[Open Babel] How to run readstring in pybel?

Hi, I got the following error. Does anybody know what is wrong? Thanks. $ cat main.py #!/usr/bin/env python import pybel mymol = pybel.readstring("smi", "") print mymol.molwt $ ./main.py Traceback (most recent call last): File "./main.py", line 5, in mymol = pybel.readstring("smi", "CC

Re: [Open Babel] How to run readstring in pybel?

7;__description__', '__email__', 'to_cx', 'from_database', 'to_graphml', 'to_database', 'exceptions', 'database_io', 'from_bytes'] On Sun, May 7, 2017 at 9:20 PM, Hongbin Yang wrote: > Hi, Peng, > > I guess you installed

Re: [Open Babel] How to run readstring in pybel?

OK. It fixed the problem. Thanks. On Sun, May 7, 2017 at 9:41 PM, David Hall wrote: > That is still the wrong pybel. You should uninstall it (i.e. pip uninstall > pybel ) > > >> On May 7, 2017, at 10:38 PM, Peng Yu wrote: >> >> Hi, I should have installed the co

[Open Babel] How to draw structure from SMILES?

Hi, Although there are many online tools (e.g., PubChem sketcher) to draw structure from SMILES, I prefer to do so locally sometimes. Could anybody show me what is the best way to do so with openbabel? Thanks. -- Regards, Peng ___ OpenBabel-discuss ma

[Open Babel] How to install pybel?

Hi, I don't see how to install pybel. https://openbabel.org/docs/dev/UseTheLibrary/Python_PybelAPI.html#pybel-api This one does seem to be the same the above one. https://pypi.org/project/pybel Could anybody let me know how to pybel that works with openbabel? Thanks. -- Regards, Peng _

Re: [Open Babel] How to install pybel?

So the documentation https://openbabel.org/docs/dev/UseTheLibrary/Python_PybelAPI.html#pybel-api is outdated? Thanks. On 10/31/19, Geoffrey Hutchison wrote: >> This one does seem to be the same the above one. >> https://pypi.org/project/pybel > > You want: > https://pypi.org/project/openbabel/

Re: [Open Babel] How to draw structure from SMILES?

I got the following error. Do you know what is wrong? Thanks. $ obabel '-:C(=O)Cl' -O acidchloride.png == *** Open Babel Error in PNG Format PNG2Format not found. Probably the Cairo library is not loaded. -1 PNG_files converted $ obabel --version No input file or fo

[Open Babel] How to obabel to stdout?

I use the following comman to print the image to stdout. Is it the best way to do so? Thanks. obabel '-:C(=O)Cl' -o png -O /dev/stdout -- Regards, Peng ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourcefor

[Open Babel] How to suppress messages from obabel?

$ obabel '-:C(=O)Cl' -O /tmp/acidchloride.png 1 molecule converted I'd like to suppress "1 molecule converted" in the above command. Is there a way to do so? Thanks. -- Regards, Peng ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourcefo

[Open Babel] Official reference of SMILES

Hi, I am wondering where is the official reference of SMILES. Is this one? Thanks. https://www.daylight.com/dayhtml/doc/theory/theory.smiles.html -- Regards, Peng ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lis

[Open Babel] How to compute the Tanimoto coefficient calculation between two structures?

Hi, Relating protein pharmacology by ligand chemistry https://www.ncbi.nlm.nih.gov/pubmed/17287757 I see the above papers Tanimoto coefficient. I am not sure how to use open-babel python code to compute the similarity between two SMILES strings. Could anybody show me how to do it? Thanks. https:

Re: [Open Babel] How to compute the Tanimoto coefficient calculation between two structures?

What is the relationship between openbabel and rdkit? What is best fingerprint nowadays for the purpose of the method described in the paper that I mentioned? Thanks. On Wed, Nov 6, 2019 at 3:49 PM Francois Berenger wrote: > On 06/11/2019 08:34, Peng Yu wrote: > > Hi, > > >

[Open Babel] Error to load pybel

Hi, I got the following error to load pybel in openbabel python module. Does anybody know what is wrong? Thanks. $ brew info open-babel open-babel: stable 3.0.0 (bottled), HEAD Chemical toolbox https://openbabel.org /usr/local/Cellar/open-babel/3.0.0 (328 files, 19.5MB) * Poured from bottle on

[Open Babel] How to install openbabel on Mac OS X?

I got the following error when I try to install openbabel. But I got errros in pip3. I also installed open-babel with brew. But it is based on python installed from homebrew? Could anybody let me know what is the correct way to install openbabel? (BTW, I want to avoid using conda if possible.) $

[Open Babel] How to convert smiles to inchikey?

Hi, I don't see how to convert smiles to inchikey in the command line. Could anybody show me how to do the conversion with openbabel? Thanks. https://openbabel.org/docs/dev/Command-line_tools/babel.html -- Regards, Peng ___ OpenBabel-discuss mailing

[Open Babel] How to convert inchikey to other formats?

Hi, I don't find how to take inchikey input and convert it to other formats. http://openbabel.org/docs/current/FileFormats/Overview.html I got the following error. Could anybody show me the correct way to make the conversion? Thanks. $ obabel -iinchikey <(echo GFAUNYMRSKVDJL-UHFFFAOYSA-N) -o sm

Re: [Open Babel] How to convert inchikey to other formats?

> There are several 'resolvers' out there for InChi Keys. > https://cactus.nci.nih.gov/blog/?tag=inchikey-resolver > http://chembl.blogspot.com/2016/03/this-python-inchi-key-resolver-will.html > > As noted, these will only work for molecules in PubChem (the NIH resolver) > and UniChem (the Chembl r

[Open Babel] How to deal with .mol2 files?

Hi, I see the following file. I see obabel can deal with mol2 format. But how to visualize it and edit it? Thanks. http://tcmspw.com/tcmspmol/MOL002088.mol2 -- Regards, Peng ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net

Re: [Open Babel] How to convert inchikey to other formats?

> They're all database lookups AFAIK. If all you want is more keys, you > need the biggest database. If ChemSpider has a larger molecule database > than PubChem, then it will be "more comprehensive". Which one is the most comprehensive according to your experience? -- Regards, Peng __

[Open Babel] How to determine a compound is a flavonoid?

Hi, I want to determine whether a compound (via SMILES or IsoSMILES) is a flavonoid. Does anybody know what is the best way to do so with babel? Thanks. -- Regards, Peng ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https