dcatoolkit 0.1.1__tar.gz → 0.1.2__tar.gz

{dcatoolkit-0.1.1/src/dcatoolkit.egg-info → dcatoolkit-0.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcatoolkit
-Version: 0.1.1
+Version: 0.1.2
 Summary: Collection of useful modules and representations for managing DCA output data.
 Author-email: Raheel Syed Ahmed <raheelsyedahmed@gmail.com>
 Maintainer-email: Raheel Syed Ahmed <raheelsyedahmed@gmail.com>
@@ -48,6 +48,7 @@ Provides-Extra: tests
 Requires-Dist: pytest; extra == "tests"
 Provides-Extra: docs
 Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: pdoc; extra == "docs"
 Requires-Dist: numpydoc; extra == "docs"
 Provides-Extra: lint
 Requires-Dist: ruffle; extra == "lint"

{dcatoolkit-0.1.1 → dcatoolkit-0.1.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "dcatoolkit"
-version = "0.1.1"
+version = "0.1.2"
 description = "Collection of useful modules and representations for managing DCA output data."
 keywords = ["dca", "toolkit", "DI", "coevolution"]
 
@@ -46,6 +46,7 @@ tests = [
 ]
 docs = [
   "sphinx",
+  "pdoc",
   "numpydoc"
 ]
 lint = [

{dcatoolkit-0.1.1 → dcatoolkit-0.1.2}/src/dcatoolkit/__init__.py

@@ -1,3 +1,3 @@
 
-__version__ = "0.1.1"
+__version__ = "0.1.2"
 from .representation import Pairs, DirectInformationData, StructureInformation, ResidueAlignment

{dcatoolkit-0.1.1 → dcatoolkit-0.1.2}/src/dcatoolkit/representation.py

@@ -1,5 +1,6 @@
 import numpy as np
 import pandas as pd
+from collections.abc import Iterable
 from scipy.spatial.distance import cdist
 
 import biotite.structure.io.pdbx as pdbx
@@ -462,6 +463,42 @@ class DirectInformationData:
         """
         return DI_data[abs(DI_data['residue1'] - DI_data['residue2']) > 4]
     
+    @staticmethod
+    def find_DI_with_residues(critical_residues_1 : Iterable[int], critical_residues_2 : Iterable[int], max_rank: Optional[int]=None, *mapped_resi_arrs: Iterable[npt.NDArray]) -> list[tuple[list, int]]:
+        """
+        Function that takes an n number of ranked, mapped DI pairs and checks to see if they're in a list of potential residue indices.
+        
+        Parameters
+        ----------
+        critical_residues_1 : collections.abc.Iterable of int
+            Specific residue indices that a DI pair will be compared to. If the first residue of the DI pair is not one of these indices, it will not be appended to results.
+        crtical_residues_2 : collections.abc.Iterable of int
+            Specific residue indices that a DI pair will be compared to. If the second residue of the DI pair is not one of these indices, it will not be appended to results.
+        threshold : int, optional
+            Maximum "rank" of the DI pair considered.
+        *mapped_resi_arrs : tuple of numpy.ndarray
+            Tuple of ranked, mapped pairs that are compared to critical residue indices and appended to results if in those indices and within threshold.
+        
+        Returns
+        -------
+        results : list of tuple of list of int, int
+            Results which consist of tuples where the first element is a list of residue1, residue2, and DI score, whereas the second element is the rank.
+        """
+        results = []
+        for mapped_resi_arr in mapped_resi_arrs:
+            # count_rank represents the rank of the DI pair being evaluated, iterating over every new row considered.
+            count_rank = 0
+            for row in mapped_resi_arr:
+                row_as_list = list(row)
+                count_rank += 1
+                if max_rank:
+                    if row_as_list[0] in critical_residues_1 and row_as_list[1] in critical_residues_2 and count_rank <= max_rank:
+                        results.append((row_as_list, count_rank))
+                else:
+                    if row_as_list[0] in critical_residues_1 and row_as_list[1] in critical_residues_2:
+                        results.append((row_as_list, count_rank))
+        return results
+
     @staticmethod
     def get_dist_commands(model1: str | int, model2: str | int, chain1: str, chain2: str, pairs: npt.NDArray, ca_only: bool=True, auth_res_ids=False) -> list[str]:
         """
@@ -543,29 +580,78 @@ class StructureInformation:
         Structure obtained from an RCSB entry with a provided pdbx/mmcif file with a specified model number.
     pdbx_file : biotite.io.pdbx.CIFFile
         mmCIF file that contains generic information and atomic information of the protein structure categorized into mmCIF blocks.
+    model_num : int
+        The model number to access from the PDB to ensure an AtomArray is returned containing the atom information of the protein structure.
 
