Adds an exception for when foldx is not found (#165)

Author: miguelgondu

src/poli/core/exceptions.py

@@ -11,3 +11,9 @@ class BudgetExhaustedException(PoliException):
     """Exception raised when the budget is exhausted."""
 
     pass
+
+
+class FoldXNotFoundException(PoliException):
+    """Exception raised when FoldX wasn't found in ~/foldx/foldx."""
+
+    pass

src/poli/objective_repository/foldx_rfp_lambo/register.py

@@ -2,22 +2,14 @@
 
 __author__ = "Simon Bartels"
 
-import logging
 from pathlib import Path
-import os
-import random
-from typing import Tuple
 
-import numpy as np
-
-# import hydra
-# import torch
 from poli.core.abstract_black_box import AbstractBlackBox
 from poli.core.abstract_problem_factory import AbstractProblemFactory
 from poli.core.problem import Problem
 from poli.core.black_box_information import BlackBoxInformation
+from poli.core.exceptions import FoldXNotFoundException
 
-from poli.core.problem_setup_information import ProblemSetupInformation
 from poli.objective_repository.foldx_rfp_lambo import PROBLEM_SEQ, CORRECT_SEQ
 from poli.core.util.isolation.instancing import instance_function_as_isolated_process
 from poli.core.util.seeding import seed_python_numpy_and_torch
@@ -47,6 +39,10 @@ def __init__(
         self.inverse_alphabet = {i + 1: AMINO_ACIDS[i] for i in range(len(AMINO_ACIDS))}
         self.inverse_alphabet[0] = "-"
 
+        if not (Path.home() / "foldx" / "foldx").exists():
+            raise FoldXNotFoundException(
+                "FoldX wasn't found in ~/foldx/foldx. Please install it."
+            )
         if not force_isolation:
             try:
                 from poli.objective_repository.foldx_rfp_lambo.isolated_function import (

src/poli/objective_repository/foldx_sasa/register.py

@@ -23,6 +23,7 @@
 from poli.core.abstract_problem_factory import AbstractProblemFactory
 from poli.core.black_box_information import BlackBoxInformation
 from poli.core.problem import Problem
+from poli.core.exceptions import FoldXNotFoundException
 
 from poli.core.util.isolation.instancing import instance_function_as_isolated_process
 
@@ -39,8 +40,6 @@ class FoldXSASABlackBox(AbstractBlackBox):
     -----------
     wildtype_pdb_path : Union[Path, List[Path]]
         The path(s) to the wildtype PDB file(s). Default is None.
-    alphabet : List[str], optional
-        The alphabet of amino acids. Default is None.
     experiment_id : str, optional
         The ID of the experiment. Default is None.
     tmp_folder : Path, optional
@@ -68,7 +67,6 @@ class FoldXSASABlackBox(AbstractBlackBox):
     def __init__(
         self,
         wildtype_pdb_path: Union[Path, List[Path]],
-        alphabet: List[str] = None,
         experiment_id: str = None,
         tmp_folder: Path = None,
         eager_repair: bool = False,
@@ -85,6 +83,10 @@ def __init__(
             num_workers=num_workers,
             evaluation_budget=evaluation_budget,
         )
+        if not (Path.home() / "foldx" / "foldx").exists():
+            raise FoldXNotFoundException(
+                "FoldX wasn't found in ~/foldx/foldx. Please install it."
+            )
         if not force_isolation:
             try:
                 from poli.objective_repository.foldx_sasa.isolated_function import (
@@ -177,7 +179,6 @@ def get_setup_information(self) -> BlackBoxInformation:
     def create(
         self,
         wildtype_pdb_path: Union[Path, List[Path]],
-        alphabet: List[str] = None,
         experiment_id: str = None,
         tmp_folder: Path = None,
         eager_repair: bool = False,
@@ -196,9 +197,6 @@ def create(
         ----------
         wildtype_pdb_path : Union[Path, List[Path]]
             Path or list of paths to the wildtype PDB files.
-        alphabet : List[str], optional
-            List of amino acid symbols. By defualt, the 20 amino acids
-            shown in poli.core.util.proteins.defaults are used.
         experiment_id : str, optional
             Identifier for the experiment.
         tmp_folder : Path, optional
@@ -259,12 +257,9 @@ def create(
 
         # We use the default alphabet if None was provided.
         # See ENCODING in foldx_utils.py
-        if alphabet is None:
-            alphabet = self.get_setup_information().get_alphabet()
 
         f = FoldXSASABlackBox(
             wildtype_pdb_path=wildtype_pdb_path,
-            alphabet=alphabet,
             experiment_id=experiment_id,
             tmp_folder=tmp_folder,
             eager_repair=eager_repair,

src/poli/objective_repository/foldx_stability/register.py

@@ -23,6 +23,7 @@
 from poli.core.black_box_information import BlackBoxInformation
 from poli.core.problem import Problem
 from poli.core.abstract_black_box import AbstractBlackBox
+from poli.core.exceptions import FoldXNotFoundException
 
