On 12/15/11 10:03 AM, David Lonie wrote:
> On Thu, Dec 15, 2011 at 12:48 PM, David Lonie wrote:
>> This seems like something that someone may have encountered before, so
>> I figured I'd ask before rolling my own solution/attempting to patch
>> the cml reader/writer.
>
> small update:
> After skim
On 11/15/11 8:22 AM, Geoff Hutchison wrote:
> Well, I'm happy to moderate less frequently. But there's a big problem
> with step (b). The only way I can think of to highlight the moderation
> process is by a reply back to a non-member posting to the list. The
> downside is that it confirms the l
On 11/10/11 1:39 PM, Chris Morley wrote:
> On 10/11/2011 17:40, Igor Filippov [Contr] wrote:
>>
>>> The confusion caused by too much choice and the deficiencies in all of
>>> the above mean that MolCore API (the proposed re-writing of the central
>>> part of the toolkit) deserves better. I am pushi
On 10/18/11 3:30 PM, My Th wrote:
> O , 2011-10-18 22:40 +0100, Chris Morley rakstīja:
>> On 18/10/2011 20:18, My Th wrote:
>>> Hi!
>>>
>>> I have problems with your version of the patch. I'm using Gentoo Linux
>>> with gcc 4.6.1.
>>>
>>> Running the test program I get this:
>>> Try finding a forc
On 8/17/11 4:16 AM, Noel O'Boyle wrote:
> Hi all,
>
> Would it break the API to add another value for the enum
> OBStereo::Winding? Current values are Clockwise and AntiClockwise: I'd
> like to add Unknown.
>
> The reason is that people seem to distinguish between unspecified
> chirality, and unkno
I subscribe to "A Word A Day" (http://wordsmith.org/words/today.html), and
today's word is "obtest". When I saw the daily email's subject line, I was
expecting it to be from this group.
Cheers,
Craig
--
WORD OF THE DAY: obtest
PRONUNCIATION:
(ob-TEST)
MEANING:
verb tr
This isn't a bug. "Si" isn't a legal SMILES string. Any element not in the
"organic subset" of C, N, O, P, S, B and the halogens must be inside brackets,
like your second example. See the SMILES specification here:
http://opensmiles.org/spec/open-smiles-3-input.html#3.1.5
Cheers,
Craig
I'm finally getting a bit of time to migrate forward to OpenBabel 2.3.0.
Question 1: I want to compile the stable 2.3.0 code, but from SVN (not the .tar
download). It looks like the right revision number is somewhere around 4265.
Is that close enough?
Question 2: Are there significant improve
On 1/21/11 7:47 AM, Geoffrey Hutchison wrote:
>> Would it be useful to pull together a list of papers that cite or use
>> Open Babel?
>
> I used a Windows program "Publish or Perish" to do this using Google Scholar
> (http://www.harzing.com/pop.htm) It gave 400 papers for Open Babel with a
> tota
On 12/21/10 1:55 PM, erapp wrote:
> All,
>
> I have a question about using OpenBabel to fragment a molecule. Is there
> any way to fragment a given molecule such that detailed information is
> provided about the given fragment (i.e. all bonds for each atom in addition
> to the other atoms in the f
On 10/28/10 4:38 AM, Noel O'Boyle wrote:
> Geoff,
>
> Well done on yet another great release.
>
> I think I speak on behalf of everyone when I say thanks to you for all
> your work pulling everything together, polishing it up and getting it
> out there.
Hear hear!
Craig
>
> - Noel
>
> --
On 10/19/10 9:58 PM, Geoffrey Hutchison wrote:
>> and there's a comment from ghutchis last year saying he should have some
>> code that does this fairly soon, so I guess this question is directed at
>> Geoff: Is this something that's stayed out because it's low priority or
>> because it turns out t
On 10/19/10 2:20 AM, Fred Ludlow wrote:
> One of the things I'd like to be able to do is component-level grouping,
> which the SMARTS matcher currently doesn't do (e.g. "[N].[O]"). However, the
> relevant entry on the bug tracker is here:
> http://sourceforge.net/tracker/index.php?func=detail&aid
working now.
