End-to-end EI+ mass spectra prediction workflow using QCxMS
Version 1 (earliest)

Galaxy Workflow End-to-end EI mass spectra prediction workflow using QCxMS (latest)

Version 1 (earliest)

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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.

SEEK ID: https://workflowhub.eu/workflows/897?version=1

DOI: 10.48546/workflowhub.workflow.897.1

Inputs

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

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	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

Galaxy Workflow End-to-end EI mass spectra prediction workflow using QCxMS (latest) Created 5th Aug 2024 at 14:53 by Helge Hecht

New version starting from a table with SMILES and NAMES to generate an SDF and then run the previous workflow.

Frozen Galaxy-Workflow-End-to-end-EI-mass-spectra-prediction-workflow-using-QCxMS 1a50bdb

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

qcxms galaxy workflow

Frozen Version-1 0007a6a

Creators and Submitter

Creators

Additional credit

RECETOX SpecDat

Submitter

Wudmir Rojas

Tool

Open Babel

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

License

MIT License

Activity

Views: 1794 Downloads: 225 Runs: 2

Created: 3rd Jun 2024 at 14:52

Last updated: 5th Aug 2024 at 15:12

End-to-end EI+ mass spectra prediction workflow using QCxMS Version 1 (earliest) Galaxy Workflow End-to-end EI mass spectra prediction workflow using QCxMS (latest) Version 1 (earliest)