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#1465 Unable to load specific mol-file (#1479)
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@even1024
even1024 authored Jan 4, 2024
1 parent c8a81a0 commit ef5dd99
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Showing 7 changed files with 359 additions and 2 deletions.
4 changes: 2 additions & 2 deletions .github/workflows/indigo-ci.yaml
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Expand Up @@ -1001,8 +1001,8 @@ jobs:
/bin/sh -c "
set -eux &&
yum install -y -y https://download.postgresql.org/pub/repos/yum/reporpms/EL-7-x86_64/pgdg-redhat-repo-latest.noarch.rpm yum-utils &&
curl -OL https://download.postgresql.org/pub/repos/yum/RPM-GPG-KEY-PGDG &&
rpm --import RPM-GPG-KEY-PGDG &&
curl -OL https://download.postgresql.org/pub/repos/yum/keys/PGDG-RPM-GPG-KEY-RHEL &&
rpm --import PGDG-RPM-GPG-KEY-RHEL &&
yumdownloader -y postgresql${{ matrix.postgres_major_version }}-devel &&
rpm -i --nodeps postgresql${{ matrix.postgres_major_version }}*.rpm &&
ls -alh /usr &&
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1 change: 1 addition & 0 deletions api/tests/integration/ref/formats/mol_to_ket.py.out
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
*** MOL to KET ***
1032-quadra.ket:SUCCEED
1046-imp_hydrogen.ket:SUCCEED
1465-lr_sugar.ket:SUCCEED
SgroupDifferent.ket:SUCCEED
acgt_1412.ket:SUCCEED
anacyclamide.ket:SUCCEED
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1 change: 1 addition & 0 deletions api/tests/integration/tests/formats/mol_to_ket.py
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Original file line number Diff line number Diff line change
Expand Up @@ -44,6 +44,7 @@ def find_diff(a, b):
"anacyclamide",
"acgt_1412",
"apamine",
"1465-lr_sugar",
]

files.sort()
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69 changes: 69 additions & 0 deletions api/tests/integration/tests/formats/molecules/1465-lr_sugar.mol
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Original file line number Diff line number Diff line change
@@ -0,0 +1,69 @@

