date:20180823

Re: [Rdkit-discuss] Alignment using LIgpargen file

2018-08-23 Thread Paolo Tosco


Dear Phuong,

you might just update the coordinates of the LigParGen PDB with the 
aligned coordinates.


Cheers,
p.


On 08/23/18 18:23, Phuong Chau wrote:

Dear Paolo,

The new chemical chemical after alignment (UNK.pdb) file is in format 
of RDKIT pdb file. Is it possible for the output in format of 
LIgParGen? I am trying to run stimulation with the aligned chemical 
but it seems like it can not read pdb file generated from RDKit.


Best,

Phuong Chau

On Wed, Aug 22, 2018 at 12:32 PM, Paolo Tosco 
mailto:paolo.tosco.m...@gmail.com>> wrote:


Dear Phuong,

it works for me with the latest RDKit release. I am wondering if
you are using an older RDKit version where maybe the PDB parser
was not assigning formal charges based on connectivity? Then you
would have to manually set the formal charge of the protonated
nitrogen atom (# 2 N) to +1.

Cheers,
p.


On 08/22/18 19:06, Phuong Chau wrote:

Hi Paolo,

I got this new error when I tried with different chemicals:

python 3DAlignmentwith3OAwithGRO.py CCNC\(N\)N_afterMD.pdb
CC\[NH2\+\]CCN_Ligpargen.pdb
[12:02:45] Explicit valence for atom # 2 N, 4, is greater than
permitted
Traceback (most recent call last):
  File "3DAlignmentwith3OAwithGRO.py", line 12, in 
    rdDistGeom.EmbedMolecule(prbMolwithH)
Boost.Python.ArgumentError: Python argument types in
    rdkit.Chem.rdDistGeom.EmbedMolecule(NoneType)
did not match C++ signature:
    EmbedMolecule(RDKit::ROMol {lvalue} mol, unsigned int
maxAttempts=0, int randomSeed=-1, bool clearConfs=True, bool
useRandomCoords=False, double boxSizeMult=2.0, bool
randNegEig=True, unsigned int numZeroFail=1, boost::python::dict
{lvalue} coordMap={}, double forceTol=0.001, bool
ignoreSmoothingFailures=False)

The second argument I also downloaded it from Ligpargen but it
gave me this error. I am not so sure why it happened.

I also attached the two files :

On Tue, Aug 21, 2018 at 3:19 PM, Paolo Tosco
mailto:paolo.tosco.m...@gmail.com>>
wrote:

Hi Phuong,

it does have hydrogens after the alignment:

$ ls
UNK_A1C198.pdb  align.py drug.pdb

$ python align.py drug.pdb UNK_A1C198.pdb

$ ls
UNK.pdb UNK_A1C198.pdb  align.py  drug.pdb

$ cat UNK.pdb
ATOM  1  C00 UNK 1 37.884  56.016  51.678  1.00
0.00   C
ATOM  2  C01 UNK 1 37.501  54.554  51.968  1.00
0.00   C
ATOM  3  C02 UNK 1 36.085  54.316  52.531  1.00
0.00   C
ATOM  4  C03 UNK 1 35.697  55.221  53.715  1.00
0.00   C
ATOM  5  C04 UNK 1 34.907  56.485  53.304  1.00
0.00   C
ATOM  6  C05 UNK 1 35.788  57.733  53.108  1.00
0.00   C
ATOM  7  C06 UNK 1 36.227  57.998  51.654  1.00
0.00   C
ATOM  8  C07 UNK 1 36.813  56.799  50.889  1.00
0.00   C
ATOM  9  H08 UNK 1 38.821  56.001  51.080  1.00
0.00   H
ATOM 10  H09 UNK 1 38.160  56.522  52.625  1.00
0.00   H
ATOM 11  H0A UNK 1 37.598  53.969  51.027  1.00
0.00   H
ATOM 12  H0B UNK 1 38.243  54.138  52.684  1.00
0.00   H
ATOM 13  H0C UNK 1 35.325  54.368  51.723  1.00
0.00   H
ATOM 14  H0D UNK 1 36.057  53.262  52.884  1.00
0.00   H
ATOM 15  H0E UNK 1 35.031  54.622  54.375  1.00
0.00   H
ATOM 16  H0F UNK 1 36.586  55.471  54.333  1.00
0.00   H
ATOM 17  H0G UNK 1 34.203  56.712  54.134  1.00
0.00   H
ATOM 18  H0H UNK 1 34.270  56.304  52.411  1.00
0.00   H
ATOM 19  H0I UNK 1 35.198  58.620  53.428  1.00
0.00   H
ATOM 20  H0J UNK 1 36.665  57.714  53.788  1.00
0.00   H
ATOM 21  H0K UNK 1 36.982  58.814  51.667  1.00
0.00   H
ATOM 22  H0M UNK 1 35.352  58.378  51.082  1.00
0.00   H
ATOM 23  H0N UNK 1 35.991  56.144  50.537  1.00
0.00   H
ATOM 24  H0O UNK 1 37.280  57.194  49.960  1.00
0.00   H
CONECT    1    2    8    9   10
CONECT    2    3   11   12
CONECT    3    4   13   14
CONECT    4    5   15   16
CONECT    5    6   17   18
CONECT    6    7   19   20
CONECT    7    8   21   22
CONECT    8   23   24
END

