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 <jasondbi...@gmail.com> 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&lk=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 <cs3...@columbia.edu> 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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