first letter is in TITLE_SPLITTERS
        # if so remove it
        if title_words and title_words[0] in TITLE_SPLITTERS:
            title_words.pop(0)

        # check for a title that is empty or consists of only a
        # title splitter to avoid a IndexError below
        if not title_words:
            return ""

        # check if last letter is in TITLE_SPLITTERS
        # if so remove it
        if title_words[-1] in TITLE_SPLITTERS:
            title_words.pop(-1)

        # rebuild the title
        title = " ".join(title_words).strip()

        return title


Instruction:
How would you code a function in Python 3 to
fetch the article title and analyze it

Response:
def get_title(self):
        """\
        Fetch the article title and analyze it
        """
        title = ''

        # rely on opengraph in case we have the data
        if "title" in list(self.article.opengraph.keys()):
            return self.clean_title(self.article.opengraph['title'])
        elif self.article.schema and "headline" in self.article.schema:
            return self.clean_title(self.article.schema['headline'])

        # try to fetch the meta headline
        meta_headline = self.parser.getElementsByTag(self.article.doc,
                                                     tag="meta",
                                                     attr="name",
                                                     value="headline")
        if meta_headline is not None and len(meta_headline) > 0:
            title = self.parser.getAttribute(meta_headline[0], 'content')
            return self.clean_title(title)

        # otherwise use the title meta
        title_element = self.parser.getElementsByTag(self.article.doc, tag='title')
        if title_element is not None and len(title_element) > 0:
            title = self.parser.getText(title_element[0])
            return self.clean_title(title)

        return title


Instruction:
Write a Python 3 function that can
return the canonical link for the article.

Response:
def get_canonical_link(self):
        """
        if the article has meta canonical link set in the url
        """
        if self.article.final_url:
            kwargs = {'tag': 'link', 'attr': 'rel', 'value': 'canonical'}
            meta = self.parser.getElementsByTag(self.article.doc, **kwargs)
            if meta is not None and len(meta) > 0:
                href = self.parser.getAttribute(meta[0], 'href')
                if href:
                    href = href.strip()
                    o = urlparse(href)
                    if not o.hostname:
                        tmp = urlparse(self.article.final_url)
                        domain = '%s://%s' % (tmp.scheme, tmp.hostname)
                        href = urljoin(domain, href)
                    return href
        return self.article.final_url


Instruction:
Write a Python 3 function that can
make any list element read like a list

Response:
def make_list_elms_pretty(self):
        """ make any list element read like a list
        """
        for elm in self.parser.getElementsByTag(self.top_node, tag='li'):
            elm.text = r'• {}'.format(elm.text)


Instruction:
Can you generate the documentation for the following Python 3 function
def close(self):
        ''' Close the network connection and perform any other required cleanup

            Note:
                Auto closed when using goose as a context manager or when garbage collected '''
        if self.fetcher is not None:
            self.shutdown_network()
        self.finalizer.atexit = False

Response: Close the network connection and perform any other required cleanup


Instruction:
Create a Python 3 function to
extract the most likely article content from the html page and return the article content as a string.

Response:
def extract(self, url=None, raw_html=None):
        ''' Extract the most likely article content from the html page

            Args:
                url (str): URL to pull and parse
                raw_html (str): String representation of the HTML page
            Returns:
                Article: Representation of the article contents \
                including other parsed and extracted metadata '''
        crawl_candidate = CrawlCandidate(self.config, url, raw_html)
        return self.__crawl(crawl_candidate)


Instruction:
Here you have a function in Python 3, explain what it does
def __crawl(self, crawl_candidate):
        ''' wrap the crawling functionality '''
        def crawler_wrapper(parser, parsers_lst, crawl_candidate):
            try:
                crawler = Crawler(self.config, self.fetcher)
                article = crawler.crawl(crawl_candidate)
            except (UnicodeDecodeError, ValueError) as ex:
                if parsers_lst:
                    parser = parsers_lst.pop(0)  # remove it also!
                    return crawler_wrapper(parser, parsers_lst, crawl_candidate)
                else:
                    raise ex
            return article

        # use the wrapper
        parsers = list(self.config.available_parsers)
        parsers.remove(self.config.parser_class)
        return crawler_wrapper(self.config.parser_class, parsers, crawl_candidate)

Response: wrap the crawling functionality


Instruction:
Can you generate the documentation for the following Python 3 function
def smart_unicode(string, encoding='utf-8', strings_only=False, errors='strict'):
    # if isinstance(s, Promise):
    #     # The input is the result of a gettext_lazy() call.
    #     return s
    return force_unicode(string, encoding, strings_only, errors)

Response: Returns a unicode object representing string.


Instruction:
Write a Python 3 script for
forcing unicode string to Unicode.

Response:
def force_unicode(string, encoding='utf-8', strings_only=False, errors='strict'):
    """
    Similar to smart_unicode, except that lazy instances are resolved to
    strings, rather than kept as lazy objects.

    If strings_only is True, don't convert (some) non-string-like objects.
    """
    # Handle the common case first, saves 30-40% in performance when s
    # is an instance of unicode. This function gets called often in that
    # setting.
    if isinstance(string, str):
        return string
    if strings_only and is_protected_type(string):
        return string
    try:
        if not isinstance(string, str):
            if hasattr(string, '__unicode__'):
                string = string.__unicode__()
            else:
                try:
                    string = str(string, encoding, errors)
                except UnicodeEncodeError:
                    if not isinstance(string, Exception):
                        raise
                    # If we get to here, the caller has passed in an Exception
                    # subclass populated with non-ASCII data without special
                    # handling to display as a string. We need to handle this
                    # without raising a further exception. We do an
                    # approximation to what the Exception's standard str()
                    # output should be.
                    string = ' '.join([force_unicode(arg, encoding,
                                                     strings_only,
                                                     errors) for arg in string])
        elif not isinstance(string, str):
            # Note: We use .decode() here, instead of unicode(s, encoding,
            # errors), so that if s is a SafeString, it ends up being a
            # SafeUnicode at the end.
            string = string.decode(encoding, errors)
    except UnicodeDecodeError as ex:
        if not isinstance(string, Exception):
            raise DjangoUnicodeDecodeError(string, *ex.args)
        else:
            # If we get to here, the caller has passed in an Exception
            # subclass populated with non-ASCII bytestring data without a
            # working unicode method. Try to handle this without raising a
            # further exception by individually forcing the exception args
            # to unicode.
            string = ' '.join([force_unicode(arg, encoding, strings_only,
                                             errors) for arg in string])
    return string


Instruction:
Make a summary of the following Python 3 code
def smart_str(string, encoding='utf-8', strings_only=False, errors='strict'):
    if strings_only and isinstance(string, (type(None), int)):
        return string
    # if isinstance(s, Promise):
    #     return unicode(s).encode(encoding, errors)
    if isinstance(string, str):
        try:
            return string.encode(encoding, errors)
        except UnicodeEncodeError:
            return string.encode('utf-8', errors)
    elif not isinstance(string, bytes):
        try:
            return str(string).encode(encoding, errors)
        except UnicodeEncodeError:
            if isinstance(string, Exception):
                # An Exception subclass containing non-ASCII data that doesn't
                # know how to print itself properly. We shouldn't raise a
                # further exception.
                return ' '.join([smart_str(arg, encoding, strings_only,
                                           errors) for arg in string])
            return str(string).encode(encoding, errors)
    else:
        return string

Response: Returns a bytestring version of s encoded as specified in encoding.


Instruction:
Can you generate a brief explanation for the following Python 3 code
def get_urls(self):
        urls = patterns(
            '',
            url(r'^upload/$', self.admin_site.admin_view(self.handle_upload), name='quill-file-upload'),
        )
        return urls + super(QuillAdmin, self).get_urls()

Response: Add URLs needed to handle image uploads.


