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In openbabel sources from FreeBSD port and latest code snapshot FindBaseType
definition looks like
OBPlugin* OBPlugin::BaseFindType(PluginMapType Map, const char* ID)
{
if(!ID || !*ID)
return NULL;
PluginMapType::iterator itr = Map.find(ID);
if(itr==Map.end())
return NULL;
else
[Oops! Sent a version as direct email and not to the list. Sending again.]
On Oct 24, 2014, at 12:05 PM, ftorazyne wrote:
Function doesn't check whether plugins loaded or not.
Which version of openbabel you use?
It gives me a version number of 2.3.90 . The _openbabel.so has a timestamp of
May
The key word is BSD. There are some differences in the dynamic library
loading which we had to sort out early on. However, we are not
responsible for the binaries provided by FreeBSD itself. If you could
compile Open babel yourself from source and check whether the problem
remains, then it's a
I have mentioned at first post that OpenBabel had been installed from ports
i.e. compiled from source code at my BSD system. I do not use pre-compilied
Linux binaries of OpenBabel.
Given enough time of course I
could do this for you but well, that's not going to happen right now.
I shall be
On Oct 24, 2014, at 4:32 PM, ftorazyne wrote:
I shall be really grateful to you if you repair this problem.
You should be aware that not going to happen right now might
mean months. I can't speak for Noel, at all, but based on what
we've worked out so far, further diagnosis requires that someone
Ah, right - I didn't know what ports is - I assumed it was a binary
package manager.
- Noel
On 24 October 2014 15:32, ftorazyne ftoraz...@mail.ru wrote:
I have mentioned at first post that OpenBabel had been installed from ports
i.e. compiled from source code at my BSD system. I do not use
On Oct 24, 2014, at 5:08 PM, Noel O'Boyle wrote:
Ah, right - I didn't know what ports is - I assumed it was a binary
package manager.
Same here!
Andrew
da...@dalkescientific.com
I send message describing this bug to port maintainer, will wait reply.
--
View this message in context:
http://forums.openbabel.org/Error-in-Pybel-readstring-smi-format-not-recognized-tp4657776p4657802.html
Sent from the General discussion mailing list archive at Nabble.com.
I have OpenBabel 2.3.2 installed from ports on FreeBSD 9.1 AMD64 machine with
Python 2.7 also installed from ports. I tried to use Pybel:
import pybel
mymol=pybel.readstring('smi','CCOC(=O)C')
mymol.addh()
mymol.make3D()
print mymol.write(format='mol2')
and received this error:
Traceback (most
Hi,
print mymol.write(format='mol2')
Try
mymol.write(mol2)
Regards,
Pascal
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Pascal Muller-3 wrote
Hi,
print mymol.write(format='mol2')
Try
mymol.write(mol2)
Regards,
Pascal
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On Oct 23, 2014, at 4:59 PM, ftorazyne wrote:
raise ValueError(%s is not a recognised Open Babel format % format)
ValueError: smi is not a recognised Open Babel format
But pybel.informats contain 'smi' key:
...
How to avoid this error?
That is certainly unexpected. Could you try both in
I put this code into file babtest.py:
#! /usr/local/bin/python
#-*- coding: utf-8 -*-
import pybel
print sorted(pybel.informats)
mymol=pybel.readstring('smi','CCOC(=O)C')
mymol.addh()
mymol.make3D()
print mymol.write(format='mol2')
and run it and this is output:
└─ ./babtest.py
['CONFIG',
On 10/23/2014 05:51 PM, ftorazyne wrote:
raise ValueError(%s is not a recognised Open Babel format % format)
ValueError: smi is not a recognised Open Babel format
Have you tried readstring(sorted(pybel.informats[-16]... -- or
whatever its index is?
--
Dimitri Maziuk
Programmer/sysadmin
I modified code in accordance with your recommendation and obtained in
general same output:
└─ ./babtest.py
['CONFIG', 'CONTCAR', 'HISTORY', 'POSCAR', 'VASP', 'abinit', 'acesout',
'acr', 'adfout', 'alc', 'arc', 'axsf', 'bgf', 'box', 'bs', 'c09out', 'c3d1',
'c3d2', 'caccrt', 'can', 'car',
On Oct 24, 2014, at 1:13 AM, ftorazyne wrote:
I modified code in accordance with your recommendation and obtained in
general same output:
I cannot explain it. Looking at the code, there are two different OBConversion
instances. There's no way that's supposed to cause a problem, but try this
On my system this code produced other output:
└─ ./babtest.py
SetInFormat False
'rsmi -- Reaction SMILES format'
'smi -- SMILES format'
'smiles -- SMILES format'
SetInFormat(smi) return False, but smi is in supported formats.
Cannot this error be connected with encoding? My system encoding is
This bug occures for other supported formats, for example, 'pdb' or 'mol2'. I
should point out that my babel as standalone program correctly converse
files from one format to other.
Cannot you send me your openbabel.py file for comparison with my one?
--
View this message in context:
On Oct 24, 2014, at 1:47 AM, ftorazyne wrote:
On my system this code produced other output:
...
SetInFormat(smi) return False, but smi is in supported formats.
Cannot this error be connected with encoding? My system encoding is UTF8 and
I every time specify this encoding in Python files.
On Oct 24, 2014, at 2:08 AM, ftorazyne wrote:
Cannot you send me your openbabel.py file for comparison with my one?
With what you've reported, the problem isn't with openbabel.py but in the
underlying C++ layer.
The only relevant code in openbabel.py is:
OBConversion.SetInFormat =
Your code returns
./babtest.py
Trying words of length 1
Trying words of length 2
Trying words of length 3
Trying words of length 4
Trying words of length 5
Trying words of length 6
I don't know C++, but I looked through latest snapshot of OpenBabel code and
saw, that there is two definitions of
On Oct 24, 2014, at 3:15 AM, ftorazyne wrote:
Your code returns
...
Trying words of length 4
Trying words of length 5
Trying words of length 6
I don't know the registration system well enough to figure out how it can be
that the formats are registered, but not available in any form.
and
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