Re: [FRIAM] Schwill Rock?

[David Eric Smith]

Would this be of any use?

https://www.molgen.de/ 

It sounded like you were doing something that you want to be fast and in-line, 
and I don’t know if MOLGEN grants an API that offers that degree of 
flexibility.  People I know who have worked with it say that it is fairly 
sophisticated in creating physically realizable molecules while still retaining 
as much combinatorics as possible. 

Eric



> On Oct 13, 2021, at 1:17 AM, Roger Critchlow  wrote:
> 
> As long as you stick to basic CNO type chemistry, you can probably figure out 
> a valid SMILES generator pretty quickly.  But it might be easier to work in 
> the explicit molecule graph instead and just use SMILES as a content name 
> string.  The things that might go wrong after the SMILES input parses 
> correctly are 1) a ring that's strained because it's too tight a turn, 2) 
> steric hindrance between bulky sidechains occupying the same space, and 3) 
> something that no one has any idea how to make.  You could probably notice 1) 
> and 2) if you track the average energy per bond.
> 
> The benzodiazepines are a classic example of structuring the search around a 
> core framework and substituting side chains onto the core.  That's the way 
> the chemists do it in the wetlab.
> 
> OpenEyes (https://www.eyesopen.com/ 
> )
>  is running some online events this month that might be interesting.
> 
> -- rec --
> 
> On Tue, Oct 12, 2021 at 5:44 PM Marcus Daniels  > wrote:
> A search algorithm that, say, proposes a prefix or a suffix to a SMILES 
> string would need to have a way to autocomplete candidates before it could 
> use these descriptors to guide an optimization because the parsing step is 
> non-trivial, never mind the sanitization step (mentioned on that web page).   
>  
> 
>  
> 
> I will deflect blame on Jon for changing the topic from music to chemicals, 
> but presumably with enough debate their aesthetic preferences in music could 
> be formalized in theory or some rule-based way, as is manifest here.
> 
>  
> 
> From: Friam mailto:friam-boun...@redfish.com>> On 
> Behalf Of Roger Critchlow
> Sent: Tuesday, October 12, 2021 2:10 PM
> To: The Friday Morning Applied Complexity Coffee Group  >
> Subject: Re: [FRIAM] Schwill Rock?
> 
>  
> 
> Hmm, when I was in the drug discovery canal, the "descriptors" that you could 
> calculate from a SMILES string were legion. 
> 
>  
> 
> Here's the list for RDKIT, 
> https://www.rdkit.org/docs/GettingStartedInPython.html#list-of-available-descriptors
>  
> .
>   There are one bunch that depend entirely on the formula and molecular 
> structure.  Then there's a whole other bunch you can compute if you generate 
> 3d structures for the molecules, possibly multiplied by the number of low 
> energy structures the molecule can adopt.
> 
>  
> 
> What kind of plausibility were you looking for?  Does the SMILES string 
> specify a real molecule?  That's hard.  There are syntax errors in SMILES, 
> failures to close rings, valency errors, charge errors.  But there are lots 
> of syntactically valid SMILES that won't match any known molecule, either 
> because they're impossible or as yet to be determined.  The pharmas all have 
> their own lists of molecules of interest, but those are proprietary.  Looks 
> like there are various online databases, none that I'm familiar with.  If the 
> SMILES parses, you can try generating a 2d depiction and a 3d structure.  
> Those will throw exceptions if things get too weird.
> 
>  
> 
> -- rec --
> 
>  
> 
> On Tue, Oct 12, 2021 at 3:22 PM Marcus Daniels  > wrote:
> 
> I was playing with RDKIT the other day, and it wasn’t obvious how to get a 
> scalar quantity of plausibility of a molecule.   It seems a SMILES string is 
> right or wrong, and then maybe there are some warnings that can be trapped.   
> However, the benefits for search or fair sampling are different than the 
> needs of correctness checks, which is deeper property.   That isn’t quite a 
> fit to the music example where aesthetic considerations are subjective.
> 
>  
> 
> From: Friam mailto:friam-boun...@redfish.com>> On 
> Behalf Of Jon Zingale
> Sent: Tuesday, October 12, 2021 12:11 PM
> To: friam@redfish.com 
> Subject: Re: [FRIAM] Schwill Rock?
> 
>  
> 
> "I mean from the perspective of aesthetics. Understanding why Pandora is 
> messing it up means sampling the deep wells."
> 
>  
> 
> Yes, but not more 

[FRIAM] Where are all the workers going?

