Re: [Rdkit-discuss] SDwriter

2016-12-16 Thread Milinda Samaraweera
This SD file is then used as an input for another program, that program is
having problems reading the sequence numbers.

Thanks,
MAK

On Fri, Dec 16, 2016 at 10:43 PM, Greg Landrum 
wrote:

> It's easy enough to make this an option, but given that it is part of the
> SDF spec (as Andrew has pointed out) the only reason I can think of to do
> so would be because it causes problems for some other piece of (likely
> commonly used) software.
>
> Are the sequence numbers causing a problem for you?
>
> -greg
>
>
>
>
>
>
> On Sat, Dec 17, 2016 at 1:46 AM +0100, "Milinda Samaraweera" <
> milindaatw...@gmail.com> wrote:
>
> Dear Users,
>>
>> I was using the SDWriter in the rdkit kit to generate a SD file with
>> mutiple entries generated using smiles and later assign SD tag data (e.g.
>> pubchem_ID, IUPAC_name, etc).
>>
>> However at the end of each tag header I noticed there is a number
>> (bolded):
>>
>> ...
>> >   * (1) *
>> N1-(2-ethylbutyl)hexane-1,3,6-triamine
>>
>> >*(1) *
>> 118903148
>>
>> ...
>> M  END
>> >   * (2)*
>> N1,N2-dimethyl-N2-[3-(methylamino)propyl]-N1-propylpropane-1,2-diamine
>>
>> >   * (2) *
>> 118883401
>>
>> What is this number and how you avoid printing this number when SDwriter
>> is used? As this number is not found in standard SD files.
>>
>> Thanks,
>> CodeMAK
>>
>>


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Re: [Rdkit-discuss] SDwriter

2016-12-16 Thread Greg Landrum
It's easy enough to make this an option, but given that it is part of the SDF 
spec (as Andrew has pointed out) the only reason I can think of to do so would 
be because it causes problems for some other piece of (likely commonly used) 
software.
Are the sequence numbers causing a problem for you?
-greg






On Sat, Dec 17, 2016 at 1:46 AM +0100, "Milinda Samaraweera" 
 wrote:










Dear Users,

I was using the SDWriter in the rdkit kit to generate a SD file with mutiple 
entries generated using smiles and later assign SD tag data (e.g. pubchem_ID, 
IUPAC_name, etc).

However at the end of each tag header I noticed there is a number (bolded):

...
>    (1) 
N1-(2-ethylbutyl)hexane-1,3,6-triamine

>    (1) 
118903148

...
M  END
>    (2) 
N1,N2-dimethyl-N2-[3-(methylamino)propyl]-N1-propylpropane-1,2-diamine

>    (2) 
118883401

What is this number and how you avoid printing this number when SDwriter is 
used? As this number is not found in standard SD files.

Thanks,
CodeMAK







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Re: [Rdkit-discuss] SDWriter from Java

2016-03-30 Thread Greg Landrum
On Wed, Mar 30, 2016 at 2:47 PM, Tim Dudgeon  wrote:

> And there's no other way to generate a SDF from Java?
> e.g. can each ROMol be converted to text in SD format and then that text
> written to the Java OutputStream?
>

There's no way to do it in a single step.
You can get the mol block and the properties individually and then use
those, but that's not particularly nice.

I *think* I can pretty easily add a static method to the SDWriter class
that takes a molecule and optional list of properties as an argument and
returns the string that would go in to the SDF. This would then
automatically show up in the wrappers (I think). Let me investigate that.

-greg
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Re: [Rdkit-discuss] SDWriter from Java

2016-03-30 Thread Tim Dudgeon

And there's no other way to generate a SDF from Java?
e.g. can each ROMol be converted to text in SD format and then that text 
written to the Java OutputStream?


Tim

On 30/03/2016 13:31, Greg Landrum wrote:

Hi Tim,

That constructor is expecting a C++ stream pointer. The takeOwnership 
flag tells it to take assume ownership of the pointer (i.e. to free up 
the memory being used by the stream when the SDWriter itself is 
free'd). I am guessing that this will not be useable from Java (and 
should probably be disabled).


There is likely a way to set up the wrappers so that Java streams are 
properly handled, but it's difficult to assess how much work that 
would be.


-greg


On Wed, Mar 30, 2016 at 2:00 PM, Tim Dudgeon > wrote:


Hi All,

this probably a pretty basic question, but I'm struggling to work out
how to use the SDWriter from Java.
The class that SWIG has generated for SDWriter has a constructor
of type:
SDWriter(SWIGTYPE_p_std__ostream outstream)
which looks like its the one I need (I need to write to a Java
OutputStream, not a file).
But I can't would out how to generate an instance of
SWIGTYPE_p_std__ostream from my Java OutputStream.
Any pointers?

