Squashed 'modules/pmi/' changes from 6473c8307f..d722206661

d722206661 Only make things flexible if asked for 10646dc022 Work around cmake 3.18.3 bug 625dca7985 Migrate to travis-ci.com git-subtree-dir: modules/pmi git-subtree-split: d7222066612e0a8bb11726345a88bf24a89e15a8
salilab · Nov 17, 2020 · 2d18e25 · 2d18e25
1 parent 295ebe9
commit 2d18e25
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Showing 4 changed files with 17 additions and 16 deletions.
diff --git a/modules/pmi/CMakeLists.txt b/modules/pmi/CMakeLists.txt
@@ -7,6 +7,10 @@ if(CMAKE_SOURCE_DIR STREQUAL CMAKE_CURRENT_SOURCE_DIR)
     cmake_policy(SET CMP0058 NEW)
   endif(POLICY CMP0058)
 
+  if(POLICY CMP0053)
+    cmake_policy(SET CMP0053 NEW)
+  endif(POLICY CMP0053)
+
   set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR}/tools)
 
   set(SWIG_EXECUTABLE swig CACHE STRING "Swig program")

diff --git a/modules/pmi/README.md b/modules/pmi/README.md
@@ -1,6 +1,6 @@
 \brief Python classes to represent, score, sample and analyze models.
 
-[![Build Status](https://travis-ci.org/salilab/pmi.svg?branch=develop)](https://travis-ci.org/salilab/pmi)
+[![Build Status](https://travis-ci.com/salilab/pmi.svg?branch=develop)](https://travis-ci.com/salilab/pmi)
 [![codecov](https://codecov.io/gh/salilab/pmi/branch/develop/graph/badge.svg)](https://codecov.io/gh/salilab/pmi)
 [![Codacy Badge](https://api.codacy.com/project/badge/Grade/bcced071b3f541449d723a774ea09026)](https://www.codacy.com/app/salilab/pmi?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=salilab/pmi&amp;utm_campaign=Badge_Grade)
 

diff --git a/modules/pmi/pyext/src/macros.py b/modules/pmi/pyext/src/macros.py
@@ -757,15 +757,14 @@ def execute_macro(self, max_rb_trans=4.0, max_rb_rot=0.04, max_bead_trans=4.0, m
                 if dname not in domains_in_rbs:
                     if domain.pdb_file != "BEADS":
                         warnings.warn(
-                              "Making %s flexible. This will likely distort "
-                              "the structure. It is strongly recommended to "
-                              "make PDB domains rigid, or use BEADS instead "
-                              "of a PDB file for flexible regions." % dname,
-                              IMP.pmi.StructureWarning)
-                    # Make both "atomic" (i.e. initialized from a PDB file)
-                    # and "non-atomic" (i.e. beads) regions flexible
+                            "No rigid bodies set for %s. Residues read from "
+                            "the PDB file will not be sampled - only regions "
+                            "missing from the PDB will be treated flexibly. "
+                            "To sample the entire sequence, use BEADS instead "
+                            "of a PDB file name" % dname,
+                            IMP.pmi.StructureWarning)
                     self.dof.create_flexible_beads(
-                            self._domain_res[nstate][dname],
+                            self._domain_res[nstate][dname][1],
                             max_trans=max_bead_trans)
 
             # add super rigid bodies

diff --git a/modules/pmi/test/test_topology_input.py b/modules/pmi/test/test_topology_input.py
@@ -107,17 +107,15 @@ def test_flexible(self):
         with warnings.catch_warnings(record=True) as cw:
             warnings.simplefilter("always")
             root_hier, dof = bs.execute_macro()
-        # Both domains (one a PDB, one beads) should be flexible
-        # There should be 12 flexible beads:
-        # Residues 1, 2, 5, 6 (taken from the PDB file)
+        # Both domains (missing regions from PDB, one beads) should be flexible
+        # There should be 6 flexible beads:
         # Beads 3, 4, 7, 8, 9, 10
-        # Resolution=10 fragments 1-2, 5-6
-        self.assertEqual(len(dof.get_movers()), 12)
+        self.assertEqual(len(dof.get_movers()), 6)
         self.assertEqual(len(dof.get_rigid_bodies()), 0)
-        self.assertEqual(len(dof.get_flexible_beads()), 12)
+        self.assertEqual(len(dof.get_flexible_beads()), 6)
         # One warning should be emitted, for the PDB domain
         w, = cw
-        self.assertIn("Making Prot1..0 flexible. This will likely distort",
+        self.assertIn("No rigid bodies set for Prot1..0.",
                       str(w.message))
         self.assertIs(w.category, IMP.pmi.StructureWarning)