Use Modeller 10 syntax

salilab · Jan 18, 2024 · 88c82e2 · 88c82e2
1 parent 2b1f821
commit 88c82e2
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Showing 3 changed files with 10 additions and 10 deletions.
diff --git a/modules/modeller/examples/imp_restraints_in_modeller.py b/modules/modeller/examples/imp_restraints_in_modeller.py
@@ -13,11 +13,11 @@
 IMP.setup_from_argv(sys.argv, "IMP restraints in Modeller")
 
 # Set up Modeller and build a model from the GGCC primary sequence
-e = modeller.environ()
+e = modeller.Environ()
 e.edat.dynamic_sphere = False
 e.libs.topology.read('${LIB}/top_heav.lib')
 e.libs.parameters.read('${LIB}/par.lib')
-modmodel = modeller.model(e)
+modmodel = modeller.Model(e)
 modmodel.build_sequence('GGCC')
 
 # Set up IMP and load the Modeller model in as a new Hierarchy
@@ -37,5 +37,5 @@
 t.append(IMP.modeller.IMPRestraints(atoms, sf))
 
 # Calculate the Modeller energy (score) for the whole protein
-sel = modeller.selection(modmodel)
+sel = modeller.Selection(modmodel)
 sel.energy()
diff --git a/modules/modeller/examples/load_modeller_model.py b/modules/modeller/examples/load_modeller_model.py
@@ -12,14 +12,14 @@
 IMP.setup_from_argv(sys.argv, "Load Modeller model")
 
 # Set up Modeller and build a model from the GGCC primary sequence
-e = modeller.environ()
+e = modeller.Environ()
 e.edat.dynamic_sphere = True
 e.libs.topology.read('${LIB}/top_heav.lib')
 e.libs.parameters.read('${LIB}/par.lib')
-modmodel = modeller.model(e)
+modmodel = modeller.Model(e)
 modmodel.build_sequence('GGCC')
 # Generate Modeller stereochemistry
-sel = modeller.selection(modmodel)
+sel = modeller.Selection(modmodel)
 modmodel.restraints.make(sel, restraint_type='STEREO', spline_on_site=False)
 
 # Set up IMP and use the ModelLoader class to load the atom coordinates

diff --git a/modules/modeller/examples/modeller_restraints_in_imp.py b/modules/modeller/examples/modeller_restraints_in_imp.py
@@ -13,16 +13,16 @@
 IMP.setup_from_argv(sys.argv, "Modeller restraints in IMP")
 
 # Set up Modeller and build a model from the GGCC primary sequence
-e = modeller.environ()
+e = modeller.Environ()
 e.edat.dynamic_sphere = False
 e.libs.topology.read('${LIB}/top_heav.lib')
 e.libs.parameters.read('${LIB}/par.lib')
-modmodel = modeller.model(e)
+modmodel = modeller.Model(e)
 modmodel.build_sequence('GGCC')
 
 # Add a simple Modeller distance restraint between the first and last atoms
-feat = modeller.features.distance(modmodel.atoms[0], modmodel.atoms[-1])
-r = modeller.forms.gaussian(feature=feat, mean=10.0, stdev=1.0,
+feat = modeller.features.Distance(modmodel.atoms[0], modmodel.atoms[-1])
+r = modeller.forms.Gaussian(feature=feat, mean=10.0, stdev=1.0,
                             group=modeller.physical.xy_distance)
 modmodel.restraints.add(r)