rdock-list-def — General Mailing List for rDock users

Re: [rDock-list-def] Links to Draft Paper, Supplemental Data

[Sergio R. C. <sru...@gm...>]

Dear Hassan,

This is an error on the text of the rDock Manual. The draft paper it refers
to corresponds to a previous draft version of the actual PLOS COMP BIOL
paper.
The details were finally removed from the draft and included in the manual.
See sections 6.1 and 6.2 for the available information and details about
the scoring functions.
Best,

Sergio


2014-12-10 21:51 GMT+01:00 Hassan Ghani <hg...@us...>:

> Hi,
>
> The Code Implementation section of the rDock User Manual says, "See the
> rDock draft
> paper for more details on the implementation of these [scoring function]
> terms".
>
> Could someone point me to the draft paper? I searched
> rdock.sourceforge.net as well as did a general Google search, but could
> not find the draft paper. I found and read the rDock paper in PLoS
> Computational Biology (April 2014), but that paper doesn't elaborate on the
> scoring function terms and I'm guessing it's not the draft paper in
> question.
>
> Additionally, could someone point me to the Supporting/Supplemental docs
> referred to in the PLoS Computational Biology paper?
>
> I really appreciate your taking the time to answer my questions!
>
> Hassan Ghani
> MD Candidate
> USC Keck School of Medicine
> Class of 2015
>
>
> ------------------------------------------------------------------------------
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>
>

[rDock-list-def] Links to Draft Paper, Supplemental Data

[Hassan G. <hg...@us...>]

Hi,

The Code Implementation section of the rDock User Manual says, "See the
rDock draft
paper for more details on the implementation of these [scoring function]
terms".

Could someone point me to the draft paper? I searched rdock.sourceforge.net
as well as did a general Google search, but could not find the draft paper.
I found and read the rDock paper in PLoS Computational Biology (April
2014), but that paper doesn't elaborate on the scoring function terms and
I'm guessing it's not the draft paper in question.

Additionally, could someone point me to the Supporting/Supplemental docs
referred to in the PLoS Computational Biology paper?

I really appreciate your taking the time to answer my questions!

Hassan Ghani
MD Candidate
USC Keck School of Medicine
Class of 2015

Re: [rDock-list-def] SCORE term corresponding to entropy?

[Szilveszter J. <szi...@gm...>]

Hi, there is no explicit entropy term, and admittedly that is one of
the main problems in docking in general. There is a score for
rotatable bonds that can give some sort of approximation, but as the
solvent (water) molecules are not considered, it is pretty crude.
The original assumption is that you can estimate the binding energy by
a linear combination of different scores including an entropy term.
Beatriz tried to invent a new scoring function using genetic
programming ( http://www.cartesiangp.co.uk/papers/gptp2004-garmendia.pdf
) that is not necessarily a linear combination of terms. It was better
in that sense that it improved the real hits, though there is no real
entropy included still. Still worth a try, but keep in mind this fancy
GP scoring function was trained on a pre-2004 version of rDock.
Szilva
PS Cheers, certainly it is David Morley who contributed the most, and
frankly I do not know the current developers but they are actively
maintaining the current version, thanks!



On Sat, Dec 6, 2014 at 12:32 AM, Hassan Ghani <gh...@gm...> wrote:
> Hi,
>
> First off, I'd like to thank the makers of rDock for all their effort and an
> excellently written opensource docking program, particularly since it allows
> explicit solvent (which is critical for me).
>
> The results SD files features numerous SCORE terms per ligand conformer. Is
> there a term that corresponds to the entropic cost of the ligand going from
> unbound -> bound?
>
> I searched the manual for any mention of entropy and did not find an answer
> to the above question, that said I apologize if it's already been documented
> and I simply missed it.
>
> Best,
> Hassan
>
> ------------------------------------------------------------------------------
> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
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>

[rDock-list-def] SCORE term corresponding to entropy?

[Hassan G. <gh...@gm...>]

Hi,

First off, I'd like to thank the makers of rDock for all their effort and
an excellently written opensource docking program, particularly since it
allows explicit solvent (which is critical for me).

