Atom coordinates in CXSMILES disrupt exact matches when do_enhanced_stereo_sss==true

[someonetookmyname]

If the CXSMILES used to query the cartridge has atom coordinates, then the query will return nothing unless do_enhanced_stereo_sss==false.

See this discussion for more details: #7190

To reproduce:

drop table if exists tst;
DROP TABLE
create table tst (pk integer, m mol);
CREATE TABLE
create index tstidx on tst using gist(m);
CREATE INDEX
insert into tst (pk, m) values (1, mol_from_ctab('
     RDKit          2D

  8  8  0  0  0  0  0  0  0  0999 V2000
    3.0000    0.0000    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.5000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7500   -1.2990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7500   -1.2990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0000    0.0000    0.0000 Br  0  0  0  0  0  0  0  0  0  0  0  0
   -0.7500    1.2990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7500    1.2990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  6
  5  7  1  0
  7  8  1  0
  8  2  1  0
M  END'));
INSERT 0 1
set rdkit.do_chiral_sss=true;
SET
set rdkit.do_enhanced_stereo_sss=true;
SET
select pk from tst where m @= 'Cl[C@H]1CC[C@H](Br)CC1'::mol;
 pk 
----
  1
(1 row)

select pk from tst where m @= 'Cl[C@H]1CC[C@H](Br)CC1 |(3,0,;1.5,0,;0.75,-1.29904,;-0.75,-1.29904,;-1.5,0,;-3,0,;-0.75,1.29904,;0.75,1.29904,)|'::mol;
 pk 
----
(0 rows)

set rdkit.do_enhanced_stereo_sss=false;
SET
select pk from tst where m @= 'Cl[C@H]1CC[C@H](Br)CC1'::mol;
 pk 
----
  1
(1 row)

select pk from tst where m @= 'Cl[C@H]1CC[C@H](Br)CC1 |(3,0,;1.5,0,;0.75,-1.29904,;-0.75,-1.29904,;-1.5,0,;-3,0,;-0.75,1.29904,;0.75,1.29904,)|'::mol;
 pk 
----
  1
(1 row)

Each above select statement would be expected to return 1 row, but 0 rows are returned when do_enhanced_stereo==true and CXSMILES contains atom coordinates.

Configuration (please complete the following information):

• RDKit version: 2023_09_6
• OS: Debian bookworm
• Python version (if relevant): n/a
• Are you using conda? No
• If you are using conda, which channel did you install the rdkit from? n/a
• If you are not using conda: how did you install the RDKit? Compiled from source

Thank you

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This issue was marked as stale because it has been open for 90 days with no activity.

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