Hi Greg – sure. So -
[cid:[email protected]]
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 <[email protected]>
Sent: Wednesday, January 31, 2024 1:45 PM
To: Tomkinson, Nicholas <[email protected]>
Cc: [email protected]
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
<[email protected]<mailto:[email protected]>> 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
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