biointerface 0.2.1__tar.gz → 0.2.3__tar.gz

{biointerface-0.2.1 → biointerface-0.2.3}/CONTRIBUTING.rst

@@ -110,7 +110,7 @@ Before you submit a pull request, check that it meets these guidelines:
 2. If the pull request adds functionality, the docs should be updated. Put
    your new functionality into a function with a docstring, and add the
    feature to the list in README.rst.
-3. The pull request should work for Python 3.8, 3.9, 3.10, 3.11, 3.12 and 3.13,
+3. The pull request should work for Python 3.10, 3.11, 3.12 and 3.13,
    and for PyPy. Make sure that the tests pass for all supported Python versions.
 
 Tips

biointerface-0.2.3/HISTORY.rst

@@ -0,0 +1,42 @@
+=======
+History
+=======
+
+0.1.0 (2025-02-08)
+------------------
+
+* First release on PyPI.
+
+
+0.2.0 (2025-02-28)
+------------------
+
+* Features: Interface class, with getter methods for atoms, dataframes etc
+
+
+0.2.1 (2025-03-1)
+------------------
+
+* Gitlab CI
+
+
+0.2.2 (2025-03-04)
+------------------
+
+* Interface methods to get residues
+
+* Interface raise error condition in case of no protein in the structure
+
+* Coverage badge on README
+
+* Full documentation
+
+
+0.2.3 (2025-03-05)
+------------------
+
+* fix: bump-my-version was updating pdbnucleicacids version too
+
+* fix: import classes instead of modules
+
+* chore: remove old tox environments

{biointerface-0.2.1 → biointerface-0.2.3}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.2
 Name: biointerface
-Version: 0.2.1
-Summary: BioInterface is a python package capable of extracting Protein-DNA interfaces from PDB/mmCif structures.
+Version: 0.2.3
+Summary: BioInterface is a Biopython based package that extracts Protein-DNA interfaces in a PDB structures.
 Author-email: Alessandro Pandolfi <alessandro.pandolfi@protonmail.com>
 Maintainer-email: Alessandro Pandolfi <alessandro.pandolfi@protonmail.com>
 License: MIT license
@@ -33,6 +33,10 @@ BioInterface
         :target: https://biointerface.readthedocs.io/en/latest/?version=latest
         :alt: Documentation Status
 
+.. image:: https://gitlab.com/MorfeoRenai/biointerface/badges/main/coverage.svg
+        :target: https://gitlab.com/MorfeoRenai/biointerface/-/commits/main
+        :alt: Coverage Status
+
 .. image:: https://pyup.io/repos/github/MorfeoRenai/biointerface/shield.svg
      :target: https://pyup.io/repos/github/MorfeoRenai/biointerface/
      :alt: Updates
@@ -62,17 +66,17 @@ You can extract a single Protein-DNA interface from a single protein chain.
 
     from Bio.PDB.MMCIFParser import MMCIFParser
     from biointerface import Interface, build_interfaces
-    
+
     # parse and build structure with Biopython
     parser = MMCIFParser()
     structure = parser.get_structure(
         structure_id="1A02", filename="1a02-assembly1.cif"
     )
-    
+
     # extract interface from a specific protein chain
     face = Interface(
         structure=structure,
-        protein_chain_id="A",
+        protein_chain_id="F",
         search_radius=5.0
     )
     face
@@ -84,9 +88,25 @@ You can extract a single Protein-DNA interface from a single protein chain.
 Check the official documentation for more information.
 
 
+Feaures
+-------
+
+* Extract one specific Protein-DNA interface in a PDB structure, given a protein chain id;
+
+* Extract all Protein-DNA interfaces in a PDB structure;
+
+* Get all interacting residues in a interface;
+
+* Get all interacting atoms in a interface;
+
+* Interface data as ``pandas`` DataFrame;
+
+
 TODO
 --------
 
+* Extract continous bound DNA sequence
+
 * Proper tests (WIP)
 
 

{biointerface-0.2.1 → biointerface-0.2.3}/README.rst

@@ -10,6 +10,10 @@ BioInterface
         :target: https://biointerface.readthedocs.io/en/latest/?version=latest
         :alt: Documentation Status
 
