[Rdkit-discuss] Is there someone who manages to compile rdkit Release_2020_03_4 from sources on a Mac?

2020-07-07 Thread Francois Berenger 

Dear rdkiters,

I am trying to repair the brew formula.

Currently, I get this when I try to compile Release_2020_03_4:

$ cd build
$ cmake -DPYTHON_EXECUTABLE=/usr/local/bin/python-3.7 
-DRDK_INSTALL_INTREE=OFF -DRDK_BUILD_INCHI_SUPPORT=ON 
-DRDK_BUILD_AVALON_SUPPORT=ON -DRDK_BUILD_PYTHON_WRAPPERS=ON 
-DCMAKE_INSTALL_PREFIX=/usr ../


-->

Not sure this one is a show stopper:
---
-- Found InChI software locally
Python Install directory
CMake Error at CMakeLists.txt:290 (install):
  install DIRECTORY given no DESTINATION!
---

This one stops the show for sure:
---
CMake Error at Code/GraphMol/FilterCatalog/CMakeLists.txt:10 (if):
  if given arguments:

"VERSION_GREATER" "2.6"

  Unknown arguments specified
---

Thanks for any help,
F.

PS: I do think cmake is the worst build system I ever encountered in my 
life...



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Re: [Rdkit-discuss] ConstrainedEmbed issue

2020-07-07 Thread Pavel Polishchuk 

Thank you, Sereina.
I understand importance of addition of hydrogens to get a reasonable 3D 
coordinates. But the situation may be not that simple.


1. Addition of hydrogen is only required for custom coordinates supplied 
from an external file. If coordinates of a template is generated with 
rdkit embedding it works without addition of explicit hydrogens.


2. I found an opposite example where addition of hydrogens breaks 
constrained embedding if custom coordinates of a template is used. And 
again if I generate coordinates of a template by rdkit everything is OK 
without addition of Hs.


These suggest that there is some issue with custom coordinates usage for 
constrained embedding.


I provided the code and output below.

Code:

data = [('1.mol', 'C[C@@H]1C1=O', 'C[C@@H]1CC[C@H](O)CC1=O'),
    ('2.mol', '[C@@H](CCC)NC(=O)c1ccc(F)cc1', 
'[C@H](CCC[C@@H](CCC)NC(=O)c1ccc(F)cc1)NC(=O)c1ccco1')]


for i, (mol_fname, smi_template, smi_child) in enumerate(data):

    print('iteration', i)

    mode = 'read template mol file, no AddHs'
    print(mode)
    mol_template = Chem.MolFromMolFile(mol_fname)
    mol_child = Chem.MolFromSmiles(smi_child)
    try:
    mol = AllChem.ConstrainedEmbed(mol_child, mol_template)
    print(mol.GetProp('EmbedRMS'))
    except ValueError as e:
    print(e)

    mode = 'read template mol file, AddHs'
    print(mode)
    mol_template = Chem.MolFromMolFile(mol_fname)
    mol_child = Chem.MolFromSmiles(smi_child)
    try:
    mol = AllChem.ConstrainedEmbed(Chem.AddHs(mol_child), mol_template)
    print(mol.GetProp('EmbedRMS'))
    except ValueError as e:
    print(e)

    mode = 'embed template mol in rdkit, no AddHs'
    print(mode)
    mol_template = Chem.MolFromSmiles(smi_template)
    AllChem.EmbedMolecule(mol_template)
    mol_child = Chem.MolFromSmiles(smi_child)
    try:
    mol = AllChem.ConstrainedEmbed(mol_child, mol_template)
    print(mol.GetProp('EmbedRMS'))
    except ValueError as e:
    print(e)

Output:

iteration 0
read template mol file, no AddHs
Could not embed molecule.
read template mol file, AddHs
0.05014807519735495
embed template mol in rdkit, no AddHs
0.12358989886023371

iteration 1
read template mol file, no AddHs
0.057937898735270194
read template mol file, AddHs
Could not embed molecule. # <-- here rdkit spends a lot of time but 
fails

embed template mol in rdkit, no AddHs
0.1012757033705761


Pavel.