[thompnickson2]

>From the New Mexican:

 

The field with the most vacancies is health care, with over 13,100 openings,
he said. Hotels and restaurants also are hurting for workers, he said.

.

 

The number of New Mexicans filing for unemployment claims has dropped from
about 50,000 in early September - when most extended federal unemployment
benefits came to an end - to just over 18,000 this week, Serna said.

 

Is everybody just "smoking cigarettes and watching Captain Kangaroo.  (Now
don't tell me; I've nothing to do.) "

 

 

Nick 

thompnicks...@gmail.com  

https://wordpress.clarku.edu/nthompson/

 


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Re: [FRIAM] Where are all the workers going?

[Merle Lefkoff]

>From the Atlantic Magazine this morning.

 “Decades of studies have shown that the people most satisfied with their
work are those who find a fundamental match between their employer’s values
and their own,” our columnist, Arthur C. Brooks, writes. “Too many people
who work hard and strive for success self-objectify as excellent work
machines and tools of performance,” Arthur explains.  “Employees love it;
bosses, not so much,” our Special Projects editor Ellen Cushing writes in
our magazine’s technology issue. The software is changing how a generation
works—and complains.  “Forget the beanbag chairs and the foosball table.
Give your staff clean air instead,” Joseph Allen, a Harvard professor,
advises.


(I'd like to add that $15/hr. is not a living wage.)

On Wed, Oct 13, 2021 at 8:34 AM  wrote:

> From the New Mexican:
>
>
>
> The field with the most vacancies is health care, with over 13,100
> openings, he said. Hotels and restaurants also are hurting for workers, he
> said.
>
> …
>
>
>
> The number of New Mexicans filing for unemployment claims has dropped from
> about 50,000 in early September — when most extended federal unemployment
> benefits came to an end — to just over 18,000 this week, Serna said.
>
>
>
> Is everybody just “smoking cigarettes and watching Captain Kangaroo.  (Now
> don’t tell me; I’ve nothing to do.) “
>
>
>
>
>
> Nick
>
> thompnicks...@gmail.com
>
> https://wordpress.clarku.edu/nthompson/
>
>
>
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> archives:
>  5/2017 thru present https://redfish.com/pipermail/friam_redfish.com/
>  1/2003 thru 6/2021  http://friam.383.s1.nabble.com/
>


-- 
Merle Lefkoff, Ph.D.
Center for Emergent Diplomacy
emergentdiplomacy.org
Santa Fe, New Mexico, USA

mobile:  (303) 859-5609
skype:  merle.lelfkoff2
twitter: @merle110

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Re: [FRIAM] Where are all the workers going?

[Jon Zingale]

"counting flowers on the wall..."

A chef friend of mine suggested yesterday that many likely left for the
construction industry.

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Re: [FRIAM] Where are all the workers going?

[uǝlƃ ☤ $]

Thanks for sending me to the Atlantic. Cushing's Slack article was great! It's 
more evidence that the chatty amongst us should start a Slack server (though 
I'd recommend Discord  instead). I didn't find the Brooks 
article. But I'm not a subscriber and I've read my last free article. 8^( If 
you can send the link, I'd be grateful. I'm still in the throes of a fugue on 
"value alignment".

