"""Utility classes to handle CIF format. This module provides classes to read in and write out mmCIF files. It is only concerned with handling syntactically correct CIF - it does not know the set of tables or the mapping to ihm objects. For that, see :mod:`ihm.dumper` for writing and :mod:`ihm.reader` for reading. See also the `stream parser example `_ and the `token reader example `_. """ # noqa: E501 import textwrap import operator import ihm from io import StringIO import inspect import re try: from . import _format except ImportError: _format = None def _write_multiline(val, fh): fh.write("\n;") fh.write(val) if not val.endswith('\n'): fh.write("\n") fh.write(";\n") class _LineWriter: def __init__(self, writer, line_len=80): self.writer = writer self.line_len = line_len self.column = 0 def write(self, val): if isinstance(val, str) and '\n' in val: _write_multiline(val, self.writer.fh) self.column = 0 return val = '.' if val is None else self.writer._repr(val) if self.column > 0: if self.line_len and self.column + len(val) + 1 > self.line_len: self.writer.fh.write("\n") self.column = 0 else: self.writer.fh.write(" ") self.column += 1 self.writer.fh.write(val) self.column += len(val) class _CifCategoryWriter: def __init__(self, writer, category): self.writer = writer self.category = category def write(self, **kwargs): self.writer._write(self.category, kwargs) def __enter__(self): return self def __exit__(self, exc_type, exc_value, traceback): pass class _CifLoopWriter: def __init__(self, writer, category, keys, line_wrap=True): self._line_wrap = line_wrap self.writer = writer self.category = category self.keys = keys # Remove characters that we can't use in Python identifiers self.python_keys = [k.replace('[', '').replace(']', '') for k in keys] self._empty_loop = True def write(self, **kwargs): if self._empty_loop: f = self.writer.fh f.write("#\nloop_\n") for k in self.keys: f.write("%s.%s\n" % (self.category, k)) self._empty_loop = False lw = _LineWriter(self.writer, line_len=80 if self._line_wrap else 0) for k in self.python_keys: lw.write(kwargs.get(k, None)) self.writer.fh.write("\n") def __enter__(self): return self def __exit__(self, exc_type, exc_value, traceback): if not self._empty_loop: self.writer.fh.write("#\n") class _Writer: """Base class for all writers""" omitted = '.' unknown = '?' _boolmap = {False: 'NO', True: 'YES'} def __init__(self, fh): self.fh = fh class CifWriter(_Writer): """Write information to a CIF file. The constructor takes a single argument - a Python filelike object to write to - and provides methods to write Python objects to that file. Most simple Python types are supported (string, float, bool, int). The Python bool type is mapped to CIF strings 'NO' and 'YES'. Floats are always represented with 3 decimal places (or in scientific notation with 3 digits of precision if smaller than 1e-3); if a different amount of precision is desired, convert the float to a string first.""" _line_wrap = True @classmethod def _set_line_wrap(cls, line_wrap): cls._line_wrap = line_wrap def flush(self): # noop - data is written as it is encountered pass def start_block(self, name): """Start a new data block in the file with the given name.""" self.fh.write('data_%s\n' % name) def end_block(self): # noop - mmCIF has no end-of-block indicator pass def category(self, category): """Return a context manager to write a CIF category. A CIF category is a simple list of key:value pairs. :param str category: the name of the category (e.g. "_struct_conf_type"). :return: an object with a single method `write` which takes keyword arguments. For example:: with writer.category("_struct_conf_type") as l: l.write(id='HELX_P', criteria=writer.unknown) """ return _CifCategoryWriter(self, category) def loop(self, category, keys): """Return a context manager to write a CIF loop. :param str category: the name of the category (e.g. "_struct_conf") :param list keys: the field keys in that category :return: an object with a single method `write` which takes keyword arguments; this can be called any number of times to add entries to the loop. Any field keys in `keys` that are not provided as arguments to `write`, or values that are the Python value `None`, will get the CIF omitted value ('.'), while arguments to `write` that are not present in `keys` will be ignored. For example:: with writer.loop("_struct_conf", ["id", "conf_type_id"]) as l: for i in range(5): l.write(id='HELX_P1%d' % i, conf_type_id='HELX_P') """ return _CifLoopWriter(self, category, keys, line_wrap=self._line_wrap) def write_comment(self, comment): """Write a simple comment to the CIF file. The comment will be wrapped if necessary for readability. See :meth:`_set_line_wrap`.""" if self._line_wrap: for line in textwrap.wrap(comment, 78): self.fh.write('# ' + line + '\n') else: self.fh.write('# ' + comment + '\n') def _write(self, category, kwargs): for key, val in sorted(kwargs.items(), key=operator.itemgetter(0)): if isinstance(val, str) and '\n' in val: self.fh.write("%s.