Craig
>
> After I set up these variables I got 100% "pass" result.
> It would be nice if this information was printed out at the end of
> "make" run.
>
> Hope this helps,
> Igor
>
> On Mon, 2010-10-18 at 13:40 -0400, Craig A. James wrot
Hmmm... "make test" didn't do too well. I suspect there's some simple linking
problem, maybe a wrong library or something. The complete logfile is attached. It looks
to me like all the failures are from a single problem related to memory corruption.
make test >test.log 2>&1 &
$ uname -a
On 10/18/10 8:54 AM, Noel O'Boyle wrote:
> Hi all,
>
> Following some problems getting agreement with the InChI DLL as
> described at
> http://baoilleach.blogspot.com/2010/10/measuring-information-loss-in-file_07.html
> (specifally the CID15550 example), I've rewritten the handling of
> cis/trans
Can someone give me a quick tutorial or point me to documentation on how to run
the entire test set? "make test" doesn't seem to do anything, and the shell
scripts in the test directory don't seem to do the trick.
Thanks,
Craig
--
On 10/15/10 1:56 PM, Geoffrey Hutchison wrote:
> I have uploaded a source-code only version of the 2.3.0 release candidate 1.
> http://sourceforge.net/projects/openbabel/files/openbabel-snapshots/2010-10-15/openbabel-2.3.0rc1-20101015-r4206.tar.gz/download
>
> Please give this a try and see if ther
On 10/14/10 6:43 AM, Tim Vandermeersch wrote:
> On Wed, Oct 13, 2010 at 8:58 PM, Geoffrey Hutchison
> wrote:
>>> 3429680: [Li+251] 24639246
>>> 3429701: [ClH+276] 24639289
>>> 3429702: [n+251]1(C)c1 24639291
I'd be happy if these were just tossed out. They're obviously not valid, and
a
On 10/14/10 5:32 AM, Steffen Neumann wrote:
> Hi
>
> On Thu, 2010-10-14 at 11:56 +0100, Noel O'Boyle wrote:
>> memcpy((char*)origCoords,(char*)_mol.GetCoordinates(),sizeof(double)*_ncoords);
>>
>> However, both origCorrds and _mol.GetCoordinates are (double*) not
>> (char*). Is this not an error?
>
On 10/11/10 11:31 AM, Tim Vandermeersch wrote:
> On Mon, Oct 11, 2010 at 7:20 PM, Craig James
> wrote:
>> If we start normalizing metallocenes, why not normalize nitro,
>> phosphate and sulfonates?
>
> To conclude, I totally agree with all of this but it is beyond the
> scope of OB 2.3.
Right,
On 10/11/10 8:52 AM, Tim Vandermeersch wrote:
> I still need to figure out how to deal with metallocene compounds
> where there are 8 or more neighbors with the same symmetry class. I
> already have a hack to handle ferrocene but we might want to extend
> this. IIRC, this might also help kekulizati
Here are the results of another 1.2 million SMILES "shuffle" tests. Each
shuffle is 20 randomized versions of one SMILES (so 24 million
canonicalizations total).
Most, maybe all of these are repeates of problems we've already encountered,
but I thought I'd include them for completeness. I thi
On 10/8/10 4:22 PM, Geoffrey Hutchison wrote:
>> c12=c3c(c4c(c5c(c1csc2)csc5)csc4)csc35860502
>> C12C(C3C(C4C(C5C1CSC5)CSC4)CSC3)CSC2 5860502
>
>> c12=c(nn2)ssnc1S 6137697
>> c12c(nn2)ssnc1S 6137697
>
> I've been looking at very similar SMILES for the kekulize code. As a general
>
Using the latest code from this morning (-r4157), I ran four processes all day
long for a total of about 280,000 SMILES. I found 12 more interesting cases
where canonicalization failed.
