Remove parse_sequence_from_file (#110)

* Add parsing test * Remove parse_sequence_from_file * update CHANGELOG --------- Co-authored-by: blancoapa <[email protected]>
pyMBE-dev · Jan 21, 2025 · 6149dc1 · 6149dc1
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -19,7 +19,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 - Code of conduct of our community `CODE_OF_CONDUCT.md`, adhering to the Contributor Covenant v2.1 (#104) 
 - New optional argument `backbone_vector` enabling to build molecules along an input vector using `pmb.create_molecule` and `pmb.create_pmb_object` (#99)
-- Unit testing for reaction methods (#86)
 - New boolean flag `--ideal` as argparse argument of `samples/globular_protein.py` enabling to run the script without setting up interactions.
 - Unit tests for `pmb.create_protein`, `pmb.enable_motion_of_rigid_object`, `pmb.protein_sequence_parser`, `pmb.define_protein`, `pmb.read_protein_vtf_in_df` (#101)
 - Library `lattice.py`, a general builder for crystaline lattices. This library is part of on-going project to support hydrogels in pyMBE. (#93)
@@ -38,6 +37,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - NumPy 2, Pandas 2 and the development version of ESPResSo are now fully supported. (#106)
 - Fixed several deprecated paths and function names in `tutorials/pyMBE_tutorial.ipynb`. (#77, #78, #79, #80, #81)
 
+### Removed
+- `pmb.parse_sequence_from_file` has been removed since it is no longer necesary to parse the sequence from pmb.df (#110)
+
 ## [0.8.0] - 2024-06-18
 
 ### Added

diff --git a/pyMBE.py b/pyMBE.py
@@ -289,9 +289,6 @@ def calculate_HH(self, molecule_name, pH_list=None, pka_set=None):
                 Z_HH.append(Z)
             else:
                 # Molecule has a sequence
-                if not isinstance(sequence, list):
-                    # If the df has been read by file, the sequence needs to be parsed.
-                    sequence = self.parse_sequence_from_file(sequence=sequence)
                 for name in sequence:
                     if name in pka_set.keys():
                         if pka_set[name]['acidity'] == 'acidic':
@@ -2318,22 +2315,6 @@ def load_pka_set(self, filename, verbose=False, overwrite=True):
                                       overwrite=overwrite)
         return
 
-    def parse_sequence_from_file(self,sequence):
-        """
-        Parses the given sequence such that it can be used in pyMBE. This function has to be used if the df was read from a file.
-
-        Args:
-            sequence(`str`): sequence to be parsed
-
-        Returns:
-            sequence(`lst`): parsed sequence
-        """
-        sequence = sequence.replace(' ', '')
-        sequence = sequence.replace("'", '')
-        sequence = sequence.split(",")[1:-1]
-        return sequence
-
-
 
     def propose_unused_type(self):
         """