%s" % (category, key)) _write_multiline(val, self.fh) else: self.fh.write("%s.%s %s\n" % (category, key, self.omitted if val is None else self._repr(val))) def _repr(self, obj): if isinstance(obj, str) and '"' not in obj \ and "'" not in obj and " " not in obj \ and len(obj) > 0 \ and not obj.startswith('_') \ and not obj.startswith('global_') \ and not obj.startswith('[') \ and obj[:5] not in ('data_', 'save_', 'loop_', 'stop_', '?', '.'): return obj elif isinstance(obj, float): if abs(obj) < 1e-3: return "%.3g" % obj else: return "%.3f" % obj elif isinstance(obj, bool): return self._boolmap[obj] elif isinstance(obj, str): return repr(obj) else: return str(obj) # Acceptable 'whitespace' characters in CIF _WHITESPACE = set(" \t") class CifParserError(Exception): """Exception raised for invalid format mmCIF files""" pass class _Token: """A token in an mmCIF file""" pass class _ValueToken(_Token): """The value of a variable in mmCIF""" pass class _OmittedValueToken(_ValueToken): """A value that is deliberately omitted (the '.' string in mmCIF)""" def as_mmcif(self): return "." class _UnknownValueToken(_ValueToken): """A value that is unknown (the '?' string in mmCIF)""" def as_mmcif(self): return "?" class _TextValueToken(_ValueToken): """The value of a variable in mmCIF as a piece of text""" __slots__ = ['txt', 'quote'] def __init__(self, txt, quote): self.txt = txt self.quote = quote def as_mmcif(self): if '\n' in self.txt or self.quote == ';': suffix = ";\n" if self.txt.endswith('\n') else "\n;\n" return ";" + self.txt + suffix elif self.quote == "'": return "'" + self.txt + "'" elif self.quote == '"' or ' ' in self.txt: return '"' + self.txt + '"' else: return self.txt class _VariableToken(_Token): """A variable name, e.g. _entry.id, in mmCIF""" __slots__ = ['category', 'keyword'] def __init__(self, val, linenum): # mmCIF categories and keywords are case insensitive, so make # everything lowercase self.category, _, self.keyword = val.lower().partition('.') if not self.category or not self.keyword: raise CifParserError("Malformed mmCIF variable name " "(%s) on line %d" % (val, linenum)) class _PreservingVariableToken(_VariableToken): """A variable name that preserves the original case of the keyword""" __slots__ = ['category', 'keyword', 'orig_keyword'] def __init__(self, val, linenum): super().__init__(val, linenum) _, _, self.orig_keyword = val.partition('.') def as_mmcif(self): if self.orig_keyword and self.orig_keyword.lower() == self.keyword: return self.category + '.' + self.orig_keyword else: return self.category + '.' + self.keyword class _CommentToken(_Token): """A comment in mmCIF without the leading '#'""" __slots__ = ['txt'] def __init__(self, txt): self.txt = txt def as_mmcif(self): return "#" + self.txt class _WhitespaceToken(_Token): """Space between other mmCIF tokens""" __slots__ = ['txt'] def __init__(self, txt): self.txt = txt def as_mmcif(self): return self.txt class _EndOfLineToken(_Token): """End of a line in an mmCIF file""" def as_mmcif(self): return "\n" class _NullToken(_Token): """Null token""" def as_mmcif(self): return "" # Return dummy values for filters that expect a variable or value token keyword = property(lambda self: None) class _DataToken(_Token): """A data_* keyword in mmCIF, denoting a new data block""" __slots__ = ['txt'] def __init__(self, txt): self.txt = txt def as_mmcif(self): return 'data_' + self.txt class _LoopToken(_Token): """A loop_ keyword in mmCIF, denoting the start of a loop construct""" def as_mmcif(self): return "loop_" class _SaveToken(_Token): """A save_* keyword in mmCIF, denoting the start or end of a save frame""" pass class _Reader: """Base class for reading a file and extracting some or all of its data.""" def _add_category_keys(self): """Populate _keys for each category by inspecting its __call__ method""" def python_to_cif(field): # Map valid Python identifiers to mmCIF keywords if field.startswith('tr_vector') or field.startswith('rot_matrix'): return re.sub(r'(\d)', r'[\1]', field) else: return field def fill_keys(h, s, attr, typ): if not hasattr(h, attr): setattr(h, attr, frozenset( python_to_cif(k) for k, v in s.annotations.items() if v is typ)) def check_extra(h, attr): extra = frozenset(getattr(h, attr)) - frozenset(h._keys) if extra: raise ValueError("For %s, %s not in _keys: %s" % (h, attr, ", ".join(extra))) for h in self.category_handler.values(): s = inspect.getfullargspec(h.