On 07/07/2020 21:41, Sunhwan Jo wrote:

Makes sense :)


On Jul 7, 2020, at 12:35 PM, Sereina Riniker 
mailto:sereina.rini...@gmail.com>> wrote:


Dear Pavel and Sunhwan,

Please note that hydrogens should always be added for the embedding 
algorithm to work properly (i.e. it’s not a walk around but what 
should be done).
See also Section “Working with 3D Molecules” in 
https://www.rdkit.org/docs/GettingStartedInPython.html


Best regards,
Sereina



On 7 Jul 2020, at 21:26, Sunhwan Jo > wrote:



The reason constraint embed didn’t work is the molecule simply can’t 
be embedded using the rdkit’s algorithm.



In [25]: mol_child = Chem.MolFromSmiles('C[C@@H]1CC[C@H](O)CC1=O')

In [26]: AllChem.EmbedMolecule(mol_child)
Out[26]: -1


See more discussion here:
https://github.com/rdkit/rdkit/issues/2996


The SMILES you posted looks valid to me and doesn’t look that 
complicated, but the anyway I think
somehow the RDKit’s algorithm tripped up and couldn’t finish 
embedding without some help. Hope

someone with more in-depth insight can help here.


Anyway, for a walk around, adding H seems to do the trick:


In [39]: mol = AllChem.AddHs(mol_child)

In [40]: AllChem.EmbedMolecule(mol)
Out[40]: 0 # worked

In [41]: AllChem.ConstrainedEmbed(mol, mol_parent)
Out[41]:  # also worked




Sunhwan




On Jul 7, 2020, at 12:36 AM, Pavel Polishchuk 
mailto:pavel_polishc...@ukr.net>> wrote:


Hi all,

  I have an issue with ConstrainedEmbed and I cannot figure out 
what exactly causes this.
  I have a molecule C[C@@H]1C1=O with 3D coordinates in 1.mol 
file (attached). And I want to generate coordinates for another 
structure with this core -

C[C@@H]1CC[C@H](O)CC1=O.

  This is usual way which causes issue with embedding and the 
corresponding error.


mol_parent = Chem.MolFromMolFile('1.mol')
mol_child = Chem.MolFromSmiles('C[C@@H]1CC[C@H](O)CC1=O')
try:
    mol = AllChem.ConstrainedEmbed(mol_child, mol_parent)
except ValueError as e:
    print(e)

  If I add explicit hydrogens the issue disappears.

mol_parent = Chem.MolFromMolFile('1.mol')
mol_child = Chem.MolFromSmiles('C[C@@H]1CC[C@H](O)CC1=O')
mol = AllChem.ConstrainedEmbed(Chem.AddHs(mol_child), mol_parent)

  If I do not use pre-defined coordinates - everything works well.

mol_parent = Chem.MolFromSmiles('C[C@@H]1C1=O')
AllChem.EmbedMolecule(mol_parent)
mol_child = Chem.MolFromSmiles('C[C@@H]1CC[C@H](O)CC1=O')
mol = AllChem.ConstrainedEmbed(mol_child, mol_parent)

  Does ugly coordinates in 1.mol file cause the

Re: [Rdkit-discuss] ConstrainedEmbed issue

2020-07-07 Thread Sunhwan Jo 
Makes sense :)


> On Jul 7, 2020, at 12:35 PM, Sereina Riniker  
> wrote:
> 
> Dear Pavel and Sunhwan,
> 
> Please note that hydrogens should always be added for the embedding algorithm 
> to work properly (i.e. it’s not a walk around but what should be done).
> See also Section “Working with 3D Molecules” in 
> https://www.rdkit.org/docs/GettingStartedInPython.html 
> 
> 
> Best regards,
> Sereina
> 
> 
> 
>> On 7 Jul 2020, at 21:26, Sunhwan Jo > > wrote:
>> 
>> 
>> The reason constraint embed didn’t work is the molecule simply can’t be 
>> embedded using the rdkit’s algorithm.
>> 
>>> In [25]: mol_child = Chem.MolFromSmiles('C[C@@H]1CC[C@H](O)CC1=O')  
>>>   
>>> 
>>> In [26]: AllChem.EmbedMolecule(mol_child)   
>>>   
>>> Out[26]: -1
>> 
>> 
>> See more discussion here:
>> https://github.com/rdkit/rdkit/issues/2996 
>> 
>> 
>> 
>> The SMILES you posted looks valid to me and doesn’t look that complicated, 
>> but the anyway I think
>> somehow the RDKit’s algorithm tripped up and couldn’t finish embedding 
>> without some help. Hope
>> someone with more in-depth insight can help here.
>> 
>> 
>> Anyway, for a walk around, adding H seems to do the trick:
>> 
>>> In [39]: mol = AllChem.AddHs(mol_child) 
>>>   
>>> 
>>> In [40]: AllChem.EmbedMolecule(mol) 
>>>   
>>> Out[40]: 0 # worked
>>> 
>>> In [41]: AllChem.ConstrainedEmbed(mol, mol_parent)  
>>>   
>>> Out[41]:  # also worked
>>> 
>> 
>> 
>> 
>> Sunhwan
>> 
>> 
>> 
>> 
>>> On Jul 7, 2020, at 12:36 AM, Pavel Polishchuk >> > wrote:
>>> 
>>> Hi all,
>>> 
>>>   I have an issue with ConstrainedEmbed and I cannot figure out what 
>>> exactly causes this.
>>>   I have a molecule C[C@@H]1C1=O with 3D coordinates in 1.mol file 
>>> (attached). And I want to generate coordinates for another structure with 
>>> this core -
>>> C[C@@H]1CC[C@H](O)CC1=O.
>>> 
>>>   This is usual way which causes issue with embedding and the corresponding 
>>> error.
>>> 
>>> mol_parent = Chem.MolFromMolFile('1.mol')
>>> mol_child = Chem.MolFromSmiles('C[C@@H]1CC[C@H](O)CC1=O')
>>> try:
>>> mol = AllChem.ConstrainedEmbed(mol_child, mol_parent)
>>> except ValueError as e:
>>> print(e)
>>> 
>>>   If I add explicit hydrogens the issue disappears.
>>> 
>>> mol_parent = Chem.MolFromMolFile('1.mol')
>>> mol_child = Chem.MolFromSmiles('C[C@@H]1CC[C@H](O)CC1=O')
>>> mol = AllChem.ConstrainedEmbed(Chem.AddHs(mol_child), mol_parent)
>>> 
>>>   If I do not use pre-defined coordinates - everything works well.
>>> 
>>> mol_parent = Chem.MolFromSmiles('C[C@@H]1C1=O')
>>> AllChem.EmbedMolecule(mol_parent)
>>> mol_child = Chem.MolFromSmiles('C[C@@H]1CC[C@H](O)CC1=O')
>>> mol = AllChem.ConstrainedEmbed(mol_child, mol_parent)
>>> 
>>>   Does ugly coordinates in 1.mol file cause the embedding issue? Or the 
>>> issue is caused by some implicit properties of a molecule? How to solve 
>>> this properly?
>>> 
>>> Kind regards,
>>> Pavel.
>>> <1.mol>___
>>> Rdkit-discuss mailing list
>>> Rdkit-discuss@lists.sourceforge.net 
>>> 
>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss 
>>> 
>> 
>> ___
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>> 
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Re: [Rdkit-discuss] ConstrainedEmbed issue

2020-07-07 Thread Sereina Riniker 
Dear Pavel and Sunhwan,

Please note that hydrogens should always be added for the embedding algorithm 
to work properly (i.e. it’s not a walk around but what should be done).
See also Section “Working with 3D Molecules” in 
https://www.rdkit.org/docs/GettingStartedInPython.html

