Updates the index, getting started and basics according to the current implementation

Author: miguelgondu

docs/protein-optimization/_autosummary/poli.core.util.alignment.is_aligned.rst

@@ -0,0 +1,29 @@
+poli.core.util.alignment.is\_aligned
+====================================
+
+.. automodule:: poli.core.util.alignment.is_aligned
+
+   
+   
+   
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      is_aligned_input
+   
+   
+
+   
+   
+   
+
+   
+   
+   
+
+
+

docs/protein-optimization/_autosummary/poli.core.util.alignment.rst

@@ -0,0 +1,31 @@
+poli.core.util.alignment
+========================
+
+.. automodule:: poli.core.util.alignment
+
+   
+   
+   
+
+   
+   
+   
+
+   
+   
+   
+
+   
+   
+   
+
+
+
+.. rubric:: Modules
+
+.. autosummary::
+   :toctree:
+   :recursive:
+
+   poli.core.util.alignment.is_aligned
+

docs/protein-optimization/_autosummary/poli.core.util.rst

@@ -1,4 +1,4 @@
-poli.core.util
+poli.core.util
 ==============
 
 .. automodule:: poli.core.util
@@ -28,6 +28,7 @@ poli.core.util
    :recursive:
 
    poli.core.util.abstract_observer
+   poli.core.util.alignment
    poli.core.util.batch
    poli.core.util.chemistry
    poli.core.util.external_observer

docs/protein-optimization/_autosummary/poli.objective_repository.gfp_cbas.gfp_gp.rst

@@ -0,0 +1,29 @@
+poli.objective\_repository.gfp\_cbas.gfp\_gp
+============================================
+
+.. automodule:: poli.objective_repository.gfp_cbas.gfp_gp
+
+   
+   
+   
+
+   
+   
+   
+
+   
+   
+   .. rubric:: Classes
+
+   .. autosummary::
+   
+      SequenceGP
+   
+   
+
+   
+   
+   
+
+
+

docs/protein-optimization/_autosummary/poli.objective_repository.gfp_cbas.rst

@@ -1,4 +1,4 @@
-poli.objective\_repository.gfp\_cbas
+poli.objective\_repository.gfp\_cbas
 ====================================
 
 .. automodule:: poli.objective_repository.gfp_cbas
@@ -30,6 +30,7 @@ poli.objective\_repository.gfp\_cbas
    poli.objective_repository.gfp_cbas.abstract_vae_wrapper
    poli.objective_repository.gfp_cbas.cbas_alphabet_preprocessing
    poli.objective_repository.gfp_cbas.cbas_wrapper
+   poli.objective_repository.gfp_cbas.gfp_gp
    poli.objective_repository.gfp_cbas.make_vae
    poli.objective_repository.gfp_cbas.register
 

docs/protein-optimization/_autosummary/poli.tests.docs_examples.test_objective_functions.rst

@@ -1,4 +1,4 @@
-poli.tests.docs\_examples.test\_objective\_functions
+poli.tests.docs\_examples.test\_objective\_functions
 ====================================================
 
 .. automodule:: poli.tests.docs_examples.test_objective_functions
@@ -15,9 +15,7 @@ poli.tests.docs\_examples.test\_objective\_functions
 
       test_aloha_example
       test_logp_example
-      test_logp_example_using_strings
       test_qed_example
-      test_qed_example_using_strings
       test_white_noise_example
 
 

docs/protein-optimization/_autosummary/poli.tests.registry.basic_objectives.test_budget_exhaustion.rst

@@ -0,0 +1,31 @@
+poli.tests.registry.basic\_objectives.test\_budget\_exhaustion
+==============================================================
+
+.. automodule:: poli.tests.registry.basic_objectives.test_budget_exhaustion
+
+   
+   
+   
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      test_budget_exhaustion_exception
+      test_budget_exhausts
+      test_num_evaluation_tracks_correctly
+   
+   
+
+   
+   
+   
+
+   
+   
+   
+
+
+

docs/protein-optimization/_autosummary/poli.tests.registry.chemistry.test_chemistry_objectives.rst

@@ -0,0 +1,38 @@
+poli.tests.registry.chemistry.test\_chemistry\_objectives
+=========================================================
+
+.. automodule:: poli.tests.registry.chemistry.test_chemistry_objectives
+
+   
+   
+   
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      test_force_registering_logp
+      test_force_registering_qed
+      test_force_registering_qed_with_context_manager
+      test_logp_is_available
+      test_penalized_logp_lambo
+      test_qed_is_available
+      test_querying_dockstring_using_selfies
+      test_querying_dockstring_using_smiles
+      test_registering_logp
+      test_registering_qed
+   
+   
+
+   
+   
+   
+
+   
+   
+   
+
+
+

docs/protein-optimization/_autosummary/poli.tests.registry.proteins.rst

@@ -28,5 +28,6 @@ poli.tests.registry.proteins
    :recursive:
 
    poli.tests.registry.proteins.test_foldx
+   poli.tests.registry.proteins.test_foldx_rfp_lambo
    poli.tests.registry.proteins.test_rasp
 

docs/protein-optimization/_autosummary/poli.tests.registry.proteins.test_foldx.rst

@@ -0,0 +1,36 @@
+poli.tests.registry.proteins.test\_foldx
+========================================
+
+.. automodule:: poli.tests.registry.proteins.test_foldx
+
+   
+   
+   
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      test_foldx_from_non_repaired_file
+      test_foldx_from_repaired_file
+      test_foldx_stability_is_available
+      test_force_registering_foldx_sasa
+      test_force_registering_foldx_stability
+      test_registering_foldx_sasa
+      test_registering_foldx_stability
+      test_registering_foldx_stability_and_sasa
+   
+   
+
+   
+   
+   
+
+   
+   
+   
+
+
+