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 __

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

On 3/23/2020 2:28 PM, Peng Yu wrote: As noted, these will only work for molecules in PubChem (the NIH resolver) and UniChem (the Chembl resolver). I see ChemSpider is mentioned here. Is it more comprehensive than PubChem and ChEMBL? Thanks. They're all database lookups AFAIK. If all you want

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

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

> PS: there is an unpractical way though: compute the inchikey of all possible >molecules, until you hit the key that you were looking for. 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-pyt

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

On 23/03/2020 12:21, Peng Yu wrote: Hi, I don't find how to take inchikey input and convert it to other formats. You should read about what really is an inchikey: https://en.wikipedia.org/wiki/International_Chemical_Identifier#InChIKey While you are at it, maybe you can read about what is a

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

inchikey is write only. On Sun, Mar 22, 2020 at 11:21 PM Peng Yu wrote: > 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 > ma

[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 smiles to inchikey?

Hi Peng, If you do >obabel -L formats, it says that inchikey is write-only. I was able to convert smiles to inchikey in two ways: >obabel -i smi benzene.smi -o inchikey -O benzene.inchikey 1 molecule converted >obabel -:"c1c1" -o inchikey -O benzene.inchikey 1 molecule converted The inchik

[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

Re: [Open Babel] how to convert

> I am wondering if you know a way to convert over 1000 outputs from mopac to > another format like sdf or mol ? each output is a molecule You don't mention what OS you use, but let's assume Linux or Mac - with a command-line: obabel *.out -osdf -m # convert all *.out files (MOPAC or otherwis

[Open Babel] how to convert

Hello, I am wondering if you know a way to convert over 1000 outputs from mopac to another format like sdf or mol ? each output is a molecule Many thanks, Mohammad -- Check out the vibrant tech community on one of the wor

Re: [Open Babel] How to convert fractional format to POSCAR

> "the client that is using Open Babel must use OBConversion::ReadFile() to > begin the conversion." This is just saying that you can't use some forms of code in C++ or Python. The command-line tools and Avogadro should handle things correctly to read / write POSCAR. I can vouch for this -- I h

Re: [Open Babel] How to convert fractional format to POSCAR

Yes, actually I do not know what does this mean (adapted from the open babel website about exporting to POSCAR): http://openbabel.org/docs/2.3.1/FileFormats/VASP_format.html "the client that is using Open Babel must use OBConversion:

Re: [Open Babel] How to convert fractional format to POSCAR

> But what I need is to export the coordinates to POSCAR. Does either > openbabel or avogadro can export other coordinates to POSCAR files? Yes. You just need to name the file POSCAR, and it should export in Vasp 5.x format. Open Babel has a few options to control the formatting. Hope that helps

Re: [Open Babel] How to convert fractional format to POSCAR

Thank you, Geoff! But what I need is to export the coordinates to POSCAR. Does either openbabel or avogadro can export other coordinates to POSCAR files? Thank you in advance! Murphy -- View this message in context: http://forums.openbabel.org/How-to-convert-fractional-format-to-POSCAR-tp4

Re: [Open Babel] How to convert fractional format to POSCAR

> seems that the most matching format of POSCAR that avogadro can offer is > fractional format, therefore I have to convert fractional format to POSCAR > format. Open Babel and Avogadro will read POSCAR files directly. Also supported include CIF, the free-form fractional, and a variety of other f

[Open Babel] How to convert fractional format to POSCAR

Dear all, May anyone tell me how to convert the fractional format to vasp POSCAR format? What I am trying to do is to build supercells using avogadro for vasp calculation. But seems that the most matching format of POSCAR that avogadro can offer is fractional format, therefore I have to convert

[Open Babel] How to convert fractional format to POSCAR?

Dear all, May anyone tell me how to convert the fractional format to vasp POSCAR format? What I am trying to do is to build supercells using avogadro for vasp calculation. But seems that the most matching format of POSCAR that avogadro can offer is fractional format, therefore I have to convert f

Re: [Open Babel] How to convert smiles code into adjacency list format

well got that allrdy, and deleted my post, but you somehow still saw it. They got a javascript called mol2adjstlst -- View this message in context: http://forums.openbabel.org/Re-How-to-convert-smiles-code-into-adjacency-list-format-tp4261731p4261845.html Sent from the General discussion maili

Re: [Open Babel] How to convert smiles code into adjacency list format

> i will need to have a format suitable for RMG (reaction mechanism > generator). > The format that RMG needs looks like that: I think you'll need to ask the RMG folks how they input data. While I know they use Open Babel, there is no "RMG format" in Open Babel. Best regards, -Geoff ---

[Open Babel] How to convert smiles code into adjacency list format

Hey Guys, i will need to have a format suitable for RMG (reaction mechanism generator). The format that RMG needs looks like that: C2H6 (mol/cm3) 1.0 1 C 0 {2,S} 2 C 0 {1,S} I have no idea how this one is called. Hope you can help me. Best -- View this message in context: http://forums.op

Re: [Open Babel] how to convert fingerprint into a 01 string

On 01/06/2010 13:25, bxiong wrote: > Dear all: > I want to calculate the fingerprint of a mol using the default FP2 > algorithm and output it as a string contains only 0 (means not set) or 1 > (means set on). through cehck the c++ source code, I get lost in those > functions. And could not find a f

Re: [Open Babel] how to convert fingerprint into a 01 string

Hi Bing, import pybel mol = pybel.readstring("smi", "CC(=O)Cl") print mol.calcfp("FP2").bits # [18, 220, 329, 330, 624, 671] So 6 bits are set. Bit number 18, 220, etc. Hopefully you can figure out the rest. Look at the Pybel code if you're interested on how this was done. - Noel On 1 June 2010

[Open Babel] how to convert fingerprint into a 01 string

Dear all: I want to calculate the fingerprint of a mol using the default FP2 algorithm and output it as a string contains only 0 (means not set) or 1 (means set on). through cehck the c++ source code, I get lost in those functions. And could not find a function to convert folded fingerprint to