Re: [Rdkit-discuss] has multiple H count specifications

[Greg Landrum]

Hi,

There are two problems here:
The warning is telling you that you've included inconsistent information
about the product in the product specification. It's a good idea to just
use dummies or plain atoms in the products and not include extra info in
the products unless you really intend to. For example, you could rewrite
your reaction SMARTS as:
"[CH2,CH3:8][OH:9].[O:1]=[O:2]>>[O:1][O:2].[C:8](=[O:9]"
or
"[CH2,CH3:8][OH:9].[O:1]=[O:2]>>[O:1][O:2].[*:8](=[O:9]"
and get correct results.

The second problem is the order in which you provide the reactants to
rxn.RunReactants(). The first reactant in the list passed to RunReactants()
corresponds to the first reactant in the reaction, the second to the second
reactant, etc. So when you rewrite your reaction to expect oxygen as the
first reactant, you need to also make sure that oxygen is passed in as the
second reactant.

-greg



On Mon, Apr 11, 2016 at 11:38 AM, 吴玲  wrote:

> *hi Greg,*
>
> *when I use the AllChem.ReactionFromSmarts and the RunReactants predict a
> reaction,just like below:*
>
> input transformation -
> *"[CH2,CH3:8][OH:9].[O:1]=[O:2]>>[OH:1][OH:2].[CH2,CH3:8](=[O:9]"*,
> input reactants-  reactants1 = *['CO','CCO','CC(C)O','COC','c1c1O',]*
> reactants2= *['O=O']*
> output product-
> CO.O=O>>OO.C=O.OO.C=O
> CCO.O=O>>OO.C[CH2]=O.OO.C[CH2]=O
> CC(C)O.O=O>>
> COC.O=O>>
> c1c1O.O=O>>
> *the result is correct ! but if I change the order,write the
> above-mentioned transformations as
> "[O:1]=[O:2].[CH2,CH3:8][OH:9]>>[OH:1][OH:2].[CH2,CH3:8](=[O:9])", there is
> no result output,and warning that atom 0 in product 1 has multiple H count
> specifications , what's the cause of this?*
> output:
> CO.O=O>>
> CCO.O=O>>
> CC(C)O.O=O>>
>  COC.O=O>>
>  c1c1O.O=O>>
>
> best wishes,
>
> monica
>
>
>
>
>
>
>
> --
> Find and fix application performance issues faster with Applications
> Manager
> Applications Manager provides deep performance insights into multiple
> tiers of
> your business applications. It resolves application problems quickly and
> reduces your MTTR. Get your free trial! http://pubads.g.doubleclick.net/
> gampad/clk?id=1444514301=/ca-pub-7940484522588532
> ___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
--
Find and fix application performance issues faster with Applications Manager
Applications Manager provides deep performance insights into multiple tiers of
your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial! http://pubads.g.doubleclick.net/
gampad/clk?id=1444514301=/ca-pub-7940484522588532___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] running RunReactants with Reactants that have a plus one charge

[Greg Landrum]

Hi,

The reactants that are part of your reaction definition are queries. If
those queries include a charge they won't match molecules that don't have a
charge. If you'd like the reactant patterns to match neutral molecules as
well as charged ones, just remove the charge from the reaction
specification.

The handling of chirality in reactions is explained in the documentation
here:
http://rdkit.org/docs/RDKit_Book.html#chirality

-greg



On Mon, Apr 11, 2016 at 9:21 AM, 吴玲  wrote:

> Hi  Greg,
> *when I run the AllChem.RunReactants with rxn'patterns that the reactant
> have a plus one charge ,like this :*
>
> '''
>patterns = [
> "[NH+:2]1[C:3][C:4][C:5][C@
> @H:6]1.[OH2:15].[O:17]=[O:18]>>[NH2+:2][C:3][C:4][C:5][C:6]=[O:17].[OH:18][OH:15]",
>
> "[NH+:2]1[C:3][C:4][C:5][CH:6]1.[OH2:15].[O:17]=[O:18]>>[NH2+:2][C:3][C:4][C:5][C:6]=[O:17].[OH:18][OH:15]",
>
> "[NH+:2]1[C:3][C:4][C:5][C:6]1.[OH2:15].[O:17]=[O:18]>>[NH2+:2][C:3][C:4][C:5][C:6]=[O:17].[OH:18][OH:15]",
>
> "[N+:2]1[C:3][C:4][C:5][C:6]1.[OH2:15].[O:17]=[O:18]>>[N+:2][C:3][C:4][C:5][C:6]=[O:17].[OH:18][OH:15]",
> ]
> rs1 = ['N11']
> rs2 = ['O']
> rs3 = ['O=O']
>
> for idx, pattern in enumerate(patterns, 1):
> rxn = ReactionFromSmarts(pattern)
>
> index = 0
> for a in rs1:
> a_ = MolFromSmiles(a)
> for b in rs2:
> b_ = MolFromSmiles(b)
> for c in rs3:
> c_ = MolFromSmiles(c)
>
> ps = [
> MolToSmiles(c) for ps in rxn.RunReactants((a_,
> b_,c_))
> for p in ps]
>
> index += 1
> print '{idx}.{index} {a}.{b}.{c}>>{ps}'.format(
> idx=idx, index=index, a=a, b=b,c=c, ps='.'.join(ps))
> '''
> *why there is no any product output ,and how should I deal with the
> atom;charge and stereoisomerism?*
> *also when I remove the charge information(*
> *patterns = [
> "[N:2]1[C:3][C:4][C:5][C:6]1.[OH2:15].[O:17]=[O:18]>>[N:2][C:3][C:4][C:5][C:6]=[O:17].[OH:18][OH:15]",]),
> it occurs an error like below:*
>   File
> "/home/qnhu/Project/Database/Rhea_Dedup/AllEcToAllRxn/Chemaxon/predict.py",
> line 48, in main3
> for p in ps]
> Boost.Python.ArgumentError: Python argument types in
> rdkit.Chem.rdmolfiles.MolToSmiles(str)
> did not match C++ signature:
> MolToSmiles(RDKit::ROMol mol, bool isomericSmiles=False, bool
> kekuleSmiles=False, int rootedAtAtom=-1, bool canonical=True, bool
> allBondsExplicit=False)
>
> *how should I do?*
> *best wishes,*
> *wl*
>
>
>
>
>
>
>
>
>
>
>
>
>
> --
> Find and fix application performance issues faster with Applications
> Manager
> Applications Manager provides deep performance insights into multiple
> tiers of
> your business applications. It resolves application problems quickly and
> reduces your MTTR. Get your free trial! http://pubads.g.doubleclick.net/
> gampad/clk?id=1444514301=/ca-pub-7940484522588532
> ___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
--
Find and fix application performance issues faster with Applications Manager
Applications Manager provides deep performance insights into multiple tiers of
your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial! http://pubads.g.doubleclick.net/
gampad/clk?id=1444514301=/ca-pub-7940484522588532___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] [Rdkit-devel] Beta of Q1 2016 release now up

[Guillaume GODIN]

Dear All,


Thanks Greg!


Using your command compilation line (see bellow), It's the first time I can 
really test mutlithread rdkit on my mac.


"cmake -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG 
-DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG 
-DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON 
-DCMAKE_INSTALL_PREFIX:PATH=/usr -DINCLUDE_INSTALL_DIR:PATH=/usr/include 
-DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc 
-DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 
-DBUILD_SHARED_LIBS:BOOL=ON -DRDK_INSTALL_INTREE=OFF 
-DCMAKE_BUILD_TYPE=RelWithDebInfo -DRDK_BUILD_INCHI_SUPPORT:BOOL=ON 
-DRDK_BUILD_THREADSAFE_SSS:BOOL=ON -DRDK_BUILD_CAIRO_SUPPORT:BOOL=ON 
-DRDK_INSTALL_STATIC_LIBS:BOOL=OFF -DRDK_USE_FLEXBISON:BOOL=ON 
-DRDK_TEST_MULTITHREADED:BOOL=ON 
-DPYTHON_EXECUTABLE:FILEPATH=/Library/Frameworks/Python.framework/Versions/2.7/bin/python"


MacBook-Pro-de-MBP:Book mbp$ time python genconformersmutiltherads.py 
numthread=1


real 0m10.941s

user 0m10.869s

sys 0m0.059s

MacBook-Pro-de-MBP:Book mbp$ time python genconformersmutiltherads.py 
numthread=4


real 0m3.979s

user 0m11.638s

sys 0m0.106s



I will try to include this now into javascript version of RDKit and build 
WebAssembly instead of simple js file. Now emscripten / binaryen project should 
allows to compile C++ into webassembly which will be the standard of Chrome/ 
Firefox / Edge in the near future if you want to have faster time execution 
compare to current javascript codes.


