[Rdkit-discuss] single SMARTS for two patterns with Boolean OR

[James T. Metz via Rdkit-discuss]

Hello,


Is it possible to write a single SMARTS for two separate patterns involving
a Boolean OR?


For example,  I want to write a single SMARTS that can match the
patterns of 


[C]-[C]  


or 


[N]-[N]


I realize that I could write something like


[C,N]-[C,N]


but that would also match "cross" patterns such as


CN and NC which I don't want.


I have tried to write


([C]-[C]), ([N\-[N])   but I have not been able to get that syntax or related
expressions (variations of parentheses, brackets, etc) to work.


Hence, if someone knows how to combine separate SMARTS expressions into
a single expression with a Boolean OR, I would be grateful.  Thank you.


Regards,
Jim Metz




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Re: [Rdkit-discuss] single SMARTS for two patterns with Boolean OR

[Dante]

Hi Jim,

Could you use the 'NOT' logical operator (!) in combination with recursive
SMARTS to eliminate the cross-matches?

Cheers,

Dante

On Tue, Sep 19, 2017 at 9:13 AM, James T. Metz via Rdkit-discuss <
rdkit-discuss@lists.sourceforge.net> wrote:

> Hello,
>
> Is it possible to write a single SMARTS for two separate patterns involving
> a Boolean OR?
>
> For example,  I want to write a single SMARTS that can match the
> patterns of
>
> [C]-[C]
>
> or
>
> [N]-[N]
>
> I realize that I could write something like
>
> [C,N]-[C,N]
>
> but that would also match "cross" patterns such as
>
> CN and NC which I don't want.
>
> I have tried to write
>
> ([C]-[C]), ([N\-[N])   but I have not been able to get that syntax or
> related
> expressions (variations of parentheses, brackets, etc) to work.
>
> Hence, if someone knows how to combine separate SMARTS expressions into
> a single expression with a Boolean OR, I would be grateful.  Thank you.
>
> Regards,
> Jim Metz
>
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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Re: [Rdkit-discuss] single SMARTS for two patterns with Boolean OR

[James T. Metz via Rdkit-discuss]

Dante,


Yes.  In principle, if one can figure out all of the possible undesired 
cross
matches.


Since my goal is to do this in RDkit and generate groups of atoms

that match, perhaps one approach is to simply use multiple RDkit pattern
matching statements (with multiple SMARTS), generate the groups of atoms, 
then combine the lists, removing identical groups.



Hmmm... Is there a more straightforward (elegant) solution?



Regards,

Jim Metz





-Original Message-
From: Dante 
To: James T. Metz 
Cc: RDKit Discuss 
Sent: Tue, Sep 19, 2017 8:45 am
Subject: Re: [Rdkit-discuss] single SMARTS for two patterns with Boolean OR



Hi Jim,


Could you use the 'NOT' logical operator (!) in combination with recursive 
SMARTS to eliminate the cross-matches?


Cheers,


Dante


On Tue, Sep 19, 2017 at 9:13 AM, James T. Metz via Rdkit-discuss 
 wrote:

Hello,


Is it possible to write a single SMARTS for two separate patterns involving
a Boolean OR?


For example,  I want to write a single SMARTS that can match the
patterns of 


[C]-[C]  


or 


[N]-[N]


I realize that I could write something like


[C,N]-[C,N]


but that would also match "cross" patterns such as


CN and NC which I don't want.


I have tried to write


([C]-[C]), ([N\-[N])   but I have not been able to get that syntax or related
expressions (variations of parentheses, brackets, etc) to work.


Hence, if someone knows how to combine separate SMARTS expressions into
a single expression with a Boolean OR, I would be grateful.  Thank you.


Regards,
Jim Metz





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Re: [Rdkit-discuss] single SMARTS for two patterns with Boolean OR

[Chris Earnshaw]

Hi

Will the recursive SMARTS [$(C-C),$(N-N)] not do the job?

I'd parse this in English as 'an atom which is EITHER an aliphatic carbon
singly bonded to an aliphatic carbon OR an aliphatic nitrogen singly bonded
to an aliphatic nitrogen'.

Regards,
Chris Earnshaw

On 19 September 2017 at 15:01, James T. Metz via Rdkit-discuss <
rdkit-discuss@lists.sourceforge.net> wrote:

> Dante,
>
> Yes.  In principle, if one can figure out all of the possible
> undesired cross
> matches.
>
> Since my goal is to do this in RDkit and generate groups of atoms
> that match, perhaps one approach is to simply use multiple RDkit pattern
> matching statements (with multiple SMARTS), generate the groups of atoms,
> then combine the lists, removing identical groups.
>
> Hmmm... Is there a more straightforward (elegant) solution?
>
> Regards,
> Jim Metz
>
>
>
> -Original Message-
> From: Dante 
> To: James T. Metz 
> Cc: RDKit Discuss 
> Sent: Tue, Sep 19, 2017 8:45 am
> Subject: Re: [Rdkit-discuss] single SMARTS for two patterns with Boolean OR
>
> Hi Jim,
>
> Could you use the 'NOT' logical operator (!) in combination with recursive
> SMARTS to eliminate the cross-matches?
>
> Cheers,
>
> Dante
>
> On Tue, Sep 19, 2017 at 9:13 AM, James T. Metz via Rdkit-discuss <
> rdkit-discuss@lists.sourceforge.net> wrote:
>
> Hello,
>
> Is it possible to write a single SMARTS for two separate patterns involving
> a Boolean OR?
>
> For example,  I want to write a single SMARTS that can match the
> patterns of
>
> [C]-[C]
>
> or
>
> [N]-[N]
>
> I realize that I could write something like
>
> [C,N]-[C,N]
>
> but that would also match "cross" patterns such as
>
> CN and NC which I don't want.
>
> I have tried to write
>
> ([C]-[C]), ([N\-[N])   but I have not been able to get that syntax or
> related
> expressions (variations of parentheses, brackets, etc) to work.
>
> Hence, if someone knows how to combine separate SMARTS expressions into
> a single expression with a Boolean OR, I would be grateful.  Thank you.
>
> Regards,
> Jim Metz
>
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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>
>
> 
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[Rdkit-discuss] Returning Z-matrix coordinates for a molecule in rdkit?

[Janusz Petkowski]

Dear RDKit Community,

I have a quick question. Is it possible to return a Z-matrix instead of the 
usual, Cartesian coordinates for a molecule in RDKit or do you know of any way 
of converting or generating Z-matrix coordinates for a batch of molecules?

Thanks!


Dr Janusz Petkowski

Research Fellow at MIT EAPS

Tel:  +1 (617) 258 - 6910
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Re: [Rdkit-discuss] Returning Z-matrix coordinates for a molecule in rdkit?

[Chris Earnshaw]

Hi

Open Babel will convert a wide range of structure formats and can produce
at least a couple of different flavours of Z-matrix, including MOPAC and
Gaussian. I'm not aware of any way to get a Z-matrix directly from RDKit
(but would be happy to find out I'm wrong).

Regards,
Chris Earnshaw

On 19 September 2017 at 16:15, Janusz Petkowski  wrote:

> Dear RDKit Community,
>
> I have a quick question. Is it possible to return a Z-matrix instead of
> the usual, Cartesian coordinates for a molecule in RDKit or do you know of
> any way of converting or generating Z-matrix coordinates for a batch of
> molecules?
>
> Thanks!
>
> Dr Janusz Petkowski
>
> Research Fellow at MIT EAPS 
>
> Tel:  +1 (617) 258 - 6910 <%28857%29%20777-6977>
>
> 
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Re: [Rdkit-discuss] single SMARTS for two patterns with Boolean OR

[James T. Metz via Rdkit-discuss]

Chris,


Thank you for your interesting suggestion, but it is not quite what I need.


For example, consider the molecule


m = Chem.MolFromSmiles("CCNN")


I am looking for one SMARTS that using the SMARTS pattern matching
capability in RDkit would return 2 groups, each group containing the two
atoms corresponding to  CC  and  NN.