But I did find this:

The Abortion Backup Plan No One Is Talking About
https://www.theatlantic.com/politics/archive/2021/10/plan-c-secret-option-mail-order-abortion/620324/

which links to this:

The Availability and Use of Medication Abortion
https://www.kff.org/womens-health-policy/fact-sheet/the-availability-and-use-of-medication-abortion/


On 10/13/21 8:04 AM, Merle Lefkoff wrote:
> From the Atlantic Magazine this morning.
> 
>  “Decades of studies have shown that the people most satisfied with their
> work are those who find a fundamental match between their employer’s values
> and their own,” our columnist, Arthur C. Brooks, writes. “Too many people
> who work hard and strive for success self-objectify as excellent work
> machines and tools of performance,” Arthur explains.  “Employees love it;
> bosses, not so much,” our Special Projects editor Ellen Cushing writes in
> our magazine’s technology issue. The software is changing how a generation
> works—and complains.  “Forget the beanbag chairs and the foosball table.
> Give your staff clean air instead,” Joseph Allen, a Harvard professor,
> advises.
> 
> 
> (I'd like to add that $15/hr. is not a living wage.)
> 
> On Wed, Oct 13, 2021 at 8:34 AM  wrote:
> 
>> From the New Mexican:
>>
>>
>>
>> The field with the most vacancies is health care, with over 13,100
>> openings, he said. Hotels and restaurants also are hurting for workers, he
>> said.
>>
>> …
>>
>>
>>
>> The number of New Mexicans filing for unemployment claims has dropped from
>> about 50,000 in early September — when most extended federal unemployment
>> benefits came to an end — to just over 18,000 this week, Serna said.
>>
>>
>>
>> Is everybody just “smoking cigarettes and watching Captain Kangaroo.  (Now
>> don’t tell me; I’ve nothing to do.) “

-- 
"Better to be slapped with the truth than kissed with a lie."
☤>$ uǝlƃ


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Re: [FRIAM] Where are all the workers going?

[thompnickson2]

“Playing solitaire till dawn with a deck of 51, …”

 

Nick Thompson

thompnicks...@gmail.com  

https://wordpress.clarku.edu/nthompson/

 

From: Friam  On Behalf Of Jon Zingale
Sent: Wednesday, October 13, 2021 11:06 AM
To: friam@redfish.com
Subject: Re: [FRIAM] Where are all the workers going?

 

"counting flowers on the wall..."

 

A chef friend of mine suggested yesterday that many likely left for the 
construction industry.


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Re: [FRIAM] Schwill Rock?

[Jon Zingale]

Thanks Roger, Marcus. I am a newbie in this area and so it might be good
for me to ask some potentially obvious questions about SMILES (since they
are used everywhere).

1. Is the SMILES isomorphism problem equivalent to the graph isomorphism
problem, or is there some advantage from being context free parsable?

2. In practice, do the edge cases that Roger mentioned effectively get
added into the rewrite rules for the grammar or are they a separate kind of
thing?

3. How is chirality handled?

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Re: [FRIAM] Schwill Rock?

[thompnickson2]

Jon, et. al, 

 

I love it when you guys talk dirty!

 

I am afraid I won’t be able to make it Friday (travel angst), so could somebody 
explain in a few sentences what is going on, here?  

 

See you all NEXT Friday. 

 

Nick 

 

Nick Thompson

thompnicks...@gmail.com  

https://wordpress.clarku.edu/nthompson/

 

From: Friam  On Behalf Of Jon Zingale
Sent: Wednesday, October 13, 2021 12:54 PM
To: friam@redfish.com
Subject: Re: [FRIAM] Schwill Rock?

 

Thanks Roger, Marcus. I am a newbie in this area and so it might be good for me 
to ask some potentially obvious questions about SMILES (since they are used 
everywhere).

 

1. Is the SMILES isomorphism problem equivalent to the graph isomorphism 
problem, or is there some advantage from being context free parsable?

 

2. In practice, do the edge cases that Roger mentioned effectively get added 
into the rewrite rules for the grammar or are they a separate kind of thing?

