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.spelling

+Biopython
+CIF
+FastA
+Jupyter
+MSA
+ModelCIF
+PAE
+PDB
+PPI
+coevolution
+modeled
+modeling
+multimer
+polypeptide
+pre
+repo
+reproducibility
+subdirectory

convert_to_modelcif.py

@@ -77,7 +77,7 @@ class _GlobalPTM(modelcif.qa_metric.Global, modelcif.qa_metric.PTM):
 
 
 class _GlobalIPTM(modelcif.qa_metric.Global, modelcif.qa_metric.IpTM):
-    # python-modelcif reads the first line of class-doc has description of a
+    # `python-modelcif` reads the first line of class-doc has description of a
     # score, so we need to allow long lines, here.
     # pylint: disable=line-too-long
     """Predicted protein-protein interface score, based on the TM-score score in [0,1]."""
@@ -111,7 +111,7 @@ class _LocalPairwisePAE(modelcif.qa_metric.LocalPairwise, _PAE):
 
 
 class _Biopython2ModelCIF(modelcif.model.AbInitioModel):
-    """Map Biopython PDB.Structure object to ihm.model"""
+    """Map Biopython `PDB.Structure()` object to `ihm.model()`."""
 
     def __init__(self, *args, **kwargs):
         """Initialise a model"""
@@ -152,7 +152,7 @@ class _Biopython2ModelCIF(modelcif.model.AbInitioModel):
         )
 
         # local scores
-        # iterate polypetide chains
+        # iterate polypeptide chains
         # local PLDDT
         i = 0
         lpae = []
@@ -239,7 +239,7 @@ def _get_step_output_method_type(method_type, protocol_steps):
     """Get the output of a protocol step of a certain type."""
     for step in protocol_steps:
         if step.method_type == method_type:
-            # modelcif.data.DataGroup is some kind of list
+            # `modelcif.data.DataGroup()` is some kind of list
             if isinstance(step.output_data, list):
                 return step.output_data
             return modelcif.data.DataGroup(step.output_data)
@@ -309,12 +309,16 @@ def _get_modelcif_protocol(
                 # add software w/o individual parameters
                 sw_grp.append(sw_dict[pss])
                 # add software with individual parameters
+                # Commented out code does not need spelling check, so disable
+                # it in Pylint
+                # pylint: disable=wrong-spelling-in-comment
                 # sw_grp.append(
                 #     modelcif.SoftwareWithParameters(
                 #         sw_dict[pss],
                 #         [modelcif.SoftwareParameter(<name>, <value>)],
                 #     )
                 # )
+                # pylint: enable=wrong-spelling-in-comment
         # ToDo: make sure AlphaPulldown is first in the SoftwareGroup() list,
         #       AlphaFold second; that influences citation order in the ModelCIF
         #       file.
@@ -334,7 +338,7 @@ def _get_modelcif_protocol(
 
 
 def _get_modelcif_ref_dbs(meta_json):
-    """Get sequence DBs used for monomer features."""
+    """Get sequence databases used for monomer features."""
     # vendor formatting for DB names/ URLs, extend on KeyError
     db_info = {
         "uniref90": {
@@ -435,13 +439,13 @@ def _store_as_modelcif(
     #        pickle files quickly exceeds reasonable storage use
     #      - 'modeling' (run_multimer_jobs.py), are the four modes reflected by
     #        the JSON data/ does the JSON data look different for each mode?
-    #      - are the scores only calculated by alpha-analysis.sif or do they
+    #      - are the scores only calculated by `alpha-analysis.sif` or do they
     #        come out of run_multimer_jobs.py? Does this go into its own step?
     #      - what about including the tabular summary?
     #      - model selection: only if just a certain model is translated to
     #        ModelCIF, or mix it with scoring step?
     #
-    #      - cancer-PPI-domains has 'coevolutin MSA'
+    #      - cancer-PPI-domains has 'coevolution MSA'
     #      - then modelling
     #      - do we have an example with a split MSA & modelling step?
     #      - model selection like for Tara
@@ -457,7 +461,7 @@ def _store_as_modelcif(
         )
     )
 
-    # write modelcif.System to file
+    # write `modelcif.System()` to file
     # NOTE: this will dump PAE on path provided in add_scores
     # -> hence we cheat by changing path and back while being exception-safe...
     oldpwd = os.getcwd()
@@ -484,7 +488,7 @@ def _store_as_modelcif(
 
 
 def _compress_cif_file(cif_file):
-    """Compress cif file and delete original."""
+    """Compress CIF file and delete original."""
     with open(cif_file, "rb") as f_in:
         with gzip.open(cif_file + ".gz", "wb") as f_out:
             shutil.copyfileobj(f_in, f_out)
@@ -495,7 +499,7 @@ def _get_model_details(cmplx_name: str, data_json: dict) -> str:
     """Get the model description."""
     ap_versions = []
     af2_version = None
-    for mnmr in data_json["__meta__"]:  # mnmr = monomer
+    for mnmr in data_json["__meta__"]:  # `mnmr = monomer`
         if (
             data_json["__meta__"][mnmr]["software"]["AlphaPulldown"]["version"]
             not in ap_versions
@@ -632,7 +636,7 @@ def _get_scores(cif_json: dict, scr_file: str) -> None:
 
 
 def _get_software_data(meta_json: dict) -> list:
-    """Turn meta data about software into modelcif.Software objects."""
+    """Turn meta data about software into `modelcif.Software()` objects."""
     cite_hhsuite = ihm.Citation(
         pmid="31521110",
         title="HH-suite3 for fast remote homology detection and deep "
@@ -651,7 +655,7 @@ def _get_software_data(meta_json: dict) -> list:
         ],
         doi="10.1186/s12859-019-3019-7",
     )
-    # {key from json: dict needed to produce sw entry plus internal key}
+    # {key from JSON: dict needed to produce software entry plus internal key}
     sw_data = {
         "AlphaFold": modelcif.Software(
             "AlphaFold-Multimer",
@@ -811,7 +815,7 @@ def _get_protocol_steps(modelcif_json):
     # model selection step <- ask if there is automated selection, if only
     # manual, skip this step here?
 
-    # ToDo: Example 1 in the GitHub repo has a 3rd step: "Evalutaion and
+    # ToDo: Example 1 in the GitHub repo has a 3rd step: "Evaluation and
     #       visualisation"
 
     return protocol
@@ -980,6 +984,3 @@ if __name__ == "__main__":
 # From former discussions:
 # - including Jupyter notebooks would require adding the pickle files to the
 #   associated files (too much storage needed for that)
-
-#  LocalWords:  ToDo AlphaPulldown PAEs dir struct coevolution MSA py modeling
-#  LocalWords:  multimer sif Jupyter aa MSAs

pyproject.toml

@@ -21,4 +21,19 @@ max-line-length = 81
 [tool.pylint.deprecated_builtins]
 # We want to use proper logging, so we can control *ALL* output bei the Abseil
 # logger, hence: deprecate 'print'
-bad-functions = ["map", "filter", "print"]
\ No newline at end of file
+bad-functions = ["map", "filter", "print"]
+
+# Run the spell check every once in a while, having it enabled always, is too
+# annoying.
+#[tool.pylint.spelling]
+#max-spelling-suggestions = 4
+#
+#spelling-dict = "en_GB"
+#
+#spelling-ignore-comment-directives = "fmt: on,fmt: off,noqa:,noqa,nosec,isort:skip,mypy:"
+#
+#spelling-ignore-words = ""
+#
+#spelling-private-dict-file = ".spelling"
+#
+#spelling-store-unknown-words = false
\ No newline at end of file