best regards,

Dr. Guillaume GODIN
Project Manager
Innovation
CORPORATE R DIVISION
DIRECT LINE +41 (0)22 780 3645
MOBILE   +41 (0)79 536 1039

Firmenich SA
RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8



De : Greg Landrum 
Envoyé : lundi 11 avril 2016 13:20
À : Gianluca Sforna
Cc : RDKit Discuss; RDKit Developers List
Objet : Re: [Rdkit-discuss] [Rdkit-devel] Beta of Q1 2016 release now up

Gianluca,

This could be the issue fixed by this PR from Matt Swain: 
https://github.com/rdkit/rdkit/pull/856

-greg


On Mon, Apr 11, 2016 at 12:32 PM, Gianluca Sforna 
> wrote:
On Thu, Apr 7, 2016 at 6:24 AM, Greg Landrum 
> wrote:
> I have tagged a beta of the next RDKit release here:
> https://github.com/rdkit/rdkit/releases/tag/Release_2016_03_1b1


Tried to rebuild the RPMs but got this right on cmake:

-- Found INCHI: /usr/lib64/libinchi.so
CMake Error at External/INCHI-API/CMakeLists.txt:64 (install):
  install TARGETS given target "Inchi" which does not exist in this
  directory.


cmake invocation as follow:

/usr/bin/cmake -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG
-DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG
-DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG
-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_PREFIX:PATH=/usr
-DINCLUDE_INSTALL_DIR:PATH=/usr/include
-DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc
-DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64
-DBUILD_SHARED_LIBS:BOOL=ON -D RDK_INSTALL_INTREE=OFF -D
CMAKE_BUILD_TYPE=RelWithDebInfo -D RDK_BUILD_INCHI_SUPPORT:BOOL=ON -D
RDK_BUILD_THREADSAFE_SSS:BOOL=ON -D RDK_BUILD_CAIRO_SUPPORT:BOOL=ON -D
RDK_INSTALL_STATIC_LIBS:BOOL=OFF -D RDK_USE_FLEXBISON:BOOL=ON -D
RDK_TEST_MULTITHREADED:BOOL=ON -D
PYTHON_EXECUTABLE:FILEPATH=/usr/bin/python2 .

I'll dig in it later, in the meanwhile if you have ideas they will be
very welcome.
**  
DISCLAIMER  
This email and any files transmitted with it, including replies and forwarded 
copies (which may contain alterations) subsequently transmitted from Firmenich, 
are confidential and solely for the use of the intended recipient. The contents 
do not represent the opinion of Firmenich except to the extent that it relates 
to their official business.  
**--
Find and fix application performance issues faster with Applications Manager
Applications Manager provides deep performance insights into multiple tiers of
your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial! http://pubads.g.doubleclick.net/
gampad/clk?id=1444514301=/ca-pub-7940484522588532___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] GetMol and GetMolFrags in C++

[Yingfeng Wang]

David,

Yes, it is very clear. I am confident to use the version Igor suggested now.

Thanks.

Yingfeng

On Mon, Apr 11, 2016 at 8:36 AM, David Hall  wrote:

> When I want to replicate one of RDKit’s python functions in C++, I go to
> the source. RDKit has very readable wrappers that make this a surprisingly
> nice approach (many other pieces of software have pretty ugly wrappers, so
> this is a major compliment to RDKit).
>
> For this, I think the source is:
>
>
> https://github.com/rdkit/rdkit/blob/master/Code/GraphMol/Wrap/MolOps.cpp#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.
>
> -David
>
>
> On Apr 11, 2016, at 8:24 AM, Yingfeng Wang  wrote:
>
> lgor,
>
> Yes, this version looks good. But, I am wondering whether I can specify
> asMols. I specify asMols in the python version of my tool, so I want to do
> the same thing for getting the same result in my C++ code. Or could you
> help me to confirm that the version you mentioned actually has the same
> effect as asMols = true?
>
> Thanks.
> Yingfeng
>
> On Sun, Apr 10, 2016 at 11:35 PM, Igor Filippov  > wrote:
>
>> Did you want
>> std::vector > >
>> RDKit::MolOps::getMolFrags ( const ROMol
>>  &  *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, Yingfeng Wang 
>> wrote:
>>
>>> Greg,
>>>
>>> Thanks. In python, I am using GetMolFrags by the following way,
>>>
>>> Chem.GetMolFrags(current_modified_mol, asMols=True, sanitizeFrags=False)
>>>
>>> However, there is not a version at the link you mentioned allows me to
>>> specify asMols. Could you please give me more hints?
>>>
>>> Thanks.
>>> Yingfeng
>>>
>>> On Sun, Apr 10, 2016 at 10:49 PM, Greg Landrum 
>>> wrote:
>>>


