qcxms-sdf/main
v0.1

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Workflow Type: Galaxy

Workflow to predict EI mass spectra using QCxMS starting from a single SDF file, containing the 3D coordinates of all atoms in the molecule. These files can typically be obtained from PubChem.

SEEK ID: https://workflowhub.eu/workflows/1350?version=1

Inputs

ID Name Description Type
Input SDF File Input SDF File An input file containing one or multiple structures with already generated conformers, for example from PubChem.
  • File

Steps

ID Name Description
1 Conversion to XYZ format toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy1
2 QCxMS neutral run toolshed.g2.bx.psu.edu/repos/recetox/qcxms_neutral_run/qcxms_neutral_run/5.2.1+galaxy6
3 QCxMS production run toolshed.g2.bx.psu.edu/repos/recetox/qcxms_production_run/qcxms_production_run/5.2.1+galaxy4
4 QCxMS get results toolshed.g2.bx.psu.edu/repos/recetox/qcxms_getres/qcxms_getres/5.2.1+galaxy3

Outputs

ID Name Description Type
fragments fragments n/a
  • File
Predicted Spectra Predicted Spectra n/a
  • File

Version History

v0.1 (earliest) Created 30th Apr 2025 at 03:01 by WorkflowHub Bot

Updated to v0.1


Frozen v0.1 b6505a2
help Creators and Submitter
Creator
  • Helge Hecht
Additional credit

RECETOX

Submitter
Tool
Open Babel
License
MIT License (MIT)
Activity

Views: 1390   Downloads: 1502   Runs: 0

Created: 30th Apr 2025 at 03:01

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