Instruction:
Can you tell what is the following Python 3 function doing
def handle_upload(self, request):
        if request.method != 'POST':
            raise Http404

        if request.is_ajax():
            try:
                filename = request.GET['quillUploadFile']
                data = request
                is_raw = True
            except KeyError:
                return HttpResponseBadRequest("Invalid file upload.")
        else:
            if len(request.FILES) != 1:
                return HttpResponseBadRequest("Can only upload 1 file at a time.")
            try:
                data = request.FILES['quillUploadFile']
                filename = data.name
                is_raw = False
            except KeyError:
                return HttpResponseBadRequest('Missing image `quillUploadFile`.')

        url = save_file(data, filename, is_raw, default_storage)
        response_data = {}
        response_data['url'] = url

        # Response content type needs to be text/html here or else
        # IE will try to download the file.
        return HttpResponse(json.dumps(response_data), content_type="text/html; charset=utf-8")

Response: Handle file uploads from WYSIWYG.


Instruction:
Here you have a function in Python 3, explain what it does
def render(self, name, value, attrs={}):
        if value is None:
            value = ''
        final_attrs = self.build_attrs(attrs, name=name)
        quill_app = apps.get_app_config('quill')
        quill_config = getattr(quill_app, self.config)

        return mark_safe(render_to_string(quill_config['template'], {
            'final_attrs': flatatt(final_attrs),
            'value': value,
            'id': final_attrs['id'],
            'config': self.config,
        }))

Response: Render the Quill WYSIWYG.


Instruction:
Can you tell what is the following Python 3 function doing
def formfield(self, **kwargs):
        defaults = {
            'form_class': RichTextFormField,
            'config': self.config,
        }
        defaults.update(kwargs)
        return super(RichTextField, self).formfield(**defaults)

Response: Get the form for field.


Instruction:
Write a Python 3 function that can
render the toolbar for the given config.

Response:
def render_toolbar(context, config):
    """Render the toolbar for the given config."""
    quill_config = getattr(quill_app, config)
    t = template.loader.get_template(quill_config['toolbar_template'])
    return t.render(context)


Instruction:
How would you explain what the following Python 3 function does
def read(self, filename=None):
        self._init_filename(filename)

        def BLANK(i):
            return "B{0:04d}".format(i)
        def COMMENT(i):
            return "C{0:04d}".format(i)

        data = odict()
        iblank = icomment = 0
        with open(self.real_filename) as mdp:
            for line in mdp:
                line = line.strip()
                if len(line) == 0:
                    iblank += 1
                    data[BLANK(iblank)] = ''
                    continue
                m = self.COMMENT.match(line)
                if m:
                    icomment += 1
                    data[COMMENT(icomment)] = m.group('value')
                    continue
                # parameter
                m = self.PARAMETER.match(line)
                if m:
                    # check for comments after parameter?? -- currently discarded
                    parameter = m.group('parameter')
                    value =  self._transform(m.group('value'))
                    data[parameter] = value
                else:
                    errmsg = '{filename!r}: unknown line in mdp file, {line!r}'.format(**vars())
                    self.logger.error(errmsg)
                    raise ParseError(errmsg)

        super(MDP,self).update(data)

Response: Read and parse mdp file filename.


Instruction:
Create a Python 3 function for
writing the dictionary to the specified mdp file.

Response:
def write(self, filename=None, skipempty=False):
        """Write mdp file to *filename*.

        :Keywords:
           *filename*
               output mdp file; default is the filename the mdp
               was read from
           *skipempty* : boolean
               ``True`` removes any parameter lines from output that
               contain empty values [``False``]

        .. Note:: Overwrites the file that the mdp was read from if no
                  *filename* supplied.
        """

        with open(self.filename(filename, ext='mdp'), 'w') as mdp:
            for k,v in self.items():
                if k[0] == 'B':        # blank line
                    mdp.write("\n")
                elif k[0] == 'C':      # comment
                    mdp.write("; {v!s}\n".format(**vars()))
                else:                  # parameter = value
                    if skipempty and (v == '' or v is None):
                        continue
                    if isinstance(v, six.string_types) or not hasattr(v, '__iter__'):
                        mdp.write("{k!s} = {v!s}\n".format(**vars()))
                    else:
                         mdp.write("{} = {}\n".format(k,' '.join(map(str, v))))


Instruction:
Implement a Python 3 function for
finding the first Gromacs command that can be found on the PATH.

Response:
def find_gromacs_command(commands):
    """Return *driver* and *name* of the first command that can be found on :envvar:`PATH`"""

    # We could try executing 'name' or 'driver name' but to keep things lean we
    # just check if the executables can be found and then hope for the best.

    commands = utilities.asiterable(commands)
    for command in commands:
        try:
            driver, name = command.split()
        except ValueError:
            driver, name = None, command

        executable = driver if driver else name
        if utilities.which(executable):
            break
    else:
        raise OSError(errno.ENOENT, "No Gromacs executable found in", ", ".join(commands))

    return driver, name


Instruction:
Here you have a function in Python 3, explain what it does
def check_mdrun_success(logfile):
    if not os.path.exists(logfile):
        return None
    with open(logfile, 'rb') as log:
        log.seek(-1024, 2)
        for line in log:
            line = line.decode('ASCII')
            if line.startswith("Finished mdrun on"):
                return True
    return False

Response: Check if mdrun finished successfully.


Instruction:
How would you code a function in Python 3 to
return double precision mdrun or single precision gromacs. mdrun_d if it cannot run.

Response:
def get_double_or_single_prec_mdrun():
    """Return double precision ``mdrun`` or fall back to single precision.

    This convenience function tries :func:`gromacs.mdrun_d` first and
    if it cannot run it, falls back to :func:`gromacs.mdrun` (without
    further checking).

    .. versionadded:: 0.5.1
    """
    try:
        gromacs.mdrun_d(h=True, stdout=False, stderr=False)
        logger.debug("using double precision gromacs.mdrun_d")
        return gromacs.mdrun_d
    except (AttributeError, GromacsError, OSError):
        # fall back to mdrun if no double precision binary
        wmsg = "No 'mdrun_d' binary found so trying 'mdrun' instead.\n"\
            "(Note that energy minimization runs better with mdrun_d.)"
        logger.warn(wmsg)
        warnings.warn(wmsg, category=AutoCorrectionWarning)
        return gromacs.mdrun


Instruction:
Write a Python 3 script to
return a simple command line to invoke the mdrun launcher.

Response:
def commandline(self, **mpiargs):
        """Returns simple command line to invoke mdrun.

        If :attr:`mpiexec` is set then :meth:`mpicommand` provides the mpi
        launcher command that prefixes the actual ``mdrun`` invocation:

           :attr:`mpiexec` [*mpiargs*]  :attr:`mdrun` [*mdrun-args*]

        The *mdrun-args* are set on initializing the class. Override
        :meth:`mpicommand` to fit your system if the simple default
        OpenMP launcher is not appropriate.
        """
        cmd = self.MDRUN.commandline()
        if self.mpiexec:
            cmd = self.mpicommand(**mpiargs) + cmd
        return cmd


Instruction:
How would you code a function in Python 3 to
return the mpi command portion of the commandline.

Response:
def mpicommand(self, *args, **kwargs):
        """Return a list of the mpi command portion of the commandline.

        Only allows primitive mpi at the moment:
           *mpiexec* -n *ncores* *mdrun* *mdrun-args*

        (This is a primitive example for OpenMP. Override it for more
        complicated cases.)
        """
        if self.mpiexec is None:
            raise NotImplementedError("Override mpiexec to enable the simple OpenMP launcher")
        # example implementation
        ncores = kwargs.pop('ncores', 8)
        return [self.mpiexec, '-n', str(ncores)]


Instruction:
Can you implement a function in Python 3 that
executes the MDrun command and return the exit code.

Response:
def run(self, pre=None, post=None, mdrunargs=None, **mpiargs):
        """Execute the mdrun command (possibly as a MPI command) and run the simulation.

