issue with aromatic rings in write.molecules()

From my email:

Hi, 

I'm running into grief with write.molecules() in rcdk.  Any molecules 
that I am inputting with an aromatic ring containing double bonds, have 
those double bonds delocalised in the output .sdf file.  

See example of the pubchem sdf for salicylic acid (Structure2D_CID_338.sdf),
 which I'm using as input.  Using load.molecules() to read this in, then write.molecules() 
to output it as Structure2D_CID_338_cdk.sdf changes the bond coding from fixed to
 delocalised in the ring.  Taking this .sdf as input in openbabel turns it back to  Structure2D_CID_338_cdk_openbabel.sdf, which has fixed position aromatic bonds again.

Is there a way to control this behavior in the write to sdf file? I have some downstream programs that
can't deal with delocalised bonds in input sdf files (Compound DIscoverer)


thanks
Tony

> sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS

Matrix products: default
BLAS:   /shared/storage/biology/rsrch/tf-PAB/lab/trl1/bin_research0/lib/R/lib/libRblas.so
LAPACK: /shared/storage/biology/rsrch/tf-PAB/lab/trl1/bin_research0/lib/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_GB          LC_NUMERIC=C            LC_TIME=en_GB
 [4] LC_COLLATE=en_GB        LC_MONETARY=en_GB       LC_MESSAGES=en_GB
 [7] LC_PAPER=en_GB          LC_NAME=en_GB           LC_ADDRESS=en_GB
[10] LC_TELEPHONE=en_GB      LC_MEASUREMENT=en_GB    LC_IDENTIFICATION=en_GB

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] rcdk_3.5.0   rcdklibs_2.3 rJava_0.9-11

loaded via a namespace (and not attached):
[1] BiocManager_1.30.10 compiler_3.6.2      parallel_3.6.2
[4] fingerprint_3.5.7   tools_3.6.2         iterators_1.0.12
[7] itertools_0.1-3     png_0.1-7

Structure2D_CID_338.sdf

338
  CDK     06292018032D

 16 16  0  0  0  0  0  0  0  0999 V2000
    2.5369   -0.0600    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1350    1.4400    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4030    1.4400    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2690   -0.0600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4030   -0.5600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1350   -0.5600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4030   -1.5600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1350   -1.5600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2690   -2.0600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2690    0.9400    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6720   -0.2500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8660   -1.8700    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6720   -1.8700    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2690   -2.6800    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0000   -0.3700    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1350    2.0600    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  5  1  0  0  0  0 
  1 15  1  0  0  0  0 
  2 10  1  0  0  0  0 
  2 16  1  0  0  0  0 
  3 10  2  0  0  0  0 
  4  5  4  0  0  0  0 
  4  6  4  0  0  0  0 
  4 10  1  0  0  0  0 
  5  7  4  0  0  0  0 
  6  8  4  0  0  0  0 
  6 11  1  0  0  0  0 
  7  9  4  0  0  0  0 
  7 12  1  0  0  0  0 
  8  9  4  0  0  0  0 
  8 13  1  0  0  0  0 
  9 14  1  0  0  0  0 
M  END
> <PUBCHEM_COMPOUND_CID>
338

> <PUBCHEM_COMPOUND_CANONICALIZED>
1

> <PUBCHEM_CACTVS_COMPLEXITY>
133

> <PUBCHEM_CACTVS_HBOND_ACCEPTOR>
3

> <PUBCHEM_CACTVS_HBOND_DONOR>
2

> <PUBCHEM_CACTVS_ROTATABLE_BOND>
1

> <PUBCHEM_CACTVS_SUBSKEYS>
AAADcYBgMAAAAAAAAAAAAAAAAAAAAAAAAAAwAAAAAAAAAAABAAAAGgAACAAADASAmAAwDoAAAgCIAiDSCAACAAAkIAAIiAEGCMgIJzaCFRKAcUAl4BEImYeIyCCOAAAAAAAIAAAAAAAAABAAAAAAAAAAAA==

> <PUBCHEM_IUPAC_OPENEYE_NAME>
2-hydroxybenzoic acid

> <PUBCHEM_IUPAC_CAS_NAME>
2-hydroxybenzoic acid

> <PUBCHEM_IUPAC_NAME_MARKUP>
2-hydroxybenzoic acid

> <PUBCHEM_IUPAC_NAME>
2-hydroxybenzoic acid

> <PUBCHEM_IUPAC_SYSTEMATIC_NAME>
2-oxidanylbenzoic acid

> <PUBCHEM_IUPAC_TRADITIONAL_NAME>
salicylic acid

> <PUBCHEM_IUPAC_INCHI>
InChI=1S/C7H6O3/c8-6-4-2-1-3-5(6)7(9)10/h1-4,8H,(H,9,10)