p.


On 08/21/18 20:46, Phuong Chau wrote:

Hi Paolo,

I tried the code, it worked with the alignment but the new
chemical after alignment still does not have any H atoms.

Re: [Rdkit-discuss] Matching Generalized Compounds

2018-08-23 Thread Kovas Palunas

Thanks for the feedback and code example!

I understand that it works to make a third query mol using MCS that matches 
both the original mols to then match with.  However, this seems like overkill 
(overly expensive) for this particular problem – as I understand it MCS can be 
very expensive depending on the compounds you are comparing.  Would it not work 
to simply override the atom.Match function with one that will always match 
dummies no matter what the other atom is?  I am not planning to compare SMARTSy 
queries with my matching with any complexity beyond simply dummy atoms.  In 
fact, as I understand it, my example compounds are not made up of any query 
atoms when they are read into rdkit – the dummies are just made into queries 
after the read by the QueryParameters code.  I am definitely not interested in 
doing generic query to query matching.

- Kovas


From: Christos Kannas 
Date: Thursday, August 23, 2018 at 7:53 AM
To: Kovas Palunas 
Cc: RDKit , Paolo Tosco 

Subject: Re: [Rdkit-discuss] Matching Generalized Compounds

Hi Kovas,

You have two fuzzy compounds that you try to match them, because our intuition 
says that any atom notation [*:1] from m1 should match the Fluorine [F:11] in 
m2 and any atom [*:14] in m2 should match Carbon [CH3:4] in m1.
The issue here is that you create two query compounds from m1 and m2 which will 
match their own specific substructures. Query to query matching is not trivial.

In order to do what you want you need a query compound that combines their 
characteristic, which is what Paolo showed.
Paolo with MCS and modifying atom properties created that query compound 
'[*:1]-[CH2:2]-[C:3](-[*:4])=[CH2:5]' or 
'[*:1]-[CH2X4:2]-[CX3:3](-[*:4])=[CH2X3:5]'
Also bare in mind that Paolo's approach changed the starting compounds, as now 
they resemble the generic query compound that combines their fuzzy atoms.

https://gist.github.com/CKannas/ac1a4791dec909552d7c8899cfaff030

Best,

Christos

Christos Kannas

Chem[o]informatics Researcher & Software Developer

[Image removed by sender. View Christos Kannas's profile on 
LinkedIn]


On Thu, 23 Aug 2018 at 12:36, Paolo Tosco 
mailto:paolo.tosco.m...@gmail.com>> wrote:

Dear Kovas,

It looks like GetSubstructMatch() only finds a match if the dummy atom is in 
the query, not if it is in the molecule they you are matching the query against.

This notebook present a possible solution off the top of my head:

https://gist.github.com/ptosco/a35ac28a14103b47096f6d6af1aec831

which does not involve changes to the C++ layer, even though it is 
computationally more expensive and will fail with disconnected fragments as it 
uses FindMCS(). There may be better solutions - this is what I came out with 
yesterday night in the little time I had available.

Cheers,
P.