 On Mon, Apr 11, 2016 at 1:35 AM, Yingfeng Wang 
 wrote:
>
>
> Thanks. Say, the current RWMol object has 10 bonds, so ids of these
> bonds should be from 1-10. Now, I remove one bond. How do I reset all nine
> bonds with ids from 1-9 (if one or two atoms are gone with this bond, I
> also want to reset the ids of these atoms).
>

 You don't need to do that, it happens automatically


> In addition, say, there are two fragments after one bond is removed.
> How do I get these two fragments as mols. In python, I can use
> Chem.GetMolFrags. But how do I get my job done in C++?
>

 There are a number of different versions of MolOps::getMolFrags(), pick
 the on that does what you like:

 http://rdkit.org/docs/cppapi/namespaceRDKit_1_1MolOps.html#ad8100d785d32fb3c173b83949766b87b

 Since the Python and C++ function/method names are often similar to
 each other, a good way to find answers like this is to google for the name
 of the Python function you are looking for and look for the link to the C++
 documentation in the results.

 Best,
 -greg

>>>
>>>
>>>
>>> --
>>> Find and fix application performance issues faster with Applications
>>> Manager
>>> Applications Manager provides deep performance insights into multiple
>>> tiers of
>>> your business applications. It resolves application problems quickly and
>>> reduces your MTTR. Get your free trial! http://pubads.g.doubleclick.net/
>>> gampad/clk?id=1444514301=/ca-pub-7940484522588532
>>> 
>>> ___
>>> Rdkit-discuss mailing list
>>> Rdkit-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>
>>>
>>
>
> --
> Find and fix application performance issues faster with Applications
> Manager
> Applications Manager provides deep performance insights into multiple
> tiers of
> your business applications. It resolves application problems quickly and
> reduces your MTTR. Get your free trial! http://pubads.g.doubleclick.net/
>
> gampad/clk?id=1444514301=/ca-pub-7940484522588532___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
>
--
Find and fix application performance issues faster with 

Re: [Rdkit-discuss] GetMol and GetMolFrags in C++

[David Hall]

When I want to replicate one of RDKit’s python functions in C++, I go to the 
source. RDKit has very readable wrappers that make this a surprisingly nice 
approach (many other pieces of software have pretty ugly wrappers, so this is a 
major compliment to RDKit).

For this, I think the source is:

https://github.com/rdkit/rdkit/blob/master/Code/GraphMol/Wrap/MolOps.cpp#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.