Let me say again that this is very impressive, a huge reduction in problem
cases!
These molecules seem to f
On 10/8/10 10:37 AM, Geoffrey Hutchison wrote:
> On Oct 8, 2010, at 12:49 PM, Craig A. James wrote:
>> So it's not creating a link for libopenbabel.so.4.0.0.
>
> I guess I'd try "make clean; make -j3" or similar. Sometimes CMake can get
> itself a bit co
On 10/8/10 9:46 AM, Craig A. James wrote:
> Hi,
>
> Where should I look to fix this? This seems to be new -- I was able to
> compile before the update this morning.
Here's one more detail:
$ find . -name 'libopenbabel.so*'
./lib/libopenbabel.so.4
./lib/libopenbabel
Hi,
Where should I look to fix this? This seems to be new -- I was able to compile
before the update this morning.
Thanks,
Craig
$ svn status -u
Status against revision: 4157
$ make; make install
...
CMake Error at src/cmake_install.cmake:41 (FILE):
file INSTALL cannot find
"/home/e
Hi,
Where should I look to fix this?
Thanks,
Craig
$ svn status -u
Status against revision: 4157
$ make; make install
...
CMake Error at src/cmake_install.cmake:41 (FILE):
file INSTALL cannot find
"/home/emi/openbabel-2-3-beta/build/lib/libopenbabel.so.4.0.0".
Call Stack (most recent
On 10/6/10 9:58 AM, Tim Vandermeersch wrote:
>> I was looking through the new canon.cpp code, and it looks like a
>> huge improvement over the original, and the tests we've been
>> running are confirming this. This is a big step forward.
>>
>> But I noticed a rather alarming lack of comments in
Hi Tim,
I was looking through the new canon.cpp code, and it looks like a huge
improvement over the original, and the tests we've been running are confirming
this. This is a big step forward.
But I noticed a rather alarming lack of comments in the new code. There are
some unfinished general
On 10/5/10 10:56 AM, Geoffrey Hutchison wrote:
> That's good! Maybe we should let you generate a file of errors
>over the next day or two(?), post it, and then make every effort
> to fix them?
The truth is, just a dozen bugs out of over a million structures is quite
remarkable. Naturally we all
On 10/5/10 10:56 AM, Geoffrey Hutchison wrote:
>
> On Oct 5, 2010, at 1:47 PM, Craig A. James wrote:
>
> That's good! Maybe we should let you generate a file of errors
> over the next day or two(?), post it, and then make every
> effort to fix them?
I had to kill everythi
On 10/5/10 10:50 AM, Craig A. James wrote:
> Here's another problem case. When I came in this morning, the babel process
> that was trying to canonicalize this was using 26GB of memory! (I should set
> some process limits!)
>
> http://www.emolecules.com/image?db=549&id
Here's another problem case. When I came in this morning, the babel process
that was trying to canonicalize this was using 26GB of memory! (I should set
some process limits!)
