biointerface 0.2.3__tar.gz → 0.3.1__tar.gz

{biointerface-0.2.3 → biointerface-0.3.1}/HISTORY.rst

@@ -2,28 +2,32 @@
 History
 =======
 
-0.1.0 (2025-02-08)
+0.3.1 (2025-03-05)
 ------------------
 
-* First release on PyPI.
+* Proper tests
 
 
-0.2.0 (2025-02-28)
+0.3.0 (2025-03-05)
 ------------------
 
-* Features: Interface class, with getter methods for atoms, dataframes etc
+* Feature: get all continous protein-bound double-strand nucleic acids;
 
 
-0.2.1 (2025-03-1)
+0.2.3 (2025-03-05)
 ------------------
 
-* Gitlab CI
+* fix: bump-my-version was updating pdbnucleicacids version too
+
+* fix: import classes instead of modules
+
+* chore: remove old tox environments
 
 
 0.2.2 (2025-03-04)
 ------------------
 
-* Interface methods to get residues
+* Interface getter methods to get residues
 
 * Interface raise error condition in case of no protein in the structure
 
@@ -32,11 +36,21 @@ History
 * Full documentation
 
 
-0.2.3 (2025-03-05)
+0.2.1 (2025-03-1)
 ------------------
 
-* fix: bump-my-version was updating pdbnucleicacids version too
+* Gitlab CI
 
-* fix: import classes instead of modules
 
-* chore: remove old tox environments
+0.2.0 (2025-02-28)
+------------------
+
+* Features: Interface class, with getter methods for atoms, dataframes etc
+
+
+0.1.0 (2025-02-08)
+------------------
+
+* First release on PyPI.
+
+* Feature: interface as pandas dataframe

{biointerface-0.2.3 → biointerface-0.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: biointerface
-Version: 0.2.3
+Version: 0.3.1
 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>
@@ -14,12 +14,21 @@ License-File: LICENSE
 License-File: AUTHORS.rst
 Requires-Dist: pandas
 Requires-Dist: biopython
-Requires-Dist: pdbnucleicacids>=0.2.1
+Requires-Dist: pdbnucleicacids>=0.2.2
 Provides-Extra: dev
-Requires-Dist: coverage; extra == "dev"
+Requires-Dist: spyder-kernels; extra == "dev"
+Requires-Dist: flake8; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
 Requires-Dist: mypy; extra == "dev"
 Requires-Dist: pytest; extra == "dev"
-Requires-Dist: ruff; extra == "dev"
+Requires-Dist: tox; extra == "dev"
+Requires-Dist: coverage; extra == "dev"
+Requires-Dist: sphinx; extra == "dev"
+Requires-Dist: watchdog; extra == "dev"
+Requires-Dist: bump-my-version; extra == "dev"
+Requires-Dist: wheel; extra == "dev"
+Requires-Dist: build; extra == "dev"
+Requires-Dist: twine; extra == "dev"
 
 ============
 BioInterface
@@ -101,13 +110,12 @@ Feaures
 
 * Interface data as ``pandas`` DataFrame;
 
+* Get all continous protein-bound double-strand nucleic acids;
+
 
 TODO
 --------
 
-* Extract continous bound DNA sequence
-
-* Proper tests (WIP)
 
 
 Credits

{biointerface-0.2.3 → biointerface-0.3.1}/README.rst

@@ -78,13 +78,12 @@ Feaures
 
 * Interface data as ``pandas`` DataFrame;
 
+* Get all continous protein-bound double-strand nucleic acids;
+
 
 TODO
 --------
 
-* Extract continous bound DNA sequence
-
-* Proper tests (WIP)
 
 
 Credits

{biointerface-0.2.3 → biointerface-0.3.1}/docs/usage.rst

@@ -35,7 +35,7 @@ You can extract a single Protein-DNA interface from a single protein chain.
     # extract interface from a specific protein chain
     face = Interface(
         structure=structure,
-        protein_chain_id="A",
+        protein_chain_id="F",
         search_radius=5.0
     )
     face
@@ -169,7 +169,7 @@ You can get all Protein-DNA interface features as a ``pandas`` DataFrame.
        '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'],
+       'dna_atom_coord_y', 'dna_atom_coord_z', 'euclidean_distance'],
       dtype='object')
 
 .. code-block:: python
@@ -178,7 +178,7 @@ You can get all Protein-DNA interface features as a ``pandas`` DataFrame.
 
