Re: [Rdkit-discuss] connecting to postgres in rdkit environment

2017-02-25 Thread Markus Sitzmann 
Maybe this one here helps, too, although it is basically the same what TJ
said:

https://devops.profitbricks.com/tutorials/install-postgresql-on-centos-7/

Markus

On Sat, Feb 25, 2017 at 11:29 PM, TJ O'Donnell  wrote:

> The server itself must be told to allow remote connections.
> You might check these two things.
> 1.  You can edit the postgresql.conf file (not sure where that is on your
> system).
>  https://www.postgresql.org/docs/9.2/static/runtime-
> config-connection.html
>  Uncomment or add the line listen_addresses='*'. You can
>  tailor that to be more specific, but try this first.
>
> 2.  The file pg_hba.conf also controls access.  Look at this:
>   https://www.postgresql.org/docs/9.3/static/auth-pg-hba-conf.html
>
> Be sure to restart the server after you make changes to these files.
>
> Hope this helps,
> TJ O'Donnell
>
>
> On Sat, Feb 25, 2017 at 12:34 PM,  wrote:
>
>> Hi,
>> I've installed rdkit on a CentOS machine using anaconda python and set up
>> a postgresql compound database in the rdkit environment. It works great on
>> the machine's console.
>> I now want to access it remotely and I'm trying to set up a jdbc postgres
>> driver to access it from a windows client but this is not working. If I
>> test the driver on the server it tells me that the connection is refused
>> and I should check that the machine is accepting TCP requests.
>>
>> I have opened the standard port that postgres uses
>> -A INPUT -m state --state NEW -m tcp -p tcp --dport 5432 -j ACCEPT
>>
>> iptables -L returns
>> ACCEPT tcp  --  anywhere anywherestate NEW
>> tcp dpt:postgres
>>
>> this is where I don't know what to check next. A few things that might be
>> relevant. If I "ps -eaf | grep post" I see four postgres processes running
>> under my username (not postgres), so I think there is a server working.
>> There is also a "system" postgresql (version 9.2) which I have connected to
>> previously a long time ago. This connection no longer works either and I
>> don't really care about that but could be an interfering factor.
>>
>> If anyone has suggestions about what to check next or solve this I'd be
>> grateful
>>
>> thanks,
>> Neil
>>
>>
>>
>> 
>> --
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>> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
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>>
>>
>
> 
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Re: [Rdkit-discuss] connecting to postgres in rdkit environment

2017-02-25 Thread TJ O'Donnell 
The server itself must be told to allow remote connections.
You might check these two things.
1.  You can edit the postgresql.conf file (not sure where that is on your
system).

https://www.postgresql.org/docs/9.2/static/runtime-config-connection.html
 Uncomment or add the line listen_addresses='*'. You can
 tailor that to be more specific, but try this first.

2.  The file pg_hba.conf also controls access.  Look at this:
  https://www.postgresql.org/docs/9.3/static/auth-pg-hba-conf.html

Be sure to restart the server after you make changes to these files.

Hope this helps,
TJ O'Donnell


On Sat, Feb 25, 2017 at 12:34 PM,  wrote:

> Hi,
> I've installed rdkit on a CentOS machine using anaconda python and set up
> a postgresql compound database in the rdkit environment. It works great on
> the machine's console.
> I now want to access it remotely and I'm trying to set up a jdbc postgres
> driver to access it from a windows client but this is not working. If I
> test the driver on the server it tells me that the connection is refused
> and I should check that the machine is accepting TCP requests.
>
> I have opened the standard port that postgres uses
> -A INPUT -m state --state NEW -m tcp -p tcp --dport 5432 -j ACCEPT
>
> iptables -L returns
> ACCEPT tcp  --  anywhere anywherestate NEW tcp
> dpt:postgres
>
> this is where I don't know what to check next. A few things that might be
> relevant. If I "ps -eaf | grep post" I see four postgres processes running
> under my username (not postgres), so I think there is a server working.
> There is also a "system" postgresql (version 9.2) which I have connected to
> previously a long time ago. This connection no longer works either and I
> don't really care about that but could be an interfering factor.
>
> If anyone has suggestions about what to check next or solve this I'd be
> grateful
>
> thanks,
> Neil
>
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> ___
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> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
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Re: [Rdkit-discuss] Question about WedgeMolBonds

2017-02-25 Thread John Mayfield 
>
> Is there something that the compute2DCoords() is doing that makes it a
> dependency for WedgeMolBonds()


Yes, calculating 2D coordinates. Look at these two molecules, they are the
same but the atoms have been positioned differently in 2D and hence the
wedging needs to be different. Therefore you need 2D coordinates before you
can (re)assign wedges.
[image: Inline images 3]
In truth since the two (2D layout and wedging) are dependant I'd probably
make the layout call the wedging automatically

John

On 25 February 2017 at 03:39, Shubbey McBean 
wrote:

> Hi, I am using WedgeMolBonds() to label converted 3D->2D conformations,
> roughly:
>
>   // ... read in 3D mol
>   assignChiralTypesFrom3D(mol);
>   assignStereochemistry(mol,true,true);
>   WedgeMolBonds(mol,());
>   compute2DCoords(...)
>
> However, this does not produce an accurate result.  In order to "fix"
> this, I need to reverse the last two calls (calling the 3D->2D _before_
> WedgeMolBonds). This seems counter-intuitive to me.  Is there something
> that the compute2DCoords() is doing that makes it a dependency for
> WedgeMolBonds()?  Or am I going about this the wrong way?  The specifics of
> my situation make it preferable to order things as stated, but it's not a
> deal-breaker.  Mostly I am just a bit stuck as to what is going on here.
>
> Thanks!
>
>
>
> 
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