Re: [Open Babel] Contributed code for new file format

[Paul Becherer]

Dear Geoff,

Perhaps I could have been a bit clearer how the files were exactly generated.

The COF files were generated by our own software and contain the QEq charges 
from our implementation. I converted those files to MOL2 files using the 
current development version of Open Babel, with "user" charges so that they 
contain the same partial charges as the COF files.

The MOL2 files are thus included mainly for convenience.

Kind regards,

Paul Becherer
Development Scientist

Culgi B.V.
Galileiweg 8
2333 BD Leiden
The Netherlands
+31-71-332-2056

From: Geoffrey Hutchison 
Sent: Thursday, March 07, 2019 17:39
To: Paul Becherer 
Cc: openbabel-discuss@lists.sourceforge.net
Subject: Re: [Open Babel] Contributed code for new file format

Dear Paul,

Thanks for the test set! (Usually, it's sufficient to post the files somewhere 
and paste in the URL or use a .tar.bz2)

To confirm - the idea is that the COF files were used to generate the MOL2 
files with the associated QEq charges.

As far as I know, many people use the same approximation for n=4 orbitals and 
above with Slater-type orbitals.

I probably won't have time for a while, but I'd like to re-visit QEq charges 
while I work to implement the new PQEq polarizable charge models from the 
Goddard group. (I have a not-so-secret desire to see a UFF-like force field 
with a polarizable charge model.)


Thanks again, it's a big help.

-Geoff

---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geo...@pitt.edu<mailto:geo...@pitt.edu>
twitter: @ghutchis
web: https://hutchison.chem.pitt.edu/


On Mar 5, 2019, at 3:34 PM, Paul Becherer 
mailto:paul.beche...@culgi.com>> wrote:

Dear Geoff,

As promised, here are the molecules we internally used for testing and 
validation of our QEq implementation. I've attached them as a tar file 
containing files in COF and MOL2 format. I tried a zip file first but 
apparently that extension is blacklisted for the mailing list. I hope the .tar 
file will work, and my apologies if you receive this twice.

The results are divided into three categories:

* Metal halides (covering Table II in the Rappé and Goddard paper; we used 
lambda = 0.5)
* Molecules (covering Tables III and (partially) IV)
* NaCl clusters (covering Figure 6)

We took some care to use the geometries from the references given in the paper.

For atoms with a principal quantum number of n = 4 and higher, the analytical 
expressions we use for the Coulomb integrals become numerically unstable. For 
those cases we use a rescaling to n = 3 (using equation 17 from Rappé and 
Goddard). For molecules involving those atoms, the deviations from the values 
in the literature are thus slightly higher.

The only molecules, as far as I know, with charges that really do not match 
those in the QEq paper of Rappé and Goddard, are lithium hydride (LiH) and 
silane (SiH4).

For SiH4 I suspect that there's an error in the table, and that the hydrogen 
charges reported for silane actually belong to the molecule directly above that 
in Table IV, which is ketene, H2C=C=O.

For LiH I don't know what the problem is. Any change to the parameters or 
functional forms for hydrogen will change the hydrogen charges on other 
molecules so that *they* no longer match, so I could not find a way to 
reproduce the LiH charges.

Kind regards,


Paul Becherer
Development Scientist

Culgi B.V.
Galileiweg 8
2333 BD Leiden
The Netherlands
+31-71-332-2056

-Original Message-
From: Geoffrey Hutchison 
mailto:geoff.hutchi...@gmail.com>>
Sent: Saturday, March 02, 2019 23:14
To: Paul Becherer mailto:paul.beche...@culgi.com>>
Cc: 
openbabel-discuss@lists.sourceforge.net<mailto:openbabel-discuss@lists.sourceforge.net>
Subject: Re: [Open Babel] Contributed code for new file format


Looking at it again now, it seems that the charges from Open Babel's QEq often 
have the wrong sign or are simply unreasonably large. I have no idea what 
causes that, as I only had a cursory look at the code. But it looks as if 
there's more going on than just the additional simplifications to QEq: even the 
QTPIE charges do not seem to reproduce those from the QTPIE paper by Chen and 
Martinez (e.g. the charges on phenol as reported in the preprint on arXiv, 
https://arxiv.org/abs/0807.2068 ). I cannot rule out that I've used the charge 
model options in the wrong way, but they seemed quite straightforward.

