Greg,
Thank you very much.
Yingfeng
On Fri, May 31, 2013 at 4:14 AM, Greg Landrum greg.land...@gmail.comwrote:
On Fri, May 31, 2013 at 7:53 AM, Yingfeng Wang ywang...@gmail.com wrote:
I think I need to add masses of all atoms for getting the mass of the
whole fragment. Am I right
let me know how to remove the
extra mass?
Thanks.
Yingfeng
On Fri, May 31, 2013 at 8:58 AM, Yingfeng Wang ywang...@gmail.com wrote:
Greg,
Thank you very much.
Yingfeng
On Fri, May 31, 2013 at 4:14 AM, Greg Landrum greg.land...@gmail.comwrote:
On Fri, May 31, 2013 at 7:53 AM, Yingfeng
How do I retrieve the dissociation energy of a bond in a molecule.
Say, I have
from rdkit import Chem
m =Chem.MolFromInchi('InChI=1S/C10H9N3O/c1-7-11-10(14)9(13-
12-7)8-5-3-2-4-6-8/h2-6H,1H3,(H,11,12,14)')
mybond = m.GetBondBetweenAtoms(8,7)
Is there a way for me to retrieve the dissociation
() is for the exact
molecular weight of the molecule. What do I observe so big difference of
mass? By the way, the mass of m calculated by the ExactMolWt () is still
less than summation of its fragments.
Thanks.
Yingfeng
On Fri, May 31, 2013 at 3:58 PM, Yingfeng Wang ywang...@gmail.com wrote:
Greg,
I got
Dear Greg,
Thank you very much! I think 'C6H5' is good enough to me.
Yingfeng
On Sun, Jun 2, 2013 at 12:25 AM, Greg Landrum greg.land...@gmail.comwrote:
On Sat, Jun 1, 2013 at 6:46 AM, Yingfeng Wang ywang...@gmail.com wrote:
Dear Greg,
Thanks.
As for
In [19]: frags = Chem.GetMolFrags
After getting the latest code by git, I install RDKit on my ubuntu 12.04.
In the step of make install, I got
CMake Error at External/INCHI-API/cmake_install.cmake:124 (FILE):
It seems the file $RDBASE/lib/libRDInchiLib.so.1.2013.06.1pre can't be
found. Please note that I have turned on the flag
2013 04:13, Yingfeng Wang ywang...@gmail.com wrote:
After getting the latest code by git, I install RDKit on my ubuntu 12.04.
In the step of make install, I got
CMake Error at External/INCHI-API/cmake_install.cmake:124 (FILE):
It seems the file $RDBASE/lib/libRDInchiLib.so.1.2013.06.1pre can't
On 2013-06-05 16:55, Yingfeng Wang wrote:
Yes, I did.
export RDBASE=/opt/RDKit_latest/latest
export LD_LIBRARY_PATH=$RDBASE/lib:$LD_LIBRARY_PATH
export PYTHONPATH=$RDBASE:$PYTHONPATH
I put them on ~/.bashrc
On Wed, Jun 5, 2013 at 10:53 AM, Jan Holst Jensen
j...@biochemfusion.comwrote
of fragments?
Thanks.
Yingfeng
On Sun, Jun 2, 2013 at 8:39 AM, Yingfeng Wang ywang...@gmail.com wrote:
Dear Greg,
Thank you very much! I think 'C6H5' is good enough to me.
Yingfeng
On Sun, Jun 2, 2013 at 12:25 AM, Greg Landrum greg.land...@gmail.comwrote:
On Sat, Jun 1, 2013 at 6:46
With the following code,
from rdkit import Chem
from rdkit.Chem import Descriptors
from rdkit.Chem import AllChem
a = Chem.MolFromSmiles([H+])
Descriptors.ExactMolWt(a)
0.0
I got mass 0.0
If I switch to Inchi format, I get same result.
a = Chem.MolFromInchi(InChI=1S/p+1)
,
On Fri, Jun 21, 2013 at 4:40 PM, Yingfeng Wang ywang...@gmail.com wrote:
With the following code,
from rdkit import Chem
from rdkit.Chem import Descriptors
from rdkit.Chem import AllChem
a = Chem.MolFromSmiles([H+])
Descriptors.ExactMolWt(a)
0.0
snip
Is it normal?
Nope. It's
-;/t19-,21-,23+,24+,41-,42-;/m0./s1
[15:30:12] WARNING: Problems/mismatches: Mobile-H( Hydrogens: Number;
Mobile-H groups: One instead of multiple, Attachment points, Number;
Charge(s): Do not match; Stereobonds/cumulenes: Missing known)
On Sat, Jun 22, 2013 at 7:59 AM, Yingfeng Wang ywang
Landrum greg.land...@gmail.comwrote:
On Tue, Jul 2, 2013 at 5:20 PM, Yingfeng Wang ywang...@gmail.com wrote:
If I have the formula, is RDKit able to generate a random compound based
on the given formula?