On 08/22/18 19:34, Kovas Palunas wrote:
Hi All,

I’m interested in having GetSubstructMatches return non-“null” results in the 
following example.  The results should lead to a match where atom 1 maps to 
atom 11, 2 to 12, etc.

m1 = Chem.MolFromSmiles('[*:1][CH2:2][C:3]([CH3:4])=[CH2:5]')
m2 = Chem.MolFromSmiles('[F:11][CH2:12][C:13]([*:14])=[CH2:15]')

### do something here so that the mols will match ###
qp = Chem.AdjustQueryParameters()
qp.makeDummiesQueries = True
m1 = Chem.AdjustQueryProperties(m1, qp)
m2 = Chem.AdjustQueryProperties(m2, qp)

# I’d like both of the following to return results
m1.GetSubstructMatches(m2)
m2.GetSubstructMatches(m1)

My understanding of why these mols currently do not match is as follows:  
because only the dummy atoms are made queries (based on my query parameter 
adjustment), when one mol is matched to another dummy 1 may match to F:11, but 
dummy 14 will then not match to methyl:14.  This is because (as I understand), 
normal atoms can only be matched by queries, and cannot match them themselves.

Potential ideas to make this work as I’d like:

  1.  Override atom.Match in the python code – not sure that this would work 
since the C++ version of this function is what would be called during 
GetSubstructMatches
  2.  Override atom.Match in the C++ code – not quite sure how to do this, or 
what side affects it might have.  Ideally the changes I make would only affect 
this example (and other similar ones)
  3.  Make all atoms in both molecules QueryAtoms, but otherwise leave them 
unchanged.  I’m not quite sure how to do this!

Does anyone have any ideas for what the best approach here would be, or knows 
if there is already built in functionality for something like this?  I’d prefer 
to not use SMARTS to construct my molecules if possible, since I don’t really 
think of them as queries, just as other molecules in the system that happen to 
not be fully specified.

- Kovas




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Re: [Rdkit-discuss] Alignment using LIgpargen file

2018-08-23 Thread Phuong Chau

Dear Paolo,

The new chemical chemical after alignment (UNK.pdb) file is in format of
RDKIT pdb file. Is it possible for the output in format of LIgParGen? I am
trying to run stimulation with the aligned chemical but it seems like it
can not read pdb file generated from RDKit.

Best,

Phuong Chau

On Wed, Aug 22, 2018 at 12:32 PM, Paolo Tosco 
wrote:

