Thank you for your kind help. It actually helped a lot. I discovered my SMARTS were wrong after sending this help request (thank you for the website suggestion, by the way) I would suggest to whoever is taking care of the guide to edit that section of the guide (paragraph 6.11 calculate TPSA) and specify better that the files must be included in the working directory (like you did). You have been very helpful. As soon as I will figure out how to make it working properly I will make a tutorial for other people with the same problem.
-----Messaggio originale----- Da: Noel O'Boyle [mailto:baoille...@gmail.com] Inviato: giovedì 1 marzo 2012 05:43 A: Samuele Sommariva Cc: openbabel-disc...@lists.sf.net Oggetto: Re: [Open Babel] Unable to use plugindefines.txt (Group additivity) Hi Samuele, Yes - it's possible - I've just checked. Step 1 - Get the existing plugindefines.txt (in C:\ProgramData\OpenBabel2.3.1\data), copy it to your working directory (e.g. C:\Temp), and edit it Step 2 - Write the file containing my property, and save it to the same directory Step 3 - Run obabel in C:\Temp C:\Temp>obabel -L descriptors abonds Number of aromatic bonds ... HF_Try Compute Entalpy of formation using group additivity ... TPSA topological polar surface area Yours SMARTS strings needed some work. To prevent errors, I edited them as follows: [CH3](-[CX4]) 11 [CH2](-[CX4])(-[CX4]) 111 [CH](-[CX4])(-[CX4])(-[CX4]) 1111 [C](-[CX4])(-[CX4])(-[CX4])(-[CX4]) 11111 ...but I still don't think they are correct, as propane gives the following: C:\Temp> obabel -:CCC -otxt --append HF_Try 288 You may find the following useful for testing SMARTS strings, e.g. http://smartsview.zbh.uni-hamburg.de/. By the way, once you figure it all out, please consider contributing the result back to Open Babel. - Noel On 29 February 2012 01:31, Samuele Sommariva <samuele.sommar...@gmail.com> wrote: > I am trying to compute Entalpy of formation (of alkanes at this time) > using group additivity. > For the sake of argument, let's use normal-propane (CCC) I am > currently running Open Babel 2.3.1 under win 7 > >From what I have understood from the Open Babel documentation > (paragraph 6.11 calculate TPSA) it should be possible to add plugins > at runtime without recompile (and that is what I am trying to do) > > My steps: > 1 - Write the plugindefines.txt file > 2 - Write the file containing my property using the sintax "group I am > looking for" TAB "number" > 3 - Save both in the C:\Program Files (x86)\OpenBabel-2.3.1 folder > > At the end of this message you can find copy of both plugindefines.txt > and HF_Groups.txt > > What I expected was to get a new descriptor called HF_Try. When I look > for descriptors, there is nothing like HF_Try, as you can see from the > screenshot > > > C:\Users\Samu>obabel -L descriptors > abonds Number of aromatic bonds > atoms Number of atoms > bonds Number of bonds > cansmi Canonical SMILES > cansmiNS Canonical SMILES without isotopes or stereo dbonds > Number of double bonds formula Chemical formula > HBA1 Number of Hydrogen Bond Acceptors 1 (JoelLib) > HBA2 Number of Hydrogen Bond Acceptors 2 (JoelLib) HBD Number of > Hydrogen Bond Donors (JoelLib) InChI IUPAC InChI identifier > InChIKey InChIKey > L5 Lipinski Rule of Five > logP octanol/water partition coefficient MR molar refractivity > MW Molecular Weight filter nF Number of Fluorine Atoms s > SMARTS filter sbonds Number of single bonds smarts SMARTS filter > tbonds Number of triple bonds title For comparing a molecule's > title TPSA topological polar surface area > > > Am I doing something wrong? Does my issue have anything to do with the > "obabel -L loaders" (about which I couldn't find any help)? > Thanks for the attention and the help > > Samuele > > > plugindefines.txt: > OBGroupContrib > HF_Try # name of descriptor > HF_Groups.txt # data file > Compute Entalpy of formation using group additivity\n # brief > description Numbers are taken from Bozzelli work! > > > HF_Groups.txt: > [CH3(-CX4)] 11 > [CH2(-CX4)(-CX4)] 111 > [CH(-CX4)(-CX4)(-CX4)] 1111 > [C(-CX4)(-CX4)(-CX4)(-CX4)] 11111 > > ---------------------------------------------------------------------- > -------- Virtualization & Cloud Management Using Capacity Planning > Cloud computing makes use of virtualization - but cloud computing also > focuses on allowing computing to be delivered as a service. > http://www.accelacomm.com/jaw/sfnl/114/51521223/ > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss ----- Nessun virus nel messaggio. Controllato da AVG - www.avg.com Versione: 10.0.1424 / Database dei virus: 2113/4844 - Data di rilascio: 01/03/2012 ------------------------------------------------------------------------------ Virtualization & Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
