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Basic sdf format input/output #107

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merged 6 commits into from
May 22, 2019
Merged

Basic sdf format input/output #107

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8a3d84b
Add basic sdf input/output https://github.com/theochem/iodata/issues/…
May 19, 2019
4ef3e0a
corrected some formatting issues
May 19, 2019
8a91e50
Checks for wrong ending in sdf file format
May 21, 2019
0becb82
Suggested changes in sdf.py
May 21, 2019
597c5a9
Last changes to test_sdf.py in load_many
May 21, 2019
cf0112b
Add using truncated function from common for wrong format at the end …
May 21, 2019
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Suggested changes in sdf.py
  • Loading branch information
Esteban Vohringer-Martinez authored and Esteban Vohringer-Martinez committed May 21, 2019
commit 0becb82a42672c71f5b315252b302195f3b279ce
9 changes: 3 additions & 6 deletions iodata/formats/sdf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -57,14 +57,11 @@ def load_one(lit: LineIterator) -> dict:
atcoords[i, 0] = float(words[0]) * angstrom
atcoords[i, 1] = float(words[1]) * angstrom
atcoords[i, 2] = float(words[2]) * angstrom
try:
atnums[i] = sym2num[words[3].title()]
except KeyError:
atnums[i] = int(words[0])
atnums[i] = sym2num.get(words[3].title())
while True:
try:
words = next(lit)
except ValueError:
except StopIteration:
raise lit.error("Molecule specification did not end properly with $$$$")
if words == "$$$$\n":
break
Expand All @@ -78,7 +75,7 @@ def load_one(lit: LineIterator) -> dict:
@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 molecueles are a simple concatenation of individual SDF files,'
# SDF files with more molecules are a simple concatenation of individual SDF files,'
# making it travial to load many frames.
while True:
try:
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