Molecule Properties

Community Extensions Indigo
#1

Hi,

In the molecule properties node, please can you add:

- Aliphatic Bonds count

- Aliphatic Atoms count

- Most Basic pKa

- Most Acidic pKa

- LogP

- LogD

- Polar Surface Area

- Number of Carbon Atoms

- Number of Non-Carbon Atoms (excluding the count of Hydrogen)

- Number of components (useful to see there are salts present)

 

Thanks

Simon.

#2

Simon,

Thank you very much for trying the Indigo nodes. Following your request, we have added the following properties:

  • Number of aliphatic atoms/bonds
  • Number of carbon atoms
  • Number of heteroatoms (non-C, non-H)

They will be available in next nightly build (i.e. tomorrow)

The number of components was already there (called "Number of connected components"). As for pKa, LogP, LogD, and Polar Surface Area, the present version of the Indigo library can not calculate these, sorry, but we can think about that properties in the future.

Regards,

Dmitry Pavlov
GGA Software Services LLC

#3

Great.

Thanks for the quick response. I will continue experimenting with these Indigo nodes

 

Thanks

 

Simon.

#4

Hi,

Is it also possible to have an option for "Number of aromatic rings".This can be a useful indicator on the worsening of solubility.

Thanks,

Simon.

#5

Thanks for the additions of, these are working as expected:

  • Number of aliphatic atoms/bonds

  • Number of carbon atoms

  • Number of heteroatoms (non-C, non-H)

    •  

    There was a couple of other additions I would like if possible which I forgot to mention:

    - Number of Rotatable Bonds

    - Hydrogen Bond Acceptors (HBAs)

    - Hydrogen Bond Donors (HBDs)

    Would it be possible to have these too. Thanks for all this extra functionality the Indigo nodes are providing :-)

    Thanks, Simon.

    #6

    Simon,

    Thank you again for your useful suggestions. We can add the "Number of aromatic rings" into the next build, but I am wondering whether it should be all rings or just SSSR (smallest set of smallest rings)? In other words, take naphtalene: should Indigo report 2 or 3 aromatic rings for it?

    As for the HBAs, HBDs, and rotatable bonds: Indigo can not calculate them directly, but you can get the result by using the Substructure Match Counter node with a SMARTS string as a query. You just connect your molecule(s) source to the first input of the Substructure Match Counter node, while to the second one you should pass a query molecule which you can obtain in the following way:

    • Table Creator (enter your SMARTS expression there) -->
    • Molecule Type Cast (cast it to the SMARTS type) -->
    • Query Molecule to Indigo (parse the SMARTS) -->
    • (to the second slot of the Substructure Match Counter)

    There are known SMARTS expressions for HBAs and HBDs, and also for the number of rotatable bonds.

    Moreover, you can calculate the TPSA this way! (you asked about the Polar Surface Area before -- is that what you want?). However, this is a bit more complicated as it involves summing the substructure match counters (multiplied by coefficients) for different SMARTS. Good news: you can download an example of TPSA calculation from the KNIME Example Flow Server, look there into 099_Community/07_Indigo/09907006_indigo-tpsa-example. There are other examples there, too.

     

    Regards,

    Dmitry

    #7

    Thanks for the detailed information, I shall try this out for RBs, HBA, HBD, and PSA. Thanks for the instructions.

    In terms of counting number of rings,I completely overlooked that you could call Napthelene 3 rings from the 2 small rings and the one larger ring!! As a chemist, I would just call Napthelene 2 rings.

    I hope this doesnt make the implementation of "the number of aromatic rings" too complicated to do.

     

    Thanks

    Simon.

    #8

    Simon,

    You can try the "Number of aromatic rings" property in today's build (923).

     

    Regards,

    Dmitry

    #9

    Brilliant, the aromatic ring count is working exactly as expected.

    Thanks very much, this will be really useful for using as a surrogate of insolubility.

    Thanks

    Simon.

    #10

    Simon, Dmitry,

     

    where these indigo nodes can be found?

    I've checked some url that is on this forum (http://tech.knime.org/forum/indigo,) but without much success.

    http://tech.knime.org/update/community-contributions/release (no success finding' indigo intergration 'nodes in 146Mo download)
    http://tech.knime.org/update/community-contributions/nightly (neither...)
    please, can you help in the matter?

    thanks in advance

    B

    #11

    BJFR: they are in the nightly updates. Here you can find detailed instructions.

    Best regads,

    Dmitry

    #12

    thank you. I found them.

    bruno

    #13

    Hi,

    Is it possible to have a minor alteration to the Molecule Properties node. Now we are spoilt for choice with many options to calculate, is it possible to have them grouped a little more logically such as:

    Molecular Formulae

    Molecular Weight

    Most Abundant Mass

    Monoisotopic Mass

    Number of Components

    Number of Atoms

    Number of Hydrogens

    Number of Heavy Atoms

    Number of Heteroatoms

    Number of Carbons

    Number of Aromatic Atoms

    Number of Aliphatic Atoms

    Number of Pseudoatoms

    Number of Visible Atoms

    Number of Chiral Centres

    Number of R Sites

    Number of Bonds

    Number of Aromatic Bonds

    Number of Aliphatic Bonds

    Number of cis/trans Bonds

    Number of Aromatic Rings

    Number of Aliphatic Rings

     

    Thanks, Simon.

    #14

    I dont know how easy it is to do, but is there a possibility for a Molecular Volume option and Polarisability ?

     

    Thanks

    Simon.

    #15

    Simon,

    I agree that having them ordered that way is much more comfortable. They follow that order in the new version (1.0.0.0000948) that is available on the nightly updates site.

     

    Best regards,

    Dmitry

    #16

    Simon,

    With the present version of Indigo code library that does not seem to be doable, sorry. We can postpone it for future versions, though.

    Best regards,

    Dmitry

    #17

    Thanks for ordering the properties more logically, its much easier to find the desired property. I'd really appreciate keeping the Molecular Volume and Polarisability properties on a wish list for the future.

    Thanks

    Simon.

    #18

    Can you add number of "hetero atoms in aliphatic ring", "htero atoms in aromatic ring". I am trying to filter carbocylic, heteroaromatic and heterocylcic[non-aromatic rings] using row filter node. But cannot do so since it picks het-atom count can occur outside a ring too.

    It would be great if we could go to the level of N-heterocycle!

    #19

    InsilicoConsulting: Done. The new properties will be available tomorrow morning in the next nightly build. You can, though, count occurrences of SMARTS: "[!#6;A;R]" and "[!#6;a;R]" in the current build to get the filters you need.

    Best regards,

    Dmitry

    #20

    Super work! Thanks! Since most drug like molecules are heterocyclic this is very important!

    cheers

    rajeev