        :Keywords:
          *pre*
             a dictionary containing keyword arguments for the :meth:`prehook`
          *post*
             a dictionary containing keyword arguments for the :meth:`posthook`
          *mdrunargs*
             a dictionary with keyword arguments for :program:`mdrun` which supersede
             **and update** the defaults given to the class constructor
          *mpiargs*
             all other keyword arguments that are processed by :meth:`mpicommand`
        """

        if pre is None:
            pre = {}
        if post is None:
            post = {}
        if mdrunargs is not None:
            try:
                self.MDRUN.gmxargs.update(mdrunargs)
            except (ValueError, TypeError):
                msg = "mdrunargs must be a dict of mdrun options, not {0}".format(mdrunargs)
                logger.error(msg)
                raise

        cmd = self.commandline(**mpiargs)

        with utilities.in_dir(self.dirname, create=False):
           try:
               self.prehook(**pre)
               logger.info(" ".join(cmd))
               rc = subprocess.call(cmd)
           except:
               logger.exception("Failed MD run for unknown reasons.")
               raise
           finally:
               self.posthook(**post)
        if rc == 0:
            logger.info("MDrun completed ok, returncode = {0:d}".format(rc))
        else:
            logger.critical("Failure in MDrun, returncode = {0:d}".format(rc))
        return rc


Instruction:
Create a Python 3 function for
running the mdrun and check if it completes.

Response:
def run_check(self, **kwargs):
        """Run :program:`mdrun` and check if run completed when it finishes.

        This works by looking at the mdrun log file for 'Finished
        mdrun on node'. It is useful to implement robust simulation
        techniques.

        :Arguments:
           *kwargs* are keyword arguments that are passed on to
           :meth:`run` (typically used for mpi things)

        :Returns:
           - ``True`` if run completed successfully
           - ``False`` otherwise
        """
        rc = None   # set to something in case we ever want to look at it later (and bomb in the try block)
        try:
            rc = self.run(**kwargs)
        except:
            logger.exception("run_check: caught exception")
        status = self.check_success()
        if status:
            logger.info("run_check: Hooray! mdrun finished successfully")
        else:
            logger.error("run_check: mdrun failed to complete run")
        return status


Instruction:
How would you code a function in Python 3 to
define functions for the top level name space.

Response:
def _define_canned_commands():
    """Define functions for the top level name space.

    Definitions are collected here so that they can all be wrapped in
    a try-except block that avoids code failing when the Gromacs tools
    are not available --- in some cases they are not necessary to use
    parts of GromacsWrapper.

    .. Note:: Any function defined here **must be listed in ``global``**!
    """
    global trj_compact, rmsd_backbone, trj_fitted, trj_xyfitted

    trj_compact = tools.Trjconv(ur='compact', center=True, boxcenter='tric', pbc='mol',
                                input=('protein','system'),
                                doc="""
Writes a compact representation of the system centered on the protein""")

    rmsd_backbone = tools.G_rms(what='rmsd', fit='rot+trans',
                                input=('Backbone','Backbone'),
                                doc="""
Computes RMSD of backbone after fitting to the backbone.""")

    trj_fitted = tools.Trjconv(fit='rot+trans',
                               input=('backbone', 'system'),
                               doc="""
Writes a trajectory fitted to the protein backbone.

Note that this does *not* center; if center is required, the *input*
selection should have the group to be centered on in second position,
e.g. ``input = ('backbone', 'Protein', System')``.
""")

    # Gromacs 4.x
    trj_xyfitted = tools.Trjconv(fit='rotxy+transxy',
                                 input=('backbone', 'protein','system'),
                                 doc="""
Writes a trajectory fitted to the protein in the XY-plane only.

This is useful for membrane proteins. The system *must* be oriented so
that the membrane is in the XY plane. The protein backbone is used
for the least square fit, centering is done for the whole protein.

Note that centering together with fitting does not always work well
and that one sometimes need two runs of trjconv: one to center and
one to fit.

.. Note:: Gromacs 4.x only""")


Instruction:
Given the following Python 3 function, write the documentation
def trj_fitandcenter(xy=False, **kwargs):
    if xy:
        fitmode = 'rotxy+transxy'
        kwargs.pop('fit', None)
    else:
        fitmode = kwargs.pop('fit', 'rot+trans')  # user can use progressive, too

    intrj = kwargs.pop('f', None)
    # get the correct suffix for the intermediate step: only trr will
    # keep velocities/forces!
    suffix = os.path.splitext(intrj)[1]
    if not suffix in ('xtc', 'trr'):
        suffix = '.xtc'
    outtrj = kwargs.pop('o', None)

    ndx = kwargs.pop('n', None)
    ndxcompact = kwargs.pop('n1', ndx)

    structures = kwargs.pop('s', None)
    if type(structures) in (tuple, list):
        try:
            compact_structure, fit_structure = structures
        except:
            raise ValueError("argument s must be a pair of tpr/pdb files or a single structure file")
    else:
        compact_structure = fit_structure = structures

    inpfit = kwargs.pop('input', ('backbone', 'protein','system'))
    try:
        _inpcompact = inpfit[1:]     # use 2nd and 3rd group for compact
    except TypeError:
        _inpcompact = None
    inpcompact = kwargs.pop('input1', _inpcompact)  # ... or the user supplied ones

    fd, tmptrj = tempfile.mkstemp(suffix=suffix, prefix='pbc_compact_')

    logger.info("Input structure for PBC:  {compact_structure!r}".format(**vars()))
    logger.info("Input structure for fit:  {fit_structure!r}".format(**vars()))
    logger.info("Input trajectory:  {intrj!r}".format(**vars()))
    logger.info("Output trajectory: {outtrj!r}".format(**vars()))
    logger.debug("Writing temporary trajectory {tmptrj!r} (will be auto-cleaned).".format(**vars()))
    sys.stdout.flush()
    try:
        gromacs.trjconv(s=compact_structure, f=intrj, o=tmptrj, n=ndxcompact,
                        ur='compact', center=True, boxcenter='tric', pbc='mol',
                        input=inpcompact, **kwargs)
        # explicitly set pbc="none" for the fitting stage (anything else will produce rubbish and/or
        # complaints from Gromacs)
        kwargs['pbc'] = "none"
        if compact_structure == fit_structure:
            # fit as ususal, including centering
            # (Is center=True really necessary? -- note, if I remove center=True then
            # I MUST fiddle inpfit as below!!)
            gromacs.trjconv(s=fit_structure, f=tmptrj, o=outtrj, n=ndx, fit=fitmode, center=True, input=inpfit, **kwargs)
        else:
            # make sure that we fit EXACTLY as the user wants
            inpfit = [inpfit[0], inpfit[-1]]
            gromacs.trjconv(s=fit_structure, f=tmptrj, o=outtrj, n=ndx, fit=fitmode, input=inpfit, **kwargs)
    finally:
        utilities.unlink_gmx(tmptrj)

Response: This function takes a list of structure files and fits the system to a compact representation and creates a compact representation of the system and centers it with the system.


Instruction:
Can you generate a brief explanation for the following Python 3 code
def cat(prefix="md", dirname=os.path.curdir, partsdir="parts", fulldir="full",
        resolve_multi="pass"):
    """Concatenate all parts of a simulation.

    The xtc, trr, and edr files in *dirname* such as prefix.xtc,
    prefix.part0002.xtc, prefix.part0003.xtc, ... are

       1) moved to the *partsdir* (under *dirname*)
       2) concatenated with the Gromacs tools to yield prefix.xtc, prefix.trr,
          prefix.edr, prefix.gro (or prefix.md) in *dirname*
       3) Store these trajectories in *fulldir*

    .. Note:: Trajectory files are *never* deleted by this function to avoid
              data loss in case of bugs. You will have to clean up yourself
              by deleting *dirname*/*partsdir*.

              Symlinks for the trajectories are *not* handled well and
              break the function. Use hard links instead.

    .. Warning:: If an exception occurs when running this function then make
                 doubly and triply sure where your files are before running
                 this function again; otherwise you might **overwrite data**.
                 Possibly you will need to manually move the files from *partsdir*
                 back into the working directory *dirname*; this should onlu overwrite
                 generated files so far but *check carefully*!

