From c45a9379b7540fea1932bc51a85c94b5ba36869d Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Mon, 29 Jun 2020 08:18:19 +0200
Subject: [PATCH] perforn alignment preprocesing in BuildRawModel
---
.../scripts/modelling_close_small_deletions.py | 4 ++--
modelling/pymod/_raw_model.py | 18 ++++++++++++++++--
modelling/tests/test_close_gaps.py | 12 ++++++++----
modelling/tests/test_modelling.py | 6 ++++--
4 files changed, 30 insertions(+), 10 deletions(-)
diff --git a/doc/tests/scripts/modelling_close_small_deletions.py b/doc/tests/scripts/modelling_close_small_deletions.py
index 9a7f2dac..caf6ad69 100644
--- a/doc/tests/scripts/modelling_close_small_deletions.py
+++ b/doc/tests/scripts/modelling_close_small_deletions.py
@@ -3,8 +3,8 @@ from promod3 import modelling
# setup
tpl = io.LoadPDB('data/gly.pdb')
-aln = seq.CreateAlignment(seq.CreateSequence('trg', 'GGG-GGG'),
- seq.CreateSequence('tpl', 'GGGAGGG'))
+aln = seq.CreateAlignment(seq.CreateSequence('trg', 'GGGG-GGGG'),
+ seq.CreateSequence('tpl', 'GGGGAGGGG'))
aln.AttachView(1, tpl.CreateFullView())
mhandle = modelling.BuildRawModel(aln)
# close small deletion
diff --git a/modelling/pymod/_raw_model.py b/modelling/pymod/_raw_model.py
index dd2b26e7..b08ae45b 100644
--- a/modelling/pymod/_raw_model.py
+++ b/modelling/pymod/_raw_model.py
@@ -15,11 +15,12 @@
# internal
from ._modelling import *
+from ._alignment_fiddling import *
# external
import ost
def BuildRawModel(aln, chain_names = None, include_ligands = False,
- spdbv_style = False):
+ spdbv_style = False, aln_preprocessing='default'):
'''Builds a raw (pseudo) model from the alignment. Can either take a single
alignment handle or an alignment handle list. Every list item is treated as a
single chain in the final raw model.
@@ -27,6 +28,9 @@ def BuildRawModel(aln, chain_names = None, include_ligands = False,
Each alignment handle must contain exactly two sequences and the second
sequence is considered the template sequence, which must have a
:class:`~ost.mol.EntityView` attached.
+
+ Before extracting the coordinates, the alignments are pre-processed
+ according to *aln_preprocessing*.
This is a basic protein core modelling algorithm that copies backbone
coordinates based on the sequence alignment. For matching residues, the
@@ -79,7 +83,11 @@ def BuildRawModel(aln, chain_names = None, include_ligands = False,
:param spdbv_style: True, if we need a model in the old SPDBV style.
:type spdbv_style: :class:`bool`
-
+
+ :param aln_preprocessing: Calls :meth:`promod3.modelling.PullTerminalDeletions`
+ if set to 'default'. Can be disabled when set
+ to False.
+
:return: Raw (pseudo) model from the alignment.
