fix style and format issues

Author: CunliangGeng

pdb2sql/StructureSimilarity.py

@@ -8,7 +8,7 @@
 class StructureSimilarity(object):
 
     def __init__(self,decoy,ref,verbose=False):
-        '''Compute structure similarity between two structures.
+        """Compute structure similarity between two structures.
 
         This class allows to compute the i-RMSD, L-RMSD, Fnat and DockQ
         score of a given conformation.
@@ -48,7 +48,7 @@ def __init__(self,decoy,ref,verbose=False):
             ...     ref_pairs='1AK4.ref_pairs')
             >>> dockQ = sim.compute_DockQScore(Fnat_fast,
             ...     lrmsd_fast,irmsd_fast)
-        '''
+        """
 
         self.decoy = decoy
         self.ref = ref
@@ -68,7 +68,7 @@ def __init__(self,decoy,ref,verbose=False):
 
     # compute the L-RMSD
     def compute_lrmsd_fast(self,lzone=None,method='svd',check=True):
-        '''Fast routine to compute the L-RMSD.
+        """Fast routine to compute the L-RMSD.
 
         L-RMSD is computed by aligning the longest chain of the decoy to
         the one of the reference and computing the RMSD of the shortest
@@ -91,7 +91,7 @@ def compute_lrmsd_fast(self,lzone=None,method='svd',check=True):
 
         See also:
             :meth:`compute_lrmsd_pdb2sql`
-        '''
+        """
 
         # create/read the lzone file
         if lzone is None:
@@ -257,8 +257,6 @@ def compute_irmsd_fast(self,izone=None,method='svd',cutoff=10,check=True):
             data_decoy  = self.get_data_zone_backbone(self.decoy,resData,return_not_in_zone=False)
             data_ref    = self.get_data_zone_backbone(self.ref,resData,return_not_in_zone=False)
 
-            atom_decoy = [ data[:3] for data in data_decoy]
-            atom_ref   = [ data[:3] for data in data_ref ]
             atom_common = data_ref.intersection(data_decoy)
             xyz_contact_decoy = self._get_xyz(self.decoy, atom_common)
             xyz_contact_ref = self._get_xyz(self.ref, atom_common)
@@ -301,7 +299,7 @@ def compute_izone(self,cutoff=10.0,save_file=True,filename=None):
         contact_ref = sql_ref.get_contact_atoms(cutoff=cutoff,extend_to_residue=True)
 
         index_contact_ref = []
-        for k,v in contact_ref.items():
+        for _,v in contact_ref.items():
         	index_contact_ref += v
 
         # get the xyz and atom identifier of the decoy contact atoms
@@ -415,7 +413,7 @@ def compute_fnat_fast(self,cutoff=5):
                             nCommon += 1
                     nTotal += 1
             else:
-                msg = f'\t FNAT: not find residue: {resA} in {decoy_name}'
+                msg = f'\t FNAT: not find residue: {resA}'
                 warnings.warn(msg)
 
         # normalize
@@ -935,10 +933,6 @@ def get_data_zone_backbone(pdb_file,resData,return_not_in_zone=False):
                 resSeq = int(line[22:26])
                 name = line[12:16].strip()
 
-                x = float(line[30:38])
-                y = float(line[38:46])
-                z = float(line[46:54])
-
                 backbone = ['C','CA','N','O']
                 if chainID in resData.keys():
 
@@ -1228,7 +1222,7 @@ def get_rotation_matrix_Kabsh(P,Q):
         A = np.dot(P.T,Q)/npts
 
         # SVD the matrix
-        V,S,W = np.linalg.svd(A)
+        V,_,W = np.linalg.svd(A)
 
         # the W matrix returned here is
         # already its transpose

pdb2sql/interface.py

@@ -1,4 +1,3 @@
-
 import numpy as np
 import itertools
 import warnings
@@ -7,10 +6,8 @@
 
 class interface(pdb2sql):
 
-    # def __init__(self, pdb):
     def __init__(self, pdb, **kwargs):
-        '''Identify interface between protein chains.'''
-
+        """Identify interface between protein chains."""
         super().__init__(pdb, **kwargs)
 
     ##########################################################################
@@ -29,7 +26,7 @@ def get_contact_atoms(
             only_backbone_atoms=False,
             excludeH=False,
             return_contact_pairs=False):
-        """get rowIDs of contact atoms.
+        """Get rowIDs of contact atoms.
 
         Args:
             cutoff (float): distance cutoff for calculating contact.
@@ -188,7 +185,7 @@ def get_contact_residues(
             excludeH=False,
             only_backbone_atoms=False,
             return_contact_pairs=False):
-        """get contact residues represented with (chain,resSeq, resname).
+        """Get contact residues represented with (chain,resSeq, resname).
 
         Args:
             cutoff (float): distance cutoff for contact calculation

pdb2sql/pdb2sqlAlchemy.py

@@ -1,7 +1,5 @@
-from sqlalchemy import *
-from sqlalchemy import Column, ForeignKey, Integer, String
+from sqlalchemy import Column, ForeignKey, Integer, String, Float
 from sqlalchemy.ext.declarative import declarative_base
-from sqlalchemy.orm import relationship
 from sqlalchemy import create_engine
 from sqlalchemy.schema import Sequence
 from sqlalchemy.orm import sessionmaker
@@ -13,7 +11,7 @@
 
 
 class ATOM(Base):
-    '''SQLAlchemy object for atoms.'''
+    """SQLAlchemy object for atoms."""
 
