diff --git a/doc/tests/CMakeLists.txt b/doc/tests/CMakeLists.txt
index 89bd4fcbd87a66d1c824e9dcf25a2dca530c6412..15ba86032f016e1d9f83003f3ef7afdd6f946511 100644
--- a/doc/tests/CMakeLists.txt
+++ b/doc/tests/CMakeLists.txt
@@ -49,6 +49,7 @@ set (DOC_TEST_SCRIPTS
scripts/modelling_loop_scoring.py
scripts/modelling_reconstruct_sidechains.py
scripts/modelling_sidechain_reconstructor.py
+ scripts/modelling_allatomrelaxer.py
scripts/sidechain_steps.py
)
diff --git a/doc/tests/scripts/modelling_allatomrelaxer.py b/doc/tests/scripts/modelling_allatomrelaxer.py
new file mode 100644
index 0000000000000000000000000000000000000000..c99244bcdd68e64d1cfb81cf6d717b1c44562e18
--- /dev/null
+++ b/doc/tests/scripts/modelling_allatomrelaxer.py
@@ -0,0 +1,27 @@
+from ost import io
+from promod3 import modelling, loop
+
+# load example (has res. numbering starting at 1)
+prot = io.LoadPDB('data/1CRN.pdb')
+res_list = prot.residues
+seqres_str = ''.join([r.one_letter_code for r in res_list])
+
+# initialize AllAtom environment and sidechain reconstructor
+env = loop.AllAtomEnv(seqres_str)
+env.SetInitialEnvironment(prot)
+sc_rec = modelling.SidechainReconstructor()
+sc_rec.AttachEnvironment(env)
+
+# "reconstruct" subset (res. num. 6..10) -> sidechains kept here
+sc_result = sc_rec.Reconstruct(6, 5)
+# setup sys creator
+ff_lookup = loop.ForcefieldLookup.GetDefault()
+mm_sys = loop.MmSystemCreator(ff_lookup)
+relaxer = modelling.AllAtomRelaxer(sc_result, mm_sys)
+# relax loop
+pot_e = relaxer.Run(sc_result, 300, 0.1)
+print "Potential energy after: %g" % pot_e
+# update environment with solution
+env.SetEnvironment(sc_result.env_pos)
+# store all positions of environment
+io.SavePDB(env.GetAllAtomPositions().ToEntity(), 'aa_relax_test.pdb')
diff --git a/doc/tests/scripts/modelling_sidechain_reconstructor.py b/doc/tests/scripts/modelling_sidechain_reconstructor.py
index 199c885643193333441080e8176c57a59b4a5f07..a39d3bf6afee1b33048dac47a473daf822f6e978 100644
--- a/doc/tests/scripts/modelling_sidechain_reconstructor.py
+++ b/doc/tests/scripts/modelling_sidechain_reconstructor.py
@@ -14,6 +14,10 @@ sc_rec.AttachEnvironment(env)
# reconstruct subset (res. num. 6..10)
res = sc_rec.Reconstruct(6, 5)
+# reconstruct two loops (6..10 and 20..25)
+res = sc_rec.Reconstruct(start_resnum_list=[6, 20],
+ num_residues_list=[5, 6],
+ chain_idx_list=[0, 0])
# update environment with solution
env.SetEnvironment(res.env_pos)
# store all positions of environment
diff --git a/doc/tests/test_doctests.py b/doc/tests/test_doctests.py
index 01a1b196890cd3ecc7a00ddd8351104a5bc7fe48..533148559befc5dc1d2fd23e01fcea2c4a2d962d 100644
--- a/doc/tests/test_doctests.py
+++ b/doc/tests/test_doctests.py
@@ -385,6 +385,14 @@ class DocTests(unittest.TestCase):
# clean up
os.remove('sc_rec_test.pdb')
+ def testModellingAllAtomRelaxer(self):
+ # run it
+ self.checkPMRun('modelling_allatomrelaxer.py', [], 0)
+ # check that result exists and is readable
+ io.LoadPDB('aa_relax_test.pdb')
+ # clean up
+ os.remove('aa_relax_test.pdb')
+
################################################################
def testSidechainSteps(self):
diff --git a/modelling/doc/loop_closing.rst b/modelling/doc/loop_closing.rst
index bd8484293aa93e1cfca17386073bc1a53bd5549e..386458ba39abdf80e0b2289a35c5eb25b7cb6463 100644
--- a/modelling/doc/loop_closing.rst
+++ b/modelling/doc/loop_closing.rst
@@ -313,6 +313,10 @@ After the reconstruction of loop sidechains with the
:class:`~promod3.modelling.SidechainReconstructor`, it may be desired to
quickly relax the loop. The :class:`AllAtomRelaxer` class takes care of that.
