Hi RDKitters,I would like to know if it's possible to set one given double bond stereo to "STEREOANY" without modifying the others?
For example, I have a molecule with two specified double bond stereo centers but want to set only one to STEREOANY and get the '3' stereo flag in bond block of the output MolBlock. I could find a GetStereo function for bonds but not its Set counterpart. With the RemoveStereochemistry function, I get the '3' stereo flag, but for both stereo double bonds.
How could I do that without building a molecule from scratch? I managed to do the same for chiral atoms.... Should I change the BondDir of all adjacent bonds to NONE? How can I make sure it won't cause any problem, for instance for allenic who can share adjacent bonds?
I attached a script and its output for more accurate description of the problem. What am I missing?
Thank you very much in advance for your help! Jose Manuel
RemoveOneDBStereoChemistry.py
Description: application/chimera
RDKIT 2015.03.1
TEST TO SET ONE GIVEN DOUBLE BOND STEREOCHEMISTRY TO 'STEREOANY'
############################ INPUT STEREOCHEMISTRY ############################
TEST_in
RDKit 2D
13 13 0 0 0 0 0 0 0 0999 V2000
-0.9060 1.3112 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6205 0.8987 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6205 0.0737 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.9060 -0.3389 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1916 0.0737 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1916 0.8987 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.9060 -1.1639 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1916 -1.5764 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5229 1.3112 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5229 2.1362 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2374 2.5487 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
0.5229 -1.1639 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.1916 2.5487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
2 3 1 0
3 4 2 0
4 5 1 0
5 6 2 0
1 6 1 0
4 7 1 0
7 8 2 0
6 9 1 0
9 10 2 0
10 11 1 0
8 12 1 0
10 13 1 0
M END
###### BONDS ######
Idx Begin End Stereo Dir
0 0 1 STEREONONE NONE
1 1 2 STEREONONE NONE
2 2 3 STEREONONE NONE
3 3 4 STEREONONE NONE
4 4 5 STEREONONE NONE
5 0 5 STEREONONE NONE
6 3 6 STEREONONE ENDUPRIGHT
7 6 7 STEREOZ NONE
8 5 8 STEREONONE ENDUPRIGHT
9 8 9 STEREOE NONE
10 9 10 STEREONONE ENDUPRIGHT
11 7 11 STEREONONE ENDDOWNRIGHT
12 9 12 STEREONONE ENDDOWNRIGHT
###### ATOMS ######
Idx Symb ChiralTag
0 C CHI_UNSPECIFIED
1 C CHI_UNSPECIFIED
2 C CHI_UNSPECIFIED
3 C CHI_UNSPECIFIED
4 C CHI_UNSPECIFIED
5 C CHI_UNSPECIFIED
6 C CHI_UNSPECIFIED
7 C CHI_UNSPECIFIED
8 C CHI_UNSPECIFIED
9 C CHI_UNSPECIFIED
10 S CHI_UNSPECIFIED
11 O CHI_UNSPECIFIED
12 C CHI_UNSPECIFIED
No flag in the bond block to specify the double bond stereochemistry.
########################## EXPLICIT STEREOCHEMISTRY ############################
TEST_allExplicitStereo
RDKit 2D
13 13 0 0 0 0 0 0 0 0999 V2000
-0.9060 1.3112 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6205 0.8987 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6205 0.0737 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.9060 -0.3389 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1916 0.0737 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1916 0.8987 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.9060 -1.1639 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1916 -1.5764 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5229 1.3112 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5229 2.1362 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2374 2.5487 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
0.5229 -1.1639 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.1916 2.5487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
2 3 1 0
3 4 2 0
4 5 1 0
5 6 2 0
1 6 1 0
4 7 1 0
7 8 2 0
6 9 1 0
9 10 2 0
10 11 1 0
8 12 1 0
10 13 1 0
M END
###### BONDS ######
Idx Begin End Stereo Dir
0 0 1 STEREONONE NONE
1 1 2 STEREONONE NONE
2 2 3 STEREONONE NONE
3 3 4 STEREONONE NONE
4 4 5 STEREONONE NONE
5 0 5 STEREONONE NONE
6 3 6 STEREONONE ENDUPRIGHT
7 6 7 STEREOZ NONE
8 5 8 STEREONONE ENDUPRIGHT
9 8 9 STEREOE NONE
10 9 10 STEREONONE ENDUPRIGHT
11 7 11 STEREONONE ENDDOWNRIGHT
12 9 12 STEREONONE ENDDOWNRIGHT
###### ATOMS ######
Idx Symb ChiralTag
0 C CHI_UNSPECIFIED
1 C CHI_UNSPECIFIED
2 C CHI_UNSPECIFIED
3 C CHI_UNSPECIFIED
4 C CHI_UNSPECIFIED
5 C CHI_UNSPECIFIED
6 C CHI_UNSPECIFIED
7 C CHI_UNSPECIFIED
8 C CHI_UNSPECIFIED
9 C CHI_UNSPECIFIED
10 S CHI_UNSPECIFIED
11 O CHI_UNSPECIFIED
12 C CHI_UNSPECIFIED
Still no flag in the bond block to specify the double bond stereochemistry.
