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

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

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

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

Associated Tutorial

Features

Thanks to...

Inputs

Steps

Outputs

Version History

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

Creators

Submitter

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

Associated Tutorial

Features

Thanks to...

Inputs

Steps

Outputs

Version History

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

Creators

Submitter

Related items

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