Revert "tmalign.py: Code cleanup"

This reverts commit 0b3aba1.

Author: jlec

tmalign.py

@@ -1,23 +1,24 @@
-"""
+'''
 (c) 2011-2012 Thomas Holder, MPI for Developmental Biology
-"""
+'''
 
 from __future__ import print_function
-from pymol import cmd, CmdException
 
 __author__ = 'Thomas Holder'
 __version__ = '1.1'
 __license__ = 'BSD-2-Clause'
 
+from pymol import cmd, CmdException
+
 
 def save_pdb_without_ter(filename, selection, **kwargs):
-    """
-    DESCRIPTION
+    '''
+DESCRIPTION
 
-    Save PDB file without TER records. External applications like TMalign and
-    DynDom stop reading PDB files at TER records, which might be undesired in
-    case of missing loops.
-    """
+Save PDB file without TER records. External applications like TMalign and
+DynDom stop reading PDB files at TER records, which might be undesired in
+case of missing loops.
+    '''
     v = cmd.get_setting_boolean('pdb_use_ter_records')
     if v:
         cmd.unset('pdb_use_ter_records')
@@ -28,34 +29,34 @@ def save_pdb_without_ter(filename, selection, **kwargs):
 
 def alignwithanymethod(mobile, target, methods='align super cealign tmalign',
                        async=1, quiet=1):
-    """
-    DESCRIPTION
+    '''
+DESCRIPTION
 
-    Align copies of mobile to target with several alignment methods
+Align copies of mobile to target with several alignment methods
 
-    ARGUMENTS
+ARGUMENTS
 
-    mobile = string: atom selection
+mobile = string: atom selection
 
-    target = string: atom selection
+target = string: atom selection
 
-    methods = string: space separated list of PyMOL commands which take
-    arguments "mobile" and "target" (in any order) {default: align super
-    cealign tmalign}
-    """
+methods = string: space separated list of PyMOL commands which take
+arguments "mobile" and "target" (in any order) {default: align super
+cealign tmalign}
+    '''
     import threading
     import time
     methods = methods.split()
     async, quiet = int(async), int(quiet)
     mobile_obj = cmd.get_object_list('first (' + mobile + ')')[0]
 
-    def myalign(method_):
-        newmobile = cmd.get_unused_name(mobile_obj + '_' + method_)
+    def myalign(method):
+        newmobile = cmd.get_unused_name(mobile_obj + '_' + method)
         cmd.create(newmobile, mobile_obj)
         start = time.time()
-        cmd.do('%s mobile=%s in %s, target=%s' % (method_, newmobile, mobile, target))
+        cmd.do('%s mobile=%s in %s, target=%s' % (method, newmobile, mobile, target))
         if not quiet:
-            print('Finished: %s (%.2f sec)' % (method_, time.time() - start))
+            print('Finished: %s (%.2f sec)' % (method, time.time() - start))
 
     for method in methods:
         if async:
@@ -66,34 +67,34 @@ def myalign(method_):
             myalign(method)
 
 
-def tmalign(mobile, target, args='', exe='TMalign', ter=0, transform=1, object_=None, quiet=0):
-    """
-    DESCRIPTION
+def tmalign(mobile, target, args='', exe='TMalign', ter=0, transform=1, object=None, quiet=0):
+    '''
+DESCRIPTION
 
-    TMalign wrapper
+TMalign wrapper
 
-    Reference: Y. Zhang and J. Skolnick, Nucl. Acids Res. 2005 33, 2302-9
-    http://zhanglab.ccmb.med.umich.edu/TM-align/
+Reference: Y. Zhang and J. Skolnick, Nucl. Acids Res. 2005 33, 2302-9
+http://zhanglab.ccmb.med.umich.edu/TM-align/
 
-    USAGE
+USAGE
 
-    tmalign mobile, target [, args [, exe ]]
+tmalign mobile, target [, args [, exe ]]
 
-    ARGUMENTS
+ARGUMENTS
 
-    mobile, target = string: atom selections
+mobile, target = string: atom selections
 
-    args = string: Extra arguments like -d0 5 -L 100
+args = string: Extra arguments like -d0 5 -L 100
 
-    exe = string: Path to TMalign executable {default: TMalign}
+exe = string: Path to TMalign executable {default: TMalign}
 
-    ter = 0/1: If ter=0, then ignore chain breaks because TMalign will stop
-    at first TER record {default: 0}
+ter = 0/1: If ter=0, then ignore chain breaks because TMalign will stop
+at first TER record {default: 0}
 
