Use Modeller 10 class names

lib/cryptosite/am_bmi.py

@@ -11,12 +11,12 @@ def get_sas(pdb, probe):
     import modeller
 
     # Read the PDB file
-    env = modeller.environ()
-    mdl = modeller.model(env)
+    env = modeller.Environ()
+    mdl = modeller.Model(env)
     mdl.read(file=pdb)
 
     # Calculate atomic accessibilities (in Biso) with appropriate probe_radius
-    myedat = modeller.energy_data()
+    myedat = modeller.EnergyData()
     myedat.radii_factor = 1.6
     mdl.write_data(edat=myedat, output='PSA ATOMIC_SOL',
                    psa_integration_step=0.05, probe_radius=probe)

lib/cryptosite/analysis.py

@@ -111,9 +111,9 @@ def get_qioft(landscape, rcut=11.):
     """Calculate Qi for all models in a landscape."""
     import modeller
     modeller.log.none()
-    e = modeller.environ()
+    e = modeller.Environ()
     e.io.hetatm = False
-    m = modeller.model(e)
+    m = modeller.Model(e)
 
     for dirname in _get_subdirectories(landscape):
         with open(os.path.join(dirname, 'list')) as fh:

lib/cryptosite/cleaning.py

@@ -15,8 +15,8 @@ def get_pdb_seq(pdb, chain):
     '''
     import modeller
 
-    e = modeller.environ()
-    m = modeller.model(e, file=pdb,
+    e = modeller.Environ()
+    m = modeller.Model(e, file=pdb,
                        model_segment=('FIRST:' + chain, 'LAST:' + chain))
     # BLAST will get confused if the PDB file contains non-standard ATOM
     # records (e.g. HIE rather than HIS)
@@ -111,29 +111,29 @@ def build_model(pdb, chains):
     and loop modeling for the rest.
     '''
     import modeller
-    from modeller.automodel import loopmodel, automodel, assess
+    from modeller.automodel import LoopModel, AutoModel, assess
 
     # --- get gaps
     gaps = get_gaps('alignment.pir')
     with open('gaps_%s.txt' % pdb, 'w') as out:
         out.write(pdb + '_mdl\t' + str(gaps))
 
     # --- set up modeling
-    env = modeller.environ()
+    env = modeller.Environ()
 
     env.io.atom_files_directory = ['.', '../atom_files']
 
-    class MyLoop(loopmodel):
+    class MyLoop(LoopModel):
         def select_loop_atoms(self):
             gaps = get_gaps('alignment.pir')
-            return modeller.selection(
+            return modeller.Selection(
                 self.residue_range(i.split(',')[0], i.split(',')[1])
                 for i in gaps)
 
         def special_restraints(self, aln):
             rsr = self.restraints
-            wholeSel = modeller.selection(self) - self.select_loop_atoms()
-            r = modeller.rigid_body(wholeSel)
+            wholeSel = modeller.Selection(self) - self.select_loop_atoms()
+            r = modeller.RigidBody(wholeSel)
             rsr.rigid_bodies.append(r)
 
     if len(gaps) > 0:
@@ -164,7 +164,7 @@ def special_restraints(self, aln):
         os.system('rm %s_X.*' % (pdb.lower(),))
 
     else:
-        a = automodel(env, alnfile='alignment.pir',
+        a = AutoModel(env, alnfile='alignment.pir',
                       knowns=pdb, sequence=pdb.lower() + '_X',
                       assess_methods=(assess.DOPE,))
         a.very_fast()
@@ -176,6 +176,6 @@ def special_restraints(self, aln):
         os.system('rm %s_X.*' % (pdb.lower(),))
 
     if len(chains) == 1:
-        mdl = modeller.model(env, file='XXX_mdl')
+        mdl = modeller.Model(env, file='XXX_mdl')
         mdl.rename_segments(segment_ids='A')
         mdl.write(file='%s_mdl.pdb' % (pdb))

lib/cryptosite/soap.py

@@ -12,7 +12,7 @@ def soap_score():
     from modeller.scripts import complete_pdb
     from modeller import soap_protein_od
 
-    env = modeller.environ()
+    env = modeller.Environ()
     env.libs.topology.read(file='$(LIB)/top_heav.lib')
     env.libs.parameters.read(file='$(LIB)/par.lib')
 
@@ -32,7 +32,7 @@ def soap_score():
             # Read a model previously generated by Modeller's automodel class
             mdl = complete_pdb(env, fil)
             # Select all atoms
-            atmsel = modeller.selection(mdl)
+            atmsel = modeller.Selection(mdl)
 
             # Assess with the above Scorer
             try:

test/mock/modeller/__init__.py

@@ -1,6 +1,6 @@
 import sys
 
 
-class environ(object):
+class Environ(object):
     def __init__(self):
         sys.exit(0)

test/test_analysis.py

@@ -34,8 +34,8 @@ def test_bad(self):
 
     def test_get_coordinates_sc(self):
         """Test get_coordinates_sc() function"""
-        e = modeller.environ()
-        m = modeller.model(e)
+        e = modeller.Environ()
+        m = modeller.Model(e)
         coord = cryptosite.analysis.get_coordinates_sc(
             m, os.path.join(TOPDIR, 'test', 'input', 'test_coord.pdb'))
         self.assertEqual(len(coord), 4)

test/test_cleaning.py

@@ -36,8 +36,8 @@ def test_detect_invalid_residue_types_ok(self):
             fname = os.path.join(tmpdir, 'test.pdb')
             with open(fname, 'w') as fh:
                 fh.write(pdb_line + '\n')
-            e = modeller.environ()
-            m = modeller.model(e, file=fname)
+            e = modeller.Environ()
+            m = modeller.Model(e, file=fname)
         cleaning._detect_invalid_residue_types(m)
 
     def test_detect_invalid_residue_types_bad(self):
@@ -53,8 +53,8 @@ def test_detect_invalid_residue_types_bad(self):
 ATOM      5  N   HSD B   3      18.511  -1.416  15.632  1.00  6.84           C
 ATOM      6  C   HSD B   3      18.511  -1.416  15.632  1.00  6.84           C
 """)
-            e = modeller.environ()
-            m = modeller.model(e, file=fname)
+            e = modeller.Environ()
+            m = modeller.Model(e, file=fname)
         self.assertRaises(cleaning.InvalidResiduesError,
                           cleaning._detect_invalid_residue_types, m)
 
@@ -108,7 +108,7 @@ def mocked_loopmodel_make(self):
             with open('input.pdb', 'w') as fh:
                 fh.write(pdb_line + '\n')
                 fh.write(pdb_line[:25] + '2' + pdb_line[26:] + '\n')
-            with utils.mocked_object(modeller.automodel.loopmodel, 'make',
+            with utils.mocked_object(modeller.automodel.LoopModel, 'make',
                                      mocked_loopmodel_make):
                 cleaning.build_model('XXX', ['A'])
             os.unlink('XXX_mdl.pdb')

test/test_soap.py

@@ -6,7 +6,7 @@
 import modeller
 import subprocess
 from modeller import soap_protein_od
-from modeller.terms import energy_term
+from modeller.terms import EnergyTerm
 
 TOPDIR = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))
 utils.set_search_paths(TOPDIR)
@@ -17,7 +17,7 @@
 # the SOAP potentials installed (even if we do have them, they are slow to
 # read in and use a lot of memory) and b) we can make sure any exceptions
 # are handled properly by the soap script
-class MockScorer(energy_term):
+class MockScorer(EnergyTerm):
     name = 'MockScorer'
 
     def __init__(self):