 .. code-block:: console
 
-        protein_chain_id prot_res_hetfield  prot_res_number  ... euclidian_distance
+        protein_chain_id prot_res_hetfield  prot_res_number  ... euclidean_distance
     0                  F                                148  ...           4.458498
     1                  F                                148  ...           3.964944
     2                  F                                148  ...           4.066739
@@ -192,3 +192,34 @@ You can get all Protein-DNA interface features as a ``pandas`` DataFrame.
     257                F                                157  ...           4.299844
 
     [258 rows x 23 columns]
+
+
+Protein-Bound Nucleic Acids
+---------------------------
+
+BioInterface can extract all double-strand nucleic acids bound by
+the input protein, as a ``DoubleStrandNucleicAcid`` class from the package
+PDBNucleicAcids_.
+
+.. code-block:: python
+
+    bound_dsna_list = face.get_bound_double_strands()
+    bound_dsna = dsna_list[0]
+    bound_dsna
+
+.. code-block:: console
+
+    <DoubleStrandNucleicAcid type='dsDNA' i-th strand='A' j-th strand='B'
+     length=9>
+
+The ``DoubleStrandNucleicAcid`` class has other useful methods.
+
+.. code-block:: python
+
+    bound_dsna.get_i_strand().get_seq()
+
+.. code-block:: console
+
+    Seq('GTTTCATAG')
+
+.. _PDBNucleicAcids: https://gitlab.com/MorfeoRenai/pdbnucleicacids

{biointerface-0.2.3 → biointerface-0.3.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "biointerface"
-version = "0.2.3"
+version = "0.3.1"
 description = "BioInterface is a Biopython based package that extracts Protein-DNA interfaces in a PDB structures."
 readme = "README.rst"
 authors = [
@@ -20,15 +20,24 @@ license = {text = "MIT license"}
 dependencies = [
     "pandas",
     "biopython",
-    "pdbnucleicacids >= 0.2.1",
+    "pdbnucleicacids >= 0.2.2",
 ]
 
 [project.optional-dependencies]
 dev = [
-    "coverage",  # testing
-    "mypy",  # linting
-    "pytest",  # testing
-    "ruff"  # linting
+    "spyder-kernels",
+    "flake8",  # lint
+    "ruff",  # lint & format
+    "mypy",  # type check
+    "pytest",  # test
+    "tox",
+    "coverage",  # test
+    "sphinx",  # docs
+    "watchdog",  # docs
+    "bump-my-version",  # tags & version
+    "wheel",  # build
+    "build",  # build
+    "twine",  # deploy
 ]
 
 [project.urls]
@@ -72,41 +81,6 @@ testpaths = [
 ]
 
 
-# bump-my-version
-# ----
-
-[tool.bumpversion]
-current_version = "0.2.3"
-parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
-serialize = ["{major}.{minor}.{patch}"]
-search = "{current_version}"
-replace = "{new_version}"
-regex = false
-ignore_missing_version = false
-ignore_missing_files = false
-tag = true
-sign_tags = false
-tag_name = "v{new_version}"
-tag_message = "Bump version: {current_version} → {new_version}"
-allow_dirty = false
-commit = true
-message = "Bump version: {current_version} → {new_version}"
-commit_args = ""
-setup_hooks = []
-pre_commit_hooks = []
-post_commit_hooks = []
-
-[[tool.bumpversion.files]]
-filename = "src/biointerface/__init__.py"
-search = "{current_version}"
-replace = "{new_version}"
-
-[[tool.bumpversion.files]]
-filename = "pyproject.toml"
-search = 'version = "{current_version}"'
-replace = 'version = "{new_version}"'
-
-
 # ruff
 # ----
 
