Re: [Open Babel] OpenCL

[Ernst-Georg Schmid]

>AFAIK OB checks all
>fingerprints in a list one by one so there is much room for
>improvement.

That is a killer for OpenCL on the GPU, because there is a considerable penalty 
for moving memory between Host and Device (GPU). Generally, you want to move 
large blocks of memory and do as much as possible on the Device before moving 
back to the Host.

AFAIK, OpenCL shines when there are independent calculations on large sets of 
numbers to do. It is not well suited for bitwise operations, string comparisons 
etc. Please note also, that literally all customer GPUs (not the dedicated 
Tesla or FireStream Accelerators) suffer severe performance degradation when 
dealing with double precision datatypes.

My 2ct is, that the forcefields probably benefit most from OpenCL on a GPU 
while things like fingerprint comparison or similarity will mostly benefit from 
running in parallel threads on the CPU. And there is a vector (MMX/SSE) unit 
around, with large registers and powerful SIMD instructions for bitwise 
operations...:-) If you use e.g. GCCs vector extensions, you don't even have to 
deal with intrinsics or assembler.

Hope that helps in finding a decision,

Ernst-Georg

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Re: [Open Babel] Weighted-rotor search

[scott_m]

That's great, many thanks for the help. One other thing, I mentioned pybel
because I haven't got the OBMol conversion from input smiles string to
output file with 3D coordinates. Would you mind giving a quick example of
this (or directing me to online documentation, I couldn't find much here)?

What I have been trying:

mol = openbabel.OBMol()
conversion = openbabel.OBConversion()
conversion.SetInAndOutFormats('smi', 'com')
conversion.ReadString(mol, 'cc')
mol.AddHydrogens()

#Next step is what I'm not sure of, how do I get the coordinates so that I
can optimize and write to file??   

cv.GetCoordinates()
cv.WriteFile(mol, 'test.com')

# But this just gives the coordinates as 0

With pybel I found the make3d() and localopt() functions very handy for this
but can't get a similar setup going with openbabel. 

Apologies if this is a bit of a new thread.

Cheers,

Scott

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Re: [Open Babel] Weighted-rotor search

[Maciek Wójcikowski]

Hello,

You should use:

ff.GetCoordinates(mol)

Where ff is your OBForceField class and mol is OBMol.

Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl


2012/7/13 scott_m 

> That's great, many thanks for the help. One other thing, I mentioned pybel
> because I haven't got the OBMol conversion from input smiles string to
> output file with 3D coordinates. Would you mind giving a quick example of
> this (or directing me to online documentation, I couldn't find much here)?
>
> What I have been trying:
>
> mol = openbabel.OBMol()
> conversion = openbabel.OBConversion()
> conversion.SetInAndOutFormats('smi', 'com')
> conversion.ReadString(mol, 'cc')
> mol.AddHydrogens()
>
> #Next step is what I'm not sure of, how do I get the coordinates so that I
> can optimize and write to file??
>
> cv.GetCoordinates()
> cv.WriteFile(mol, 'test.com')
>
> # But this just gives the coordinates as 0
>
> With pybel I found the make3d() and localopt() functions very handy for
> this
> but can't get a similar setup going with openbabel.
>
> Apologies if this is a bit of a new thread.
>
> Cheers,
>
> Scott
>
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> View this message in context:
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>
>
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[Open Babel] (no subject)

[James Jack]

I have what may be a simple question.  I'm taking the 2D molfile for Naproxen:



[cid:image001.png@01CD5F96.2CB3DAD0]



When I convert this to a 3D molfile with "add explicit H" checked in the 
OpenBabel GUI or I try the same in code the OH seems to become O- (O with a 
negative charge).



Even if I use Cheshire to sprout explicit H everywhere necessary first, 
including the OH abbreviation I still get an O- in the resulting 3D molfile 
from OpenBabel:



[cid:image002.png@01CD5F96.2CB3DAD0]



Do you know why that is and how I can prevent it?



A customer of yours and ours has seen the Draw add-ins I have written with 
other 3D geometry calculators and asked if I could do this with OpenBabel and 
I'm almost there.



Best Regards,



James



[cid:image003.jpg@01CD5F96.2CB3DAD0]


James Jack PhD.
Principal Solutions Architect, ELM Solution Architects Team

Accelrys Ltd
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Re: [Open Babel] Weighted-rotor search

[scott_m]

Thanks for the reply but that doesn't seem to be working for me (code below).
If I just want to get a rough set of coordinates, what should I do? I see
that gen3d (see link below) does a weighted rotor search as part of the
process of making 3d coords but I wanted to just get the 3d coords and
specify my own weighted rotor search conditions. 

mol = openbabel.OBMol()
cv = openbabel.OBConversion()
cv.SetInAndOutFormats('smi', outfile_type)
cv.ReadString(mol, smiles_string)
mol.AddHydrogens()
ff = openbabel.OBForceField.FindForceField("MMFF94")
ff.GetCoordinates(mol)

gen3d source code:
http://openbabel.svn.sf.net/viewvc/openbabel/openbabel/trunk/src/ops/gen3d.cpp?revision=4307&view=markup





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Re: [Open Babel] Weighted-rotor search

[Chris Morley]

On 13/07/2012 14:46, scott_m wrote:
> Thanks for the reply but that doesn't seem to be working for me (code below).
> If I just want to get a rough set of coordinates, what should I do? I see
> that gen3d (see link below) does a weighted rotor search as part of the
> process of making 3d coords but I wanted to just get the 3d coords and
> specify my own weighted rotor search conditions.

But you have to start with something. gen3D is quite quick. See my reply 
to James Jack on how it is used in C++. The python would be similar.

Chris
>
> mol = openbabel.OBMol()
> cv = openbabel.OBConversion()
> cv.SetInAndOutFormats('smi', outfile_type)
> cv.ReadString(mol, smiles_string)
> mol.AddHydrogens()
> ff = openbabel.OBForceField.FindForceField("MMFF94")
> ff.GetCoordinates(mol)
>
> gen3d source code:
> http://openbabel.svn.sf.net/viewvc/openbabel/openbabel/trunk/src/ops/gen3d.cpp?revision=4307&view=markup



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Re: [Open Babel] Weighted-rotor search

[scott_m]

Thanks Chris, do you have a link for that?

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Re: [Open Babel] (no subject)

[Chris Morley]

On 11/07/2012 18:51, James Jack wrote:
>
> When I convert this to a 3D molfile with "add explicit H" checked in the
> OpenBabel GUI or I try the same in code the OH seems to become O- (O
> with a negative charge).
>
In the GUI you need to check "Add hydrogens (make explicit)" but have 
the editbox labelled "Add hydrogens appropriate for this pH" on the next 
line empty.

In code something like
  pMol->AddHydrogens(false, false);

But this may not be necessary.

If you use "Generate 3D coordinates" in the GUI or something like
  OBOp* pOp = OBOp::FindType("gen3D");
  if(pOp)
   pOp->Do(pMol);
in code, explicit hydrogens are added automatically.

Chris

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