Workflow Type: Galaxy
Open
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
- Includes Galaxy Workflow Tests
- Includes a Galaxy Workflow Report
- Uses Galaxy Workflow Comments
Thanks to...
Workflow Author(s): RECETOX SpecDat
Tutorial Author(s): Julia Jakiela, Helge Hecht
Inputs
ID | Name | Description | Type |
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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. |
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Number of conformers to generate | Number of conformers to generate | By default one conformer |
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Optimization Levels | Optimization Levels | Level of accuracy for the optimization |
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QC Method | QC Method | Available: GFN1-xTB and GFN2-xTB |
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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 |
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XYZ output | XYZ output | n/a |
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optimized output | optimized output | n/a |
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[.in] output | [.in] output | n/a |
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[.xyz] output | [.xyz] output | n/a |
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[.start] output | [.start] output | n/a |
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res output | res output | n/a |
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MSP output | MSP output | n/a |
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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
Attributions
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