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#2041 - Monomer could be saved to RXN V3000 format but can't be load…
…ed back - exception (#2700)
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,4 @@ | ||
| *** RXN to KET *** | ||
| 2485-bad-layout.ket:SUCCEED | ||
| 2531-bad-layout.ket:SUCCEED | ||
| rxn3000-with-macro.ket:SUCCEED |
358 changes: 358 additions & 0 deletions
358
api/tests/integration/tests/formats/reactions/rxn3000-with-macro.rxn
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,358 @@ | ||
| $RXN V3000 | ||
|
|
||
| -INDIGO- 1220241444 | ||
|
|
||
| M V30 COUNTS 2 1 | ||
| M V30 BEGIN REACTANT | ||
| M V30 BEGIN CTAB | ||
| M V30 COUNTS 1 0 0 0 0 | ||
| M V30 BEGIN ATOM | ||
| M V30 1 5hMedC 10.225 -7.375 0.0 0 CLASS=RNA SEQID=1 | ||
| 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/5hMedC/5hMedC NATREPLACE=RNA/C | ||
| M V30 BEGIN CTAB | ||
| M V30 COUNTS 23 24 3 0 0 | ||
| M V30 BEGIN ATOM | ||
| M V30 1 C 15.2737 -8.09693 0.0 0 CFG=1 | ||
| M V30 2 O 16.1872 -7.69022 0.0 0 | ||
| M V30 3 C 16.8564 -8.43336 0.0 0 CFG=2 | ||
| M V30 4 C 16.3564 -9.29938 0.0 0 | ||
| M V30 5 C 15.3782 -9.09143 0.0 0 CFG=2 | ||
| M V30 6 C 14.4077 -7.59693 0.0 0 | ||
| M V30 7 O 14.4077 -6.59693 0.0 0 | ||
| M V30 8 H 13.5416 -6.09693 0.0 0 | ||
| M V30 9 O 14.6351 -9.76056 0.0 0 | ||
| M V30 10 P 13.684 -9.45154 0.0 0 | ||
| M V30 11 O 12.9409 -10.1207 0.0 0 | ||
| M V30 12 O 13.4761 -8.47339 0.0 0 | ||
| M V30 13 O 13.8919 -10.4297 0.0 0 | ||
| M V30 14 N 17.8509 -8.32882 0.0 0 | ||
| M V30 15 C 18.3509 -9.19485 0.0 0 | ||
| M V30 16 C 19.3509 -9.19485 0.0 0 | ||
| M V30 17 C 19.8509 -8.32882 0.0 0 | ||
| M V30 18 N 19.3509 -7.46279 0.0 0 | ||
| M V30 19 C 18.3509 -7.46279 0.0 0 | ||
| M V30 20 O 17.8509 -6.59677 0.0 0 | ||
| M V30 21 N 20.8509 -8.3288 0.0 0 | ||
| M V30 22 C 19.8509 -10.0609 0.0 0 | ||
| M V30 23 O 19.3509 -10.9269 0.0 0 | ||
| M V30 END ATOM | ||
| M V30 BEGIN BOND | ||
| M V30 1 1 1 5 | ||
| M V30 2 1 5 4 | ||
| M V30 3 1 4 3 | ||
| M V30 4 1 3 2 | ||
| M V30 5 1 2 1 | ||
| M V30 6 1 1 6 CFG=1 | ||
| M V30 7 1 6 7 | ||
| M V30 8 1 7 8 | ||
| M V30 9 1 5 9 CFG=3 | ||
| M V30 10 1 9 10 | ||
| M V30 11 1 10 11 | ||
| M V30 12 1 10 12 | ||
| M V30 13 2 10 13 | ||
| M V30 14 1 3 14 CFG=1 | ||
| M V30 15 1 19 14 | ||
| M V30 16 1 14 15 | ||
| M V30 17 2 15 16 | ||
| M V30 18 1 16 17 | ||
| M V30 19 2 17 18 | ||
| M V30 20 1 18 19 | ||
| M V30 21 2 19 20 | ||
| M V30 22 1 17 21 | ||
| M V30 23 1 16 22 | ||
| M V30 24 1 22 23 | ||
| M V30 END BOND | ||
| M V30 BEGIN COLLECTION | ||
| M V30 MDLV30/STEABS ATOMS=(3 1 3 5) | ||
| M V30 END COLLECTION | ||
