[Rdkit-discuss] New problem compiling RDKit on Windows

[James Davidson]

Dear All,

For quite some time I have been successfully compiling RDKit on Windows using 
Visual Studio 2012.
However, recently (and perhaps triggered by a recent VS update that I accepted) 
I am getting errors.

The problem seems to be in Wrap.h (line 133):

<<< .mine


VS is complaining "error C2059: syntax error:'<<'"  and the corresponding error 
when inspecting the code is "Error: expected a declaration".
Does anyone have any suggestions for working through this?

Kind regards

James

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Re: [Rdkit-discuss] New problem compiling RDKit on Windows

[James Davidson]

Oops - accidentally hit send just now (if you see a previous message)!  Let's 
try that again!

Hi Greg,

>  That looks like a leftover from a source-control conflict. I can't find it 
> in github:
>  https://github.com/rdkit/rdkit/blob/master/Code/RDBoost/Wrap.h#L133
>  
>  Could it be that you are pulling from github and that you had local 
> modifications to the file that lead to a conflict?

Sorry for the delayed response - I have only just got a chance to relook at 
this.
I have wiped everything and started again.  I now get some different errors, 
but they are still centred around Wrap.h (and hc.c).  The first error - which 
may lead onto the rest(?) is in Wrap.h line 136:


#defined RDUNUSED
20>c:\rdkit\code\rdboost\Wrap.h(136): fatal error C1021: invalid preprocessor 
command 'defined'

I have some recollection that I started by modifying this to try and mend 
things last time - so maybe that explains why Wrap.h could have been 
conflicted...
Anyway - I guess I will try again and see if it helps; but it seems that there 
is a problem - at least for Visual Studio(?)

Kind regards

James

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Re: [Rdkit-discuss] New problem compiling RDKit on Windows

[James Davidson]

That looks like a leftover from a source-control conflict. I can't find it in 
github:
https://github.com/rdkit/rdkit/blob/master/Code/RDBoost/Wrap.h#L133

Could it be that you are pulling from github and that you had local 
modifications to the file that lead to a conflict?



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Re: [Rdkit-discuss] New problem compiling RDKit on Windows

[James Davidson]

Hi again, Greg

>  If you still have problems with this (or hc.c), please let me know,

hc.c fails to compile.
The errors are shown below, and then I get related linking errors.  I'm hoping 
all the errors are related(?)
The first line affected is line 42:

static doublereal inf = 1e20;

