End-to-end spectra predictions: multi atoms dataset
Version 1

Workflow Type: Galaxy

Galaxy Workflow Documentation: In-Silico Mass Spectra Prediction Using Semi-Empirical Quantum Chemistry


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.


ID Name Description Type
List of molecules #main/List of molecules Global input dataset
  • File
Number of conformers to generate #main/Number of conformers to generate By default one conformer
  • int
Optimization Levels #main/Optimization Levels Level of accuracy for the optimization
  • string
QC Method #main/QC Method Available: GFN1-xTB and GFN2-xTB
  • string


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


ID Name Description Type
MSP output #main/MSP output n/a
  • File
XYZ output #main/XYZ output n/a
  • File
[.in] output #main/[.in] output n/a
  • File
[.start] output #main/[.start] output n/a
  • File
[.xyz] output #main/[.xyz] output n/a
  • File
conformer_output #main/conformer_output n/a
  • File
optimized output #main/optimized output n/a
  • File
res output #main/res output n/a
  • File

Version History

Version 1 (earliest) Created 3rd Jun 2024 at 14:52 by Wudmir Rojas

qcxms galaxy workflow

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Additional credit


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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Created: 3rd Jun 2024 at 14:52

Last updated: 4th Jun 2024 at 13:18

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