Ironically, the code for both QEq and QTPIE in Open Babel were contributed by 
Chen. But I've heard similar things about the signs and magnitudes of the QEq 
charges. Naturally, considering the source of the code, I didn't question the 
results at the time, but it's been several years with off-and-on questions 
about it.


I can send the molecule geometries that we used in validating our QEq against 
the Rappé and Goddard article, if that would be of help, or run our QEq 
implementation on a set of molecules of your choice 

Re: [Open Babel] Contributed code for new file format

[Geoffrey Hutchison]

Dear Paul,

Thanks for the test set! (Usually, it's sufficient to post the files somewhere 
and paste in the URL or use a .tar.bz2)

To confirm - the idea is that the COF files were used to generate the MOL2 
files with the associated QEq charges.

As far as I know, many people use the same approximation for n=4 orbitals and 
above with Slater-type orbitals.

I probably won't have time for a while, but I'd like to re-visit QEq charges 
while I work to implement the new PQEq polarizable charge models from the 
Goddard group. (I have a not-so-secret desire to see a UFF-like force field 
with a polarizable charge model.)


Thanks again, it's a big help.

-Geoff

---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geo...@pitt.edu
twitter: @ghutchis
web: https://hutchison.chem.pitt.edu/

> On Mar 5, 2019, at 3:34 PM, Paul Becherer  wrote:
> 
> Dear Geoff,
> 
> As promised, here are the molecules we internally used for testing and 
> validation of our QEq implementation. I've attached them as a tar file 
> containing files in COF and MOL2 format. I tried a zip file first but 
> apparently that extension is blacklisted for the mailing list. I hope the 
> .tar file will work, and my apologies if you receive this twice.
> 
> The results are divided into three categories:
> 
> * Metal halides (covering Table II in the Rappé and Goddard paper; we used 
> lambda = 0.5)
> * Molecules (covering Tables III and (partially) IV)
> * NaCl clusters (covering Figure 6)
> 
> We took some care to use the geometries from the references given in the 
> paper.
> 
> For atoms with a principal quantum number of n = 4 and higher, the analytical 
> expressions we use for the Coulomb integrals become numerically unstable. For 
> those cases we use a rescaling to n = 3 (using equation 17 from Rappé and 
> Goddard). For molecules involving those atoms, the deviations from the values 
> in the literature are thus slightly higher.
> 
> The only molecules, as far as I know, with charges that really do not match 
> those in the QEq paper of Rappé and Goddard, are lithium hydride (LiH) and 
> silane (SiH4).
> 
> For SiH4 I suspect that there's an error in the table, and that the hydrogen 
> charges reported for silane actually belong to the molecule directly above 
> that in Table IV, which is ketene, H2C=C=O.
> 
> For LiH I don't know what the problem is. Any change to the parameters or 
> functional forms for hydrogen will change the hydrogen charges on other 
> molecules so that *they* no longer match, so I could not find a way to 
> reproduce the LiH charges.
> 
> Kind regards,
> 
> 
> Paul Becherer
> Development Scientist
> 
> Culgi B.V.
> Galileiweg 8
> 2333 BD Leiden
> The Netherlands
> +31-71-332-2056
> 
> -Original Message-
> From: Geoffrey Hutchison  
> Sent: Saturday, March 02, 2019 23:14
> To: Paul Becherer 
> Cc: openbabel-discuss@lists.sourceforge.net
> Subject: Re: [Open Babel] Contributed code for new file format
> 
>> Looking at it again now, it seems that the charges from Open Babel's QEq 
>> often have the wrong sign or are simply unreasonably large. I have no idea 
>> what causes that, as I only had a cursory look at the code. But it looks as 
>> if there's more going on than just the additional simplifications to QEq: 
>> even the QTPIE charges do not seem to reproduce those from the QTPIE paper 
>> by Chen and Martinez (e.g. the charges on phenol as reported in the preprint 
>> on arXiv, https://arxiv.org/abs/0807.2068 ). I cannot rule out that I've 
>> used the charge model options in the wrong way, but they seemed quite 
>> straightforward.
> 
> Ironically, the code for both QEq and QTPIE in Open Babel were contributed by 
> Chen. But I've heard similar things about the signs and magnitudes of the QEq 
> charges. Naturally, considering the source of the code, I didn't question the 
> results at the time, but it's been several years with off-and-on questions 
> about it.
> 
>> I can send the molecule geometries that we used in validating our QEq 
>> against the Rappé and Goddard article, if that would be of help, or run our 
>> QEq implementation on a set of molecules of your choice and send back the 
>> results. Our coverage of elements is limited to that in the original paper, 
>> which covers H, Li, C, N, O, F, Na, Si, P, S, Cl, K, Br, Rb, I, Cs.
> 
> If you're willing to send some molecule geometries and charges, that would be 
> very helpful. I probably won't have time to evaluate the code until the 
> summer, but having a validation set would be a helpful contribution.
> 
> Incidentally, I've been following the work by the Goddard group on their new 
> po

