Re: [Rdkit-discuss] Contractors working with the RDKit?

2011-03-20 Thread Evgueni Kolossov
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

Re: [Rdkit-discuss] Build on Windows

2010-07-30 Thread Evgueni Kolossov
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

Re: [Rdkit-discuss] Build on Windows

2010-07-30 Thread Evgueni Kolossov
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

Re: [Rdkit-discuss] Build on Windows

2010-07-30 Thread Evgueni Kolossov
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

Re: [Rdkit-discuss] Build on Windows

2010-07-29 Thread Evgueni Kolossov
, 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

Re: [Rdkit-discuss] Build on Windows

2010-07-28 Thread Evgueni Kolossov
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

Re: [Rdkit-discuss] Build on Windows

2010-07-28 Thread Evgueni Kolossov
, 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

Re: [Rdkit-discuss] Build on Windows

2010-07-28 Thread Evgueni Kolossov
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

Re: [Rdkit-discuss] Build on Windows

2010-07-28 Thread Evgueni Kolossov
: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

Re: [Rdkit-discuss] Q2 2010 Release

2010-07-02 Thread Evgueni Kolossov
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

Re: [Rdkit-discuss] Q2 2010 Release

2010-07-01 Thread Evgueni Kolossov
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

Re: [Rdkit-discuss] Q2 2010 Release

2010-07-01 Thread Evgueni Kolossov
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

[Rdkit-discuss] Installation on Windows

2010-06-22 Thread Evgueni Kolossov
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

Re: [Rdkit-discuss] about building RDKit on VS 2008

2010-04-19 Thread Evgueni Kolossov
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

Re: [Rdkit-discuss] about building RDKit on VS 2008

2010-04-19 Thread Evgueni Kolossov
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

Re: [Rdkit-discuss] MOL_SPTR_VECT

2010-02-11 Thread Evgueni Kolossov
: 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

Re: [Rdkit-discuss] MOL_SPTR_VECT

2010-02-05 Thread Evgueni Kolossov
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

[Rdkit-discuss] MOL_SPTR_VECT

2010-02-04 Thread Evgueni Kolossov
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 {

Re: [Rdkit-discuss] SubstructMatch

2009-12-02 Thread Evgueni Kolossov
),(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

[Rdkit-discuss] SubstructMatch

2009-12-01 Thread Evgueni Kolossov
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

Re: [Rdkit-discuss] SubstructMatch

2009-12-01 Thread Evgueni Kolossov
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

[Rdkit-discuss] Fwd: SubstructMatch

2009-12-01 Thread Evgueni Kolossov
-- 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

Re: [Rdkit-discuss] Substructure search

2009-11-07 Thread Evgueni Kolossov
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

Re: [Rdkit-discuss] Substructure search

2009-11-06 Thread Evgueni Kolossov
? 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

Re: [Rdkit-discuss] Substructure search

2009-11-05 Thread Evgueni Kolossov
, 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

[Rdkit-discuss] fragments aromaticity

2009-10-19 Thread Evgueni Kolossov
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

Re: [Rdkit-discuss] fragments aromaticity

2009-10-19 Thread Evgueni Kolossov
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

Re: [Rdkit-discuss] Fragmentation

2009-08-14 Thread Evgueni Kolossov
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

Re: [Rdkit-discuss] Fragmentation

2009-08-13 Thread Evgueni Kolossov
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

Re: [Rdkit-discuss] Fragmentation

2009-08-13 Thread Evgueni Kolossov
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

Re: [Rdkit-discuss] Fragmentation

2009-08-12 Thread Evgueni Kolossov
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

Re: [Rdkit-discuss] Fragmentation

2009-08-11 Thread Evgueni Kolossov
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

Re: [Rdkit-discuss] Fragmentation

2009-08-10 Thread 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

Re: [Rdkit-discuss] Fragmentation

2009-07-21 Thread Evgueni Kolossov
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()

Re: [Rdkit-discuss] Fragmentation

2009-07-20 Thread Evgueni Kolossov
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

Re: [Rdkit-discuss] Fragmentation

2009-07-16 Thread Evgueni Kolossov
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

Re: [Rdkit-discuss] beta of Q2 release available

2009-06-21 Thread 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

Re: [Rdkit-discuss] Cannot read compounds containing nitro group?

2009-05-26 Thread Evgueni Kolossov
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

[Rdkit-discuss] Fwd: Question

2009-05-01 Thread Evgueni Kolossov
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

Re: [Rdkit-discuss] Fwd: Question

2009-05-01 Thread Evgueni Kolossov
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

Re: [Rdkit-discuss] Question

2009-04-30 Thread Evgueni Kolossov
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

[Rdkit-discuss] IronPython

2009-04-09 Thread Evgueni Kolossov
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

Re: [Rdkit-discuss] Beta of next release up.

2009-03-25 Thread Evgueni Kolossov
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

Re: [Rdkit-discuss] Compiling for VS 2008

2009-02-12 Thread Evgueni Kolossov
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

Re: [Rdkit-discuss] Compiling for VS 2008

2009-02-12 Thread Evgueni Kolossov
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

Re: [Rdkit-discuss] Compiling for VS 2008

2009-02-11 Thread Evgueni Kolossov
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

[Rdkit-discuss] Fragmentation

2008-09-11 Thread Evgueni Kolossov
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

[Rdkit-discuss] computeBalabanJ

2008-09-10 Thread Evgueni Kolossov
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

Re: [Rdkit-discuss] Rings

2008-08-20 Thread Evgueni Kolossov
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

Re: [Rdkit-discuss] Calculation of atomic descriptors, Code snippet

2008-08-18 Thread Evgueni Kolossov
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

Re: [Rdkit-discuss] Calculation of atomic descriptors, Code snippet

2008-08-17 Thread Evgueni Kolossov
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

Re: [Rdkit-discuss] Mol property

2008-08-13 Thread Evgueni Kolossov
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

Re: [Rdkit-discuss] SD File output

2008-08-08 Thread Evgueni Kolossov
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

[Rdkit-discuss] VS2005 solution

2008-07-22 Thread Evgueni Kolossov
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