Hi Greg – sure. So -
[cid:image001.png@01DA544C.50E20B90]
If I have a V2000 with or without the chiral flag:
ACCLDraw01312413482D
8 8 0 0 1 0 0 0 0 0999 V2000
4.6334 -6.5969 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.6563 -6.0064 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
6.6791 -6.5969 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0
6.6791 -7.7781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.6563 -8.3686 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.6334 -7.7781 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
5.6563 -4.8257 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.6109 -8.3684 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
3 2 1 0 0 0 0
4 3 1 0 0 0 0
5 4 1 0 0 0 0
1 6 1 0 0 0 0
6 5 1 0 0 0 0
2 7 1 1 0 0 0
6 8 1 1 0 0 0
M END
ACCLDraw01312413492D
8 8 0 0 0 0 0 0 0 0999 V2000
4.6334 -6.5969 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.6563 -6.0064 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
6.6791 -6.5969 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0
6.6791 -7.7781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.6563 -8.3686 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.6334 -7.7781 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
5.6563 -4.8257 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.6109 -8.3684 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
3 2 1 0 0 0 0
4 3 1 0 0 0 0
5 4 1 0 0 0 0
1 6 1 0 0 0 0
6 5 1 0 0 0 0
2 7 1 1 0 0 0
6 8 1 1 0 0 0
M END
I’d expect the enhanced collections to be output in V3000 format. In this case
the chiral flag is also set but that’s not a biggy for me. (I wish the chiral
flag didn’t exist in V3000.)
ACCLDraw01312413472D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 8 8 0 0 1
M V30 BEGIN ATOM
M V30 1 C 4.6334 -6.5969 0 0
M V30 2 C 5.6563 -6.0064 0 0 CFG=2
M V30 3 N 6.6791 -6.5969 0 0 CFG=3
M V30 4 C 6.6791 -7.7781 0 0
M V30 5 C 5.6563 -8.3686 0 0
M V30 6 C 4.6334 -7.7781 0 0 CFG=1
M V30 7 C 5.6563 -4.8257 0 0
M V30 8 C 3.6109 -8.3684 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 3 2
M V30 3 1 4 3
M V30 4 1 5 4
M V30 5 1 1 6
M V30 6 1 6 5
M V30 7 1 2 7 CFG=1
M V30 8 1 6 8 CFG=1
M V30 END BOND
M V30 BEGIN COLLECTION
M V30 MDLV30/STEABS ATOMS=(2 2 6)
M V30 END COLLECTION
M V30 END CTAB
M END
ACCLDraw01312413492D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 8 8 0 0 0
M V30 BEGIN ATOM
M V30 1 C 4.6334 -6.5969 0 0
M V30 2 C 5.6563 -6.0064 0 0 CFG=2
M V30 3 N 6.6791 -6.5969 0 0 CFG=3
M V30 4 C 6.6791 -7.7781 0 0
M V30 5 C 5.6563 -8.3686 0 0
M V30 6 C 4.6334 -7.7781 0 0 CFG=1
M V30 7 C 5.6563 -4.8257 0 0
M V30 8 C 3.6109 -8.3684 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 3 2
M V30 3 1 4 3
M V30 4 1 5 4
M V30 5 1 1 6
M V30 6 1 6 5
M V30 7 1 2 7 CFG=1
M V30 8 1 6 8 CFG=1
M V30 END BOND
M V30 BEGIN COLLECTION
M V30 MDLV30/STERAC1 ATOMS=(2 6 2)
M V30 END COLLECTION
M V30 END CTAB
M END
Cheers
Nick
From: Greg Landrum <greg.land...@gmail.com>
Sent: Wednesday, January 31, 2024 1:45 PM
To: Tomkinson, Nicholas <nick.tomkin...@astrazeneca.com>
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] V2000 to V3000 enhanced stereo question
Hi Nick,
Can you provide an example of exactly what you would like to have happen?
-greg
On Tue, Jan 30, 2024 at 5:46 PM Tomkinson, Nicholas
<nick.tomkin...@astrazeneca.com<mailto:nick.tomkin...@astrazeneca.com>> wrote:
I am trying to convert a simple V2000 molfile with or without the chiral flag
into a V3000 molfile but this does not create an enhanced stereo collection in
the V3000 molfile. This is a requirement for another application that does not
handle V2000/V3000 mixtures well. Is there anyway of forcing the writing of the
enhanced collection in this context?
Thanks
Nick
________________________________
AstraZeneca UK Limited is a company incorporated in England and Wales with
registered number:03674842 and its registered office at 1 Francis Crick Avenue,
Cambridge Biomedical Campus, Cambridge, CB2 0AA.
This e-mail and its attachments are intended for the above named recipient only
and may contain confidential and privileged information. If they have come to
you in error, you must not copy or show them to anyone; instead, please reply
to this e-mail, highlighting the error to the sender and then immediately
delete the message. For information about how AstraZeneca UK Limited and its
affiliates may process information, personal data and monitor communications,
please see our privacy notice at
www.astrazeneca.com<https://www.astrazeneca.com>
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net<mailto:Rdkit-discuss@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss<https://lists.sourceforge.net/lists/listinfo/rdkit-discuss>
________________________________
AstraZeneca UK Limited is a company incorporated in England and Wales with
registered number:03674842 and its registered office at 1 Francis Crick Avenue,
Cambridge Biomedical Campus, Cambridge, CB2 0AA.
This e-mail and its attachments are intended for the above named recipient only
and may contain confidential and privileged information. If they have come to
you in error, you must not copy or show them to anyone; instead, please reply
to this e-mail, highlighting the error to the sender and then immediately
delete the message. For information about how AstraZeneca UK Limited and its
affiliates may process information, personal data and monitor communications,
please see our privacy notice at
www.astrazeneca.com<https://www.astrazeneca.com>
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