@@ -134,8 +108,11 @@ envlist = ["py310", "py311", "py312", "py313"]
 [tool.tox.env_run_base]  # Configurazione generale per tutti gli ambienti di test
 description = "Run the tests with pytest"
 deps = [
-    #"pytest-cov",  # Esempio di dipendenza per la coverage dei test
-    "-r requirements-dev.txt"  # Se hai un file requirements per lo sviluppo
+    "flake8",  # lint
+    "ruff",  # lint & format
+    "mypy",  # type check
+    "pytest",  # test
+    #"-r requirements-dev.txt"  # Se hai un file requirements per lo sviluppo
 ]
 commands = [["pytest"]]
 
@@ -162,3 +139,37 @@ description = "Run the tests on Python 3.13"
 #deps = ["flake8"]
 #commands = ["flake8 src tests"]
 
+
+# bump-my-version
+# ----
+
+[tool.bumpversion]
+current_version = "0.3.1"
+parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
+serialize = ["{major}.{minor}.{patch}"]
+search = "{current_version}"
+replace = "{new_version}"
+regex = false
+ignore_missing_version = false
+ignore_missing_files = false
+tag = true
+sign_tags = false
+tag_name = "v{new_version}"
+tag_message = "Bump version: {current_version} → {new_version}"
+allow_dirty = false
+commit = true
+message = "Bump version: {current_version} → {new_version}"
+commit_args = ""
+setup_hooks = []
+pre_commit_hooks = []
+post_commit_hooks = []
+
+[[tool.bumpversion.files]]
+filename = "src/biointerface/__init__.py"
+search = "{current_version}"
+replace = "{new_version}"
+
+[[tool.bumpversion.files]]
+filename = "pyproject.toml"
+search = 'version = "{current_version}"'
+replace = 'version = "{new_version}"'

{biointerface-0.2.3 → biointerface-0.3.1}/src/biointerface/__init__.py

@@ -4,6 +4,6 @@ from biointerface.core import Interface, build_interfaces
 
 __author__ = """Alessandro Pandolfi"""
 __email__ = "alessandro.pandolfi@protonmail.com"
-__version__ = "0.2.3"
+__version__ = "0.3.1"
 
 __all__ = ["Interface", "build_interfaces"]

{biointerface-0.2.3 → biointerface-0.3.1}/src/biointerface/core.py

@@ -13,53 +13,15 @@ from Bio.PDB.PDBExceptions import PDBConstructionException
 
 import pandas as pd
 
-from PDBNucleicAcids.NucleicAcid import NABuilder
+from PDBNucleicAcids.NucleicAcid import (
+    NABuilder,
+    DSNABuilder,
+    DoubleStrandNucleicAcid,
+)
 
+import copy
 
-def build_interfaces(structure, search_radius=5.0) -> list:
-    """
-    Extract all Protein-DNA interfaces found in a structure.
-
-    Parameters
-    ----------
-    structure : Bio.PDB.Structure
-        Biopython Structure entity.
-    search_radius : float | int, optional
-        Search radius, measured in Armstrong, within which Protein-DNA
-        interactions are found. Default is 5.0
-
-    Returns
-    -------
-    list
-        List of all Protein-DNA interfaces found in a structure.
-
-    """
-    # build nucleic acids
-    builder = NABuilder()
-    na_list = builder.build_nucleic_acids(structure)
-    if not na_list:
-        return []
-
-    # dna_chain_ids = list({na.get_chain_id() for na in na_list})
-
-    # build peptides
-    builder = PPBuilder()
-    pp_list = builder.build_peptides(structure)
-    if not pp_list:
-        return []
-
-    prot_chain_ids = list({pp[0].parent.id for pp in pp_list})
-
-    face_list = []
-    for prot_chain_id in prot_chain_ids:
-        face = Interface(
-            structure=structure,
-            protein_chain_id=prot_chain_id,
-            search_radius=search_radius,
-        )
-        face_list.append(face)
-
-    return face_list
+import warnings
 
 
 class Interface:
@@ -90,7 +52,7 @@ class Interface:
             {atom.parent.parent.id for atom in dna_atoms}
         )
 
-    def __repr__(self):
+    def __repr__(self) -> str:
         """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=\
@@ -98,7 +60,7 @@ class Interface:
 
     def _extract_contacts(self) -> list[tuple[Atom]]:
         """
-        Extract interface contacts.
+        Extract interface contacts (PRIVATE).
 
