Update peptides_proteins.rst #433
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| # Create an amino acid sequence using the fromString() method of the AASequence class. | ||
| # In this example, we will use the amino acid sequence "TESTMTECSTMTESTR" | ||
| sequence = poms.AASequence.fromString("TESTMTECSTMTESTR") | ||
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| # We use the names "Oxidation (M)" and "Carbamidomethyl (C)" for the variable and fixed modifications, respectively. | ||
| variable_mod_names = [b"Oxidation (M)"] | ||
| fixed_mod_names = [b"Carbamidomethyl (C)"] | ||
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| variable_modifications = poms.ModifiedPeptideGenerator.getModifications(variable_mod_names) | ||
| fixed_modifications = poms.ModifiedPeptideGenerator.getModifications(fixed_mod_names) | ||
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| variable_modifications = poms.ModifiedPeptideGenerator.getModifications(variable_mod_names) | |
| fixed_modifications = poms.ModifiedPeptideGenerator.getModifications(fixed_mod_names) | |
| variable_modifications = poms.ModifiedPeptideGenerator.getModifications( | |
| variable_mod_names | |
| ) | |
| fixed_modifications = poms.ModifiedPeptideGenerator.getModifications( | |
| fixed_mod_names | |
| ) | |
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| poms.ModifiedPeptideGenerator.applyFixedModifications(fixed_modifications, sequence) | ||
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| poms.ModifiedPeptideGenerator.applyFixedModifications(fixed_modifications, sequence) | |
| poms.ModifiedPeptideGenerator.applyFixedModifications( | |
| fixed_modifications, sequence | |
| ) | |
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| # Define the maximum number of variable modifications allowed | ||
| max_variable_mods = 1 | ||
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| # Print the modified peptides generated using Fixed modifications and their mono-isotopic mass. | ||
| print("Fixed:", sequence.toString()) | ||
| print("Mono-isotopic mass:", sequence.getMonoWeight()) | ||
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| for peptide in peptides_with_variable_modifications: | ||
| print("Variable:", peptide.toString()) | ||
| print("Mono-isotopic mass:", peptide.getMonoWeight()) | ||
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look more good Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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| variable_modifications = poms.ModifiedPeptideGenerator.getModifications(variable_mod_names) | ||
| fixed_modifications = poms.ModifiedPeptideGenerator.getModifications(fixed_mod_names) | ||
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| variable_modifications = poms.ModifiedPeptideGenerator.getModifications(variable_mod_names) | |
| fixed_modifications = poms.ModifiedPeptideGenerator.getModifications(fixed_mod_names) | |
| variable_modifications = poms.ModifiedPeptideGenerator.getModifications( | |
| variable_mod_names | |
| ) | |
| fixed_modifications = poms.ModifiedPeptideGenerator.getModifications( | |
| fixed_mod_names | |
| ) | |
Arslan-Siraj
approved these changes
Mar 1, 2024
| @@ -13,7 +13,6 @@ some commonly used operations like chemical formula, weight, and isotope distrib | |||
| The example below shows how amino acid sequences can be created and how basic mass calculations are conducted. | |||
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| .. code-block:: python | |||
| :linenos: | |||
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Why are these removed?
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Instead of removing this line, I fixed in next commits of format issue.
added 3 commits
March 5, 2024 15:23
| @@ -335,41 +335,42 @@ In this tutorial, we will cover a step-by-step guide on how to use the pyopenms | |||
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| .. code-block:: python | |||
| :linenos: | |||
| import pyopenms as poms | |||
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| import pyopenms as poms | |||
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| import pyopenms as poms | |
| import pyopenms as poms |
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| # Create an amino acid sequence using the fromString() method of the AASequence class. | ||
| # In this example, we will use the amino acid sequence "TESTMTECSTMTESTR" | ||
| sequence = poms.AASequence.fromString("TESTMTECSTMTESTR") |
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[blacken-docs] reported by reviewdog 🐶
Suggested change
| # Create an amino acid sequence using the fromString() method of the AASequence class. | |
| # In this example, we will use the amino acid sequence "TESTMTECSTMTESTR" | |
| sequence = poms.AASequence.fromString("TESTMTECSTMTESTR") | |
| # Create an amino acid sequence using the fromString() method of the AASequence class. | |
| # In this example, we will use the amino acid sequence "TESTMTECSTMTESTR" | |
| sequence = poms.AASequence.fromString("TESTMTECSTMTESTR") |
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| # We use the names "Oxidation (M)" and "Carbamidomethyl (C)" for the variable and fixed modifications, respectively. | ||
| variable_mod_names = [b"Oxidation (M)"] | ||
| fixed_mod_names = [b"Carbamidomethyl (C)"] |
There was a problem hiding this comment.