Re: [Open Babel] Contributed code for new file format

[Paul Becherer]

Dear Geoff,

As promised, here are the molecules we internally used for testing and 
validation of our QEq implementation. I've attached them as a tar file 
containing files in COF and MOL2 format. I tried a zip file first but 
apparently that extension is blacklisted for the mailing list. I hope the .tar 
file will work, and my apologies if you receive this twice.

The results are divided into three categories:

* Metal halides (covering Table II in the Rappé and Goddard paper; we used 
lambda = 0.5)
* Molecules (covering Tables III and (partially) IV)
* NaCl clusters (covering Figure 6)

We took some care to use the geometries from the references given in the paper.

For atoms with a principal quantum number of n = 4 and higher, the analytical 
expressions we use for the Coulomb integrals become numerically unstable. For 
those cases we use a rescaling to n = 3 (using equation 17 from Rappé and 
Goddard). For molecules involving those atoms, the deviations from the values 
in the literature are thus slightly higher.

The only molecules, as far as I know, with charges that really do not match 
those in the QEq paper of Rappé and Goddard, are lithium hydride (LiH) and 
silane (SiH4).

For SiH4 I suspect that there's an error in the table, and that the hydrogen 
charges reported for silane actually belong to the molecule directly above that 
in Table IV, which is ketene, H2C=C=O.

For LiH I don't know what the problem is. Any change to the parameters or 
functional forms for hydrogen will change the hydrogen charges on other 
molecules so that *they* no longer match, so I could not find a way to 
reproduce the LiH charges.

Kind regards,


Paul Becherer
Development Scientist

Culgi B.V.
Galileiweg 8
2333 BD Leiden
The Netherlands
+31-71-332-2056

-Original Message-
From: Geoffrey Hutchison  
Sent: Saturday, March 02, 2019 23:14
To: Paul Becherer 
Cc: openbabel-discuss@lists.sourceforge.net
Subject: Re: [Open Babel] Contributed code for new file format

> Looking at it again now, it seems that the charges from Open Babel's QEq 
> often have the wrong sign or are simply unreasonably large. I have no idea 
> what causes that, as I only had a cursory look at the code. But it looks as 
> if there's more going on than just the additional simplifications to QEq: 
> even the QTPIE charges do not seem to reproduce those from the QTPIE paper by 
> Chen and Martinez (e.g. the charges on phenol as reported in the preprint on 
> arXiv, https://arxiv.org/abs/0807.2068 ). I cannot rule out that I've used 
> the charge model options in the wrong way, but they seemed quite 
> straightforward.

Ironically, the code for both QEq and QTPIE in Open Babel were contributed by 
Chen. But I've heard similar things about the signs and magnitudes of the QEq 
charges. Naturally, considering the source of the code, I didn't question the 
results at the time, but it's been several years with off-and-on questions 
about it.

> I can send the molecule geometries that we used in validating our QEq against 
> the Rappé and Goddard article, if that would be of help, or run our QEq 
> implementation on a set of molecules of your choice and send back the 
> results. Our coverage of elements is limited to that in the original paper, 
> which covers H, Li, C, N, O, F, Na, Si, P, S, Cl, K, Br, Rb, I, Cs.

If you're willing to send some molecule geometries and charges, that would be 
very helpful. I probably won't have time to evaluate the code until the summer, 
but having a validation set would be a helpful contribution.