Your suggested recursive SMARTS  and code below



pattern = Chem.MolFromSmarts('[$(C-C),$(N-N)]')
match = m.GetSubstructMatches(pattern)
match


returns



((0,), (1,), (2,), (3,))


The output I am trying to achieve, instead, is



((0,1), (2,3))


Is there a single SMARTS that will do that?



Regards,

Jim Metz










-Original Message-
From: Chris Earnshaw 
To: James T. Metz 
Cc: Rdkit-discuss@lists.sourceforge.net 
Sent: Tue, Sep 19, 2017 10:13 am
Subject: Re: [Rdkit-discuss] single SMARTS for two patterns with Boolean OR




Hi


Will the recursive SMARTS [$(C-C),$(N-N)] not do the job?

I'd parse this in English as 'an atom which is EITHER an aliphatic carbon 
singly bonded to an aliphatic carbon OR an aliphatic nitrogen singly bonded to 
an aliphatic nitrogen'.


Regards,

Chris Earnshaw



On 19 September 2017 at 15:01, James T. Metz via Rdkit-discuss 
 wrote:

Dante,


Yes.  In principle, if one can figure out all of the possible undesired 
cross
matches.


Since my goal is to do this in RDkit and generate groups of atoms

that match, perhaps one approach is to simply use multiple RDkit pattern
matching statements (with multiple SMARTS), generate the groups of atoms, 
then combine the lists, removing identical groups.



Hmmm... Is there a more straightforward (elegant) solution?



Regards,

Jim Metz






-Original Message-
From: Dante 
To: James T. Metz 
Cc: RDKit Discuss 
Sent: Tue, Sep 19, 2017 8:45 am
Subject: Re: [Rdkit-discuss] single SMARTS for two patterns with Boolean OR



Hi Jim,


Could you use the 'NOT' logical operator (!) in combination with recursive 
SMARTS to eliminate the cross-matches?


Cheers,


Dante


On Tue, Sep 19, 2017 at 9:13 AM, James T. Metz via Rdkit-discuss 
 wrote:

Hello,


Is it possible to write a single SMARTS for two separate patterns involving
a Boolean OR?


For example,  I want to write a single SMARTS that can match the
patterns of 


[C]-[C]  


or 


[N]-[N]


I realize that I could write something like


[C,N]-[C,N]


but that would also match "cross" patterns such as


CN and NC which I don't want.


I have tried to write


([C]-[C]), ([N\-[N])   but I have not been able to get that syntax or related
expressions (variations of parentheses, brackets, etc) to work.


Hence, if someone knows how to combine separate SMARTS expressions into
a single expression with a Boolean OR, I would be grateful.  Thank you.


Regards,
Jim Metz





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Re: [Rdkit-discuss] single SMARTS for two patterns with Boolean OR

[Chris Earnshaw]

Hmm, that makes it distinctly trickier. Recursive SMARTS work at the level
of single atoms and their environment, rather than treating a group of
atoms together, so I suspect it isn't possible to create a single SMARTS to
give the match information you need in one go. I'd be very pleased to find
out I'm wrong!

If you could use a small script it's pretty trivial of course -
m = Chem.MolFromSmiles("CCNN")
p1 = Chem.MolFromSmarts("C-C")
p2 = Chem.MolFromSmarts("N-N")
m1 = m.GetSubstructMatches(p1)
m2 = m.GetSubstructMatches(p2)
m1 + m2

which gives ((0, 1), (2, 3)) as required, but if you have a specific need
for the 'single SMARTS' approach that's not much use. Sorry not to be more
helpful...