+.. image:: https://gitlab.com/MorfeoRenai/biointerface/badges/main/coverage.svg
+        :target: https://gitlab.com/MorfeoRenai/biointerface/-/commits/main
+        :alt: Coverage Status
+
 .. image:: https://pyup.io/repos/github/MorfeoRenai/biointerface/shield.svg
      :target: https://pyup.io/repos/github/MorfeoRenai/biointerface/
      :alt: Updates
@@ -39,17 +43,17 @@ You can extract a single Protein-DNA interface from a single protein chain.
 
     from Bio.PDB.MMCIFParser import MMCIFParser
     from biointerface import Interface, build_interfaces
-    
+
     # parse and build structure with Biopython
     parser = MMCIFParser()
     structure = parser.get_structure(
         structure_id="1A02", filename="1a02-assembly1.cif"
     )
-    
+
     # extract interface from a specific protein chain
     face = Interface(
         structure=structure,
-        protein_chain_id="A",
+        protein_chain_id="F",
         search_radius=5.0
     )
     face
@@ -61,9 +65,25 @@ You can extract a single Protein-DNA interface from a single protein chain.
 Check the official documentation for more information.
 
 
+Feaures
+-------
+
+* Extract one specific Protein-DNA interface in a PDB structure, given a protein chain id;
+
+* Extract all Protein-DNA interfaces in a PDB structure;
+
+* Get all interacting residues in a interface;
+
+* Get all interacting atoms in a interface;
+
+* Interface data as ``pandas`` DataFrame;
+
+
 TODO
 --------
 
+* Extract continous bound DNA sequence
+
 * Proper tests (WIP)
 
 

