We can do this kind of work at Scientific Software Solutions Ltd. (
www.scisoftpro.com), especially with C++
Regards,
Evgueni
On 20 March 2011 05:46, Greg Landrum greg.land...@gmail.com wrote:
Dear all,
I was recently asked if there was anyone out there who was able to do
contract
wrote:
Hi Evgueni,
On Thu, Jul 29, 2010 at 9:08 PM, Evgueni Kolossov ekolos...@gmail.com
wrote:
- I am sure I included install in the bjam command line
- I have only
/c/boost/lib/libboost_regex-vc90-mt-1_43.lib
and
/c/boost/lib/libboost_regex-vc90-mt.lib
-and I have not added 1.43
Greg,
I do not understand:
.\bjam.exe toolset=msvc link=shared --with-regex release install
or
.\bjam.exe toolset=msvc link=static --with-regex release install?
Regards,
Evgueni
On 30 July 2010 09:44, Greg Landrum greg.land...@gmail.com wrote:
On Fri, Jul 30, 2010 at 9:55 AM, Evgueni
Ok this way it works...
Regards,
Evgueni
On 30 July 2010 09:52, Greg Landrum greg.land...@gmail.com wrote:
On Fri, Jul 30, 2010 at 10:50 AM, Evgueni Kolossov ekolos...@gmail.com
wrote:
Greg,
I do not understand:
.\bjam.exe toolset=msvc link=shared --with-regex release install
,
On Wed, Jul 28, 2010 at 4:04 PM, Evgueni Kolossov ekolos...@gmail.com
wrote:
I am trying to rebuild RDKit on Windows using boost 1_43 and cannot go
through the configuration stage with CMake:
There's been a lot of activity on this thread (thanks to everyone for
pitching in), and a lot
Tried Run cmake with -DBoost_LIBRARYDIR=whatever
but it still cannot find regex
On 28 July 2010 15:07, Noel O'Boyle baoille...@gmail.com wrote:
On 28 July 2010 15:04, Evgueni Kolossov ekolos...@gmail.com wrote:
Dear Greg,
I am trying to rebuild RDKit on Windows using boost 1_43 and cannot
, at 16:14, Evgueni Kolossov wrote:
Tried Run cmake with -DBoost_LIBRARYDIR=whatever
but it still cannot find regex
On 28 July 2010 15:07, Noel O'Boyle baoille...@gmail.com wrote:
On 28 July 2010 15:04, Evgueni Kolossov ekolos...@gmail.com wrote:
Dear Greg,
I am trying to rebuild RDKit
No, what is this for?
On 28 July 2010 15:31, Peter Schmidtke pschmid...@ub.edu wrote:
Did you ./boostrap boost with regex using :
./bootstrap.sh --prefix=$HOME/pool --libdir=$HOME/pool/lib
--with-libraries=python,regex
?
On 28/07/2010, at 16:28, Evgueni Kolossov wrote:
Yes
:34, Evgueni Kolossov wrote:
No, what is this for?
On 28 July 2010 15:31, Peter Schmidtke pschmid...@ub.edu wrote:
Did you ./boostrap boost with regex using :
./bootstrap.sh --prefix=$HOME/pool --libdir=$HOME/pool/lib
--with-libraries=python,regex
?
On 28/07/2010, at 16:28, Evgueni
Thank you very much
Regards,
Evgueni
On 2 July 2010 07:11, Greg Landrum greg.land...@gmail.com wrote:
Hi Evgueni,
On Fri, Jul 2, 2010 at 8:06 AM, Evgueni Kolossov ekolos...@gmail.com
wrote:
Thank you very much. I understood I need to rebuild again to have all
libraries in one place
Dear Greg,
I was sure bison and flex are part of cygwin installation but cannot find
executables.
Can you suggest anything?
Regards,
Evgueni
On 1 July 2010 13:06, Greg Landrum greg.land...@gmail.com wrote:
On Thu, Jul 1, 2010 at 1:38 PM, Evgueni Kolossov ekolos...@gmail.com
wrote:
Greg
Dear Noel,
Thank you very much - done upgrade anyway and now can find bison and flex
Regards,
Evgueni
On 1 July 2010 13:45, Noel O'Boyle baoille...@gmail.com wrote:
On 1 July 2010 13:43, Evgueni Kolossov ekolos...@gmail.com wrote:
Dear Greg,
I was sure bison and flex are part of cygwin
Hi Greg,
I have decided now to move into latest version and got couple of questions:
- What the latest boost version you can recommend?