    :Keywords:
        *prefix*
            deffnm of the trajectories [md]
        *resolve_multi"
            how to deal with multiple "final" gro or pdb files: normally there should
            only be one but in case of restarting from the checkpoint of a finished
            simulation one can end up with multiple identical ones.
              - "pass" : do nothing and log a warning
              - "guess" : take prefix.pdb or prefix.gro if it exists, otherwise the one of
                          prefix.partNNNN.gro|pdb with the highes NNNN
        *dirname*
            change to *dirname* and assume all tarjectories are located there [.]
        *partsdir*
             directory where to store the input files (they are moved out of the way);
             *partsdir* must be manually deleted [parts]
        *fulldir*
             directory where to store the final results [full]
    """

    gmxcat = {'xtc': gromacs.trjcat,
              'trr': gromacs.trjcat,
              'edr': gromacs.eneconv,
              'log': utilities.cat,
              }

    def _cat(prefix, ext, partsdir=partsdir, fulldir=fulldir):
        filenames = glob_parts(prefix, ext)
        if ext.startswith('.'):
            ext = ext[1:]
        outfile = os.path.join(fulldir, prefix + '.' + ext)
        if not filenames:
            return None
        nonempty_files = []
        for f in filenames:
            if os.stat(f).st_size == 0:
                logger.warn("File {f!r} is empty, skipping".format(**vars()))
                continue
            if os.path.islink(f):
                # TODO: re-write the symlink to point to the original file
                errmsg = "Symbolic links do not work (file %(f)r), sorry. " \
                    "CHECK LOCATION OF FILES MANUALLY BEFORE RUNNING gromacs.cbook.cat() AGAIN!" % vars()
                logger.exception(errmsg)
                raise NotImplementedError(errmsg)
            shutil.move(f, partsdir)
            nonempty_files.append(f)
        filepaths = [os.path.join(partsdir, f) for f in nonempty_files]
        gmxcat[ext](f=filepaths, o=outfile)
        return outfile

    _resolve_options = ("pass", "guess")
    if not resolve_multi in _resolve_options:
        raise ValueError("resolve_multi must be one of %(_resolve_options)r, "
                         "not %(resolve_multi)r" % vars())

    if fulldir == os.path.curdir:
        wmsg = "Using the current directory as fulldir can potentially lead to data loss if you run this function multiple times."
        logger.warning(wmsg)
        warnings.warn(wmsg, category=BadParameterWarning)

    with utilities.in_dir(dirname, create=False):
        utilities.mkdir_p(partsdir)
        utilities.mkdir_p(fulldir)
        for ext in ('log', 'edr', 'trr', 'xtc'):
            logger.info("[%(dirname)s] concatenating %(ext)s files...", vars())
            outfile = _cat(prefix, ext, partsdir)
            logger.info("[%(dirname)s] created %(outfile)r", vars())
        for ext in ('gro', 'pdb'):              # XXX: ugly, make method out of parts?
            filenames = glob_parts(prefix, ext)
            if len(filenames) == 0:
                continue                        # goto next ext
            elif len(filenames) == 1:
                pick = filenames[0]
            else:
                if resolve_multi == "pass":
                    logger.warning("[%(dirname)s] too many output structures %(filenames)r, "
                                   "cannot decide which one --- resolve manually!", vars())
                    for f in filenames:
                        shutil.move(f, partsdir)
                    continue                    # goto next ext
                elif resolve_multi == "guess":
                    pick = prefix + '.' + ext
                    if not pick in filenames:
                        pick = filenames[-1]  # filenames are ordered with highest parts at end
            final = os.path.join(fulldir, prefix + '.' + ext)
            shutil.copy(pick, final)  # copy2 fails on nfs with Darwin at least
            for f in filenames:
                shutil.move(f, partsdir)
            logger.info("[%(dirname)s] collected final structure %(final)r "
                        "(from %(pick)r)", vars())

    partsdirpath = utilities.realpath(dirname, partsdir)
    logger.warn("[%(dirname)s] cat() complete in %(fulldir)r but original files "
                "in %(partsdirpath)r must be manually removed", vars())

Response: Concatenate all parts of a simulation into a single file.


Instruction:
How would you implement a function in Python 3 that
finds files from a continuation run

Response:
def glob_parts(prefix, ext):
    """Find files from a continuation run"""
    if ext.startswith('.'):
        ext = ext[1:]
    files = glob.glob(prefix+'.'+ext) + glob.glob(prefix+'.part[0-9][0-9][0-9][0-9].'+ext)
    files.sort()   # at least some rough sorting...
    return files


Instruction:
Make a summary of the following Python 3 code
def grompp_qtot(*args, **kwargs):
    qtot_pattern = re.compile('System has non-zero total charge: *(?P<qtot>[-+]?\d*\.\d+([eE][-+]\d+)?)')
    # make sure to capture ALL output
    kwargs['stdout'] = False
    kwargs['stderr'] = False
    rc, output, error = grompp_warnonly(*args, **kwargs)
    gmxoutput = "\n".join([x for x in [output, error] if x is not None])
    if rc != 0:
        # error occured and we want to see the whole output for debugging
        msg = "grompp_qtot() failed. See warning and screen output for clues."
        logger.error(msg)
        import sys
        sys.stderr.write("=========== grompp (stdout/stderr) ============\n")
        sys.stderr.write(gmxoutput)
        sys.stderr.write("===============================================\n")
        sys.stderr.flush()
        raise GromacsError(rc, msg)
    qtot = 0
    for line in gmxoutput.split('\n'):
        m = qtot_pattern.search(line)
        if m:
            qtot = float(m.group('qtot'))
            break
    logger.info("system total charge qtot = {qtot!r}".format(**vars()))
    return qtot

Response: Run gromacs. grompp and return the total charge of the system.


Instruction:
Here you have a function in Python 3, explain what it does
def _mdp_include_string(dirs):
    include_paths = [os.path.expanduser(p) for p in dirs]
    return ' -I'.join([''] + include_paths)

Response: Generate a string that can be added to a mdp include line.


Instruction:
Here you have a function in Python 3, explain what it does
def add_mdp_includes(topology=None, kwargs=None):
    if kwargs is None:
        kwargs = {}

    include_dirs = ['.', '..']      # should . & .. always be added?
    if topology is not None:
        # half-hack: find additional itps in the same directory as the topology
        topology_dir = os.path.dirname(topology)
        include_dirs.append(topology_dir)

    include_dirs.extend(asiterable(kwargs.pop('includes', [])))  # includes can be a list or a string

    # 1. setdefault: we do nothing if user defined include
    # 2. modify input in place!
    kwargs.setdefault('include', _mdp_include_string(include_dirs))
    return kwargs

Response: This function adds the mdp include files to the top - level file that are included in the current directory.


Instruction:
Can you generate a brief explanation for the following Python 3 code
def filter_grompp_options(**kwargs):
    grompp_options = ('f','po','c','r','rb','n','p','pp','o','t','e',  # files
                      'h', 'noh', 'version', 'noversion', 'nice', 'v', 'nov',
                      'time', 'rmvsbds', 'normvsbds', 'maxwarn', 'zero', 'nozero',
                      'renum', 'norenum')
    grompp = dict((k,v) for k,v in kwargs.items() if k in grompp_options)
    other =  dict((k,v) for k,v in kwargs.items() if k not in grompp_options)
    return grompp, other

Response: Returns one dictionary only containing valid grompp options and everything else.


Instruction:
Implement a Python 3 function for
creating a portable topology file.

Response:
def create_portable_topology(topol, struct, **kwargs):
    """Create a processed topology.

    The processed (or portable) topology file does not contain any
    ``#include`` statements and hence can be easily copied around. It
    also makes it possible to re-grompp without having any special itp
    files available.