The results SD files features numerous SCORE terms per ligand conformer. Is
there a term that corresponds to the entropic cost of the ligand going from
unbound -> bound?

I searched the manual for any mention of entropy and did not find an answer
to the above question, that said I apologize if it's already been
documented and I simply missed it.

Best,
Hassan

[rDock-list-def] error with a parallel rDocking on a computer with 4 CPUs without job scheduler

[Jose M. G. <jos...@un...>]

Dear rDockers,

I found the problem. My SDF records contained the molecules' SMILES 
descriptions as properties and and it seems that for larger molecules 
the string was too long for rDock.
I could fix this by removing the corresponding fields from my SDF and 
now it runs fine.

Cheers,
Jose Manuel

[rDock-list-def] error with a parallel rDocking on a computer with 4 CPUs without job scheduler

[Jose M. G. <jos...@un...>]

Dear rDock communauty,

I noticed a strange behavior of rDock recently. Here is the short story...

I tried to dock a database on multiple CPUs without using a job 
scheduler, as none was already installed on this particular computer and 
I needed to start the docking quickly for the weekend...

To do so, I followed this tutorial (1). I have 4 CPUs on my computer, so 
I splitted the input ligands file in 4 even parts and I 'submitted' 4 
jobs using the following syntax in a bash script (snippet at reference 2).
When I checked, all jobs were running simultaneously, as I wished.
However, I noticed a very strange behavior when I came back this 
morning. No job finished but all stopped without printing any error 
message at very different times (3). Here is an example of the relevant 
part of one of the log files : (4).

Did anyone try the tutorial (1) and noticed the same behavior? Do you 
have insight about what could have caused it?
Could this be resolved by a job scheduler, such as PBS or Condor?

Thank you for your help!!!

Jose Manuel

Additional Informations :
OS: Centos 6.5
CPUs type :  Intel(R) Core(TM) i7 CPU 950 @ 3.07GH

REFERENCES :
(1) http://rdock.sourceforge.net/how-to-run-rdock-in-parallel/

(2)
#/bin/bash

for file in *sd; do
     out=$(echo $file | cut -d. -f1)'_out'
     rbdock -i $file -o $out -r $protein.prm -p dock.prm -n 20  > 
$out.log 2>&1 &
done

(3)
job1 - Nov 23 11:22
job2 - Nov 20 16:06
job3 - Nov 21 00:29
job4 - Nov 21 10:09

(4)
**************************************************
RECORD #4577
NAME:   previousLigand
RANDOM_NUMBER_SEED:           1164231034

**************************************************
RECORD #4578

Re: [rDock-list-def] How to see if section pharma has been enabled

[Jan D. <ja...@gm...>]

Thank you Sergio that solved it!
Jan

On Monday, November 10, 2014, Sergio Ruiz Carmona <sru...@gm...>
wrote:

> Hi Jan,
>
> In the output that rDock writes to the command line you will have
> something like the following text:
>
> ***********************************************
>> The rDock program is licensed under GNU-LGPLv3.0.
>> http://rdock.sourceforge.net/
>> [ ... ]
>> ***********************************************
>>
>> Command line args:
>>  -i FILE.sd
>>  [ ... ]
>>  -n 50
>> Reading polar hydrogens only from ligand SD file
>> DOCKING PROTOCOL:
>> [ ... ]
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> *RbtPharmaSF: Reading mandatory ph4 constraints from FILE.restrReading
>> EXP constraint file(-3,3,-4) 0.5 1.91 0.25 DonCreating ph4 for Dontype
>> EXPReading EXP constraint file(-3,4,-6) 0.5 1.74 0.25 AccCreating ph4 for
>> Acctype EXPReading EXP constraint file(1,1.5,-4) 0.5 1.68 0.25 HydCreating
>> ph4 for Hydtype EXPRbtPharmaSF: No optional ph4 constraints file found*
>> No solvent
>> ------------- Terminate filter 0------------
>> if (SCORE.NRUNS - 49 ) > 0 then
>> 0.0
>> else
>> -1.0
>> end
>>
>> **************************************************
>> RECORD #1
>
> [ ... ]
>
>
> The lines in boldface (from "RbtParmaSF: Reading ..." to "No Solvent")
> correspond to the pharmacophoric constraints: 3 mandatory in "FILE.restr"
> with the corresponding parameters also written and no optional constraints.
> Best regards,
>
> Sergio
>
>
>
> 2014-11-10 12:21 GMT+01:00 Jan Domanski <ja...@gm...
> <javascript:_e(%7B%7D,'cvml','ja...@gm...');>>:
>
>> Hi guys,
>>
>> I have a section pharma defined in my dock.prm file, pointing to some
>> .const files. How to make sure that rdock has read those in correctly and
>> is actually using them?
>>
>> Thanks,
>>
>> - Jan
>>
>>
>> ------------------------------------------------------------------------------
>>
>> _______________________________________________
>> rDock-list-def mailing list
>> rDo...@li...
>> <javascript:_e(%7B%7D,'cvml','rDo...@li...');>
>> https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>>
>>
>

