From 2548e9523f6d94b6770a6f679c754203a90a47af Mon Sep 17 00:00:00 2001
From: Berk Onat <b.onat@warwick.ac.uk>
Date: Tue, 12 Dec 2017 17:10:24 +0000
Subject: [PATCH] Update Readme file and main routine to match new
improvements.
---
README.md | 13 +++++++++++++
pymolfile/pymolfile.py | 18 +++++++++++-------
2 files changed, 24 insertions(+), 7 deletions(-)
diff --git a/README.md b/README.md
index 9aea7d7..a24361e 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,17 @@
# pymolfile
+
+#### Version: 0.0.3
+What is new?
+* Added script to change printf/fprintf to stdout and stderr at C level on molfile plugins to make the package compatiable with NOMAD parsers.
+* Added "nowarnings" option to OpenMolfile to prevent user warnings.
+
+Anything in mind for additional improvements?
+* C level silencing modifications are mandatory. This might be optional with a setup.py parameter.
+* pymolfile only supports read fucntions at plugins. Write functions might also be added to convert data to other formats.
+
+Needs precaution when using?
+* Recursive initialization of OpenMolfile leads to breaks at trajectory class when an outer calling function fails (Ex: in MDDataAccess package) since trajectory file can still be open and can not be closed properly without a delete call.
+
#### Version: 0.0.2
Python interface for molfile plugins.
diff --git a/pymolfile/pymolfile.py b/pymolfile/pymolfile.py
index 7396a23..f1dcaa5 100644
--- a/pymolfile/pymolfile.py
+++ b/pymolfile/pymolfile.py
@@ -512,9 +512,10 @@ class OpenMolfile(object):
self.kwords["silent"])
#libpymolfile.molfile_finish()
else:
- warnings.warn("Pymolfile can not find a plugin to open the '" +
- self.kwords["topology_format"] + "' file format of the file " +
- self.kwords["topology"])
+ if self.kwords["nowarnings"] is True:
+ warnings.warn("Pymolfile can not find a plugin to open the '" +
+ self.kwords["topology_format"] + "' file format of the file " +
+ self.kwords["topology"])
if self.fplugin[1][5] == 1:
num_atoms = 0
@@ -531,8 +532,9 @@ class OpenMolfile(object):
num_atoms,
self.kwords["silent"])
else:
- warnings.warn("Pymolfile can not find a plugin to open the '" + self.kwords["file_format"] +
- "' file format of the file " + self.kwords["file_name"])
+ if self.kwords["nowarnings"] is True:
+ warnings.warn("Pymolfile can not find a plugin to open the '" + self.kwords["file_format"] +
+ "' file format of the file " + self.kwords["file_name"])
def initialize_settings(self):
#global MOLFILE_PLUGINS
@@ -553,7 +555,8 @@ class OpenMolfile(object):
"topology_format" : None,
"topology_plugin" : None,
"natoms" : None,
- "silent" : False
+ "silent" : False,
+ "nowarnings" : False
}
#if not C_MOLFILE_PLUGINS:
@@ -574,7 +577,8 @@ class OpenMolfile(object):
"topology_format" : None,
"topology_plugin" : None,
"natoms" : None,
- "silent" : False
+ "silent" : False,
+ "nowarnings" : False
})
def __del__(self):
--
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