Removed strip() calls to avoid trimming ATOM/HETATM lines

pdb_b.py

@@ -76,11 +76,10 @@ def _alter_bfactor(fhandle, bfactor):
     #bfactor = str(round(bfactor, 2)).rjust(6)
     bfactor = "{0:>6.2f}".format(bfactor)
     for line in fhandle:
-        line = line.strip()
         if coord_re.match(line):
-            yield line[:60] + bfactor + line[66:] + '\n'
+            yield line[:60] + bfactor + line[66:]
         else:
-            yield line + '\n'
+            yield line
 
 if __name__ == '__main__':
 

pdb_chain.py

@@ -78,11 +78,10 @@ def _alter_chain(fhandle, chain_id):
     chain_id = chain_id
 
     for line in fhandle:
-        line = line.strip()
         if coord_re.match(line):
-            yield line[:21] + chain_id[0] + line[22:] + '\n'
+            yield line[:21] + chain_id[0] + line[22:]
         else:
-            yield line + '\n'
+            yield line
 
 if __name__ == '__main__':
     # Check Input

pdb_chainxseg.py

@@ -54,16 +54,15 @@ def _swap_chainxseg(fhandle):
     fhandle = fhandle
 
     for line in fhandle:
-        line = line.strip()
         if coord_re.match(line):
             size_of_line = len(line)
             # Pad short lines
             if size_of_line < 80:
                 padding = 80 - size_of_line
                 line = line + ' '*padding
-            yield line[:72] + line[21].ljust(4) + line[76:] + '\n'
+            yield line[:72] + line[21].ljust(4) + line[76:]
         else:
-            yield line + '\n'
+            yield line
 
 if __name__ == '__main__':
     # Check Input

pdb_join.py

@@ -60,7 +60,7 @@ def _join_pdb(pdb_list):
         pdb_data.append('MODEL     {0:>4d}'.format(i_model))
         with open(pdb_f, 'r') as handle:
             for line in handle:
-                line = line.strip()
+                line = line.strip('\n')
                 if coord_re.match(line):
                     pdb_data.append(line)
                     model_auids.add(auid(line))

pdb_occ.py

@@ -75,11 +75,10 @@ def _alter_occupancy(fhandle, occup):
     coord_re = re.compile('^(ATOM|HETATM)')
     occup = str(round(occup, 2)).rjust(6)
     for line in fhandle:
-        line = line.strip()
         if coord_re.match(line):
-            yield line[:54] + occup + line[60:] + '\n'
+            yield line[:54] + occup + line[60:]
         else:
-            yield line + '\n'
+            yield line
 
 if __name__ == '__main__':
 

pdb_reatom.py

@@ -76,12 +76,11 @@ def _renumber_pdb_atoms(fhandle, satomi):
     satomi = satomi
 
     for line in fhandle:
-        line = line.strip()
         if coord_re.match(line):
-            yield line[:6] + str(satomi).rjust(5) + line[11:] + '\n'
+            yield line[:6] + str(satomi).rjust(5) + line[11:]
             satomi += 1
         else:
-            yield line + '\n'
+            yield line
 
 if __name__ == '__main__':
 

pdb_reres.py

@@ -75,15 +75,14 @@ def _renumber_pdb_residue(fhandle, sresid):
     resi = sresid - 1
     prev_resi = None
     for line in fhandle:
-        line = line.strip()
         if line.startswith(('ATOM', 'HETATM', 'TER')):
             if line[22:26] != prev_resi:
                 prev_resi = line[22:26]
                 resi += 1
 
-            yield line[:22] + str(resi).rjust(4) + line[26:] + '\n'
+            yield line[:22] + str(resi).rjust(4) + line[26:]
         else:
-            yield line + '\n'
+            yield line
 
 if __name__ == '__main__':
 

pdb_rplchain.py

@@ -76,11 +76,10 @@ def _alter_chain(fhandle, ori_chain, new_chain):
         new_chain = ' '
 
     for line in fhandle:
-        line = line.strip()
         if coord_re.match(line) and line[21] == ori_chain:
-            yield line[:21] + new_chain + line[22:] + '\n'
+            yield line[:21] + new_chain + line[22:]
         else:
-            yield line + '\n'
+            yield line
 
 if __name__ == '__main__':
     # Check Input

pdb_seg.py

@@ -77,11 +77,10 @@ def _alter_segid(fhandle, seg_id):
     seg_id = seg_id[0:4].ljust(4)
 
     for line in fhandle:
-        line = line.strip()
         if coord_re.match(line):
-            yield line[:72] + seg_id + line[76:] + '\n'
+            yield line[:72] + seg_id + line[76:]
         else:
-            yield line + '\n'
+            yield line
 
 if __name__ == '__main__':
     # Check Input

pdb_selchain.py

@@ -77,9 +77,8 @@ def _select_chain(fhandle, chain_id):
     chain_id = chain_id
 
     for line in fhandle:
-        line = line.strip()
         if coord_re.match(line) and line[21] == chain_id:
-            yield line + '\n'
+            yield line
 
 if __name__ == '__main__':
     # Check Input

pdb_selseg.py

@@ -77,9 +77,8 @@ def _select_seg(fhandle, seg_id):
     seg_id = seg_id
 
     for line in fhandle:
-        line = line.strip()
         if coord_re.match(line) and line[72:76].strip() == seg_id:
-            yield line + '\n'
+            yield line
 
 if __name__ == '__main__':
     # Check Input

pdb_splitchain.py

@@ -56,7 +56,6 @@ def _extract_chains(fhandle):
 
     for line in fhandle:
         if coord_re.match(line):
-            line = line.strip()
             # ATOM/HETATM line
             if prev_chain != line[21]:
                 if not line[21] in chain_atoms:
@@ -67,7 +66,7 @@ def _extract_chains(fhandle):
                 prev_chain = line[21]
                 chain_ids.append(line[21])
             else:
-                cur_chain.append(line + '\n')
+                cur_chain.append(line)
 
     # Output chains to files
     for c_id in chain_ids:

pdb_splitmodel.py

@@ -54,10 +54,9 @@ def _extract_models(fhandle):
     output_handle = None
 
     for line in fhandle:
-        line = line.strip()
         if coord_re.match(line):
             # ATOM/HETATM line
-            output_handle.write(line + '\n')
+            output_handle.write(line)
         elif line.startswith('MODEL'):
             model_no = line.split()[-1]
             output_handle = open(fname_root + '_' + model_no + '.pdb', 'w')

pdb_splitseg.py

@@ -55,7 +55,6 @@ def _extract_segments(fhandle):
     prev_segment, segment_atoms = None, []
 
     for line in fhandle:
-        line = line.strip()
         if coord_re.match(line):
             # ATOM/HETATM line
             if prev_segment != line[72:76]:
@@ -66,10 +65,10 @@ def _extract_segments(fhandle):
                     output_handle.write('END\n')
                     output_handle.close()
                     segment_atoms = []
-                segment_atoms.append(line + '\n')
+                segment_atoms.append(line)
                 prev_segment = line[72:76]
             else:
-                segment_atoms.append(line + '\n')
+                segment_atoms.append(line)
 
     # Output last chain to file
     output_handle = open(fname_root + '_' + segment_atoms[-1][72:76].strip() + '.pdb', 'w')

pdb_striphet.py

@@ -52,9 +52,8 @@ def _remove_hetatm(fhandle):
 
     coord_re = re.compile('^ATOM')
     for line in fhandle:
-        line = line.strip()
         if coord_re.match(line):
-            yield line + '\n'   
+            yield line
 
 if __name__ == '__main__':