Incidentally, I've been following the work by the Goddard group on their new 
polarizable QEq model (e.g., PQEq2) and I'm trying to get a test set together 
for an independent implantation of those.

-Geoff


QEQ_results.tar
Description: QEQ_results.tar
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Re: [Open Babel] Contributed code for new file format

[Geoffrey Hutchison]

> Looking at it again now, it seems that the charges from Open Babel's QEq 
> often have the wrong sign or are simply unreasonably large. I have no idea 
> what causes that, as I only had a cursory look at the code. But it looks as 
> if there's more going on than just the additional simplifications to QEq: 
> even the QTPIE charges do not seem to reproduce those from the QTPIE paper by 
> Chen and Martinez (e.g. the charges on phenol as reported in the preprint on 
> arXiv, https://arxiv.org/abs/0807.2068 ). I cannot rule out that I've used 
> the charge model options in the wrong way, but they seemed quite 
> straightforward.

Ironically, the code for both QEq and QTPIE in Open Babel were contributed by 
Chen. But I've heard similar things about the signs and magnitudes of the QEq 
charges. Naturally, considering the source of the code, I didn't question the 
results at the time, but it's been several years with off-and-on questions 
about it.

> I can send the molecule geometries that we used in validating our QEq against 
> the Rappé and Goddard article, if that would be of help, or run our QEq 
> implementation on a set of molecules of your choice and send back the 
> results. Our coverage of elements is limited to that in the original paper, 
> which covers H, Li, C, N, O, F, Na, Si, P, S, Cl, K, Br, Rb, I, Cs.

If you're willing to send some molecule geometries and charges, that would be 
very helpful. I probably won't have time to evaluate the code until the summer, 
but having a validation set would be a helpful contribution.

Incidentally, I've been following the work by the Goddard group on their new 
polarizable QEq model (e.g., PQEq2) and I'm trying to get a test set together 
for an independent implantation of those.

-Geoff

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Re: [Open Babel] Contributed code for new file format

[Paul Becherer]

Dear Geoff,

We're in the process of adding our existing tests to the Open Babel source. 
This will contain a number of 'authentic' files that have not been generated by 
Open Babel.

Concerning your questions on QEq: we have implemented our own version, 
following the original paper by Rappé and Goddard [J. Phys. Chem 95 (1991) 
3358] as closely as possible. That was around 2010-2011.

We did take a look at the Open Babel implementation (which was then new) but we 
decided to make our own implementation. We had noticed that Open Babel makes a 
number of simplifications for QEq (hydrogen parameters not charge-dependent and 
using Gaussians instead of Slater-type orbitals for the Coulomb integrals). 
Perhaps more importantly, the charges did not seem to match very well with the 
ones from the Rappé and Goddard paper.

Looking at it again now, it seems that the charges from Open Babel's QEq often 
have the wrong sign or are simply unreasonably large. I have no idea what 
causes that, as I only had a cursory look at the code. But it looks as if 
there's more going on than just the additional simplifications to QEq: even the 
QTPIE charges do not seem to reproduce those from the QTPIE paper by Chen and 
Martinez (e.g. the charges on phenol as reported in the preprint on arXiv, 
https://arxiv.org/abs/0807.2068 ). I cannot rule out that I've used the charge 
model options in the wrong way, but they seemed quite straightforward.

I can send the molecule geometries that we used in validating our QEq against 
the Rappé and Goddard article, if that would be of help, or run our QEq 
implementation on a set of molecules of your choice and send back the results. 
Our coverage of elements is limited to that in the original paper, which covers 
H, Li, C, N, O, F, Na, Si, P, S, Cl, K, Br, Rb, I, Cs.

Kind regards,

Paul Becherer
Development Scientist

Culgi B.V.
Galileiweg 8
2333 BD Leiden
The Netherlands
+31-71-332-2056

-Original Message-
From: Geoffrey Hutchison  
Sent: Friday, February 22, 2019 03:38
To: Paul Becherer 
Cc: openbabel-discuss@lists.sourceforge.net
Subject: Re: [Open Babel] Contributed code for new file format

> We could not really find hard guidelines for coding standards, or what kinds 
> of tests are desired, so I'd appreciate any feedback on that. The code in the 
> patch is based on the exampleformat.cpp template and was further developed by 
> two colleagues and myself at Culgi. We presently test conversion to and from 
> the MOL and MOL2 formats in our own test suite.