         Raises
         ------
@@ -262,7 +224,7 @@ chain id: {self.protein_chain_id}"
             Atom element
             Atomic coordinates (x, y, z)
             From both protein and DNA atoms
-            Euclidean distance
+            Euclidean distance between atom pair in contact
 
         Returns
         -------
@@ -273,7 +235,6 @@ chain id: {self.protein_chain_id}"
         data = []
 
         for na_atom, prot_atom in self.contacts:
-
             prot_res_hetfield = prot_atom.parent.id[0]
             prot_res_number = prot_atom.parent.id[1]
             prot_res_icode = prot_atom.parent.id[2]
@@ -297,7 +258,7 @@ chain id: {self.protein_chain_id}"
             dna_atom_coord_y = na_atom.coord[1]
             dna_atom_coord_z = na_atom.coord[2]
 
-            euclidian_distance = na_atom - prot_atom
+            euclidean_distance = na_atom - prot_atom
 
             row = (
                 self.protein_chain_id,
@@ -322,7 +283,7 @@ chain id: {self.protein_chain_id}"
                 dna_atom_coord_x,
                 dna_atom_coord_y,
                 dna_atom_coord_z,
-                euclidian_distance,
+                euclidean_distance,
             )
 
             data.append(row)
@@ -352,12 +313,126 @@ chain id: {self.protein_chain_id}"
                 "dna_atom_coord_x",
                 "dna_atom_coord_y",
                 "dna_atom_coord_z",
-                "euclidian_distance",
+                "euclidean_distance",
             ],
         )
 
         return df
 
+    def get_bound_double_strands(self) -> list[DoubleStrandNucleicAcid]:
+        """
+        Get all double-strand nucleic acids bound by the protein.
+
+        The output double stranded nucleic acids (DSNAs) are subsequences
+        of the full DSNAs found in the structure,
+        since proteins usually do not bind the whole DSNA.
+
+        This method allows for "gaps" of unbound base-pairs inside the
+        DSNA, only the base pairs at the ends are trimmed accourding
+        to being protein-bound or not.
+
+        A visual example of "gaps":
+            ``Input full DSNA:            GATATACAAGCCA``
+
+            ``Protein-bound:                ****  **``
+
+            ``Output protein-bound DSNA:    TATACAAG``
+
+        Returns
+        -------
+        bound_dsna_list : list[DoubleStrandNucleicAcid]
+            List of double-strand nucleic acids bound by the protein.
+
+        """
+        bound_nucleotides = self.get_nucleotides()
+
+        builder = DSNABuilder()
+        dsna_list = builder.build_double_strands(self.structure)
+        bound_dsna_list = []
+        for dsna in dsna_list:
+            bound_dsna = copy.copy(dsna)
+            while (
+                bound_dsna[0].i_res not in bound_nucleotides
+                and bound_dsna[0].j_res not in bound_nucleotides
+            ):
+                # if the FIRST base pair isn't bound by protein
+                # then discard it and check the next FIRST base pair
+                bound_dsna.pop(0)
+
+            while (
+                bound_dsna[-1].i_res not in bound_nucleotides
+                and bound_dsna[-1].j_res not in bound_nucleotides
+            ):
+                # if the LAST base pair isn't bound by protein
+                # then discard it and check the next LAST base pair
+                bound_dsna.pop(-1)
+
+            if len(bound_dsna) > 0:
+                # in this case, there is an actual bound DSNA
+                bound_dsna_list.append(bound_dsna)
+
+                for bp in bound_dsna:
+                    if (
+                        bp.i_res not in bound_nucleotides
+                        and bp.j_res not in bound_nucleotides
+                    ):
+                        warnings.warn(
+                            f"Warning: there are unbound base-pairs \
+inside the resulting DoubleStrandNucleicAcid - {bp}"
+                        )
+
+        return bound_dsna_list
+
+
+def build_interfaces(structure, search_radius=5.0) -> list[Interface]:
+    """
+    Extract all Protein-DNA interfaces found in a structure.
+
+    Parameters
+    ----------
+    structure : Bio.PDB.Structure
+        Biopython Structure entity.
+    search_radius : float | int, optional
+        Search radius, measured in Armstrong, within which Protein-DNA
+        interactions are found. Default is 5.0
+
+    Returns
+    -------
+    list
+        List of all Protein-DNA interfaces found in a structure.
+
+    """
+    # build nucleic acids
+    builder = NABuilder()
+    na_list = builder.build_nucleic_acids(structure)
+    if not na_list:
+        return []
+
+    # dna_chain_ids = list({na.get_chain_id() for na in na_list})
+
+    # build peptides
+    builder = PPBuilder()
+    pp_list = builder.build_peptides(structure)
+    if not pp_list:
+        return []
+
+    prot_chain_ids = list({pp[0].parent.id for pp in pp_list})
+
+    face_list = []
+    for prot_chain_id in prot_chain_ids:
+        # extract interface
+        face = Interface(
+            structure=structure,
+            protein_chain_id=prot_chain_id,
+            search_radius=search_radius,
+        )
+
+        # skip empty interfaces
+        if len(face.get_atomic_contacts()) > 0:
+            face_list.append(face)
+
+    return face_list
+
 
