Re: [Rdkit-discuss] SMARTS for Joback and Reid method

2017-11-09 Thread Emanuel Ehmki 
Dear Chenyang,

at http://smartsview.zbh.uni-hamburg.de/ you will find a useful tool to
visualize your Smarts pattern and also get them checked for correctness.

Best,
Emanuel

Jason Biggs  schrieb am Do., 9. Nov. 2017 um
00:51 Uhr:

> Chenyang,
> I haven't looked at your smarts strings yet, but I do have this list of
> SMARTS strings for the joback method I compiled myself (for use here:
> https://www.wolframalpha.com/input/?i=2,3-methano-5,6-dichloroindene=3
> ).
>
> Perhaps this can be of use.  If you spot any mistakes, please let me know
>
> Jason
>
> $JobackSubstructures={
>
> {"Methyl","-CH3", "[CX4H3]"},
>
> {"SecondaryAcyclic", "-CH2-", "[!R;CX4H2]"},
>
> {"TertiaryAcyclic",">CH-", "[!R;CX4H]"},
>
> {"QuaternaryAcyclic", ">C<", "[!R;CX4H0]"},
>
> {"PrimaryAlkene", "=CH2", "[CX3H2]"},
>
> {"SecondaryAlkeneAcyclic", "=CH-", "[!R;CX3H1;!$([CX3H1](=O))]"},
>
> {"TertiaryAlkeneAcyclic", "=C<", "[$([!R;#6X3H0]);!$([!R;#6X3H0]=[#8])]"},
>
> {"CumulativeAlkene", "=C=", "[$([CX2H0](=*)=*)]"},
>
> {"TerminalAlkyne", "\[Congruent]CH","[$([CX2H1]#[!#7])]"},
>
> {"InternalAlkyne","\[Congruent]C-","[$([CX2H0]#[!#7])]"},
>
> {"SecondaryCyclic", "-CH2- (ring)", "[R;CX4H2]"},
>
> {"TertiaryCyclic", ">CH- (ring)", "[R;CX4H]"},
>
> {"QuaternaryCyclic", ">C< (ring)", "[R;CX4H0]"},
>
> {"SecondaryAlkeneCyclic", "=CH- (ring)", "[R;CX3H1,cX3H1]"},
>
> {"TertiaryAlkeneCyclic", "=C<
> (ring)","[$([R;#6X3H0]);!$([R;#6X3H0]=[#8])]"},
>
> {"Fluoro", "-F", "[F]"},
>
> {"Chloro", "-Cl", "[Cl]"},
>
> {"Bromo", "-Br", "[Br]"},
>
> {"Iodo", "-I", "[I]"},
>
> {"Alcohol","-OH", "[OX2H;!$([OX2H]-[#6]=[O]);!$([OX2H]-a)]"},(* alcohol -
> not matching a carboxylic acid *)
>
> {"Phenol","-OH", "[$([OX2H]-a)]"},
>
> {"EtherAcyclic", "-O-", "[OX2H0;!R;!$([OX2H0]-[#6]=[#8])]"},
>
> {"EtherCyclic", "-O- (ring)", "[#8X2H0;R;!$([#8X2H0]~[#6]=[#8])]"},
>
> {"CarbonylAcyclic", ">C=O",
> "[$([CX3H0](=[OX1]));!$([CX3](=[OX1])-[OX2]);!R]=O"},
>
> {"CarbonylCyclic", ">C=O
> (ring)","[$([#6X3H0](=[OX1]));!$([#6X3](=[#8X1])~[#8X2]);R]=O"},
>
> {"Aldehyde","O=CH-","[CX3H1](=O)"},
>
> {"CarboxylicAcid", "COOH", "[OX2H]-[C]=O"},
>
> {"Ester", "-C(=O)O-",
> "[#6X3H0;!$([#6X3H0](~O)(~O)(~O))](=[#8X1])[#8X2H0]"},
>
> {"OxygenDoubleBondOther", "=O",
> "[OX1H0;!$([OX1H0]~[#6X3]);!$([OX1H0]~[#7X3]~[#8])]"},
>
> {"PrimaryAmino","NH2", "[NX3H2]"},
>
> {"SecondaryAminoAcyclic",">NH", "[NX3H1;!R]"},
>
> {"SecondaryAminoCyclic",">NH (ring)", "[#7X3H1;R]"},
>
> {"TertiaryAmino", ">N-","[#7X3H0;!$([#7](~O)~O)]"}, (* Tertiary amine
> except nitro group *)
>
> {"ImineCyclic","=N- (ring)","[#7X2H0;R]"},
>
> {"ImineAcyclic","=N-","[#7X2H0;!R]"},
>
> {"Aldimine", "=NH", "[#7X2H1]"},
>
> {"Cyano", "-C\[Congruent]N","[#6X2]#[#7X1H0]"},
>
> {"Nitro", "NO2", "[$([#7X3,#7X3+][!#8])](=[O])~[O-]"},
>
> {"Thiol", "-SH", "[SX2H]"},
>
> {"ThioetherAcyclic", "-S-", "[#16X2H0;!R]"},
>
> {"ThioetherCyclic", "-S- (ring)", "[#16X2H0;R]"}
>
> };
>
> Jason Biggs
>
>
> On Wed, Nov 8, 2017 at 4:52 PM, Chenyang Shi  wrote:
>
>> Hi everyone,
>>
>> I have been recently working on a project that implements Joback method
>> using RDKit (https://en.wikipedia.org/wiki/Joback_method).
>>
>> I believe the core to the success of this project is to make the 41
>> functional groups correctly represented by SMARTS code. I have compiled my
>> own codes, see attachment. I would appreciate your review of it and let me
>> know if you spot errors.
>>
>> I think building a robust/well-tested SMARTS database (though small in my
>> case) would be helpful to others and other projects.
>>
>> Thank you,
>> Chenyang
>>
>> PS: The ones highlighted red in the document are robust.
>>
>>
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>>
>
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Re: [Rdkit-discuss] How to generate bioisosters?