Re: [rDock-list-def] How to see if section pharma has been enabled

[Sergio R. C. <sru...@gm...>]

Hi Jan,

In the output that rDock writes to the command line you will have something
like the following text:

***********************************************
> The rDock program is licensed under GNU-LGPLv3.0.
> http://rdock.sourceforge.net/
> [ ... ]
> ***********************************************
>
> Command line args:
>  -i FILE.sd
>  [ ... ]
>  -n 50
> Reading polar hydrogens only from ligand SD file
> DOCKING PROTOCOL:
> [ ... ]
>
>
>
>
>
>
>
>
>
>
> *RbtPharmaSF: Reading mandatory ph4 constraints from FILE.restrReading EXP
> constraint file(-3,3,-4) 0.5 1.91 0.25 DonCreating ph4 for Dontype
> EXPReading EXP constraint file(-3,4,-6) 0.5 1.74 0.25 AccCreating ph4 for
> Acctype EXPReading EXP constraint file(1,1.5,-4) 0.5 1.68 0.25 HydCreating
> ph4 for Hydtype EXPRbtPharmaSF: No optional ph4 constraints file found*
> No solvent
> ------------- Terminate filter 0------------
> if (SCORE.NRUNS - 49 ) > 0 then
> 0.0
> else
> -1.0
> end
>
> **************************************************
> RECORD #1

[ ... ]


The lines in boldface (from "RbtParmaSF: Reading ..." to "No Solvent")
correspond to the pharmacophoric constraints: 3 mandatory in "FILE.restr"
with the corresponding parameters also written and no optional constraints.
Best regards,

Sergio



2014-11-10 12:21 GMT+01:00 Jan Domanski <ja...@gm...>:

> Hi guys,
>
> I have a section pharma defined in my dock.prm file, pointing to some
> .const files. How to make sure that rdock has read those in correctly and
> is actually using them?
>
> Thanks,
>
> - Jan
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> rDock-list-def mailing list
> rDo...@li...
> https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>
>

[rDock-list-def] How to see if section pharma has been enabled

[Jan D. <ja...@gm...>]

Hi guys,

I have a section pharma defined in my dock.prm file, pointing to some
.const files. How to make sure that rdock has read those in correctly and
is actually using them?

Thanks,

- Jan

Re: [rDock-list-def] Using density dx files as pharmacophore definitions

[Jan D. <ja...@gm...>]

Oh, I see. Many thanks for the answer Daniel!
I'll send any further questions on mdmix to its mailing list ;)

- Jan

On 8 November 2014 01:00, Daniel Álvarez García <alg...@gm...>
wrote:

> The file format is briefly described in page 34 of the manual.
> This is an example of a .const file:
>
>  -3.000   3.000   -4.000 0.50  Don
>  -3.000   4.000   -6.000 0.50  Acc
>   1.000   1.500   -4.000 1.00  Hyd
>
> As you see, it's very simple: center, tolerance and type.
> And the section to include in the prm file is this one
> (supposing al three are mandatory and the file is named mandatory.const):
>
> ################################
> # PHARMACOPHORIC RESTRAINTS
> ################################
> SECTION PHARMA
>     SCORING_FUNCTION RbtPharmaSF
>     WEIGHT 1.0
>     CONSTRAINTS_FILE mandatory.const
> END_SECTION
>
> Regarding the transformation of the density map to
> coordinates as I did for HSP90, please write to pymdmix mailing list,
> (https://sourceforge.net/p/mdmix/mailman/) the topic will better fit
> there
> and will help other users as well ;)
>
> Thanks!
>
> Daniel
>
> El 08/11/2014, a las 01:03, Jan Domanski escribió:
>
> Hi Daniel,
>
> Many thanks for a speedy reply! mdmix looks much better than hand-crafted
> tools I have for that purpose ;)
>
> Regarding the pharmacophore, is there a ready tutorial somewhere showing
> how the .const file should be structured? The only thing I could find in
> the manual was adding the mandatory and optional.const files to the .prm
> file. An example of what you did for HSP90 in the paper would be awesome.
>
> Thanks,
>
> - Jan
>
> On 7 November 2014 23:58, Daniel Álvarez García <alg...@gm...
> > wrote:
>
>> Hi Jan,
>>
>> it is not possible to directly use a density file as a pharmacophore
>> model. You will need to pre-process the grid information
>> to extract the relevant coordinates and write a standard pharmacophore
>> file as described in the documentation.
>>
>> If you need help to extract coordinates from a grid file, take a look at
>> this software: mdmix.sourceforge.net.
>> The python package contains useful objects and functions to deal with
>> grid data. Contact me for further info on this.
>>
>> Daniel
>>
>>
>>
>> El 08/11/2014, a las 00:04, Jan Domanski escribió:
>>
>> > Hi guys,
>> >
>> > Is it possible to use density (.dx) files in the rDock pharmacophore
>> model? Do I understand correctly that now the pharmacophore model is just a
>> bunch of xyz for each pharmacophore type with a weight parameter?
>> >
>> > Thanks,
>> >
>> > - Jan
>> >
>> ------------------------------------------------------------------------------
>> > _______________________________________________
>> > rDock-list-def mailing list
>> > rDo...@li...
>> > https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>>
>>
>
>

Re: [rDock-list-def] Using density dx files as pharmacophore definitions

[Daniel Á. G. <alg...@gm...>]

The file format is briefly described in page 34 of the manual.
This is an example of a .const file:

 -3.000   3.000   -4.000 0.50  Don
 -3.000   4.000   -6.000 0.50  Acc
  1.000   1.500   -4.000 1.00  Hyd

As you see, it's very simple: center, tolerance and type. 
And the section to include in the prm file is this one
(supposing al three are mandatory and the file is named mandatory.const):

################################
# PHARMACOPHORIC RESTRAINTS
################################
SECTION PHARMA
    SCORING_FUNCTION RbtPharmaSF
    WEIGHT 1.0
    CONSTRAINTS_FILE mandatory.const
END_SECTION

Regarding the transformation of the density map to 
coordinates as I did for HSP90, please write to pymdmix mailing list, 
(https://sourceforge.net/p/mdmix/mailman/) the topic will better fit there 
and will help other users as well ;)

Thanks!

Daniel

El 08/11/2014, a las 01:03, Jan Domanski escribió:

> Hi Daniel, 
> 
> Many thanks for a speedy reply! mdmix looks much better than hand-crafted tools I have for that purpose ;)
> 
> Regarding the pharmacophore, is there a ready tutorial somewhere showing how the .const file should be structured? The only thing I could find in the manual was adding the mandatory and optional.const files to the .prm file. An example of what you did for HSP90 in the paper would be awesome. 
> 
> Thanks,
> 
> - Jan
> 
> On 7 November 2014 23:58, Daniel Álvarez García <alg...@gm...> wrote:
> Hi Jan,
> 
> it is not possible to directly use a density file as a pharmacophore model. You will need to pre-process the grid information
> to extract the relevant coordinates and write a standard pharmacophore file as described in the documentation.
> 
> If you need help to extract coordinates from a grid file, take a look at this software: mdmix.sourceforge.net.
> The python package contains useful objects and functions to deal with grid data. Contact me for further info on this.
> 
> Daniel
> 
> 
> 
> El 08/11/2014, a las 00:04, Jan Domanski escribió:
> 
> > Hi guys,
> >
> > Is it possible to use density (.dx) files in the rDock pharmacophore model? Do I understand correctly that now the pharmacophore model is just a bunch of xyz for each pharmacophore type with a weight parameter?
> >
> > Thanks,
> >
> > - Jan
> > ------------------------------------------------------------------------------
> > _______________________________________________
> > rDock-list-def mailing list
> > rDo...@li...
> > https://lists.sourceforge.net/lists/listinfo/rdock-list-def
> 
> 

