"""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>`_.
""" # noqa: E501
from __future__ import print_function
import sys
import textwrap
import operator
# getargspec is deprecated in Python 3, but getfullargspec has a very
# similar interface
try:
from inspect import getfullargspec as getargspec
except ImportError: # pragma: no cover
from inspect import getargspec
import re
try:
from . import _format
except ImportError:
_format = None
# Python 3 has no 'long' type, so use 'int' instead
if sys.version_info[0] >= 3:
_long_type = int
else: # pragma: no cover
_long_type = long # noqa: F821
def _write_multiline(val, fh):
fh.write("\n;")
fh.write(val)
if not val.endswith('\n'):
fh.write("\n")
fh.write(";\n")
class _LineWriter(object):
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(object):
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(object):
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(object):
"""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:
return "%.3g" % obj
else:
return "%.3f" % obj
elif isinstance(obj, bool):
return self._boolmap[obj]
# Don't use repr(x) if type(x) == long since that adds an 'L' suffix,
# which isn't valid mmCIF syntax. _long_type = long only on Python 2.
elif isinstance(obj, _long_type):
return "%d" % obj
else:
return repr(obj)
# Acceptable 'whitespace' characters in CIF
_WHITESPACE = set(" \t")
[docs]
class CifParserError(Exception):
"""Exception raised for invalid format mmCIF files"""
pass
class _Token(object):
"""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)"""
pass
class _UnknownValueToken(_ValueToken):
"""A value that is unknown (the '?' string in mmCIF)"""
pass
class _TextValueToken(_ValueToken):
"""The value of a variable in mmCIF as a piece of text"""
__slots__ = ['txt']
def __init__(self, txt):
self.txt = 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 _DataToken(_Token):
"""A data_* keyword in mmCIF, denoting a new data block"""
pass
class _LoopToken(_Token):
"""A loop_ keyword in mmCIF, denoting the start of a loop construct"""
pass
class _SaveToken(_Token):
"""A save_* keyword in mmCIF, denoting the start or end of a save frame"""
pass
class _Reader(object):
"""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
for h in self.category_handler.values():
if not hasattr(h, '_keys'):
h._keys = [python_to_cif(x)
for x in getargspec(h.__call__)[0][1:]]
[docs]
class CifReader(_Reader):
"""Class to read an mmCIF file and extract some or all of its data.
Use :meth:`read_file` to actually read the file.
: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
`unkonwn` 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)
self._c_format = _format.ihm_reader_new(c_file)
self.category_handler = category_handler
self.unknown_category_handler = unknown_category_handler
self.unknown_keyword_handler = unknown_keyword_handler
self._category_data = {}
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
if sys.version_info[0] == 2: # pragma: no cover
def _read_line(self):
return self.fh.readline()
else:
def _read_line(self):
line = self.fh.readline()
if isinstance(line, bytes):
return line.decode('latin-1')
else:
return line
def __del__(self):
if hasattr(self, '_c_format'):
_format.ihm_reader_free(self._c_format)
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]))
return end + 1 # Step past the closing quote
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."""
# Skip initial whitespace
while start_pos < strlen and line[start_pos] in _WHITESPACE:
start_pos += 1
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
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()
elif val.startswith('save_'):
tok = _SaveToken()
elif val.startswith('_'):
tok = _VariableToken(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) # don't alter case of values
self._tokens.append(tok)
return end_pos
def _tokenize(self, line):
"""Break up a line into tokens, populating self._tokens"""
self._tokens = []
if line.startswith('#'):
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]
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:
val = valtoken.txt
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):
"""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] = token.txt
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 _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]
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)
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, 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:
eof, 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 != 0