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#2236 Import/export multi-tails in KET #2295

Merged
merged 26 commits into from
Sep 4, 2024
Merged

#2236 Import/export multi-tails in KET #2295

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5fb70df
multitale rendering
even1024 Aug 27, 2024
c486842
multitale rendering
even1024 Aug 27, 2024
04f46e1
multitale rendering
even1024 Aug 27, 2024
39cca9f
multitale rendering
even1024 Aug 27, 2024
d0a2269
multitale rendering
even1024 Aug 27, 2024
ebd0589
multitale rendering
even1024 Aug 28, 2024
098fe53
fix positions
even1024 Aug 30, 2024
aea9531
new err case
even1024 Aug 31, 2024
836bca7
layout debug
even1024 Sep 1, 2024
b3c13cb
layout and model
even1024 Sep 2, 2024
8deaa6b
layout and model
even1024 Sep 2, 2024
28f5c9b
layout and model
even1024 Sep 3, 2024
0167a3f
clang format
even1024 Sep 3, 2024
34064a4
clang format
even1024 Sep 3, 2024
0196154
clang format
even1024 Sep 3, 2024
372d4bc
constructor fix
even1024 Sep 3, 2024
11c3e7b
const fix
even1024 Sep 3, 2024
c63b011
int fix
even1024 Sep 3, 2024
64cbed1
comments fix
even1024 Sep 3, 2024
172a14d
comments fix
even1024 Sep 3, 2024
170434f
int fix
even1024 Sep 3, 2024
0ac3493
missing refs
even1024 Sep 3, 2024
18b2fb2
update refs
even1024 Sep 3, 2024
5151042
Merge branch 'master' of github.com:epam/Indigo into 2234-model-impor…
even1024 Sep 4, 2024
c7d3f42
refactor
even1024 Sep 4, 2024
e92d7a3
refactor
even1024 Sep 4, 2024
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3 changes: 2 additions & 1 deletion api/c/indigo/src/indigo_layout.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -101,7 +101,8 @@ CEXPORT int indigoLayout(int object)
else if (IndigoBaseReaction::is(obj))
{
BaseReaction& rxn = obj.getBaseReaction();
bool no_layout = rxn.intermediateCount() || rxn.specialConditionsCount() || rxn.meta().getNonChemicalMetaCount();
bool no_layout = rxn.intermediateCount() || rxn.specialConditionsCount() || rxn.meta().getNonChemicalMetaCount() ||
obj.type == IndigoObject::PATHWAY_REACTION || rxn.multitaleCount();
if (!no_layout)
{
ReactionLayout rl(rxn, self.smart_layout);
Expand Down
27 changes: 21 additions & 6 deletions api/c/indigo/src/indigo_savers.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -32,12 +32,15 @@
#include "molecule/sequence_saver.h"
#include "molecule/smiles_saver.h"
#include "reaction/canonical_rsmiles_saver.h"
#include "reaction/pathway_reaction.h"
#include "reaction/pathway_reaction_json_saver.h"
#include "reaction/reaction_cdxml_saver.h"
#include "reaction/reaction_cml_saver.h"
#include "reaction/reaction_json_saver.h"
#include "reaction/rsmiles_saver.h"
#include "reaction/rxnfile_loader.h"
#include "reaction/rxnfile_saver.h"

#include <memory>

#include "indigo_io.h"
Expand Down Expand Up @@ -714,12 +717,24 @@ CEXPORT int indigoSaveJson(int item, int output)
}
else if (IndigoBaseReaction::is(obj))
{
ReactionJsonSaver saver(out);
self.initReactionJsonSaver(saver);
BaseReaction& rxn = obj.getBaseReaction();
saver.saveReaction(rxn);
out.flush();
return 1;
if (obj.type == IndigoObject::PATHWAY_REACTION)
{
PathwayReactionJsonSaver jn(out);
self.initReactionJsonSaver(jn);
BaseReaction& br = obj.getBaseReaction();
jn.saveReaction(dynamic_cast<PathwayReaction&>(br));
out.flush();
return 1;
}
else
{
ReactionJsonSaver saver(out);
self.initReactionJsonSaver(saver);
BaseReaction& rxn = obj.getBaseReaction();
saver.saveReaction(rxn);
out.flush();
return 1;
}
}
else if (IndigoKetDocument::is(obj))
{
Expand Down
2 changes: 2 additions & 0 deletions api/tests/integration/ref/reaction/pathway.py.out
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Original file line number Diff line number Diff line change
Expand Up @@ -6,3 +6,5 @@ pathway5.rdf:SUCCEED
pathway6.rdf:SUCCEED
pathway7.rdf:SUCCEED
pathway8.rdf:SUCCEED
pathway9.rdf:SUCCEED
pathway10.rdf:SUCCEED
8 changes: 7 additions & 1 deletion api/tests/integration/tests/reaction/pathway.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,16 +27,22 @@ def find_diff(a, b):
"pathway6",
"pathway7",
"pathway8",
"pathway9",
"pathway10",
]