Re: [rDock-list-def] Using density dx files as pharmacophore definitions

[Jan D. <ja...@gm...>]

Hi Daniel,

Many thanks for a speedy reply! mdmix looks much better than hand-crafted
tools I have for that purpose ;)

Regarding the pharmacophore, is there a ready tutorial somewhere showing
how the .const file should be structured? The only thing I could find in
the manual was adding the mandatory and optional.const files to the .prm
file. An example of what you did for HSP90 in the paper would be awesome.

Thanks,

- Jan

On 7 November 2014 23:58, Daniel Álvarez García <alg...@gm...>
wrote:

> Hi Jan,
>
> it is not possible to directly use a density file as a pharmacophore
> model. You will need to pre-process the grid information
> to extract the relevant coordinates and write a standard pharmacophore
> file as described in the documentation.
>
> If you need help to extract coordinates from a grid file, take a look at
> this software: mdmix.sourceforge.net.
> The python package contains useful objects and functions to deal with grid
> data. Contact me for further info on this.
>
> Daniel
>
>
>
> El 08/11/2014, a las 00:04, Jan Domanski escribió:
>
> > Hi guys,
> >
> > Is it possible to use density (.dx) files in the rDock pharmacophore
> model? Do I understand correctly that now the pharmacophore model is just a
> bunch of xyz for each pharmacophore type with a weight parameter?
> >
> > Thanks,
> >
> > - Jan
> >
> ------------------------------------------------------------------------------
> > _______________________________________________
> > rDock-list-def mailing list
> > rDo...@li...
> > https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>
>

Re: [rDock-list-def] Using density dx files as pharmacophore definitions

[Daniel Á. G. <alg...@gm...>]

Hi Jan,

it is not possible to directly use a density file as a pharmacophore model. You will need to pre-process the grid information
to extract the relevant coordinates and write a standard pharmacophore file as described in the documentation. 

If you need help to extract coordinates from a grid file, take a look at this software: mdmix.sourceforge.net.
The python package contains useful objects and functions to deal with grid data. Contact me for further info on this.

Daniel



El 08/11/2014, a las 00:04, Jan Domanski escribió:

> Hi guys, 
> 
> Is it possible to use density (.dx) files in the rDock pharmacophore model? Do I understand correctly that now the pharmacophore model is just a bunch of xyz for each pharmacophore type with a weight parameter?
> 
> Thanks,
> 
> - Jan
> ------------------------------------------------------------------------------
> _______________________________________________
> rDock-list-def mailing list
> rDo...@li...
> https://lists.sourceforge.net/lists/listinfo/rdock-list-def

[rDock-list-def] Using density dx files as pharmacophore definitions

[Jan D. <ja...@gm...>]

Hi guys,

Is it possible to use density (.dx) files in the rDock pharmacophore model?
Do I understand correctly that now the pharmacophore model is just a bunch
of xyz for each pharmacophore type with a weight parameter?

Thanks,

- Jan

Re: [rDock-list-def] sdreport Molecular Weight

[Sergio R. C. <sru...@gm...>]

Dear Parker,

There is a binary script called "rblist" that outputs physicochemical
properties, including molecular weight, of the entries in an sd file.
For example, running the following command:

*rblist -iSDFILE.sd*

will produce the following output:

***********************************************
> The rDock program is licensed under GNU-LGPLv3.0.
> http://rdock.sourceforge.net/
> [...]
> Date:           Wed Oct 22 10:39:34 2014
> ***********************************************
> Command line args:
> -iSDFILE.sd
> RECORD  NAME                          #ATOMS  #BONDS  MW      #ROT    #HBD
>    #HBA    #AROM   #GUAN   #LIPOC
> 1       ZINC03831630                  34      38      449.506 4       3
>     5       5       0       21
> 2       ZINC00603011                  32      35      402.476 7       4
>     7       3       0       18