http://www.emolecules.com/image?db=549&id=716941&width=500&height=500
C12[Pr]3456789%10%11%12%13(C1C3C%13C24)(C1C9C%10C
On 10/5/10 2:21 AM, Chris Morley wrote:
> On 05/10/2010 01:40, Craig A. James wrote:
>> Here's a POB (plain old bug) in the latest source code:
>>
>> echo "[Cl+]" | babel -i smi -o can
>> [ClH+]
>
> This is not what I get with the lat
On 10/5/10 1:06 AM, Noel O'Boyle wrote:
> On 5 October 2010 02:58, Geoffrey Hutchison wrote:
>>
>> On Oct 4, 2010, at 5:15 PM, Craig A. James wrote:
>>
>>> Something has gone badly wrong with the canonicalizer -- these are awful
>>> SMILES. The e
Here's another molecule with two different canonical SMILES. In this case, the
molecule is very simple:
http://www.emolecules.com/image?db=549&id=513261&width=500&height=500
[C@@H]([...@h](CO)O)([C@@H](CO)O)O
[...@h]([C@@H](CO)O)([...@h](CO)O)O
It's another case with that's symmetrica
Here's a POB (plain old bug) in the latest source code:
echo "[Cl+]" | babel -i smi -o can
[ClH+]
The SMILES specification says that no matter what is inside of the brackets for
an atom, it can't be changed. Hydrogens and charge in particular, no matter
whether they make sense or not, mu
Here's another problem case:
[Cl].[Cl-].[Cl+]
There are six ways to write this SMILES, and the canonicalizer doesn't
distinguish them:
[Cl-].Cl.[Cl+]
Cl.[Cl-].[Cl+]
[Cl-].[Cl+].Cl
Cl.[Cl+].[Cl-]
[Cl+].[Cl-].Cl
[Cl+].Cl.[Cl-]
If you add an
On 10/4/10 2:10 PM, Noel O'Boyle wrote:
> Hello all,
>
> Back on the 19/03/2009 I emailed to this list with the subject
> "Canonical SMILES performance" about a test set of around 18000
> PubChem 3D structures. I did the following analysis:
> (1) sdf -> can
> (2) sdf -> smi -> can
> (3) diff of
I was going to run some tests on the latest OpenBabel code, but before I got
started I ran into a fairly serious problem:
echo "Oc1c1" | babel -i smi -o can
c1(c1)O
echo "Oc1c1O" | babel -i smi -o can
c1(c(1)O)O
Something has gone badly wrong with the canonicalizer -- these are
Hi Noel,
> Can you have a look at this structure? OB says that there is only a
> single cis/trans stereogenic unit...is this correct?
I didn't see a reply to this, so I checked ... there is only a single cis/trans
unit in this molecule. The other double bond has two cyclohexanes with
identical
On 9/27/10 4:24 AM, Noel O'Boyle wrote:
> To summarise, I need to make a decision on how to handle cis/trans
> stereochem at ring closures in SMILES and I think that Daylight are
> wrong.
>
> Daylight has the following: (a) C/C=C/1NC1 is the same as (b)
> C/C=C1NC\1 and (c) C/C=C/1NC\1
>
> The cons
On 9/22/10 1:33 PM, Geoffrey Hutchison wrote:
>> Is there any harm in printing SP (and the other point groups) by default?
>> Are
>> we worried that it will break other SMILES parsers?
>
> That would be my worry. That we'd print SP or TB or whatever, and users would
> come back and complain it'
On 9/22/10 8:27 AM, Geoffrey Hutchison wrote:
> IMHO, since very little software handles SP stereo information, it should
> be enabled as an option to output with SMILES or canonical SMILES.
Is there any harm in printing SP (and the other point groups) by default? Are
we worried that it will br
On 8/23/10 1:17 PM, Noel O'Boyle wrote:
>> The function's name doesn't seem right. Aren't wedge and hash 2D
>> concepts, not 0D, even if coordinates do not appear in the function?
>> It's from 0D to 2D?
>
> Actually, to complicate it further, wedge and hash are 3D concepts.
> How about TetStereoToW
On 7/30/10 10:06 AM, Geoffrey Hutchison wrote:
> Hans De Winter and Silicos whipped up a 2-page quick reference PDF intended
> to be printed double-sided on one sheet of paper. They wish to distribute it
> at EuroQSAR, and I've suggested distributing it at the ACS Boston meeting.
>
> Please let u
A while back I had a problem with OpenBabel shared libraries, but I can't find
the discussion in the archives.