    :Arguments:
      *topol*
          topology file
      *struct*
          coordinat (structure) file

    :Keywords:
      *processed*
          name of the new topology file; if not set then it is named like
          *topol* but with ``pp_`` prepended
      *includes*
          path or list of paths of directories in which itp files are
          searched for
      *grompp_kwargs**
          other options for :program:`grompp` such as ``maxwarn=2`` can
          also be supplied

    :Returns: full path to the processed topology
    """
    _topoldir, _topol = os.path.split(topol)
    processed = kwargs.pop('processed', os.path.join(_topoldir, 'pp_'+_topol))
    grompp_kwargs, mdp_kwargs = filter_grompp_options(**kwargs)
    mdp_kwargs = add_mdp_includes(topol, mdp_kwargs)
    with tempfile.NamedTemporaryFile(suffix='.mdp') as mdp:
        mdp.write('; empty mdp file\ninclude = {include!s}\n'.format(**mdp_kwargs))
        mdp.flush()
        grompp_kwargs['p'] = topol
        grompp_kwargs['pp'] = processed
        grompp_kwargs['f'] =  mdp.name
        grompp_kwargs['c'] = struct
        grompp_kwargs['v'] = False
        try:
            gromacs.grompp(**grompp_kwargs)
        finally:
            utilities.unlink_gmx('topol.tpr', 'mdout.mdp')
    return utilities.realpath(processed)


Instruction:
Can you tell what is the following Python 3 function doing
def get_volume(f):
    fd, temp = tempfile.mkstemp('.gro')
    try:
        rc,out,err = gromacs.editconf(f=f, o=temp, stdout=False)
    finally:
        os.unlink(temp)
    return [float(x.split()[1]) for x in out.splitlines()
            if x.startswith('Volume:')][0]

Response: Return the volume in nm^3 of structure file f.


Instruction:
How would you implement a function in Python 3 that
edits values in a Gromacs mdp file.

Response:
def edit_mdp(mdp, new_mdp=None, extend_parameters=None, **substitutions):
    """Change values in a Gromacs mdp file.

    Parameters and values are supplied as substitutions, eg ``nsteps=1000``.

    By default the template mdp file is **overwritten in place**.

    If a parameter does not exist in the template then it cannot be substituted
    and the parameter/value pair is returned. The user has to check the
    returned list in order to make sure that everything worked as expected. At
    the moment it is not possible to automatically append the new values to the
    mdp file because of ambiguities when having to replace dashes in parameter
    names with underscores (see the notes below on dashes/underscores).

    If a parameter is set to the value ``None`` then it will be ignored.

    :Arguments:
        *mdp* : filename
            filename of input (and output filename of ``new_mdp=None``)
        *new_mdp* : filename
            filename of alternative output mdp file [None]
        *extend_parameters* : string or list of strings
            single parameter or list of parameters for which the new values
            should be appended to the existing value in the mdp file. This
            makes mostly sense for a single parameter, namely 'include', which
            is set as the default. Set to ``[]`` to disable. ['include']
        *substitutions*
            parameter=value pairs, where parameter is defined by the Gromacs
            mdp file; dashes in parameter names have to be replaced by
            underscores. If a value is a list-like object then the items are
            written as a sequence, joined with spaces, e.g. ::

               ref_t=[310,310,310] --->  ref_t = 310 310 310

    :Returns:
        Dict of parameters that have *not* been substituted.

    **Example** ::

       edit_mdp('md.mdp', new_mdp='long_md.mdp', nsteps=100000, nstxtcout=1000, lincs_iter=2)

    .. Note::

       * Dashes in Gromacs mdp parameters have to be replaced by an underscore
         when supplied as python keyword arguments (a limitation of python). For example
         the MDP syntax is  ``lincs-iter = 4`` but the corresponding  keyword would be
         ``lincs_iter = 4``.
       * If the keyword is set as a dict key, eg ``mdp_params['lincs-iter']=4`` then one
         does not have to substitute.
       * Parameters *aa_bb* and *aa-bb* are considered the same (although this should
         not be a problem in practice because there are no mdp parameters that only
         differ by a underscore).
       * This code is more compact in ``Perl`` as one can use ``s///`` operators:
         ``s/^(\s*${key}\s*=\s*).*/$1${val}/``

    .. SeeAlso:: One can also load the mdp file with
                :class:`gromacs.formats.MDP`, edit the object (a dict), and save it again.
    """
    if new_mdp is None:
        new_mdp = mdp
    if extend_parameters is None:
        extend_parameters = ['include']
    else:
        extend_parameters = list(asiterable(extend_parameters))

    # None parameters should be ignored (simple way to keep the template defaults)
    substitutions = {k: v for k,v in substitutions.items() if v is not None}

    params = list(substitutions.keys())   # list will be reduced for each match

    def demangled(p):
        """Return a RE string that matches the parameter."""
        return p.replace('_', '[-_]')  # must catch either - or _

    patterns = {parameter:
                      re.compile("""\
                       (?P<assignment>\s*{0!s}\s*=\s*)  # parameter == everything before the value
                       (?P<value>[^;]*)              # value (stop before comment=;)
                       (?P<comment>\s*;.*)?          # optional comment
                       """.format(demangled(parameter)), re.VERBOSE)
                     for parameter in substitutions}

    with tempfile.TemporaryFile() as target:
        with open(mdp, 'rb') as src:
            logger.info("editing mdp = {0!r}: {1!r}".format(mdp, substitutions.keys()))
            for line in src:
                line = line.decode('utf-8')
                new_line = line.strip()  # \n must be stripped to ensure that new line is built without break
                for p in params[:]:
                    m = patterns[p].match(new_line)
                    if m:
                        # I am too stupid to replace a specific region in the string so I rebuild it
                        # (matching a line and then replacing value requires TWO re calls)
                        #print 'line:' + new_line
                        #print m.groupdict()
                        if m.group('comment') is None:
                            comment = ''
                        else:
                            comment = " "+m.group('comment')
                        assignment = m.group('assignment')
                        if not assignment.endswith(' '):
                            assignment += ' '
                        # build new line piece-wise:
                        new_line = assignment
                        if p in extend_parameters:
                            # keep original value and add new stuff at end
                            new_line += str(m.group('value')) + ' '
                        # automatically transform lists into space-separated string values
                        value = " ".join(map(str, asiterable(substitutions[p])))
                        new_line += value + comment
                        params.remove(p)
                        break
                target.write((new_line+'\n').encode('utf-8'))
        target.seek(0)
        # XXX: Is there a danger of corrupting the original mdp if something went wrong?
        with open(new_mdp, 'wb') as final:
            shutil.copyfileobj(target, final)

     # return all parameters that have NOT been substituted
    if len(params) > 0:
        logger.warn("Not substituted in {new_mdp!r}: {params!r}".format(**vars()))
    return {p: substitutions[p] for p in params}


Instruction:
How would you explain what the following Python 3 function does
def edit_txt(filename, substitutions, newname=None):
    if newname is None:
        newname = filename

    # No sanity checks (figure out later how to give decent diagnostics).
    # Filter out any rules that have None in replacement.
    _substitutions = [{'lRE': re.compile(str(lRE)),
                       'sRE': re.compile(str(sRE)),
                       'repl': repl}
                      for lRE,sRE,repl in substitutions if repl is not None]

    with tempfile.TemporaryFile() as target:
        with open(filename, 'rb') as src:
            logger.info("editing txt = {0!r} ({1:d} substitutions)".format(filename, len(substitutions)))
            for line in src:
                line = line.decode("utf-8")
                keep_line = True
                for subst in _substitutions:
                    m = subst['lRE'].match(line)
                    if m:              # apply substition to this line?
                        logger.debug('match:    '+line.rstrip())
                        if subst['repl'] is False:   # special rule: delete line
                            keep_line = False
                        else:                        # standard replacement
                            line = subst['sRE'].sub(str(subst['repl']), line)
                            logger.debug('replaced: '+line.rstrip())
                if keep_line:
                    target.write(line.encode('utf-8'))
                else:
                    logger.debug("Deleting line %r", line)

        target.seek(0)
        with open(newname, 'wb') as final:
            shutil.copyfileobj(target, final)
    logger.info("edited txt = {newname!r}".format(**vars()))

Response: Primitive text file stream editor.


