Re: [Rdkit-discuss] Merge two fragments at connection point

2016-03-10 Thread Steven Combs
the Transform methods in RDKit in time!) Steven Combs On Thu, Mar 10, 2016 at 12:23 AM, Greg Landrum <greg.land...@gmail.com> wrote: > Hi Steven, > > On Mon, Mar 7, 2016 at 5:03 PM, Steven Combs <steven.com...@gmail.com> > wrote: > >> >> I am developer for

[Rdkit-discuss] Merge two fragments at connection point

2016-03-07 Thread Steven Combs
reate a bond between the parent atom's hydrogen to a specific atom on mol2). Is replaceSubstructs the way to go? I am not exactly sure how to set up the query for this. Steven Combs -- Transform Data into Opportunity. Acc

[Rdkit-discuss] mmFF minimization in context of two ligands/binding pocket

2016-04-01 Thread Steven Combs
on the combine molecule. The steps would look like this -use combineMols() for all residues -use mmFF on the complex 2) Use a hacked version of MCS from here: http://rdkit.blogspot.com/2013/12/using-allchemconstrainedembed.html Is there a better way of doing this? I am using the C++ api. Steven

Re: [Rdkit-discuss] sdf reading error between osx and windows

2016-04-27 Thread Steven Combs
and that fixed it. Thanks again Paolo! Steven Combs On Wed, Apr 27, 2016 at 12:28 PM, Steven Combs <steven.com...@gmail.com> wrote: > I will give that a try and let you know! > > On Wed, Apr 27, 2016 at 12:20 PM, Paolo Tosco <paolo.to...@unito.it> > wrote: > >&g

[Rdkit-discuss] sdf reading error between osx and windows

2016-04-27 Thread Steven Combs
while( ! supplier.atEnd() ) { ::RDKit::ROMolOP mol( supplier.next() ); if( mol ) { mol_vector.push_back( mol ); } } } Regards, Steven Combs basic_fragments.sdf Description: Binary data ---

[Rdkit-discuss] MolFromPDBBlock and heterocycles

2016-09-07 Thread Steven Combs
[CH]1[NH][CH]([C]([H])([H])[CH]([OH])[OH])[CH]([C]([H])([H])[C]([H])([H])[H])[CH]([CH]([OH])[CH]2[CH]([H])[CH]([H])[CH]([H])[CH]([N]([H])[H])[CH]2[H])[CH]1[N]([C]([H])([H])[H])[C]([H])([H])[H] Steven Combs tes

[Rdkit-discuss] windows 32 shared library

2016-10-14 Thread Steven Combs
Has anyone compiled rdkit into a 32bit shared library dll? Steven Combs -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link

[Rdkit-discuss] Reactions saved as ctfile RD format

2017-03-01 Thread Steven Combs
Hi, Is there a way to save out reactions in the RD file format specified by the CTFile format specifications or should I just write out my own format? Steven Combs -- Check out the vibrant tech community on one