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| name: Changelog Enforcer | ||
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| on: # yamllint disable-line rule:truthy | ||
| pull_request: | ||
| types: [opened, synchronize, reopened, ready_for_review, labeled, unlabeled] | ||
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| jobs: | ||
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| changelog: | ||
| runs-on: ubuntu-latest | ||
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| steps: | ||
| - uses: actions/checkout@v3 | ||
| - uses: dangoslen/changelog-enforcer@v3 | ||
| with: | ||
| skipLabels: 'skip-changelog' |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,5 @@ | ||
| """Class for working with MMCIF files.""" | ||
|
|
||
| # BioPandas | ||
| # Authors: Arian Jamasb <[email protected]>, | ||
| # Authors: Sebastian Raschka <[email protected]> | ||
|
|
@@ -69,56 +70,76 @@ def read_mmcif(self, path): | |
| self.code = self.data["entry"]["id"][0].lower() | ||
| return self | ||
|
|
||
| def fetch_mmcif(self, pdb_code: Optional[str] = None, uniprot_id: Optional[str] = None, source: str = "pdb"): | ||
| def fetch_mmcif( | ||
| self, | ||
| pdb_code: Optional[str] = None, | ||
| uniprot_id: Optional[str] = None, | ||
| source: str = "pdb", | ||
| ): | ||
| """Fetches mmCIF file contents from the Protein Databank at rcsb.org or AlphaFold database at https://alphafold.ebi.ac.uk/. | ||
| . | ||
| . | ||
| Parameters | ||
| ---------- | ||
| pdb_code : str, optional | ||
| A 4-letter PDB code, e.g., `"3eiy"` to retrieve structures from the PDB. Defaults to `None`. | ||
| Parameters | ||
| ---------- | ||
| pdb_code : str, optional | ||
| A 4-letter PDB code, e.g., `"3eiy"` to retrieve structures from the PDB. Defaults to `None`. | ||
| uniprot_id : str, optional | ||
| A UniProt Identifier, e.g., `"Q5VSL9"` to retrieve structures from the AF2 database. Defaults to `None`. | ||
| uniprot_id : str, optional | ||
| A UniProt Identifier, e.g., `"Q5VSL9"` to retrieve structures from the AF2 database. Defaults to `None`. | ||
| source : str | ||
| The source to retrieve the structure from | ||
| (`"pdb"`, `"alphafold2-v3"` or `"alphafold2-v4"`). Defaults to `"pdb"`. | ||
| source : str | ||
| The source to retrieve the structure from | ||
| (`"pdb"`, `"alphafold2-v3"` or `"alphafold2-v4"`). Defaults to `"pdb"`. | ||
| Returns | ||
| --------- | ||
| self | ||
| Returns | ||
| --------- | ||
| self | ||
| """ | ||
| # Sanitize input | ||
| invalid_input_identifier_1 = pdb_code is None and uniprot_id is None | ||
| invalid_input_identifier_2 = pdb_code is not None and uniprot_id is not None | ||
| invalid_input_combination_1 = uniprot_id is not None and source == "pdb" | ||
| invalid_input_identifier_2 = ( | ||
| pdb_code is not None and uniprot_id is not None | ||
| ) | ||
| invalid_input_combination_1 = ( | ||
| uniprot_id is not None and source == "pdb" | ||
| ) | ||
| invalid_input_combination_2 = pdb_code is not None and source in { | ||
| "alphafold2-v3", "alphafold2-v4"} | ||
| "alphafold2-v3", | ||
| "alphafold2-v4", | ||
| } | ||
|
|
||
| if invalid_input_identifier_1 or invalid_input_identifier_2: | ||
| raise ValueError( | ||
| "Please provide either a PDB code or a UniProt ID.") | ||
| "Please provide either a PDB code or a UniProt ID." | ||
| ) | ||
|
|
||
| if invalid_input_combination_1: | ||
| raise ValueError( | ||
| "Please use a 'pdb_code' instead of 'uniprot_id' for source='pdb'.") | ||
| "Please use a 'pdb_code' instead of 'uniprot_id' for source='pdb'." | ||