     __tablename__ = 'ATOM'
     rowID = Column(Integer, primary_key=True)
@@ -41,16 +39,16 @@ def __init__(
             sqlfile=None,
             fix_chainID=False,
             verbose=False):
-        '''Use sqlAlchemy to load the database.'''
+        """Use sqlAlchemy to load the database."""
         super().__init__(pdbfile, sqlfile, fix_chainID, verbose)
         self._create_sql()
 
     def _create_sql(self):
 
         # sqlalchemy init
-        self.engine = create_engine('sqlite:///:memory:')
-        Base.metadata.create_all(self.engine)
-        DBSession = sessionmaker(bind=self.engine)
+        self.conn = create_engine('sqlite:///:memory:')
+        Base.metadata.create_all(self.conn)
+        DBSession = sessionmaker(bind=self.conn)
         self.session = DBSession()
 
         # read the pdb file a pure python way
@@ -82,11 +80,11 @@ def _create_sql(self):
                     del_copy['chainID'] = [72, 73]
                 if line[del_copy['chainID'][0]] == ' ':
                     raise ValueError('chainID not found sorry')
-                _check_format_ = False
+                _check_format = False
 
             # browse all attribute of each atom
             at = {}
-            for ik, (colname, coltype) in enumerate(self.col.items()):
+            for _, (colname, coltype) in enumerate(self.col.items()):
 
                 # get the piece of data
                 if colname in del_copy.keys():
@@ -126,7 +124,8 @@ def _create_sql(self):
         fi.close()
 
     def get(self, attribute=None, **kwargs):
-        '''Exectute a simple SQL query that extracts values of attributes for certain condition.
+        """Exectute a simple SQL query that extracts values of attributes for
+        certain condition.
 
         Args :
             attribute (str) : attribute to retreive eg : ['x','y,'z'], 'xyz', 'resSeq'
@@ -139,7 +138,7 @@ def get(self, attribute=None, **kwargs):
 
         Example :
         >>> db.get('x,y,z',chainID='A',no_name=['H']")
-        '''
+        """
 
         # parse the commas in the attribute
         if attribute is not None:
@@ -223,7 +222,7 @@ def get(self, attribute=None, **kwargs):
                         1 if attribute == 'rowID' else atom.__dict__[attribute] for atom in atom_list]
 
     def update(self, attribute, values, **kwargs):
-        '''Update the database.
+        """Update the database.
 
         Args:
             attribute (str) : string of attribute names eg. ['x','y,'z'], 'xyz', 'resSeq'
@@ -232,7 +231,7 @@ def update(self, attribute, values, **kwargs):
                                   to the number of attributes and atoms selected
 
             kwargs : selection arguments eg : name = ['CA','O'], chainID = 'A', no_name = ['H']
-        '''
+        """
 
         # parse the commas in the attribute
         if ',' in attribute:

pdb2sql/pdb2sql_base.py

@@ -1,7 +1,4 @@
-import sqlite3
-import subprocess as sp
 import os
-import numpy as np
 from time import time
 
 
@@ -13,7 +10,7 @@ def __init__(
             sqlfile=None,
             fix_chainID=False,
             verbose=False):
-        '''Base class for the definition of sql database.
+        """Base class for the definition of sql database.
 
         Args:
             pdbfile (str, list(str/bytes), ndarray) : name of pdbfile or
@@ -23,8 +20,7 @@ def __init__(
             fix_chainID (bool, optinal): check if the name of the chains
                 are A,B,C, .... and fix it if not.
             verbose (bool): probably print stuff
-        '''
-
+        """
         self.pdbfile = pdbfile
         self.sqlfile = sqlfile
         self.fix_chainID = fix_chainID
@@ -89,7 +85,7 @@ def get(self, atnames, **kwargs):
         raise NotImplementedError()
 
     def get_xyz(self, **kwargs):
-        '''Shortcut to get the xyz coordinates.'''
+        """Shortcut to get the xyz coordinates."""
         return self.get('x,y,z', **kwargs)
 
     def get_residues(self, **kwargs):
@@ -121,19 +117,19 @@ def update(self, attribute, values, **kwargs):
         raise NotImplementedError()
 
     def update_xyz(self, xyz, **kwargs):
-        '''Update the xyz coordinates.'''
+        """Update the xyz coordinates."""
         self.update('x,y,z', xyz, **kwargs)
 
     def update_column(self, colname, values, index=None):
-        '''Update a single column.'''
+        """Update a single column."""
         raise NotImplementedError()
 
     def add_column(self, colname, coltype='FLOAT', default=0):
-        '''Add a new column to the ATOM table.'''
+        """Add a new column to the ATOM table."""
         raise NotImplementedError()
 
     def exportpdb(self, fname, append=False, periodic=False, **kwargs):
-        '''Export a PDB file with kwargs selection.'''
+        """Export a PDB file with kwargs selection."""
 
         if append:
             f = open(fname, 'a')
@@ -147,7 +143,7 @@ def exportpdb(self, fname, append=False, periodic=False, **kwargs):
         f.close()
 
     def sql2pdb(self, **kwargs):
-        """Convert SQL data to PDB formatted lines
+        """Convert SQL data to PDB formatted lines.
 
         Returns:
             list: pdb-format lines
@@ -181,7 +177,8 @@ def sql2pdb(self, **kwargs):
         return pdb
 
     def _format_atomname(self, data):
-        """Format atom name to align with PDB reqireuments:
+        """Format atom name to align with PDB reqireuments.
+
              - alignment of one-letter atom name starts at column 14,
              - while two-letter atom name such as FE starts at column 13.