- I believe before it was requirement to install some additional boost
libraries. Is it still required or not?
Regards,
Evgueni
--
Dr. Evgueni Kolossov (PhD
projects on VS
2008.
Could you give me some tips about how to add RDKit library to VS 2008
develop projects on it?
Best regards,
Jongyoung Joung
--
Dr. Evgueni Kolossov (PhD)
ekolos...@gmail.com
Scientific Software Solutions Ltd.
www.scisoftpro.com
Tel. +44(0)1628 647 333
Mob. +44(0
Dear Greg,
Thanks for suggestion - I am still on the old version.
It just making it easier...
Regards,
Evgueni
On 19 April 2010 10:39, Greg Landrum greg.land...@gmail.com wrote:
Dear Evgueni,
2010/4/19 Evgueni Kolossov ekolos...@gmail.com:
You need to add to your project:
- Additional
:
Hi Evgueni,
On Wed, Feb 10, 2010 at 11:02 AM, Evgueni Kolossov ekolos...@gmail.com
wrote:
Dear Greg,
I just cannot understand what's going on - please take a look below:
std::string strSmiles = [*];
RDKit::RWMol *fragMol = new RDKit::RWMol();
fragMol = RDKit::SmilesToMol
greg.land...@gmail.com wrote:
Hi Evgueni,
On Thu, Feb 4, 2010 at 5:25 PM, Evgueni Kolossov ekolos...@gmail.com
wrote:
I have a vector RDKit::MOL_SPTR_VECT m_vF.
Vector is populated Ok.
Now i am trying to get mols from this vector:
nCount = 0;
RDKit::ROMol *fMol = new RDKit::ROMol
Hi Greg,
I have a vector RDKit::MOL_SPTR_VECT m_vF.
Vector is populated Ok.
Now i am trying to get mols from this vector:
nCount = 0;
RDKit::ROMol *fMol = new RDKit::ROMol(*m_vF[nCount]);
This will compile OK but will throw an exception on execution in
T * operator- () const
{
),(3,12),(4,13))
[16][5]((0,10),(1,11),(2,12),(3,18),(4,19))
I need actually to get finally for this example:
[1][5]((0,1),(1,2),(2,3),(3,8),(4,7))
[12] [5]((0,9),(1,10),(2,11),(3,12),(4,13))
in all other matches overlap is over 1.
Regards,
Evgueni
2009/12/1 Evgueni Kolossov ekolos
Hi Greg,
I have enclosed 2 files - images for structure and fragment. When using
unsigned int SubstructMatch() I am getting value = 17!!! Looking like
function is not taking in account atom types and flag uniquify is not
working at all - or may be I am missing something? Can you please comment on
Yes, Greg,
I believe that result 17 matches for this fragment does not make any sense
2009/12/1 Greg Landrum greg.land...@gmail.com
Dear Evgueni,
On Tue, Dec 1, 2009 at 10:21 AM, Evgueni Kolossov ekolos...@gmail.com
wrote:
I have enclosed 2 files - images for structure and fragment
-- Forwarded message --
From: Evgueni Kolossov ekolos...@gmail.com
Date: 2009/12/1
Subject: Re: [Rdkit-discuss] SubstructMatch
To: Greg Landrum greg.land...@gmail.com
Fragment: *
Structure: S=C(CC1C1)N1CCC(c2nc[nH]c2)CC1
Code
take bond in account as it is but use match any for dummy atom
Regards,
Evgueni
2009/11/7 Greg Landrum greg.land...@gmail.com
Combining two answers into one:
On Fri, Nov 6, 2009 at 7:59 AM, Evgueni Kolossov ekolos...@gmail.com
wrote:
Hi Greg,
Yes, this is solution I been thinking about
?
Regards,
Evgueni
2009/11/6 Evgueni Kolossov ekolos...@gmail.com
Hi Greg,
Yes, this is solution I been thinking about as well but there is 2
problems:
1. It will slow dawn mapping process which is slow already
2. What atom to use for replacement?
What if I will just remove this atom(s
, Nov 4, 2009 at 7:54 PM, Greg Landrum greg.land...@gmail.com
wrote:
On Wed, Nov 4, 2009 at 3:26 PM, Evgueni Kolossov ekolos...@gmail.com
wrote:
I found that SubstructMatch would not work if query is a fragment (with
*
atoms).
Can you suggest solution for this problem?