+Example usage:
+
+.. literalinclude:: ../../../tests/doc/scripts/modelling_allatomrelaxer.py
+
.. class:: AllAtomRelaxer(sc_data, mm_system_creator)
Setup relaxer for a given sidechain reconstruction result and a given MM
diff --git a/modelling/doc/sidechain_reconstruction.rst b/modelling/doc/sidechain_reconstruction.rst
index 52e4b1c720c2ccc320a9531cb574833413040b88..72e93a0a96a3f793542c32062748295655c010b7 100644
--- a/modelling/doc/sidechain_reconstruction.rst
+++ b/modelling/doc/sidechain_reconstruction.rst
@@ -61,7 +61,8 @@ SidechainReconstructor Class
the result.
:type build_disulfids: :class:`bool`
- :param optimize_subrotamers: Flag, whether the :func:`SubrotamerOptimizer`
+ :param optimize_subrotamers: Flag, whether the
+ :func:`~promod3.sidechain.SubrotamerOptimizer`
with default parametrization should be called
if we're dealing with FRM rotamers.
:type optimize_subrotamers: :class:`bool`
@@ -98,12 +99,13 @@ SidechainReconstructor Class
.. method:: Reconstruct(start_resnum, num_residues, chain_idx=0)
Reconstruct(start_resnum_list, num_residues_list, chain_idx_list)
- Reconstruct sidechains for one or several loops (extracted from environment).
- All residues in the loop(s) are expected to contain valid CB positions
- (or CA for GLY), which are used to look for other potentially relevant
- residues in the surrounding. The resulting structural data will contain all
- residues in the loop(s) and in the surrounding with all backbone and
- sidechain heavy atom positions set.
+ Reconstruct sidechains for one or several loops extracted from environment.
+ Overlapping loops are merged and 0-length loops are removed. All residues in
+ the loop(s) are expected to contain valid CB positions (or CA for GLY),
+ which are used to look for other potentially relevant residues in the
+ surrounding. The resulting structural data will contain all residues in the
+ loop(s) and in the surrounding with all backbone and sidechain heavy atom
+ positions set.
Note that the structural data of the loop(s) is expected to be in the linked
environment before calling this!
@@ -115,9 +117,9 @@ SidechainReconstructor Class
:param chain_idx: Chain the loop belongs to.
:type chain_idx: :class:`int`
- :param start_resnum_list: Start of loops.
+ :param start_resnum_list: Starts of loops.
:type start_resnum_list: :class:`list` of :class:`int`
- :param num_residues_list: Length of loops.
+ :param num_residues_list: Lengths of loops.
:type num_residues_list: :class:`list` of :class:`int`
:param chain_idx_list: Chains the loops belong to.
:type chain_idx_list: :class:`list` of :class:`int`
@@ -172,13 +174,22 @@ The SidechainReconstructionData class
:type: :class:`~promod3.loop.AllAtomEnvPositions`
- .. attribute:: length
+ .. attribute:: loop_start_indices
+ loop_lengths
- Length of the residues used to generate this result. The first *length*
- residues in *env_pos* are guaranteed to belong to the actual input, all the
- rest comes from the close environment.
+ The first *sum(loop_lengths)* residues in
+ :attr:`~promod3.loop.AllAtomEnvPositions.res_indices` of *env_pos* are
+ guaranteed to belong to the actual input, all the rest comes from the close
+ environment.
- :type: :class:`int`
+ Each input loop (apart from overlapping and 0-length loops) is defined by an
+ entry in *loop_start_indices* and *loop_lengths*. For loop *i_loop*,
+ *res_indices[loop_start_indices[i_loop]]* is the N-stem and
+ *res_indices[loop_start_indices[i_loop] + loop_lengths[i_loop] - 1]* is the
+ C-stem of the loop. The loop indices are contiguous in *res_indices* between
+ the stems.
+
+ :type: :class:`list` of :class:`int`
.. attribute:: rotamer_res_indices