| ) | ||
| elif invalid_input_combination_2: | ||
| raise ValueError( | ||
| f"Please use a 'uniprot_id' instead of 'pdb_code' for source={source}.") | ||
| f"Please use a 'uniprot_id' instead of 'pdb_code' for source={source}." | ||
| ) | ||
|
|
||
| if source == "pdb": | ||
| self.mmcif_path, self.mmcif_text = self._fetch_mmcif(pdb_code) | ||
| elif source == "alphafold2-v3": | ||
| af2_version = 3 | ||
| self.mmcif_path, self.mmcif_text = self._fetch_af2(uniprot_id, af2_version) | ||
| self.mmcif_path, self.mmcif_text = self._fetch_af2( | ||
| uniprot_id, af2_version | ||
| ) | ||
| elif source == "alphafold2-v4": | ||
| af2_version = 4 | ||
| self.mmcif_path, self.mmcif_text = self._fetch_af2(uniprot_id, af2_version) | ||
| self.mmcif_path, self.mmcif_text = self._fetch_af2( | ||
| uniprot_id, af2_version | ||
| ) | ||
| else: | ||
| raise ValueError(f"Invalid source: {source}." | ||
| " Please use one of 'pdb', 'alphafold2-v3' or 'alphafold2-v4'.") | ||
| raise ValueError( | ||
| f"Invalid source: {source}." | ||
| " Please use one of 'pdb', 'alphafold2-v3' or 'alphafold2-v4'." | ||
| ) | ||
|
|
||
| self._df = self._construct_df(text=self.mmcif_text) | ||
| return self | ||
|
|
@@ -129,7 +150,8 @@ def _construct_df(self, text: str): | |
| self.data = data | ||
| df: Dict[str, pd.DataFrame] = {} | ||
| full_df = pd.DataFrame.from_dict( | ||
| data["atom_site"], orient="index").transpose() | ||
| data["atom_site"], orient="index" | ||
| ).transpose() | ||
| full_df = full_df.astype(mmcif_col_types, errors="ignore") | ||
| df["ATOM"] = pd.DataFrame(full_df[full_df.group_PDB == "ATOM"]) | ||
| df["HETATM"] = pd.DataFrame(full_df[full_df.group_PDB == "HETATM"]) | ||
|
|
@@ -148,8 +170,9 @@ def _fetch_mmcif(pdb_code): | |
| response = urlopen(url) | ||
| txt = response.read() | ||
| txt = ( | ||
| txt.decode( | ||
| "utf-8") if sys.version_info[0] >= 3 else txt.encode("ascii") | ||
| txt.decode("utf-8") | ||
| if sys.version_info[0] >= 3 | ||
| else txt.encode("ascii") | ||
| ) | ||
| except HTTPError as e: | ||
| print(f"HTTP Error {e.code}") | ||
|
|
@@ -166,11 +189,15 @@ def _fetch_af2(uniprot_id: str, af2_version: int = 3): | |
| try: | ||
| response = urlopen(url) | ||
| txt = response.read() | ||
| txt = txt.decode('utf-8') if sys.version_info[0] >= 3 else txt.encode('ascii') | ||
| txt = ( | ||
| txt.decode("utf-8") | ||
| if sys.version_info[0] >= 3 | ||
| else txt.encode("ascii") | ||
| ) | ||
| except HTTPError as e: | ||
| print(f'HTTP Error {e.code}') | ||
| print(f"HTTP Error {e.code}") | ||
| except URLError as e: | ||
| print(f'URL Error {e.args}') | ||
| print(f"URL Error {e.args}") | ||
| return url, txt | ||
|
|
||
| @staticmethod | ||
|
|
@@ -184,7 +211,8 @@ def _read_mmcif(path): | |
| openf = gzip.open | ||
| else: | ||
| allowed_formats = ", ".join( | ||
| (".cif", ".cif.gz", ".mmcif", ".mmcif.gz")) | ||
| (".cif", ".cif.gz", ".mmcif", ".mmcif.gz") | ||
| ) | ||
| raise ValueError( | ||
| f"Wrong file format; allowed file formats are {allowed_formats}" | ||
| ) | ||
|
|
@@ -194,8 +222,9 @@ def _read_mmcif(path): | |
|
|
||
| if path.endswith(".gz"): | ||
| txt = ( | ||
| txt.decode( | ||
| "utf-8") if sys.version_info[0] >= 3 else txt.encode("ascii") | ||
| txt.decode("utf-8") | ||
| if sys.version_info[0] >= 3 | ||
| else txt.encode("ascii") | ||
| ) | ||
| return path, txt | ||
|
|
||
|
|
@@ -271,14 +300,19 @@ def _get_mainchain( | |
| def _get_hydrogen(df, invert): | ||
| """Return only hydrogen atom entries from a DataFrame""" | ||