It's not, but it is kind of an interesting problem to think about.[1]
-greg
[1] Note
I failed to install RDKit on CentOS.
The error message is
[ 85%] Built target MolChemicalFeatures
Linking CXX executable testSLNParse
[ 85%] Built target rdSLNParse
/home/yingfeng/software/boost/boost_1_54_0/stage/lib/libboost_regex.so:
undefined reference to
Gianluca,
I am using CentOS 5.8. But I am just a regular user. So I prefer to install
RDkit by building it from source.
Thanks.
Yingfeng
On Mon, Jul 15, 2013 at 5:51 AM, Gianluca Sforna gia...@gmail.com wrote:
On Sun, Jul 14, 2013 at 10:57 PM, Yingfeng Wang ywang...@gmail.com
wrote:
I
Hi Greg,
I just tried 1.51, and got same problem.
Thanks.
Yingfeng
On Mon, Jul 15, 2013 at 7:49 AM, Yingfeng Wang ywang...@gmail.com wrote:
Greg,
I also tried boost 1.49.0, and met same problem. If necessary, I can try
1.51.
Yingfeng
On Mon, Jul 15, 2013 at 5:02 AM, Greg Landrum
, but
did you try pulling boost with Yum? I was able to get RDKit, and the Java
wrappers, to cleanly compile on CentOS 6.4 with that flavor of boost.
Matt
On Mon, Jul 15, 2013 at 9:39 PM, Greg Landrum greg.land...@gmail.comwrote:
On Mon, Jul 15, 2013 at 7:49 AM, Yingfeng Wang ywang
Matthew,
Thanks.
Yingfeng
On Tue, Jul 16, 2013 at 10:11 AM, Matthew Lardy mla...@gmail.com wrote:
Yingfeng,
That's really unfortunate! Hopefully, you can punch through this quickly!
Best,
Matthew
On Tue, Jul 16, 2013 at 5:29 AM, Yingfeng Wang ywang...@gmail.com wrote:
Matthew
at 7:49 AM, Yingfeng Wang ywang...@gmail.com wrote:
I also tried boost 1.49.0, and met same problem. If necessary, I can try
1.51.
hmm, ok, so much for that idea. Let's try something else.
On Sunday, July 14, 2013, Yingfeng Wang wrote:
I failed to install RDKit on CentOS.
The error
I have two different compounds with the same formula. But I got different
mass.
sInchi =
InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/p-1/t3-/m0/s1
current_mol = Chem.MolFromInchi(sInchi)
current_mass = Descriptors.ExactMolWt(current_mol)
print current_mass
On 19 December 2013 11:18, Yingfeng Wang ywang...@gmail.com wrote:
Peter,
Thanks. Is there is a way to calculate the neutral mass of a compound
even if the Inchi indicates that this compound is negatively charged?
Yingfeng
On Wed, Dec 18, 2013 at 7:50 PM, Peter Gedeck peter.ged
I want to draw a 2D figure of a compound. And I follow the example given at
the following link,
http://www.rdkit.org/docs/GettingStartedInPython.html
My code is given as follows,
from rdkit.Chem import AllChem
from rdkit import Chem
m = Chem.MolFromSmiles('c1nccc2n1ccc2')
-condition Violation
On Wed, Feb 19, 2014 at 3:27 PM, Yingfeng Wang ywang...@gmail.com wrote:
Adrian,
I meet a weird case.
import matplotlib.offsetbox
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import Draw
m = Chem.MolFromSmiles('ccc[nH]c')
I got
non-ring
try:
AllChem.Compute2DCoords(m)
for second example:
m = Chem.MolFromSmiles('C(=O)OCCO')
AllChem.Compute2DCoords(m)
2014-02-19 21:46 GMT+01:00 Yingfeng Wang ywang...@gmail.com:
Here are more details.
If I use
m = Chem.MolFromSmiles('ccc[nH]c', sanitize=False
According to the following link,
http://www.rdkit.org/docs/RDKit_Book.html
I get sample code for identifying identify anti-aromatic bonds like
from rdkit import Chem
m=Chem.MolFromSmiles('O=C1C=CC(=O)C2=C1OC=CO2')
m.GetBondBetweenAtoms(6,7).GetIsAromatic()
Is there a way to identify
()
Is there a way to identify anti-aromatic bonds using Rdkit?
Thanks.