| M V30 BEGIN SGROUP | ||
| M V30 1 SUP 1 ATOMS=(1 8) XBONDS=(1 8) BRKXYZ=(9 0.433013 -0.250000 0.000000- | ||
| M V30 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=H CLASS=- | ||
| M V30 LGRP | ||
| M V30 2 SUP 2 ATOMS=(1 11) XBONDS=(1 11) BRKXYZ=(9 0.371574 0.334564 0.00000- | ||
| M V30 0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=OH CLAS- | ||
| M V30 S=LGRP | ||
| M V30 3 SUP 3 ATOMS=(21 1 2 3 4 5 6 7 9 10 12 13 14 15 16 17 18 19 20 21 22 - | ||
| M V30 23) XBONDS=(2 8 11) BRKXYZ=(9 -0.433013 0.250000 0.000000 -0.371574 -0- | ||
| M V30 .334564 0.000000 0.000000 0.000000 0.000000) LABEL=5hMedC CLASS=RNA SA- | ||
| M V30 P=(3 7 8 Al) SAP=(3 10 11 Br) NATREPLACE=RNA/C | ||
| M V30 END SGROUP | ||
| M V30 END CTAB | ||
| M V30 TEMPLATE 2 LINKER/PEG-2/PEG-2 | ||
| M V30 BEGIN CTAB | ||
| M V30 COUNTS 9 8 3 0 0 | ||
| M V30 BEGIN ATOM | ||
| M V30 1 O -3.8999 -0.3833 0.0 0 | ||
| M V30 2 C -2.5999 0.3667 0.0 0 | ||
| M V30 3 C -1.3 -0.3833 0.0 0 | ||
| M V30 4 O 0.0 0.3667 0.0 0 | ||
| M V30 5 C 1.3 -0.3833 0.0 0 | ||
| M V30 6 C 2.6 0.3667 0.0 0 | ||
| M V30 7 O 3.9 -0.3833 0.0 0 | ||
| M V30 8 H 4.9394 0.2164 0.0 0 | ||
| M V30 9 H -4.9394 0.2164 0.0 0 | ||
| M V30 END ATOM | ||
| M V30 BEGIN BOND | ||
| M V30 1 1 1 2 | ||
| M V30 2 1 2 3 | ||
| M V30 3 1 3 4 | ||
| M V30 4 1 4 5 | ||
| M V30 5 1 5 6 | ||
| M V30 6 1 6 7 | ||
| M V30 7 1 7 8 | ||
| M V30 8 1 1 9 | ||
| M V30 END BOND | ||
| M V30 BEGIN SGROUP | ||
| M V30 1 SUP 1 ATOMS=(1 9) XBONDS=(1 8) BRKXYZ=(9 0.519750 -0.299850 0.000000- | ||
| M V30 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=H CLASS=- | ||
| M V30 LGRP | ||
| M V30 2 SUP 2 ATOMS=(1 8) XBONDS=(1 7) BRKXYZ=(9 -0.519700 -0.299850 0.00000- | ||
| M V30 0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=H CLASS- | ||
| M V30 =LGRP | ||
| M V30 3 SUP 3 ATOMS=(7 1 2 3 4 5 6 7) XBONDS=(2 8 7) BRKXYZ=(9 -0.519750 0.2- | ||
| M V30 99850 0.000000 0.519700 0.299850 0.000000 0.000000 0.000000 0.000000) - | ||
| M V30 LABEL=PEG-2 CLASS=LINKER SAP=(3 1 9 Al) SAP=(3 7 8 Br) | ||
| M V30 END SGROUP | ||
| M V30 END CTAB | ||
| M V30 END TEMPLATE | ||
| M V30 BEGIN CTAB | ||
| M V30 COUNTS 1 0 0 0 0 | ||
| M V30 BEGIN ATOM | ||
| M V30 1 PEG-2 12.5 -7.4 0.0 0 CLASS=LINKER | ||
| 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/5hMedC/5hMedC NATREPLACE=RNA/C | ||
| M V30 BEGIN CTAB | ||
| M V30 COUNTS 23 24 3 0 0 | ||
| M V30 BEGIN ATOM | ||
| M V30 1 C 15.2737 -8.09693 0.0 0 CFG=1 | ||
| M V30 2 O 16.1872 -7.69022 0.0 0 | ||
| M V30 3 C 16.8564 -8.43336 0.0 0 CFG=2 | ||
| M V30 4 C 16.3564 -9.29938 0.0 0 | ||