We would definitely appreciate some "authentic" files for testing. I should get 
the broader round-trip test suite going again, but having "original" files 
(i.e., not created by Open Babel) is definitely a help when testing.

One side question - your website mentions QEq charges. Are you using the OB 
code for that? There has been some question as to the OB implementation of QEq 
charges, but there obviously isn't an open test set. If you have an independent 
implementation, I'd be curious to compare point charges across a range of 
molecules.

Thanks,
-Geoff


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Re: [Open Babel] Contributed code for new file format

[Chris Swain via OpenBabel-discuss]

Once implemented I’d be delighted to publicise it. One of the things I’ve been 
trying to do is encourage people to not reinvent the wheel and use existing 
cheminformatics libraries.

https://www.macinchem.org/reviews/scientificsoftware/toolkits.php 


Cheers

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Re: [Open Babel] Contributed code for new file format

[Geoffrey Hutchison]

> We could not really find hard guidelines for coding standards, or what kinds 
> of tests are desired, so I'd appreciate any feedback on that. The code in the 
> patch is based on the exampleformat.cpp template and was further developed by 
> two colleagues and myself at Culgi. We presently test conversion to and from 
> the MOL and MOL2 formats in our own test suite.

We would definitely appreciate some "authentic" files for testing. I should get 
the broader round-trip test suite going again, but having "original" files 
(i.e., not created by Open Babel) is definitely a help when testing.

One side question - your website mentions QEq charges. Are you using the OB 
code for that? There has been some question as to the OB implementation of QEq 
charges, but there obviously isn't an open test set. If you have an independent 
implementation, I'd be curious to compare point charges across a range of 
molecules.

Thanks,
-Geoff

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Re: [Open Babel] Contributed code for new file format

[Noel O'Boyle]

Hi Paul,

Sounds great.

It'd be definitely nice to have some test cases to ensure that it actually
works as intended and will keep working. It's sound like you have some
already. I can help integrate these if you wish. There is also information
over at
https://open-babel.readthedocs.io/en/latest/Contributing/Testing.html

The usual way to submit code is via Github - this also helps us keep track
of things. Are you happy to send a pull request via that route?

Regarding release forms, I don't think that's something we can help with.
We don't require it. That is, it's between you and your employer whether
you have permission to give us this code under the GPL.

Regards,
- Noel

On Wed, 20 Feb 2019 at 18:07, Paul Becherer  wrote:

> Dear all,
>
> At the software company that I work for (Culgi B.V., Leiden, The
> Netherlands, ​https://www.culgi.com/), we have been using Open Babel for
> a while now, for conversion between our file format and other formats. To
> get this working, we have added a file format to the Open Babel source, and
> we currently build a 'custom' executable with this extra file.
>
> To comply with the GNU GPL we do not link our proprietary software to Open
> Babel, but just run the executable using input and output files, and we've
> always made the modified Open Babel source available to our users under the
> GPL.
>
> Of course in the long run it would be easier for us, and for our users, to
> have this file format support integrated into the regular Open Babel
> distribution. We'd like to contribute the code that we use for that. I have
> attached a patch that should work against the latest source from GitHub.
>
> As it will be primarily our customers and ourselves who will benefit from
> this (at least at this time) we're willing to assume responsibility for
> maintaining this code for the foreseeable future.
>
> We could not really find hard guidelines for coding standards, or what
> kinds of tests are desired, so I'd appreciate any feedback on that. The
> code in the patch is based on the exampleformat.cpp template and was
> further developed by two colleagues and myself at Culgi. We presently test
> conversion to and from the MOL and MOL2 formats in our own test suite.
>
> I can imagine that some kind of release form or other document from my
> employer is required before the code can be integrated into the regular
> Open Babel source. I'd be very grateful if anyone could guide us through
> any formalities here.
>
>
> Kind regards,
>
> Paul Becherer
>
> Development Scientist
>
> Culgi B.V.
> Galileiweg 8
> 2333 BD Leiden
> The Netherlands
>
> Phone: + 31 71 33 22 056
> www.culgi.com
>
>
>
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