 

3. How is chirality handled?


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Re: [FRIAM] Schwill Rock?

[Marcus Daniels]

Thanks for putting more care into the answer than I did the question.  😊   I 
don’t have a problem here, was just riffing on the conversation.   I suspected 
the way to do this was use a latent representation and since Jon is talking 
about conformations, perhaps he already has it.

From: Friam  On Behalf Of Roger Critchlow
Sent: Tuesday, October 12, 2021 10:17 PM
To: The Friday Morning Applied Complexity Coffee Group 
Subject: Re: [FRIAM] Schwill Rock?

As long as you stick to basic CNO type chemistry, you can probably figure out a 
valid SMILES generator pretty quickly.  But it might be easier to work in the 
explicit molecule graph instead and just use SMILES as a content name string.  
The things that might go wrong after the SMILES input parses correctly are 1) a 
ring that's strained because it's too tight a turn, 2) steric hindrance between 
bulky sidechains occupying the same space, and 3) something that no one has any 
idea how to make.  You could probably notice 1) and 2) if you track the average 
energy per bond.

The benzodiazepines are a classic example of structuring the search around a 
core framework and substituting side chains onto the core.  That's the way the 
chemists do it in the wetlab.

OpenEyes (https://www.eyesopen.com/) is running some online events this month 
that might be interesting.

-- rec --

On Tue, Oct 12, 2021 at 5:44 PM Marcus Daniels 
mailto:mar...@snoutfarm.com>> wrote:
A search algorithm that, say, proposes a prefix or a suffix to a SMILES string 
would need to have a way to autocomplete candidates before it could use these 
descriptors to guide an optimization because the parsing step is non-trivial, 
never mind the sanitization step (mentioned on that web page).

I will deflect blame on Jon for changing the topic from music to chemicals, but 
presumably with enough debate their aesthetic preferences in music could be 
formalized in theory or some rule-based way, as is manifest here.

From: Friam mailto:friam-boun...@redfish.com>> On 
Behalf Of Roger Critchlow
Sent: Tuesday, October 12, 2021 2:10 PM
To: The Friday Morning Applied Complexity Coffee Group 
mailto:friam@redfish.com>>
Subject: Re: [FRIAM] Schwill Rock?

Hmm, when I was in the drug discovery canal, the "descriptors" that you could 
calculate from a SMILES string were legion.

Here's the list for RDKIT, 
https://www.rdkit.org/docs/GettingStartedInPython.html#list-of-available-descriptors.
  There are one bunch that depend entirely on the formula and molecular 
structure.  Then there's a whole other bunch you can compute if you generate 3d 
structures for the molecules, possibly multiplied by the number of low energy 
structures the molecule can adopt.

What kind of plausibility were you looking for?  Does the SMILES string specify 
a real molecule?  That's hard.  There are syntax errors in SMILES, failures to 
close rings, valency errors, charge errors.  But there are lots of 
syntactically valid SMILES that won't match any known molecule, either because 
they're impossible or as yet to be determined.  The pharmas all have their own 
lists of molecules of interest, but those are proprietary.  Looks like there 
are various online databases, none that I'm familiar with.  If the SMILES 
parses, you can try generating a 2d depiction and a 3d structure.  Those will 
throw exceptions if things get too weird.

-- rec --

On Tue, Oct 12, 2021 at 3:22 PM Marcus Daniels 
mailto:mar...@snoutfarm.com>> wrote:
I was playing with RDKIT the other day, and it wasn’t obvious how to get a 
scalar quantity of plausibility of a molecule.   It seems a SMILES string is 
right or wrong, and then maybe there are some warnings that can be trapped.   
However, the benefits for search or fair sampling are different than the needs 
of correctness checks, which is deeper property.   That isn’t quite a fit to 
the music example where aesthetic considerations are subjective.