| M V30 5 C 15.3782 -9.09143 0.0 0 CFG=2 | ||
| M V30 6 C 14.4077 -7.59693 0.0 0 | ||
| M V30 7 O 14.4077 -6.59693 0.0 0 | ||
| M V30 8 H 13.5416 -6.09693 0.0 0 | ||
| M V30 9 O 14.6351 -9.76056 0.0 0 | ||
| M V30 10 P 13.684 -9.45154 0.0 0 | ||
| M V30 11 O 12.9409 -10.1207 0.0 0 | ||
| M V30 12 O 13.4761 -8.47339 0.0 0 | ||
| M V30 13 O 13.8919 -10.4297 0.0 0 | ||
| M V30 14 N 17.8509 -8.32882 0.0 0 | ||
| M V30 15 C 18.3509 -9.19485 0.0 0 | ||
| M V30 16 C 19.3509 -9.19485 0.0 0 | ||
| M V30 17 C 19.8509 -8.32882 0.0 0 | ||
| M V30 18 N 19.3509 -7.46279 0.0 0 | ||
| M V30 19 C 18.3509 -7.46279 0.0 0 | ||
| M V30 20 O 17.8509 -6.59677 0.0 0 | ||
| M V30 21 N 20.8509 -8.3288 0.0 0 | ||
| M V30 22 C 19.8509 -10.0609 0.0 0 | ||
| M V30 23 O 19.3509 -10.9269 0.0 0 | ||
| M V30 END ATOM | ||
| M V30 BEGIN BOND | ||
| M V30 1 1 1 5 | ||
| M V30 2 1 5 4 | ||
| M V30 3 1 4 3 | ||
| M V30 4 1 3 2 | ||
| M V30 5 1 2 1 | ||
| M V30 6 1 1 6 CFG=1 | ||
| M V30 7 1 6 7 | ||
| M V30 8 1 7 8 | ||
| M V30 9 1 5 9 CFG=3 | ||
| M V30 10 1 9 10 | ||
| M V30 11 1 10 11 | ||
| M V30 12 1 10 12 | ||
| M V30 13 2 10 13 | ||
| M V30 14 1 3 14 CFG=1 | ||
| M V30 15 1 19 14 | ||
| M V30 16 1 14 15 | ||
| M V30 17 2 15 16 | ||
| M V30 18 1 16 17 | ||
| M V30 19 2 17 18 | ||
| M V30 20 1 18 19 | ||
| M V30 21 2 19 20 | ||
| M V30 22 1 17 21 | ||
| M V30 23 1 16 22 | ||
| M V30 24 1 22 23 | ||
| M V30 END BOND | ||
| M V30 BEGIN COLLECTION | ||
| M V30 MDLV30/STEABS ATOMS=(3 1 3 5) | ||
| M V30 END COLLECTION | ||
| M V30 BEGIN SGROUP | ||
| M V30 1 SUP 1 ATOMS=(1 8) XBONDS=(1 8) BRKXYZ=(9 0.433013 -0.250000 0.000000- | ||
| M V30 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=H CLASS=- | ||
| M V30 LGRP | ||
| M V30 2 SUP 2 ATOMS=(1 11) XBONDS=(1 11) BRKXYZ=(9 0.371574 0.334564 0.00000- | ||
| M V30 0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=OH CLAS- | ||
| M V30 S=LGRP | ||
| M V30 3 SUP 3 ATOMS=(21 1 2 3 4 5 6 7 9 10 12 13 14 15 16 17 18 19 20 21 22 - | ||
| M V30 23) XBONDS=(2 8 11) BRKXYZ=(9 -0.433013 0.250000 0.000000 -0.371574 -0- | ||
| M V30 .334564 0.000000 0.000000 0.000000 0.000000) LABEL=5hMedC CLASS=RNA SA- | ||
| M V30 P=(3 7 8 Al) SAP=(3 10 11 Br) NATREPLACE=RNA/C | ||
| M V30 END SGROUP | ||
| M V30 END CTAB | ||
| M V30 TEMPLATE 2 LINKER/PEG-2/PEG-2 | ||
| M V30 BEGIN CTAB | ||
| M V30 COUNTS 9 8 3 0 0 | ||
| M V30 BEGIN ATOM | ||
| M V30 1 O -3.8999 -0.3833 0.0 0 | ||
| M V30 2 C -2.5999 0.3667 0.0 0 | ||
| M V30 3 C -1.3 -0.3833 0.0 0 | ||
| M V30 4 O 0.0 0.3667 0.0 0 | ||
| M V30 5 C 1.3 -0.3833 0.0 0 | ||
| M V30 6 C 2.6 0.3667 0.0 0 | ||
| M V30 7 O 3.9 -0.3833 0.0 0 | ||