Kind regards

James


Error   2426error C2143: syntax error : missing ';' before 'type'   
C:\RDKit\Code\ML\Cluster\Murtagh\hc.c   42  1   hc
Error   2427error C2275: 'integer' : illegal use of this type as an 
expression  C:\RDKit\Code\ML\Cluster\Murtagh\hc.c   45  1   hc
Error   2428error C2146: syntax error : missing ';' before identifier 
'i__1'C:\RDKit\Code\ML\Cluster\Murtagh\hc.c   45  1   hc
Error   2429error C2065: 'i__1' : undeclared identifier 
C:\RDKit\Code\ML\Cluster\Murtagh\hc.c   45  1   hc
Error   2430error C2065: 'i__2' : undeclared identifier 
C:\RDKit\Code\ML\Cluster\Murtagh\hc.c   45  1   hc
Error   2431error C2275: 'doublereal' : illegal use of this type as an 
expression   C:\RDKit\Code\ML\Cluster\Murtagh\hc.c   46  1   hc
Error   2432error C2146: syntax error : missing ';' before identifier 
'd__1'C:\RDKit\Code\ML\Cluster\Murtagh\hc.c   46  1   hc
Error   2433error C2065: 'd__1' : undeclared identifier 
C:\RDKit\Code\ML\Cluster\Murtagh\hc.c   46  1   hc
Error   2434error C2065: 'd__2' : undeclared identifier 
C:\RDKit\Code\ML\Cluster\Murtagh\hc.c   46  1   hc
Error   2435error C2143: syntax error : missing ';' before 'type'   
C:\RDKit\Code\ML\Cluster\Murtagh\hc.c   49  1   hc
Error   2436error C2143: syntax error : missing ';' before 'type'   
C:\RDKit\Code\ML\Cluster\Murtagh\hc.c   50  1   hc
Error   2437error C2143: syntax error : missing ';' before 'type'   
C:\RDKit\Code\ML\Cluster\Murtagh\hc.c   51  1   hc
Error   2438error C2143: syntax error : missing ';' before 'type'   
C:\RDKit\Code\ML\Cluster\Murtagh\hc.c   52  1   hc
Error   2439error C2143: syntax error : missing ';' before 'type'   
C:\RDKit\Code\ML\Cluster\Murtagh\hc.c   53  1   hc
Error   2440error C2143: syntax error : missing ';' before 'type'   
C:\RDKit\Code\ML\Cluster\Murtagh\hc.c   54  1   hc
Error   2441error C2143: syntax error : missing ';' before 'type'   
C:\RDKit\Code\ML\Cluster\Murtagh\hc.c   55  1   hc
Error   2442error C2143: syntax error : missing ';' before 'type'   
C:\RDKit\Code\ML\Cluster\Murtagh\hc.c   56  1   hc
Error   2443error C2065: 'i__1' : undeclared identifier 
C:\RDKit\Code\ML\Cluster\Murtagh\hc.c   72  1   hc
Error   2444error C2065: 'i__' : undeclared identifier  
C:\RDKit\Code\ML\Cluster\Murtagh\hc.c   73  1   hc
Error   2445error C2065: 'i__1' : undeclared identifier 
C:\RDKit\Code\ML\Cluster\Murtagh\hc.c   73  1   hc
Error   2446error C2065: 'i__' : undeclared identifier  
C:\RDKit\Code\ML\Cluster\Murtagh\hc.c   74  1   hc
Error   2447error C2065: 'i__' : undeclared identifier  
C:\RDKit\Code\ML\Cluster\Murtagh\hc.c   75  1   hc
Error   2448error C2065: 'ncl' : undeclared identifier  
C:\RDKit\Code\ML\Cluster\Murtagh\hc.c   77  1   hc
Error   2449error C2065: 'i__1' : undeclared identifier 
C:\RDKit\Code\ML\Cluster\Murtagh\hc.c   79  1   hc
Error   2450error C2065: 'ind' : undeclared identifier  
C:\RDKit\Code\ML\Cluster\Murtagh\hc.c   80  1   hc
Error   2451error C2065: 'i__1' : undeclared identifier 
C:\RDKit\Code\ML\Cluster\Murtagh\hc.c   80  1   hc
Error   2452error C2065: 'ind' : undeclared identifier  
C:\RDKit\Code\ML\Cluster\Murtagh\hc.c   81  1   hc
Error   2453error C2065: 'i__1' : undeclared identifier 
C:\RDKit\Code\ML\Cluster\Murtagh\hc.c   90  1   hc
Error   2454error C2065: 'i__' : undeclared identifier  
C:\RDKit\Code\ML\Cluster\Murtagh\hc.c   91  1   hc
Error   2455error C2065: 'i__1' : undeclared identifier 
C:\RDKit\Code\ML\Cluster\Murtagh\hc.c   91  1   hc
Error   2456error C2065: 'dmin__' : undeclared identifier   
C:\RDKit\Code\ML\Cluster\Murtagh\hc.c   92  1   hc
Error   2457error C2065: 'inf' : undeclared identifier  
C:\RDKit\Code\ML\Cluster\Murtagh\hc.c   92  1   hc
Error   2458error C2065: 'i__2' : undeclared identifier 
C:\RDKit\Code\ML\Cluster\Murtagh\hc.c   93  1   hc
Error   2459error C2065: 'j' : undeclared identifier
C:\RDKit\Code\ML\Cluster\Murtagh\hc.c   94  1   hc
Error   2460error C2065: 'i__' : undeclared identifier  
C:\RDKit\Code\ML\Cluster\Murtagh\hc.c   94  1   hc
Error   2461error C2065: 'i__2' : undeclared identifier 
C:\RDKit\Code\ML\Cluster\Murtagh\hc.c   94  1   hc
Error   2462error C2065: 'ind' : undeclared iden

[Rdkit-discuss] Problem adding hydrogens to peptides

[James Davidson]

Dear All,

Enthused by all the great talks at the UGM, for the last couple of days I have 
been getting more hands-on with RDKit than I have in quite a while!
I was keen to work with some peptides/proteins in 3D, but am having some 
problems when adding hydrogens...