     Attributes
     ----------
-    struct_ref_seq : zip
-        zipped version of parallel arrays that contain chain ids, beginning align indices of the sequence, and beginning align indices of the auth sequence.
+    self.atom_data : numpy.ndarray, optional
+        Entries in the format 'ATOM', residue index, chain ID, auth residue index, auth chain ID, model number
+    self.het_atom_data : numpy.ndarray, optional
+        Array of entries in the format 'HETATM', residue index, chain ID, auth residue index, auth chain ID, model number
+    self.unique_chains : numpy.ndarray, optional
+        Array of unique asym_id entries which corresponds to unique chain IDs.
+    self.chain_auth_dict : dict of str, str, optional
+        Uses chain id as a key and provides auth chain id as a value. 
+    self.res_auth_dict : dict of str, tuple of int, int or optional 
+        Uses chain id as a key and an array of residue index and auth residue index as a value.
     """
-    def __init__(self, structure, pdbx_file: pdbx.CIFFile):
+    def __init__(self, structure, pdbx_file: pdbx.CIFFile, model_num: int):
         self.structure = structure
         self.pdbx_file = pdbx_file
-        strand_ids = []
-        align_beg = []
-        auth_align_beg = []
-        # Obtain struct ref seq information (chain names, beginning residue, and the corresponding protein beginning residue)
-        for col_name, col in self.pdbx_file[list(self.pdbx_file.keys())[0]]['struct_ref_seq'].items():
-            if col_name == "pdbx_strand_id":
-                    strand_ids = col.data.array
-            if col_name == "seq_align_beg":
-                    align_beg = col.data.array
-            if col_name == "pdbx_auth_seq_align_beg": 
-                    auth_align_beg = col.data.array
-        # Put all three lists together
-        self.struct_ref_seq = zip(strand_ids, align_beg, auth_align_beg)
-                
+        self.model_num = model_num
+        self.generate_auth_info()
+
+    def generate_auth_info(self) -> None:
+        """
+        Ran as part of constructor function. Generates information needed to access auth information including auth_seq_id and auth_asym_id, which correspond to alternative chain ids and alternative residue indices.
+        
+        Note
+        ----
+        See attributes for details.
+        
+        Returns
+        -------
+        None
+        """
+        if len(self.pdbx_file.keys()) > 0:
+            self.first_block = list(self.pdbx_file)[0]
+            self.atom_site_category = self.pdbx_file[self.first_block].get('atom_site')
+            self.chain_auth_dict = {}
+            self.res_auth_dict = {}
+            if self.atom_site_category:
+                group_pdbs = []
+                seq_ids = []
+                asym_ids = []
+                auth_seq_ids = []
+                auth_asym_ids = []
+                model_nums = []
+                for col_name, col in self.atom_site_category.items():
+                    if col_name == 'group_PDB':
+                        group_pdbs = col.as_array()
+                    elif col_name == 'label_seq_id':
+                        seq_ids = col.as_array()
+                    elif col_name == 'label_asym_id':
+                        asym_ids = col.as_array()
+                    elif col_name == 'auth_seq_id':
+                        auth_seq_ids = col.as_array()
+                    elif col_name == 'auth_asym_id':
+                        auth_asym_ids = col.as_array()
+                    elif col_name == 'pdbx_PDB_model_num':
+                        model_nums = col.as_array()
+
+                atom_site_data = np.unique(np.column_stack((group_pdbs, seq_ids, asym_ids, auth_seq_ids, auth_asym_ids, model_nums)), axis=0)
+                atom_site_data = atom_site_data[atom_site_data[:,5] == str(self.model_num)]
+                self.atom_data = atom_site_data[atom_site_data[:,0] == "ATOM"]
+                self.het_atom_data = atom_site_data[atom_site_data[:,0] == "HETATM"]
+                self.unique_chains = np.unique(self.atom_data[:,2])
+                for unique_chain in self.unique_chains:
+                    unique_entry = self.atom_data[self.atom_data[:,2] == unique_chain][0]
+                    self.chain_auth_dict[unique_entry[2]] = unique_entry[4]
+                    self.res_auth_dict[unique_entry[2]] = unique_entry[[1,3]].astype('int')
+        else:
+            self.atom_site_category = None
+
     @staticmethod
     def fetch_pdb(pdb_id: str, model_num: int=1, struc_format: str="mmcif") -> 'StructureInformation':
         """
@@ -594,7 +680,7 @@ class StructureInformation:
         if fetched_data is None:
             raise TypeError("RCSB fetch failed. Try fetch again.")
         pdbx_file = pdbx.CIFFile.read(fetched_data)
-        return StructureInformation(pdbx.get_structure(pdbx_file=pdbx_file, model=model_num, use_author_fields=False), pdbx_file)
+        return StructureInformation(pdbx.get_structure(pdbx_file=pdbx_file, model=model_num, use_author_fields=False), pdbx_file, model_num)
     
