Dear Emanuel,

Thank you for pointing at SMARTSviewer; it is a good place to check our
codes.

Cheers,
Chenyang

On Thu, Nov 9, 2017 at 4:44 AM, Emanuel Ehmki <emanuel.eh...@gmail.com>
wrote:

> 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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