A quick summary: There was a table define in a .cpp file (like the elements
table?) that had no references to it in OpenBabel, so the linker wasn't
including it in the .so file, result
On 7/5/10 8:40 AM, Geoffrey Hutchison wrote:
>
> On Jul 5, 2010, at 11:39 AM, Craig A. James wrote:
>
>> Do you mean it's now -gen2D? That's not right. The defacto standard for
>> UNIX/Linux is...
>
> No, no. He means that the documentation somehow dro
On 7/2/10 4:44 AM, Tim Vandermeersch wrote:
> Hi,
>
> I have put the "old" aromaticity algorithm back since unit tests were
> failing. I tried to debug the problem but didn't get far. When Craig
> has time to look at this, I can merge this again.
>
> Although electron counting isn't the problem wit
On 7/4/10 1:45 PM, Chris Morley wrote:
> On 04/07/2010 21:11, Noel O'Boyle wrote:
>> 2010/7/4 Konstantin Tokarev:
>>>
>>>
>>> 04.07.10, 23:37, "Noel O'Boyle":
>>>
On 30 June 2010 22:49, Chris Morley wrote:
> On 30/06/2010 12:24, Noel O'Boyle wrote:
>> On 30 June 2010 12:16
On 7/2/10 4:44 AM, Tim Vandermeersch wrote:
> Hi,
>
> I have put the "old" aromaticity algorithm back since unit tests were
> failing. I tried to debug the problem but didn't get far. When Craig
> has time to look at this, I can merge this again.
>
> Although electron counting isn't the problem wit
On 6/23/10 9:44 AM, Tim Vandermeersch wrote:
>> Sorry to keep nagging, but the remaining test failure seems to be real
>> bug: http://my.cdash.org/testDetails.php?test=2416695&build=76838
>>
>> It says that babel -ismi -osmi
>> '[nH]1c2c2c2c3C(=O)NCc3c3c4c4[nH]c3c12' gives
>> '[nH]1c2c2
On 6/21/10 2:49 PM, Tim Vandermeersch wrote:
>> The LSSR algorithm is simple:
>>
>> for S in (3, 4, 5, 6, ...)
>> find all rings of size S, add to LSSR
>> if all cyclic atoms and bonds are included in at
>> least one ring in the LSSR, quit
>
> This would give 10 rings for cubane wi
On 6/21/10 6:32 PM, Tim Vandermeersch wrote:
> On Tue, Jun 22, 2010 at 3:17 AM, Geoffrey Hutchison
> wrote:
>>> The changes are in svn trunk. The current test set (aromatics.smi,
>>> attype.00.smi& nci.smi) is not good though.
>>
>> By that, I assume you mean that the current test set is not suf
BTW, I sent Geoff some new kekulize.cpp code this morning. If anyone's
interested, here are the comments that describe how it works. Comments
welcome... Note that "SSSR" could/should be replaced by "LSSR" since LSSR is
easier to compute for these very large molecules. We've been using the ne
On 6/21/10 1:21 PM, Tim Vandermeersch wrote:
> Craig: Do you have test cases for aromaticity?
No, there's nothing that I know of that exercises all of the cases that should
be tested.
Craig
--
ThinkGeek and WIRED's Gee
On 6/21/10 1:21 PM, Tim Vandermeersch wrote:
>> For most "ordinary" molecules, the LSSR is the same as the SSSR. The LSSR
>> and
>> SSSR only differ with "cage" structures, where the rings themselves form
>> rings,
>> i.e. when there exists a set of R rings that "covers" all atoms, but R is
>
The recent discussion of SSSR bugs prompted me to dig back through my emails to
one I wrote on 20 November 2007 to the BlueObelisk mailing list. Here it is in
its entirety.
Craig
Andrew suggested an algorithmic description of aromaticity. I think this is a
On 6/15/10 10:12 AM, Geoffrey Hutchison wrote:
> I think there are two classes of documentation:
> 1) Developer-level docs (e.g., tutorials, API, etc.).
>
> 2) User-level tutorials.