| M V30 8 H 4.9394 0.2164 0.0 0 | ||
| M V30 9 H -4.9394 0.2164 0.0 0 | ||
| M V30 END ATOM | ||
| M V30 BEGIN BOND | ||
| M V30 1 1 1 2 | ||
| M V30 2 1 2 3 | ||
| M V30 3 1 3 4 | ||
| M V30 4 1 4 5 | ||
| M V30 5 1 5 6 | ||
| M V30 6 1 6 7 | ||
| M V30 7 1 7 8 | ||
| M V30 8 1 1 9 | ||
| M V30 END BOND | ||
| M V30 BEGIN SGROUP | ||
| M V30 1 SUP 1 ATOMS=(1 9) XBONDS=(1 8) BRKXYZ=(9 0.519750 -0.299850 0.000000- | ||
| M V30 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=H CLASS=- | ||
| M V30 LGRP | ||
| M V30 2 SUP 2 ATOMS=(1 8) XBONDS=(1 7) BRKXYZ=(9 -0.519700 -0.299850 0.00000- | ||
| M V30 0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=H CLASS- | ||
| M V30 =LGRP | ||
| M V30 3 SUP 3 ATOMS=(7 1 2 3 4 5 6 7) XBONDS=(2 8 7) BRKXYZ=(9 -0.519750 0.2- | ||
| M V30 99850 0.000000 0.519700 0.299850 0.000000 0.000000 0.000000 0.000000) - | ||
| M V30 LABEL=PEG-2 CLASS=LINKER SAP=(3 1 9 Al) SAP=(3 7 8 Br) | ||
| M V30 END SGROUP | ||
| M V30 END CTAB | ||
| M V30 END TEMPLATE | ||
| M V30 END REACTANT | ||
| M V30 BEGIN PRODUCT | ||
| M V30 BEGIN CTAB | ||
| M V30 COUNTS 1 0 0 0 0 | ||
| M V30 BEGIN ATOM | ||
| M V30 1 C 15.3206 -7.40254 0.0 0 | ||
| 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/5hMedC/5hMedC NATREPLACE=RNA/C | ||
| M V30 BEGIN CTAB | ||
| M V30 COUNTS 23 24 3 0 0 | ||
| M V30 BEGIN ATOM | ||
| M V30 1 C 15.2737 -8.09693 0.0 0 CFG=1 | ||
| M V30 2 O 16.1872 -7.69022 0.0 0 | ||
| M V30 3 C 16.8564 -8.43336 0.0 0 CFG=2 | ||
| M V30 4 C 16.3564 -9.29938 0.0 0 | ||
| M V30 5 C 15.3782 -9.09143 0.0 0 CFG=2 | ||
| M V30 6 C 14.4077 -7.59693 0.0 0 | ||
| M V30 7 O 14.4077 -6.59693 0.0 0 | ||
| M V30 8 H 13.5416 -6.09693 0.0 0 | ||
| M V30 9 O 14.6351 -9.76056 0.0 0 | ||
| M V30 10 P 13.684 -9.45154 0.0 0 | ||
| M V30 11 O 12.9409 -10.1207 0.0 0 | ||
| M V30 12 O 13.4761 -8.47339 0.0 0 | ||
| M V30 13 O 13.8919 -10.4297 0.0 0 | ||
| M V30 14 N 17.8509 -8.32882 0.0 0 | ||
| M V30 15 C 18.3509 -9.19485 0.0 0 | ||
| M V30 16 C 19.3509 -9.19485 0.0 0 | ||
| M V30 17 C 19.8509 -8.32882 0.0 0 | ||
| M V30 18 N 19.3509 -7.46279 0.0 0 | ||
| M V30 19 C 18.3509 -7.46279 0.0 0 | ||
| M V30 20 O 17.8509 -6.59677 0.0 0 | ||
| M V30 21 N 20.8509 -8.3288 0.0 0 | ||
| M V30 22 C 19.8509 -10.0609 0.0 0 | ||
| M V30 23 O 19.3509 -10.9269 0.0 0 | ||
| M V30 END ATOM | ||
| M V30 BEGIN BOND | ||
| M V30 1 1 1 5 | ||
| M V30 2 1 5 4 | ||
| M V30 3 1 4 3 | ||
| M V30 4 1 3 2 | ||
| M V30 5 1 2 1 | ||
| M V30 6 1 1 6 CFG=1 | ||
| M V30 7 1 6 7 | ||
| M V30 8 1 7 8 | ||
| M V30 9 1 5 9 CFG=3 | ||
| M V30 10 1 9 10 | ||
| M V30 11 1 10 11 | ||
| M V30 12 1 10 12 | ||