biointerface-0.2.3/docs/usage.rst

@@ -0,0 +1,194 @@
+=====
+Usage
+=====
+
+To use BioInterface in a Python project:
+
+.. code-block:: python
+
+    import biointerface
+
+
+Extract One Protein-DNA Interface
+---------------------------------
+
+You can extract a single Protein-DNA interface from a single protein chain.
+
+.. code-block:: python
+
+    from Bio.PDB.PDBList import PDBList
+    from Bio.PDB.MMCIFParser import MMCIFParser
+    from biointerface import Interface
+
+    # retrive file from PDB using Biopython
+    pdbl = PDBList()
+    pdbl.retrieve_pdb_file(pdb_code="1A02", pdir=".")
+    pdbl.retrieve_assembly_file(pdb_code="1A02", assembly_num=1, pdir=".")
+    # ... or else use your own
+
+    # parse and build structure with Biopython
+    parser = MMCIFParser()
+    structure = parser.get_structure(
+        structure_id="1A02", filename="1a02-assembly1.cif"
+    )
+
+    # extract interface from a specific protein chain
+    face = Interface(
+        structure=structure,
+        protein_chain_id="A",
+        search_radius=5.0
+    )
+    face
+
+
+.. code-block:: console
+
+    <Interface chains=F:BA contacts=258 search_radius=5.0>
+
+
+Extract All Protein-DNA Interfaces
+----------------------------------
+
+You can also extract all Protein-DNA interface from an entire structure.
+
+.. code-block:: python
+
+    from biointerface import build_interfaces
+
+    face_list = build_interfaces(structure=structure, search_radius=5.0)
+    face_list
+
+.. code-block:: console
+
+    [<Interface chains=J:BA contacts=189 search_radius=5.0>,
+     <Interface chains=F:BA contacts=258 search_radius=5.0>,
+     <Interface chains=N:BA contacts=529 search_radius=5.0>]
+
+
+Get All Interacting Residues
+----------------------------
+
+You can access all interacting residues in a Protein-DNA interface, both
+aminoacids and nucleotides.
+
+.. code-block:: python
+
+    face.get_aminoacids()
+
+.. code-block:: console
+
+    [<Residue ARG het=  resseq=144 icode= >,
+     <Residue ALA het=  resseq=151 icode= >,
+     <Residue ARG het=  resseq=158 icode= >,
+     <Residue ASN het=  resseq=147 icode= >,
+     <Residue LYS het=  resseq=148 icode= >,
+     <Residue LYS het=  resseq=153 icode= >,
+     <Residue SER het=  resseq=154 icode= >,
+     <Residue ARG het=  resseq=155 icode= >,
+     <Residue ALA het=  resseq=150 icode= >,
+     <Residue ARG het=  resseq=143 icode= >,
+     <Residue ARG het=  resseq=146 icode= >,
+     <Residue ARG het=  resseq=157 icode= >]
+
+.. code-block:: python
+
+    face.get_nucleotides()
+
+.. code-block:: console
+
+    [<Residue DT het=  resseq=4015 icode= >,
+     <Residue DC het=  resseq=4016 icode= >,
+     <Residue DT het=  resseq=4014 icode= >,
+     <Residue DG het=  resseq=5007 icode= >,
+     <Residue DA het=  resseq=4017 icode= >,
+     <Residue DT het=  resseq=4018 icode= >,
+     <Residue DT het=  resseq=5006 icode= >,
+     <Residue DC het=  resseq=5003 icode= >,
+     <Residue DA het=  resseq=5005 icode= >,
+     <Residue DG het=  resseq=4012 icode= >,
+     <Residue DT het=  resseq=4013 icode= >,
+     <Residue DT het=  resseq=5004 icode= >]
+
+
+Get All Interacting Atoms
+-------------------------
+
+You can access all interacting atoms in a Protein-DNA interface.
+
+First of all you can get all interacting atoms as atom pairs.
+
+.. code-block:: python
+
+    contacts = face.get_atomic_contacts()
+    contacts[:5]
+
+.. code-block:: console
+
+    [(<Atom C5'>, <Atom NZ>),
+     (<Atom C5'>, <Atom CE>),
+     (<Atom O5'>, <Atom NZ>),
+     (<Atom O5'>, <Atom CE>),
+     (<Atom O5'>, <Atom CD>)]
+
+You can also get all Protein or DNA interacting atoms, independently.
+
+.. code-block:: python
+
+    atoms = face.get_protein_atoms()
+    atoms[:5]
+
+.. code-block:: console
+
+    [<Atom CZ>, <Atom N>, <Atom NE>, <Atom CD>, <Atom CG>]
+
+.. code-block:: python
+
+    atoms = face.get_dna_atoms()
+    atoms[:5]
+
+.. code-block:: console
+
+    [<Atom P>, <Atom C5'>, <Atom C6>, <Atom C5>, <Atom C4'>]
+
+
+Interface Data as DataFrame
+---------------------------
+
+You can get all Protein-DNA interface features as a ``pandas`` DataFrame.
+
+.. code-block:: python
+
+    df = face.get_interface_data()
+    df.columns
+
+.. code-block:: console
+
+    Index(['protein_chain_id', 'prot_res_hetfield', 'prot_res_number',
+       'prot_res_icode', 'prot_res_name', 'prot_atom_name', 'prot_atom_altloc',
+       'prot_atom_element', 'prot_atom_coord_x', 'prot_atom_coord_y',
+       'prot_atom_coord_z', 'dna_chain_id', 'dna_res_hetfield',
+       'dna_res_number', 'dna_res_icode', 'dna_res_name', 'dna_atom_name',
+       'dna_atom_altloc', 'dna_atom_element', 'dna_atom_coord_x',
+       'dna_atom_coord_y', 'dna_atom_coord_z', 'euclidian_distance'],
+      dtype='object')
+
+.. code-block:: python
+
+    df
+
+.. code-block:: console
+
+        protein_chain_id prot_res_hetfield  prot_res_number  ... euclidian_distance
+    0                  F                                148  ...           4.458498
+    1                  F                                148  ...           3.964944
+    2                  F                                148  ...           4.066739
+    3                  F                                148  ...           3.271817
+    4                  F                                148  ...           4.217340
+    ...              ...               ...              ...  ...                ...
+    253                F                                154  ...           4.644194
+    254                F                                150  ...           4.594888
+    255                F                                150  ...           4.784895
+    256                F                                157  ...           4.904832
+    257                F                                157  ...           4.299844
+
+    [258 rows x 23 columns]

