Re: [Rdkit-discuss] error while calculating rms and shape tanimoto

2016-09-22 Thread Amit singh 
Hi
>>Files 1.pdb and 2.pdb do not contain CONECT records (so missing bond
orders?).

 I removed  CONECT records from Files a.pdb and b.pdb. still code is
running fine

>>File 1.pdb contains an atom with name BR43. Maybe the PDB parser can't
parse that (seems valid to me, FWTW).

 Also tried to run by removing BR43 from the file. Still same error.


Amit


On Thu, Sep 22, 2016 at 4:26 PM, Paul Emsley 
wrote:

>
>
> File 1.pdb contains an atom with name BR43. Maybe the PDB parser can't
> parse that (seems valid to me, FWTW).
>
> Paul
>
>
>
> On 22/09/16 11:15, Amit singh wrote:
>
> Hi
>
> Files a.pdb and b.pdb are from RDKit test data (working fine)
>
> Files 1.pdb and 2.pdb (other than test data, which are giving error)
>
> On Thu, Sep 22, 2016 at 3:03 PM, Greg Landrum 
> wrote:
>
>> HI Amit,
>>
>>
>> On Thu, Sep 22, 2016 at 9:23 AM, Amit singh 
>> wrote:
>>
>>>
>>> I am a new entry in this discussion forum and also for RDKit
>>>
>>
>> Welcome!
>>
>>
>>> I am trying to calculate shape tanimoto  and rms between two molecules
>>> (PDB files) from 3D functionality of RDKit.
>>> Code is working fine for the pdb files given in test data.
>>> But gives error whenever I uses other pdb files
>>>
>>> 
>>> >>> rms = rdMolAlign.AlignMol(mol1, mol2)
>>> Traceback (most recent call last):
>>>   File "", line 1, in 
>>> RuntimeError: std::exception
>>> ---
>>> It looks like there is a problem in input files, but help required
>>>
>>
>> In order to be able to answer the question, we need a bit more
>> information. Can you please share what files you loaded mol1 and mol2 from
>> so that we can reproduce the problem?
>>
>> -greg
>>
>>
>
>
>
>
>
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Re: [Rdkit-discuss] error while calculating rms and shape tanimoto

2016-09-22 Thread Paul Emsley 
Files 1.pdb and 2.pdb do not contain CONECT records (so missing bond 
orders?).


File 1.pdb contains an atom with name BR43. Maybe the PDB parser can't 
parse that (seems valid to me, FWTW).


Paul


On 22/09/16 11:15, Amit singh wrote:

Hi

Files a.pdb and b.pdb are from RDKit test data (working fine)

Files 1.pdb and 2.pdb (other than test data, which are giving error)

On Thu, Sep 22, 2016 at 3:03 PM, Greg Landrum > wrote:


HI Amit,


On Thu, Sep 22, 2016 at 9:23 AM, Amit singh > wrote:


I am a new entry in this discussion forum and also for RDKit


Welcome!

I am trying to calculate shape tanimoto and rms between two
molecules (PDB files) from 3D functionality of RDKit.
Code is working fine for the pdb files given in test data.
But gives error whenever I uses other pdb files


>>> rms = rdMolAlign.AlignMol(mol1, mol2)
Traceback (most recent call last):
  File "", line 1, in 
RuntimeError: std::exception
---
It looks like there is a problem in input files, but help required


In order to be able to answer the question, we need a bit more
information. Can you please share what files you loaded mol1 and
mol2 from so that we can reproduce the problem?

-greg




--

Dr. Amit Kumar
Scientist B
National Institute of Cancer Prevention and Research
(Formly Institute of Cytology and Preventive Oncology)
 I-7, Sector - 39, Noida - 201301 Uttar Pradesh



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Re: [Rdkit-discuss] error while calculating rms and shape tanimoto

2016-09-22 Thread Amit singh 
Hi

Files a.pdb and b.pdb are from RDKit test data (working fine)

Files 1.pdb and 2.pdb (other than test data, which are giving error)

On Thu, Sep 22, 2016 at 3:03 PM, Greg Landrum 
wrote:

> HI Amit,
>
>
> On Thu, Sep 22, 2016 at 9:23 AM, Amit singh  wrote:
>
>>
>> I am a new entry in this discussion forum and also for RDKit
>>
>
> Welcome!
>
>
>> I am trying to calculate shape tanimoto  and rms between two molecules
>> (PDB files) from 3D functionality of RDKit.
>> Code is working fine for the pdb files given in test data.
>> But gives error whenever I uses other pdb files
>>
>> 
>> >>> rms = rdMolAlign.AlignMol(mol1, mol2)
>> Traceback (most recent call last):
>>   File "", line 1, in 
>> RuntimeError: std::exception
>> ---
>> It looks like there is a problem in input files, but help required
>>
>
> In order to be able to answer the question, we need a bit more
> information. Can you please share what files you loaded mol1 and mol2 from
> so that we can reproduce the problem?
>
> -greg
>
>


-- 

Dr. Amit Kumar
Scientist B
National Institute of Cancer Prevention and Research
(Formly Institute of Cytology and Preventive Oncology)
 I-7, Sector - 39, Noida - 201301 Uttar Pradesh


b.pdb
Description: application/aportisdoc


a.pdb
Description: application/aportisdoc


2.pdb
Description: application/aportisdoc


1.pdb
Description: application/aportisdoc
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Re: [Rdkit-discuss] error while calculating rms and shape tanimoto

2016-09-22 Thread Greg Landrum 
HI Amit,


On Thu, Sep 22, 2016 at 9:23 AM, Amit singh  wrote:

>
> I am a new entry in this discussion forum and also for RDKit
>

Welcome!


> I am trying to calculate shape tanimoto  and rms between two molecules
> (PDB files) from 3D functionality of RDKit.
> Code is working fine for the pdb files given in test data.
> But gives error whenever I uses other pdb files
>
> 
> >>> rms = rdMolAlign.AlignMol(mol1, mol2)
> Traceback (most recent call last):
>   File "", line 1, in 
> RuntimeError: std::exception
> ---
> It looks like there is a problem in input files, but help required
>

In order to be able to answer the question, we need a bit more information.
Can you please share what files you loaded mol1 and mol2 from so that we
can reproduce the problem?

-greg
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