     @staticmethod
     def read_pdb_mmCIF(pdb_filepath: str, model_num: int=1) -> 'StructureInformation':
@@ -614,7 +700,7 @@ class StructureInformation:
             StructureInformation generated from pdbx.get_structure() function using the pdbx file fetched from RCSB. The pdbx file is also supplied as an argument.
         """
         pdbx_file = pdbx.CIFFile.read(pdb_filepath)
-        return StructureInformation(pdbx.get_structure(pdbx_file, model=model_num, use_author_fields=False), pdbx_file)
+        return StructureInformation(pdbx.get_structure(pdbx_file, model=model_num, use_author_fields=False), pdbx_file, model_num)
     
     def get_chain_specific_structure(self, ca_only: bool, chain1: str, chain2: str, remove_hetero=True) -> tuple:
         """
@@ -669,6 +755,31 @@ class StructureInformation:
         dist_matrix = cdist(chain1_structure.coord, chain2_structure.coord)
         return (chain1_structure, chain2_structure, dist_matrix)
     
+    def get_shift_values(self, chain1: str, chain2: str) -> tuple[int, int]:
+        """
+        Get shift values needed for production of auth residue ids.
+        
+        Parameters
+        ----------
+        chain1 : str
+            Name of the chain id present in the struct_ref_seq block of cif files referring to the second column of residues.
+        chain2 : str
+            Name of the chain id present in the struct_ref_seq block of cif files referring to the second column of residues.
+
+        Returns
+        -------
+        (shift1, shift2) : tuple of int, int
+            Tuple containing both shift values, the difference between the auth_res_id and res_id.
+        """
+        shift1 = 0
+        shift2 = 0
+        if self.atom_site_category:
+            shift1 = abs(self.res_auth_dict[chain1][0] - self.res_auth_dict[chain1][1])
+            shift2 = abs(self.res_auth_dict[chain2][0] - self.res_auth_dict[chain2][1])
+            return shift1, shift2
+        else:
+            return shift1, shift2
+
     def get_min_dist_atom_info(self, pairs: npt.NDArray, chain1: str, chain2: str) -> npt.NDArray:
         """
         Generate a ndarray of residue ids and their corresponding atom names such that the distance is the minimum between the initial residues provided.
@@ -687,15 +798,7 @@ class StructureInformation:
         min_dist_pairs_atoms_arr : numpy.ndarray
             Structured ndarray that has residue indices, auth residue indices (corresponding to the protein numbering), and atomic names in the format {'names': ['residue1','residue2','auth_residue1','auth_residue2','atom_name1','atom_name2'], 'formats': [int,int,str,str]}
         """
-        shift1 = 0
-        shift2 = 0
-        for row in list(self.struct_ref_seq):
-            ref_seq_chain, ref_seq_beg, auth_ref_seq_beg = row
-            if ref_seq_chain == chain1:
-                shift1 = int(auth_ref_seq_beg) - int(ref_seq_beg)
-            if ref_seq_chain == chain2:
-                shift2 = int(auth_ref_seq_beg) - int(ref_seq_beg)
-            
+        shift1, shift2 = self.get_shift_values(chain1, chain2)
         chain1_structure, chain2_structure = self.get_chain_specific_structure(ca_only=False, chain1=chain1, chain2=chain2, remove_hetero=True)
         min_dist_pairs_atoms = []
         for row in pairs:
@@ -711,11 +814,11 @@ class StructureInformation:
             # Generate the auth ids of the residues in the pairs ndarray
             auth_res_id1 = row['residue1'] + shift1
             auth_res_id2 = row['residue2'] + shift2
-            min_dist_pairs_atoms.append((row['residue1'], row['residue2'],auth_res_id1, auth_res_id2, chain1_res1_structure[ind[0]].atom_name, chain2_res2_structure[ind[1]].atom_name))
+            min_dist_pairs_atoms.append((row['residue1'], row['residue2'], auth_res_id1, auth_res_id2, chain1_res1_structure[ind[0]].atom_name, chain2_res2_structure[ind[1]].atom_name))
         min_dist_pairs_atoms_arr = np.array(min_dist_pairs_atoms, dtype={'names': ['residue1','residue2','auth_residue1','auth_residue2','atom_name1','atom_name2'], 'formats': [int,int,int,int,'<U10','<U10']})
         return min_dist_pairs_atoms_arr
 