> <PUBCHEM_IUPAC_INCHIKEY>
YGSDEFSMJLZEOE-UHFFFAOYSA-N

> <PUBCHEM_XLOGP3>
2.3

> <PUBCHEM_EXACT_MASS>
138.031694

> <PUBCHEM_MOLECULAR_FORMULA>
C7H6O3

> <PUBCHEM_MOLECULAR_WEIGHT>
138.12

> <PUBCHEM_OPENEYE_CAN_SMILES>
C1=CC=C(C(=C1)C(=O)O)O

> <PUBCHEM_OPENEYE_ISO_SMILES>
C1=CC=C(C(=C1)C(=O)O)O

> <PUBCHEM_CACTVS_TPSA>
57.5

> <PUBCHEM_MONOISOTOPIC_WEIGHT>
138.031694

> <PUBCHEM_TOTAL_CHARGE>
0

> <PUBCHEM_HEAVY_ATOM_COUNT>
10

> <PUBCHEM_ATOM_DEF_STEREO_COUNT>
0

> <PUBCHEM_ATOM_UDEF_STEREO_COUNT>
0

> <PUBCHEM_BOND_DEF_STEREO_COUNT>
0

> <PUBCHEM_BOND_UDEF_STEREO_COUNT>
0

> <PUBCHEM_ISOTOPIC_ATOM_COUNT>
0

> <PUBCHEM_COMPONENT_COUNT>
1

> <PUBCHEM_CACTVS_TAUTO_COUNT>
-1

> <PUBCHEM_COORDINATE_TYPE>
1
5
255

> <PUBCHEM_BONDANNOTATIONS>
4  5  8
4  6  8
5  7  8
6  8  8
7  9  8
8  9  8

$$$$

Structure2D_CID_338_cdk_openbabel.sdf

338
 OpenBabel06292018072D

 16 16  0  0  0  0  0  0  0  0999 V2000
    2.5369   -0.0600    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1350    1.4400    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4030    1.4400    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2690   -0.0600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4030   -0.5600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1350   -0.5600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4030   -1.5600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1350   -1.5600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2690   -2.0600    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2690    0.9400    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6720   -0.2500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8660   -1.8700    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6720   -1.8700    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2690   -2.6800    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0000   -0.3700    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1350    2.0600    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  5  1  0  0  0  0
  1 15  1  0  0  0  0
  2 10  1  0  0  0  0
  2 16  1  0  0  0  0
  3 10  2  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  4 10  1  0  0  0  0
  5  7  1  0  0  0  0
  6  8  2  0  0  0  0
  6 11  1  0  0  0  0
  7  9  2  0  0  0  0
  7 12  1  0  0  0  0
  8  9  1  0  0  0  0
  8 13  1  0  0  0  0
  9 14  1  0  0  0  0
M  END
>  <PUBCHEM_COMPOUND_CID>
338

>  <PUBCHEM_COMPOUND_CANONICALIZED>
1

>  <PUBCHEM_CACTVS_COMPLEXITY>
133

>  <PUBCHEM_CACTVS_HBOND_ACCEPTOR>
3

>  <PUBCHEM_CACTVS_HBOND_DONOR>
2

>  <PUBCHEM_CACTVS_ROTATABLE_BOND>
1

>  <PUBCHEM_CACTVS_SUBSKEYS>
AAADcYBgMAAAAAAAAAAAAAAAAAAAAAAAAAAwAAAAAAAAAAABAAAAGgAACAAADASAmAAwDoAAAgCIAiDSCAACAAAkIAAIiAEGCMgIJzaCFRKAcUAl4BEImYeIyCCOAAAAAAAIAAAAAAAAABAAAAAAAAAAAA==

>  <PUBCHEM_IUPAC_OPENEYE_NAME>
2-hydroxybenzoic acid

>  <PUBCHEM_IUPAC_CAS_NAME>
2-hydroxybenzoic acid

>  <PUBCHEM_IUPAC_NAME_MARKUP>
2-hydroxybenzoic acid

>  <PUBCHEM_IUPAC_NAME>
2-hydroxybenzoic acid

>  <PUBCHEM_IUPAC_SYSTEMATIC_NAME>
2-oxidanylbenzoic acid

>  <PUBCHEM_IUPAC_TRADITIONAL_NAME>
salicylic acid

>  <PUBCHEM_IUPAC_INCHI>
InChI=1S/C7H6O3/c8-6-4-2-1-3-5(6)7(9)10/h1-4,8H,(H,9,10)