From: Friam mailto:friam-boun...@redfish.com>> On 
Behalf Of Jon Zingale
Sent: Tuesday, October 12, 2021 12:11 PM
To: friam@redfish.com
Subject: Re: [FRIAM] Schwill Rock?

"I mean from the perspective of aesthetics. Understanding why Pandora is 
messing it up means sampling the deep wells."

Yes, but not more than one has to. This is why I am advocating for methods like 
a weighted ensemble. The working analogy for me comes from drug discovery. It 
doesn't make a lot of sense to probe the same old sites and the same old 
conformations.

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Re: [FRIAM] Where are all the workers going?

[uǝlƃ ☤ $]

And:

https://aidaccess.org/en/
https://aidaccess.org/en/page/952476/texas-bans-abortion-after-6-weeks-of-pregnancy

Exploring the feasibility of obtaining mifepristone and misoprostol from the 
internet
https://www.sciencedirect.com/science/article/pii/S0010782417304754

On 10/13/21 9:00 AM, uǝlƃ ☤>$ wrote:
> Thanks for sending me to the Atlantic. Cushing's Slack article was great! 
> It's more evidence that the chatty amongst us should start a Slack server 
> (though I'd recommend Discord  instead). I didn't find 
> the Brooks article. But I'm not a subscriber and I've read my last free 
> article. 8^( If you can send the link, I'd be grateful. I'm still in the 
> throes of a fugue on "value alignment".
> 
> But I did find this:
> 
> The Abortion Backup Plan No One Is Talking About
> https://www.theatlantic.com/politics/archive/2021/10/plan-c-secret-option-mail-order-abortion/620324/
> 
> which links to this:
> 
> The Availability and Use of Medication Abortion
> https://www.kff.org/womens-health-policy/fact-sheet/the-availability-and-use-of-medication-abortion/
> 
> 
> On 10/13/21 8:04 AM, Merle Lefkoff wrote:
>> From the Atlantic Magazine this morning.
>>
>>  “Decades of studies have shown that the people most satisfied with their
>> work are those who find a fundamental match between their employer’s values
>> and their own,” our columnist, Arthur C. Brooks, writes. “Too many people
>> who work hard and strive for success self-objectify as excellent work
>> machines and tools of performance,” Arthur explains.  “Employees love it;
>> bosses, not so much,” our Special Projects editor Ellen Cushing writes in
>> our magazine’s technology issue. The software is changing how a generation
>> works—and complains.  “Forget the beanbag chairs and the foosball table.
>> Give your staff clean air instead,” Joseph Allen, a Harvard professor,
>> advises.
>>
>>
>> (I'd like to add that $15/hr. is not a living wage.)
>>
>> On Wed, Oct 13, 2021 at 8:34 AM  wrote:
>>
>>> From the New Mexican:
>>>
>>>
>>>
>>> The field with the most vacancies is health care, with over 13,100
>>> openings, he said. Hotels and restaurants also are hurting for workers, he
>>> said.
>>>
>>> …
>>>
>>>
>>>
>>> The number of New Mexicans filing for unemployment claims has dropped from
>>> about 50,000 in early September — when most extended federal unemployment
>>> benefits came to an end — to just over 18,000 this week, Serna said.
>>>
>>>
>>>
>>> Is everybody just “smoking cigarettes and watching Captain Kangaroo.  (Now
>>> don’t tell me; I’ve nothing to do.) “
> 

-- 
"Better to be slapped with the truth than kissed with a lie."
☤>$ uǝlƃ


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Re: [FRIAM] Schwill Rock?

[Jon Zingale]

@EricS Thanks for that resource. I shared it with my coworkers.

@Marcus My office neighbor works with weighted ensemble and so most of what
I am thinking about there is related to my discussions with him. Those
discussions are mostly in the frame of molecular dynamics and related
algorithms. That's typically where I am most at home, but it is really good
to get a wider picture of the kinds of things others do.

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Re: [FRIAM] Where are all the workers going?

