fix: do not create empty reaction product

[lpatiny]

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[lpatiny]

@targos I didn't succeed to update openchemlib in this project. Before I fill a bug report could you try to update this branch to the last version of OCL ?

I did npm run copy-openchemlib

But then the build yields to an error

npm run build-java

> [email protected] build-java
> npm run build-java-min && npm run build-java-debug


> [email protected] build-java-min
> node scripts/build.js build --mode=min

node:internal/errors:985
  const err = new Error(message);
              ^

Error: Command failed: java -Xmx2G -cp src:/Users/lpatiny/gwt/gwt-2.12.1/gwt-dev.jar:/Users/lpatiny/gwt/gwt-2.12.1/gwt-user.jar com.google.gwt.dev.Compiler com.actelion.research.gwt.Js -logLevel ERROR -XnocheckCasts -XnoclassMetadata -nodraftCompile -nocheckAssertions -generateJsInteropExports -optimize 9 -style OBFUSCATED -sourceLevel 17 -failOnError
    at genericNodeError (node:internal/errors:985:15)
    at wrappedFn (node:internal/errors:539:14)
    at checkExecSyncError (node:child_process:925:11)
    at Object.execFileSync (node:child_process:961:15)
    at compile (file:///Users/lpatiny/git/cheminfo/openchemlib-js/scripts/build.js:184:27)
    at run (file:///Users/lpatiny/git/cheminfo/openchemlib-js/scripts/build.js:75:5)
    at file:///Users/lpatiny/git/cheminfo/openchemlib-js/scripts/build.js:65:1 {
  status: 1,
  signal: null,
  output: [
    null,
    Buffer(544) [Uint8Array] [
       67, 111, 109, 112, 105, 108, 105, 110, 103,  32, 109, 111,
      100, 117, 108, 101,  32,  99, 111, 109,  46,  97,  99, 116,
      101, 108, 105, 111, 110,  46, 114, 101, 115, 101,  97, 114,
       99, 104,  46, 103, 119, 116,  46,  74, 115,  10,  32,  32,
       32,  84, 114,  97,  99, 105, 110, 103,  32,  99, 111, 109,
      112, 105, 108, 101,  32, 102,  97, 105, 108, 117, 114, 101,
       32, 112,  97, 116, 104,  32, 102, 111, 114,  32, 116, 121,
      112, 101,  32,  39,  99, 111, 109,  46,  97,  99, 116, 101,
      108, 105, 111, 110,
      ... 444 more items
    ],
    Buffer(0) [Uint8Array] []
  ],
  pid: 64173,
  stdout: Buffer(544) [Uint8Array] [
     67, 111, 109, 112, 105, 108, 105, 110, 103,  32, 109, 111,
    100, 117, 108, 101,  32,  99, 111, 109,  46,  97,  99, 116,
    101, 108, 105, 111, 110,  46, 114, 101, 115, 101,  97, 114,
     99, 104,  46, 103, 119, 116,  46,  74, 115,  10,  32,  32,
     32,  84, 114,  97,  99, 105, 110, 103,  32,  99, 111, 109,
    112, 105, 108, 101,  32, 102,  97, 105, 108, 117, 114, 101,
     32, 112,  97, 116, 104,  32, 102, 111, 114,  32, 116, 121,
    112, 101,  32,  39,  99, 111, 109,  46,  97,  99, 116, 101,
    108, 105, 111, 110,
    ... 444 more items
  ],
  stderr: Buffer(0) [Uint8Array] []

[targos]

In this PR your are reverting the submodule back to an old commit. Here on main we are tracking https://github.com/cheminfo/openchemlib/tree/68a858e6e08e2fdf5f6ce856bc9562ebf34cf26f. This PR sets it to https://github.com/cheminfo/openchemlib/tree/c8b24f7a48bcc6e5bebcba9df16c1b64bfedcb48

[targos]

Only the PDB parser changed in the actelion repo since the last update. I can update it but don't expect any changes to the reactions.

[lpatiny]

Ok no need to update then. Thanks.

[lpatiny]

Blocked by:

• Problem in reaction idCode ? Actelion/openchemlib#158

[targos]

I guess this was replaced by #353