Re: [Rdkit-discuss] problem using RDKit c++ class to read sdf file
Hi Sergio,
You need to provide the filename when you construct the SDMolSupplier.
Here's some sample code from one of the RDKit tests that demonstrates how
to use the supplier:
https://github.com/rdkit/rdkit/blob/master/Code/GraphMol/FileParsers/testMolSupplier.cpp#L42
(that file contains other examples of using the suppliers too)
-greg
On Tue, Jul 14, 2015 at 7:10 AM, Wong, Sergio E. wrote:
> Dear RDKit users;
>
> I am trying to read a sdf file using the following code:
>
> #include
> #include
> #include
> #include
> #include
> #include
>
> int main()
> {
> RDKit::SDMolSupplier supplier;
>
> supplier.init();
> supplier.SDMolSupplier("PubChem_info_dat.sdf");
>
> return 0;
>
> }
>
> When I try to compile it, I get the following error:
>
> test.c: In function ‘int main()’:
> test.c:19:10: error: invalid use of ‘RDKit::SDMolSupplier::SDMolSupplier’
> supplier.SDMolSupplier("PubChem_info_dat.sdf");
> ^
>
> Can anyone suggest anything?
>
> Thanks!
> -Sergio
>
>
>
>
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[Rdkit-discuss] problem using RDKit c++ class to read sdf file
Dear RDKit users;
I am trying to read a sdf file using the following code:
#include
#include
#include
#include
#include
#include
int main()
{
RDKit::SDMolSupplier supplier;
supplier.init();
supplier.SDMolSupplier("PubChem_info_dat.sdf");
return 0;
}
When I try to compile it, I get the following error:
test.c: In function ‘int main()’:
test.c:19:10: error: invalid use of ‘RDKit::SDMolSupplier::SDMolSupplier’
supplier.SDMolSupplier("PubChem_info_dat.sdf");
^
Can anyone suggest anything?
Thanks!
-Sergio
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Re: [Rdkit-discuss] Rev. 5775 (Windows) - pyGraphMolWrap test fails
Just a quick FYI that Paolo's PR has been accepted in github.
I'm still digging out from the email from last week, so I'm slow.
-greg
On Tue, Jul 14, 2015 at 12:23 AM, Paolo Tosco wrote:
> Hi James,
>
> I just submitted a pull request about this; a patch is attached to this
> e-mail. To apply the patch, cd to $RDBASE and issue the following command:
>
> patch -p0 < patch20150713.txt
>
> Best,
> p.
>
>
> On 13/07/2015 15:16, James Davidson wrote:
>
> Dear All,
>
>
>
> I have just built revision 5775 on Windows, and the pyGraphMolWrap test
> fails. The relevant bit of the verbose output is below:
>
>
>
> 78: ERROR: testGithub498 (__main__.TestCase)
>
> 78: --
>
> 78: Traceback (most recent call last):
>
> 78: File "C:/RDKit/Code/GraphMol/Wrap/rough_test.py", line 3033, in
> testGithub498
>
> 78: outf = gzip.open(tempfile.mktemp(),'wt+')
>
> 78: File "C:\Anaconda\lib\gzip.py", line 34, in open
>
> 78: return GzipFile(filename, mode, compresslevel)
>
> 78: File "C:\Anaconda\lib\gzip.py", line 94, in __init__
>
> 78: fileobj = self.myfileobj = __builtin__.open(filename, mode or 'rb')
>
> 78: ValueError: Invalid mode ('wt+b')
>
>
>
>
>
> This seems to be due to a difference in python/gzip behaviour on Windows
> vs. eg Linux:
>
>
>
> *On Ubuntu (Anaconda python):*
>
>
>
> In [1]: import tempfile, gzip
>
> In [2]: outf = gzip.open(tempfile.mktemp(), 'wt+')
>
> In [3]:
>
>
>
>
>
> *On Windows (again Anaconda python):*
>
>
>
> In [1]: import tempfile, gzip
>
> In [2]: outf = gzip.open(tempfile.mktemp(), 'wt+')
>
> ---
>
> ValueErrorTraceback (most recent call last)
>
> in ()
>
> > 1 outf = gzip.open(tempfile.mktemp(), 'wt+')
>
>
>
> C:\Anaconda\lib\gzip.pyc in open(filename, mode, compresslevel)
>
> 32
>
> 33 """
>
> ---> 34 return GzipFile(filename, mode, compresslevel)
>
> 35
>
> 36 class GzipFile(io.BufferedIOBase):
>
>
>
> C:\Anaconda\lib\gzip.pyc in __init__(self, filename, mode, compresslevel,
> fileobj, mtime)
>
> 92 mode += 'b'
>
> 93 if fileobj is None:
>
> ---> 94 fileobj = self.myfileobj = __builtin__.open(filename,
> mode or 'rb')
>
> 95 if filename is None:
>
> 96 # Issue #13781: os.fdopen() creates a fileobj with a
> bogus name
>
>
>
> ValueError: Invalid mode ('wt+b')
>
>
>
> In [3]:
>
>
>
>
>
>
>
> Is this an easy one to fix?