__call__) if not hasattr(h, '_keys'): h._keys = [python_to_cif(x) for x in s.args[1:]] fill_keys(h, s, '_int_keys', int) fill_keys(h, s, '_float_keys', float) fill_keys(h, s, '_bool_keys', bool) bad_keys = frozenset(k for k, v in s.annotations.items() if v not in (int, float, str, bool)) if bad_keys: raise ValueError("For %s, bad annotations: %s" % (h, ", ".join(bad_keys))) check_extra(h, '_int_keys') check_extra(h, '_float_keys') check_extra(h, '_bool_keys') class _CifTokenizer: def __init__(self, fh): self.fh = fh self._tokens = [] self._token_index = 0 self._linenum = 0 # Read a line from the file. Treat it as ASCII (not Unicode) # but be tolerant of 8-bit characters by assuming latin-1 encoding def _read_line(self): line = self.fh.readline() if isinstance(line, bytes): return line.decode('latin-1') else: return line def _read_multiline_token(self, first_line, ignore_multiline): """Read a semicolon-delimited (multiline) token""" lines = [first_line[1:]] # Skip initial semicolon start_linenum = self._linenum while True: self._linenum += 1 nextline = self._read_line() if nextline == '': raise CifParserError( "End of file while reading multiline " "string which started on line %d" % start_linenum) elif nextline.startswith(';'): # Strip last newline lines[-1] = lines[-1].rstrip('\r\n') self._tokens = [_TextValueToken("".join(lines), ';')] return elif not ignore_multiline: lines.append(nextline) def _handle_quoted_token(self, line, strlen, start_pos, quote_type): """Given the start of a quoted string, find the end and add a token for it""" quote = line[start_pos] # Get the next quote that is followed by whitespace (or line end). # In mmCIF a quote within a string is not considered an end quote as # long as it is not followed by whitespace. end = start_pos while True: end = line.find(quote, end + 1) if end == -1: raise CifParserError("%s-quoted string not terminated " "at line %d" % (quote_type, self._linenum)) elif end == strlen - 1 or line[end + 1] in _WHITESPACE: # A quoted string is always a literal string, even if it is # "?" or ".", not an unknown/omitted value self._tokens.append(_TextValueToken(line[start_pos + 1:end], quote)) return end + 1 # Step past the closing quote def _skip_initial_whitespace(self, line, strlen, start_pos): while start_pos < strlen and line[start_pos] in _WHITESPACE: start_pos += 1 return start_pos def _extract_line_token(self, line, strlen, start_pos): """Extract the next token from the given line starting at start_pos, populating self._tokens. The new start_pos is returned.""" start_pos = self._skip_initial_whitespace(line, strlen, start_pos) if start_pos >= strlen: return strlen if line[start_pos] == '"': return self._handle_quoted_token(line, strlen, start_pos, "Double") elif line[start_pos] == "'": return self._handle_quoted_token(line, strlen, start_pos, "Single") elif line[start_pos] == "#": # Comment - discard the rest of the line self._handle_comment(line, start_pos) return strlen else: # Find end of token (whitespace or end of line) end_pos = start_pos while end_pos < strlen and line[end_pos] not in _WHITESPACE: end_pos += 1 val = line[start_pos:end_pos] if val == 'loop_': tok = _LoopToken() elif val.startswith('data_'): tok = _DataToken(val[5:]) elif val.startswith('save_'): tok = _SaveToken() elif val.startswith('_'): tok = self._handle_variable_token(val, self._linenum) elif val == '.': tok = _OmittedValueToken() elif val == '?': tok = _UnknownValueToken() else: # Note that we do no special processing for other reserved # words (global_, save_, stop_). But the probability of # them occurring where we expect a value is pretty small. tok = _TextValueToken(val, None) # don't alter case of values self._tokens.append(tok) return end_pos def _handle_variable_token(self, val, linenum): return _VariableToken(val, linenum) def _handle_comment(self, line, start_pos): """Potentially handle a comment that spans line[start_pos:].""" pass def _tokenize(self, line): """Break up a line into tokens, populating self._tokens""" self._tokens = [] if line.startswith('#'): self._handle_comment(line, 0) return # Skip comment lines start_pos = 0 strlen = len(line) while start_pos < strlen: start_pos = self._extract_line_token(line, strlen, start_pos) def _unget_token(self): """Push back the last token returned by _get_token() so it can be read again""" self._token_index -= 1 def _get_token(self, ignore_multiline=False): """Get the next :class:`_Token` from an mmCIF file, or None on end of file. If ignore_multiline is TRUE, the string contents of any multiline value tokens (those that are semicolon-delimited) are not stored in memory. """ while len(self._tokens) <= self._token_index: # No tokens left - read the next non-blank line in self._linenum += 1 line = self._read_line() if line == '': # End of file return if line.startswith(';'): self._read_multiline_token(line, ignore_multiline) else: self._tokenize(line.rstrip('\r\n')) self._token_index = 0 self._token_index += 1 return self._tokens[self._token_index - 1] class _PreservingCifTokenizer(_CifTokenizer): """A tokenizer subclass which preserves comments, case and