Chris Earnshaw


On 19 September 2017 at 16:50, James T. Metz  wrote:

> Chris,
>
> Thank you for your interesting suggestion, but it is not quite what I
> need.
>
> For example, consider the molecule
>
> m = Chem.MolFromSmiles("CCNN")
>
> I am looking for one SMARTS that using the SMARTS pattern matching
> capability in RDkit would return 2 groups, each group containing the two
> atoms corresponding to  CC  and  NN.
>
> Your suggested recursive SMARTS  and code below
>
> pattern = Chem.MolFromSmarts('[$(C-C),$(N-N)]')
> match = m.GetSubstructMatches(pattern)
> match
>
> returns
>
> ((0,), (1,), (2,), (3,))
>
>
> The output I am trying to achieve, instead, is
>
>
> ((0,1), (2,3))
>
>
> Is there a single SMARTS that will do that?
>
>
> Regards,
>
> Jim Metz
>
>
>
>
>
>
> -Original Message-
> From: Chris Earnshaw 
> To: James T. Metz 
> Cc: Rdkit-discuss@lists.sourceforge.net  sourceforge.net>
> Sent: Tue, Sep 19, 2017 10:13 am
> Subject: Re: [Rdkit-discuss] single SMARTS for two patterns with Boolean OR
>
> Hi
>
> Will the recursive SMARTS [$(C-C),$(N-N)] not do the job?
>
> I'd parse this in English as 'an atom which is EITHER an aliphatic carbon
> singly bonded to an aliphatic carbon OR an aliphatic nitrogen singly bonded
> to an aliphatic nitrogen'.
>
> Regards,
> Chris Earnshaw
>
> On 19 September 2017 at 15:01, James T. Metz via Rdkit-discuss <
> rdkit-discuss@lists.sourceforge.net> wrote:
>
> Dante,
>
> Yes.  In principle, if one can figure out all of the possible
> undesired cross
> matches.
>
> Since my goal is to do this in RDkit and generate groups of atoms
> that match, perhaps one approach is to simply use multiple RDkit pattern
> matching statements (with multiple SMARTS), generate the groups of atoms,
> then combine the lists, removing identical groups.
>
> Hmmm... Is there a more straightforward (elegant) solution?
>
> Regards,
> Jim Metz
>
>
>
> -Original Message-
> From: Dante 
> To: James T. Metz 
> Cc: RDKit Discuss 
> Sent: Tue, Sep 19, 2017 8:45 am
> Subject: Re: [Rdkit-discuss] single SMARTS for two patterns with Boolean OR
>
> Hi Jim,
>
> Could you use the 'NOT' logical operator (!) in combination with recursive
> SMARTS to eliminate the cross-matches?
>
> Cheers,
>
> Dante
>
> On Tue, Sep 19, 2017 at 9:13 AM, James T. Metz via Rdkit-discuss <
> rdkit-discuss@lists.sourceforge.net> wrote:
>
> Hello,
>
> Is it possible to write a single SMARTS for two separate patterns involving
> a Boolean OR?
>
> For example,  I want to write a single SMARTS that can match the
> patterns of
>
> [C]-[C]
>
> or
>
> [N]-[N]
>
> I realize that I could write something like
>
> [C,N]-[C,N]
>
> but that would also match "cross" patterns such as
>
> CN and NC which I don't want.
>
> I have tried to write
>
> ([C]-[C]), ([N\-[N])   but I have not been able to get that syntax or
> related
> expressions (variations of parentheses, brackets, etc) to work.
>
> Hence, if someone knows how to combine separate SMARTS expressions into
> a single expression with a Boolean OR, I would be grateful.  Thank you.
>
> Regards,
> Jim Metz
>
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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>
>
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Re: [Rdkit-discuss] single SMARTS for two patterns with Boolean OR

[James T. Metz via Rdkit-discuss]

Chris,


Thanks again.  I thought of this idea also as I was eating my lunch!


One could create a "hyper SMARTS" using one or more vertical pipes


[C]-[C]|[N]-[N]


Then use PYTHON to check for the existence of a vertical pipe in the 
string.  
If it exists, then split the hyper SMARTS string using the vertical pipe 
character.
Then process each of the separated SMARTS strings in a loop, generate the list
of atoms for each iteration of the loop (each SMARTS), and keep adding the 
groups
of atoms (as you did in your example code below).


I think the vertical pipe is probably a good choice for a separator, since 
it

is not used in normal SMARTS and hence would not be confused with some 
regular SMARTS expression.


This is clearly not as elegant as I was hoping for, but should work just 
fine.


Thanks again.