> Dear Phuong,
>
> it works for me with the latest RDKit release. I am wondering if you are
> using an older RDKit version where maybe the PDB parser was not assigning
> formal charges based on connectivity? Then you would have to manually set
> the formal charge of the protonated nitrogen atom (# 2 N) to +1.
>
> Cheers,
> p.
>
> On 08/22/18 19:06, Phuong Chau wrote:
>
> Hi Paolo,
>
> I got this new error when I tried with different chemicals:
>
> python 3DAlignmentwith3OAwithGRO.py CCNC\(N\)N_afterMD.pdb
> CC\[NH2\+\]CCN_Ligpargen.pdb
> [12:02:45] Explicit valence for atom # 2 N, 4, is greater than permitted
> Traceback (most recent call last):
>   File "3DAlignmentwith3OAwithGRO.py", line 12, in 
> rdDistGeom.EmbedMolecule(prbMolwithH)
> Boost.Python.ArgumentError: Python argument types in
> rdkit.Chem.rdDistGeom.EmbedMolecule(NoneType)
> did not match C++ signature:
> EmbedMolecule(RDKit::ROMol {lvalue} mol, unsigned int maxAttempts=0,
> int randomSeed=-1, bool clearConfs=True, bool useRandomCoords=False, double
> boxSizeMult=2.0, bool randNegEig=True, unsigned int numZeroFail=1,
> boost::python::dict {lvalue} coordMap={}, double forceTol=0.001, bool
> ignoreSmoothingFailures=False)
>
> The second argument I also downloaded it from Ligpargen but it gave me
> this error. I am not so sure why it happened.
>
> I also attached the two files :
>
> On Tue, Aug 21, 2018 at 3:19 PM, Paolo Tosco 
> wrote:
>
>> Hi Phuong,
>>
>> it does have hydrogens after the alignment:
>>
>> $ ls
>> UNK_A1C198.pdb  align.py  drug.pdb
>>
>> $ python align.py drug.pdb UNK_A1C198.pdb
>>
>> $ ls
>> UNK.pdb  UNK_A1C198.pdb  align.py  drug.pdb
>> $ cat UNK.pdb
>> ATOM  1  C00 UNK 1  37.884  56.016  51.678  1.00
>> 0.00   C
>> ATOM  2  C01 UNK 1  37.501  54.554  51.968  1.00
>> 0.00   C
>> ATOM  3  C02 UNK 1  36.085  54.316  52.531  1.00
>> 0.00   C
>> ATOM  4  C03 UNK 1  35.697  55.221  53.715  1.00
>> 0.00   C
>> ATOM  5  C04 UNK 1  34.907  56.485  53.304  1.00
>> 0.00   C
>> ATOM  6  C05 UNK 1  35.788  57.733  53.108  1.00
>> 0.00   C
>> ATOM  7  C06 UNK 1  36.227  57.998  51.654  1.00
>> 0.00   C
>> ATOM  8  C07 UNK 1  36.813  56.799  50.889  1.00
>> 0.00   C
>> ATOM  9  H08 UNK 1  38.821  56.001  51.080  1.00
>> 0.00   H
>> ATOM 10  H09 UNK 1  38.160  56.522  52.625  1.00
>> 0.00   H
>> ATOM 11  H0A UNK 1  37.598  53.969  51.027  1.00
>> 0.00   H
>> ATOM 12  H0B UNK 1  38.243  54.138  52.684  1.00
>> 0.00   H
>> ATOM 13  H0C UNK 1  35.325  54.368  51.723  1.00
>> 0.00   H
>> ATOM 14  H0D UNK 1  36.057  53.262  52.884  1.00
>> 0.00   H
>> ATOM 15  H0E UNK 1  35.031  54.622  54.375  1.00
>> 0.00   H
>> ATOM 16  H0F UNK 1  36.586  55.471  54.333  1.00
>> 0.00   H
>> ATOM 17  H0G UNK 1  34.203  56.712  54.134  1.00
>> 0.00   H
>> ATOM 18  H0H UNK 1  34.270  56.304  52.411  1.00
>> 0.00   H
>> ATOM 19  H0I UNK 1  35.198  58.620  53.428  1.00
>> 0.00   H
>> ATOM 20  H0J UNK 1  36.665  57.714  53.788  1.00
>> 0.00   H
>> ATOM 21  H0K UNK 1  36.982  58.814  51.667  1.00
>> 0.00   H
>> ATOM 22  H0M UNK 1  35.352  58.378  51.082  1.00
>> 0.00   H
>> ATOM 23  H0N UNK 1  35.991  56.144  50.537  1.00
>> 0.00   H
>> ATOM 24  H0O UNK 1  37.280  57.194  49.960  1.00
>> 0.00   H
>> CONECT1289   10
>> CONECT23   11   12
>> CONECT34   13   14
>> CONECT45   15   16
>> CONECT56   17   18
>> CONECT67   19   20
>> CONECT78   21   22
>> CONECT8   23   24
>> END
>>
>> p.
>>
>>
>> On 08/21/18 20:46, Phuong Chau wrote:
>>
>> Hi Paolo,
>>
>> I tried the code, it worked with the alignment but the new chemical after
>> alignment still does not have any H atoms. If I add H after alignment, it
>> has weird structure with H atoms. Would you please show me how to fix this
>> problem?
>>
>> Best,
>> Phuong Chau
>>
>> On Tue, Aug 21, 2018 at 8:01 AM, Paolo Tosco 
>> wrote:
>>
>>> Hi Phuong,
>>>
>>> If you wish to retain Hs you just need to set removeHs = False when you
>>> call MolFromPDBFile():
>>>
>>> # align.py
>>>
>>> import sys
>>> from rdkit import Chem
>>> from rdkit.Chem import rdDistGeom, rdMolAlign, rdForceFieldHelpers
>>> from rdkit import Chem
>>>
>>>

Re: [Rdkit-discuss] Matching Generalized Compounds

2018-08-23 Thread Christos Kannas

Hi Kovas,

You have two fuzzy compounds that you try to match them, because our
intuition says that any atom notation [*:1] from m1 should match the
Fluorine [F:11] in m2 and any atom [*:14] in m2 should match Carbon [CH3:4]
in m1.
The issue here is that you create two query compounds from m1 and m2 which
will match their own specific substructures. Query to query matching is not
trivial.

