epam / epam/Indigo

Substructure Reaction Bingo/PostgreSQL (Explicit H issue)

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#134 1 comment 0 reactions 1 assignee Claimed by @mkviatkovskii View on GitHub
Bingo
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C++
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134
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2d 11h
Merged PRs (30d)
24

Description

Currently running Bingo on postgreSQL database and developping substructure reaction queries. I get results no problem on substrure reactions but explicit hydrogens and atom-mapping on queries do not seem to give appropriate results. For example the following query gives the following result (it shouldn't).

**QUERY:**
SELECT *
FROM reactions
WHERE reaction_mdl_rxn_format @ ('$RXN

1 1 0
$MOL

Ketcher 02211910492D 1 1.00000 0.00000 0

9 9 0 0 0 999 V2000
4.7000 -4.5993 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.5090 -5.1871 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.2000 -6.1382 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
4.2000 -6.1382 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.8910 -5.1871 0.0000 C 0 0 0 0 0 0 0 0 0 1 0 0
3.6322 -4.2212 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
2.9251 -5.4459 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
4.4412 -3.6334 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
5.2000 -3.7333 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0
2 3 1 0 0 0
3 4 1 0 0 0
4 5 1 0 0 0
5 1 1 0 0 0
5 6 1 0 0 0
5 7 1 0 0 0
1 8 1 0 0 0
1 9 1 0 0 0
M END
$MOL

Ketcher 02211910492D 1 1.00000 0.00000 0

6 6 0 0 0 999 V2000
12.6867 -4.7747 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.5822 -5.7692 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
11.6040 -5.9771 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.1040 -5.1111 0.0000 C 0 0 0 0 0 0 0 0 0 1 0 0
11.7732 -4.3680 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.3969 -4.4040 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0
2 3 1 0 0 0
3 4 1 0 0 0
4 5 1 0 0 0
5 1 1 0 0 0
4 6 1 0 0 0
M END
','ALL')::bingo.rsub

**RESULT:**
$RXN

1 1
$MOL

Ketcher 04231811342D 1 1.00000 0.00000 0

8 7 0 0 0 999 V2000
5.2500 -5.0757 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
4.4410 -4.4879 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.7500 -3.5368 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.7500 -3.5368 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.0590 -4.4879 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.1622 -2.7278 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
7.0100 -4.7969 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.3750 -5.6250 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0
2 3 1 0 0 0
3 4 1 0 0 0
4 5 1 0 0 0
5 1 1 0 0 0
3 6 1 6 0 0
5 7 1 1 0 0
M END
$MOL

Ketcher 04231811332D 1 1.00000 0.00000 0

14 14 0 0 0 999 V2000
5.2500 -5.0757 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
4.4410 -4.4879 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.7500 -3.5368 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.7500 -3.5368 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.0590 -4.4879 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.1622 -2.7278 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
7.0100 -4.7969 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.2500 -6.0757 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.3840 -6.5757 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
6.1160 -6.5757 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
6.1160 -7.5757 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.9821 -8.0757 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.2500 -8.0757 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.1160 -8.5757 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0
2 3 1 0 0 0
3 4 1 0 0 0
4 5 1 0 0 0
5 1 1 0 0 0
3 6 1 6 0 0
5 7 1 1 0 0
1 8 1 0 0 0
8 9 2 0 0 0
8 10 1 0 0 0
10 11 1 0 0 0
11 12 1 0 0 0
11 13 1 0 0 0
11 14 1 0 0 0
M END

David

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