| return ( | ||
| df[(df["type_symbol"] != "H")] if invert else df[( | ||
| df["type_symbol"] == "H")] | ||
| df[(df["type_symbol"] != "H")] | ||
| if invert | ||
| else df[(df["type_symbol"] == "H")] | ||
| ) | ||
|
|
||
| @staticmethod | ||
| def _get_heavy(df, invert): | ||
| """Return only heavy atom entries from a DataFrame""" | ||
| return df[df["type_symbol"] == "H"] if invert else df[df["type_symbol"] != "H"] | ||
| return ( | ||
| df[df["type_symbol"] == "H"] | ||
| if invert | ||
| else df[df["type_symbol"] != "H"] | ||
| ) | ||
|
|
||
| @staticmethod | ||
| def _get_calpha(df, invert, atom_col: str = "auth_atom_id"): | ||
|
|
@@ -288,7 +322,11 @@ def _get_calpha(df, invert, atom_col: str = "auth_atom_id"): | |
| @staticmethod | ||
| def _get_carbon(df, invert): | ||
| """Return carbon atom entries from a DataFrame""" | ||
| return df[df["type_symbol"] != "C"] if invert else df[df["type_symbol"] == "C"] | ||
| return ( | ||
| df[df["type_symbol"] != "C"] | ||
| if invert | ||
| else df[df["type_symbol"] == "C"] | ||
| ) | ||
|
|
||
| def amino3to1( | ||
| self, | ||
|
|
@@ -339,8 +377,9 @@ def amino3to1( | |
| indices.append(ind) | ||
| cmp = num | ||
|
|
||
| transl = tmp.iloc[indices][residue_col].map( | ||
| amino3to1dict).fillna(fillna) | ||
| transl = ( | ||
| tmp.iloc[indices][residue_col].map(amino3to1dict).fillna(fillna) | ||
| ) | ||
|
|
||
| return pd.concat((tmp.iloc[indices][chain_col], transl), axis=1) | ||
|
|
||
|
|
@@ -425,7 +464,9 @@ def distance(self, xyz=(0.00, 0.00, 0.00), records=("ATOM", "HETATM")): | |
|
|
||
| return np.sqrt( | ||
| np.sum( | ||
| df[["Cartn_x", "Cartn_y", "Cartn_z"]].subtract(xyz, axis=1) ** 2, axis=1 | ||
| df[["Cartn_x", "Cartn_y", "Cartn_z"]].subtract(xyz, axis=1) | ||
| ** 2, | ||
| axis=1, | ||
| ) | ||
| ) | ||
|
|
||
|
|
@@ -451,7 +492,9 @@ def distance_df(df, xyz=(0.00, 0.00, 0.00)): | |
| """ | ||
| return np.sqrt( | ||
| np.sum( | ||
| df[["Cartn_x", "Cartn_y", "Cartn_z"]].subtract(xyz, axis=1) ** 2, axis=1 | ||
| df[["Cartn_x", "Cartn_y", "Cartn_z"]].subtract(xyz, axis=1) | ||
| ** 2, | ||
| axis=1, | ||
| ) | ||
| ) | ||
|
|
||
|
|
@@ -485,7 +528,11 @@ def read_mmcif_from_list(self, mmcif_lines): | |
| self.code = self.data["entry"]["id"][0].lower() | ||
| return self | ||
|
|
||
| def convert_to_pandas_pdb(self, offset_chains: bool = True, records: List[str] = ["ATOM", "HETATM"]) -> PandasPdb: | ||
| def convert_to_pandas_pdb( | ||
| self, | ||
| offset_chains: bool = True, | ||
| records: List[str] = ["ATOM", "HETATM"], | ||
| ) -> PandasPdb: | ||
| """Returns a PandasPdb object with the same data as the PandasMmcif | ||
| object. | ||
|
|
@@ -525,10 +572,15 @@ def convert_to_pandas_pdb(self, offset_chains: bool = True, records: List[str] = | |
|
|
||
| # Update atom numbers | ||
| if offset_chains: | ||
| offsets = pandaspdb.df["ATOM"]["chain_id"].astype( | ||
| "category").cat.codes | ||
| pandaspdb.df["ATOM"]["atom_number"] = pandaspdb.df["ATOM"]["atom_number"] + offsets | ||
| offsets = ( | ||
| pandaspdb.df["ATOM"]["chain_id"].astype("category").cat.codes | ||
| ) | ||
| pandaspdb.df["ATOM"]["atom_number"] = ( | ||
| pandaspdb.df["ATOM"]["atom_number"] + offsets | ||
| ) | ||
| hetatom_offset = offsets.max() + 1 | ||
| pandaspdb.df["HETATM"]["atom_number"] = pandaspdb.df["HETATM"]["atom_number"] + hetatom_offset | ||
| pandaspdb.df["HETATM"]["atom_number"] = ( | ||
| pandaspdb.df["HETATM"]["atom_number"] + hetatom_offset | ||
| ) | ||
|
|
||
| return pandaspdb | ||
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