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Features 2.9

Zachary Charlop-Powers

2024-03-04

Source: ../vignettes/Features_29.Rmd
Features_29.Rmd

CDK 2.9 Release Notes Vignettes

CDK 2.9 Release Notes

rJava

RXN Arrows

https://github.com/cdk/cdk/pull/927

library(rcdklibs)
library(depict)


# Java Imports
sp <- J('org.openscience.cdk.smiles.SmilesParser')
silentchemobject <- J("org.openscience.cdk.silent.SilentChemObjectBuilder")
smiles_parser <- new(sp, silentchemobject$getInstance())
ReactionManipulator <- J('org.openscience.cdk.tools.manipulator.ReactionManipulator')
IReaction <- J('org.openscience.cdk.interfaces.IReaction')
dg <- .jnew('org.openscience.cdk.depict.DepictionGenerator')

to_svg <- function(grd) {
  svg_str <- grd$toSvgStr()
  svg_list <- strsplit(svg_str, "\n")[[1]]
  paste(svg_list[3:length(svg_list)], collapse="\n")
}


abbreviations <- .jnew('org.openscience.cdk.depict.Abbreviations')
abbreviations$add("[Al+3].[Cl-].[Cl-].[Cl-] AlCl3")
## [1] TRUE
abbreviations$add("ClCCl DCM")
## [1] TRUE
abbreviations$setContractToSingleLabel(TRUE)
rxn <- smiles_parser$parseReactionSmiles("[CH3:9][CH:8]([CH3:10])[c:7]1[cH:11][cH:12][cH:13][cH:14][cH:15]1.[CH2:3]([CH2:4][C:5](=[O:6])Cl)[CH2:2][Cl:1]>[Al+3].[Cl-].[Cl-].[Cl-].C(Cl)Cl>[CH3:9][CH:8]([CH3:10])[c:7]1[cH:11][cH:12][c:13]([cH:14][cH:15]1)[C:5](=[O:6])[CH2:4][CH2:3][CH2:2][Cl:1] |f:2.3.4.5| Friedel-Crafts acylation [3.10.1]")

# note `as.list`
for (mol in as.list(ReactionManipulator$getAllAtomContainers(rxn))) {
 abbreviations$apply(mol) 
}

rxn$setDirection(IReaction$Direction$NO_GO)
svg  <- depiction() |> depict(rxn)
to_svg(svg)

[1] “Generated by the Chemistry Development Kit (http://github.com/cdk)”

rxn <- smiles_parser$parseReactionSmiles("[CH3:9][CH:8]([CH3:10])[c:7]1[cH:11][cH:12][cH:13][cH:14][cH:15]1.[CH2:3]([CH2:4][C:5](=[O:6])Cl)[CH2:2][Cl:1]>[Al+3].[Cl-].[Cl-].[Cl-].C(Cl)Cl>[CH3:9][CH:8]([CH3:10])[c:7]1[cH:11][cH:12][c:13]([cH:14][cH:15]1)[C:5](=[O:6])[CH2:4][CH2:3][CH2:2][Cl:1] |f:2.3.4.5| Friedel-Crafts acylation [3.10.1]")

for (mol in as.list(ReactionManipulator$getAllAtomContainers(rxn))) {
 abbreviations$apply(mol) 
}

rxn$setDirection(IReaction$Direction$RETRO_SYNTHETIC)
svg  <- depiction() |> depict(rxn)
to_svg(svg)

[1] “Generated by the Chemistry Development Kit (http://github.com/cdk)”

rxn <- smiles_parser$parseReactionSmiles("[CH3:9][CH:8]([CH3:10])[c:7]1[cH:11][cH:12][cH:13][cH:14][cH:15]1.[CH2:3]([CH2:4][C:5](=[O:6])Cl)[CH2:2][Cl:1]>[Al+3].[Cl-].[Cl-].[Cl-].C(Cl)Cl>[CH3:9][CH:8]([CH3:10])[c:7]1[cH:11][cH:12][c:13]([cH:14][cH:15]1)[C:5](=[O:6])[CH2:4][CH2:3][CH2:2][Cl:1] |f:2.3.4.5| Friedel-Crafts acylation [3.10.1]")

for (mol in as.list(ReactionManipulator$getAllAtomContainers(rxn))) {
 abbreviations$apply(mol) 
}

rxn$setDirection(IReaction$Direction$BIDIRECTIONAL)
svg  <- depiction() |> depict(rxn)
to_svg(svg)