Instruction:
Can you generate the documentation for the following Python 3 function
def remove_molecules_from_topology(filename, **kwargs):
    marker = kwargs.pop('marker', None)
    if marker is None:
        marker = "; Gromacs auto-generated entries follow:"
    logger.debug("Scrubbed [ molecules ]: marker = %(marker)r", vars())

    p_marker = re.compile("\s*{0!s}".format(marker))
    p_molecule = re.compile("\s*[\w+_-]+\s+\d+\s*(;.*)?$")
    with tempfile.TemporaryFile() as target:
        with open(filename, 'rb') as src:
            autogenerated = False
            n_removed = 0
            for line in src:
                line = line.decode('utf-8')
                if p_marker.match(line):
                    autogenerated = True
                if autogenerated and p_molecule.match(line):
                    n_removed += 1
                    continue  # remove by skipping
                target.write(line.encode('utf-8'))
        if autogenerated and n_removed > 0:
            target.seek(0)
            with open(filename, 'wb') as final:   # overwrite original!
                shutil.copyfileobj(target, final)
            logger.info("Removed %(n_removed)d autogenerated [ molecules ] from "
                        "topol = %(filename)r" % vars())
    return n_removed

Response: Remove molecules from a topology file.


Instruction:
Given the following Python 3 function, write the documentation
def make_ndx_captured(**kwargs):
    kwargs['stdout']=False   # required for proper output as described in doc
    user_input = kwargs.pop('input',[])
    user_input = [cmd for cmd in user_input if cmd != 'q']  # filter any quit
    kwargs['input'] = user_input + ['', 'q']                # necessary commands
    return gromacs.make_ndx(**kwargs)

Response: This function will take a list of n - dimensional items and return a new list of n - dimensional items.


Instruction:
Implement a function in Python 3 to
return a list of index groups in the index file ndx.

Response:
def get_ndx_groups(ndx, **kwargs):
    """Return a list of index groups in the index file *ndx*.

    :Arguments:
        - *ndx*  is a Gromacs index file.
        - kwargs are passed to :func:`make_ndx_captured`.

    :Returns:
        list of groups as supplied by :func:`parse_ndxlist`

    Alternatively, load the index file with
    :class:`gromacs.formats.NDX` for full control.
    """
    fd, tmp_ndx = tempfile.mkstemp(suffix='.ndx')
    kwargs['o'] = tmp_ndx
    try:
        g = parse_ndxlist(make_ndx_captured(n=ndx, **kwargs)[1])
    finally:
        utilities.unlink_gmx(tmp_ndx)
    return g


Instruction:
Implement a function in Python 3 to
parse output from make_ndx to build list of index groups

Response:
def parse_ndxlist(output):
    """Parse output from make_ndx to build list of index groups::

      groups = parse_ndxlist(output)

    output should be the standard output from ``make_ndx``, e.g.::

       rc,output,junk = gromacs.make_ndx(..., input=('', 'q'), stdout=False, stderr=True)

    (or simply use

       rc,output,junk = cbook.make_ndx_captured(...)

    which presets input, stdout and stderr; of course input can be overriden.)

    :Returns:
       The function returns a list of dicts (``groups``) with fields

       name
           name of the groups
       nr
           number of the group (starts at 0)
       natoms
           number of atoms in the group

    """

    m = NDXLIST.search(output)    # make sure we pick up a proper full list
    grouplist = m.group('LIST')
    return parse_groups(grouplist)


Instruction:
Here you have a function in Python 3, explain what it does
def parse_groups(output):
    groups = []
    for line in output.split('\n'):
        m = NDXGROUP.match(line)
        if m:
            d = m.groupdict()
            groups.append({'name': d['GROUPNAME'],
                           'nr': int(d['GROUPNUMBER']),
                           'natoms': int(d['NATOMS'])})
    return groups

Response: Parse make_ndx output and return groups as a list of dicts.


Instruction:
Here you have a function in Python 3, explain what it does
def gmx_resid(self, resid):
        try:
            gmx_resid = int(self.offset[resid])
        except (TypeError, IndexError):
            gmx_resid = resid + self.offset
        except KeyError:
            raise KeyError("offset must be a dict that contains the gmx resid for {0:d}".format(resid))
        return gmx_resid

Response: Returns the Gromacs index by transforming with offset.


Instruction:
Can you tell what is the following Python 3 function doing
def combine(self, name_all=None, out_ndx=None, operation='|', defaultgroups=False):
        if not operation in ('|', '&', False):
            raise ValueError("Illegal operation {0!r}, only '|' (OR) and '&' (AND) or False allowed.".format(
                             operation))
        if name_all is None and operation:
            name_all = self.name_all or operation.join(self.indexfiles)
        if out_ndx is None:
            out_ndx = self.output

        if defaultgroups:
            # make a default file (using the original ndx where provided!!)
            fd, default_ndx = tempfile.mkstemp(suffix='.ndx', prefix='default__')
            try:
                self.make_ndx(o=default_ndx, input=['q'])
            except:
                utilities.unlink_gmx(default_ndx)
                raise
            ndxfiles = [default_ndx]
        else:
            ndxfiles = []

        ndxfiles.extend(self.indexfiles.values())

        if operation:
            # combine multiple selections and name them
            try:
                fd, tmp_ndx = tempfile.mkstemp(suffix='.ndx', prefix='combined__')
                # combine all selections by loading ALL temporary index files
                operation = ' '+operation.strip()+' '
                cmd = [operation.join(['"{0!s}"'.format(gname) for gname in self.indexfiles]),
                       '', 'q']
                rc,out,err = self.make_ndx(n=ndxfiles, o=tmp_ndx, input=cmd)
                if self._is_empty_group(out):
                    warnings.warn("No atoms found for {cmd!r}".format(**vars()),
                                  category=BadParameterWarning)

                # second pass for naming, sigh (or: use NDX ?)
                groups = parse_ndxlist(out)
                last = groups[-1]
                # name this group
                name_cmd = ["name {0:d} {1!s}".format(last['nr'], name_all), 'q']
                rc,out,err = self.make_ndx(n=tmp_ndx, o=out_ndx, input=name_cmd)
                # For debugging, look at out and err or set stdout=True, stderr=True
                # TODO: check out if at least 1 atom selected
                ##print "DEBUG: combine()"
                ##print out
            finally:
                utilities.unlink_gmx(tmp_ndx)
                if defaultgroups:
                    utilities.unlink_gmx(default_ndx)
        else:
            # just write individual groups in one file (name_all --> None)
            rc,out,err = self.make_ndx(n=ndxfiles, o=out_ndx, input=['','q'])

        return name_all, out_ndx

Response: Combine individual groups into a single one and write output.


Instruction:
Create a Python 3 function for
writing individual named groups to out_ndx.

Response:
def write(self, out_ndx=None, defaultgroups=False):
        """Write individual (named) groups to *out_ndx*."""
        name_all, out_ndx = self.combine(operation=False, out_ndx=out_ndx, defaultgroups=defaultgroups)
        return out_ndx


Instruction:
How would you explain what the following Python 3 function does
def cat(self, out_ndx=None):
        if out_ndx is None:
            out_ndx = self.output
        self.make_ndx(o=out_ndx, input=['q'])
        return out_ndx

Response: Concatenate input index files into a new index file.


Instruction:
How would you explain what the following Python 3 function does
def parse_selection(self, selection, name=None):

        if type(selection) is tuple:
            # range
            process = self._process_range
        elif selection.startswith('@'):
            # verbatim make_ndx command
            process = self._process_command
            selection = selection[1:]
        else:
            process = self._process_residue
        return process(selection, name)

Response: Retuns ( groupname filename ) with index group.