I have uploaded a GIST to demonstrate the issue (apologies - the py3Dmol js 
doesn't render in the nbviewer, but this doesn't affect understanding):
https://gist.github.com/jepdavidson/f5220187c18be0fc9e119f9da2e7d955

The main problem is that added hydrogens don't automatically get assigned 
monomer info from the monomer they are being added to, but there are other 
issues as well (the hydrogens are marked 'HETATM', the occupancy for the ATOM 
blocks are set to "-nan", and the CONECT block doesn't list the added Hs).

Propagating the monomer info from the amino acids to the added Hs isn't too 
difficult (can call atom.GetNeighbors() and take the info from the neighbouring 
atom) - but there are also some preferred (or required?) naming and numbering 
conventions to adhere to ("H" for the backbone NH, "HA" for the hydrogen on the 
alpha carbon, etc).

Perhaps I am missing something here (a secret 'flavour' option? :)) - but if 
not, it would be interesting to hear what behaviour others would expect when 
adding explicit hydrogens (I think the same issues will relate to any sequence 
where monomer information is present).

Kind regards

James

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[Rdkit-discuss] RDKit patch releases in conda?

[James Davidson]

Dear All,

I think I probably know the answer to this already, but wanted to double check 
- did any of the four 2016_03 patch releases ever get pushed to conda?
I only seem to get 2016_03_1 with "conda update -c 
https://conda.anaconda.org/rdkit rdkit"

(if not available then I guess this is academic with 2016_09_1 around the 
corner?)

Kind regards

James

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Re: [Rdkit-discuss] RDKit patch releases in conda?

[James Davidson]

Hi Greg (and Riccardo),

> Riccardo had pushed binaries for Linux and I have done most of the mac 
> versions, but doing windows builds, which I suspect is what you want, is 
> enough of a barrier that we haven't done those.
> There is an ongoing discussion about resolving this problem, but it is 
> non-trivial.
It sounds like there is a chance that Riccardo will look at a win64 2016_03 
patch build for conda (which would be geat!)

> P.S. Obligatory plug: this is a matter of focusing resources on an 
> less-than-pleasant task; exactly the kind of thing that RDKit 
> maintenance/support customers can reasonably request.
That sounds fair...

Kind regards

James


_____
From: James Davidson 
Sent: Wednesday, November 2, 2016 2:32 PM
Subject: [Rdkit-discuss] RDKit patch releases in conda?
To: 

Dear All,
 
I think I probably know the answer to this already, but wanted to double check 
– did any of the four 2016_03 patch releases ever get pushed to conda?
I only seem to get 2016_03_1 with “conda update –c 
https://conda.anaconda.org/rdkit rdkit”
 
(if not available then I guess this is academic with 2016_09_1 around the 
corner?)
 
Kind regards
 
James

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Re: [Rdkit-discuss] RDKit patch releases in conda?

[James Davidson]

Hi Riccardo,

> are you working on Windows? Pre-built conda packages targeting the 2016.03 
> patch releases are at this time only available for linux and osx.
Yes, I'm afraid so...

> an additional patch release was tagged before the UGM, and I think it wasn't 
> yet pushed to the anaconda channel. if there's interest for making this 
> revision available,
>  I can try to include some windows packages (for the amd64 platform at 
> least), otherwise it might make sense to wait for the upcoming release?
I would definitely be interested in this (py2 and py3) for win64, but if it is 
anything more than a small amount of work, then please don't do it just for me!

Kind regards

James

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[Rdkit-discuss] Stereochemistry issue for spirocycles/pseudochiral centres(?)