{biointerface-0.2.1 → biointerface-0.2.3}/pyproject.toml

@@ -4,8 +4,8 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "biointerface"
-version = "0.2.1"
-description = "BioInterface is a python package capable of extracting Protein-DNA interfaces from PDB/mmCif structures."
+version = "0.2.3"
+description = "BioInterface is a Biopython based package that extracts Protein-DNA interfaces in a PDB structures."
 readme = "README.rst"
 authors = [
   {name = "Alessandro Pandolfi", email = "alessandro.pandolfi@protonmail.com"}
@@ -32,7 +32,6 @@ dev = [
 ]
 
 [project.urls]
-
 bugs = "https://gitlab.com/MorfeoRenai/biointerface/-/issues"
 changelog = "https://gitlab.com/MorfeoRenai/biointerface/-/blob/main/HISTORY.rst"
 homepage = "https://gitlab.com/MorfeoRenai/biointerface"
@@ -44,8 +43,6 @@ package-dir = {"" = "src"}
 "*" = ["*.*"]
 
 
-
-
 # Mypy
 # ----
 
@@ -64,8 +61,6 @@ allow_untyped_defs = true
 disable_error_code = "attr-defined"
 
 
-
-
 # pytest
 # ----
 
@@ -77,13 +72,11 @@ testpaths = [
 ]
 
 
-
-
 # bump-my-version
 # ----
 
 [tool.bumpversion]
-current_version = "0.2.1"
+current_version = "0.2.3"
 parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
 serialize = ["{major}.{minor}.{patch}"]
 search = "{current_version}"
@@ -91,7 +84,7 @@ replace = "{new_version}"
 regex = false
 ignore_missing_version = false
 ignore_missing_files = false
-tag = false
+tag = true
 sign_tags = false
 tag_name = "v{new_version}"
 tag_message = "Bump version: {current_version} → {new_version}"
@@ -110,10 +103,8 @@ replace = "{new_version}"
 
 [[tool.bumpversion.files]]
 filename = "pyproject.toml"
-search = "{current_version}"
-replace = "{new_version}"
-
-
+search = 'version = "{current_version}"'
+replace = 'version = "{new_version}"'
 
 
 # ruff
@@ -131,8 +122,6 @@ show-fixes = true
 extend-select = ["E501"]
 
 
-
-
 # tox
 # ----
 
@@ -140,7 +129,7 @@ extend-select = ["E501"]
 #requires = ["tox>=4.19"]
 requires = ["tox"]
 # Elenco delle versioni di Python con cui testare
-envlist = ["py38", "py39", "py310", "py311", "py312", "py313"]
+envlist = ["py310", "py311", "py312", "py313"]
 
 [tool.tox.env_run_base]  # Configurazione generale per tutti gli ambienti di test
 description = "Run the tests with pytest"
@@ -155,12 +144,6 @@ commands = [["pytest"]]
 #deps = ["mypy==1.11.2", "types-cachetools>=5.5.0.20240820", "types-chardet>=5.0.4.6"]
 #commands = [["mypy", "src{/}tox"], ["mypy", "tests"]]
 
-[tool.tox.env.py38]
-description = "Run the tests on Python 3.8"
-
-[tool.tox.env.py39]
-description = "Run the tests on Python 3.9"
-
 [tool.tox.env.py310]
 description = "Run the tests on Python 3.10"
 
@@ -178,3 +161,4 @@ description = "Run the tests on Python 3.13"
 #description = "Run linting"
 #deps = ["flake8"]
 #commands = ["flake8 src tests"]
+

{biointerface-0.2.1 → biointerface-0.2.3}/src/biointerface/__init__.py

@@ -4,6 +4,6 @@ from biointerface.core import Interface, build_interfaces
 
 __author__ = """Alessandro Pandolfi"""
 __email__ = "alessandro.pandolfi@protonmail.com"
-__version__ = "0.2.1"
+__version__ = "0.2.3"
 