[Steve Smith]

This is total speculation/projection:

Maybe people in service roles got a wake up call to their
vulnerability.  Maybe the relief programs gave *some* of them to find
alternative lifestyles or employment so they don't have to go back to
that position.  And likely the personal service categories might be even
more acutely involved since their work would nominally involve more risk
of being exposed to COVID and/or exposing others.   Health care workers
would seem to top that list, adding the kind of grief they apparently
get from the anti-crowd who want to paint them as snowflakes or even
crisis-actors   Thankless shite all the way around.

On 10/13/21 8:33 AM, thompnicks...@gmail.com wrote:
>
> From the New Mexican:
>
>  
>
> The field with the most vacancies is health care, with over 13,100
> openings, he said. Hotels and restaurants also are hurting for
> workers, he said.
>
> …
>
>  
>
> The number of New Mexicans filing for unemployment claims has dropped
> from about 50,000 in early September — when most extended federal
> unemployment benefits came to an end — to just over 18,000 this week,
> Serna said.
>
>  
>
> Is everybody just “smoking cigarettes and watching Captain Kangaroo. 
> (Now don’t tell me; I’ve nothing to do.) “
>
>  
>
>  
>
> Nick
>
> thompnicks...@gmail.com 
>
> https://wordpress.clarku.edu/nthompson/
> 
>
>  
>
>
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Re: [FRIAM] Where are all the workers going?

[Steve Smith]

I first heard this in my early teens and at that point in my life had
never known anyone who was "idle poor", I knew idle rich (technically
just professional/merchant class?) and I knew bony-fingers poor.   There
was something captivating about thethis song almost celebrating
idle-poor status/circumstance.  


On 10/13/21 10:35 AM, thompnicks...@gmail.com wrote:
>
> “Playing solitaire till dawn with a deck of 51, …”
>
>  
>
> Nick Thompson
>
> thompnicks...@gmail.com 
>
> https://wordpress.clarku.edu/nthompson/
> 
>
>  
>
> *From:* Friam  *On Behalf Of *Jon Zingale
> *Sent:* Wednesday, October 13, 2021 11:06 AM
> *To:* friam@redfish.com
> *Subject:* Re: [FRIAM] Where are all the workers going?
>
>  
>
> "counting flowers on the wall..."
>
>  
>
> A chef friend of mine suggested yesterday that many likely left for
> the construction industry.
>
>
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Re: [FRIAM] Schwill Rock?

[Stephen Guerin]

On Wed, Oct 13, 2021 at 11:09 AM  wrote:

> Jon, et. al,
>
>
>
> I love it when you guys talk dirty!
>
>
>
> I am afraid I won’t be able to make it Friday (travel angst), so could
> somebody explain in a few sentences what is going on, here?
>

A few Google searches related to

"Smiles Chemistry notation"  "David Weininger Daylight" "Santa Fe
Infomesa" " OpenEye" "cheminformatics bioinformatics"

Weininger's Cheshire Grin: What lives on his SMILES. RIP.


>

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Re: [FRIAM] Schwill Rock?

[Jon Zingale]

Oh, and here is a good article on the SMILES isomorphism problem:
https://depth-first.com/articles/2021/10/06/molecular-graph-canonicalization/

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[FRIAM] Geometrical Mechanics

[Jon Zingale]

I would love to have a reading group around this:
https://harrydole.com/Mac%20Lane/Geometrical%20Mechanics%20v1%201-22.pdf

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Re: [FRIAM] Geometrical Mechanics

[Frank Wimberly]

I don't know if it's the same thing but it must be related.  I started to
study some papers on robot kinematics.  Shortly thereafter I got promoted
into a position in the public policy school so I never got very far into
those papers.

Let me know what develops.

