From 57f42c7827681e070dcd39c43647d807f16233b9 Mon Sep 17 00:00:00 2001
From: Fabrice ALLAIN <fabrice.allain@pasteur.fr>
Date: Tue, 30 May 2017 19:16:17 +0200
Subject: [PATCH] Bug revision: removed hard coded lines...
---
ariaec/converter.py | 9 ++-------
1 file changed, 2 insertions(+), 7 deletions(-)
diff --git a/ariaec/converter.py b/ariaec/converter.py
index 1f23336..7a43b47 100644
--- a/ariaec/converter.py
+++ b/ariaec/converter.py
@@ -839,7 +839,6 @@ class AriaEcXMLConverter(AriaXMLConverter):
res2:
list_type :
type of atoms in the product (Default value = "min")
- product :
res1 :
res2 :
@@ -920,7 +919,7 @@ class AriaEcXMLConverter(AriaXMLConverter):
((idx1, atm1), (idx2, atm2)) for (atm1, atm2) in
list(itertools.product(atms1, atms2))]
- def _pdbdistmaps(self, sequence):
+ def _pdbdistmaps(self):
# TODO: use precision level, actually we only use SsAaAtmMaps
precision_level = self.settings.setup.config.get(
"pdbdistance_level", "ss")
@@ -1089,7 +1088,7 @@ class AriaEcXMLConverter(AriaXMLConverter):
# if '_upper_bound' in bound.lower())}
# targetmaps.subfill(pdbdict, level=1)
# targetmaps = SsAaAtmMap()
- targetmaps = self._pdbdistmaps(sequence)
+ targetmaps = self._pdbdistmaps()
else:
# retourne fixed AtmMap
raise ValueError("Unknown distance_type %s or wrong distance file" %
@@ -1285,10 +1284,6 @@ class AriaEcXMLConverter(AriaXMLConverter):
# Define Residue lists for the contact. Those lists contains
# normally only one element by default except if we introduce
# neighbors with neigh_flag triggered
- # TODO: REMOVE !!!!!
- neigh_flag = True
- adr_flag = False
- contribs_type = "same"
subcontacts = self.neighcontact(subcontacts, max_seqidx - 1) if neigh_flag \
else [subcontacts]
--
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