-David


> On Apr 11, 2016, at 8:24 AM, Yingfeng Wang  wrote:
> 
> lgor,
> 
> Yes, this version looks good. But, I am wondering whether I can specify 
> asMols. I specify asMols in the python version of my tool, so I want to do 
> the same thing for getting the same result in my C++ code. Or could you help 
> me to confirm that the version you mentioned actually has the same effect as 
> asMols = true?
> 
> Thanks.
> Yingfeng
> 
> On Sun, Apr 10, 2016 at 11:35 PM, Igor Filippov  > wrote:
> Did you want
> std::vector> > 
> RDKit::MolOps::getMolFrags ( const ROMol 
>  &  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, Yingfeng Wang  > wrote:
> Greg,
> 
> Thanks. In python, I am using GetMolFrags by the following way,
> 
> Chem.GetMolFrags(current_modified_mol, asMols=True, sanitizeFrags=False)
> 
> However, there is not a version at the link you mentioned allows me to 
> specify asMols. Could you please give me more hints?
> 
> Thanks.
> Yingfeng
> 
> On Sun, Apr 10, 2016 at 10:49 PM, Greg Landrum  > wrote:
> 
> 
> On Mon, Apr 11, 2016 at 1:35 AM, Yingfeng Wang  > wrote:
> 
> Thanks. Say, the current RWMol object has 10 bonds, so ids of these bonds 
> should be from 1-10. Now, I remove one bond. How do I reset all nine bonds 
> with ids from 1-9 (if one or two atoms are gone with this bond, I also want 
> to reset the ids of these atoms).
> 
> You don't need to do that, it happens automatically
>  
> In addition, say, there are two fragments after one bond is removed. How do I 
> get these two fragments as mols. In python, I can use Chem.GetMolFrags. But 
> how do I get my job done in C++?
> 
> There are a number of different versions of MolOps::getMolFrags(), pick the 
> on that does what you like:
> http://rdkit.org/docs/cppapi/namespaceRDKit_1_1MolOps.html#ad8100d785d32fb3c173b83949766b87b
>  
> 
> 
> Since the Python and C++ function/method names are often similar to each 
> other, a good way to find answers like this is to google for the name of the 
> Python function you are looking for and look for the link to the C++ 
> documentation in the results. 
> 
> Best,
> -greg
> 
> 
> --
> Find and fix application performance issues faster with Applications Manager
> Applications Manager provides deep performance insights into multiple tiers of
> your business applications. It resolves application problems quickly and
> reduces your MTTR. Get your free trial! http://pubads.g.doubleclick.net/
> gampad/clk?id=1444514301=/ca-pub-7940484522588532 
> 
> ___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net 
> 
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss 
> 
> 
> 
> 
> --
> Find and fix application performance issues faster with Applications Manager
> Applications Manager provides deep performance insights into multiple tiers of
> your business applications. It resolves application problems quickly and
> reduces your MTTR. Get your free trial! http://pubads.g.doubleclick.net/
> gampad/clk?id=1444514301=/ca-pub-7940484522588532___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

--
Find and fix application performance issues faster with Applications Manager
Applications Manager provides deep 

Re: [Rdkit-discuss] GetMol and GetMolFrags in C++

[Yingfeng Wang]

lgor,

Yes, this version looks good. But, I am wondering whether I can specify
asMols. I specify asMols in the python version of my tool, so I want to do
the same thing for getting the same result in my C++ code. Or could you
help me to confirm that the version you mentioned actually has the same
effect as asMols = true?

Thanks.
Yingfeng

On Sun, Apr 10, 2016 at 11:35 PM, Igor Filippov 
wrote:

> Did you want
> std::vector> >
> RDKit::MolOps::getMolFrags ( const ROMol
>  &  *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, Yingfeng Wang 
> wrote:
>
>> Greg,
>>
>> Thanks. In python, I am using GetMolFrags by the following way,
>>
>> Chem.GetMolFrags(current_modified_mol, asMols=True, sanitizeFrags=False)
>>
>> However, there is not a version at the link you mentioned allows me to
>> specify asMols. Could you please give me more hints?
>>
>> Thanks.
>> Yingfeng
>>
>> On Sun, Apr 10, 2016 at 10:49 PM, Greg Landrum 
>> wrote:
>>
>>>
>>>
>>> On Mon, Apr 11, 2016 at 1:35 AM, Yingfeng Wang 
>>> wrote:


 Thanks. Say, the current RWMol object has 10 bonds, so ids of these
 bonds should be from 1-10. Now, I remove one bond. How do I reset all nine
 bonds with ids from 1-9 (if one or two atoms are gone with this bond, I
 also want to reset the ids of these atoms).

>>>
>>> You don't need to do that, it happens automatically
>>>
>>>
 In addition, say, there are two fragments after one bond is removed.
 How do I get these two fragments as mols. In python, I can use
 Chem.GetMolFrags. But how do I get my job done in C++?

>>>
>>> There are a number of different versions of MolOps::getMolFrags(), pick
>>> the on that does what you like:
>>>
>>> http://rdkit.org/docs/cppapi/namespaceRDKit_1_1MolOps.html#ad8100d785d32fb3c173b83949766b87b
>>>
>>> Since the Python and C++ function/method names are often similar to each
>>> other, a good way to find answers like this is to google for the name of
>>> the Python function you are looking for and look for the link to the C++
>>> documentation in the results.
>>>
>>> Best,
>>> -greg
>>>
>>
>>
>>
>> --
>> Find and fix application performance issues faster with Applications
>> Manager
>> Applications Manager provides deep performance insights into multiple
>> tiers of
>> your business applications. It resolves application problems quickly and
>> reduces your MTTR. Get your free trial! http://pubads.g.doubleclick.net/
>> gampad/clk?id=1444514301=/ca-pub-7940484522588532
>> 
>> ___
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>>
>
--
Find and fix application performance issues faster with Applications Manager
Applications Manager provides deep performance insights into multiple tiers of
your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial! http://pubads.g.doubleclick.net/
gampad/clk?id=1444514301=/ca-pub-7940484522588532___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] [Rdkit-devel] Beta of Q1 2016 release now up

