From 410a489b5a0953bfe9cb5ff32547a2e132487e40 Mon Sep 17 00:00:00 2001
From: Rafal Gumienny <r.gumienny@unibas.ch>
Date: Wed, 25 Apr 2018 11:45:10 +0200
Subject: [PATCH] fix: SCHWED-3121 Use calpha_only fron LoadPDB and LoadMMCIF
---
actions/ost-compare-structures | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index b244c22c0..b12ceedf5 100644
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -491,11 +491,7 @@ def _ReadStructureFile(path, c_alpha_only=False, fault_tolerant=False,
"""
def _Select(entity):
- calpha_message = "Selecting only C-alpha atoms"
selection_message = "Selecting %s" % selection
- if c_alpha_only:
- ost.LogInfo(calpha_message)
- entity = entity.Select("aname=CA")
if selection:
ost.LogInfo(selection_message)
entity = entity.Select(selection)
@@ -505,7 +501,10 @@ def _ReadStructureFile(path, c_alpha_only=False, fault_tolerant=False,
if not os.path.isfile(path):
raise IOError("%s is not a file" % path)
try:
- entity = LoadPDB(path, fault_tolerant=fault_tolerant)
+ entity = LoadPDB(
+ path,
+ fault_tolerant=fault_tolerant,
+ calpha_only=c_alpha_only)
if not entity.IsValid():
raise IOError("Provided file does not contain valid entity.")
entity.SetName(os.path.basename(path))
@@ -516,7 +515,8 @@ def _ReadStructureFile(path, c_alpha_only=False, fault_tolerant=False,
tmp_entity, cif_info = LoadMMCIF(
path,
info=True,
- fault_tolerant=fault_tolerant)
+ fault_tolerant=fault_tolerant,
+ calpha_only=c_alpha_only)
if len(cif_info.biounits) == 0:
tbu = MMCifInfoBioUnit()
tbu.id = 'ASU of ' + entity.pdb_id
--
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