TP_predict/7c9ef951bf6emaster
TP_predict/
7c9ef951bf6emaster
/
/
READme.txt
READme.txt
Created by Leo Trostel on 17.08.2022
This is a READme file for "smiles_to_mass_and_inclusion_list.py"
Purpose:
The purpose of the script is to generate a mass lists, which can be imported into Compound Discoverer.
It also creates inclusion lists for positive and negative mode for the use on a QExactivePlus.
Input:
The scripts needs 1 txt file as input that contains the SMILES of compounds (one string per line).
Output:
Mass list as csv file that can be imported into Compound Discoverer and 2 inclusion lists.
Important:
The script uses the PubChem database and for every compound a request is sent, thus the code can run for some time.
The csv files can be opened in Microsoft Excel and brought to a more readable form
by selection of the "A" column and apply: Data > Text to columns > Next > Next > Finish > Ok
However, this will override the Structure column and can not be imported into Compound Discoverer anymore.
Nevertheless, it can be saved as an xlsx file, thus converting it to the Excel Workbook format.
Step by step guide for non-python users:
1. download Anaconda (link: https://docs.anaconda.com/anaconda/install/index.html) and install it, then run Anaconda Navigator
2. create new environment under the environment tab, select python version 3.6.13
3. you need to install some python packages for this script to work:
3.1. go to environments, click "play button" on newly created environment, open Terminal
3.2. run following lines individually (need to confirm: type "y" and press enter)(might take a while):
conda install -c rdkit rdkit
pip install pubchempy
3.3. check if pandas is installed and active according to: https://docs.anaconda.com/anaconda/navigator/tutorials/pandas/
4. open anaconda navigator, go to home tab, check if "Applications on" is set to the new environment
5. click gear icon on "Spyder" > install specific version > 5.0.5 and wait for installation to finish
6. click launch button below "Spyder"
7. open the script: "smiles_to_mass_and_inclusion_list.py"
8. change the pathway of the input files according to the filepath on your harddrive
9. click somewhere in the left window and press F5 or click "Run File", if Run settings windows appears, click run
10. wait for the script to finish running (you can see the progress in the bottom right window, "Script finished successfully" marks end of script)
This is a READme file for "smiles_to_mass_and_inclusion_list.py"
Purpose:
The purpose of the script is to generate a mass lists, which can be imported into Compound Discoverer.
It also creates inclusion lists for positive and negative mode for the use on a QExactivePlus.
Input:
The scripts needs 1 txt file as input that contains the SMILES of compounds (one string per line).
Output:
Mass list as csv file that can be imported into Compound Discoverer and 2 inclusion lists.
Important:
The script uses the PubChem database and for every compound a request is sent, thus the code can run for some time.
The csv files can be opened in Microsoft Excel and brought to a more readable form
by selection of the "A" column and apply: Data > Text to columns > Next > Next > Finish > Ok
However, this will override the Structure column and can not be imported into Compound Discoverer anymore.
Nevertheless, it can be saved as an xlsx file, thus converting it to the Excel Workbook format.
Step by step guide for non-python users:
1. download Anaconda (link: https://docs.anaconda.com/anaconda/install/index.html) and install it, then run Anaconda Navigator
2. create new environment under the environment tab, select python version 3.6.13
3. you need to install some python packages for this script to work:
3.1. go to environments, click "play button" on newly created environment, open Terminal
3.2. run following lines individually (need to confirm: type "y" and press enter)(might take a while):
conda install -c rdkit rdkit
pip install pubchempy
3.3. check if pandas is installed and active according to: https://docs.anaconda.com/anaconda/navigator/tutorials/pandas/
4. open anaconda navigator, go to home tab, check if "Applications on" is set to the new environment
5. click gear icon on "Spyder" > install specific version > 5.0.5 and wait for installation to finish
6. click launch button below "Spyder"
7. open the script: "smiles_to_mass_and_inclusion_list.py"
8. change the pathway of the input files according to the filepath on your harddrive
9. click somewhere in the left window and press F5 or click "Run File", if Run settings windows appears, click run
10. wait for the script to finish running (you can see the progress in the bottom right window, "Script finished successfully" marks end of script)
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