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

2016-04-11 Thread 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

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

2016-04-11 Thread 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
> 
> 
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> your business applications. It resolves application problems quickly and
> reduces your MTTR. Get your free trial! http://pubads.g.doubleclick.net/
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> 
> 
> 
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Re: [Rdkit-discuss] GetMol and GetMolFrags in C++

2016-04-11 Thread 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
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>>
>>
>
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Re: [Rdkit-discuss] GetMol and GetMolFrags in C++

2016-04-10 Thread Igor Filippov 
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
>>
>
>
>
> --
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> Manager
> Applications Manager provides deep performance insights into multiple
> tiers of
> your business applications. It resolves application problems quickly and
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Re: [Rdkit-discuss] GetMol and GetMolFrags in C++

2016-04-10 Thread Yingfeng Wang 
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
>
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Re: [Rdkit-discuss] GetMol and GetMolFrags in C++

2016-04-10 Thread Greg Landrum 
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
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Re: [Rdkit-discuss] GetMol and GetMolFrags in C++

2016-04-10 Thread Yingfeng Wang 
Brian,

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). 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++?

Again, thank you very much!

Yingfeng

On Sun, Apr 10, 2016 at 6:31 PM, Brian Kelley  wrote:

> In C++ you don'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 Kelley
>
> > On Apr 10, 2016, at 6:27 PM, Yingfeng Wang  wrote:
> >
> > 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
> >
> --
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Re: [Rdkit-discuss] GetMol and GetMolFrags in C++

2016-04-10 Thread Brian Kelley 
In C++ you don'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 Kelley

> On Apr 10, 2016, at 6:27 PM, Yingfeng Wang  wrote:
> 
> 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
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[Rdkit-discuss] GetMol and GetMolFrags in C++

2016-04-10 Thread Yingfeng Wang 
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
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