Right, I agree with Geoff. My comments about in-line documentation are only
applicable to API and class descriptio
On 6/8/10 9:59 AM, Tim Vandermeersch wrote:
> Andrew has raised some important issues with outdated docs etc. I
> think we should turn all wiki pages into in-source documentation
> (using doxygen for example) that is updated nightly. The current wiki
> is just not suited for maintainability IMHO, t
Noel O'Boyle wrote:
> Does anyone have any ideas about how to stop inchi complaining about
> undefined stereocenters? We know it's undefined - we don't need to
> hear all about it.
>
pybel.readstring("smi", "FC(Br)(Cl)I").write("inchi")
> ==
> *** Open Babel Warnin
Craig A. James wrote:
> Chris Morley wrote:
>> In the V2000 MOL file interpreter in the trunk code (potentially for
>> v2.3.0), numbers need to be right-justified in their fields. So the
>> first molecule in the drugbank dataset ( http://www.drugbank.ca/ )
>> fai
Chris Morley wrote:
> In the V2000 MOL file interpreter in the trunk code (potentially for
> v2.3.0), numbers need to be right-justified in their fields. So the
> first molecule in the drugbank dataset ( http://www.drugbank.ca/ )
> fails silently with 0 atoms, 0 bonds. I cannot find a justificat
Andreas Maunz wrote:
> can't figure out what's wrong with this SMARTS:
> F-c1:c:c2:c(:c(:c:n:c:2:c:c:1-N1-C-C-N-C-C-1)-C(-O)=O)=O
There's nothing wrong with it. There's a bug in the SMARTS parser. This is
the same thing, which also gives an error:
Fc1cc2c(c(cnc2cc:1N1CCNCC1)C(O)=O)=O
If
Andrew Dalke wrote:
> On Dec 14, 2009, at 9:28 PM, Geoffrey Hutchison wrote:
>> Craig, do you have another solution? Is there a wild-card or dummy atom for
>> the canonical SMILES?
>
> I haven't been tracking this, so just a reflex action pointing out "*".
As Andrew points out, "*" is a possible
Noel O'Boyle wrote:
> Actually just thought of a way to create canonical SMARTS string.
> Craig, do you have code for generating all possible SMILES strings for
> a particular molecule? If so, then I could do this for each fragment,
> do string replacement to create the corresponding SMARTS, and pi
Igor Filippov wrote:
> I'm not sure what everybody means - when I search for "OpenBabel" the
> first link that comes up is openbabel.org - like always.
> What exactly is the problem?
Go to google.com, and BEFORE you search, click on "Search Settings" at the top.
Scroll down, find the "Safe Search
Geoffrey Hutchison wrote:
>> Now, it's filtered from the search list with "strict search" but not
>> "moderate".
>
> That's truly weird. We should do a careful search through the wiki to look
> for spam links. That's the only thing I can imagine.
I wonder if there are words that we use in chemis
Noel O'Boyle wrote:
> Uncle Al claims no possible SMILES for his chiralanes:
>
> http://www.coronene.com/blog/?p=1128#comment-8794
>
> Perhaps a worthy challenge for our new stereocode
I'm not sure what the challenge is. The molecule plainly has a distinct mirror
image. Ignoring hydrogens
Tim Vandermeersch wrote:
> Hi Craig,
> ...
