Executable Path Resolution

executable-path-resolution

Summary

Locates and validates required external executables in the system PATH and verifies their installed versions meet minimum thresholds before a dependent scientific application (QCxMS2) can execute. This skill automates dependency verification to prevent silent failures or version-incompatible runs.

When to use

When preparing to run QCxMS2 or similar multi-tool orchestration software that depends on five or more external programs with strict version floors. Specifically: before any QCxMS2 mass spectra calculation is attempted, or when setting up a new computational environment where xtb, CREST, molbar, orca, and geodesic_interpolate must all be available and sourced.

When NOT to use

• The application does not invoke external programs or has no external dependencies with version constraints.
• Executables are already dynamically linked or bundled within a container/virtual environment where PATH resolution is not needed.
• User has already manually verified all dependencies offline and does not require automated validation before each run.

Inputs

• system PATH environment variable
• executable names: xtb, CREST, molbar, orca, geodesic_interpolate
• minimum version thresholds (hardcoded: xtb >6.7.1, CREST ≥3.0.2, molbar ≥1.1.3, orca ≥6.0.0)

Outputs

• validation report (CSV or JSON)
• executable location paths (absolute or relative)
• extracted version strings per executable
• pass/fail status per dependency
• structured summary of all results with explicit version numbers and minimum requirements

How to apply

For each required executable (xtb, CREST, molbar, orca, geodesic_interpolate), query the system PATH using platform-specific lookup tools ('which' on Unix, 'where' on Windows) to locate the binary. Invoke the version-reporting flag (typically --version or -V) on each located executable and parse the output to extract the semantic version string. Compare the extracted version against the minimum thresholds: xtb > 6.7.1, CREST ≥ 3.0.2, molbar ≥ 1.1.3, orca ≥ 6.0.0; for geodesic_interpolate, confirm presence even if version output is unavailable. Record pass/fail for each dependency and generate a structured validation report (CSV or JSON format) with explicit version numbers found, minimum requirements, and pass/fail status. Halt QCxMS2 execution if any dependency fails validation.

Related tools

• xtb (Semiempirical quantum chemistry engine; QCxMS2 invokes xtb for geometry optimizations and electronic structure in mass spectrum calculations) — https://github.com/grimme-lab/xtb
• CREST (Conformer ensemble sampler; QCxMS2 uses CREST to generate molecular conformer ensembles for fragmentation analysis) — https://github.com/crest-lab/crest
• molbar (Molecular structure manipulation and visualization utility; QCxMS2 requires it for bond breaking and molecular editing in fragmentation workflows) — https://git.rwth-aachen.de/bannwarthlab/molbar
• orca (Quantum chemistry package; QCxMS2 invokes orca for high-level ab initio calculations of ionization and fragmentation) — https://orcaforum.kofo.mpg.de
• geodesic_interpolate (Reaction pathway interpolation tool (optional); enhances geodesic path generation in molecular geometry space for fragmentation networks) — https://github.com/virtualzx-nad/geodesic-interpolate
• QCxMS2 (Primary orchestrator; manages the entire workflow and calls this skill to validate external dependencies before mass spectrum calculation) — https://github.com/grimme-lab/QCxMS2

Examples

which xtb && xtb --version && which crest && crest --version && which molbar && molbar --version && which orca && orca --version && which geodesic_interpolate

Evaluation signals

• All five executable locations are successfully resolved and reported with non-empty absolute or relative paths.
• Version strings extracted from each executable match expected semantic versioning format (e.g., '6.7.2', '3.0.2').
• Each extracted version is compared correctly against its minimum threshold; pass signal returned only if xtb > 6.7.1, CREST ≥ 3.0.2, molbar ≥ 1.1.3, orca ≥ 6.0.0.
• Validation report is generated in valid CSV or JSON format with columns/keys: executable_name, path, version_found, minimum_required, status (pass/fail).
• QCxMS2 blocks calculation initiation with an error message if any dependency is missing or fails version check; successful validation allows calculation to proceed.

Limitations

• Manual installation and sourcing of external programs is required before this skill can succeed; the skill does not install or configure dependencies automatically.
• Version reporting flag (--version or -V) must be supported by the target executable; some tools may use non-standard version output formats, requiring custom parsing.
• geodesic_interpolate lacks a standardized version reporting mechanism, so presence-only validation is performed; version check is skipped for this tool.
• The skill relies on system PATH environment variable; executables in non-standard locations or shadowed by other executables with the same name may yield false positives or negatives.
• No changelog is provided in the QCxMS2 repository, so version compatibility matrices and deprecation timelines are not documented; thresholds may become outdated.

Evidence

• [other] QCxMS2 requires users to manually ensure installation and sourcing of five external programs with minimum version thresholds: xtb (version > 6.7.1), CREST (version >= 3.0.2), molbar (version >= 1.1.3), orca (version >= 6.0.0), and geodesic_interpolate, prior to executing any QCxMS2 calculations.: "QCxMS2 requires users to manually ensure installation and sourcing of five external programs with minimum version thresholds: xtb (version > 6.7.1), CREST (version >= 3.0.2), molbar (version >="
• [other] Query the system PATH and attempt to locate each required executable: xtb, CREST, molbar, orca, and geodesic_interpolate using standard command-line tools (e.g., 'which' on Unix or 'where' on Windows). For each located executable, invoke version-reporting flags (typically --version or -V) and parse the output to extract the version string.: "Query the system PATH and attempt to locate each required executable: xtb, CREST, molbar, orca, and geodesic_interpolate using standard command-line tools (e.g., 'which' on Unix or 'where' on"
• [other] Compare extracted versions against the minimum thresholds: xtb > 6.7.1, CREST ≥ 3.0.2, molbar ≥ 1.1.3, orca ≥ 6.0.0; for geodesic_interpolate, confirm presence without version check if version output is unavailable.: "Compare extracted versions against the minimum thresholds: xtb > 6.7.1, CREST ≥ 3.0.2, molbar ≥ 1.1.3, orca ≥ 6.0.0; for geodesic_interpolate, confirm presence without version check"
• [other] Record pass/fail outcome for each dependency and generate a structured validation report (CSV or JSON) summarizing all results with explicit version numbers found and minimum requirements.: "Record pass/fail outcome for each dependency and generate a structured validation report (CSV or JSON) summarizing all results with explicit version numbers found and minimum requirements"
• [readme] For any installation make sure that you have correctly installed and sourced the following external programs before attempting any calculations with QCxMS2: "For any installation make sure that you have correctly installed and sourced the following external programs before attempting any calculations with QCxMS2"