*** empty log message ***

Bio/PDB/NeighborSearch.py

@@ -11,15 +11,15 @@
 
 class NeighborSearch:
     """
-    This module can be used in two ways:
+    This class can be used for two related purposes:
 
     1. To find all atoms/residues/chains/models/structures within radius 
-    of a given query vector. 
+    of a given query position. 
 
     2. To find all atoms/residues/chains/models/structures that are within 
     a fixed radius of each other.
 
-    NeighborSearch makes use of the KD tree C++ module.
+    NeighborSearch makes use of the Bio.KDTree C++ module, so it's fast.
     """
     def __init__(self, atom_list, bucket_size=10):
         """

Bio/PDB/PDBIO.py

@@ -3,28 +3,55 @@
 __doc__="Output of PDB files."
 
 
-ATOM_FORMAT_STRING="%s%5i %-4s%c%3s %c%4i%c   %8.3f%8.3f%8.3f%6.2f%6.2f      %4s%2s%2s\n"
+_ATOM_FORMAT_STRING="%s%5i %-4s%c%3s %c%4i%c   %8.3f%8.3f%8.3f%6.2f%6.2f      %4s%2s%2s\n"
 
 
 class Select:
     """
-    Dummy class.
-    This selects which entities will be written out.
+    Default selection (everything) during writing - can be used as base class
+    to implement selective output. This selects which entities will be written out.
     """
+
+    def __repr__(self):
+        return "<Select all>"
+
     def accept_model(self, model):
+        """
+        Overload this to reject models for output.
+        """
         return 1
 
     def accept_chain(self, chain):
+        """
+        Overload this to reject chains for output.
+        """
         return 1
 
     def accept_residue(self, residue):
+        """
+        Overload this to reject residues for output.
+        """
         return 1
 
     def accept_atom(self, atom):
+        """
+        Overload this to reject atoms for output.
+        """
         return 1
 
 
 class PDBIO:
+    """
+    Write a Structure object (or a subset of a Structure object) as a PDB file.
+
+
+    Example:
+        >>> p=PDBParser()
+        >>> s=p.get_structure("1fat", "1fat.pdb")
+        >>> io=PDBIO()
+        >>> io.set_structure(s)
+        >>> io.save("out.pdb")
+    """
     def __init__(self):
         pass
 
@@ -47,7 +74,7 @@ def _get_atom_line(self, atom, hetfield, segid, atom_number, resname,
         args=(record_type, atom_number, name, altloc, resname, chain_id,
             resseq, icode, x, y, z, occupancy, bfactor, segid,
             element, charge)
-        return ATOM_FORMAT_STRING % args
+        return _ATOM_FORMAT_STRING % args
 
     # Public methods
 

Bio/PDB/Residue.py

@@ -12,11 +12,11 @@
 __doc__="Residue class, used by Structure objects."
 
 
-atom_name_dict={}
-atom_name_dict["N"]=1
-atom_name_dict["CA"]=2
-atom_name_dict["C"]=3
-atom_name_dict["O"]=4
+_atom_name_dict={}
+_atom_name_dict["N"]=1
+_atom_name_dict["CA"]=2
+_atom_name_dict["C"]=3
+_atom_name_dict["O"]=4
 
 
 class Residue(Entity):
@@ -53,12 +53,12 @@ def _sort(self, a1, a2):
         name2=a2.get_name()
         if name1==name2:
             return(cmp(a1.get_altloc(), a2.get_altloc()))
-        if atom_name_dict.has_key(name1):
-            index1=atom_name_dict[name1]
+        if _atom_name_dict.has_key(name1):
+            index1=_atom_name_dict[name1]
         else:
             index1=None
-        if atom_name_dict.has_key(name2):
-            index2=atom_name_dict[name2]
+        if _atom_name_dict.has_key(name2):
+            index2=_atom_name_dict[name2]
         else:
             index2=None
         if index1 and index2:

Bio/PDB/parse_pdb_header.py

@@ -109,7 +109,13 @@ def _nice_case(line):
     return s
 
 def parse_pdb_header(file):
-    """Returns the header lines for a pdb entry."""
+    """
+    Returns the header lines of a pdb file as a dictionary.
+
+    Dictionary keys are: head, deposition_date, release_date, structure_method,
+    resolution, structure_reference, journal_reference, author and
+    compound.
+    """
     header=[]
     f=open(filename,'r')
     while f: