Renamed one argument

Manual.html

@@ -131,9 +131,9 @@ This is the most powerful way to use PDBFixer.  It allows you to script the proc
 <p>
 PDBFixer is based on OpenMM, and to use its Python API you should first be familiar with the OpenMM API.  Consult the OpenMM documentation for details.  In everything that follows, I will assume you are already familiar with OpenMM.
 <p>
-To use PDBFixer create a <tt>PDBFixer</tt> object, passing to its constructor a <tt>PdbStructure</tt> object containing the structure to process.  You then call a series of methods on it to perform various transformations.  When all the transformations are done, you can get the new structure from its <tt>topology</tt> and <tt>positions</tt> fields.  The overall outline of your code will look something like this:
+To use PDBFixer create a <tt>PDBFixer</tt> object, passing to its constructor the file to process.  You then call a series of methods on it to perform various transformations.  When all the transformations are done, you can get the new structure from its <tt>topology</tt> and <tt>positions</tt> fields.  The overall outline of your code will look something like this:
 <tt><pre>
-fixer = PDBFixer(file=open('myfile.pdb'))
+fixer = PDBFixer(filename='myfile.pdb')
 # ...
 # Call various methods on the PDBFixer
 # ...
@@ -213,7 +213,7 @@ Here is a complete example that ties this together.  It adds all missing atoms i
 <tt><pre>
 from pdbfixer import PDBFixer
 from simtk.openmm.app import PDBFile
-fixer = PDBFixer(file=open('myfile.pdb'))
+fixer = PDBFixer(filename='myfile.pdb')
 fixer.findMissingResidues()
 fixer.findNonstandardResidues()
 fixer.replaceNonstandardResidues()
@@ -227,7 +227,7 @@ PDBFile.writeFile(fixer.topology, fixer.positions, open('output.pdb', 'w'))
 
 Suppose you want to keep only the first chain in the file and remove all the others.  To do this, call <tt>removeChains()</tt>:
 <tt><pre>
-<span style="color:grey">fixer = PDBFixer(file=open('myfile.pdb'))</span>
+<span style="color:grey">fixer = PDBFixer(filename='myfile.pdb')</span>
 numChains = len(list(fixer.topology.chains()))
 fixer.removeChains(range(1, numChains))
 <span style="color:grey">fixer.findMissingResidues()</span>

pdbfixer/pdbfixer.py

@@ -133,14 +133,14 @@ class PDBFixer(object):
     """PDBFixer implements many tools for fixing problems in PDB files.
     """
     
-    def __init__(self, filename=None, file=None, url=None, pdbid=None):
+    def __init__(self, filename=None, pdbfile=None, url=None, pdbid=None):
         """Create a new PDBFixer instance to fix problems in a PDB file.
         
         Parameters
         ----------
         filename : str, optional, default=None
             A filename specifying the file from which the PDB file is to be read.
-        file : file, optional, default=None
+        pdbfile : file, optional, default=None
             A file-like object from which the PDB file is to be read.
             The file is not closed after reading.
         url : str, optional, default=None
@@ -150,7 +150,7 @@ class PDBFixer(object):
             
         Notes
         -----
-        Only one of structure, filename, file, url, or pdbid may be specified or an exception will be thrown.
+        Only one of structure, filename, pdbfile, url, or pdbid may be specified or an exception will be thrown.
             
         Examples
         --------
@@ -160,7 +160,7 @@ class PDBFixer(object):
         >>> pdbid = '1VII'
         >>> url = 'http://www.rcsb.org/pdb/files/%s.pdb' % pdbid
         >>> file = urlopen(url)
-        >>> fixer = PDBFixer(file=file)
+        >>> fixer = PDBFixer(pdbfile=file)
 
         Start from a filename.
         
@@ -182,17 +182,17 @@ class PDBFixer(object):
         """
         
         # Check to make sure only one option has been specified.
-        if bool(filename) + bool(file) + bool(url) + bool(pdbid) != 1:
-            raise Exception("Exactly one option [filename, file, url, pdbid] must be specified.")
+        if bool(filename) + bool(pdbfile) + bool(url) + bool(pdbid) != 1:
+            raise Exception("Exactly one option [filename, pdbfile, url, pdbid] must be specified.")
 
         if filename:
             # A local file has been specified.
             file = open(filename, 'r')                
             structure = PdbStructure(file)
             file.close()
-        elif file:
+        elif pdbfile:
             # A file-like object has been specified.
-            structure = PdbStructure(file)  
+            structure = PdbStructure(pdbfile)  
         elif url:
             # A URL has been specified.
             file = urlopen(url)