Best regards,
Sereina



> On 7 Jul 2020, at 21:26, Sunhwan Jo  wrote:
> 
> 
> The reason constraint embed didn’t work is the molecule simply can’t be 
> embedded using the rdkit’s algorithm.
> 
>> In [25]: mol_child = Chem.MolFromSmiles('C[C@@H]1CC[C@H](O)CC1=O')   
>>  
>> 
>> In [26]: AllChem.EmbedMolecule(mol_child)
>>  
>> Out[26]: -1
> 
> 
> See more discussion here:
> https://github.com/rdkit/rdkit/issues/2996 
> 
> 
> 
> The SMILES you posted looks valid to me and doesn’t look that complicated, 
> but the anyway I think
> somehow the RDKit’s algorithm tripped up and couldn’t finish embedding 
> without some help. Hope
> someone with more in-depth insight can help here.
> 
> 
> Anyway, for a walk around, adding H seems to do the trick:
> 
>> In [39]: mol = AllChem.AddHs(mol_child)  
>>  
>> 
>> In [40]: AllChem.EmbedMolecule(mol)  
>>  
>> Out[40]: 0 # worked
>> 
>> In [41]: AllChem.ConstrainedEmbed(mol, mol_parent)   
>>  
>> Out[41]:  # also worked
>> 
> 
> 
> 
> Sunhwan
> 
> 
> 
> 
>> On Jul 7, 2020, at 12:36 AM, Pavel Polishchuk > > wrote:
>> 
>> Hi all,
>> 
>>   I have an issue with ConstrainedEmbed and I cannot figure out what exactly 
>> causes this.
>>   I have a molecule C[C@@H]1C1=O with 3D coordinates in 1.mol file 
>> (attached). And I want to generate coordinates for another structure with 
>> this core -
>> C[C@@H]1CC[C@H](O)CC1=O.
>> 
>>   This is usual way which causes issue with embedding and the corresponding 
>> error.
>> 
>> mol_parent = Chem.MolFromMolFile('1.mol')
>> mol_child = Chem.MolFromSmiles('C[C@@H]1CC[C@H](O)CC1=O')
>> try:
>> mol = AllChem.ConstrainedEmbed(mol_child, mol_parent)
>> except ValueError as e:
>> print(e)
>> 
>>   If I add explicit hydrogens the issue disappears.
>> 
>> mol_parent = Chem.MolFromMolFile('1.mol')
>> mol_child = Chem.MolFromSmiles('C[C@@H]1CC[C@H](O)CC1=O')
>> mol = AllChem.ConstrainedEmbed(Chem.AddHs(mol_child), mol_parent)
>> 
>>   If I do not use pre-defined coordinates - everything works well.
>> 
>> mol_parent = Chem.MolFromSmiles('C[C@@H]1C1=O')
>> AllChem.EmbedMolecule(mol_parent)
>> mol_child = Chem.MolFromSmiles('C[C@@H]1CC[C@H](O)CC1=O')
>> mol = AllChem.ConstrainedEmbed(mol_child, mol_parent)
>> 
>>   Does ugly coordinates in 1.mol file cause the embedding issue? Or the 
>> issue is caused by some implicit properties of a molecule? How to solve this 
>> properly?
>> 
>> Kind regards,
>> Pavel.
>> <1.mol>___
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net 
>> 
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
> 
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[Rdkit-discuss] ConstrainedEmbed issue

2020-07-07 Thread Pavel Polishchuk 

Hi all,

  I have an issue with ConstrainedEmbed and I cannot figure out what 
exactly causes this.
  I have a molecule C[C@@H]1C1=O with 3D coordinates in 1.mol file 
(attached). And I want to generate coordinates for another structure 
with this core -

C[C@@H]1CC[C@H](O)CC1=O.

  This is usual way which causes issue with embedding and the 
corresponding error.


mol_parent = Chem.MolFromMolFile('1.mol')
mol_child = Chem.MolFromSmiles('C[C@@H]1CC[C@H](O)CC1=O')
try:
    mol = AllChem.ConstrainedEmbed(mol_child, mol_parent)
except ValueError as e:
    print(e)

  If I add explicit hydrogens the issue disappears.

mol_parent = Chem.MolFromMolFile('1.mol')
mol_child = Chem.MolFromSmiles('C[C@@H]1CC[C@H](O)CC1=O')
mol = AllChem.ConstrainedEmbed(Chem.AddHs(mol_child), mol_parent)

  If I do not use pre-defined coordinates - everything works well.

mol_parent = Chem.MolFromSmiles('C[C@@H]1C1=O')
AllChem.EmbedMolecule(mol_parent)
mol_child = Chem.MolFromSmiles('C[C@@H]1CC[C@H](O)CC1=O')
mol = AllChem.ConstrainedEmbed(mol_child, mol_parent)

  Does ugly coordinates in 1.mol file cause the embedding issue? Or the 
issue is caused by some implicit properties of a molecule? How to solve 
this properly?


Kind regards,
Pavel.


1.mol
Description: MOL mdl chemical test
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