-    def get_contacts(self, ca_only: bool, threshold: float, chain1: str, chain2: str) -> set[tuple[int, int]]:
+    def get_contacts(self, ca_only: bool, threshold: float, chain1: str, chain2: str, auth_contacts: bool=False) -> set[tuple[int, int]]:
         """
         Get contacts from the structure attribute where the distance between two residues is less than the threshold.
 
@@ -729,15 +832,47 @@ class StructureInformation:
             Chain id corresponding to the first column of residues in the structure.
         chain2 : str
             Chain id corresponding to the second column of residues in the structure.
+        auth_contacts : bool
+            True if supplying alt_ids for residues indices, False if cif residue indexing is needed.
 
         Returns
         -------
         contacts_set : set of tuple of ints
             Set of contacts, tuples with "residue1" and "residue2" from the structure that are within the distance threshold.
         """
+        shift1, shift2 = self.get_shift_values(chain1, chain2)
         chain1_structure, chain2_structure, dist_matrix = self.generate_dist_matrix(ca_only, chain1, chain2)
-        contacts = np.argwhere(dist_matrix <= threshold)
+        thresh_ind = np.argwhere(dist_matrix <= threshold)
         contacts_set = set()
-        for contact in contacts:
-            contacts_set.add((chain1_structure[contact[0]].res_id, chain2_structure[contact[1]].res_id))
-        return contacts_set
+        for indices in thresh_ind:
+            chain1_atom = chain1_structure[indices[0]]
+            chain2_atom = chain2_structure[indices[1]]
+            res1 = chain1_atom.res_id
+            res2 = chain2_atom.res_id
+            if not(chain1==chain2 and res1 >= res2):
+                if auth_contacts:
+                    contacts_set.add((res1 + shift1, res2 + shift2))
+                else:
+                    contacts_set.add((res1, res2))
+        return contacts_set
+    
+    @staticmethod
+    def write_contacts_set(filepath : str, contacts_set : set[tuple[int, int]]) -> None:
+        """
+        Write the contacts generated from get_contacts or general set of tuples of pairs.
+
+        Parameters
+        ----------
+        filepath : str
+            Path of file to output contacts_set to.
+        contacts_set : set of tuple of int, int
+            Set of tuples of pairs that represent contacts.
+        
+        Returns
+        -------
+        None
+        """
+        contacts_list = list(sorted(contacts_set))
+        with open(filepath, 'w') as fs:
+            for pair in contacts_list:
+                fs.write(str(pair[0]) + "\t" + str(pair[1]) + "\n")

{dcatoolkit-0.1.1 → dcatoolkit-0.1.2/src/dcatoolkit.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcatoolkit
-Version: 0.1.1
+Version: 0.1.2
 Summary: Collection of useful modules and representations for managing DCA output data.
 Author-email: Raheel Syed Ahmed <raheelsyedahmed@gmail.com>
 Maintainer-email: Raheel Syed Ahmed <raheelsyedahmed@gmail.com>
@@ -48,6 +48,7 @@ Provides-Extra: tests
 Requires-Dist: pytest; extra == "tests"
 Provides-Extra: docs
 Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: pdoc; extra == "docs"
 Requires-Dist: numpydoc; extra == "docs"
 Provides-Extra: lint
 Requires-Dist: ruffle; extra == "lint"

{dcatoolkit-0.1.1 → dcatoolkit-0.1.2}/src/dcatoolkit.egg-info/requires.txt

@@ -7,6 +7,7 @@ scipy>=1.11.0
 
 [docs]
 sphinx
+pdoc
 numpydoc
 
 [lint]