(Also, what does the boolean takeownership param of the similar
constructor do?)


Tim




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Re: [Rdkit-discuss] SDWriter from Java

2016-03-30 Thread Greg Landrum
Hi Tim,

That constructor is expecting a C++ stream pointer. The takeOwnership flag
tells it to take assume ownership of the pointer (i.e. to free up the
memory being used by the stream when the SDWriter itself is free'd). I am
guessing that this will not be useable from Java (and should probably be
disabled).

There is likely a way to set up the wrappers so that Java streams are
properly handled, but it's difficult to assess how much work that would be.

-greg


On Wed, Mar 30, 2016 at 2:00 PM, Tim Dudgeon  wrote:

> Hi All,
>
> this probably a pretty basic question, but I'm struggling to work out
> how to use the SDWriter from Java.
> The class that SWIG has generated for SDWriter has a constructor of type:
> SDWriter(SWIGTYPE_p_std__ostream outstream)
> which looks like its the one I need (I need to write to a Java
> OutputStream, not a file).
> But I can't would out how to generate an instance of
> SWIGTYPE_p_std__ostream from my Java OutputStream.
> Any pointers?
>
> (Also, what does the boolean takeownership param of the similar
> constructor do?)
>
>
> Tim
>
>
>
>
> --
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
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Re: [Rdkit-discuss] SDWriter kekulizes by default

2014-01-06 Thread Greg Landrum
Hi Michal,

On Mon, Jan 6, 2014 at 3:30 PM, Michal Krompiec
michal.kromp...@gmail.comwrote:

 Hello Greg,
  Chem.MolToSmiles(Chem.MolFromSmiles('O=C1NC=CC1=C1C=C(-c2nccc2)NC1=O'))
 [14:25:55] Can't kekulize mol


The problem is, once again, in the pyrrole:
In [2]: Chem.MolFromSmiles('O=C1NC=CC1=C1C=C(-c2nccc2)NC1=O')
[15:38:53] Can't kekulize mol

If you add the explicit H, everything works:

In [3]: Chem.MolFromSmiles('O=C1NC=CC1=C1C=C(-c2[nH]ccc2)NC1=O')
Out[3]: rdkit.Chem.rdchem.Mol at 0x108d22910

This smiles was generated from ChemSketch. OpenBabel converts it to
 O=C1NC=CC1=C1C=C(c2[nH]ccc2)NC1=O which is correctly interpreted by
 RDKit (no problems with kekulization).
 But IMHO both representations are correct, am I wrong?


The SMILES c1cccn1 does not really contain sufficient information to figure
out what the user meant. The RDKit does not, in general, try to guess
intent, so it fails on that form. Daylight's depictor also does not process
that form of pyrrole.

It's possible to imagine adding a special case for pyrrole, but something
like Cc1nncc1 would still cause problems.

The fact that you're getting those SMILES at all is really a bug in
ChemSketch. It should be adding the H.

-greg
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Re: [Rdkit-discuss] SDWriter kekulizes by default

2013-12-06 Thread Michal Krompiec
Dear Greg,
It seems that all examples I found are in fact incorrect (due to an
error during conversion of SDF produced by ISIS Draw with OpenBabel)
and contain this bit:
c1(sc(c2c1nsn2)) which was meant to be: c1scc2N=S=Nc12.
By the way, ChemSketch understands c1(sc(c2c1nsn2)) as N1SNc2cscc12.
So it is not a bug in your code, unless you consider the fused
thiadiazole ring aromatic.
Best wishes,
Michal

On 5 December 2013 12:19, Greg Landrum greg.land...@gmail.com wrote:
 Hi Michal,

 On Thu, Dec 5, 2013 at 11:52 AM, Michal Krompiec michal.kromp...@gmail.com
 wrote:

 Hello,
 Is it possible to suppress kekulization by SDWriter? I get the
 following error on a call to SDWriter.write:
 ValueError: Sanitization error: Can't kekulize mol
 But some molecules can't be kekulized using RDKit's algorithm, even
 though they are otherwise 'correct'.


 hmm, I'd love to see examples of those if you can share them.


 I browsed the sources and it seems that SDWriter calls MolToMolBlock
 with the default parameter kekulize=True. Can this parameter be
 exposed in SDWriter?


 Yep, I'll get it in for the next release.

 -greg


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Re: [Rdkit-discuss] SDWriter kekulizes by default

2013-12-05 Thread Greg Landrum
Hi Michal,

On Thu, Dec 5, 2013 at 11:52 AM, Michal Krompiec
michal.kromp...@gmail.comwrote:

 Hello,
 Is it possible to suppress kekulization by SDWriter? I get the
 following error on a call to SDWriter.write:
 ValueError: Sanitization error: Can't kekulize mol
 But some molecules can't be kekulized using RDKit's algorithm, even
 though they are otherwise 'correct'.


hmm, I'd love to see examples of those if you can share them.


 I browsed the sources and it seems that SDWriter calls MolToMolBlock
 with the default parameter kekulize=True. Can this parameter be
 exposed in SDWriter?


Yep, I'll get it in for the next release.

-greg
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Re: [Rdkit-discuss] 'SDWriter' object has no attribute 'close

2010-06-10 Thread markus kossner
Cedric MORETTI wrote:

 Hello all,

 I have I little problem with RDKIT( I hope :D)

 My program don’t arrive to close the SDwriter whereas I put the 
 command “writer.close()” and Chem.SDWriter.close() in the end of programm

 I just let the part of the code that is import for understand the 
 problem and the error.

 I have the error when the program has finished to read the file

 Tks

 C

 from sys import *

 #from ChemScript11 import *

 from cinfony import rdk

 from rdkit import Chem

 import time

 reader1 = Chem.SDMolSupplier(sys.argv[0])

 writer = Chem.SDWriter(sys.argv[1])

 z = 0

 for mol in reader1:

 “

 [Blablablablabla ( It’s to simulate a code)]

 writer.write(mol)

 writer.close()

 reader1.close()

 Chem.SDWriter.close()

 Traceback (most recent call last):

 File C:\Scripttravail\supermain.py, line 18, in module

 exec(file.read())

 File string, line 51, in module

 AttributeError: 'SDWriter' object has no attribute 'close

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Hi Cedric,
the Chem.SDWriter Object does not need to be closed, does it? It is 
automatically closed at the end of your program.
It doesn't even have a method that is named 'close()' like the ones you 
might know from python text file I/O objects.
This is what the Traceback error complains when it says :
-AttributeError: 'SDWriter' object has no attribute 'close'
So you should go well with simply deleting the three lines at the end of 
your script that give the .close() commands.
Hope this helps,
Markus

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Re: [Rdkit-discuss] 'SDWriter' object has no attribute 'close

2010-06-10 Thread Cedric MORETTI
Markus thank you, you responded to my problem.
I had read the manual RDKIT and I could not see where you need to close 
SDWRITER.
So I do not understand my error.
C
 

-Original Message-
From: markus kossner [mailto:m.koss...@tu-bs.de] 
Sent: jeudi, 10. juin 2010 15:43
To: Cedric MORETTI
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] 'SDWriter' object has no attribute 'close

Cedric MORETTI wrote:

 Hello all,

 I have I little problem with RDKIT( I hope :D)

 My program don't arrive to close the SDwriter whereas I put the 
 command writer.close() and Chem.SDWriter.close() in the end of programm

 I just let the part of the code that is import for understand the 
 problem and the error.

 I have the error when the program has finished to read the file

 Tks

 C

 from sys import *

 #from ChemScript11 import *

 from cinfony import rdk

 from rdkit import Chem

 import time

 reader1 = Chem.SDMolSupplier(sys.argv[0])

 writer = Chem.SDWriter(sys.argv[1])

 z = 0

 for mol in reader1:

 

 [Blablablablabla ( It's to simulate a code)]

 writer.write(mol)

 writer.close()

 reader1.close()

 Chem.SDWriter.close()

 Traceback (most recent call last):

 File C:\Scripttravail\supermain.py, line 18, in module

 exec(file.read())

 File string, line 51, in module

 AttributeError: 'SDWriter' object has no attribute 'close

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 DISCLAIMER
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 The contents do not represent the opinion of Firmenich except to the extent 
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Hi Cedric,
the Chem.SDWriter Object does not need to be closed, does it? It is 
automatically closed at the end of your program.
It doesn't even have a method that is named 'close()' like the ones you 
might know from python text file I/O objects.
This is what the Traceback error complains when it says :
-AttributeError: 'SDWriter' object has no attribute 'close'
So you should go well with simply deleting the three lines at the end of 
your script that give the .close() commands.
Hope this helps,
Markus
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do not represent the opinion of Firmenich except to the extent that it relates 
to their official business.
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