---
Frank C. Wimberly
140 Calle Ojo Feliz,
Santa Fe, NM 87505

505 670-9918
Santa Fe, NM

On Wed, Oct 13, 2021, 3:09 PM Jon Zingale  wrote:

> I would love to have a reading group around this:
> https://harrydole.com/Mac%20Lane/Geometrical%20Mechanics%20v1%201-22.pdf
>
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>

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Re: [FRIAM] Geometrical Mechanics

[Frank Wimberly]

p.s.  I was going to start with a book called Robot Manipulators by Richard
Paul.  I just looked at my copy and it has a stamp on it that says, "Do not
remove from Robotics Institute."  I feel bad about that.

---
Frank C. Wimberly
140 Calle Ojo Feliz,
Santa Fe, NM 87505

505 670-9918
Santa Fe, NM

On Wed, Oct 13, 2021, 3:19 PM Frank Wimberly  wrote:

> I don't know if it's the same thing but it must be related.  I started to
> study some papers on robot kinematics.  Shortly thereafter I got promoted
> into a position in the public policy school so I never got very far into
> those papers.
>
> Let me know what develops.
>
> ---
> Frank C. Wimberly
> 140 Calle Ojo Feliz,
> Santa Fe, NM 87505
>
> 505 670-9918
> Santa Fe, NM
>
> On Wed, Oct 13, 2021, 3:09 PM Jon Zingale  wrote:
>
>> I would love to have a reading group around this:
>> https://harrydole.com/Mac%20Lane/Geometrical%20Mechanics%20v1%201-22.pdf
>>
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>>
>

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Re: [FRIAM] Schwill Rock?

[David Eric Smith]

On 3:

https://depth-first.com/articles/2020/05/04/stereochemistry-and-atom-parity-in-smiles/
 




> On Oct 13, 2021, at 12:54 PM, Jon Zingale  wrote:
> 
> Thanks Roger, Marcus. I am a newbie in this area and so it might be good for 
> me to ask some potentially obvious questions about SMILES (since they are 
> used everywhere).
> 
> 1. Is the SMILES isomorphism problem equivalent to the graph isomorphism 
> problem, or is there some advantage from being context free parsable?
> 
> 2. In practice, do the edge cases that Roger mentioned effectively get added 
> into the rewrite rules for the grammar or are they a separate kind of thing?
> 
> 3. How is chirality handled?
> 
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Re: [FRIAM] Geometrical Mechanics

[Jon Zingale]

Books want to be free, Frank.
Do what is in your heart.

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Re: [FRIAM] Geometrical Mechanics

[Frank Wimberly]

I suspect Marc Raibert handed it to me and said, "Read this" so I took it
without seeing the "do not remove" stamp.

---
Frank C. Wimberly
140 Calle Ojo Feliz,
Santa Fe, NM 87505

505 670-9918
Santa Fe, NM

On Wed, Oct 13, 2021, 3:56 PM Jon Zingale  wrote:

> Books want to be free, Frank.
> Do what is in your heart.
>
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>

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Re: [FRIAM] Schwill Rock?

[Roger Critchlow]

On Wed, Oct 13, 2021 at 12:55 PM Jon Zingale  wrote:

> Thanks Roger, Marcus. I am a newbie in this area and so it might be good
> for me to ask some potentially obvious questions about SMILES (since they
> are used everywhere).
>
> 1. Is the SMILES isomorphism problem equivalent to the graph isomorphism
> problem, or is there some advantage from being context free parsable?
>
> Equivalent to graph isomorphism with labelled vertices, having an atomic
weight allows you to break some degeneracies.

2. In practice, do the edge cases that Roger mentioned effectively get
> added into the rewrite rules for the grammar or are they a separate kind of
> thing?
>
> The edge cases are yours to deal with, they're totally legit potential
molecular structures, they'd be difficult to impossible to realize as
material structures, you have to pick where to draw the line.  And as to
whether it's impossible or only difficult to make, opinions may vary, and
many a chemist makes her reputation by showing a compound is only difficult
to make, but it can take years, or decades.

3. How is chirality handled?
>

>
Eric's link looks good.  Having some physical models to manipulate is
highly recommended.

-- rec --

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