permit atomic input to deformAtoms

prody/dynamics/sampling.py

@@ -260,8 +260,8 @@ def deformAtoms(atoms, mode, rmsd=None, replace=False, scale=None):
     generate a coordinate set with given RMSD distance to the active coordinate
     set."""
 
-    if not isinstance(atoms, AtomGroup):
-        raise TypeError('atoms must be an AtomGroup, not {0}'
+    if not isinstance(atoms, Atomic):
+        raise TypeError('atoms must be an Atomic object, not {0}'
                         .format(type(atoms)))
     if not isinstance(mode, VectorBase):
         raise TypeError('mode must be a Mode or Vector instance, '
@@ -280,15 +280,12 @@ def deformAtoms(atoms, mode, rmsd=None, replace=False, scale=None):
         rmsd = float(rmsd)
         # rmsd = ( ((scalar * array)**2).sum() / n_atoms )**0.5
         scalar = (atoms.numAtoms() * rmsd**2 / (array**2).sum())**0.5
+        scale *= scalar
         LOGGER.info('Mode is scaled by {0}.'.format(scalar))
-        if replace is False:
-            atoms.addCoordset(atoms.getCoords() + array * scalar * scale)
-        else:
-            atoms.setCoords(atoms.getCoords() + array * scalar * scale)
+
+    if replace is False:
+        atoms.addCoordset(atoms.getCoords() + array * scale)
     else:
-        if replace is False:
-            atoms.addCoordset(atoms.getCoords() + array * scale)
-        else:
-            atoms.setCoords(atoms.getCoords() + array * scale)
+        atoms.setCoords(atoms.getCoords() + array * scale)
 
 

prody/proteins/cifheader.py

@@ -745,8 +745,11 @@ def _getReference(lines):
             except:
                 continue
             if what == 'AUTH':
-                surname, initials = value.split(',')
-                author = initials+surname
+                try:
+                    surname, initials = value.split(',')
+                    author = initials+surname
+                except ValueError:
+                    author = value
                 authors.append(author.strip().upper())
 
         ref['authors'] = authors

prody/proteins/localpdb.py

@@ -212,12 +212,15 @@ def fetchPDB(*pdb, **kwargs):
     if len(pdb) == 1 and isinstance(pdb[0], list):
         pdb = pdb[0]
 
-    identifiers = checkIdentifiers(*pdb)
-
     folder = kwargs.get('folder', '.')
     compressed = kwargs.get('compressed')
     format_ = kwargs.get('format', 'pdb')
 
+    if format_ != 'emd':
+        identifiers = checkIdentifiers(*pdb)
+    else:
+        identifiers = pdb
+
     # check *folder* specified by the user, usually pwd ('.')
     filedict = findPDBFiles(folder, compressed=compressed, 
                             format=format_)

prody/proteins/pdbfile.py

@@ -214,13 +214,15 @@ def _parsePDB(pdb, **kwargs):
         if filename is None:
             try:
                 LOGGER.warn("Trying to parse mmCIF file instead")
+                chain = kwargs.pop('chain', chain)
                 return parseMMCIF(pdb+chain, **kwargs)
-            except:
+            except OSError:
                 try:
                     LOGGER.warn("Trying to parse EMD file instead")
+                    chain = kwargs.pop('chain', chain)
                     return parseEMD(pdb+chain, **kwargs)
                 except:
-                    raise IOError('PDB file for {0} could not be downloaded.'
+                    raise IOError('PDB file for {0} could not be parsed.'
                                 .format(pdb))
         pdb = filename
     if title is None:

prody/proteins/wwpdb.py

@@ -254,7 +254,22 @@ def fetchPDBviaHTTP(*pdb, **kwargs):
     output_folder = kwargs.pop('folder', None)
     compressed = bool(kwargs.pop('compressed', True))
 
-    extension = '.pdb'
+    format = kwargs.get('format', 'pdb')
+    noatom = bool(kwargs.pop('noatom', False))
+    if format == 'pdb':
+        extension = '.pdb'
+    elif format == 'xml':
+        if noatom:
+            extension = '-noatom.xml'
+        else:
+            extension = '.xml'
+    elif format == 'cif':
+        extension = '.cif'
+    elif format == 'emd' or format == 'map':
+        extension = '.map'
+    else:
+        raise ValueError(repr(format) + ' is not valid format')
+
     local_folder = pathPDBFolder()
     if local_folder:
         local_folder, is_divided = local_folder
@@ -294,7 +309,10 @@ def fetchPDBviaHTTP(*pdb, **kwargs):
             filenames.append(None)
             continue
         try:
-            handle = openURL(getURL(pdb))
+            url = getURL(pdb)
+            if kwargs.get('format', 'pdb') != 'pdb':
+                url = url.replace('.pdb', extension)
+            handle = openURL(url)
         except Exception as err:
             LOGGER.warn('{0} download failed ({1}).'.format(pdb, str(err)))
             failure += 1

prody/tests/proteins/test_wwpdb.py

@@ -15,15 +15,15 @@
 LOGGER.verbosity = 'none'
 
 
-class TestFTP(unittest.TestCase):
+class TestHTTP(unittest.TestCase):
 
     def setUp(self):
 
         self.pdb = ['1ubi', '1aar', 'arg', 1234]
         self.fns = []
         self.len = [683, 1218, None, None]
-        self.fetch = fetchPDBviaFTP
-        self.protocol = 'FTP'
+        self.fetch = fetchPDBviaHTTP
+        self.protocol = 'HTTP'
 
 
     @dec.slow
@@ -69,12 +69,3 @@ def tearDown(self):
                 pass
             except:
                 pass
-
-class TestHTTP(TestFTP):
-
-    def setUp(self):
-
-        TestFTP.setUp(self)
-        self.fetch = fetchPDBviaHTTP
-        self.protocol = 'HTTP'
-