########################## REMOVE ALL STEREOCHEMISTRY ##########################
TEST_allStereoRemoved
RDKit 2D
13 13 0 0 0 0 0 0 0 0999 V2000
-0.9060 1.3112 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6205 0.8987 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6205 0.0737 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.9060 -0.3389 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1916 0.0737 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1916 0.8987 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.9060 -1.1639 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1916 -1.5764 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5229 1.3112 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5229 2.1362 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2374 2.5487 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
0.5229 -1.1639 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.1916 2.5487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
2 3 1 0
3 4 2 0
4 5 1 0
5 6 2 0
1 6 1 0
4 7 1 0
7 8 2 3
6 9 1 0
9 10 2 3
10 11 1 0
8 12 1 0
10 13 1 0
M END
###### BONDS ######
Idx Begin End Stereo Dir
0 0 1 STEREONONE NONE
1 1 2 STEREONONE NONE
2 2 3 STEREONONE NONE
3 3 4 STEREONONE NONE
4 4 5 STEREONONE NONE
5 0 5 STEREONONE NONE
6 3 6 STEREONONE NONE
7 6 7 STEREONONE NONE
8 5 8 STEREONONE NONE
9 8 9 STEREONONE NONE
10 9 10 STEREONONE NONE
11 7 11 STEREONONE NONE
12 9 12 STEREONONE NONE
###### ATOMS ######
Idx Symb ChiralTag
0 C CHI_UNSPECIFIED
1 C CHI_UNSPECIFIED
2 C CHI_UNSPECIFIED
3 C CHI_UNSPECIFIED
4 C CHI_UNSPECIFIED
5 C CHI_UNSPECIFIED
6 C CHI_UNSPECIFIED
7 C CHI_UNSPECIFIED
8 C CHI_UNSPECIFIED
9 C CHI_UNSPECIFIED
10 S CHI_UNSPECIFIED
11 O CHI_UNSPECIFIED
12 C CHI_UNSPECIFIED
These are the flags I want in the bond block, but the BondStereo is set to
STEREONONE instead of STEREOANY.
########################### REMOVE 8-9 DB STEREOCHEMISTRY
##########################
TEST_OneStereoDBRemoved?
RDKit 2D
13 13 0 0 0 0 0 0 0 0999 V2000
-0.9060 1.3112 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6205 0.8987 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6205 0.0737 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.9060 -0.3389 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1916 0.0737 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1916 0.8987 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.9060 -1.1639 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1916 -1.5764 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5229 1.3112 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5229 2.1362 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2374 2.5487 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
0.5229 -1.1639 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.1916 2.5487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
2 3 1 0
3 4 2 0
4 5 1 0
5 6 2 0
1 6 1 0
4 7 1 0
7 8 2 0
6 9 1 0
9 10 2 0
10 11 1 0
8 12 1 0
10 13 1 0
M END
###### BONDS ######
Idx Begin End Stereo Dir
0 0 1 STEREONONE NONE
1 1 2 STEREONONE NONE
2 2 3 STEREONONE NONE
3 3 4 STEREONONE NONE
4 4 5 STEREONONE NONE
5 0 5 STEREONONE NONE
6 3 6 STEREONONE ENDUPRIGHT
7 6 7 STEREOZ NONE
8 5 8 STEREONONE ENDUPRIGHT
9 8 9 STEREOE UNKNOWN
10 9 10 STEREONONE ENDUPRIGHT
11 7 11 STEREONONE ENDDOWNRIGHT
12 9 12 STEREONONE ENDDOWNRIGHT
###### ATOMS ######
Idx Symb ChiralTag
0 C CHI_UNSPECIFIED
1 C CHI_UNSPECIFIED
2 C CHI_UNSPECIFIED
3 C CHI_UNSPECIFIED
4 C CHI_UNSPECIFIED
5 C CHI_UNSPECIFIED
6 C CHI_UNSPECIFIED
7 C CHI_UNSPECIFIED
8 C CHI_UNSPECIFIED
9 C CHI_UNSPECIFIED
10 S CHI_UNSPECIFIED
11 O CHI_UNSPECIFIED
12 C CHI_UNSPECIFIED
I don't get any 'cis or trans' flags in the bond block and the other stereo db
BondDir is changed.
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