Regards,

Jim Met








-Original Message-
From: Chris Earnshaw 
To: James T. Metz 
Cc: Rdkit-discuss@lists.sourceforge.net 
Sent: Tue, Sep 19, 2017 11:45 am
Subject: Re: [Rdkit-discuss] single SMARTS for two patterns with Boolean OR





Hmm, that makes it distinctly trickier. Recursive SMARTS work at the level of 
single atoms and their environment, rather than treating a group of atoms 
together, so I suspect it isn't possible to create a single SMARTS to give the 
match information you need in one go. I'd be very pleased to find out I'm wrong!


If you could use a small script it's pretty trivial of course -
m = Chem.MolFromSmiles("CCNN")
p1 = Chem.MolFromSmarts("C-C")
p2 = Chem.MolFromSmarts("N-N")
m1 = m.GetSubstructMatches(p1)
m2 = m.GetSubstructMatches(p2)

m1 + m2



which gives ((0, 1), (2, 3)) as required, but if you have a specific need for 
the 'single SMARTS' approach that's not much use. Sorry not to be more 
helpful...


Chris Earnshaw








On 19 September 2017 at 16:50, James T. Metz  wrote:

Chris,


Thank you for your interesting suggestion, but it is not quite what I need.


For example, consider the molecule


m = Chem.MolFromSmiles("CCNN")


I am looking for one SMARTS that using the SMARTS pattern matching
capability in RDkit would return 2 groups, each group containing the two
atoms corresponding to  CC  and  NN.


Your suggested recursive SMARTS  and code below



pattern = Chem.MolFromSmarts('[$(C-C),$(N-N)]')
match = m.GetSubstructMatches(pattern)
match


returns



((0,), (1,), (2,), (3,))



The output I am trying to achieve, instead, is





((0,1), (2,3))



Is there a single SMARTS that will do that?





Regards,


Jim Metz














-Original Message-
From: Chris Earnshaw 
To: James T. Metz 

Cc: Rdkit-discuss@lists.sourceforge.net 
Sent: Tue, Sep 19, 2017 10:13 am
Subject: Re: [Rdkit-discuss] single SMARTS for two patterns with Boolean OR




Hi


Will the recursive SMARTS [$(C-C),$(N-N)] not do the job?

I'd parse this in English as 'an atom which is EITHER an aliphatic carbon 
singly bonded to an aliphatic carbon OR an aliphatic nitrogen singly bonded to 
an aliphatic nitrogen'.


Regards,

Chris Earnshaw



On 19 September 2017 at 15:01, James T. Metz via Rdkit-discuss 
 wrote:

Dante,


Yes.  In principle, if one can figure out all of the possible undesired 
cross
matches.


Since my goal is to do this in RDkit and generate groups of atoms

that match, perhaps one approach is to simply use multiple RDkit pattern
matching statements (with multiple SMARTS), generate the groups of atoms, 
then combine the lists, removing identical groups.



Hmmm... Is there a more straightforward (elegant) solution?



Regards,

Jim Metz






-Original Message-
From: Dante 
To: James T. Metz 
Cc: RDKit Discuss 
Sent: Tue, Sep 19, 2017 8:45 am
Subject: Re: [Rdkit-discuss] single SMARTS for two patterns with Boolean OR



Hi Jim,


Could you use the 'NOT' logical operator (!) in combination with recursive 
SMARTS to eliminate the cross-matches?


Cheers,


Dante


On Tue, Sep 19, 2017 at 9:13 AM, James T. Metz via Rdkit-discuss 
 wrote:

Hello,


Is it possible to write a single SMARTS for two separate patterns involving
a Boolean OR?


For example,  I want to write a single SMARTS that can match the
patterns of 


[C]-[C]  


or 


[N]-[N]


I realize that I could write something like


[C,N]-[C,N]


but that would also match "cross" patterns such as


CN and NC which I don't want.


I have tried to write


([C]-[C]), ([N\-[N])   but I have not been able to get that syntax or related
expressions (variations of parentheses, brackets, etc) to work.


Hence, if someone knows how to combine separate SMARTS expressions into
a single expression with a Boolean OR, I would be grateful.  Thank you.


Regards,
Jim Metz





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