From cfb041e7016cdb0d6e5f64ebf8fb63ee2bc23c5d Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 9 Nov 2018 16:02:48 +0100
Subject: [PATCH] The user can now add profiles to the build-model action
---
actions/doc/index.rst | 24 +++++++++++++++++++++++-
actions/pm-build-model | 5 ++++-
2 files changed, 27 insertions(+), 2 deletions(-)
diff --git a/actions/doc/index.rst b/actions/doc/index.rst
index 6f997647..56a0e2a5 100644
--- a/actions/doc/index.rst
+++ b/actions/doc/index.rst
@@ -20,7 +20,7 @@ with
.. code-block:: console
$ pm build-model [-h] (-f <FILE> | -c <FILE> | -j <OBJECT>|<FILE>)
- (-p <FILE> | -e <FILE>) [-o <FILENAME>]
+ (-p <FILE> | -e <FILE>) [-s <FILE>] [-o <FILENAME>]
Example usage:
@@ -105,6 +105,28 @@ sequence names are:
Example: ``... -p data/2jlp.pdb.gz``, where the pdb file has chains ``A``,
``B``, ``C`` and the template sequence is named ``2jlp.A|55``.
+
+You can optionally specify sequence profiles to be added (``-s``) and linked
+to the corresponding target sequences. This has an impact on loop scoring with
+the database approach.
+The profiles can be provided as plain files or gzipped. Following file
+extensions are understood: .hhm, .hhm.gz, .pssm, .pssm.gz.
+
+* The profiles are mapped based on exact matches towards the gapless
+ target sequences from the provided alignment files,
+ i.e. one profile is mapped to several chains in case of homo-oligomers
+
+* Every profile must have a unique sequence to avoid ambiguities
+
+* All or nothing - You cannot provide profiles for only a subset of
+ target sequences
+
+Example usage:
+
+.. code-block:: console
+
+ $ pm build-model -f aln.fasta -p tpl.pdb -s prof.hhm
+
Possible exit codes of the action:
- 0: all went well
diff --git a/actions/pm-build-model b/actions/pm-build-model
index 1dcd882c..f7155293 100755
--- a/actions/pm-build-model
+++ b/actions/pm-build-model
@@ -23,6 +23,7 @@ ost.PushVerbosityLevel(2)
parser = pm3argparse.PM3ArgumentParser(__doc__, action=True)
parser.AddAlignment()
parser.AddStructure(attach_views=True)
+parser.AddProfile()
parser.AssembleParser()
parser.add_argument('-o', '--model-file', metavar='<FILENAME>', type=str,
default='model.pdb', help='File to store model coordinates'+
@@ -43,11 +44,13 @@ for aln in opts.alignments:
for i in range(1, aln.GetCount()):
ost.mol.alg.AssignSecStruct(aln.GetSequence(i).GetAttachedView())
-
# model it
try:
# get raw model
mhandle = modelling.BuildRawModel(opts.alignments)
+ # add profiles if any
+ if len(opts.profiles) > 0:
+ modelling.SetSequenceProfiles(mhandle, opts.profiles)
# build final model
final_model = modelling.BuildFromRawModel(mhandle)
except Exception as ex:
--
GitLab