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| # Copyright (C) 2002, Thomas Hamelryck ([email protected]) | |
| # | |
| # This file is part of the Biopython distribution and governed by your | |
| # choice of the "Biopython License Agreement" or the "BSD 3-Clause License". | |
| # Please see the LICENSE file that should have been included as part of this | |
| # package. | |
| """Turn an mmCIF file into a dictionary.""" | |
| from Bio.File import as_handle | |
| class MMCIF2Dict(dict): | |
| """Parse a mmCIF file and return a dictionary.""" | |
| def __init__(self, filename): | |
| """Parse a mmCIF file and return a dictionary. | |
| Arguments: | |
| - file - name of the PDB file OR an open filehandle | |
| """ | |
| self.quote_chars = ["'", '"'] | |
| self.whitespace_chars = [" ", "\t"] | |
| with as_handle(filename) as handle: | |
| loop_flag = False | |
| key = None | |
| tokens = self._tokenize(handle) | |
| try: | |
| token = next(tokens) | |
| except StopIteration: | |
| return # for Python 3.7 and PEP 479 | |
| self[token[0:5]] = token[5:] | |
| i = 0 | |
| n = 0 | |
| for token in tokens: | |
| if token.lower() == "loop_": | |
| loop_flag = True | |
| keys = [] | |
| i = 0 | |
| n = 0 | |
| continue | |
| elif loop_flag: | |
| # The second condition checks we are in the first column | |
| # Some mmCIF files (e.g. 4q9r) have values in later columns | |
| # starting with an underscore and we don't want to read | |
| # these as keys | |
| if token.startswith("_") and (n == 0 or i % n == 0): | |
| if i > 0: | |
| loop_flag = False | |
| else: | |
| self[token] = [] | |
| keys.append(token) | |
| n += 1 | |
| continue | |
| else: | |
| self[keys[i % n]].append(token) | |
| i += 1 | |
| continue | |
| if key is None: | |
| key = token | |
| else: | |
| self[key] = [token] | |
| key = None | |
| # Private methods | |
| def _splitline(self, line): | |
| # See https://www.iucr.org/resources/cif/spec/version1.1/cifsyntax for the syntax | |
| in_token = False | |
| # quote character of the currently open quote, or None if no quote open | |
| quote_open_char = None | |
| start_i = 0 | |
| for (i, c) in enumerate(line): | |
| if c in self.whitespace_chars: | |
| if in_token and not quote_open_char: | |
| in_token = False | |
| yield line[start_i:i] | |
| elif c in self.quote_chars: | |
| if not quote_open_char and not in_token: | |
| quote_open_char = c | |
| in_token = True | |
| start_i = i + 1 | |
| elif c == quote_open_char and ( | |
| i + 1 == len(line) or line[i + 1] in self.whitespace_chars | |
| ): | |
| quote_open_char = None | |
| in_token = False | |
| yield line[start_i:i] | |
| elif c == "#" and not in_token: | |
| # Skip comments. "#" is a valid non-comment char inside of a | |
| # quote and inside of an unquoted token (!?!?), so we need to | |
| # check that the current char is not in a token. | |
| return | |
| elif not in_token: | |
| in_token = True | |
| start_i = i | |
| if in_token: | |
| yield line[start_i:] | |
| if quote_open_char: | |
| raise ValueError("Line ended with quote open: " + line) | |
| def _tokenize(self, handle): | |
| empty = True | |
| for line in handle: | |
| empty = False | |
| if line.startswith("#"): | |
| continue | |
| elif line.startswith(";"): | |
| # The spec says that leading whitespace on each line must be | |
| # preserved while trailing whitespace may be stripped. The | |
| # trailing newline must be stripped. | |
| token_buffer = [line[1:].rstrip()] | |
| for line in handle: | |
| line = line.rstrip() | |
| if line.startswith(";"): | |
| yield "\n".join(token_buffer) | |
| line = line[1:] | |
| if line and line[0] not in self.whitespace_chars: | |
| raise ValueError("Missing whitespace") | |
| break | |
| token_buffer.append(line) | |
| else: | |
| raise ValueError("Missing closing semicolon") | |
| yield from self._splitline(line.strip()) | |
| if empty: | |
| raise ValueError("Empty file.") | |