whitespace""" def _tokenize(self, line): _CifTokenizer._tokenize(self, line) self._tokens.append(_EndOfLineToken()) def _handle_comment(self, line, start_pos): self._tokens.append(_CommentToken(line[start_pos + 1:])) def _handle_variable_token(self, val, linenum): return _PreservingVariableToken(val, linenum) def _skip_initial_whitespace(self, line, strlen, start_pos): end_pos = start_pos while end_pos < strlen and line[end_pos] in _WHITESPACE: end_pos += 1 if end_pos > start_pos: self._tokens.append(_WhitespaceToken(line[start_pos:end_pos])) return end_pos class _CategoryTokenGroup: """A group of tokens which set a single data item""" def __init__(self, vartoken, valtoken): self.vartoken, self.valtoken = vartoken, valtoken def __str__(self): return ("<_CategoryTokenGroup(%s, %s)>" % (self.vartoken.as_mmcif(), self.valtoken.token.as_mmcif())) def as_mmcif(self): return self.vartoken.as_mmcif() + self.valtoken.as_mmcif() + "\n" def __set_value(self, val): self.valtoken.value = val category = property(lambda self: self.vartoken.category) keyword = property(lambda self: self.vartoken.keyword) value = property(lambda self: self.valtoken.value, __set_value) class _LoopHeaderTokenGroup: """A group of tokens that form the start of a loop_ construct""" def __init__(self, looptoken, category, keywords, end_spacers): self._loop, self.category = looptoken, category self.keywords = keywords self.end_spacers = end_spacers def keyword_index(self, keyword): """Get the zero-based index of the given keyword, or ValueError""" return [k.token.keyword for k in self.keywords].index(keyword) def __str__(self): return ("<_LoopHeaderTokenGroup(%s, %s)>" % (self.category, str([k.token.keyword for k in self.keywords]))) def as_mmcif(self): all_tokens = [self._loop] + self.keywords + self.end_spacers return "".join(x.as_mmcif() for x in all_tokens) class _LoopRowTokenGroup: """A group of tokens that represent one row in a loop_ construct""" def __init__(self, items): self.items = items def as_mmcif(self): return "".join(x.as_mmcif() for x in self.items) class _SpacedToken: """A token with zero or more leading whitespace or newline tokens""" def __init__(self, spacers, token): self.spacers, self.token = spacers, token def as_mmcif(self): return ("".join(x.as_mmcif() for x in self.spacers) + self.token.as_mmcif()) def __get_value(self): if isinstance(self.token, _OmittedValueToken): return None elif isinstance(self.token, _UnknownValueToken): return ihm.unknown else: return self.token.txt def __set_value(self, val): if val is None: self.token = _OmittedValueToken() elif val is ihm.unknown: self.token = _UnknownValueToken() elif isinstance(self.token, _TextValueToken): self.token.txt = val else: self.token = _TextValueToken(val, quote=None) value = property(__get_value, __set_value) class Filter: """Base class for filters used by :meth:`CifTokenReader.read_file`. Typically, a subclass such as :class:`ChangeValueFilter` is used when reading an mmCIF file. :param str target: the mmCIF data item this filter should act on. It can be the full name of the data item (including category) such as ``_entity.type``; or just the attribute or keyword name such as ``.type_symbol`` which would match any category (e.g. ``_atom_site.type_symbol``). """ def __init__(self, target): ts = target.lower().split('.') if len(ts) == 1 or not ts[0]: self.category = None elif ts[0].startswith('_'): self.category = ts[0] else: self.category = '_' + ts[0] self.keyword = ts[-1] def _set_category_from_target(self, target): if target.startswith('_'): self.category = target else: self.category = '_' + target self.keyword = None def match_token_category(self, tok): """Return true iff the given token matches the target's category""" return self.category is None or tok.category == self.category def match_token_keyword(self, tok): """Return true iff the given token matches the target's category and keyword""" return self.match_token_category(tok) and tok.keyword == self.keyword def filter_category(self, tok): """Filter the given category token. :return: the original token (which may have been modified), a replacement token, or None if the token should be deleted. """ raise NotImplementedError def filter_loop_header(self, tok): """Filter the given loop header token. :return: the original token (which must not have been modified), a replacement token, or None if the token should be deleted. If the header token is replaced or deleted, all of the original loop rows will also be deleted. """ return tok def get_loop_filter(self, tok): """Given a loop header token, potentially return a handler for each loop row token. This function is also permitted to alter the header in place (but not replace or remove it). Keywords should not be removed from the header (as that may confuse other filters) but can be replaced with null tokens. :return: a callable which will be called for each loop row token (and acts like :meth:`filter_category`), or None if no filtering is needed for this loop. """ raise NotImplementedError class ChangeValueFilter(Filter): """Change any token that sets a data item to ``old`` to be ``new``. For example, this could be used to rename certain chains, or change all residues of a certain type. :param str old: The existing value of the data item. :param str new: The new value of the data item. See :class:`Filter` for a description of the ``target`` parameter. """ def __init__(self, target, old, new): super().