Yingfeng
On Mon, Aug 24, 2015 at 9:38 PM, Yingfeng Wang ywang...@gmail.com wrote:
According to the following link,
http://www.rdkit.org/docs/RDKit_Book.html
I get sample code for identifying identify anti-aromatic bonds like
from
Could anyone please share your experience with identifying non-aromatic
bonds using RDKit? I would greatly appreciate your help.
Yingfeng
On Mon, Aug 24, 2015 at 9:42 PM, Yingfeng Wang ywang...@gmail.com wrote:
Sorry, my previous email has a typo.
According to the following link,
http
://rdkit.org/docs/RDKit_Book.html#aromaticity
-greg
On Thu, Aug 27, 2015 at 5:36 PM, Yingfeng Wang ywang...@gmail.com wrote:
Greg,
Thanks. I believe identifying anti-aromatic bonds even just with simple
rings will be very helpful to my project. Could you please give me some
links or sample codes
was
> executed.
> If it's when you ran the program: please show the results of "ldd EXENAME"
> where EXENAME is the program you're running.
>
> Best.
> -greg
>
>
> On Mon, May 30, 2016 at 5:25 AM, Yingfeng Wang <ywang...@gmail.com> wrote:
>
>> I use the fo
-lSubgraphs -lSubstructMatch
-L/home/wyf/anaconda3/pkgs/boost-1.60.0-py27_0/lib -lboost_system
-lboost_filesystem
Hope my experience can help others to avoid the similar problem.
Thanks.
Yingfeng
On Tue, May 31, 2016 at 10:22 PM, Yingfeng Wang <ywang...@gmail.com> wrote:
> Greg,
>
> I
I use the following setting for Apple LLVM version 6.0 (clang-600.0.57).
CXXFLAGS= -Wall -O2 -std=c++11 -I ${RDBASE}/Code -I ${RDBASE}/lib -I
${RDBASE}/External -I ${BOOSTBASE}/include
LDFLAGS=-L${RDBASE}/lib -lAlignment -lCatalogs -lChemReactions
-lChemTransforms -lChemicalFeatures
oubled times, but it's easy enough to try.
>
> -P.
>
> On Wed, Mar 16, 2016 at 8:46 AM, Yingfeng Wang <ywang...@gmail.com> wrote:
>
>> Peter,
>>
>> Thanks. Do you mean
>>
>> -lLibA_static -lLibB_static -lLibC_static -lLibA_static -lLibB_static
>>
, 2016 at 8:16 AM, Greg Landrum <greg.land...@gmail.com>
wrote:
>
>
> On Sat, Mar 12, 2016 at 5:00 AM, Yingfeng Wang <ywang...@gmail.com> wrote:
>
>> Greg,
>>
>> Thanks. Your suggestion solves my problem. I add the following part in my
>> compiling comma
After installing RDKit, I try to compile the following code in main.cpp,
#include
#include
using namespace RDKit;
using namespace std;
int main(int argc, const char * argv[]) {
string curInchi =
"InChI=1S/C10H9N3O/c1-7-11-10(14)9(13-12-7)8-5-3-2-4-6-8/h2-6H,1H3,(H,11,12,14)";
braries. If you are using
> the InChI code, you need to link against: RDInchiLib, InChi, GraphMol, and
> RDGeneral. There may be a few others as well.
>
> -greg
>
>
>
>
>
> On Sat, Mar 12, 2016 at 5:13 AM, Yingfeng Wang <ywang...@gmail.com> wrote:
>
>>
.land...@gmail.com>
> wrote:
>
>> Though that would be useful information, I'm afraid that's not something
>> I've ever put together.
>>
>> -greg
>>
>>
>>
>> On Tue, Mar 15, 2016 at 6:26 PM, Yingfeng Wang <ywang...@gmail.com>
>> wrot
onst ROMol
> <http://rdkit.org/docs/cppapi/classRDKit_1_1ROMol.html> & *mol*, bool
> *sanitizeFrags* = true,
> by any chance? This will return a vector of ROMol's which correspond to
> the contiguous fragments.
>
> Igor
>
>
> On Sun, Apr 10, 2016 at 11:04 PM,
#L483
>
> There is a nice if-else that shows you how to get the behaviors of asMols
> = False, then asMols=True. There is obviously a little bit of manipulation
> to get the output into python, but hopefully it is clear how one might make
> a similar pure C++ function.
>
> -
, Apr 10, 2016 at 10:49 PM, Greg Landrum <greg.land...@gmail.com>
wrote:
>
>
> On Mon, Apr 11, 2016 at 1:35 AM, Yingfeng Wang <ywang...@gmail.com> wrote:
>>
>>
>> Thanks. Say, the current RWMol object has 10 bonds, so ids of these bonds
>> should be from
In python, I have GetMol() for Chem.EditableMol. I can also use
Chem.GetMolFrags(...). Could you please help me to know how to get similar
functions in C++?