| M V30 13 2 10 13 | ||
| M V30 14 1 3 14 CFG=1 | ||
| M V30 15 1 19 14 | ||
| M V30 16 1 14 15 | ||
| M V30 17 2 15 16 | ||
| M V30 18 1 16 17 | ||
| M V30 19 2 17 18 | ||
| M V30 20 1 18 19 | ||
| M V30 21 2 19 20 | ||
| M V30 22 1 17 21 | ||
| M V30 23 1 16 22 | ||
| M V30 24 1 22 23 | ||
| M V30 END BOND | ||
| M V30 BEGIN COLLECTION | ||
| M V30 MDLV30/STEABS ATOMS=(3 1 3 5) | ||
| M V30 END COLLECTION | ||
| M V30 BEGIN SGROUP | ||
| M V30 1 SUP 1 ATOMS=(1 8) XBONDS=(1 8) BRKXYZ=(9 0.433013 -0.250000 0.000000- | ||
| M V30 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=H CLASS=- | ||
| M V30 LGRP | ||
| M V30 2 SUP 2 ATOMS=(1 11) XBONDS=(1 11) BRKXYZ=(9 0.371574 0.334564 0.00000- | ||
| M V30 0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=OH CLAS- | ||
| M V30 S=LGRP | ||
| M V30 3 SUP 3 ATOMS=(21 1 2 3 4 5 6 7 9 10 12 13 14 15 16 17 18 19 20 21 22 - | ||
| M V30 23) XBONDS=(2 8 11) BRKXYZ=(9 -0.433013 0.250000 0.000000 -0.371574 -0- | ||
| M V30 .334564 0.000000 0.000000 0.000000 0.000000) LABEL=5hMedC CLASS=RNA SA- | ||
| M V30 P=(3 7 8 Al) SAP=(3 10 11 Br) NATREPLACE=RNA/C | ||
| M V30 END SGROUP | ||
| M V30 END CTAB | ||
| M V30 TEMPLATE 2 LINKER/PEG-2/PEG-2 | ||
| M V30 BEGIN CTAB | ||
| M V30 COUNTS 9 8 3 0 0 | ||
| M V30 BEGIN ATOM | ||
| M V30 1 O -3.8999 -0.3833 0.0 0 | ||
| M V30 2 C -2.5999 0.3667 0.0 0 | ||
| M V30 3 C -1.3 -0.3833 0.0 0 | ||
| M V30 4 O 0.0 0.3667 0.0 0 | ||
| M V30 5 C 1.3 -0.3833 0.0 0 | ||
| M V30 6 C 2.6 0.3667 0.0 0 | ||
| M V30 7 O 3.9 -0.3833 0.0 0 | ||
| M V30 8 H 4.9394 0.2164 0.0 0 | ||
| M V30 9 H -4.9394 0.2164 0.0 0 | ||
| M V30 END ATOM | ||
| M V30 BEGIN BOND | ||
| M V30 1 1 1 2 | ||
| M V30 2 1 2 3 | ||
| M V30 3 1 3 4 | ||
| M V30 4 1 4 5 | ||
| M V30 5 1 5 6 | ||
| M V30 6 1 6 7 | ||
| M V30 7 1 7 8 | ||
| M V30 8 1 1 9 | ||
| M V30 END BOND | ||
| M V30 BEGIN SGROUP | ||
| M V30 1 SUP 1 ATOMS=(1 9) XBONDS=(1 8) BRKXYZ=(9 0.519750 -0.299850 0.000000- | ||
| M V30 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=H CLASS=- | ||
| M V30 LGRP | ||
| M V30 2 SUP 2 ATOMS=(1 8) XBONDS=(1 7) BRKXYZ=(9 -0.519700 -0.299850 0.00000- | ||
| M V30 0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=H CLASS- | ||
| M V30 =LGRP | ||
| M V30 3 SUP 3 ATOMS=(7 1 2 3 4 5 6 7) XBONDS=(2 8 7) BRKXYZ=(9 -0.519750 0.2- | ||
| M V30 99850 0.000000 0.519700 0.299850 0.000000 0.000000 0.000000 0.000000) - | ||
| M V30 LABEL=PEG-2 CLASS=LINKER SAP=(3 1 9 Al) SAP=(3 7 8 Br) | ||
| M V30 END SGROUP | ||
| M V30 END CTAB | ||
| M V30 END TEMPLATE | ||
| M V30 END PRODUCT | ||
| M END |
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