__init__(target) self.old, self.new = old, new def filter_category(self, tok): if self.match_token_keyword(tok) and tok.value == self.old: tok.value = self.new return tok def get_loop_filter(self, tok): if self.match_token_category(tok): try: keyword_index = tok.keyword_index(self.keyword) except ValueError: return def loop_filter(t): if t.items[keyword_index].value == self.old: t.items[keyword_index].value = self.new return t return loop_filter class ChangeFuncValueFilter(Filter): """Change any token that sets a data item to x to be f(x). For example, this could be used to perform a search and replace on a string, or match against a regex. :param callable func: A function that is given the existing value of the data item, the category name (e.g. ``_atom_site``), and the keyword name (e.g. ``auth_seq_id``), and should return the new value of the data item (perhaps unchanged). See :class:`Filter` for a description of the ``target`` parameter. """ def __init__(self, target, func): super().__init__(target) self.func = func def filter_category(self, tok): if self.match_token_keyword(tok): tok.value = self.func(tok.value, tok.category, tok.keyword) return tok def get_loop_filter(self, tok): if self.match_token_category(tok): try: keyword_index = tok.keyword_index(self.keyword) except ValueError: return def loop_filter(t): item = t.items[keyword_index] item.value = self.func(item.value, tok.category, self.keyword) return t return loop_filter class RemoveItemFilter(Filter): """Remove any token from the file that sets the given data item. See :class:`Filter` for a description of the ``target`` parameter. """ def filter_category(self, tok): if self.match_token_keyword(tok): return None else: return tok def get_loop_filter(self, tok): if self.match_token_category(tok): try: keyword_index = tok.keyword_index(self.keyword) except ValueError: return # Remove keyword from loop header tok.keywords[keyword_index].spacers = [] tok.keywords[keyword_index].token = _NullToken() def loop_filter(t): # Remove item from loop row (we don't want to pop from # t.items as other filters may reference later indexes) spc = t.items[keyword_index].spacers if len(spc) > 0 and isinstance(spc[0], _EndOfLineToken): del spc[1:] else: t.items[keyword_index].spacers = [] t.items[keyword_index].token = _NullToken() return t return loop_filter class ChangeKeywordFilter(Filter): """Change the keyword in any applicable token to be ``new``. :param str new: The new keyword. See :class:`Filter` for a description of the ``target`` parameter. """ def __init__(self, target, new): super().__init__(target) self.new = new def filter_category(self, tok): if self.match_token_keyword(tok): tok.vartoken.keyword = self.new return tok def get_loop_filter(self, tok): if self.match_token_category(tok): try: keyword_index = tok.keyword_index(self.keyword) except ValueError: return tok.keywords[keyword_index].token.keyword = self.new class ReplaceCategoryFilter(Filter): """Replace any token from the file that sets the given category. This can also be used to completely remove a category if no replacement is given. :param str target: the mmCIF category name this filter should act on, such as ``_entity``. :param str raw_cif: if given, text in mmCIF format which should replace the first instance of the category. :param dumper: if given, a dumper object that should generate mmCIF output to replace the first instance of the category. :type dumper: :class:`ihm.dumper.Dumper` :param system: the System that the given dumper will work on. :type system: :class:`ihm.System` """ class _RawCifToken(_Token): __slots__ = ['txt'] category = keyword = None def __init__(self, txt): self.txt = txt def as_mmcif(self): return self.txt def __init__(self, target, raw_cif=None, dumper=None, system=None): self._set_category_from_target(target) self.raw_cif = raw_cif self.dumper = dumper self.system = system #: The number of times the category was found in the mmCIF file self.num_matches = 0 def _get_replacement_token(self): if self.num_matches > 1: return None if self.raw_cif: return self._RawCifToken(self.raw_cif) elif self.dumper and self.system: fh = StringIO() writer = CifWriter(fh) self.dumper.finalize(self.system) self.dumper.dump(self.system, writer) return self._RawCifToken(fh.getvalue()) def