In order to do what you want you need a query compound that combines their
characteristic, which is what Paolo showed.
Paolo with MCS and modifying atom properties created that query compound
'[*:1]-[CH2:2]-[C:3](-[*:4])=[CH2:5]' or
'[*:1]-[CH2X4:2]-[CX3:3](-[*:4])=[CH2X3:5]'
Also bare in mind that Paolo's approach changed the starting compounds, as
now they resemble the generic query compound that combines their fuzzy
atoms.

https://gist.github.com/CKannas/ac1a4791dec909552d7c8899cfaff030

Best,

Christos

Christos Kannas

Chem[o]informatics Researcher & Software Developer

[image: View Christos Kannas's profile on LinkedIn]



On Thu, 23 Aug 2018 at 12:36, Paolo Tosco 
wrote:

> Dear Kovas,
>
> It looks like GetSubstructMatch() only finds a match if the dummy atom is
> in the query, not if it is in the molecule they you are matching the query
> against.
>
> This notebook present a possible solution off the top of my head:
>
> https://gist.github.com/ptosco/a35ac28a14103b47096f6d6af1aec831
>
> which does not involve changes to the C++ layer, even though it is
> computationally more expensive and will fail with disconnected fragments as
> it uses FindMCS(). There may be better solutions - this is what I came out
> with yesterday night in the little time I had available.
>
> Cheers,
> P.
>
> On 08/22/18 19:34, Kovas Palunas wrote:
>
> Hi All,
>
>
>
> I’m interested in having GetSubstructMatches return non-“null” results in
> the following example.  The results should lead to a match where atom 1
> maps to atom 11, 2 to 12, etc.
>
>
>
> m1 = Chem.MolFromSmiles('[*:1][CH2:2][C:3]([CH3:4])=[CH2:5]')
>
> m2 = Chem.MolFromSmiles('[F:11][CH2:12][C:13]([*:14])=[CH2:15]')
>
>
>
> ### do something here so that the mols will match ###
>
> qp = Chem.AdjustQueryParameters()
>
> qp.makeDummiesQueries = True
>
> m1 = Chem.AdjustQueryProperties(m1, qp)
>
> m2 = Chem.AdjustQueryProperties(m2, qp)
>
>
>
> # I’d like both of the following to return results
>
> m1.GetSubstructMatches(m2)
>
> m2.GetSubstructMatches(m1)
>
>
>
> My understanding of why these mols currently do not match is as follows:
>  because only the dummy atoms are made queries (based on my query parameter
> adjustment), when one mol is matched to another dummy 1 may match to F:11,
> but dummy 14 will then not match to methyl:14.  This is because (as I
> understand), normal atoms can only be matched by queries, and cannot match
> them themselves.
>
>
>
> Potential ideas to make this work as I’d like:
>
>1. Override atom.Match in the python code – not sure that this would
>work since the C++ version of this function is what would be called during
>GetSubstructMatches
>2. Override atom.Match in the C++ code – not quite sure how to do
>this, or what side affects it might have.  Ideally the changes I make would
>only affect this example (and other similar ones)
>3. Make all atoms in both molecules QueryAtoms, but otherwise leave
>them unchanged.  I’m not quite sure how to do this!
>
>
>
> Does anyone have any ideas for what the best approach here would be, or
> knows if there is already built in functionality for something like this?
> I’d prefer to not use SMARTS to construct my molecules if possible, since I
> don’t really think of them as queries, just as other molecules in the
> system that happen to not be fully specified.
>
>
>
> - Kovas
>
>
>
>
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>
>
>
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Re: [Rdkit-discuss] Matching Generalized Compounds

2018-08-23 Thread Paolo Tosco


Dear Kovas,

It looks like GetSubstructMatch() only finds a match if the dummy atom 
is in the query, not if it is in the molecule they you are matching the 
query against.


