def _add_provenance_nodes(self, rmf, rt):
"""Add *Provenance nodes under rt. Return the root."""
softpf = RMF.SoftwareProvenanceFactory(rmf)
scriptpf = RMF.ScriptProvenanceFactory(rmf)
strucpf = RMF.StructureProvenanceFactory(rmf)
samppf = RMF.SampleProvenanceFactory(rmf)
filtpf = RMF.FilterProvenanceFactory(rmf)
clustpf = RMF.ClusterProvenanceFactory(rmf)
clust_node = rt.add_child("clustering", RMF.PROVENANCE)
clust = clustpf.get(clust_node)
clust.set_members(10)
filt_node = clust_node.add_child("filtering", RMF.PROVENANCE)
filt = filtpf.get(filt_node)
filt.set_method("Total score")
filt.set_threshold(250.)
filt.set_frames(4)
samp_node = filt_node.add_child("sampling", RMF.PROVENANCE)
samp = samppf.get(samp_node)
samp.set_method("Monte Carlo")
samp.set_frames(100)
samp.set_iterations(10)
samp.set_replicas(8)
struc_node = samp_node.add_child("structure", RMF.PROVENANCE)
struc = strucpf.get(struc_node)
struc.set_filename(os.path.abspath('foo.pdb'))
struc.set_chain('X')
# Test default
self.assertEqual(struc.get_residue_offset(), 0)
struc.set_residue_offset(42)
script_node = struc_node.add_child("script", RMF.PROVENANCE)
script = scriptpf.get(script_node)
script.set_filename(os.path.abspath('test.py'))
soft_node = script_node.add_child("software", RMF.PROVENANCE)
soft = softpf.get(soft_node)
soft.set_name('RMF')
soft.set_version('1.0.1')
soft.set_location('https://test.url')
return clust_node
def _check_provenance_nodes(self, rmf, prov_root):
softpf = RMF.SoftwareProvenanceFactory(rmf)
scriptpf = RMF.ScriptProvenanceFactory(rmf)
strucpf = RMF.StructureProvenanceFactory(rmf)
filtpf = RMF.FilterProvenanceFactory(rmf)
samppf = RMF.SampleProvenanceFactory(rmf)
clustpf = RMF.ClusterProvenanceFactory(rmf)
self.assertTrue(clustpf.get_is(prov_root))
clust = clustpf.get(prov_root)
self.assertEqual(clust.get_members(), 10)
filt_node = prov_root.get_children()[0]
self.assertTrue(filtpf.get_is(filt_node))
filt = filtpf.get(filt_node)
self.assertEqual(filt.get_method(), "Total score")
self.assertAlmostEqual(filt.get_threshold(), 250., delta=0.1)
self.assertEqual(filt.get_frames(), 4)
samp_node = filt_node.get_children()[0]
self.assertTrue(samppf.get_is(samp_node))
samp = samppf.get(samp_node)
self.assertEqual(samp.get_frames(), 100)
self.assertEqual(samp.get_iterations(), 10)
self.assertEqual(samp.get_replicas(), 8)
self.assertEqual(samp.get_method(), "Monte Carlo")
struc_node = samp_node.get_children()[0]
self.assertTrue(strucpf.get_is(struc_node))
struc = strucpf.get(struc_node)
self.assertEqual(struc.get_filename(), os.path.abspath('foo.pdb'))
self.assertEqual(struc.get_chain(), 'X')
self.assertEqual(struc.get_residue_offset(), 42)
script_node = struc_node.get_children()[0]
self.assertTrue(scriptpf.get_is(script_node))
script = scriptpf.get(script_node)
self.assertEqual(script.get_filename(), os.path.abspath('test.py'))
soft_node = script_node.get_children()[0]
self.assertTrue(softpf.get_is(soft_node))
soft = softpf.get(soft_node)
self.assertEqual(soft.get_name(), 'RMF')
self.assertEqual(soft.get_version(), '1.0.1')
self.assertEqual(soft.get_location(), 'https://test.url')
def make_cluster_centroid(infname, frame, outfname, cluster_index,
cluster_size, precision, density, path):
import RMF
# If we have new enough IMP/RMF, do our own RMF slicing with provenance
if hasattr(RMF.NodeHandle, 'replace_child'):
print(infname, outfname)
inr = RMF.open_rmf_file_read_only(infname)
outr = RMF.create_rmf_file(outfname)
cpf = RMF.ClusterProvenanceFactory(outr)
RMF.clone_file_info(inr, outr)
RMF.clone_hierarchy(inr, outr)
RMF.clone_static_frame(inr, outr)
inr.set_current_frame(RMF.FrameID(frame))
outr.add_frame("f0")
RMF.clone_loaded_frame(inr, outr)
rn = outr.get_root_node()
children = rn.get_children()
if len(children) == 0:
return
rn = children[0] # Should be the top-level IMP node
prov = [c for c in rn.get_children() if c.get_type() == RMF.PROVENANCE]
if not prov:
return
prov = prov[0]
# Add cluster-provenance info
newp = rn.replace_child(prov, "cluster.%d" % cluster_index,
RMF.PROVENANCE)
cp = cpf.get(newp)
cp.set_members(cluster_size)
cp.set_precision(precision)
cp.set_density(os.path.abspath(density))
else:
# Otherwise, fall back to RMF's command line tool
import subprocess
print(infname, frame, outfname)
subprocess.call(
['rmf_slice', path + infname, '-f',
str(frame), outfname])
