From b70d56269a5688da3ba65bbc8e6ea1f03986f044 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 20 Nov 2019 14:17:58 +0100
Subject: [PATCH] set universal_newlines flag in Popen
This enables string encoding in passed streams => stdout and stderr
---
modules/bindings/pymod/cadscore.py | 14 ++++++++------
1 file changed, 8 insertions(+), 6 deletions(-)
diff --git a/modules/bindings/pymod/cadscore.py b/modules/bindings/pymod/cadscore.py
index 6d5bb0b9a..90fa77e4a 100644
--- a/modules/bindings/pymod/cadscore.py
+++ b/modules/bindings/pymod/cadscore.py
@@ -185,16 +185,19 @@ def _RunCAD(tmp_dir, mode, cad_bin_path, old_regime):
os.path.join(tmp_dir,
"cadtemp"))
- ps1=subprocess.Popen(command1, shell=True, stdout=subprocess.PIPE)
+ ps1=subprocess.Popen(command1, shell=True, stdout=subprocess.PIPE,
+ universal_newlines=True)
ps1.wait()
- ps2=subprocess.Popen(command2, shell=True, stdout=subprocess.PIPE)
+ ps2=subprocess.Popen(command2, shell=True, stdout=subprocess.PIPE,
+ universal_newlines=True)
ps2.wait()
lines=ps2.stdout.readlines()
try:
globalAA=_ParseCADGlobal(lines)
except:
raise RuntimeError("CAD calculation failed")
- ps3=subprocess.Popen(command3, shell=True, stdout=subprocess.PIPE)
+ ps3=subprocess.Popen(command3, shell=True, stdout=subprocess.PIPE,
+ universal_newlines=True)
ps3.wait()
lines=ps3.stdout.readlines()
try:
@@ -225,7 +228,8 @@ def _RunCAD(tmp_dir, mode, cad_bin_path, old_regime):
if old_regime:
cmd.append("--old-regime")
cmd = ' '.join(cmd)
- ps = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE)
+ ps = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE,
+ universal_newlines=True)
ps.wait()
try:
globalAA = _ParseVoronotaGlobal(ps.stdout.readlines())
@@ -246,11 +250,9 @@ def _RunCAD(tmp_dir, mode, cad_bin_path, old_regime):
def _HasInsertionCodes(model, reference):
for r in model.residues:
if r.GetNumber().GetInsCode() != "\0":
- print(r)
return True
for r in reference.residues:
if r.GetNumber().GetInsCode() != "\0":
- print(r)
return True
return False
--
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