>  <PUBCHEM_IUPAC_INCHIKEY>
YGSDEFSMJLZEOE-UHFFFAOYSA-N

>  <PUBCHEM_XLOGP3>
2.3

>  <PUBCHEM_EXACT_MASS>
138.031694

>  <PUBCHEM_MOLECULAR_FORMULA>
C7H6O3

>  <PUBCHEM_MOLECULAR_WEIGHT>
138.12

>  <PUBCHEM_OPENEYE_CAN_SMILES>
C1=CC=C(C(=C1)C(=O)O)O

>  <PUBCHEM_OPENEYE_ISO_SMILES>
C1=CC=C(C(=C1)C(=O)O)O

>  <PUBCHEM_CACTVS_TPSA>
57.5

>  <PUBCHEM_MONOISOTOPIC_WEIGHT>
138.031694

>  <PUBCHEM_TOTAL_CHARGE>
0

>  <PUBCHEM_HEAVY_ATOM_COUNT>
10

>  <PUBCHEM_ATOM_DEF_STEREO_COUNT>
0

>  <PUBCHEM_ATOM_UDEF_STEREO_COUNT>
0

>  <PUBCHEM_BOND_DEF_STEREO_COUNT>
0

>  <PUBCHEM_BOND_UDEF_STEREO_COUNT>
0

>  <PUBCHEM_ISOTOPIC_ATOM_COUNT>
0

>  <PUBCHEM_COMPONENT_COUNT>
1

>  <PUBCHEM_CACTVS_TAUTO_COUNT>
-1

>  <PUBCHEM_COORDINATE_TYPE>
1
5
255

>  <PUBCHEM_BONDANNOTATIONS>
4  5  8
4  6  8
5  7  8
6  8  8
7  9  8
8  9  8

$$$$

further tests and input/output files attached. The problem seems to be that implicit H typing is lost in the write.molecules() process.

files.zip

library("rcdk")
Loading required package: rcdklibs
Loading required package: rJava

load structure from downloaded pubchem .sdf

mols <- load.molecules("Structure2D_CID_338.sdf")

plot structure

img <- view.image.2d(mols[[1]])
plot.new()
rasterImage(img, 0, 0, 1, 1)
savePlot("Structure2D_CID_338.png")
dev.off()
null device
1

write to sdf

write.molecules(mols, "Structure2D_CID_338_cdk.sdf", write.props = TRUE)

load and re plot

mols2 <- load.molecules("Structure2D_CID_338_cdk.sdf")

img2 <- view.image.2d(mols2[[1]])
Error in .jcall(mi, "[B", "getBytes", as.integer(depictor$getWidth()), :
java.lang.NullPointerException: One or more atoms had an undefined number of implicit hydrogens
plot.new()
rasterImage(img2, 0, 0, 1, 1)
Error in rasterImage(img2, 0, 0, 1, 1) : object 'img2' not found
savePlot("Structure2D_CID_338_cdk.png")
dev.off()
null device
1

sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS

Matrix products: default
BLAS: /shared/storage/biology/rsrch/tf-PAB/lab/trl1/bin_research0/lib/R/lib/libRblas.so
LAPACK: /shared/storage/biology/rsrch/tf-PAB/lab/trl1/bin_research0/lib/R/lib/libRlapack.so

locale:
[1] LC_CTYPE=en_GB LC_NUMERIC=C LC_TIME=en_GB
[4] LC_COLLATE=en_GB LC_MONETARY=en_GB LC_MESSAGES=en_GB
[7] LC_PAPER=en_GB LC_NAME=en_GB LC_ADDRESS=en_GB
[10] LC_TELEPHONE=en_GB LC_MEASUREMENT=en_GB LC_IDENTIFICATION=en_GB

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] rcdk_3.5.0 rcdklibs_2.3 rJava_0.9-11

loaded via a namespace (and not attached):
[1] compiler_3.6.2 parallel_3.6.2 fingerprint_3.5.7 iterators_1.0.12
[5] itertools_0.1-3 png_0.1-7

@trljcl

@trljcl apologies for the delay

I am looking at this again and agree that the hydrogens are lost. The write command is a wrapper of CDK's SDFWriter. Can you post this issue on the CDK user list? If it is explained/fixed in CDK, I can help get equivalent functionality in rCDK.

# suport for your theory
mols[[1]]$getAtomCount()
# 16
mols2[[1]]$getAtomCount()
# 10

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issue with aromatic rings in `write.molecules()` #108

Structure2D_CID_338.sdf

Structure2D_CID_338_cdk_openbabel.sdf

load structure from downloaded pubchem .sdf

plot structure

write to sdf

load and re plot

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issue with aromatic rings in write.molecules() #108

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Structure2D_CID_338.sdf

Structure2D_CID_338_cdk_openbabel.sdf

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trljcl commented on Jun 30, 2020

load structure from downloaded pubchem .sdf

plot structure

write to sdf

load and re plot

zachcp commented on Jul 20, 2020

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issue with aromatic rings in `write.molecules()` #108