For example, I remove two bonds in an RWMol object, how do I use GetMol()
and GetMolFrags(...) in C++?
Thanks.
Yingfeng
on't have to, RWMol can be sent to any function that takes an
> ROMol.
>
> Actually, this is true now in Python as well.
>
> In C++ if you really need to copy the molecule:
>
> ROMol mol = new ROMol( *rwmol );
>
> But you really don't have to.
>
>
> Brian Kelle
ect that builds a test project against a built
> distribution. It could prove useful as a basis for building C++ extensions.
>
> Basically we would hedge our bets and just link against everything :)
>
> Cheers,
> Brian
>
> On Wed, Mar 16, 2016 at 8:47 AM, Yingfeng Wang <ywan
call should fix your problem.
>
> Kind regards,
> Paolo
>
>
> On 4/13/2016 16:48, Yingfeng Wang wrote:
>
> This is my C++ code.
>
>
> #include
> #include
> #include
> #include
> #include
>
> using namespace RDKit;
> using namespac
!bond->getOwningMol().getRingInfo()->isInitialized()) {
> MolOps::findSSSR(bond->getOwningMol());
> }
> return bond->getOwningMol().getRingInfo()->numBondRings(bond->getIdx())
> != 0;
> }
>
>
> On Wed, Apr 13, 2016 at 11:59 AM, Yingfeng Wang <ywan
I try to use minGW to build rdkit_2016_09_2, which is from the following
link.
https://github.com/rdkit/rdkit/archive/Release_2016_09_2.zip
cmake command is
cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++
-DMSVC_RUNTIME_DLL="C:\Windows\System32\msvcr100.dll"
-DBOOST_ROOT="C:\boost"
CMD shell using mingw32-make.exe.
>
> Make sure you start from a clean build directory before issuing the cmake
> command.
>
> Cheers,
> p.
>
>
> On 12/20/16 04:47, Yingfeng Wang wrote:
>
> I try to use minGW to build rdkit_2016_09_2, which is from the following
>
Paolo,
Could you please let me know the version of your minGW and how you got or
built boost with minGW. I kept getting errors like "duplicate section" with
different size.
Thanks.
Yingfeng
On Tue, Dec 20, 2016 at 10:13 AM, Yingfeng Wang <ywang...@gmail.com> wrote:
> P
Andreas,
Could you please share your Makefile? I am also using the C++ API of RDKit
on Mac. This is my current Makefile.
CC= g++
OPENMPFLAG=#-fopenmp
CXXFLAGS=-Wall -O2 -std=c++11 -I${RDBASE}/Code -I${RDBASE}/lib
-I${RDBASE}/External -I${BOOSTBASE}/include -I${EGGBASE}
LDFLAGS=-L${RDBASE}/lib
egin];
> to:
> Atom *atom = (*pCurrentROMol)[*atBegin];
> or, even simpler:
> auto atom = (*pCurrentROMol)[*atBegin];
>
> things should work.
> -greg
>
>
> On Wed, Dec 12, 2018 at 12:36 AM Yingfeng Wang wrote:
>
>> I am using the C++ library of RDKit on Mac.
g to copy the
> atom, and control ownership with the shared_ptr?
>
> - dan nealschneider
>
> (né wandschneider)
>
> Senior Developer
> Schr*ö*dinger, Inc
> Portland, OR
>
>
>
>
> On Tue, Dec 11, 2018 at 3:36 PM Yingfeng Wang wrote:
>
>> I am using the C++
InRing(bond.get())) ? "ring|" : "linear|" );
...
++firstB;
}
However, I still have a question. Why "Atom *atom" and "Bond *bond" do not
work? Yes, "auto" solves the problem, but I feel it just covers the
essential issue.
Thanks.
Yingfeng
On We
I am using the C++ library of RDKit on Mac. My C++ code works with
RDKit_2017_09_3. However, after I switch to RDKit 2018_03_4, I got the
following error when compiling my C++ source code.
*Database.cpp:148:33: **error: **no viable conversion from 'const
RDKit::Atom *' to*
*
Jason,
I can see the image :-)
Yingfeng
On Mon, Dec 17, 2018 at 10:01 AM Jason Biggs wrote:
> Is this the same issue as https://github.com/rdkit/rdkit/issues/1852?
> where the input string specifies a trans double bond in a ring but
> EmbedMolecule returns a cis configuration? I get
Greg,
I figure it out. Adding const should work.
const Atom *atom = (*pCurrentROMol)[*atBegin];
Thanks.
Yingfeng
On Wed, Dec 12, 2018 at 10:21 AM Yingfeng Wang wrote:
> Greg,
>
> I figure out the problem. Removing "->get()" can solve the problem.
>
> Here is th
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