Instruction:
How would you explain what the following Python 3 function does
def _process_command(self, command, name=None):

        self._command_counter += 1
        if name is None:
            name = "CMD{0:03d}".format(self._command_counter)

        # Need to build it with two make_ndx calls because I cannot reliably
        # name the new group without knowing its number.
        try:
            fd, tmp_ndx = tempfile.mkstemp(suffix='.ndx', prefix='tmp_'+name+'__')
            cmd = [command, '', 'q']   # empty command '' necessary to get list
            # This sometimes fails with 'OSError: Broken Pipe' --- hard to debug
            rc,out,err = self.make_ndx(o=tmp_ndx, input=cmd)
            self.check_output(out, "No atoms found for selection {command!r}.".format(**vars()), err=err)
            # For debugging, look at out and err or set stdout=True, stderr=True
            # TODO: check '  0 r_300_&_ALA_&_O     :     1 atoms' has at least 1 atom
            ##print "DEBUG: _process_command()"
            ##print out
            groups = parse_ndxlist(out)
            last = groups[-1]
            # reduce and name this group
            fd, ndx = tempfile.mkstemp(suffix='.ndx', prefix=name+'__')
            name_cmd = ["keep {0:d}".format(last['nr']),
                        "name 0 {0!s}".format(name), 'q']
            rc,out,err = self.make_ndx(n=tmp_ndx, o=ndx, input=name_cmd)
        finally:
            utilities.unlink_gmx(tmp_ndx)

        return name, ndx

Response: Process a make_ndx command and return name and temp index file.


Instruction:
Can you tell what is the following Python 3 function doing
def _process_residue(self, selection, name=None):

        if name is None:
            name = selection.replace(':', '_')

        # XXX: use _translate_residue() ....
        m = self.RESIDUE.match(selection)
        if not m:
            raise ValueError("Selection {selection!r} is not valid.".format(**vars()))

        gmx_resid = self.gmx_resid(int(m.group('resid')))
        residue = m.group('aa')
        if len(residue) == 1:
            gmx_resname = utilities.convert_aa_code(residue) # only works for AA
        else:
            gmx_resname = residue                            # use 3-letter for any resname
        gmx_atomname = m.group('atom')
        if gmx_atomname is None:
            gmx_atomname = 'CA'

        #: select residue <gmx_resname><gmx_resid> atom <gmx_atomname>
        _selection = 'r {gmx_resid:d} & r {gmx_resname!s} & a {gmx_atomname!s}'.format(**vars())
        cmd = ['keep 0', 'del 0',
               _selection,
               'name 0 {name!s}'.format(**vars()),
               'q']
        fd, ndx = tempfile.mkstemp(suffix='.ndx', prefix=name+'__')
        rc,out,err = self.make_ndx(n=self.ndx, o=ndx, input=cmd)
        self.check_output(out, "No atoms found for "
                          "%(selection)r --> %(_selection)r" % vars())
        # For debugging, look at out and err or set stdout=True, stderr=True
        ##print "DEBUG: _process_residue()"
        ##print out

        return name, ndx

Response: Process a residue atom selection and return name and temp index file.


Instruction:
Can you create a Python 3 function that
processes a range selection.

Response:
def _process_range(self, selection, name=None):
        """Process a range selection.

        ("S234", "A300", "CA")   --> selected all CA in this range
        ("S234", "A300")         --> selected all atoms in this range

        .. Note:: Ignores residue type, only cares about the resid (but still required)
        """

        try:
            first, last, gmx_atomname = selection
        except ValueError:
            try:
                first, last = selection
                gmx_atomname = '*'
            except:
                logger.error("%r is not a valid range selection", selection)
                raise
        if name is None:
            name = "{first!s}-{last!s}_{gmx_atomname!s}".format(**vars())

        _first = self._translate_residue(first, default_atomname=gmx_atomname)
        _last = self._translate_residue(last, default_atomname=gmx_atomname)

        _selection = 'r {0:d} - {1:d} & & a {2!s}'.format(_first['resid'], _last['resid'], gmx_atomname)
        cmd = ['keep 0', 'del 0',
               _selection,
               'name 0 {name!s}'.format(**vars()),
               'q']
        fd, ndx = tempfile.mkstemp(suffix='.ndx', prefix=name+'__')
        rc,out,err = self.make_ndx(n=self.ndx, o=ndx, input=cmd)
        self.check_output(out, "No atoms found for "
                          "%(selection)r --> %(_selection)r" % vars())
        # For debugging, look at out and err or set stdout=True, stderr=True
        ##print "DEBUG: _process_residue()"
        ##print out

        return name, ndx


Instruction:
Create a Python 3 function to
translate a single residue to make_ndx syntax.

Response:
def _translate_residue(self, selection, default_atomname='CA'):
        """Translate selection for a single res to make_ndx syntax."""
        m = self.RESIDUE.match(selection)
        if not m:
            errmsg = "Selection {selection!r} is not valid.".format(**vars())
            logger.error(errmsg)
            raise ValueError(errmsg)

        gmx_resid = self.gmx_resid(int(m.group('resid')))    # magic offset correction
        residue = m.group('aa')
        if len(residue) == 1:
            gmx_resname = utilities.convert_aa_code(residue) # only works for AA
        else:
            gmx_resname = residue                            # use 3-letter for any resname

        gmx_atomname = m.group('atom')
        if gmx_atomname is None:
            gmx_atomname = default_atomname

        return {'resname':gmx_resname, 'resid':gmx_resid, 'atomname':gmx_atomname}


Instruction:
Given the following Python 3 function, write the documentation
def rp(self, *args):
        try:
            p = os.path.join(*args)
            if os.path.isabs(p):
                return p
        except TypeError:
            pass
        return utilities.realpath(self.dirname, *args)

Response: Return canonical path to file under *dirname* with components *args*


Instruction:
How would you code a function in Python 3 to
center the tpr and xtc of the current tpr reference structure.

Response:
def center_fit(self, **kwargs):
        """Write compact xtc that is fitted to the tpr reference structure.

        See :func:`gromacs.cbook.trj_fitandcenter` for details and
        description of *kwargs* (including *input*, *input1*, *n* and
        *n1* for how to supply custom index groups). The most important ones are listed
        here but in most cases the defaults should work.

        :Keywords:
           *s*
             Input structure (typically the default tpr file but can be set to
             some other file with a different conformation for fitting)
           *n*
             Alternative index file.
           *o*
             Name of the output trajectory.
           *xy* : Boolean
             If ``True`` then only fit in xy-plane (useful for a membrane normal
             to z). The default is ``False``.
           *force*
             - ``True``: overwrite existing trajectories
             - ``False``: throw a IOError exception
             - ``None``: skip existing and log a warning [default]

        :Returns:
              dictionary with keys *tpr*, *xtc*, which are the names of the
              the new files
        """
        kwargs.setdefault('s', self.tpr)
        kwargs.setdefault('n', self.ndx)
        kwargs['f'] = self.xtc
        kwargs.setdefault('o', self.outfile(self.infix_filename(None, self.xtc, '_centfit', 'xtc')))
        force = kwargs.pop('force', self.force)

        logger.info("Centering and fitting trajectory {f!r}...".format(**kwargs))
        with utilities.in_dir(self.dirname):
            if not self.check_file_exists(kwargs['o'], resolve="indicate", force=force):
                trj_fitandcenter(**kwargs)
            logger.info("Centered and fit trajectory: {o!r}.".format(**kwargs))
        return {'tpr': self.rp(kwargs['s']), 'xtc': self.rp(kwargs['o'])}