 from poli.core.util.seeding import seed_python_numpy_and_torch
 
@@ -39,9 +40,6 @@ class FoldXStabilityBlackBox(AbstractBlackBox):
     ----------
     wildtype_pdb_path : Union[Path, List[Path]]
         The path(s) to the wildtype PDB file(s).
-    alphabet : List[str], optional
-        The alphabet of amino acids. By default, we use the 20
-        amino acids shown in poli.core.util.proteins.defaults.
     experiment_id : str, optional
         The ID of the experiment (default is None).
     tmp_folder : Path, optional
@@ -74,7 +72,6 @@ class FoldXStabilityBlackBox(AbstractBlackBox):
     def __init__(
         self,
         wildtype_pdb_path: Union[Path, List[Path]],
-        alphabet: List[str] = None,
         experiment_id: str = None,
         tmp_folder: Path = None,
         eager_repair: bool = False,
@@ -91,6 +88,10 @@ def __init__(
             num_workers=num_workers,
             evaluation_budget=evaluation_budget,
         )
+        if not (Path.home() / "foldx" / "foldx").exists():
+            raise FoldXNotFoundException(
+                "FoldX wasn't found in ~/foldx/foldx. Please install it."
+            )
         if not force_isolation:
             try:
                 from poli.objective_repository.foldx_stability.isolated_function import (
@@ -173,7 +174,6 @@ def get_setup_information(self) -> BlackBoxInformation:
     def create(
         self,
         wildtype_pdb_path: Union[Path, List[Path]],
-        alphabet: List[str] = None,
         experiment_id: str = None,
         tmp_folder: Path = None,
         eager_repair: bool = False,
@@ -248,15 +248,9 @@ def create(
         # By this point, we know that wildtype_pdb_path is a
         # list of Path objects.
 
-        if alphabet is None:
-            # We use the default alphabet.
-            # See AMINO_ACIDS in foldx_utils.py
-            alphabet = self.get_setup_information().get_alphabet()
-
         # TODO: add support for a larger batch-size.
         f = FoldXStabilityBlackBox(
             wildtype_pdb_path=wildtype_pdb_path,
-            alphabet=alphabet,
             experiment_id=experiment_id,
             tmp_folder=tmp_folder,
             eager_repair=eager_repair,

src/poli/objective_repository/foldx_stability_and_sasa/register.py

@@ -25,6 +25,7 @@
 from poli.core.black_box_information import BlackBoxInformation
 from poli.core.problem import Problem
 from poli.core.abstract_problem_factory import AbstractProblemFactory
+from poli.core.exceptions import FoldXNotFoundException
 
 
 from poli.core.util.seeding import seed_python_numpy_and_torch
@@ -44,8 +45,6 @@ class FoldXStabilityAndSASABlackBox(AbstractBlackBox):
     -----------
     wildtype_pdb_path : Union[Path, List[Path]]
         The path(s) to the wildtype PDB file(s).
-    alphabet : List[str], optional
-        The alphabet of amino acids. Default is None.
     experiment_id : str, optional
         The ID of the experiment. Default is None.
     tmp_folder : Path, optional
@@ -73,7 +72,6 @@ class FoldXStabilityAndSASABlackBox(AbstractBlackBox):
     def __init__(
         self,
         wildtype_pdb_path: Union[Path, List[Path]],
-        alphabet: List[str] = None,
         experiment_id: str = None,
         tmp_folder: Path = None,
         eager_repair: bool = False,
@@ -90,6 +88,10 @@ def __init__(
             num_workers=num_workers,
             evaluation_budget=evaluation_budget,
         )
+        if not (Path.home() / "foldx" / "foldx").exists():
+            raise FoldXNotFoundException(
+                "FoldX wasn't found in ~/foldx/foldx. Please install it."
+            )
         if not force_isolation:
             try:
                 from poli.objective_repository.foldx_stability_and_sasa.isolated_function import (
@@ -181,7 +183,6 @@ def get_setup_information(self) -> BlackBoxInformation:
     def create(
         self,
         wildtype_pdb_path: Union[Path, List[Path]],
-        alphabet: List[str] = None,
         experiment_id: str = None,
         tmp_folder: Path = None,
         eager_repair: bool = False,
@@ -200,9 +201,6 @@ def create(
         ----------
         wildtype_pdb_path : Union[Path, List[Path]]
             Path or list of paths to the wildtype PDB files.
-        alphabet : List[str], optional
-            List of amino acid symbols. By default, we use the
-            20 amino acids shown in poli.core.util.proteins.defaults.
         experiment_id : str, optional
             Identifier for the experiment.
         tmp_folder : Path, optional
@@ -261,12 +259,8 @@ def create(
 
         # We use the default alphabet if None was provided.
         # See ENCODING in foldx_utils.py
-        if alphabet is None:
-            alphabet = self.get_setup_information().get_alphabet()
-
         f = FoldXStabilityAndSASABlackBox(
             wildtype_pdb_path=wildtype_pdb_path,
-            alphabet=alphabet,
             experiment_id=experiment_id,
             tmp_folder=tmp_folder,
             eager_repair=eager_repair,