 __all__ = ["Interface", "build_interfaces"]

{biointerface-0.2.1 → biointerface-0.2.3}/src/biointerface/core.py

@@ -2,9 +2,13 @@
 
 from Bio.PDB.Polypeptide import PPBuilder
 from Bio.PDB.NeighborSearch import NeighborSearch
-from Bio.PDB import Atom
+from Bio.PDB.Residue import Residue
+from Bio.PDB.Atom import Atom
+from Bio.PDB.PDBExceptions import PDBConstructionException
 
-# from Bio.PDB import Structure, Model, Chain, Residue
+# from Bio.PDB.Structure import Structure
+# from Bio.PDB.Model import Model
+# from Bio.PDB.Chain import Chain
 # from Bio.PDB import MMCIFIO
 
 import pandas as pd
@@ -82,18 +86,31 @@ class Interface:
         self.contacts = self._extract_contacts()
 
         dna_atoms = self.get_dna_atoms()
-        self.dna_chain_ids = list(
+        self._dna_chain_ids = list(
             {atom.parent.parent.id for atom in dna_atoms}
         )
 
     def __repr__(self):
         """Return string representation of the nucleic acid."""
         return f"<Interface chains={self.protein_chain_id}:\
-{''.join(self.dna_chain_ids)} contacts={len(self.contacts)} search_radius=\
+{''.join(self._dna_chain_ids)} contacts={len(self.contacts)} search_radius=\
 {self.search_radius}>"
 
     def _extract_contacts(self) -> list[tuple[Atom]]:
-        """Extract interface contacts."""
+        """
+        Extract interface contacts.
+
+        Raises
+        ------
+        PDBConstructionException
+            In case of `protein_chain_id` not being a protein chain.
+
+        Returns
+        -------
+        list[tuple[Atom]]
+            List of pairs of atoms, first one is DNA, second is proteic.
+
+        """
         # get all the atoms from the nucleic acids, in most cases DNA
         na_builder = NABuilder()
         na_list = na_builder.build_nucleic_acids(self.structure)
@@ -108,6 +125,14 @@ class Interface:
         protein_chain = self.structure[0][self.protein_chain_id]
         pp_builder = PPBuilder()
         pp_list = pp_builder.build_peptides(protein_chain)
+
+        # check if given chain id is actually a protein
+        if not pp_list:
+            raise PDBConstructionException(
+                f"No polypeptides found in the input protein \
+chain id: {self.protein_chain_id}"
+            )
+
         pp_atoms = []
         for pp in pp_list:
             for res in pp:
@@ -163,6 +188,18 @@ class Interface:
 
         return contacts
 
+    def get_atomic_contacts(self) -> list[tuple[Atom]]:
+        """
+        Get interface contacts as pairs of atoms.
+
+        Returns
+        -------
+        list[tuple[Atom]]
+            List of pairs of atoms, first one is DNA, second is proteic.
+
+        """
+        return self.contacts
+
     def get_protein_atoms(self) -> list[Atom]:
         """
         Get only protein atoms in the protein-DNA interface.
@@ -187,6 +224,30 @@ class Interface:
         """
         return list({atom_pair[0] for atom_pair in self.contacts})
 
+    def get_aminoacids(self) -> list[Residue]:
+        """
+        Get only protein residues in the protein-DNA interface.
+
+        Returns
+        -------
+        list[Residue]
+            List of protein reisudes in the interface.
+
+        """
+        return list({atom_pair[1].parent for atom_pair in self.contacts})
+
+    def get_nucleotides(self) -> list[Residue]:
+        """
+        Get only DNA residues in the protein-DNA interface.
+
+        Returns
+        -------
+        list[Residue]
+            List of DNA residues in the interface.
+
+        """
+        return list({atom_pair[0].parent for atom_pair in self.contacts})
+
     def get_interface_data(self) -> pd.DataFrame:
         """
         Get all data from the interface, as a dataframe.

