Re: [Rdkit-discuss] UFF energy question(s)...
Doh -- of course ... THANKS
any comments about the second part of my query?
"Also, any ideas what the energy units returned from ff.CalcEnergy() are?"
The UFF values vary wildly from the ones offered by obenergy using UFF
forcefield (this doesn't mean they are wrong of course, just want to
understand why)
OBenergy UFF (kJ/mol)
TOTAL ENERGY = 603.32957 kJ/mol
TOTAL ENERGY = 582.35037 kJ/mol
TOTAL ENERGY = 483.29385 kJ/mol
TOTAL ENERGY = 504.88763 kJ/mol
TOTAL ENERGY = 555.16601 kJ/mol
TOTAL ENERGY = 579.55593 kJ/mol
TOTAL ENERGY = 581.58096 kJ/mol
TOTAL ENERGY = 557.90448 kJ/mol
TOTAL ENERGY = 532.21012 kJ/mol
TOTAL ENERGY = 503.59585 kJ/mol
RDKit Calc Energy (UFF) for exactly the same molecules...
16700300.472
154163.203
132597.990
124078.437
140688.066
4863030.479
20278658.428
3690505.452
145837.684
150862.539
Some of the values I see for other molecules are huge - 4083891061152.739
(but this is not the case when I use obenergy to calculate the energy
values)
Cheers
-
Jean-Paul Ebejer
Early Stage Researcher
On 13 January 2012 13:11, Stiefl, Nikolaus wrote:
> Hi JP,
>
> ** **
>
> When you generate a mol from a smiles I don’t think a conformer is added
> by default.
>
> ** **
>
> So you have to do this yourself:
>
> ** **
>
> molecule = Chem.MolFromSmiles('')
>
> mol_h = AllChem.AddHs(molecule)
>
> mol_h.AddConformer(Chem.Conformer(mol_h.GetNumAtoms()))
>
> ff = AllChem.UFFGetMoleculeForceField(mol_h)
>
> energy_value = str(ff.CalcEnergy())
>
> print energy_value
>
> ** **
>
> Should at least get rid of the error ... not that the above code is tested
> ... plus it obviously doesn’t make any sense since all coordinates will be
> 0.0 L
>
> ** **
>
> Ciao
>
> Nik
>
> ** **
>
> ** **
>
> *From:* JP [mailto:jeanpaul.ebe...@inhibox.com]
> *Sent:* Friday, January 13, 2012 1:07 PM
> *To:* rdkit-discuss@lists.sourceforge.net
> *Subject:* [Rdkit-discuss] UFF energy question(s)...
>
> ** **
>
> ** **
>
> Hi there, (using RDKit 2011.09.01)
>
> ** **
>
> Any ideas why
>
> ** **
>
> molecule = Chem.MolFromSmiles('')
>
> mol_h = AllChem.AddHs(molecule)
>
> ff = AllChem.UFFGetMoleculeForceField(mol_h)
>
> energy_value = str(ff.CalcEnergy())
>
> print energy_value
>
> ** **
>
> Gives me:
>
> ** **
>
> Traceback (most recent call last):
>
> File "./energy_test.py", line 8, in
>
> ff = AllChem.UFFGetMoleculeForceField(mol_h)
>
> ValueError: Bad Conformer Id
>
> ** **
>
> There are no conformers in the molecule - so the default (implicit) confId
> -1 should do the work no?
>
> This code somehow works when I use suppliers...
>
> ** **
>
> Also, any ideas what the energy units returned from ff.CalcEnergy() are?
> They must be in calories (not K/cal) as they are massive. Correct?
>
>
> -
> Jean-Paul Ebejer
> Early Stage Researcher
>
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Re: [Rdkit-discuss] UFF energy question(s)...
Hi JP,
When you generate a mol from a smiles I don't think a conformer is added by
default.