:rtype: :class:`ModellingHandle`
@@ -129,4 +137,10 @@ def BuildRawModel(aln, chain_names = None, include_ligands = False,
raise RuntimeError('aln must be of type ost.seq.AlignmentHandle or '\
'ost.seq.AlignmentList')
+ if aln_preprocessing == 'default':
+ temp = ost.seq.AlignmentList()
+ for a in aln_list:
+ temp.append(PullTerminalDeletions(a))
+ aln_list = temp
+
return MHandleFromAln(aln_list, name_list, include_ligands, spdbv_style)
diff --git a/modelling/tests/test_close_gaps.py b/modelling/tests/test_close_gaps.py
index f2eb4882..9b88c4fb 100644
--- a/modelling/tests/test_close_gaps.py
+++ b/modelling/tests/test_close_gaps.py
@@ -175,7 +175,8 @@ class CloseGapsTests(unittest.TestCase):
aln = seq.CreateAlignment(seq.CreateSequence('trg', 'GGG-GGG'),
seq.CreateSequence('tpl', 'GGGAGGG'))
aln.AttachView(1, tpl.CreateFullView())
- mhandle = modelling.BuildRawModel(aln)
+ # disable aln_preprocessing as deletion would be removed
+ mhandle = modelling.BuildRawModel(aln, aln_preprocessing=False)
self.assertEqual(len(mhandle.gaps), 1)
# close it
nlogs = len(self.log.messages['INFO'])
@@ -202,7 +203,8 @@ class CloseGapsTests(unittest.TestCase):
alns = seq.AlignmentList()
alns.append(aln_A)
alns.append(aln_B)
- mhandle = modelling.BuildRawModel(alns)
+ # disable aln_preprocessing as one of the deletions would be removed
+ mhandle = modelling.BuildRawModel(alns, aln_preprocessing=False)
self.assertEqual(len(mhandle.gaps), 2)
# do it
modelling.CloseSmallDeletions(mhandle)
@@ -581,7 +583,8 @@ class CloseGapsTests(unittest.TestCase):
seq.CreateSequence('trg', 'NGG----------------------RVE'),
seq.CreateSequence('tpl', 'NGGTLLIPNGTYHFLGIQMKSNVHIRVE'))
aln.AttachView(1, tpl.CreateFullView())
- mhandle = modelling.BuildRawModel(aln)
+ # disable aln_preprocessing as the deletion would be removed
+ mhandle = modelling.BuildRawModel(aln, aln_preprocessing=False)
self.assertEqual(len(mhandle.gaps), 1)
modelling.CloseLargeDeletions(mhandle, self.structure_db,
num_fragments=100)
@@ -596,7 +599,8 @@ class CloseGapsTests(unittest.TestCase):
seq.CreateSequence('trg', 'GAGAGAGANG--LLIPNGTYHFLGIQMKSNVHIRVE'),
seq.CreateSequence('tpl', '--------NGGTLLIPNGTYHFLGIQMKSNVHIRVE'))
aln.AttachView(1, tpl.CreateFullView())
- mhandle = modelling.BuildRawModel(aln)
+ # disable aln_preprocessing as the deletion would be removed
+ mhandle = modelling.BuildRawModel(aln, aln_preprocessing=False)
modelling.RemoveTerminalGaps(mhandle)
self.assertEqual(len(mhandle.gaps), 1)
modelling.CloseLargeDeletions(mhandle, self.structure_db,
diff --git a/modelling/tests/test_modelling.py b/modelling/tests/test_modelling.py
index 382b1035..f8e8b946 100644
--- a/modelling/tests/test_modelling.py
+++ b/modelling/tests/test_modelling.py
@@ -109,7 +109,8 @@ class ModellingTests(unittest.TestCase):
tpl = io.LoadPDB('data/gly.pdb')
aln = io.LoadAlignment('data/del.fasta')
aln.AttachView(1, tpl.CreateFullView())
- result = modelling.BuildRawModel(aln)
+ # disable aln_preprocessing to keep the deletion in the example aln
+ result = modelling.BuildRawModel(aln, aln_preprocessing=False)
residues = result.model.residues
self.assertEqual(len(result.gaps), 1)
self.assertEqual(result.gaps[0].before, residues[2])
@@ -432,7 +433,8 @@ class ModellingTests(unittest.TestCase):
seq.CreateSequence('trg', 'TLNGFTVPAGNTLVLN---PDKG--ATVTM-A'),
seq.CreateSequence('tpl', 'N-GG-TLLI--PNGTYHFLGIQMKSNVHIRVE'))
aln.AttachView(1, tpl.CreateFullView())
- mhandle = modelling.BuildRawModel(aln)
+ # disable aln_preprocessing to also keep the small deletion in the end
+ mhandle = modelling.BuildRawModel(aln, aln_preprocessing=False)
# check
self.assertEqual(len(mhandle.gaps), 6)
self.assertEqual(modelling.ClearGaps(mhandle, mhandle.gaps[1]), 1)
--
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