私はobabelツールを使用してSDFファイルセットをPDBファイルに一括変換しています。
obabel *.sdf -opdb --gen3d -m
約50000個のファイルがあり、合計12個の警告が表示されます（下記の警告）。
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 2 stereocenter(s) in this molecule ()
with Atom Ids as follows: 1 5
Warning: Stereochemistry is wrong, using the distance geometry method instead
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 2 stereocenter(s) in this molecule ()
with Atom Ids as follows: 2 4
Warning: Stereochemistry is wrong, using the distance geometry method instead
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 3 stereocenter(s) in this molecule ()
with Atom Ids as follows: 1 3 4
Warning: Stereochemistry is wrong, using the distance geometry method instead
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 4 stereocenter(s) in this molecule ()
with Atom Ids as follows: 0 2 3 4
Warning: Stereochemistry is wrong, using the distance geometry method instead
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 2 stereocenter(s) in this molecule ()
with Atom Ids as follows: 1 12
Warning: Stereochemistry is wrong, using the distance geometry method instead
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 1 stereocenter(s) in this molecule ()
with Atom Ids as follows: 0
Warning: Stereochemistry is wrong, using the distance geometry method instead
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 1 stereocenter(s) in this molecule ()
with Atom Ids as follows: 1
Warning: Stereochemistry is wrong, using the distance geometry method instead
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 2 stereocenter(s) in this molecule ()
with Atom Ids as follows: 0 2
Warning: Stereochemistry is wrong, using the distance geometry method instead
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 2 stereocenter(s) in this molecule ()
with Atom Ids as follows: 0 11
Warning: Stereochemistry is wrong, using the distance geometry method instead
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 3 stereocenter(s) in this molecule ()
with Atom Ids as follows: 0 2 13
Warning: Stereochemistry is wrong, using the distance geometry method instead
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 1 stereocenter(s) in this molecule ()
with Atom Ids as follows: 0
Warning: Stereochemistry is wrong, using the distance geometry method instead
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 1 stereocenter(s) in this molecule ()
with Atom Ids as follows: 0
Warning: Stereochemistry is wrong, using the distance geometry method instead
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 1 stereocenter(s) in this molecule ()
with Atom Ids as follows: 0
Warning: Stereochemistry is wrong, using the distance geometry method instead
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 1 stereocenter(s) in this molecule ()
with Atom Ids as follows: 0
Warning: Stereochemistry is wrong, using the distance geometry method instead
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 5 stereocenter(s) in this molecule ()
with Atom Ids as follows: 8 9 30 31 52
Warning: Stereochemistry is wrong, using the distance geometry method instead
この警告を生成した正確な12個のファイルをどのように確認できますか？
編集する：
提案されているように--errorlevel 3を試してみました。しかし、残念ながら、これはエラーを引き起こす正確なリガンドを識別するのに役立ちません。コード出力を貼り付けました。以前と似ています。
obabel *.sdf -opdb --gen3d --errorlevel 3 -m
obabel *.sdf -opdb --gen3d --errorlevel 3 -m
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 2 stereocenter(s) in this molecule ()
with Atom Ids as follows: 1 5
Warning: Stereochemistry is wrong, using the distance geometry method instead
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 2 stereocenter(s) in this molecule ()
with Atom Ids as follows: 2 4
Warning: Stereochemistry is wrong, using the distance geometry method instead
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 3 stereocenter(s) in this molecule ()
with Atom Ids as follows: 1 3 4
Warning: Stereochemistry is wrong, using the distance geometry method instead
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 4 stereocenter(s) in this molecule ()
with Atom Ids as follows: 0 2 3 4
Warning: Stereochemistry is wrong, using the distance geometry method instead
==============================
*** Open Babel Warning in CorrectStereoAtoms
Could not correct 2 stereocenter(s) in this molecule ()
with Atom Ids as follows: 1 12
Warning: Stereochemistry is wrong, using the distance geometry method instead
ベストアンサー1
ソフトウェアについてはわかりませんが、ファイル間の相互依存関係がない場合は、次のことを実行できます。
for i in *.sdf; do
echo "$i"
obabel "$i" -opdb --gen3d
done