That's
Hi Greg,
I got a small problem with the fragments - aromatic cycles coming with all
bonds as double. If I save it into SDF and open SDF than it all Ok.
I believe I saw somewhere fix for this. Can you please point me to the right
place?
Regards,
Evgueni
at 12:06 PM, Evgueni Kolossov ekolos...@gmail.com
wrote:
I got a small problem with the fragments - aromatic cycles coming with
all
bonds as double. If I save it into SDF and open SDF than it all Ok.
I believe I saw somewhere fix for this. Can you please point me to the
right
place?
hmm
Some more fixes
2009/8/13 Greg Landrum greg.land...@gmail.com
Dear Evgueni,
Thanks for the contribution. I am travelling at the moment, but I will
try to find some time review the code over the next few days.
Best Regards,
-greg
attachment: salts.zip
Sorry - forgot that anion in nitro group and perchlorate can be affected -
fixed now.
Regards,
Evgueni
2009/8/13 Evgueni Kolossov ekolos...@gmail.com
Hi Greg,
I have enclosed files for class CSalts which is doing salt stripping.
The main function (StripSalt) taking a few arguments:
- RDKit
Bug found and fixed.
2009/8/13 Evgueni Kolossov ekolos...@gmail.com
Sorry - forgot to fix one more things.
Now it's final.
Regards,
Evgueni
2009/8/13 Evgueni Kolossov ekolos...@gmail.com
Sorry - forgot that anion in nitro group and perchlorate can be affected -
fixed now.
Regards
mol, bool
sanitizeFrags=true, INT_VECT *frags=0) will return the vector of
fragments
as ROMol's?
yes, that is correct.
-greg
--
Dr. Evgueni Kolossov (PhD)
ekolos...@gmail.com
Tel. +44(0)1628 627168
Mob. +44(0)7812070446
need to remove H+ from it.
Any thought about this?
You could loop through the molecule and set the formal charges to
zero. You'll have to be figure out some way to solve the problems this
will cause with nitro groups (and related substructures) though.
-greg
--
Dr. Evgueni Kolossov
() function in ChemTransforms that does the
work, but it needs to be fed with a set of substructure definitions
for the salts. There isn't currently such a thing distributed with the
RDKit.
-greg
--
Dr. Evgueni Kolossov (PhD)
ekolos...@gmail.com
Tel. +44(0)1628 627168
Mob. +44(0)7812070446
Thank you very much
2009/7/21 Greg Landrum greg.land...@gmail.com
On Tue, Jul 21, 2009 at 8:09 AM, Evgueni Kolossovekolos...@gmail.com
wrote:
One more question - is there function to get how many structures is in
mol?
MolOps::getMolFrags()
with a set of substructure definitions
for the salts. There isn't currently such a thing distributed with the
RDKit.
-greg
--
Dr. Evgueni Kolossov (PhD)
ekolos...@gmail.com
Tel. +44(0)1628 627168
Mob. +44(0)7812070446
Hi Greg,
What's the best way to check for duplicate in this smart pointers vector of
fragments when adding a new fragment to the vector?
Regards,
Evgueni
-Original Message-
From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: 26 June 2009 19:45
To: Evgueni Kolossov
Dear Greg,
Can you please explain the usage of atom labels Q, A, and *. I know that *
used in fragments. Where you using Q and A?
Regards,
Evgueni
2009/6/21 Greg Landrum greg.land...@gmail.com
Dear all,
It's getting to be time for the next RDKit release. Yesterday I tagged
the Q2 2009
Hi Greg,
One additional question about this subject:
If we have molecules in both tautomeric forms:'C[N+](=O)([O-])' and
CN(=O)(=O)'
than what we will have after SmilesToMol() and MolToSmiles() (which will
sanitise molecule)?
Regards,
Evgueni
2009/5/25 Greg Landrum greg.land...@gmail.com
to particular record
number. Is it possible with pickle files?
Regards,
Evgueni
2009/4/30 Greg Landrum greg.land...@gmail.com:
There really isn't a maximum. It depends on the number of atoms,
number of bonds, and number of conformers.
On Thu, Apr 30, 2009 at 9:09 PM, Evgueni Kolossov ekolos
Ok Greg,
What if we will try to define the format and start with the record separator
- may be use the same as SDF?
Index file can be created during the writing.