This notebook present a possible solution off the top of my head:

https://gist.github.com/ptosco/a35ac28a14103b47096f6d6af1aec831

which does not involve changes to the C++ layer, even though it is 
computationally more expensive and will fail with disconnected fragments 
as it uses FindMCS(). There may be better solutions - this is what I 
came out with yesterday night in the little time I had available.


Cheers,
P.


On 08/22/18 19:34, Kovas Palunas wrote:


Hi All,

I’m interested in having GetSubstructMatches return non-“null” results 
in the following example.  The results should lead to a match where 
atom 1 maps to atom 11, 2 to 12, etc.


m1 = Chem.MolFromSmiles('[*:1][CH2:2][C:3]([CH3:4])=[CH2:5]')

m2 = Chem.MolFromSmiles('[F:11][CH2:12][C:13]([*:14])=[CH2:15]')

### do something here so that the mols will match ###

qp = Chem.AdjustQueryParameters()

qp.makeDummiesQueries = True

m1 = Chem.AdjustQueryProperties(m1, qp)

m2 = Chem.AdjustQueryProperties(m2, qp)

# I’d like both of the following to return results

m1.GetSubstructMatches(m2)

m2.GetSubstructMatches(m1)

My understanding of why these mols currently do not match is as 
follows:  because only the dummy atoms are made queries (based on my 
query parameter adjustment), when one mol is matched to another dummy 
1 may match to F:11, but dummy 14 will then not match to methyl:14.  
This is because (as I understand), normal atoms can only be matched by 
queries, and cannot match them themselves.


Potential ideas to make this work as I’d like:

 1. Override atom.Match in the python code – not sure that this would
work since the C++ version of this function is what would be
called during GetSubstructMatches
 2. Override atom.Match in the C++ code – not quite sure how to do
this, or what side affects it might have.  Ideally the changes I
make would only affect this example (and other similar ones)
 3. Make all atoms in both molecules QueryAtoms, but otherwise leave
them unchanged.  I’m not quite sure how to do this!

Does anyone have any ideas for what the best approach here would be, 
or knows if there is already built in functionality for something like 
this?  I’d prefer to not use SMARTS to construct my molecules if 
possible, since I don’t really think of them as queries, just as other 
molecules in the system that happen to not be fully specified.


- Kovas



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Re: [Rdkit-discuss] cartridge license?

2018-08-23 Thread Roman Bolzern

Dear Andrew,

My bad, excuse me fooling around.

Thanks for the clarification. I wanted to really make sure if also the 
cartridge can be used for commercial purposes. I also reached the same 
conclusions, but didn't know about the CC licenses for documentation hint.

Thanks for taking your time!

Best regards,
Roman

-Ursprüngliche Nachricht-
Von: Andrew Dalke  
Gesendet: Donnerstag, 23. August 2018 09:47
An: Roman Bolzern 
Cc: Rdkit-discuss@lists.sourceforge.net
Betreff: Re: [Rdkit-discuss] cartridge license?

On Aug 23, 2018, at 07:18, Roman Bolzern  wrote:
> Dear RDKittens,

I would prefer to not be called a 'kitten'.

> https://www.rdkit.org/docs/Cartridge.html#license, and at the bottom it says 
> “This work is licensed under the Creative Commons Attribution-ShareAlike 4.0 
> License”,
  ...
> Is “this work” only the code in this docs page? Or what does this mean for a 
> business use case? What exactly do we have to share, what not?

Before that sentence is the line "This document is copyright ..." At the top of 
the page it says: "This document is a tutorial and reference guide for the 
RDKit PostgreSQL cartridge." I regard that as saying that "this work" is a 
synonym for 'this document' and meant to refer to the tutorial and reference 
guide document.

To verify that, I looked at the source code, available online at 
https://github.com/rdkit/rdkit/tree/master/Code/PgSQL/rdkit . The files all 
appear to have the standard BSD license, and they do not mention the CC 
license. 

The FAQ at https://creativecommons.org/faq/ suggests "While we recommend 
against using a CC license on software itself, CC licenses may be used for 
software documentation, as well as for separate artistic elements such as game 
art or music." This supports the hypothesis that the Attribution-ShareAlike 4.0 
License is only meant to apply to the documentation.