>
>
>
> Kind regards
>
>
>
> James
>
> __
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Re: [Rdkit-discuss] AP / DP descriptors
Hi Michael, On Sun, Jul 5, 2015 at 2:43 PM, Michael Reutlinger wrote: > > I would like to use a machine learning method with the AP and DP > descriptors as described by Robert Sheridan. > > AP descriptors are the 'atom pair' descriptors from Carhart et al. 1985 > and I think they are already available in RDKIT. > Indeed, they are. > DP 'donor−acceptor pair', called 'BP' in Kearsley et al. 1996, is a > reduced pharmacophore version of AP. > > I would like to know if you think there is a straightforward way to use > the existing AP functionality (maybe using atomInvariants) to reproduce > the descriptor as described in Kearsley et al.? > Yes, if you have a way to assign integer invariants (atom types) to atoms that correspond to the BP features described in Kearsley et al. then it would be very straightforward to use those in the calculation. Note that the RDKit atom pair code does require that all atoms have a type (i.e. you can't have atoms that are ignored like some pharmacophore methods would do), but looking at the paper it seems like this isn't a problem: any atom that doesn't get assigned to one of the other classes just gets put into class 7: "other". The paper does not, unfortunately, include enough information to directly implement the fingerprint: you will need to come up with definitions (probably SMARTS-based?) for the the 6 atom classes. I've thought several times about adding the fingerprint-types from the paper to the RDKit (and then testing them out using Sereina's benchmarking platform), but this has always ended up getting hung-up on the missing atom-type definitions. -greg -- Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Rev. 5775 (Windows) - pyGraphMolWrap test fails
Hi James,
I just submitted a pull request about this; a patch is attached to this
e-mail. To apply the patch, cd to $RDBASE and issue the following command:
patch -p0 < patch20150713.txt
Best,
p.
On 13/07/2015 15:16, James Davidson wrote:
Dear All,
I have just built revision 5775 on Windows, and the pyGraphMolWrap
test fails. The relevant bit of the verbose output is below:
78: ERROR: testGithub498 (__main__.TestCase)
78: --
78: Traceback (most recent call last):
78: File "C:/RDKit/Code/GraphMol/Wrap/rough_test.py", line 3033, in
testGithub498
78: outf = gzip.open(tempfile.mktemp(),'wt+')
78: File "C:\Anaconda\lib\gzip.py", line 34, in open
78: return GzipFile(filename, mode, compresslevel)
78: File "C:\Anaconda\lib\gzip.py", line 94, in __init__
78: fileobj = self.myfileobj = __builtin__.open(filename, mode or
'rb')
78: ValueError: Invalid mode ('wt+b')
This seems to be due to a difference in python/gzip behaviour on
Windows vs. eg Linux:
*On Ubuntu (Anaconda python):*
In [1]: import tempfile, gzip
In [2]: outf = gzip.open(tempfile.mktemp(), 'wt+')
In [3]:
*On Windows (again Anaconda python):*
In [1]: import tempfile, gzip
In [2]: outf = gzip.open(tempfile.mktemp(), 'wt+')
---
ValueError Traceback (most recent call last)
in ()
> 1 outf = gzip.open(tempfile.mktemp(), 'wt+')
C:\Anaconda\lib\gzip.pyc in open(filename, mode, compresslevel)
32
33 """
---> 34 return GzipFile(filename, mode, compresslevel)
35
36 class GzipFile(io.BufferedIOBase):
C:\Anaconda\lib\gzip.pyc in __init__(self, filename, mode,
compresslevel, fileobj, mtime)
92 mode += 'b'
93 if fileobj is None:
---> 94 fileobj = self.myfileobj =
__builtin__.open(filename, mode or 'rb')
95 if filename is None:
96 # Issue #13781: os.fdopen() creates a fileobj with
a bogus name
ValueError: Invalid mode ('wt+b')
In [3]:
Is this an easy one to fix?