{biointerface-0.2.1 → biointerface-0.2.3}/src/biointerface.egg-info/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.2
 Name: biointerface
-Version: 0.2.1
-Summary: BioInterface is a python package capable of extracting Protein-DNA interfaces from PDB/mmCif structures.
+Version: 0.2.3
+Summary: BioInterface is a Biopython based package that extracts Protein-DNA interfaces in a PDB structures.
 Author-email: Alessandro Pandolfi <alessandro.pandolfi@protonmail.com>
 Maintainer-email: Alessandro Pandolfi <alessandro.pandolfi@protonmail.com>
 License: MIT license
@@ -33,6 +33,10 @@ BioInterface
         :target: https://biointerface.readthedocs.io/en/latest/?version=latest
         :alt: Documentation Status
 
+.. image:: https://gitlab.com/MorfeoRenai/biointerface/badges/main/coverage.svg
+        :target: https://gitlab.com/MorfeoRenai/biointerface/-/commits/main
+        :alt: Coverage Status
+
 .. image:: https://pyup.io/repos/github/MorfeoRenai/biointerface/shield.svg
      :target: https://pyup.io/repos/github/MorfeoRenai/biointerface/
      :alt: Updates
@@ -62,17 +66,17 @@ You can extract a single Protein-DNA interface from a single protein chain.
 
     from Bio.PDB.MMCIFParser import MMCIFParser
     from biointerface import Interface, build_interfaces
-    
+
     # parse and build structure with Biopython
     parser = MMCIFParser()
     structure = parser.get_structure(
         structure_id="1A02", filename="1a02-assembly1.cif"
     )
-    
+
     # extract interface from a specific protein chain
     face = Interface(
         structure=structure,
-        protein_chain_id="A",
+        protein_chain_id="F",
         search_radius=5.0
     )
     face
@@ -84,9 +88,25 @@ You can extract a single Protein-DNA interface from a single protein chain.
 Check the official documentation for more information.
 
 
+Feaures
+-------
+
+* Extract one specific Protein-DNA interface in a PDB structure, given a protein chain id;
+
+* Extract all Protein-DNA interfaces in a PDB structure;
+
+* Get all interacting residues in a interface;
+
+* Get all interacting atoms in a interface;
+
+* Interface data as ``pandas`` DataFrame;
+
+
 TODO
 --------
 
+* Extract continous bound DNA sequence
+
 * Proper tests (WIP)
 
 

biointerface-0.2.1/HISTORY.rst

@@ -1,14 +0,0 @@
-=======
-History
-=======
-
-0.1.0 (2025-02-08)
-------------------
-
-* First release on PyPI.
-
-
-0.2.0 (2025-02-28)
-------------------
-
-* Feature: Interface class, with getter methods for atoms, dataframes etc

biointerface-0.2.1/docs/usage.rst

@@ -1,55 +0,0 @@
-=====
-Usage
-=====
-
-To use BioInterface in a Python project:
-
-.. code-block:: python
-
-    import biointerface
-
-You can extract a single Protein-DNA interface from a single protein chain.
-
-.. code-block:: python
-
-    from Bio.PDB.PDBList import PDBList
-    from Bio.PDB.MMCIFParser import MMCIFParser
-    from biointerface import Interface, build_interfaces
-
-    # retrive file from PDB using Biopython
-    pdbl = PDBList()
-    pdbl.retrieve_pdb_file(pdb_code="1A02", pdir=".")
-    pdbl.retrieve_assembly_file(pdb_code="1A02", assembly_num=1, pdir=".")
-    # ... or else use your own
-    
-    # parse and build structure with Biopython
-    parser = MMCIFParser()
-    structure = parser.get_structure(
-        structure_id="1A02", filename="1a02-assembly1.cif"
-    )
-    
-    # extract interface from a specific protein chain
-    face = Interface(
-        structure=structure,
-        protein_chain_id="A",
-        search_radius=5.0
-    )
-    face
-
-
-.. code-block:: console
-
-    <Interface chains=F:BA contacts=258 search_radius=5.0>
-
-You can also extract all Protein-DNA interface from an entire structure.
-
-.. code-block:: python
-
-    face_list = build_interfaces(structure=structure, search_radius=5.0)
-    face_list
-
-.. code-block:: console
-
-    [<Interface chains=J:BA contacts=189 search_radius=5.0>,
-     <Interface chains=F:BA contacts=258 search_radius=5.0>,
-     <Interface chains=N:BA contacts=529 search_radius=5.0>]