> The new stereo code doesn't need these extra hydrogens. The added
> hydrogens you are seeing are probably added in
> OBMol2Cansmi::AddHydrogenToChiralCenters (smilesformat.cpp)
Huh. My own code. I assumed this was a new bug so I guessed it was in the
Noel O'Boyle wrote:
> 2009/11/18 Craig A. James :
>> Tim,
>>
>> I've run into a problem: OpenBabel add a hydrogen to any potentially-chiral
>> carbon that doesn't have four bonds, for example, when it parses "ClC(Br)I"
>> (but not "
Tim,
I've run into a problem: OpenBabel add a hydrogen to any potentially-chiral
carbon that doesn't have four bonds, for example, when it parses "ClC(Br)I"
(but not "ClC(Cl)Br" since it can't be chiral). I'm pretty sure it's the new
stereo code that's doing this, but I haven't dug into it yet
Geoffrey Hutchison wrote:
>> I need certain things fixed, and I have to do it now, using OpenBabel 2. I
>> need a pragmatic, short-term solution. The questions I'm asking are:
>> - Whether there's any interest by others in the work I'll be doing
>> - Whether the current aromaticity detection i
Andrew Dalke wrote:
> On Oct 29, 2009, at 7:49 PM, Chris Swain wrote:
>> The SMILES definition of aromaticity would seem to be an excellent
>> solution.
>
> Except when it isn't. That's why different people and different
> software have different aromaticity models.
>
> I wrote some about this
o an OpenSMARTS specification, I think the "D" should be
highly discouraged. But that's a topic for another day...
Craig
Andrew Dalke wrote:
> On Oct 29, 2009, at 6:33 PM, Craig A. James wrote:
>> 1. The "D" or "degree" in SMARTS
>>
>> [#
Geoffrey Hutchison wrote:
>
> On Oct 29, 2009, at 2:40 PM, Craig A. James wrote:
>
>> This is a good topic for OpenBabel 3. There really is no such thing
>> as an "aromatic atom". Aromaticity is only a property of bonds and
>> ring systems. It might
In fact, now that I think about it more...
Craig A. James wrote:
> I have just a small amount more work to do before kekule.cpp is ready to
> check back in. It has to do with molecules like this:
> c1ccc2c(c1)c132c13
>
> http://depict.emolecules.com/cgi-bin/mymol/de
Geoffrey Hutchison wrote:
>
> On Oct 23, 2009, at 11:03 AM, Craig A. James wrote:
>
>> I've now got a new version of expand_kekulize() in kekule.cpp, it
>> solves a fullerene correctly in a few milliseconds. There's still a
>> lot of work to do on the det
This is just a quick summary of the technical problems I've discovered. I'm
putting them here so that if I've overlooked something, or anyone has insights
that I've missed, we can discuss them.
1. The "D" or "degree" in SMARTS
[#6D2] is supposed to mean a a carbon atom with two bonds. However
Geoff and I have had a short private conversation about aromaticity, and I had
some ideas that are better expressed here on the discussion board.
Currently, OpenBabel's aromaticity (typer.cpp) is pretty well broken. It seems
to accept most correct structures, ordinary stuff like benzenes and py
Tim and Geoff,
Thanks for the pointer, it worked.
Tim Vandermeersch wrote:
>>
>>int start_idx = ring->_path[0];
>>OBAtom *start_atom = GetAtomById(start_idx);
>
> GetAtomById is meant to be used together with the unique ids (GetId),
> not indexes (1...N). These unique ids initially go fr
I'm baffled by the following, and can only assume I have some misunderstanding
of how atom Idx's are stored.
I asked for an SSSR using GetSSSR(), then take the first ring from the SSSR.
Then I wanted something simple: one atom from that ring. So I take the first
IDX from ring->_path, like thi
Noel O'Boyle wrote:
> I'm trying to profile an optimization using MMFF94 (obminimize) using
> OB22x and gprof as follows:
I'll second Geoff's recommendation of valgrind. It works on unmodified code,
and runs it in a virtual machine that measures EVERY instruction that's
executed. No sampling,
Tim Vandermeersch wrote:
> On Tue, Sep 29, 2009 at 10:50 PM, Noel O'Boyle wrote:
>> Nice work. http://timvdm.blogspot.com/2009/09/automorphism-group-bliss.html
>>
>> Does this mean you've solved the problem?
>
> Yes, but to continue towards correct canonical codes, we still need to
> do some matr
86 matches
Mail list logo
