When parsing surechembl V3000 mols with CFG information in the atom block, CDK gives the following warnings:
org.openscience.cdk.io.MDLV3000Reader WARN: Not parsing key: CFG
org.openscience.cdk.io.MDLV3000Reader WARN: Not parsing key: CFG
org.openscience.cdk.io.MDLV3000Reader WARN: Not parsing key: CFG
org.openscience.cdk.io.MDLV3000Reader WARN: Not parsing key: CFG
Mol Example:
Mrv1719003161910112D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 35 39 0 0 1
M V30 BEGIN ATOM
M V30 1 N -0.2679 -0.0569 0 0
M V30 2 C -1.1731 -1.3028 0 0
M V30 3 N -0.2679 -2.5487 0 0
M V30 4 C 1.1967 -2.0728 0 0
M V30 5 C 1.1967 -0.5328 0 0
M V30 6 C 2.5304 0.2372 0 0
M V30 7 C 3.8641 -0.5328 0 0
M V30 8 C 3.8641 -2.0728 0 0
M V30 9 C 2.5304 -2.8428 0 0
M V30 10 C 5.1978 0.2372 0 0
M V30 11 O 5.1978 1.7772 0 0
M V30 12 N 6.5315 -0.5328 0 0
M V30 13 C -0.7438 -4.0133 0 0
M V30 14 C 1.793 -4.8376 0 0
M V30 15 C 0.2867 -5.1578 0 0 CFG=2
M V30 16 O -0.1892 -6.6224 0 0
M V30 17 C 0.8413 -7.7669 0 0 CFG=2
M V30 18 C 2.3476 -7.4467 0 0
M V30 19 N 2.8235 -5.982 0 0
M V30 20 C 0.3654 -9.2315 0 0
M V30 21 O 2.5304 -4.3828 0 0
M V30 22 C 3.8641 -5.1528 0 0
M V30 23 N -5.0231 0.0309 0 0
M V30 24 C -3.4831 0.0309 0 0
M V30 25 C -2.7131 -1.3028 0 0
M V30 26 C -3.4831 -2.6365 0 0
M V30 27 C -5.0231 -2.6365 0 0
M V30 28 C -5.7931 -1.3028 0 0
M V30 29 N -7.3331 -1.3028 0 0
M V30 30 C -8.2383 -2.5487 0 0 CFG=2
M V30 31 C -9.7029 -2.0728 0 0
M V30 32 C -9.7029 -0.5328 0 0
M V30 33 C -8.2383 -0.0569 0 0 CFG=2
M V30 34 C -7.7624 -4.0133 0 0
M V30 35 C -7.7624 1.4077 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 2 1 2
M V30 2 1 2 3
M V30 3 1 3 4
M V30 4 1 1 5
M V30 5 1 4 5
M V30 6 2 5 6
M V30 7 1 6 7
M V30 8 2 7 8
M V30 9 1 8 9
M V30 10 2 4 9
M V30 11 2 10 11
M V30 12 1 10 12
M V30 13 1 7 10
M V30 14 1 15 14
M V30 15 1 15 16
M V30 16 1 17 16
M V30 17 1 17 18
M V30 18 1 18 19
M V30 19 1 14 19
M V30 20 1 17 20 CFG=3
M V30 21 1 15 13 CFG=3
M V30 22 1 3 13
M V30 23 1 21 22
M V30 24 1 9 21
M V30 25 2 23 24
M V30 26 1 24 25
M V30 27 2 25 26
M V30 28 1 26 27
M V30 29 2 27 28
M V30 30 1 23 28
M V30 31 1 30 29
M V30 32 1 30 31
M V30 33 1 31 32
M V30 34 1 33 32
M V30 35 1 33 29
M V30 36 1 30 34 CFG=1
M V30 37 1 33 35 CFG=3
M V30 38 1 28 29
M V30 39 1 2 25
M V30 END BOND
M V30 END CTAB
M END
> <ID>
SCHEMBL20798387
> <InChI>
InChI=1S/C26H34N6O3/c1-15-5-6-16(2)32(15)23-8-7-18(12-29-23)26-30-21-9-19(25(27)33)10-22(34-4)24(21)31(26)14-20-13-28-11-17(3)35-20/h7-10,12,15-17,20,28H,5-6,11,13-14H2,1-4H3,(H2,27,33)/t15-,16-,17-,20-/m0/s1
> <InChIKey>
HYFVUNXGVWUHSK-BOSXTWCSSA-N
> <MW>
478.597
$$$$
The CFG information in the atom block is lost after parsing of the molecule is complete. Is this intentional? The structural rendering appears accurate using just the CFG information from the bond block.
Using cdk-bundle Version 2.3.
When parsing surechembl V3000 mols with CFG information in the atom block, CDK gives the following warnings:
Mol Example:
The CFG information in the atom block is lost after parsing of the molecule is complete. Is this intentional? The structural rendering appears accurate using just the CFG information from the bond block.
Using cdk-bundle Version 2.3.