filter_category(self, tok): if self.match_token_category(tok): self.num_matches += 1 return self._get_replacement_token() else: return tok def filter_loop_header(self, tok): return self.filter_category(tok) def get_loop_filter(self, tok): return None class CifTokenReader(_PreservingCifTokenizer): """Read an mmCIF file and break it into tokens. Unlike :class:`CifReader` which extracts selected data from an mmCIF file, this class operates on the file at a lower level, splitting it into tokens, and preserving data such as comments and whitespace. This can be used for various housekeeping tasks directly on an mmCIF file, such as changing chain IDs or renaming categories or data items. Use :meth:`read_file` to actually read the file. :param file fh: Open handle to the mmCIF file """ def __init__(self, fh): super().__init__(fh) def read_file(self, filters=None): """Read the file and yield tokens and/or token groups. The exact type of the tokens is subject to change and is not currently documented; however, each token or group object has an ``as_mmcif`` method which returns the corresponding text in mmCIF format. Thus, the file can be reconstructed by concatenating the result of ``as_mmcif`` for all tokens. :exc:`CifParserError` will be raised if the file cannot be parsed. :param filters: if a list of :class:`Filter` objects is provided, the read tokens will be modified or removed by each of these filters before being returned. :type filters: sequence of :class:`Filter` :return: tokens and/or token groups. """ if filters is None: return self._read_file_internal() else: return self._read_file_with_filters(filters) def _read_file_with_filters(self, filters): loop_filters = None remove_all_loop_rows = False for tok in self._read_file_internal(): if isinstance(tok, _CategoryTokenGroup): tok = self._filter_category(tok, filters) elif isinstance(tok, ihm.format._LoopHeaderTokenGroup): new_tok = self._filter_loop_header(tok, filters) if new_tok is not tok: tok = new_tok remove_all_loop_rows = True else: remove_all_loop_rows = False loop_filters = [f.get_loop_filter(tok) for f in filters] loop_filters = [f for f in loop_filters if f is not None] # Did filters remove all keywords from the loop? if all(isinstance(k.token, _NullToken) for k in tok.keywords): tok = None remove_all_loop_rows = True elif isinstance(tok, ihm.format._LoopRowTokenGroup): if remove_all_loop_rows: tok = None elif loop_filters: tok = self._filter_loop(tok, loop_filters) if tok is not None: yield tok def _filter_category(self, tok, filters): for f in filters: tok = f.filter_category(tok) if tok is None: return return tok def _filter_loop_header(self, tok, filters): orig_tok = tok for f in filters: tok = f.filter_loop_header(tok) if tok is not orig_tok: break return tok def _filter_loop(self, tok, filters): for f in filters: tok = f(tok) if tok is None: return return tok def _read_file_internal(self): while True: token = self._get_token() if token is None: break if isinstance(token, _VariableToken): yield self._read_value(token) elif isinstance(token, _LoopToken): for tok in self._read_loop(token): yield tok # Did we hit the end of the file? if self._token_index < 0: break else: yield token def _get_spaced_token(self): """Get the next token plus any number of leading space/EOL tokens""" spacers = [] while True: token = self._get_token() if isinstance(token, (_EndOfLineToken, _WhitespaceToken)): spacers.append(token) else: return _SpacedToken(spacers, token) def _read_value(self, vartoken): """Read a line that sets a single value, e.g. "_entry.id 1YTI""" spval = self._get_spaced_token() if not isinstance(spval.token, _ValueToken): raise CifParserError( "No valid value found for %s.%s on line %d" % (vartoken.category, vartoken.keyword, self._linenum)) eoltok = self._get_token() if not isinstance(eoltok, _EndOfLineToken): raise CifParserError( "No end of line after %s.%s on line %d" % (vartoken.category, vartoken.keyword, self._linenum)) return _CategoryTokenGroup(vartoken, spval) def _read_loop(self, looptoken): """Handle a loop_ construct""" header = self._read_loop_header(looptoken) # Record original number of keywords, in case the header token # is filtered num_keywords = len(header.keywords) yield header for line in self._read_loop_data(num_keywords): yield line def _read_loop_header(self, looptoken): """Read the set of keywords for a loop_ construct""" category = None keywords = [] while True: spt = self._get_spaced_token() if isinstance(spt.token, _VariableToken): if category is None: category = spt.token.category elif category != spt.token.category: raise CifParserError( "mmCIF files cannot contain multiple " "categories within a single loop at line %d" % self._linenum) keywords.append(spt) elif isinstance(spt.token, _ValueToken): # OK, end of keywords; proceed on to values self._unget_token() return _LoopHeaderTokenGroup(looptoken, category, keywords, spt.spacers) else: raise CifParserError("Was expecting a keyword or value for " "loop at line %d" % self._linenum) def _read_loop_data(self, num_keywords): """Read the data for a loop_ construct""" while True: items = [] for i in range(num_keywords): spt = self._get_spaced_token() if isinstance(spt.token, _ValueToken): items.append(spt) elif i == 0: # OK, end of the loop for s in spt.spacers: yield s if spt.token is not None: self._unget_token() return else: raise CifParserError( "Wrong number of data values in loop " "(should be an exact multiple of the number " "of keys) at line %d" % self._linenum) yield _LoopRowTokenGroup(items) def _int_type_handler(txt, linenum): try: return int(txt) except ValueError as exc: raise ValueError("%s at line %d" % (str(exc), linenum)) def _float_type_handler(txt, linenum): try: return float(txt) except ValueError as exc: raise ValueError("%s at line %d" % (str(exc), linenum)) class _BoolTypeHandler: _bool_map = {'YES': True, 'NO': False} def __init__(self, omitted): self.omitted = omitted def __call__(self, txt, linenum): return self._bool_map.get(txt.upper(), self.omitted) def _str_type_handler(txt, linenum): return txt class CifReader(_Reader, _CifTokenizer): """Class to read an mmCIF file and extract some or all of its data. Use :meth:`read_file` to actually read the file. See also :class:`CifTokenReader` for a class that operates on the lower-level structure of an mmCIF file, preserving data such as comments and whitespace. :param file fh: Open handle to the mmCIF file :param dict category_handler: A dict to handle data extracted from the file. Keys are category names (e.g. "_entry") and values are objects that have a `__call__` method and `not_in_file`, `omitted`, and `unknown` attributes. The names of the arguments to this `__call__` method are mmCIF keywords that are extracted from the file (for the keywords tr_vector[N] and rot_matrix[N][M] simply omit the [ and ] characters, since these are not valid for Python identifiers). The object will be called with the data from the file as a set of strings, or `not_in_file`, `omitted` or `unknown` for any keyword that is not present in the file, the mmCIF omitted value (.), or mmCIF unknown value (?) respectively. (mmCIF keywords are case insensitive, so this class always treats them as lowercase regardless of the file contents.) :param unknown_category_handler: A callable (or `None`) that is called for each category in the file that isn't handled; it is given two arguments: the name of the category, and the line in the file at which the category was encountered (if known, otherwise None). :param unknown_keyword_handler: A callable (or `None`) that is called for each keyword in the file that isn't handled (within a category that is handled); it is given three arguments: the names of the category and keyword, and the line in the file at which the keyword was encountered (if known, otherwise None). """ def __init__(self, fh, category_handler, unknown_category_handler=None, unknown_keyword_handler=None): if _format is not None: c_file = _format.ihm_file_new_from_python(fh, False) self._c_format = _format.ihm_reader_new(c_file, False) self.category_handler = category_handler self.unknown_category_handler = unknown_category_handler self.unknown_keyword_handler = unknown_keyword_handler self._category_data = {} _CifTokenizer.__init__(self, fh) def __del__(self): if hasattr(self, '_c_format'): _format.ihm_reader_free(self._c_format) def _read_value(self, vartoken): """Read a line that sets a single value, e.g. "_entry.id 1YTI""" # Only read the value if we're interested in this category and key if vartoken.category in self.category_handler: if vartoken.keyword \ in self.category_handler[vartoken.category]._keys: valtoken = self._get_token() if isinstance(valtoken, _ValueToken): ch = self.category_handler[vartoken.category] if vartoken.category not in self._category_data: self._category_data[vartoken.category] = {} if isinstance(valtoken, _OmittedValueToken): val = ch.omitted elif isinstance(valtoken, _UnknownValueToken): val = ch.unknown else: tc = self._get_type_handler(ch, vartoken.keyword) val = tc(valtoken.txt, self._linenum) self._category_data[vartoken.category][vartoken.keyword] \ = val else: raise CifParserError( "No valid value found for %s.