Re: [Open Babel] Fwd: C++ / segfault / "open file" change?

d244948450ae >>> >>> improves this to only 3,866 molecules not being successfully roundtripped. >>> Unfortunately, deleting that code also means the pyridinium cation no >>> longer works, which has made me not want to remove it, but instead try to >>> f

Re: [Open Babel] Fwd: C++ / segfault / "open file" change?

nium cation no longer > works, which has made me not want to remove it, but instead try to find a fix > that solves both this and the bug the code meant to fix. > > -David > > > > >> On Fri, Jul 4, 2014 at 5:44 AM, Paolo Tosco wrote: >> Dear Pascal, >>

Re: [Open Babel] Fwd: C++ / segfault / "open file" change?

2014-05-09 10:51 GMT+02:00 Subject: Re: [Open Babel] C++ / segfault / "open file" change? To: babel <mailto:openbabel-discuss@lists.sourceforge.net>> Hi, Well, I got a little further. Now, it's working with version 2.3.1, but not 2.3.2 and 2.3.90. It seems somehow r

Re: [Open Babel] REAL FIX: Atom charge lost in 2.3.x SDF-to-SMILES conversion

e a nice day, p. -- ====== Paolo Tosco, Ph.D.Phone: +39 011 6707680 Department of Drug ScienceFax: +39 011 6707687 and TechnologyMob: +39 348 5537206 Via Pietro Giuria, 9 10125 Torino, Italy http://open3da

Re: [Open Babel] REAL FIX: Atom charge lost in 2.3.x SDF-to-SMILES conversion

y(to, sto.c_str()); return(rval); } My only worry is that the (char *)to parameter passed in has to be long enough to hold the (char*)from parameter. I assume it is. Craig On Thu, May 17, 2012 at 4:06 PM, Paolo Tosco <mailto:paolo.to...@unito.it>> wrote: Actually that sizeof in

[Open Babel] REAL FIX: Atom charge lost in 2.3.x SDF-to-SMILES conversion

tting _type[OBATOM_TYPE_LEN] in OBAtom and replacing sizeof(to) with OBATOM_TYPE_LEN in bool OBTypeTable::Translate(char *to, const char *from). A new patch is attached. Cheers, p. -- == Paolo Tosco, Ph.D.Phone: +39 011 67

[Open Babel] SOLVED: Atom charge lost in 2.3.x SDF-to-SMILES conversion

and, most importantly, patches atom.h. Cheers, p. -- ====== Paolo Tosco, Ph.D.Phone: +39 011 6707680 Department of Drug ScienceFax: +39 011 6707687 and TechnologyMob: +39 348 5537206 Via Pietro Giuri

Re: [Open Babel] Atom charge lost in 2.3.x SDF-to-SMILES conversion

7;t resolve my > issue. OBForceField only seems to be called if I use the --gen3D option. > > Best regards, > Craig > > On Thu, May 17, 2012 at 3:03 AM, Paolo Tosco mailto:paolo.to...@unito.it&

Re: [Open Babel] Atom charge lost in 2.3.x SDF-to-SMILES conversion

ons that you patched are never called at all during the >> SDF-to-SMILES conversion process, so the patch doesn't resolve my >> issue. OBForceField only seems to be called if I use the --gen3D option. >> >> Best regards, >> Craig >> >> On Thu, May 17,

Re: [Open Babel] Atom charge lost in 2.3.x SDF-to-SMILES conversion

.com/jaw/sfrnl04242012/114/50122263/ ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- == Paolo Tos

Re: [Open Babel] What about adding AddNonPolarH, DelPolarH, DelNonPolarH?

h but if you can address this issue I'm sure we can accept it. Thanks, Tim -- ====== Paolo Tosco, Ph.D.Phone: +39 011 6707680 Department of Drug ScienceFax: +39 011 6707687 and TechnologyM

[Open Babel] What about adding AddNonPolarH, DelPolarH, DelNonPolarH?

en.patch Cheers, Paolo -- ====== Paolo Tosco, Ph.D.Phone: +39 011 6707680 Department of Drug ScienceFax: +39 011 6707687 and TechnologyMob: +39 348 5537206 Via Pietro Giuria, 9 10125 Torino, Italy http://open3dali

Re: [Open Babel] Conversion mol2/sdf --> smi : generate [2H]

lop and > publish your website. http://p.sf.net/sfu/ms-webmatrix-sf > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > -- ==

[Open Babel] Small regression?

t;D" in output1.txt), hence the inability to assign correct MMFF types. Thanks, bye Paolo -- ====== Paolo Tosco, Ph.D.Phone: +39 011 6707680 Department of Drug ScienceFax: +39 011 6707687 and Technology

[Open Babel] Small regression?

t;D" in output1.txt), hence the inability to assign correct MMFF types. Thanks, bye Paolo -- ====== Paolo Tosco, Ph.D.Phone: +39 011 6707680 Department of Drug ScienceFax: +39 011 6707687 and Technology

[Open Babel] One more MMFF94-related patch

of charges (e.g. because a pdb was imported), Cu(II) and Fe(III) are assigned by default Thanks once again for all your work and collaboration. Cheers, Paolo -- Paolo Tosco, Ph.D. Phone: +39 011 6707680

[Open Babel] more MMFF94 bug fixes

-- Paolo Tosco, Ph.D. Phone: +39 011 6707680 Dipartimento di ScienzaFax: +39 011 6707687 e Tecnologia del Farmaco Mob: +39 348 5537206 Via Pietro Giuria, 9 E-mail: paolo.to...@unito.it I-10125 Torino Italy

[Open Babel] MMFF94 type 48 and OpenBabel

;BOSum() >= 2) { oxygenCount = sulphurCount = 0; FOR_NBORS_OF_ATOM (nbr, atom) { -- ==== Paolo Tosco, Ph.D. Phone: +39 011 6707680 Dipartimento di ScienzaFax: +39 011 6707687 e T

[Open Babel] pyridinium and MMFF94

nitrogen), while all formal charges are set to zero. On the contrary, correct atom typing is observed for pyridine. Best regards, Paolo Tosco -- Paolo Tosco, Ph.D. Phone: +39 011 6707680 Dipartimento di Scienza