[Greg Landrum]

Gianluca,

This could be the issue fixed by this PR from Matt Swain:
https://github.com/rdkit/rdkit/pull/856

-greg


On Mon, Apr 11, 2016 at 12:32 PM, Gianluca Sforna  wrote:

> On Thu, Apr 7, 2016 at 6:24 AM, Greg Landrum 
> wrote:
> > I have tagged a beta of the next RDKit release here:
> > https://github.com/rdkit/rdkit/releases/tag/Release_2016_03_1b1
>
>
> Tried to rebuild the RPMs but got this right on cmake:
>
> -- Found INCHI: /usr/lib64/libinchi.so
> CMake Error at External/INCHI-API/CMakeLists.txt:64 (install):
>   install TARGETS given target "Inchi" which does not exist in this
>   directory.
>
>
> cmake invocation as follow:
>
> /usr/bin/cmake -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG
> -DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG
> -DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG
> -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_PREFIX:PATH=/usr
> -DINCLUDE_INSTALL_DIR:PATH=/usr/include
> -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc
> -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64
> -DBUILD_SHARED_LIBS:BOOL=ON -D RDK_INSTALL_INTREE=OFF -D
> CMAKE_BUILD_TYPE=RelWithDebInfo -D RDK_BUILD_INCHI_SUPPORT:BOOL=ON -D
> RDK_BUILD_THREADSAFE_SSS:BOOL=ON -D RDK_BUILD_CAIRO_SUPPORT:BOOL=ON -D
> RDK_INSTALL_STATIC_LIBS:BOOL=OFF -D RDK_USE_FLEXBISON:BOOL=ON -D
> RDK_TEST_MULTITHREADED:BOOL=ON -D
> PYTHON_EXECUTABLE:FILEPATH=/usr/bin/python2 .
>
> I'll dig in it later, in the meanwhile if you have ideas they will be
> very welcome.
>
--
Find and fix application performance issues faster with Applications Manager
Applications Manager provides deep performance insights into multiple tiers of
your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial! http://pubads.g.doubleclick.net/
gampad/clk?id=1444514301=/ca-pub-7940484522588532___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] [Rdkit-devel] Beta of Q1 2016 release now up

[Gianluca Sforna]

On Thu, Apr 7, 2016 at 6:24 AM, Greg Landrum  wrote:
> I have tagged a beta of the next RDKit release here:
> https://github.com/rdkit/rdkit/releases/tag/Release_2016_03_1b1


Tried to rebuild the RPMs but got this right on cmake:

-- Found INCHI: /usr/lib64/libinchi.so
CMake Error at External/INCHI-API/CMakeLists.txt:64 (install):
  install TARGETS given target "Inchi" which does not exist in this
  directory.


cmake invocation as follow:

/usr/bin/cmake -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG
-DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG
-DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG
-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_PREFIX:PATH=/usr
-DINCLUDE_INSTALL_DIR:PATH=/usr/include
-DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc
-DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64
-DBUILD_SHARED_LIBS:BOOL=ON -D RDK_INSTALL_INTREE=OFF -D
CMAKE_BUILD_TYPE=RelWithDebInfo -D RDK_BUILD_INCHI_SUPPORT:BOOL=ON -D
RDK_BUILD_THREADSAFE_SSS:BOOL=ON -D RDK_BUILD_CAIRO_SUPPORT:BOOL=ON -D
RDK_INSTALL_STATIC_LIBS:BOOL=OFF -D RDK_USE_FLEXBISON:BOOL=ON -D
RDK_TEST_MULTITHREADED:BOOL=ON -D
PYTHON_EXECUTABLE:FILEPATH=/usr/bin/python2 .

I'll dig in it later, in the meanwhile if you have ideas they will be
very welcome.