Kind regards
James
__
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*** Code/GraphMol/Wrap/rough_test.new.pyMon Jul 13 23:19:32 2015
--- Code/GraphMol/Wrap/rough_test.orig.py Mon Jul 13 23:18:35 2015
***
*** 3030,3040
def testGithub498(self):
import gzip,tempfile
! if (sys.version_info < (3, 0)):
! mode = 'w+'
! else:
! mode = 'wt+'
! outf = gzip.open(tempfile.mktemp(), mode)
m = Chem.MolFromSmiles('C')
w = Chem.SDWriter(outf)
w.write(m)
--- 3030,3036
def testGithub498(self):
import gzip,tempfile
! outf = gzip.open(tempfile.mktemp(), 'wt+')
m = Chem.MolFromSmiles('C')
w = Chem.SDWriter(outf)
w.write(m)
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Re: [Rdkit-discuss] Rev. 5775 (Windows) - pyGraphMolWrap test fails
Looks like the problem opening the file with the extra parameters used ('t+')
as the gzip module just sticks a 'b' on the end of the opening mode
if mode and 'b' not in mode:
mode += 'b'
The test should run if line 3033 is changed from
outf = gzip.open(tempfile.mktemp(),'wt+')
to
outf = gzip.open(tempfile.mktemp(),'wb+')
which I would put right but I still have zero idea how to use git :)
The more interesting question is why does this work on Unix/Mac but not on
Windows, and why do you get this error when it's not in the gzip code?
Best,
Nick
Nicholas C. Firth | PhD Student | Cancer Therapeutics
The Institute of Cancer Research | 15 Cotswold Road | Belmont | Sutton | Surrey
| SM2 5NG
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W www.icr.ac.uk
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[cid:image001.gif@01CE053D.51D3C4E0]
On 13 Jul 2015, at 15:16, James Davidson
mailto:j.david...@vernalis.com>> wrote:
gzip.pyc
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[Rdkit-discuss] Rev. 5775 (Windows) - pyGraphMolWrap test fails
Dear All,
I have just built revision 5775 on Windows, and the pyGraphMolWrap test fails.
The relevant bit of the verbose output is below:
78: ERROR: testGithub498 (__main__.TestCase)
78: --
78: Traceback (most recent call last):
78: File "C:/RDKit/Code/GraphMol/Wrap/rough_test.py", line 3033, in
testGithub498
78: outf = gzip.open(tempfile.mktemp(),'wt+')
78: File "C:\Anaconda\lib\gzip.py", line 34, in open
78: return GzipFile(filename, mode, compresslevel)
78: File "C:\Anaconda\lib\gzip.py", line 94, in __init__
78: fileobj = self.myfileobj = __builtin__.open(filename, mode or 'rb')
78: ValueError: Invalid mode ('wt+b')
This seems to be due to a difference in python/gzip behaviour on Windows vs. eg
Linux:
On Ubuntu (Anaconda python):
In [1]: import tempfile, gzip
In [2]: outf = gzip.open(tempfile.mktemp(), 'wt+')
In [3]:
On Windows (again Anaconda python):
In [1]: import tempfile, gzip
In [2]: outf = gzip.open(tempfile.mktemp(), 'wt+')
---
ValueErrorTraceback (most recent call last)
in ()
> 1 outf = gzip.open(tempfile.mktemp(), 'wt+')
C:\Anaconda\lib\gzip.pyc in open(filename, mode, compresslevel)
32
33 """
---> 34 return GzipFile(filename, mode, compresslevel)
35
36 class GzipFile(io.BufferedIOBase):
C:\Anaconda\lib\gzip.pyc in __init__(self, filename, mode, compresslevel,
fileobj, mtime)
92 mode += 'b'
93 if fileobj is None:
---> 94 fileobj = self.myfileobj = __builtin__.open(filename, mode
or 'rb')
95 if filename is None:
96 # Issue #13781: os.fdopen() creates a fileobj with a bogus
name
ValueError: Invalid mode ('wt+b')
In [3]:
Is this an easy one to fix?
Kind regards
James
__
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To access trading company registration and address details, please go to the
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