If you need sdreport to do it, you should modify the sdfile in order to add
a field with the MW for each entry. In that case, the executed command
should be something like this:

*sdreport -t'MW' SDFILE.sd*

Hope this helps!
Best,

Sergio

2014-10-21 17:58 GMT+02:00 Parker de Waal <Par...@va...>:

> Hello,
>
> I’d like to have sdreport output the molecular weight of the compound
> being docked. After a number of attempts I was unable to perform this.
>
> Could someone provide insight into how to do this?
>
> Best,
> Parker
>
>
> ------------------------------------------------------------------------------
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> _______________________________________________
> rDock-list-def mailing list
> rDo...@li...
> https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>

[rDock-list-def] sdreport Molecular Weight

[Parker de W. <Par...@va...>]

Hello,

I’d like to have sdreport output the molecular weight of the compound being docked. After a number of attempts I was unable to perform this.

Could someone provide insight into how to do this?

Best,
Parker

Re: [rDock-list-def] missing function for measuring angles

[Szilveszter J. <szi...@gm...>]

Hi,

I am afraid you are looking for an other mailing list, likely the one
called: rdkit-devel http://sourceforge.net/p/rdkit/mailman/

This list is for the rDock package: http://rdock.sourceforge.net/ and
has nothing to do with rdkit.

Cheers:
Szilva


On Mon, Oct 13, 2014 at 1:09 PM, Jose Manuel Gally
<jos...@un...> wrote:
> Dear rdkitters,
>
> I cannot find the functions GetAngleDeg and GetAngleRad which should be in
> rdMolTransforms according to the docs:
> http://www.rdkit.org/Python_Docs/rdkit.Chem.rdMolTransforms-module.html
>
> Here are the modules listed in rdMolTransforms with dir command:
> ['CanonicalizeConformer', 'CanonicalizeMol', 'ComputeCanonicalTransform',
> 'ComputeCentroid', 'TransformConformer', '__doc__', '__file__', '__name__',
> '__package__']
>
> I am working with the latest build of rdkit on Centos 6.5 (x64).
>
> Is the documentation out-dated or is it something wrong with my
> installation?
>
> Thank you for your help!
>
> Cheers,
> José-Manuel Gally
>
> ------------------------------------------------------------------------------
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> _______________________________________________
> rDock-list-def mailing list
> rDo...@li...
> https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>

[rDock-list-def] missing function for measuring angles

[Jose M. G. <jos...@un...>]

Dear rdkitters,

I cannot find the functions GetAngleDeg and GetAngleRad which should be 
in rdMolTransforms according to the docs:
http://www.rdkit.org/Python_Docs/rdkit.Chem.rdMolTransforms-module.html

Here are the modules listed in rdMolTransforms with dir command:
['CanonicalizeConformer', 'CanonicalizeMol', 
'ComputeCanonicalTransform', 'ComputeCentroid', 'TransformConformer', 
'__doc__', '__file__', '__name__', '__package__']

I am working with the latest build of rdkit on Centos 6.5 (x64).

Is the documentation out-dated or is it something wrong with my 
installation?

Thank you for your help!

Cheers,
José-Manuel Gally
//

Re: [rDock-list-def] docking small molecule - small molecule

[Sergio R. C. <sru...@gm...>]

Dear Mirko,

I am not really sure about what you want to do.
rDock is a program for docking small molecules to macromolecules (proteins
or RNA).
If you need to dock small molecules against small molecules, I am afraid
rDock can not help you.
Best,

Sergio


2014-09-28 13:46 GMT+02:00 mirko busato <mir...@gm...>:

> Dear users,
>
> I am new user,
>
>  I would like to do a virtual screening of 30 or less monomers (ligands)
> against a receptor (not a protein but a small molecule for
> example  beta-agonists, beta blockers and some drugs  ) to understand which
> monomers are most likely to bind the receptor.
>
> Could I use rDock in my case?
>
> Thank you very much,
>
> Mirko
>
>
>
>
>
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[rDock-list-def] docking small molecule - small molecule

[mirko b. <mir...@gm...>]

Dear users,

I am new user,

 I would like to do a virtual screening of 30 or less monomers (ligands)
against a receptor (not a protein but a small molecule for
example  beta-agonists, beta blockers and some drugs  ) to understand which
monomers are most likely to bind the receptor.