--
Find and fix application performance issues faster with Applications Manager
Applications Manager provides deep performance insights into multiple tiers of
your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial! http://pubads.g.doubleclick.net/
gampad/clk?id=1444514301=/ca-pub-7940484522588532
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] has multiple H count specifications

[吴玲]

hi Greg,

when I use the AllChem.ReactionFromSmarts and the RunReactants predict a 
reaction,just like below:

input transformation - 
"[CH2,CH3:8][OH:9].[O:1]=[O:2]>>[OH:1][OH:2].[CH2,CH3:8](=[O:9]",
input reactants-  reactants1 = ['CO','CCO','CC(C)O','COC','c1c1O',]  
reactants2= ['O=O']
output product-
CO.O=O>>OO.C=O.OO.C=O
CCO.O=O>>OO.C[CH2]=O.OO.C[CH2]=O
CC(C)O.O=O>>
COC.O=O>>
c1c1O.O=O>>
the result is correct ! but if I change the order,write the above-mentioned 
transformations as 
"[O:1]=[O:2].[CH2,CH3:8][OH:9]>>[OH:1][OH:2].[CH2,CH3:8](=[O:9])", there is no 
result output,and warning that atom 0 in product 1 has multiple H count 
specifications , what's the cause of this?
output:
CO.O=O>>
CCO.O=O>>
CC(C)O.O=O>>
 COC.O=O>>
 c1c1O.O=O>>

best wishes,

monica

 
--
Find and fix application performance issues faster with Applications Manager
Applications Manager provides deep performance insights into multiple tiers of
your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial! http://pubads.g.doubleclick.net/
gampad/clk?id=1444514301=/ca-pub-7940484522588532___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] running RunReactants with Reactants that have a plus one charge

[吴玲]

Hi  Greg,
when I run the AllChem.RunReactants with rxn'patterns that the reactant have a 
plus one charge ,like this :
  
'''
   patterns = [

"[NH+:2]1[C:3][C:4][C:5][C@@H:6]1.[OH2:15].[O:17]=[O:18]>>[NH2+:2][C:3][C:4][C:5][C:6]=[O:17].[OH:18][OH:15]",

"[NH+:2]1[C:3][C:4][C:5][CH:6]1.[OH2:15].[O:17]=[O:18]>>[NH2+:2][C:3][C:4][C:5][C:6]=[O:17].[OH:18][OH:15]",

"[NH+:2]1[C:3][C:4][C:5][C:6]1.[OH2:15].[O:17]=[O:18]>>[NH2+:2][C:3][C:4][C:5][C:6]=[O:17].[OH:18][OH:15]",

"[N+:2]1[C:3][C:4][C:5][C:6]1.[OH2:15].[O:17]=[O:18]>>[N+:2][C:3][C:4][C:5][C:6]=[O:17].[OH:18][OH:15]",
]
rs1 = ['N11']
rs2 = ['O']
rs3 = ['O=O']

for idx, pattern in enumerate(patterns, 1):
rxn = ReactionFromSmarts(pattern)
  
index = 0
for a in rs1:
a_ = MolFromSmiles(a)
for b in rs2:
b_ = MolFromSmiles(b)
for c in rs3:
c_ = MolFromSmiles(c)

ps = [
MolToSmiles(c) for ps in rxn.RunReactants((a_, b_,c_))
for p in ps]

index += 1
print '{idx}.{index} {a}.{b}.{c}>>{ps}'.format(
idx=idx, index=index, a=a, b=b,c=c, ps='.'.join(ps))
'''
why there is no any product output ,and how should I deal with the atom;charge 
and stereoisomerism?
also when I remove the charge information(patterns = [ 
"[N:2]1[C:3][C:4][C:5][C:6]1.[OH2:15].[O:17]=[O:18]>>[N:2][C:3][C:4][C:5][C:6]=[O:17].[OH:18][OH:15]",
]), it occurs an error like below:
  File 
"/home/qnhu/Project/Database/Rhea_Dedup/AllEcToAllRxn/Chemaxon/predict.py", 
line 48, in main3
for p in ps]
Boost.Python.ArgumentError: Python argument types in
rdkit.Chem.rdmolfiles.MolToSmiles(str)
did not match C++ signature:
MolToSmiles(RDKit::ROMol mol, bool isomericSmiles=False, bool 
kekuleSmiles=False, int rootedAtAtom=-1, bool canonical=True, bool 
allBondsExplicit=False)

how should I do?
best wishes,
wl










 --
Find and fix application performance issues faster with Applications Manager
Applications Manager provides deep performance insights into multiple tiers of
your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial! http://pubads.g.doubleclick.net/
gampad/clk?id=1444514301=/ca-pub-7940484522588532___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss