Re: [Rdkit-discuss] write sdf properties without position number

[Nicolas Bosc]

It’s for an old internal tool that we are updating. It has apparently some 
strict parsing rules at the moment.

> On 6 May 2020, at 10:37, Greg Landrum  wrote:
> 
> Out of curiousity, which software are you using that can't read those index 
> values?
> 
> On Wed, May 6, 2020 at 11:25 AM Nicolas Bosc  > wrote:
> Hi Paolo,
> 
> Thank you. You spoonfed me!
> 
> Nicolas
> 
>> On 5 May 2020, at 17:25, Paolo Tosco > > wrote:
>> 
>> Hi Nicolas,
>> 
>> quick and dirty solution: strip it with a regex, e.g.
>> 
>> sed 's|^\(>  <.*>\) *([0-9]*)|\1|'
>> 
>> HTH,
>> p.
>> 
>> On 05/05/2020 16:35, Nicolas Bosc wrote:
>>> Hi RDKit users,
>>> 
>>> Writing molecules in a sdf with properties automatically add a number after 
>>> the property name which is the position of the associated molecule in the 
>>> file:
>>> >(1) 
>>> CHEMBL123
>>> 
>>> How can I change this so there is no number? The program that I am using to 
>>> read the sdf file fails because of this...
>>> 
>>> Thanks,
>>> 
>>> Nicolas
>>> 
>>> 
>>> 
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>>> 
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>>> 
> 
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Re: [Rdkit-discuss] write sdf properties without position number

[Greg Landrum]

Out of curiousity, which software are you using that can't read those index
values?

On Wed, May 6, 2020 at 11:25 AM Nicolas Bosc  wrote:

> Hi Paolo,
>
> Thank you. You spoonfed me!
>
> Nicolas
>
> On 5 May 2020, at 17:25, Paolo Tosco  wrote:
>
> Hi Nicolas,
>
> quick and dirty solution: strip it with a regex, e.g.
>
> sed 's|^\(>  <.*>\) *([0-9]*)|\1|'
>
> HTH,
> p.
> On 05/05/2020 16:35, Nicolas Bosc wrote:
>
> Hi RDKit users,
>
> Writing molecules in a sdf with properties automatically add a number
> after the property name which is the position of the associated molecule in
> the file:
> >   * (1) *
> CHEMBL123
>
> How can I change this so there is no number? The program that I am using
> to read the sdf file fails because of this...
>
> Thanks,
>
> Nicolas
>
>
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>
>
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Re: [Rdkit-discuss] write sdf properties without position number

[Nicolas Bosc]

Hi Paolo,

Thank you. You spoonfed me!

Nicolas

> On 5 May 2020, at 17:25, Paolo Tosco  wrote:
> 
> Hi Nicolas,
> 
> quick and dirty solution: strip it with a regex, e.g.
> 
> sed 's|^\(>  <.*>\) *([0-9]*)|\1|'
> 
> HTH,
> p.
> 
> On 05/05/2020 16:35, Nicolas Bosc wrote:
>> Hi RDKit users,
>> 
>> Writing molecules in a sdf with properties automatically add a number after 
>> the property name which is the position of the associated molecule in the 
>> file:
>> >(1) 
>> CHEMBL123
>> 
>> How can I change this so there is no number? The program that I am using to 
>> read the sdf file fails because of this...
>> 
>> Thanks,
>> 
>> Nicolas
>> 
>> 
>> 
>> ___
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net 
>> 
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss 
>> 

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Re: [Rdkit-discuss] write sdf properties without position number

[Paolo Tosco]

Hi Nicolas,

quick and dirty solution: strip it with a regex, e.g.

sed 's|^\(>  <.*>\) *([0-9]*)|\1|'

HTH,
p.

On 05/05/2020 16:35, Nicolas Bosc wrote:

Hi RDKit users,

Writing molecules in a sdf with properties automatically add a number 
after the property name which is the position of the associated 
molecule in the file:

>   * (1) *
CHEMBL123

How can I change this so there is no number? The program that I am 
using to read the sdf file fails because of this...


Thanks,

Nicolas


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