-INDIGO-01042412382D

0 0 0 0 0 0 0 0 0 0 0 V3000
M V30 BEGIN CTAB
M V30 COUNTS 1 0 0 0 0
M V30 BEGIN ATOM
M V30 1 LR 10.125 6.675 0.0 0 CLASS=RNA
M V30 END ATOM
M V30 BEGIN BOND
M V30 END BOND
M V30 END CTAB
M V30 BEGIN TEMPLATE
M V30 TEMPLATE 1 RNA/LR/LR NATREPLACE=RNA/R
M V30 BEGIN CTAB
M V30 COUNTS 13 14 4 0 0
M V30 BEGIN ATOM
M V30 1 O -0.9702 0.0384 0.0 0
M V30 2 C 0.5413 -0.5559 0.0 0 CFG=1
M V30 3 C -1.5602 -1.0669 0.0 0 CFG=2
M V30 4 C 1.9236 0.0726 0.0 0 CFG=2
M V30 5 C -0.2063 -1.7187 0.0 0 CFG=1
M V30 6 O 1.5616 1.5445 0.0 0
M V30 7 C 0.3744 0.9413 0.0 0
M V30 8 O -2.6751 -0.6231 0.0 0
M V30 9 O -0.9999 1.5445 0.0 0
M V30 10 H -1.1323 2.7372 0.0 0
M V30 11 H 2.4387 2.3633 0.0 0
M V30 12 C 0.6245 -2.0152 0.0 0
M V30 13 O 0.0798 -3.2622 0.0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 1 3
M V30 3 1 2 4
M V30 4 1 2 7 CFG=1
M V30 5 1 3 5
M V30 6 1 3 8 CFG=3
M V30 7 1 4 5
M V30 8 1 6 11
M V30 9 1 7 9
M V30 10 1 9 10
M V30 11 1 2 12 CFG=3
M V30 12 1 12 13
M V30 13 1 5 13 CFG=1
M V30 14 1 4 6 CFG=1
M V30 END BOND
M V30 BEGIN COLLECTION
M V30 MDLV30/STEABS ATOMS=(4 2 3 4 5)
M V30 END COLLECTION
M V30 BEGIN SGROUP
M V30 1 SUP 1 ATOMS=(1 10) XBONDS=(1 10) BRKXYZ=(9 0.066200 -0.596350 0.0000-
M V30 00 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=H CLAS-
M V30 S=LGRP
M V30 2 SUP 2 ATOMS=(1 11) XBONDS=(1 8) BRKXYZ=(9 -0.438550 -0.409400 0.0000-
M V30 00 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=H CLAS-
M V30 S=LGRP
M V30 3 SUP 3 ATOMS=(1 8) XBONDS=(1 6) BRKXYZ=(9 0.557450 -0.221900 0.000000-
M V30 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=OH CLASS-
M V30 =LGRP
M V30 4 SUP 4 ATOMS=(10 1 2 3 4 5 6 7 9 12 13) XBONDS=(3 6 8 10) BRKXYZ=(9 --
M V30 0.557450 0.221900 0.000000 0.438550 0.409400 0.000000 0.000000 0.00000-
M V30 0 0.000000) BRKXYZ=(9 -0.066200 0.596350 0.000000 0.000000 0.000000 0.-
M V30 000000 0.000000 0.000000 0.000000) LABEL=LR CLASS=RNA SAP=(3 9 10 Al) -
M V30 SAP=(3 6 11 Br) SAP=(3 3 8 Cx) NATREPLACE=RNA/R
M V30 END SGROUP
M V30 END CTAB
M V30 END TEMPLATE
M END
274 changes: 274 additions & 0 deletions api/tests/integration/tests/formats/ref/1465-lr_sugar.ket
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@@ -0,0 +1,274 @@
{
"root": {
"nodes": [
{
"$ref": "monomer0"
}
],
"connections": [],
"templates": [
{
"$ref": "monomerTemplate-LR_1"
}
]
},
"monomer0": {
"type": "monomer",
"id": "0",
"position": {
"x": 10.125,
"y": 6.675000190734863
},
"alias": "LR",
"templateId": "LR_1"
},
"monomerTemplate-LR_1": {
"type": "monomerTemplate",
"id": "LR_1",
"class": "RNA",
"classHELM": "RNA",
"alias": "LR",
"name": "LR",
"naturalAnalogShort": "R",
"attachmentPoints": [
{
"attachmentAtom": 8,
"leavingGroup": {
"atoms": [
9
]
}
},
{
"attachmentAtom": 5,
"leavingGroup": {
"atoms": [
10
]
}
},
{
"attachmentAtom": 2,
"leavingGroup": {
"atoms": [
7
]
}
}
],
"atoms": [
{
"label": "O",
"location": [
-0.9702000021934509,
0.03840000182390213,
0.0
]
},
{
"label": "C",
"location": [
0.5412999987602234,
-0.555899977684021,
0.0
]
},
{
"label": "C",
"location": [
-1.5601999759674073,
-1.0669000148773194,
0.0
],
"stereoLabel": "abs"
},
{
"label": "C",
"location": [
1.9235999584197999,
0.07259999960660935,
0.0
],
"stereoLabel": "abs"
},
{
"label": "C",
"location": [
-0.20630000531673432,
-1.7187000513076783,
0.0
],
"stereoLabel": "abs"
},
{
"label": "O",
"location": [
1.5615999698638917,
1.5444999933242798,
0.0
]
},
{
"label": "C",
"location": [
0.37439998984336855,
0.9412999749183655,
0.0
]
},
{
"label": "O",
"location": [
-2.675100088119507,
-0.6230999827384949,
0.0
]
},
{
"label": "O",
"location": [
-0.9998999834060669,
1.5444999933242798,
0.0
]
},
{
"label": "H",
"location": [
-1.1323000192642213,
2.7372000217437746,
0.0
]
},
{
"label": "H",
"location": [
2.438699960708618,
2.363300085067749,
0.0
]
},
{
"label": "C",
"location": [
0.6244999766349793,
-2.015199899673462,
0.0
]
},
{
"label": "O",
"location": [
0.07980000227689743,
-3.262200117111206,
0.0
]
}
],
"bonds": [
{
"type": 1,
"atoms": [
0,
1
]
},
{
"type": 1,
"atoms": [
0,
2
]
},
{
"type": 1,
"atoms": [
1,
3
]
},
{
"type": 1,
"atoms": [
1,
6
],
"stereo": 1
},
{
"type": 1,
"atoms": [
2,
4
]
},
{
"type": 1,
"atoms": [
2,
7
],
"stereo": 6
},
{
"type": 1,
"atoms": [
3,
4
]
},
{
"type": 1,
"atoms": [
5,
10
]
},
{
"type": 1,
"atoms": [
6,
8
]
},
{
"type": 1,
"atoms": [
8,
9
]
},
{
"type": 1,
"atoms": [
1,
11
],
"stereo": 6
},
{
"type": 1,
"atoms": [
11,
12
]
},
{
"type": 1,
"atoms": [
4,
12
],
"stereo": 1
},
{
"type": 1,
"atoms": [
3,
5
],
"stereo": 1
}
]
}
}
1 change: 1 addition & 0 deletions core/indigo-core/molecule/molfile_loader.h
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Original file line number Diff line number Diff line change
Expand Up @@ -49,6 +49,7 @@ namespace indigo

void loadMolecule(Molecule& mol);
void loadQueryMolecule(QueryMolecule& mol);
void copyProperties(const MolfileLoader& loader);

// for Rxnfiles v3000
void loadCtab3000(Molecule& mol);
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