Source code for iodata.formats.sdf

# IODATA is an input and output module for quantum chemistry.
# Copyright (C) 2011-2019 The IODATA Development Team
# This file is part of IODATA.
# IODATA is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 3
# of the License, or (at your option) any later version.
# IODATA is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this program; if not, see <>
# --
"""SDF file format.

Usually, the different frames in a trajectory describe different geometries of the same
molecule, with atoms in the same order. The ``load_many`` and ``dump_many`` functions
below can also handle an SDF file with different molecules, e.g. a molecular database.

from typing import TextIO, Iterator

import numpy as np

from ..docstrings import (document_load_one, document_load_many, document_dump_one,
from ..iodata import IOData
from ..periodic import sym2num, num2sym
from ..utils import angstrom, LineIterator

__all__ = []

PATTERNS = ['*.sdf']

[docs]@document_load_one("SDF", ['atcoords', 'atnums', 'title']) def load_one(lit: LineIterator) -> dict: """Do not edit this docstring. It will be overwritten.""" title = next(lit).strip() # The next two lines are general comments next(lit) next(lit) words = next(lit).split() size = int(words[0]) atcoords = np.empty((size, 3), float) atnums = np.empty(size, int) for i in range(size): words = next(lit).split() atcoords[i, 0] = float(words[0]) * angstrom atcoords[i, 1] = float(words[1]) * angstrom atcoords[i, 2] = float(words[2]) * angstrom atnums[i] = sym2num.get(words[3].title()) while True: try: words = next(lit) except StopIteration: lit.error("Molecule specification did not end properly with $$$$") if words == "$$$$\n": break return { 'title': title, 'atcoords': atcoords, 'atnums': atnums }
[docs]@document_load_many("SDF", ['atcoords', 'atnums', 'title']) def load_many(lit: LineIterator) -> Iterator[dict]: """Do not edit this docstring. It will be overwritten.""" # SDF files with more molecules are a simple concatenation of individual SDF files,' # making it travial to load many frames. while True: try: yield load_one(lit) except StopIteration: return
[docs]@document_dump_one("SDF", ['atcoords', 'atnums'], ['title']) def dump_one(f: TextIO, data: IOData): """Do not edit this docstring. It will be overwritten.""" print(data.title or 'Created with IOData', file=f) print('', file=f) print('', file=f) print(data.natom, file=f) for i in range(data.natom): n = num2sym[data.atnums[i]] x, y, z = data.atcoords[i] / angstrom print(f'{x:15.10f} {y:15.10f} {z:15.10f} {n:2s}', file=f) print('$$$$', file=f)
[docs]@document_dump_many("SDF", ['atcoords', 'atnums'], ['title']) def dump_many(f: TextIO, datas: Iterator[IOData]): """Do not edit this docstring. It will be overwritten.""" # Similar to load_many, this is relatively easy. for data in datas: dump_one(f, data)