End-to-end EI+ mass spectra prediction workflow using QCxMS
1.0

Workflow Type: Galaxy

This workflow predict in-silico mass spectra using semi-empirical quantum physics method.

Associated Tutorial

This workflows is part of the tutorial Predicting EI+ mass spectra with QCxMS, available in the GTN

Features

Thanks to...

Workflow Author(s): RECETOX SpecDat

Tutorial Author(s): Julia Jakiela, Helge Hecht

gtn star logo followed by the word workflows

Inputs

ID Name Description Type
Input Molecules with SMILES and NAME without a header. Input Molecules with SMILES and NAME without a header. First column should containe the name of the molecule, the second should contain the SMILES code.
  • File
Number of conformers to generate Number of conformers to generate By default one conformer
  • int?
Optimization Levels Optimization Levels Level of accuracy for the optimization
  • string
QC Method QC Method Available: GFN1-xTB and GFN2-xTB
  • string

Steps

ID Name Description
4 Cut SMILES column toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1
5 Cut NAME column toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1
6 Split file toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2
7 Split file toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2
8 Parse parameter value param_value_from_file
9 Convert compounds from SMILES to SDF and add the name as title. toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy0
10 Merge the individual SDF files toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1
11 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
12 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
13 xTB molecular optimization Semi-empirical optimization toolshed.g2.bx.psu.edu/repos/recetox/xtb_molecular_optimization/xtb_molecular_optimization/6.6.1+galaxy3
14 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+galaxy4
15 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+galaxy3
16 Filter failed datasets Remove failed runs __FILTER_FAILED_DATASETS__
17 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+galaxy2

Outputs

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

Version History

1.0 (earliest) Created 7th Oct 2024 at 14:08 by Helena Rasche

Added/updated 4 files


Open master 5875e30
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Views: 207   Downloads: 47

Created: 7th Oct 2024 at 14:08

Last updated: 7th Oct 2024 at 14:08

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