Regards,
Evgueni
2009/5/1 Greg Landrum greg.land...@gmail.com
On Fri, May 1, 2009 at 8:06 AM, Evgueni Kolossov ekolos...@gmail.com
Compounds.sqlt
There is, no doubt, some overhead associated with the sqlite data, but
this gives a rough estimate.
-greg
On Thu, Apr 30, 2009 at 10:55 AM, Evgueni Kolossov ekolos...@gmail.com
wrote:
and what's the length of Pickles?
2009/4/30 Evgueni Kolossov ekolos...@gmail.com:
Greg
Dear Greg,
Do you know about IronPython (
http://www.codeplex.com/Wiki/View.aspx?ProjectName=IronPython)?
It actually combining Visual Studio and Python.
It can be very interesting solution for RDKit. What you think?
Regards,
Evgueni
Thank you very much!
Regards,
Evgueni
2009/3/25 Greg Landrum greg.land...@gmail.com
[Redirected to the list because the question is of general interest]
Hi Evgueni,
On Wed, Mar 25, 2009 at 10:56 AM, Evgueni Kolossov
ekolos...@btinternet.com wrote:
Got some problems with looping over
boost site I can only get 1.38 (the latest) but not
1.36. What you will suggest?
Regards,
Evgueni
2009/2/11 Evgueni Kolossov ekolos...@gmail.com
Thanks - will try to rebuild with msvc-9 option
Regards,
Evgueni
2009/2/11 Greg Landrum greg.land...@gmail.com
You can specify the version of msvc
Thank you very much
2009/2/12 Greg Landrum greg.land...@gmail.com
Dear Evgueni,
On Thu, Feb 12, 2009 at 10:22 AM, Evgueni Kolossov ekolos...@gmail.com
wrote:
Thank you very much - it all works now.
Glad to hear it.
Another question - I still have boost 1.35 and I have noticed you
Yes,
This is why I am talking about new boost version...
It refer to libraries of RDKit built with the old version.
Regards,
Evgueni
2009/2/11 Greg Landrum greg.land...@gmail.com
Dear Evgueni,
On Wed, Feb 11, 2009 at 4:38 PM, Evgueni Kolossov ekolos...@gmail.com
wrote:
I have attached
Hi Greg,
Can you please describe (or forward me to description) what rules you
applied for fragmentation process. Can they be modified, etc.
Regards,
Evgueni
Hi Greg,
I am trying to use your function to calculate Balaban index J:
doubel dResult = RDKit::MolOps::computeBalabanJ(*mol, true, true, 0, false)
and getting linker problems (see enclosed file). Probably need to #include
some files?
Can you help please?
Regards,
Evgueni
Error 7
So, RingInfo::numRings return the number of smallest rings?
2008/8/20 Greg Landrum greg.land...@gmail.com
Dear Evgueni,
On Wed, Aug 20, 2008 at 11:46 AM, Evgueni Kolossov ekolos...@gmail.com
wrote:
Is there any way to get separately total number of Rings and number of
SMALLEST rings
Thanks Greg,
Will this give the SHORTEST distance?
Regards,
Evgueni
2008/8/18 Greg Landrum greg.land...@gmail.com
On Mon, Aug 18, 2008 at 12:42 PM, Evgueni Kolossov ekolos...@gmail.com
wrote:
Thanks Greg - this is works.
Another question:
Can you please provide an example of use MolOps
2008/8/17 Evgueni Kolossov ekolos...@gmail.com
Thanks Greg,
But this is not enough:
unsigned int minRingSize=ringInfo-
minAtomRingSize(atomIdx);
for(VECT_INT_VECT_CI ringIt=ringInfo-atomRings().begin();
ringIt!=ringInfo-atomRings().end();++ringIt){
if(ringIt-size()==minRingSize
in Python. The default
behavior is the same as before: to show all properties.
-greg
On Mon, Aug 11, 2008 at 2:24 PM, Evgueni Kolossov ekolos...@gmail.com
wrote:
Hi Greg,
ROMol::getPropList() will return not only properties from the SDFile but
also some default properties.
Is there way(param
Dear Greg,
Can you please show how to extract text from stringstream (which in your
case actually ostream) into string?
ROMol *mol;
mol = SmilesToMol(strSmile);
ostream *ss = new stringstream();
SDWriter *writer = new SDWriter(ss, false);
writer-write(*mol);
string strMolStructure;
//Now we want
Hi,
If anybody interested, I have made single RDKit.sln as well as separate
solutions for each dll in RDKit for Visual Studio 2005. All builds OK.
Regards,
Evgueni
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