Update peptides_proteins.rst (#433)

* Update peptides_proteins.rst

checked for spacing etc.

* Update docs/source/user_guide/peptides_proteins.rst

look more good

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

* Revert "Update docs/source/user_guide/peptides_proteins.rst
"

This reverts commit 17c8b19.

* Revert "Update peptides_proteins.rst"

This reverts commit 885ae45.

* Applying Fixed or Variable Modifications to Sequences fixed in doc

---------

Co-authored-by: Arslan Siraj <[email protected]>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Arslan <[email protected]>

docs/source/user_guide/peptides_proteins.rst

@@ -335,41 +335,42 @@ In this tutorial, we will cover a step-by-step guide on how to use the pyopenms
 
 .. code-block:: python
     :linenos:
-    import pyopenms as poms
+    
+        import pyopenms as poms
 
-# 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")
 
-# 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)"]
 
-# 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)
+        # 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)
 
-# Define the maximum number of variable modifications allowed
-max_variable_mods = 1
+        # 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)
+        # 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)
 
-# 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())
 
-# 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())
     
 The above code outputs: