"""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 <https://github.com/ihmwg/python-ihm/blob/main/examples/stream_parser.py>`_
and the `token reader example <https://github.com/ihmwg/python-ihm/blob/main/examples/token_reader.py>`_.
""" # 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
[docs]
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
[docs]
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
[docs]
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)
[docs]
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(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 and obj != 0.0:
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")
[docs]
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)
[docs]
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
[docs]
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
[docs]
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
[docs]
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
[docs]
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
[docs]
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
[docs]
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
[docs]
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
[docs]
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
[docs]
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
[docs]
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)
[docs]
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
[docs]
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)
[docs]
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