Cheers,

Andrew
da...@dalkescientific.com

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Re: [Rdkit-discuss] cartridge license?

2018-08-23 Thread Andrew Dalke

On Aug 23, 2018, at 07:18, Roman Bolzern  wrote:
> Dear RDKittens,

I would prefer to not be called a 'kitten'.

> https://www.rdkit.org/docs/Cartridge.html#license, and at the bottom it says 
> “This work is licensed under the Creative Commons Attribution-ShareAlike 4.0 
> License”,
  ...
> Is “this work” only the code in this docs page? Or what does this mean for a 
> business use case? What exactly do we have to share, what not?

Before that sentence is the line "This document is copyright ..." At the top of 
the page it says: "This document is a tutorial and reference guide for the 
RDKit PostgreSQL cartridge." I regard that as saying that "this work" is a 
synonym for 'this document' and meant to refer to the tutorial and reference 
guide document.

To verify that, I looked at the source code, available online at 
https://github.com/rdkit/rdkit/tree/master/Code/PgSQL/rdkit . The files all 
appear to have the standard BSD license, and they do not mention the CC 
license. 

The FAQ at https://creativecommons.org/faq/ suggests "While we recommend 
against using a CC license on software itself, CC licenses may be used for 
software documentation, as well as for separate artistic elements such as game 
art or music." This supports the hypothesis that the Attribution-ShareAlike 4.0 
License is only meant to apply to the documentation.

Cheers,

Andrew
da...@dalkescientific.com

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Re: [Rdkit-discuss] 2018_03_2 md5 checksum problems

2018-08-23 Thread Juuso Lehtivarjo

Hi,

encountered this too. At least for me the problem was self-built cmake
that did not automatically support https/ssl, which caused the empty
downloads.
The solution was to re-build cmake using the following instructions:
https://github.com/ruslo/hunter/issues/328#issuecomment-198672048

Cheers,
Juuso
On Fri, Jun 29, 2018 at 12:28 AM Kaushik Lakkaraju  wrote:
>
> master.tar.gz is empty.
>
> kaushik@kuta:/data/kaushik/src/rdkit-Release_2018_03_2/External/CoordGen$ du 
> -sh *
>
> 4.0K CMakeLists.txt
>
> 8.0K CoordGen.h
>
> 16K Wrap
>
> 0 master.tar.gz
>
> 12K test.cpp
>
>
>
> On Thu, Jun 28, 2018 at 4:39 PM, Dan Nealschneider 
>  wrote:
>>
>> Oh, good point (that the version is pinned). I guess that I saw an md5 
>> mismatch which I addressed by submitting 
>> https://github.com/rdkit/rdkit/pull/1904. That case caused a md5sum mismatch 
>> because the reference md5sum was being compared to a different library. It 
>> would be interesting to know which library is stored in 
>> /data/kaushik/src/rdkit-Release_2018_03_2/External/CoordGen/master.tar.gz 
>> (Is it actually maeparser, or is it coordgen?).
>>
>>
>> - dan nealschneider
>>
>> (né wandschneider)
>>
>> Senior Developer
>> Schrödinger, Inc
>> Portland, OR
>>
>>
>>
>>
>> On Thu, Jun 28, 2018 at 1:13 PM Kaushik Lakkaraju  
>> wrote:
>>>
>>> Thanks for helping out Greg and Dan.
>>>
>>> @Greg, rdkit version 2018_03_2.
>>>
>>> -Kaushik
>>>
>>>
>>> On Thu, Jun 28, 2018 at 3:53 PM, Greg Landrum  
>>> wrote:



 On Thu, Jun 28, 2018 at 12:52 PM Greg Landrum  
 wrote:
>
> I don't think that should be a problem. The versions should already be 
> pinned to a particular commit of both libraries in this case:
> https://github.com/rdkit/rdkit/blob/Release_2018_03_2/External/CoordGen/CMakeLists.txt
>
> I'm somewhat confused that you're seeing md5 errors at all since the 
> 2018.03.2 version of the code doesn't have md5s for this package.


 Sorry, mis-spoke here. The coordgen download isn't checking an md5 but the 
 maeparser download is.

 I'm not at all sure where the problem is coming from though.

