139 create dedicated rfp foldx stability sasa and revert foldx stability sasa

src/poli/objective_repository/__init__.py

@@ -81,6 +81,18 @@
     pass
 
 
+try:
+    from .rfp_foldx_stability_and_sasa.register import (
+        RFPFoldXStabilityAndSASAProblemFactory,
+    )
+
+    AVAILABLE_PROBLEM_FACTORIES[
+        "rfp_foldx_stability_and_sasa"
+    ] = RFPFoldXStabilityAndSASAProblemFactory
+except (ImportError, FileNotFoundError):
+    pass
+
+
 try:
     from .penalized_logp_lambo.register import PenalizedLogPLamboProblemFactory
 

src/poli/objective_repository/foldx_stability_and_sasa/register.py

@@ -17,7 +17,6 @@
 """
 from pathlib import Path
 from typing import List, Tuple, Union
-import warnings
 
 import numpy as np
 
@@ -205,8 +204,6 @@ def create(
         parallelize: bool = False,
         num_workers: int = None,
         evaluation_budget: int = float("inf"),
-        n_starting_points: int = None,
-        strict: bool = False,
     ) -> Tuple[AbstractBlackBox, np.ndarray, np.ndarray]:
         """
         Create a FoldXSASABlackBox object and compute the initial values of wildtypes.
@@ -235,11 +232,7 @@ def create(
             Number of worker processes for parallel computation.
         evaluation_budget:  int, optional
             The maximum number of function evaluations. Default is infinity.
-        n_starting_points: int, optional
-            Size of D_0. Default is all available data.
-            The minimum number of sequence is given by the Pareto front of the RFP problem, ie. you cannot have less sequences than that.
-        strict: bool, optional
-            Enable RuntimeErrors if number of starting sequences different to requested number of sequences.
+
         Returns
         -------
         Tuple[AbstractBlackBox, np.ndarray, np.ndarray]
@@ -280,56 +273,10 @@ def create(
         if alphabet is None:
             alphabet = self.get_setup_information().get_alphabet()
 
-        if n_starting_points is None:
-            n_starting_points = len(wildtype_pdb_path)
-
-        # For a comparable RFP definition we require the sequences of the Pareto front:
-        pareto_sequences_name_pdb_dict = {
-            "DsRed.M1": "2VAD",
-            "DsRed.T4": "2VAE",
-            "mScarlet": "5LK4",
-            "AdRed": "6AA7",
-            "mRouge": "3NED",
-            "RFP630": "3E5V",
-        }
-
-        if strict and n_starting_points < len(pareto_sequences_name_pdb_dict):
-            raise RuntimeError(
-                f"Initial number of sequences too low!\nMinimum size {len(pareto_sequences_name_pdb_dict)} , requested {n_starting_points}"
-            )
-
-        remaining_n_starting_points = max(
-            n_starting_points - len(pareto_sequences_name_pdb_dict.values()), 0
-        )
-        # filter minimal required Pareto sequences
-        pareto_pdb_files = [
-            p
-            for p in wildtype_pdb_path
-            if any(
-                [
-                    bool(_pdb.lower() in str(p).lower())
-                    for _pdb in pareto_sequences_name_pdb_dict.values()
-                ]
-            )
-        ]
-        if len(pareto_pdb_files) != len(pareto_sequences_name_pdb_dict):
-            raise RuntimeError(
-                f"The provided PDB files list is incomplete!\n Required={','.join(list(pareto_sequences_name_pdb_dict.values()))} provided files={pareto_pdb_files}"
-            )
-
-        remaining_wildtype_pdb_files = list(
-            set(wildtype_pdb_path) - set(pareto_pdb_files)
-        )
-        np.random.shuffle(remaining_wildtype_pdb_files)
-        remaining_wildtype_pdb_files = remaining_wildtype_pdb_files[
-            :remaining_n_starting_points
-        ]  # subselect w.r.t. requested number of sequences
-        pdb_files_for_black_box: List = pareto_pdb_files + remaining_wildtype_pdb_files
-
         problem_info = self.get_setup_information()
         f = FoldXStabilityAndSASABlackBox(
             info=problem_info,
-            wildtype_pdb_path=pdb_files_for_black_box,
+            wildtype_pdb_path=wildtype_pdb_path,
             alphabet=alphabet,
             experiment_id=experiment_id,
             tmp_folder=tmp_folder,
@@ -345,8 +292,7 @@ def create(
         # a vector of wildtype sequences. These are padded to
         # match the maximum length with empty strings.
         wildtype_amino_acids_ = []
-        for pdb_file in pdb_files_for_black_box:
-            # NOTE: we require the elements of the pareto front for this problem to be well-defined
+        for pdb_file in wildtype_pdb_path:
             wildtype_residues = parse_pdb_as_residues(pdb_file)
             wildtype_amino_acids_.append(
                 [
@@ -363,19 +309,9 @@ def create(
         ]
 
         x0 = np.array(wildtype_amino_acids).reshape(
-            len(pdb_files_for_black_box), longest_wildtype_length
+            len(wildtype_pdb_path), longest_wildtype_length
         )
 
-        if n_starting_points is not None and x0.shape[0] != n_starting_points:
-            if strict:
-                raise RuntimeError(
-                    f"Requested number of starting sequences different to loaded!\nRequested n={n_starting_points}, loaded n={x0.shape[0]}"
-                )
-            else:
-                warnings.warn(
-                    f"Requested number of starting sequences different to loaded!\nRequested n={n_starting_points}, loaded n={x0.shape[0]}"
-                )
-
         f_0 = f(x0)
 
         return f, x0, f_0

src/poli/objective_repository/rfp_foldx_stability_and_sasa/__init__.py

@@ -0,0 +1 @@
+"""A black box for computing stability and solvent accessible surface area (SASA) using FoldX on a particular RFP problem with a defined Pareto front."""

src/poli/objective_repository/rfp_foldx_stability_and_sasa/environment.yml

@@ -0,0 +1,13 @@
+name: poli__protein
+channels:
+  - defaults
+  - conda-forge
+dependencies:
+  - python=3.9
+  - pip
+  - pip:
+    - biopython
+    - python-levenshtein
+    - numpy
+    - pdb-tools
+    - "git+https://github.com/MachineLearningLifeScience/poli.git@dev"