for filename in files:
rxn = indigo.loadReactionFromFile(
os.path.join(input_path, filename + ".rdf")
)
rxn_ref = open(os.path.join(ref_path, filename) + ".ket", "r").read()

rxn_txt = rxn.json()

# with open(os.path.join(ref_path, filename) + ".ket", "w") as file:
# file.write(rxn_txt)

rxn_ref = open(os.path.join(ref_path, filename) + ".ket", "r").read()

diff = find_diff(rxn_ref, rxn_txt)
if not diff:
print(filename + ".rdf:SUCCEED")
Expand Down
279 changes: 279 additions & 0 deletions api/tests/integration/tests/reaction/reactions/pathway10.rdf
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Original file line number Diff line number Diff line change
@@ -0,0 +1,279 @@
$RDFILE 1
$RFMT
$RXN

-INDIGO- 0903241149

2 3
$MOL

-INDIGO-09032411492D

5 5 0 0 0 0 0 0 0 0999 V2000
5.1216 -4.8963 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.1179 -3.9012 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.1096 -4.8834 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.1071 -3.9012 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.4000 -3.1941 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 4 1 0 0 0 0
4 3 1 0 0 0 0
3 1 1 0 0 0 0
4 5 1 0 0 0 0
M END
$MOL

-INDIGO-09032411492D

4 4 0 0 0 0 0 0 0 0999 V2000
6.9387 -4.8812 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.9400 -4.8812 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.4394 -4.0163 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.4394 -3.0163 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 1 1 0 0 0 0
3 4 1 0 0 0 0
M END
$MOL

-INDIGO-09032411492D

6 6 0 0 0 0 0 0 0 0999 V2000
15.0894 -3.3537 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
15.5898 -4.8938 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
15.8990 -3.9476 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
14.5890 -4.8938 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
14.2797 -3.9476 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
15.0894 -2.3537 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
1 5 1 0 0 0 0
5 4 2 0 0 0 0
4 2 1 0 0 0 0
2 3 2 0 0 0 0
3 1 1 0 0 0 0
1 6 1 0 0 0 0
M END
$MOL

-INDIGO-09032411492D

4 4 0 0 0 0 0 0 0 0999 V2000
17.6887 -4.6312 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
18.6900 -4.6312 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
18.1894 -3.7663 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
18.4482 -2.8004 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 1 1 0 0 0 0
3 4 1 0 0 0 0
M END
$MOL

-INDIGO-09032411492D

5 5 0 0 0 0 0 0 0 0999 V2000
21.4966 -4.7213 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
21.4929 -3.7262 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
20.4846 -4.7084 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
20.4821 -3.7262 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
22.2000 -3.0191 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 4 1 0 0 0 0
4 3 1 0 0 0 0
3 1 1 0 0 0 0
2 5 1 0 0 0 0
M END

$RFMT
$RXN

-INDIGO- 0903241151

2 2
$MOL

-INDIGO-09032411512D

5 5 0 0 0 0 0 0 0 0999 V2000
4.9844 -5.1799 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.4848 -6.7200 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.7940 -5.7738 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.4840 -6.7200 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.1747 -5.7738 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 5 1 0 0 0 0
5 4 2 0 0 0 0
4 2 1 0 0 0 0
2 3 2 0 0 0 0
3 1 1 0 0 0 0
M END
$MOL

-INDIGO-09032411512D

6 6 0 0 0 0 0 0 0 0999 V2000
7.7442 -5.3751 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.4745 -5.3746 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.6110 -4.8750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.4745 -6.3755 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.7442 -6.3800 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.6132 -6.8750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3 1 2 0 0 0 0
1 5 1 0 0 0 0
5 6 2 0 0 0 0
6 4 1 0 0 0 0
4 2 2 0 0 0 0
2 3 1 0 0 0 0
M END
$MOL

-INDIGO-09032411512D

5 5 0 0 0 0 0 0 0 0999 V2000
16.2665 -6.3225 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
16.2628 -5.3274 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
15.2546 -6.3096 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
15.2521 -5.3274 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
17.2288 -5.0686 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 4 1 0 0 0 0
4 3 1 0 0 0 0
3 1 1 0 0 0 0
2 5 1 0 0 0 0
M END
$MOL

-INDIGO-09032411512D

6 6 0 0 0 0 0 0 0 0999 V2000
19.7433 -5.3250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
19.7433 -6.3250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
20.6093 -6.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
21.4753 -6.3250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
21.4753 -5.3250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
20.6093 -4.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6 1 1 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
4 5 1 0 0 0 0
5 6 1 0 0 0 0
M END

$RFMT
$RXN

-INDIGO- 0903241152

5 1
$MOL

-INDIGO-09032411522D

4 4 0 0 0 0 0 0 0 0999 V2000
2.3905 -7.2966 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.3917 -7.2966 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.8912 -6.4316 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.1500 -5.4657 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 1 1 0 0 0 0
3 4 1 0 0 0 0
M END
$MOL

-INDIGO-09032411522D

6 6 0 0 0 0 0 0 0 0999 V2000
6.3501 -5.7811 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.3501 -6.7811 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.2161 -7.2811 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.0821 -6.7811 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.0821 -5.7811 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.2161 -5.2811 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6 1 1 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
4 5 1 0 0 0 0
5 6 1 0 0 0 0
M END
$MOL

-INDIGO-09032411522D

5 5 0 0 0 0 0 0 0 0999 V2000
11.2466 -6.8822 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.2429 -5.8871 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.2347 -6.8693 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.2322 -5.8871 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.9500 -5.1800 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 4 1 0 0 0 0
4 3 1 0 0 0 0
3 1 1 0 0 0 0
2 5 1 0 0 0 0
M END
$MOL

-INDIGO-09032411522D

6 6 0 0 0 0 0 0 0 0999 V2000
14.7162 -5.7111 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
15.2166 -7.2512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
15.5258 -6.3049 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
14.2158 -7.2512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
13.9064 -6.3049 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
14.7162 -4.7111 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
1 5 1 0 0 0 0
5 4 2 0 0 0 0
4 2 1 0 0 0 0
2 3 2 0 0 0 0
3 1 1 0 0 0 0
1 6 1 0 0 0 0
M END
$MOL

-INDIGO-09032411522D

5 5 0 0 0 0 0 0 0 0999 V2000
18.5922 -6.8581 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
18.5885 -5.8630 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
17.5803 -6.8452 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
17.5778 -5.8630 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
19.5544 -5.6042 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 4 1 0 0 0 0
4 3 1 0 0 0 0
3 1 1 0 0 0 0
2 5 1 0 0 0 0
M END
$MOL

-INDIGO-09032411522D

12 12 0 0 1 0 0 0 0 0999 V2000
30.0095 -4.9233 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
30.0095 -6.7984 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
28.1901 -7.7389 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
26.3706 -6.7985 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
28.1845 -4.9233 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
25.5727 -5.5176 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
29.0997 -5.3824 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
29.0997 -6.3338 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
28.1845 -6.7985 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
27.2749 -6.3340 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
27.2749 -5.3825 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
26.3706 -4.9235 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6 12 1 0 0 0 0
11 5 1 0 0 0 0
5 7 1 0 0 0 0
7 8 1 0 0 0 0
8 9 1 0 0 0 0
9 10 1 0 0 0 0
10 11 1 0 0 0 0
11 12 1 1 0 0 0
7 1 1 6 0 0 0
8 2 1 6 0 0 0
9 3 1 6 0 0 0
10 4 1 6 0 0 0
M END
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