From 346d90c4448e36dc81cb495a33a20b7308ee4399 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Sat, 10 Nov 2018 00:36:26 +0100
Subject: [PATCH] add some options to build-sidechains action
---
actions/doc/index.rst | 14 ++++++++++++--
actions/pm-build-sidechains | 20 ++++++++++++++++++--
2 files changed, 30 insertions(+), 4 deletions(-)
diff --git a/actions/doc/index.rst b/actions/doc/index.rst
index 3e3c611b..450ffa57 100644
--- a/actions/doc/index.rst
+++ b/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
+
diff --git a/actions/pm-build-sidechains b/actions/pm-build-sidechains
index a04cd7b1..c7ceb244 100644
--- a/actions/pm-build-sidechains
+++ b/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()
--
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