End-to-end spectra predictions: multi atoms dataset Version 1
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Galaxy Workflow Documentation: In-Silico Mass Spectra Prediction Using Semi-Empirical Quantum Chemistry
Overview
This workflow predicts in-silico mass spectra using a semi-empirical quantum chemistry method. It involves generating and optimizing molecular conformers and simulating their mass spectra with computational chemistry tools. The workflow receives an SDF file as input and outputs the mass spectrum in MSP file format.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| List of molecules | #main/List of molecules | Global input dataset |
|
| Number of conformers to generate | #main/Number of conformers to generate | By default one conformer |
|
| Optimization Levels | #main/Optimization Levels | Level of accuracy for the optimization |
|
| QC Method | #main/QC Method | Available: GFN1-xTB and GFN2-xTB |
|
Steps
| ID | Name | Description |
|---|---|---|
| 4 | Generate conformers | Generate 3D conformers from SDF input for each molecule. It requires the number of conformers as an input parameter. Default parameters value is 1. toolshed.g2.bx.psu.edu/repos/bgruening/ctb_im_conformers/ctb_im_conformers/1.1.4+galaxy0 |
| 5 | Molecular format conversion | Convert the conformer to cartesian coordinate (XYZ) format toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy0 |
| 6 | xTB molecular optimization | Semi-empirical optimization toolshed.g2.bx.psu.edu/repos/recetox/xtb_molecular_optimization/xtb_molecular_optimization/6.6.1+galaxy1 |
| 7 | QCxMS neutral run | Produce preparation input files for production runs toolshed.g2.bx.psu.edu/repos/recetox/qcxms_neutral_run/qcxms_neutral_run/5.2.1+galaxy3 |
| 8 | QCxMS production run | Calculate the mass spectra for a given molecule using QCxMS. It generates .res files, which are collected and converted into MSP format in the last step toolshed.g2.bx.psu.edu/repos/recetox/qcxms_production_run/qcxms_production_run/5.2.1+galaxy2 |
| 9 | Filter failed datasets | Remove failed runs __FILTER_FAILED_DATASETS__ |
| 10 | QCxMS get results | Produce simulated mass spectra into MSP file format. toolshed.g2.bx.psu.edu/repos/recetox/qcxms_getres/qcxms_getres/5.2.1+galaxy1 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| MSP output | #main/MSP output | n/a |
|
| XYZ output | #main/XYZ output | n/a |
|
| [.in] output | #main/[.in] output | n/a |
|
| [.start] output | #main/[.start] output | n/a |
|
| [.xyz] output | #main/[.xyz] output | n/a |
|
| conformer_output | #main/conformer_output | n/a |
|
| optimized output | #main/optimized output | n/a |
|
| res output | #main/res output | n/a |
|
Version History
Version 1 (earliest) Created 3rd Jun 2024 at 14:52 by Wudmir Rojas
qcxms galaxy workflow
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Version-10007a6a
Creators and SubmitterCreators
Additional credit
RECETOX SpecDat
Submitter
Tool
Citation
Ahmad, Z., Hecht, H., & Rojas, W. (2024). End-to-end spectra predictions: multi atoms dataset. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.897.1
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Views: 711 Downloads: 89
Created: 3rd Jun 2024 at 14:52
Last updated: 4th Jun 2024 at 13:18
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Related items
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https://orcid.org/0000-0001-6744-996X
Teams: RECETOX SpecDatRI
Organizations: Masaryk University
Teams: RECETOX SpecDatRI, RECETOX, usegalaxy-eu, ELIXIR Metabolomics
Organizations: Masaryk University, RECETOX
https://orcid.org/0000-0001-6744-996X
Advanced Teams list for this Workflow with search and filtering
Spectrometric Data Processing & Analysis Department of RECETOX.