Could I use rDock in my case?

Thank you very much,

Mirko

Re: [rDock-list-def] PMF Scoring function in rDock

[Szilveszter J. <szi...@gm...>]

Hi,

As far as I remember, the PMF scoring was not really good for docking.
My guess is because the PMF functions are not smooth enough, hence you
can find the smoothing part in the source tree, but honestly I have
never had a chance to test it thoroughly. Still, you can re-score the
final docked poses with PMF, but you have to have a slightly modified
cavity preparation. The cavity border have to be larger to make sure
the PMF scoring function (that is summing up relatively long-range
atom interactions) can reach atoms furher away.

Using 4dfr as sample try:


rbcavity -was -r4dfr.prm -b16
rbcalcgrid -o_vdw1.grd -r4dfr.prm -pcalcgrid_vdw1.prm  -g0.3 -b1.0
rbcalcgrid -o_vdw5.grd -r4dfr.prm -pcalcgrid_vdw5.prm  -g0.3 -b1.0
rbdock -i4dfr_lignad.sd -odocked -r4dfr.prm -pdock.prm -n 100 -an -ap
rbdock -idocked.sd -odocked_pmf -r4dfr.prm -pscore_pmf.prm -n 1 -an -ap

You will find an additional <SCORE.INTER.PMF> entry in the resulting
ligand file.
Hope it helps:
Szilva



On Fri, Aug 22, 2014 at 12:28 PM, Szilveszter Juhos
<szi...@gm...> wrote:
> Hi,
> Indeed it is Ingos pmf - I will be next to my computer on Sunday, and will
> be able to give a longer answer.
> Cheers
> Szilva
>
> On Aug 22, 2014 12:04 PM, "Jose Manuel Gally"
> <jos...@un...> wrote:
>>
>> Dear fellow rDockers,
>>
>> I noticed that there was a RbtPMFIdxSF.prm scoring function in the
>> $RB_ROOT/data/sf directory. I couldn't find any reference to it neither
>> in the User or Reference Guides nor any explicit call to it in the
>> protocol files located at the $RB_ROOT/data/scripts repertory.
>> A quick look into the literature let me think that this might actually
>> be a Potential Mean Force scoring function (maybe as described here:
>> http://pubs.acs.org/doi/abs/10.1021/jm050038s ?), but without
>> confirmation I cannot know for sure.
>> I tried to test it by replacing some other scoring functions called in
>> the protocol files, but this only gave me errors, which is probably
>> because I didn't find the right place yet.
>>
>> Hence my following questions:
>>      1) Is the PMF scoring function the one presented in the paper from
>> Ingo Muegge?
>>      2) How could one implement it into the dock.prm protocol to compare
>> the obtained scores?
>>
>> I apologize if these questions are trivial, I am actually fairly new at
>> docking and C++... Many thanks for your help!
>>
>> Cheers,
>> Jose Manuel Gally
>> version of rDock: rDock_2013.1
>>
>>
>> ------------------------------------------------------------------------------
>> Slashdot TV.
>> Video for Nerds.  Stuff that matters.
>> http://tv.slashdot.org/
>> _______________________________________________
>> rDock-list-def mailing list
>> rDo...@li...
>> https://lists.sourceforge.net/lists/listinfo/rdock-list-def

Re: [rDock-list-def] PMF Scoring function in rDock

[Szilveszter J. <szi...@gm...>]

Hi,
Indeed it is Ingos pmf - I will be next to my computer on Sunday, and will
be able to give a longer answer.
Cheers
Szilva
On Aug 22, 2014 12:04 PM, "Jose Manuel Gally" <
jos...@un...> wrote:

> Dear fellow rDockers,
>
> I noticed that there was a RbtPMFIdxSF.prm scoring function in the
> $RB_ROOT/data/sf directory. I couldn't find any reference to it neither
> in the User or Reference Guides nor any explicit call to it in the
> protocol files located at the $RB_ROOT/data/scripts repertory.
> A quick look into the literature let me think that this might actually
> be a Potential Mean Force scoring function (maybe as described here:
> http://pubs.acs.org/doi/abs/10.1021/jm050038s ?), but without
> confirmation I cannot know for sure.
> I tried to test it by replacing some other scoring functions called in
> the protocol files, but this only gave me errors, which is probably
> because I didn't find the right place yet.
>
> Hence my following questions:
>      1) Is the PMF scoring function the one presented in the paper from
> Ingo Muegge?
>      2) How could one implement it into the dock.prm protocol to compare
> the obtained scores?
>
> I apologize if these questions are trivial, I am actually fairly new at
> docking and C++... Many thanks for your help!
>
> Cheers,
> Jose Manuel Gally
> version of rDock: rDock_2013.1
>
>
> ------------------------------------------------------------------------------
> Slashdot TV.
> Video for Nerds.  Stuff that matters.
> http://tv.slashdot.org/
> _______________________________________________
> rDock-list-def mailing list
> rDo...@li...
> https://lists.sourceforge.net/lists/listinfo/rdock-list-def
>

[rDock-list-def] PMF Scoring function in rDock

[Jose M. G. <jos...@un...>]

Dear fellow rDockers,

I noticed that there was a RbtPMFIdxSF.prm scoring function in the 
$RB_ROOT/data/sf directory. I couldn't find any reference to it neither 
in the User or Reference Guides nor any explicit call to it in the 
protocol files located at the $RB_ROOT/data/scripts repertory.
A quick look into the literature let me think that this might actually 
be a Potential Mean Force scoring function (maybe as described here: 
http://pubs.acs.org/doi/abs/10.1021/jm050038s ?), but without 
confirmation I cannot know for sure.
I tried to test it by replacing some other scoring functions called in 
the protocol files, but this only gave me errors, which is probably 
because I didn't find the right place yet.

Hence my following questions:
     1) Is the PMF scoring function the one presented in the paper from 
Ingo Muegge?
     2) How could one implement it into the dock.prm protocol to compare 
the obtained scores?

I apologize if these questions are trivial, I am actually fairly new at 
docking and C++... Many thanks for your help!

Cheers,
Jose Manuel Gally
version of rDock: rDock_2013.1

Re: [rDock-list-def] Visualizing top unique ligands

[Sergio R. C. <sru...@gm...>]

Dear Parker,

rDock provides some ancillary scripts that can help you in these tasks (see
sdfilter, sdsort in the Manual).
A typical sequence for obtaining a file with the top50 poses would be:

1.- For sorting all the poses per each ligand according to their score and
keeping the best one of each.

sdsort -n -s -fSCORE ALL_RESULTS.sd | sdfilter -f'$_COUNT == 1' >
>  ALL_RESULTS_1poseperlig.sd


2.- For sorting all the ligands by SCORE.INTER:

sdsort -n -fSCORE.INTER ALL_RESULTS_1poseperlig.sd >
> ALL_RESULTS_1poseperlig_sorted.sd


3.- For keeping the best 50 scoring ligands:

sdfilter -f'$_REC < 51' ALL_RESULTS_1poseperlig_sorted.sd >
> ALL_RESULTS_1poseperlig_sorted_TOP50.sd


Finally, you can just take a look at this generated sdfile with a molecular
viewer.
Best regards,

Sergio Ruiz



2014-07-06 3:10 GMT+02:00 Parker de Waal <Par...@va...>:

> Hello Everyone,
>
> After running a HTVS against the NCI DTP (273,000 compounds) database I
> would like to visualize the top 50 unique compounds before ordering them to
> test in vitro.
>
> Does anyone know if rDock has this capability? Or will I have to write an
> awk script to perform this for me?
>
> Best,
> Parker
>
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[rDock-list-def] Visualizing top unique ligands

[Parker de W. <Par...@va...>]

Hello Everyone,

After running a HTVS against the NCI DTP (273,000 compounds) database I would like to visualize the top 50 unique compounds before ordering them to test in vitro.

Does anyone know if rDock has this capability? Or will I have to write an awk script to perform this for me?

Best,
Parker