So you have to do this yourself:
molecule = Chem.MolFromSmiles('')
mol_h = AllChem.AddHs(molecule)
mol_h.AddConformer(Chem.Conformer(mol_h.GetNumAtoms()))
ff = AllChem.UFFGetMoleculeForceField(mol_h)
energy_value = str(ff.CalcEnergy())
print energy_value
Should at least get rid of the error ... not that the above code is tested ...
plus it obviously doesn't make any sense since all coordinates will be 0.0 :(
Ciao
Nik
From: JP [mailto:jeanpaul.ebe...@inhibox.com]
Sent: Friday, January 13, 2012 1:07 PM
To: rdkit-discuss@lists.sourceforge.net
Subject: [Rdkit-discuss] UFF energy question(s)...
Hi there, (using RDKit 2011.09.01)
Any ideas why
molecule = Chem.MolFromSmiles('')
mol_h = AllChem.AddHs(molecule)
ff = AllChem.UFFGetMoleculeForceField(mol_h)
energy_value = str(ff.CalcEnergy())
print energy_value
Gives me:
Traceback (most recent call last):
File "./energy_test.py", line 8, in
ff = AllChem.UFFGetMoleculeForceField(mol_h)
ValueError: Bad Conformer Id
There are no conformers in the molecule - so the default (implicit) confId -1
should do the work no?
This code somehow works when I use suppliers...
Also, any ideas what the energy units returned from ff.CalcEnergy() are? They
must be in calories (not K/cal) as they are massive. Correct?
-
Jean-Paul Ebejer
Early Stage Researcher
--
RSA(R) Conference 2012
Mar 27 - Feb 2
Save $400 by Jan. 27
Register now!
http://p.sf.net/sfu/rsa-sfdev2dev2___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] UFF energy question(s)...
Hi there, (using RDKit 2011.09.01)
Any ideas why
molecule = Chem.MolFromSmiles('')
mol_h = AllChem.AddHs(molecule)
ff = AllChem.UFFGetMoleculeForceField(mol_h)
energy_value = str(ff.CalcEnergy())
print energy_value
Gives me:
Traceback (most recent call last):
File "./energy_test.py", line 8, in
ff = AllChem.UFFGetMoleculeForceField(mol_h)
ValueError: Bad Conformer Id
There are no conformers in the molecule - so the default (implicit) confId
-1 should do the work no?
This code somehow works when I use suppliers...
Also, any ideas what the energy units returned from ff.CalcEnergy() are?
They must be in calories (not K/cal) as they are massive. Correct?
-
Jean-Paul Ebejer
Early Stage Researcher
--
RSA(R) Conference 2012
Mar 27 - Feb 2
Save $400 by Jan. 27
Register now!
http://p.sf.net/sfu/rsa-sfdev2dev2___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Gobbi_Pharm2D
I think I found the solution by myself: from rdkit.Chem.Pharm2D import Gobbi_Pharm2D fds=Gobbi_Pharm2D.factory.featFactory.GetFeatureDefs() followed by fds['COO'] = 'C(=O)O' COOPattern = Chem.MolFromSmarts(fds['COO']) and now I can search for carboxylic groups as well. the interested reaeder might be interested why Gobbi_Pharm2D is being used at all - because the new SMARTS is rather simple. This is due to the fact I just wanted to give a simple example. Cheers, Paul > > Dear RDKitters, > > > is there any way of tailoring the Gobbi_Pharm2D fingerprints? > > Or to state it that way: > Is it possible to code his own definitions which can be used for queryin? > > > > Cheers & Thanks, > Paul This message and any attachment are confidential and may be privileged or otherwise protected from disclosure. If you are not the intended recipient, you must not copy this message or attachment or disclose the contents to any other person. If you have received this transmission in error, please notify the sender immediately and delete the message and any attachment from your system. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not accept liability for any omissions or errors in this message which may arise as a result of E-Mail-transmission or for damages resulting from any unauthorized changes of the content of this message and any attachment thereto. Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not guarantee that this message is free of viruses and does not accept liability for any damages caused by any virus transmitted therewith. Click http://www.merckgroup.com/disclaimer to access the German, French, Spanish and Portuguese versions of this disclaimer. -- RSA(R) Conference 2012 Mar 27 - Feb 2 Save $400 by Jan. 27 Register now! http://p.sf.net/sfu/rsa-sfdev2dev2 ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