-    SEE ALSO
+SEE ALSO
 
-    tmscore, mmalign
-    """
+tmscore, mmalign
+    '''
     import subprocess
     import tempfile
     import os
@@ -104,8 +105,8 @@ def tmalign(mobile, target, args='', exe='TMalign', ter=0, transform=1, object_=
     mobile_filename = tempfile.mktemp('.pdb', 'mobile')
     target_filename = tempfile.mktemp('.pdb', 'target')
     matrix_filename = tempfile.mktemp('.txt', 'matrix')
-    mobile_ca_sele = '(%s) and (not hetatm) and name CA and alt +A' % mobile
-    target_ca_sele = '(%s) and (not hetatm) and name CA and alt +A' % target
+    mobile_ca_sele = '(%s) and (not hetatm) and name CA and alt +A' % (mobile)
+    target_ca_sele = '(%s) and (not hetatm) and name CA and alt +A' % (target)
 
     if ter:
         save = cmd.save
@@ -121,7 +122,7 @@ def tmalign(mobile, target, args='', exe='TMalign', ter=0, transform=1, object_=
         process = subprocess.Popen(args, stdout=subprocess.PIPE)
         lines = process.stdout.readlines()
     except OSError:
-        print('Cannot execute "%s", please provide full path to TMscore or TMalign executable' % exe)
+        print('Cannot execute "%s", please provide full path to TMscore or TMalign executable' % (exe))
         raise CmdException
     finally:
         os.remove(mobile_filename)
@@ -148,7 +149,7 @@ def tmalign(mobile, target, args='', exe='TMalign', ter=0, transform=1, object_=
         elif line.lower().startswith(' -------- rotation matrix'):
             rowcount = 1
         elif line.startswith('(":" denotes'):
-            alignment = [line_it.next().rstrip() for _ in range(3)]
+            alignment = [line_it.next().rstrip() for i in range(3)]
         else:
             match = re_score.search(line)
             if match is not None:
@@ -166,10 +167,10 @@ def tmalign(mobile, target, args='', exe='TMalign', ter=0, transform=1, object_=
     matrix.extend([0, 0, 0, 1])
 
     if int(transform):
-        cmd.transform_selection('byobject (%s)' % mobile, matrix, homogenous=1)
+        cmd.transform_selection('byobject (%s)' % (mobile), matrix, homogenous=1)
 
     # alignment object
-    if object_ is not None:
+    if object is not None:
         mobile_idx, target_idx = [], []
         space = {'mobile_idx': mobile_idx, 'target_idx': target_idx}
         cmd.iterate(mobile_ca_sele, 'mobile_idx.append("%s`%d" % (model, index))', space=space)
@@ -180,61 +181,61 @@ def tmalign(mobile, target, args='', exe='TMalign', ter=0, transform=1, object_=
         for i, aa in enumerate(alignment[2]):
             if aa == '-':
                 target_idx.insert(i, None)
-        if len(mobile_idx) == len(target_idx) == len(alignment[2]):
+        if (len(mobile_idx) == len(target_idx) == len(alignment[2])):
             cmd.rms_cur(
                 ' '.join(idx for (idx, m) in zip(mobile_idx, alignment[1]) if m in ':.'),
                 ' '.join(idx for (idx, m) in zip(target_idx, alignment[1]) if m in ':.'),
-                cycles=0, matchmaker=4, object=object_)
+                cycles=0, matchmaker=4, object=object)
         else:
             print('Could not load alignment object')
 
     if not quiet and r is not None:
-        print('Found in output TM-score = %.4f' % r)
+        print('Found in output TM-score = %.4f' % (r))
 
     return r
 
 
 def tmscore(mobile, target, args='', exe='TMscore', quiet=0, **kwargs):
-    """
-    DESCRIPTION
+    '''
+DESCRIPTION
 
-    TMscore wrapper
+TMscore wrapper
 
-    Reference: Yang Zhang and Jeffrey Skolnick, Proteins 2004 57: 702-710
-    http://zhanglab.ccmb.med.umich.edu/TM-score/
+Reference: Yang Zhang and Jeffrey Skolnick, Proteins 2004 57: 702-710
+http://zhanglab.ccmb.med.umich.edu/TM-score/
 
-    ARGUMENTS
+ARGUMENTS
 
-    mobile, target = string: atom selections
+mobile, target = string: atom selections
 
-    args = string: Extra arguments like -d 5
+args = string: Extra arguments like -d 5
 
-    exe = string: Path to TMscore executable {default: TMscore}
+exe = string: Path to TMscore executable {default: TMscore}
 
-    ter = 0/1: If ter=0, then ignore chain breaks because TMscore will stop
-    at first TER record {default: 0}
+ter = 0/1: If ter=0, then ignore chain breaks because TMscore will stop
+at first TER record {default: 0}
 
-    SEE ALSO
+SEE ALSO
 
-    tmalign, mmalign
-    """
+tmalign, mmalign
+    '''
     kwargs.pop('_self', None)
     return tmalign(mobile, target, args, exe, quiet=quiet, **kwargs)
 
 
 def mmalign(mobile, target, args='', exe='MMalign', ter=0, transform=1, quiet=0):
-    """
-    DESCRIPTION
+    '''
+DESCRIPTION
 
-    MMalign wrapper
+MMalign wrapper
 
-    Reference: S. Mukherjee and Y. Zhang, Nucleic Acids Research 2009; 37: e83
-    http://zhanglab.ccmb.med.umich.edu/MM-align/
+Reference: S. Mukherjee and Y. Zhang, Nucleic Acids Research 2009; 37: e83
+http://zhanglab.ccmb.med.umich.edu/MM-align/
 
-    SEE ALSO
+SEE ALSO
 
-    tmalign, tmscore
-    """
+tmalign, tmscore
+    '''
     return tmalign(mobile, target, args, exe, ter, transform, quiet=quiet)
 
 # pymol commands