 -greg



>
> @Kaushik: which version of the RDKit source are you using?
>
> -greg
>
>
>
>
> On Thu, Jun 28, 2018 at 12:46 PM Dan Nealschneider 
>  wrote:
>>
>> I've noticed this as well, I think it's because maeparser has been 
>> updated since it was pinned within RDKit. You can work around this by 
>> downloading the mae[arser manually to External outside the make process. 
>> This may also be required for coordgen. I'll also submit a PR to either 
>> ignore the md5sum for these packages for now (this is what is done for 
>> other fast moving packages) or to get the correct tagged version of 
>> these libraries.
>>
>> - dan nealschneider
>>
>> (né wandschneider)
>>
>> Senior Developer
>> Schrödinger, Inc
>> Portland, OR
>>
>>
>>
>>
>> On Mon, Jun 25, 2018 at 2:19 PM Kaushik Lakkaraju  
>> wrote:
>>>
>>> Hi all,
>>>
>>> I am trying to install rdkit from source on Ubuntu 14.04 using the 
>>> following commands. I have a previously compiled 2016 version on the 
>>> same machine, so my paths for boost, python etc are already set.
>>>
>>> The following is my sequence of steps:
>>>
>>> 1) wget https://github.com/rdkit/rdkit/archive/Release_2018_03_2.tar.gz
>>>
>>> 2) tar -xvzf Release_2018_03_2.tar.gz
>>>
>>> 3) cd rdkit-Release_2018_03_2
>>>
>>> 4) mkdir build
>>>
>>> 5) cd build
>>>
>>> 6) cmake .. -DCMAKE_INSTALL_PREFIX=/data/kaushik/apps/rdkit-2018
>>>
>>> Upon doing so, I bump into configuration errors :
>>>
>>> -- Boost version: 1.59.0
>>>
>>> -- Found the following Boost libraries:
>>>
>>> --   python
>>>
>>> PYTHON Py_ENABLE_SHARED: 1
>>>
>>> PYTHON USING LINK LINE: -pthread -shared -Wl,-O1 
>>> -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro 
>>> -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes 
>>> -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4 
>>> -Wformat -Werror=format-security
>>>
>>> -- Could NOT find Eigen3 (missing:  EIGEN3_INCLUDE_DIR 
>>> EIGEN3_VERSION_OK) (Required is at least version "2.91.0")
>>>
>>> Eigen3 not found, disabling the Descriptors3D build.
>>>
>>> -- Boost version: 1.59.0
>>>
>>> -- Found the following Boost libraries:
>>>
>>> --   serialization
>>>
>>> == Using strict rotor definition
>>>
>>> Downloading 
>>> https://codeload.github.com/schrodinger/maeparser/tar.gz/83368293dcc0eb07562dadfb7728b8d18d23a6cb...
>>>
>>> CMake Error at Code/cmake/Modules/RDKitUtils.cmake:194 (MESSAGE):
>>>
>>>   The md5 checksum for
>>>
>>>   
>>>

[Rdkit-discuss] cartridge license?

2018-08-23 Thread Roman Bolzern

Dear RDKittens,

I noticed your business-friendly BSD license that is mentioned everywhere, but 
now I stumbled upon this docs page for the cartridge at 
https://www.rdkit.org/docs/Cartridge.html#license, and at the bottom it says 
"This work is licensed under the Creative Commons Attribution-ShareAlike 4.0 
License", which states:
ShareAlike - If you remix, transform, or build upon the material, you must 
distribute your contributions under the same license as the original.

Is "this work" only the code in this docs page? Or what does this mean for a 
business use case? What exactly do we have to share, what not?

Thanks and kind regards,
Roman

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Re: [Rdkit-discuss] Alignment using LIgpargen file

Re: [Rdkit-discuss] Matching Generalized Compounds

Re: [Rdkit-discuss] Alignment using LIgpargen file

Re: [Rdkit-discuss] Matching Generalized Compounds

Re: [Rdkit-discuss] Matching Generalized Compounds

Re: [Rdkit-discuss] cartridge license?

Re: [Rdkit-discuss] cartridge license?

Re: [Rdkit-discuss] 2018_03_2 md5 checksum problems

[Rdkit-discuss] cartridge license?

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