[1] “Generated by the Chemistry Development Kit (http://github.com/cdk)”

rxn <- smiles_parser$parseReactionSmiles("c1c(Cl)cccc1[N-][N+]#N>>c1c(Cl)cccc1N=[N+]=[N-]")


for (mol in as.list(ReactionManipulator$getAllAtomContainers(rxn))) {
 abbreviations$apply(mol) 
}

rxn$setDirection(IReaction$Direction$RESONANCE)
svg  <- depiction() |> depict(rxn)
to_svg(svg)

[1] “Generated by the Chemistry Development Kit (http://github.com/cdk)”

Multi-Step Smiles 

SmilesParser sp = new SmilesParser(SilentChemObjectBuilder.getInstance());
IReactionSet rset = sp.parseReactionSetSmiles("[Pb]>>[Ag]>>[Au] lead-to-silver-to-gold");
multi_smiles <- "ClC1=NC=2N(C(=C1)N(CC3=CC=CC=C3)CC4=CC=CC=C4)N=CC2C(OCC)=O>C1(=CC(=CC(=N1)C)N)N2C[C@H](CCC2)O.O1CCOCC1.CC1(C2=C(C(=CC=C2)P(C3=CC=CC=C3)C4=CC=CC=C4)OC5=C(C=CC=C15)P(C6=CC=CC=C6)C7=CC=CC=C7)C.C=1C=CC(=CC1)\\C=C\\C(=O)\\C=C\\C2=CC=CC=C2.C=1C=CC(=CC1)\\C=C\\C(=O)\\C=C\\C2=CC=CC=C2.C=1C=CC(=CC1)\\C=C\\C(=O)\\C=C\\C2=CC=CC=C2.[Pd].[Pd].[Cs]OC(=O)O[Cs]>C1(=CC(=CC(=N1)C)NC2=NC=3N(C(=C2)N(CC4=CC=CC=C4)CC5=CC=CC=C5)N=CC3C(OCC)=O)N6C[C@H](CCC6)O>CO.C1CCOC1.O.O[Li]>C1(=CC(=CC(=N1)C)NC2=NC=3N(C(=C2)N(CC4=CC=CC=C4)CC5=CC=CC=C5)N=CC3C(O)=O)N6C[C@H](CCC6)O>CN(C)C(=[N+](C)C)ON1C2=C(C=CC=N2)N=N1.F[P-](F)(F)(F)(F)F.[NH4+].[Cl-].CN(C)C=O.CCN(C(C)C)C(C)C>C1(=CC(=CC(=N1)C)NC2=NC=3N(C(=C2)N(CC4=CC=CC=C4)CC5=CC=CC=C5)N=CC3C(N)=O)N6C[C@H](CCC6)O>>C1(=CC(=CC(=N1)C)NC2=NC=3N(C(=C2)N)N=CC3C(N)=O)N4C[C@H](CCC4)O |f:4.5.6.7.8,16.17,18.19|  US20190241576A1"

rxn_set <- smiles_parser$parseReactionSetSmiles(multi_smiles)
svg  <- depiction() |> depict(rxn_set)
to_svg(svg)

[1] “Generated by the Chemistry Development Kit (http://github.com/cdk)”

Features 2.8

Maygen 

maygen_cls    <- J('org.openscience.cdk.structgen.maygen.Maygen')
#smioutout_cls <- J('org.openscience.cdk.structgen.maygen.SmiOutputConsumer')
silentchemobject <- J("org.openscience.cdk.silent.SilentChemObjectBuilder")
smigen_cls    <- J('org.openscience.cdk.smiles.SmilesGenerator')
smigen <- .jnew('org.openscience.cdk.smiles.SmilesGenerator')
#IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();
#SmilesGenerator smigen = new SmilesGenerator(SmiFlavor.Default);


maygen <- new(maygen_cls, silentchemobject$getInstance())
maygen$setFormula("C3Cl2H4")


# smigen$create()
# consumer
# maygen$setConsumer(mol)
# maygen$run()


# StringWriter sw = new StringWriter();
# maygen.setConsumer(new SmiOutputConsumer(sw));

# StringWriter sw = new StringWriter();
# SdfOutputConsumer consumer = new SdfOutputConsumer(sw);
# consumer.setCoordinates(true);
        
# maygen.setConsumer(mol -> {
#              try {
#                  System.out.println(smigen.create(mol));
#              } catch (CDKException ignore) { }
#          });
# 
# int count = maygen.getCount(); // number of structures generated