Instruction:
Can you tell what is the following Python 3 function doing
def fit(self, xy=False, **kwargs):
        kwargs.setdefault('s', self.tpr)
        kwargs.setdefault('n', self.ndx)
        kwargs['f'] = self.xtc
        force = kwargs.pop('force', self.force)
        if xy:
            fitmode = 'rotxy+transxy'
            kwargs.pop('fit', None)
            infix_default = '_fitxy'
        else:
            fitmode = kwargs.pop('fit', 'rot+trans')  # user can use 'progressive', too
            infix_default = '_fit'

        dt = kwargs.get('dt')
        if dt:
            infix_default += '_dt{0:d}ps'.format(int(dt))    # dt in ps

        kwargs.setdefault('o', self.outfile(self.infix_filename(None, self.xtc, infix_default, 'xtc')))
        fitgroup = kwargs.pop('fitgroup', 'backbone')
        kwargs.setdefault('input', [fitgroup, "system"])

        if kwargs.get('center', False):
            logger.warn("Transformer.fit(): center=%(center)r used: centering should not be combined with fitting.", kwargs)
            if len(kwargs['inputs']) != 3:
                logger.error("If you insist on centering you must provide three groups in the 'input' kwarg: (center, fit, output)")
                raise ValuError("Insufficient index groups for centering,fitting,output")

        logger.info("Fitting trajectory %r to with xy=%r...", kwargs['f'], xy)
        logger.info("Fitting on index group %(fitgroup)r", vars())
        with utilities.in_dir(self.dirname):
            if self.check_file_exists(kwargs['o'], resolve="indicate", force=force):
                logger.warn("File %r exists; force regenerating it with force=True.", kwargs['o'])
            else:
                gromacs.trjconv(fit=fitmode, **kwargs)
                logger.info("Fitted trajectory (fitmode=%s): %r.", fitmode, kwargs['o'])
        return {'tpr': self.rp(kwargs['s']), 'xtc': self.rp(kwargs['o'])}

Response: Fit the tpr reference structure to the output trajectory.


Instruction:
Can you tell what is the following Python 3 function doing
def strip_water(self, os=None, o=None, on=None, compact=False,
                    resn="SOL", groupname="notwater", **kwargs):
        """Write xtc and tpr with water (by resname) removed.

        :Keywords:
           *os*
              Name of the output tpr file; by default use the original but
              insert "nowater" before suffix.
           *o*
              Name of the output trajectory; by default use the original name but
              insert "nowater" before suffix.
           *on*
              Name of a new index file (without water).
           *compact*
              ``True``: write a compact and centered trajectory
              ``False``: use trajectory as it is [``False``]
           *centergroup*
              Index group used for centering ["Protein"]

              .. Note:: If *input* is provided (see below under *kwargs*)
                        then *centergroup* is ignored and the group for
                        centering is taken as the first entry in *input*.

           *resn*
              Residue name of the water molecules; all these residues are excluded.
           *groupname*
              Name of the group that is generated by subtracting all waters
              from the system.
           *force* : Boolean
             - ``True``: overwrite existing trajectories
             - ``False``: throw a IOError exception
             - ``None``: skip existing and log a warning [default]
           *kwargs*
              are passed on to :func:`gromacs.cbook.trj_compact` (unless the
              values have to be set to certain values such as s, f, n, o
              keywords). The *input* keyword is always mangled: Only the first
              entry (the group to centre the trajectory on) is kept, and as a
              second group (the output group) *groupname* is used.

        :Returns:
              dictionary with keys *tpr*, *xtc*, *ndx* which are the names of the
              the new files

        .. warning:: The input tpr file should *not* have *any position restraints*;
                     otherwise Gromacs will throw a hissy-fit and say

                     *Software inconsistency error: Position restraint coordinates are
                     missing*

                     (This appears to be a bug in Gromacs 4.x.)
        """
        force = kwargs.pop('force', self.force)

        newtpr = self.outfile(self.infix_filename(os, self.tpr, '_nowater'))
        newxtc = self.outfile(self.infix_filename(o, self.xtc, '_nowater'))
        newndx = self.outfile(self.infix_filename(on, self.tpr, '_nowater', 'ndx'))

        nowater_ndx = self._join_dirname(newtpr, "nowater.ndx")    # refers to original tpr

        if compact:
            TRJCONV = trj_compact
            # input overrides centergroup
            if kwargs.get('centergroup') is not None and 'input' in kwargs:
                logger.warn("centergroup = %r will be superceded by input[0] = %r", kwargs['centergroup'], kwargs['input'][0])
            _input = kwargs.get('input', [kwargs.get('centergroup', 'Protein')])
            kwargs['input'] = [_input[0], groupname]  # [center group, write-out selection]
            del _input
            logger.info("Creating a compact trajectory centered on group %r", kwargs['input'][0])
            logger.info("Writing %r to the output trajectory", kwargs['input'][1])
        else:
            TRJCONV = gromacs.trjconv
            kwargs['input'] = [groupname]
            logger.info("Writing %r to the output trajectory (no centering)", kwargs['input'][0])
        # clean kwargs, only legal arguments for Gromacs tool trjconv should remain
        kwargs.pop("centergroup", None)

        NOTwater = "! r {resn!s}".format(**vars())  # make_ndx selection ("not water residues")
        with utilities.in_dir(self.dirname):
            # ugly because I cannot break from the block
            if not self.check_file_exists(newxtc, resolve="indicate", force=force):
                # make no-water index
                B = IndexBuilder(struct=self.tpr, selections=['@'+NOTwater],
                                 ndx=self.ndx, out_ndx=nowater_ndx)
                B.combine(name_all=groupname, operation="|", defaultgroups=True)
                logger.debug("Index file for water removal: %r", nowater_ndx)

                logger.info("TPR file without water {newtpr!r}".format(**vars()))
                gromacs.tpbconv(s=self.tpr, o=newtpr, n=nowater_ndx, input=[groupname])

                logger.info("NDX of the new system %r", newndx)
                gromacs.make_ndx(f=newtpr, o=newndx, input=['q'], stderr=False, stdout=False)
                # PROBLEM: If self.ndx contained a custom group required for fitting then we are loosing
                #          this group here. We could try to merge only this group but it is possible that
                #          atom indices changed. The only way to solve this is to regenerate the group with
                #          a selection or only use Gromacs default groups.

                logger.info("Trajectory without water {newxtc!r}".format(**vars()))
                kwargs['s'] = self.tpr
                kwargs['f'] = self.xtc
                kwargs['n'] = nowater_ndx
                kwargs['o'] = newxtc
                TRJCONV(**kwargs)

                logger.info("pdb and gro for visualization")
                for ext in 'pdb', 'gro':
                    try:
                        # see warning in doc ... so we don't use the new xtc but the old one
                        kwargs['o'] = self.filename(newtpr, ext=ext)
                        TRJCONV(dump=0, stdout=False, stderr=False, **kwargs)  # silent
                    except:
                        logger.exception("Failed building the water-less %(ext)s. "
                                         "Position restraints in tpr file (see docs)?" % vars())
            logger.info("strip_water() complete")

        self.nowater[self.rp(newxtc)] = Transformer(dirname=self.dirname, s=newtpr,
                                           f=newxtc, n=newndx, force=force)
        return {'tpr':self.rp(newtpr), 'xtc':self.rp(newxtc), 'ndx':self.rp(newndx)}

Response: This function is used to remove water from the output tpr file.


Instruction:
Can you generate the documentation for the following Python 3 function
def strip_fit(self, **kwargs):
        kwargs.setdefault('fit', 'rot+trans')
        kw_fit = {}
        for k in ('xy', 'fit', 'fitgroup', 'input'):
            if k in kwargs:
                kw_fit[k] = kwargs.pop(k)

        kwargs['input'] = kwargs.pop('strip_input', ['Protein'])
        kwargs['force'] = kw_fit['force'] = kwargs.pop('force', self.force)

        paths = self.strip_water(**kwargs)    # updates self.nowater
        transformer_nowater = self.nowater[paths['xtc']]  # make sure to get the one we just produced
        return transformer_nowater.fit(**kw_fit)

Response: Strip water and fit to the remaining system.


Instruction:
Explain what the following Python 3 code does
def _join_dirname(self, *args):
        # extra function because I need to use it in a method that defines
        # the kwarg 'os', which collides with os.path...
        return os.path.join(os.path.dirname(args[0]), *args[1:])

Response: join_dirname - Joins the directory name of the base directory of the log file.