#8143 System allow to load monomers with invalid HELM aliases (spaces are not allowed)

[Copilot]

How the feature works? / How did you fix the issue?

Monomers with HELM aliases containing spaces were being accepted into the macromolecule library instead of being rejected with a clear error. This adds alias validation during library updates so invalid entries are skipped and the required error is logged.

• Library validation: enforce HELM alias format on load and skip invalid monomers with the prescribed error text
• Tests: add a unit test covering invalid HELM alias rejection

const helmAliasRegex = /^[A-Za-z0-9_-*]+$/;
if (newMonomer.props?.aliasHELM && !helmAliasRegex.test(newMonomer.props.aliasHELM)) {
  KetcherLogger.error(
    `Load of "${newMonomer.props.MonomerName}" monomer has failed, monomer definition contains invalid HELM alias value. The HELM alias must consist only of uppercase and lowercase letters, numbers, hyphens (-), underscores (_), and asterisks (*), spaces prohibited.`,
  );
  return;
}

Check list

• unit-tests written
• e2e-tests written
• documentation updated
• PR name follows the pattern #1234 – issue name
• branch name doesn't contain '#'
• PR is linked with the issue
• base branch (master or release/xx) is correct
• task status changed to "Code review"
• reviewers are notified about the pull request

Original prompt

---

This section details on the original issue you should resolve

<issue_title>System allow to load monomers with invalid HELM aliases (spaces are not allowed)</issue_title>
<issue_description>Steps to Reproduce

1. Open Macromolecules - Flex mode (clean canvas)
2. Go to console and execute following commands:

_Peptide1

await ketcher.updateMonomersLibrary('\n  -INDIGO-10092516592D\n\n  0  0  0  0  0  0  0  0  0  0  0 V3000\nM  V30 BEGIN CTAB\nM  V30 COUNTS 1 0 0 0 0\nM  V30 BEGIN ATOM\nM  V30 1 _Peptide1 10.0194 -9.20822 0.0 0 CLASS=AA SEQID=1\nM  V30 END ATOM\nM  V30 BEGIN BOND\nM  V30 END BOND\nM  V30 END CTAB\nM  V30 BEGIN TEMPLATE\nM  V30 TEMPLATE 1 AA/_Peptide1/_Peptide1/ NATREPLACE=AA/A\nM  V30 BEGIN CTAB\nM  V30 COUNTS 9 8 3 0 0\nM  V30 BEGIN ATOM\nM  V30 1 H -2.394 0.508 0.0 0\nM  V30 2 C -1.528 0.008 0.0 0\nM  V30 3 C -0.662 0.508 0.0 0\nM  V30 4 C 0.204 0.008 0.0 0\nM  V30 5 C -1.528 -0.992 0.0 0\nM  V30 6 C -0.662 -1.492 0.0 0\nM  V30 7 C 1.17 0.267 0.0 0\nM  V30 8 C 1.428 1.233 0.0 0\nM  V30 9 H 2.394 1.492 0.0 0\nM  V30 END ATOM\nM  V30 BEGIN BOND\nM  V30 1 1 1 2\nM  V30 2 1 2 3\nM  V30 3 1 3 4\nM  V30 4 1 2 5\nM  V30 5 1 5 6\nM  V30 6 1 4 7\nM  V30 7 1 7 8\nM  V30 8 1 8 9\nM  V30 END BOND\nM  V30 BEGIN SGROUP\nM  V30 1 SUP 1 ATOMS=(1 1) XBONDS=(1 1) BRKXYZ=(9 0.433000 -0.250000 0.000000-\nM  V30  0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=H CLASS=-\nM  V30 LGRP\nM  V30 2 SUP 2 ATOMS=(1 9) XBONDS=(1 8) BRKXYZ=(9 -0.483000 -0.129500 0.00000-\nM  V30 0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=H CLASS-\nM  V30 =LGRP\nM  V30 3 SUP 3 ATOMS=(7 2 3 4 5 6 7 8) XBONDS=(2 1 8) BRKXYZ=(9 -0.433000 0.2-\nM  V30 50000 0.000000 0.483000 0.129500 0.000000 0.000000 0.000000 0.000000) -\nM  V30 LABEL=_Peptide1 CLASS=AA SAP=(3 2 1 Al) SAP=(3 8 9 Br) NATREPLACE=AA/A\nM  V30 END SGROUP\nM  V30 END CTAB\nM  V30 END TEMPLATE\nM  END\n>  <type>\nmonomerTemplate\n\n>  <modificationType>\nNatural amino acid2222222;ssssss;\n\n>  <aliasHELM>\n_Peptide1 Spaces are not allowed for HELM\n\n>  <idtAliases>\nbase=_Peptide1\n\n$$$$\n', { format: 'sdf' })

Actual behavior
_Peptide1 unsplit nucleotide appears in the library

Expected behavior
Monomer doesn't appear at the Library
System throws an error in console: Load of "_Nucleotide1" monomer has failed, monomer definition contains invalid HELM alias value. The HELM alias must consist only of uppercase and lowercase letters, numbers, hyphens (-), underscores (_), and asterisks (*), spaces prohibited.

As per requirement:

The HELM symbol must be a string of uppercase and lowercase letters, numbers, hyphens (-), underscores (), and asterisks (*) (spaces prohibited). If that is not true, an error message appears in the console: "The HELM alias must consist only of uppercase and lowercase letters, numbers, hyphens (-), underscores (), and asterisks (*), spaces prohibited."

If a monomer/preset property is incorrect for whatever reason: skip that monomers, load the rest and throw an error with monomer name and details

Environment details:

• Ketcher Version 3.9.0-rc.1 Build at 2025-10-02; 16:35:40
• Indigo Version 1.37.0-rc.1.0-gca09660df-wasm32-wasm-clang-19.0.0
• Chrome Version 141.0.7390.55 (Official Build) (64-bit)
• Win10

Related issue: epam/Indigo#3161</issue_description>

Comments on the Issue (you are @copilot in this section)

• Fixes System allow to load monomers with invalid HELM aliases (spaces are not allowed) #8143

---

💬 We'd love your input! Share your thoughts on Copilot coding agent in our 2 minute survey.