2018-02-05 Thread Emanuel Ehmki 
Dear Alexis,

as far as I know, this would be the SMARTS string with recursive pattern:
[$(C1=CN=[CH1][CH1]=N1),$(C1=[CH1]N=C[CH1]=N1),$(C1=[CH1]N=[CH1]C=N1),$(OC1=[CH1]C=NO1),$(OC1=NOC=[CH1]1),$(C1=CN=C([NX3])O1),$([#6X4]([#6X4](F)(F)(F))[NX3]),$(C(C#N)=NO),$(N1N=NN=C1),$(N1N=NC=[N]1),$(N1N=NC=[CH1]1),$(C1=NOC=N1),$(C1=NN=C[OX2]1),$(C1=NN=C[NH1]1),$([C]1(COC1)[OX2]),$([C]1(COC1)[NX3]),$(C([NX3H1])=N[CX4H3]),$([CX4]1([CX4][CX4]1)[NX3]),$([#16X4+2]([NX3])([OX1-])([OX1-])),$([#16X4]([NX3])(=[OX1])(=[OX1])),$([CX3](=[CX3])(F)),$([OX2][CX3](=[OX1])),$([NX3][CX3](=[OX1]))]

I don't know what you want to match specifically, but some of your pattern
won't match SMILES that are written as the aromatic form of the molecule
instead of the localized form.

Best wishes,
Emanuel

Alexis Parenty  schrieb am Mo., 5. Feb. 2018
um 10:07 Uhr:

> Dear RDKiters,
>
> I would like to generate the bioisosters of amides from a large list of
> structures:
>
> The smarts patterns for the bioisosters  of amides I am interested in is:
>
> smarts_path = ['C1=CN=[CH1][CH1]=N1', 'C1=[CH1]N=C[CH1]=N1',
> 'C1=[CH1]N=[CH1]C=N1', 'OC1=[CH1]C=NO1', 'OC1=NOC=[CH1]1',
> 'C1=CN=C([NX3])O1', '[#6X4]([#6X4](F)(F)(F))[NX3]', 'C(C#N)=NO',
> 'N1N=NN=C1', 'N1N=NC=[N]1', 'N1N=NC=[CH1]1', 'C1=NOC=N1', 'C1=NN=C[OX2]1',
> 'C1=NN=C[NH1]1', '[C]1(COC1)[OX2]', '[C]1(COC1)[NX3]',
> 'C([NX3H1])=N[CX4H3]', '[CX4]1([CX4][CX4]1)[NX3]',
> '[#16X4+2]([NX3])([OX1-])([OX1-])', '[#16X4]([NX3])(=[OX1])(=[OX1])',
> '[CX3](=[CX3])(F)', '[OX2][CX3](=[OX1])', '[NX3][CX3](=[OX1])']
>
> How would you best "disconnect the amide moiety" of a structure and
> "replace" it with the recursive smarts pattern of its bioisosters? The
> bioster matching patern above must be contained within a single smarts, so
> I think I need recursive smarts, right?
>
> Any directions would be very much appreciated.
>
> Best,
>
> Alexis
>
>
>
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[Rdkit-discuss] MMPA implementation in C++

2020-03-27 Thread Emanuel Ehmki 
Dear all,

I was just checking out the MMPA implementation in the C++ code. Do I miss
something or was only the fragmentation ported to C++ from Python?
If that is the case, is there a specific reason why the indexing part was
not ported?

Kind regards,
Emanuel
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