[Open Babel] help in using molprint2D

Hi everybody, I'm running Open Babel 2.3.1 in GNU/LinuxDebian OS. I'm interested in using molprint2D fingerprints. As described in openbabel manual the following command should gives the list of molprint2D fingerprint for each molecule: /obabel -ismi test.smi -ompd/ As described in manual the fo

Re: [Open Babel] erroneous structures when the option "-p" is activated

Hey Douglas, thank you for your help and for the information provided. I'll take this into account. I hope somebody could fix this bug soon. The '-p' option seems so useful to me. Cheers! -- View this message in context: http://forums.openbabel.org/erroneous-structures-when-the-option-p-is-act

[Open Babel] erroneous structures when the option "-p" is activated

Hi guys! I'm using Open Babel 2.3.1 in a GNU/Linux (2.6.32-5-amd64) machine with debian OS. openbabel generate erroneous structures when the option "-p" to add hydrogens appropriate for a certain pH is activated and the output is SMILES or canonical SMILES. An example is provided with 3 files: http

Re: [Open Babel] obabel crash while removing salt (removing counter-ions)

Hi Chris, Thank you so much for your fast reply and solution. Indeed the problematic molecule can be bypassed as you suggested! -- View this message in context: http://forums.openbabel.org/obabel-crash-while-removing-salt-removing-counter-ions-tp4561055p4561399.html Sent from the General disc

[Open Babel] obabel crash while removing salt (removing counter-ions)

Hi all, I'm using Open Babel 2.3.1 running on a GNU/Linux OS. I used to work with molecules DB in SMILES format. Normally with obabel you can remove counter-ions (with the flag '-r', which remove all but the largest contiguous fragment) with the following command: /obabel -ismi file.smi -r -osmi

Re: [Open Babel] Calculating partial charges with openbabel of a positively charged molecule

Hi Christos, Please, can you tell us if you're using the tag "--partialcharge gasteiger" or not, in your calculation? I was having the same problem with many charged molecules. I noticed that if you do NOT use that tag, obabel correctly calculate the partial charges. For example if you're calcula

Re: [Open Babel] Is there any other way to generate unique SMILES ?

I'm agree to what is said above: calculating molecular similarity basing on SMILES alignment is not a good idea. A so better alternative, already explored by several researcher is the "lingo method", which can accurately calculate molecular similarity with SMILES, but it's not based on an alignment

[Open Babel] Wrong gasteiger atomic partial charges. BUG?

Hi guys, I've a problem using the last Open Babel 2.3.1 in an GNU/Linux ubuntu OS. When I convert an sdf file to a mol2 (or whatever other format) using the "--partialcharge gasteiger" option, I obtain molecules with wrong partial charges. case A) obabel -isdf mols_charged.sdf -omol2 --partialcha

Re: [Open Babel] how 2 calculate partial charges indipendently from those of input file?

Hi Geoff, thank you for your quick reply! Maybe I didn't express me very well, I'll try to explain. If I pass to obabel a file where there are no charges, it correctly generate gasteiger charges on the output. Anyway if I pass to babel a file with some dummy charges, where let say that the sum of t

[Open Babel] how 2 calculate partial charges indipendently from those of input file?

Hi guys! I want to add a specific type of partial atomic charge (e.g gasteiger) to a mol2 file without taking into account the partial charges already present in the input file. If I use openbabel with the following command: obabel input.mol2 --partialcharge gasteiger -O output.mol2 I obtain that

Re: [Open Babel] very strange canonical SMILES (BUG? or normal behaviour)

OK guys, thank you so much for your explanation!!! Now it results clear to me. I asked because I've never seen before an EXPLICIT definition of regio-isomery on a SMILES so I couldn't understand. I was believing that in SMILES the regio-isomery definition was simply following the chemistry cis-tr

[Open Babel] very strange canonical SMILES (BUG? or normal behaviour)

Hi guys! I have the following molecule in smiles format: [O-]S(=O)(=O)c1ccc2NC(=O)\C(=C3/Nc4c4C3=O)c2c1 When I canonize it with openbabel I obtain the following: O=C1Nc2c(/C/1=C\1/Nc3c(C1=O)3)cc(cc2)S(=O)(=O)[O-] The molecule is not very strange and it has just ONE double bound over whic