 # def export_atom_list(structure_id, atom_list, out_filepath):
 #     """Export atom list."""

{biointerface-0.2.3 → biointerface-0.3.1}/src/biointerface.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: biointerface
-Version: 0.2.3
+Version: 0.3.1
 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>
@@ -14,12 +14,21 @@ License-File: LICENSE
 License-File: AUTHORS.rst
 Requires-Dist: pandas
 Requires-Dist: biopython
-Requires-Dist: pdbnucleicacids>=0.2.1
+Requires-Dist: pdbnucleicacids>=0.2.2
 Provides-Extra: dev
-Requires-Dist: coverage; extra == "dev"
+Requires-Dist: spyder-kernels; extra == "dev"
+Requires-Dist: flake8; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
 Requires-Dist: mypy; extra == "dev"
 Requires-Dist: pytest; extra == "dev"
-Requires-Dist: ruff; extra == "dev"
+Requires-Dist: tox; extra == "dev"
+Requires-Dist: coverage; extra == "dev"
+Requires-Dist: sphinx; extra == "dev"
+Requires-Dist: watchdog; extra == "dev"
+Requires-Dist: bump-my-version; extra == "dev"
+Requires-Dist: wheel; extra == "dev"
+Requires-Dist: build; extra == "dev"
+Requires-Dist: twine; extra == "dev"
 
 ============
 BioInterface
@@ -101,13 +110,12 @@ Feaures
 
 * Interface data as ``pandas`` DataFrame;
 
+* Get all continous protein-bound double-strand nucleic acids;
+
 
 TODO
 --------
 
-* Extract continous bound DNA sequence
-
-* Proper tests (WIP)
 
 
 Credits

{biointerface-0.2.3 → biointerface-0.3.1}/src/biointerface.egg-info/SOURCES.txt

@@ -28,4 +28,6 @@ src/biointerface.egg-info/dependency_links.txt
 src/biointerface.egg-info/requires.txt
 src/biointerface.egg-info/top_level.txt
 tests/__init__.py
-tests/test_biointerface.py
+tests/test_biointerface.py
+tests/test_core.py
+tests/data/gattaca.cif

biointerface-0.3.1/src/biointerface.egg-info/requires.txt

@@ -0,0 +1,18 @@
+pandas
+biopython
+pdbnucleicacids>=0.2.2
+
+[dev]
+spyder-kernels
+flake8
+ruff
+mypy
+pytest
+tox
+coverage
+sphinx
+watchdog
+bump-my-version
+wheel
+build
+twine