add some options to build-sidechains action

actions/doc/index.rst

@@ -147,8 +147,8 @@ You can (re-)construct the sidechains in a model from the command line.
 
 .. code-block:: console
 
-  $ usage: build-sidechains [-h] (-p <FILE> | -e <FILE>) [-o <FILENAME>] [-k] 
-                            [-n] [-r]
+  $ usage: build-sidechains [-h] (-p <FILE> | -e <FILE>) [-o <FILENAME>] [-k] [-n]
+                            [-r] [-i] [-s]
 
 Example usage:
 
@@ -180,3 +180,13 @@ Several flags control the modelling behaviour:
 
   Do not use rotamers with subrotamers
 
+.. option:: -i, --backbone-independent
+
+  Use backbone independent rotamer library 
+  (from :meth:`promod3.sidechain.LoadLib`) instead of the default backbone 
+  dependent one (from :meth:`promod3.sidechain.LoadBBDepLib`)
+
+.. option:: -s, --no-subrotamer-optimization
+
+  Dont do subrotamer optimization if flexible rotamer model is used
+

actions/pm-build-sidechains

@@ -11,7 +11,7 @@ Example usage:
 import os
 import ost
 from ost import io, settings
-from promod3 import modelling
+from promod3 import modelling, sidechain
 from promod3.core import pm3argparse, helper
 
 # make sure we see output when passing '-h'
@@ -32,6 +32,12 @@ parser.add_argument('-n', '--no-disulfids', action='store_true',
                          'optimization')
 parser.add_argument('-r', '--rigid-rotamers', action='store_true',
                     help='Do not use rotamers with subrotamers')
+parser.add_argument('-i', '--backbone-independent', action='store_true',
+                    help='Use backbone independent rotamer library instead ' +
+                         'of the default backbone dependent one')
+parser.add_argument('-s', '--no-subrotamer-optimization', action='store_true',
+                    help='Dont do subrotamer optimization if flexible ' +
+                         'rotamer model is used.')
 
 opts = parser.Parse()
 
@@ -45,10 +51,20 @@ rotamer_model = "frm"
 if opts.rigid_rotamers:
     rotamer_model = "rrm"
 
+lib = None
+if opts.backbone_independent:
+    lib = sidechain.LoadLib()
+
+opt_subrot = True
+if opts.no_subrotamer_optimization:
+    opt_subrot = False
+
 # do sidechain modelling
 modelling.ReconstructSidechains(prot, keep_sidechains=opts.keep_sidechains,
                                 build_disulfids=opts.no_disulfids==False, 
-                                rotamer_model=rotamer_model)
+                                rotamer_model=rotamer_model, 
+                                rotamer_library=lib, 
+                                optimize_subrotamers=opt_subrot)
 
 # output
 ost.PopVerbosityLevel()