%s on line %d" % (vartoken.category, vartoken.keyword, self._linenum)) elif self.unknown_keyword_handler is not None: self.unknown_keyword_handler(vartoken.category, vartoken.keyword, self._linenum) elif self.unknown_category_handler is not None: self.unknown_category_handler(vartoken.category, self._linenum) def _read_loop_keywords(self): """Read the set of keywords for a loop_ construct""" category = None keywords = [] first_line = None keyword_lines = [] while True: token = self._get_token() if isinstance(token, _VariableToken): if category is None: category = token.category first_line = self._linenum elif category != token.category: raise CifParserError( "mmCIF files cannot contain multiple " "categories within a single loop at line %d" % self._linenum) keywords.append(token.keyword) keyword_lines.append(self._linenum) elif isinstance(token, _ValueToken): # OK, end of keywords; proceed on to values self._unget_token() return category, keywords, keyword_lines, first_line else: raise CifParserError("Was expecting a keyword or value for " "loop at line %d" % self._linenum) def _read_loop_data(self, handler, num_wanted_keys, keyword_indices, type_handlers): """Read the data for a loop_ construct""" data = [handler.not_in_file] * num_wanted_keys while True: for i, index in enumerate(keyword_indices): token = self._get_token() if isinstance(token, _ValueToken): if index >= 0: if isinstance(token, _OmittedValueToken): data[index] = handler.omitted elif isinstance(token, _UnknownValueToken): data[index] = handler.unknown else: data[index] = type_handlers[index](token.txt, self._linenum) elif i == 0: # OK, end of the loop self._unget_token() return else: raise CifParserError( "Wrong number of data values in loop " "(should be an exact multiple of the number " "of keys) at line %d" % self._linenum) handler(*data) def _get_type_handler(self, category_handler, keyword): """Return a function that converts keyword string into desired type""" if keyword in category_handler._int_keys: return _int_type_handler elif keyword in category_handler._bool_keys: return _BoolTypeHandler(category_handler.omitted) elif keyword in category_handler._float_keys: return _float_type_handler else: return _str_type_handler def _read_loop(self): """Handle a loop_ construct""" (category, keywords, keyword_lines, first_line) = self._read_loop_keywords() # Skip data if we don't have a handler for it if category in self.category_handler: ch = self.category_handler[category] type_handlers = [self._get_type_handler(ch, k) for k in ch._keys] wanted_key_index = {} for i, k in enumerate(ch._keys): wanted_key_index[k] = i indices = [wanted_key_index.get(k, -1) for k in keywords] if self.unknown_keyword_handler is not None: for k, i, line in zip(keywords, indices, keyword_lines): if i == -1: self.unknown_keyword_handler(category, k, line) self._read_loop_data(ch, len(ch._keys), indices, type_handlers) elif self.unknown_category_handler is not None: self.unknown_category_handler(category, first_line) def read_file(self): """Read the file and extract data. Category handlers will be called as data becomes available - for ``loop_`` constructs, this will be once for each row in the loop; for categories (e.g. ``_entry.id model``), this will be once at the very end of the file. If the C-accelerated _format module is available, then it is used instead of the (much slower) Python tokenizer. :exc:`CifParserError` will be raised if the file cannot be parsed. :return: True iff more data blocks are available to be read. """ self._add_category_keys() if hasattr(self, '_c_format'): return self._read_file_c() def call_all_categories(): for cat, data in self._category_data.items(): ch = self.category_handler[cat] ch(*[data.get(k, ch.not_in_file) for k in ch._keys]) # Clear category data for next call to read_file() self._category_data = {} ndata = 0 in_save = False while True: token = self._get_token(ignore_multiline=True) if token is None: break if isinstance(token, _VariableToken): self._read_value(token) elif isinstance(token, _DataToken): ndata += 1 # Only read the first data block if ndata > 1: # Allow reading the next data block self._unget_token() break elif isinstance(token, _LoopToken): self._read_loop() # Did we hit the end of the file? if self._token_index < 0: break elif isinstance(token, _SaveToken): in_save = not in_save if not in_save: call_all_categories() for handler in self.category_handler.values(): handler.end_save_frame() call_all_categories() return ndata > 1 def _read_file_c(self): """Read the file using the C parser""" _format.ihm_reader_remove_all_categories(self._c_format) for category, handler in self.category_handler.items(): func = getattr(handler, '_add_c_handler', None) \ or _format.add_category_handler func(self._c_format, category, handler._keys, frozenset(handler._int_keys), frozenset(handler._float_keys), frozenset(handler._bool_keys), handler) if self.unknown_category_handler is not None: _format.add_unknown_category_handler(self._c_format, self.unknown_category_handler) if self.unknown_keyword_handler is not None: _format.add_unknown_keyword_handler(self._c_format, self.unknown_keyword_handler) try: ret_ok, more_data = _format.ihm_read_file(self._c_format) except _format.FileFormatError as exc: # Convert to the same exception used by the Python code raise CifParserError(str(exc)) return more_data