[blacken-docs] reported by reviewdog 🐶
Suggested change
| # We use the names "Oxidation (M)" and "Carbamidomethyl (C)" for the variable and fixed modifications, respectively. | |
| variable_mod_names = [b"Oxidation (M)"] | |
| fixed_mod_names = [b"Carbamidomethyl (C)"] | |
| # We use the names "Oxidation (M)" and "Carbamidomethyl (C)" for the variable and fixed modifications, respectively. | |
| variable_mod_names = [b"Oxidation (M)"] | |
| fixed_mod_names = [b"Carbamidomethyl (C)"] |
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| # We then use the getModifications() method of the ModifiedPeptideGenerator class to get the modifications for these names. | ||
| variable_modifications = poms.ModifiedPeptideGenerator.getModifications(variable_mod_names) | ||
| fixed_modifications = poms.ModifiedPeptideGenerator.getModifications(fixed_mod_names) | ||
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| # Apply the fixed modifications to the amino acid sequence | ||
| poms.ModifiedPeptideGenerator.applyFixedModifications(fixed_modifications, sequence) | ||
| # Apply the fixed modifications to the amino acid sequence | ||
| poms.ModifiedPeptideGenerator.applyFixedModifications(fixed_modifications, sequence) |
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| # We then use the getModifications() method of the ModifiedPeptideGenerator class to get the modifications for these names. | |
| variable_modifications = poms.ModifiedPeptideGenerator.getModifications(variable_mod_names) | |
| fixed_modifications = poms.ModifiedPeptideGenerator.getModifications(fixed_mod_names) | |
| # Apply the fixed modifications to the amino acid sequence | |
| poms.ModifiedPeptideGenerator.applyFixedModifications(fixed_modifications, sequence) | |
| # Apply the fixed modifications to the amino acid sequence | |
| poms.ModifiedPeptideGenerator.applyFixedModifications(fixed_modifications, sequence) | |
| # We then use the getModifications() method of the ModifiedPeptideGenerator class to get the modifications for these names. | |
| variable_modifications = poms.ModifiedPeptideGenerator.getModifications( | |
| variable_mod_names | |
| ) | |
| fixed_modifications = poms.ModifiedPeptideGenerator.getModifications( | |
| fixed_mod_names | |
| ) |
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| # Define the maximum number of variable modifications allowed | ||
| max_variable_mods = 1 |
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| # Define the maximum number of variable modifications allowed | |
| max_variable_mods = 1 | |
| # Apply the fixed modifications to the amino acid sequence | |
| poms.ModifiedPeptideGenerator.applyFixedModifications( | |
| fixed_modifications, sequence | |
| ) |
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| # Generate the modified peptides | ||
| peptides_with_variable_modifications = [] | ||
| keep_unmodified_in_result = False | ||
| poms.ModifiedPeptideGenerator.applyVariableModifications(variable_modifications, sequence, max_variable_mods, | ||
| peptides_with_variable_modifications, | ||
| keep_unmodified_in_result) |
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| # Generate the modified peptides | |
| peptides_with_variable_modifications = [] | |
| keep_unmodified_in_result = False | |
| poms.ModifiedPeptideGenerator.applyVariableModifications(variable_modifications, sequence, max_variable_mods, | |
| peptides_with_variable_modifications, | |
| keep_unmodified_in_result) | |
| # Define the maximum number of variable modifications allowed | |
| max_variable_mods = 1 | |
| # Generate the modified peptides | |
| peptides_with_variable_modifications = [] | |
| keep_unmodified_in_result = False | |
| poms.ModifiedPeptideGenerator.applyVariableModifications( | |
| variable_modifications, | |
| sequence, | |
| max_variable_mods, | |
| peptides_with_variable_modifications, | |
| keep_unmodified_in_result, | |
| ) |
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| # Print the modified peptides generated using Fixed modifications and their mono-isotopic mass. | ||
| print("Fixed:", sequence.toString()) | ||
| print("Mono-isotopic mass:", sequence.getMonoWeight()) |
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| # Print the modified peptides generated using Fixed modifications and their mono-isotopic mass. | |
| print("Fixed:", sequence.toString()) | |
| print("Mono-isotopic mass:", sequence.getMonoWeight()) | |
| # Print the modified peptides generated using Fixed modifications and their mono-isotopic mass. | |
| print("Fixed:", sequence.toString()) | |
| print("Mono-isotopic mass:", sequence.getMonoWeight()) |
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| # Print the modified peptides generated using variable modifications and their mono-isotopic mass. | ||
| for peptide in peptides_with_variable_modifications: | ||
| print("Variable:", peptide.toString()) | ||
| print("Mono-isotopic mass:", peptide.getMonoWeight()) | ||
|
|
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| # Print the modified peptides generated using variable modifications and their mono-isotopic mass. | |
| for peptide in peptides_with_variable_modifications: | |
| print("Variable:", peptide.toString()) | |
| print("Mono-isotopic mass:", peptide.getMonoWeight()) | |
| # Print the modified peptides generated using variable modifications and their mono-isotopic mass. | |
| for peptide in peptides_with_variable_modifications: | |
| print("Variable:", peptide.toString()) | |
| print("Mono-isotopic mass:", peptide.getMonoWeight()) |
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checked for spacing etc.