[James Davidson]

Dear All,

I have hit what I think is a problem with stereochemistry perception/handling 
for certain types of pseudochiral and/or spirocyclic systems.
Basically I am observing that some types of input tetrahedral stereochemical 
information gets lost when an RDKit molecule is generated.
But I only realised this because I was wanting to generate conformers and was 
seeing stereochemical scrambling...

Anyway, an example with pictures will probably explain things better:
https://gist.github.com/jepdavidson/fdfbf6366a17f4829de3d4de22f3b442

Any help/advice appreciated.

Kind regards

James

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Re: [Rdkit-discuss] Stereochemistry issue for spirocycles/pseudochiral centres(?)

[James Davidson]

Hi Greg (et al.),

Thanks for looking into it.
And thanks to Paolo, who gave me a good workaround suggestion – which was to 
desymmetrise the spirocyclic centre by modifying the isotope on one of the 
neighbours.
This is good for attended processing of single molecules, but not so good for 
unattended processing of unknown molecules…

Reading in molecules with sanitize=False is a good start, but my first thought 
was then to do some sort of rSMARTS transform to automate the isomer assignment.
It soon became apparent that this wasn’t the way to go – as abilities are 
limited with an unsanitised molecule(!).

So I ended-up with the following:

m3 = Chem.MolFromSmiles('O[C@H]1CC[C@]11CC[C@@](Cl)(Br)CC1', sanitize=False)
for atom in m3.GetAtoms():
print "Stereo:", atom.GetChiralTag(), "Neighbours:", [n.GetSymbol() for n 
in atom.GetNeighbors()]  # chiral centres currently intact

# Find possible spirocentres
for atom in m3.GetAtoms():
if len(atom.GetNeighbors()) == 4 and atom.IsInRing() and 
atom.GetChiralTag() != 'CHI_UNSPECIFIED':
# We have found a candidate spirocentre modify a neighbour at random
first_neighbour = atom.GetNeighbors()[0]
first_neighbour.SetIsotope(100)
Chem.SanitizeMol(m3)  # Now we can sanitise
test3_mols = summarise_conformers(m3)  # and generate the conformers (as before)
sdf = Chem.SDWriter('test3.sdf')  # and write them out (but resetting the 
isotopes first)
for mol in test3_mols:
for atom in mol.GetAtoms():
if atom.GetIsotope() == 100:
atom.SetIsotope(0)
sdf.write(mol)


GIST is updated to include this:  
https://gist.github.com/jepdavidson/fdfbf6366a17f4829de3d4de22f3b442

Kind regards

James


From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: 08 February 2017 03:45
To: James Davidson
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] Stereochemistry issue for spirocycles/pseudochiral 
centres(?)

Hi James,

This is definitely a bug. The problem seems to be connected to the way what the 
RDKit calls "ring stereochemistry" is handled when there are spiro linkages.

Here's the github issue: https://github.com/rdkit/rdkit/issues/1294

I'll take a look.

Best,
-greg



On Tue, Feb 7, 2017 at 8:32 PM, James Davidson 
mailto:j.david...@vernalis.com>> wrote:
Dear All,

I have hit what I think is a problem with stereochemistry perception/handling 
for certain types of pseudochiral and/or spirocyclic systems.
Basically I am observing that some types of input tetrahedral stereochemical 
information gets lost when an RDKit molecule is generated.
But I only realised this because I was wanting to generate conformers and was 
seeing stereochemical scrambling…

Anyway, an example with pictures will probably explain things better:
https://gist.github.com/jepdavidson/fdfbf6366a17f4829de3d4de22f3b442

Any help/advice appreciated.

Kind regards

James

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[Rdkit-discuss] Is it possible to get a breakdown of conformational energy terms?

[James Davidson]

Dear All,

Recently I have been assessing some ligand conformations from crystal 
structures to identify any non-ideal bond lengths, angles, torsions, or 
non-bonded contacts.
What I am doing at the moment is adding some positional constraints to the 
crystallographic heavy atom positions, and calculating the energy before and 
after minimisation:

>>>   m = Chem.MolFromMolFile('input.mol')
>>>   mh = AllChem.AddHs(m, addCoords=True)
>>>   mp = AllChem.MMFFGetMoleculeProperties(mh, mmffVariant='MMFF94s')
>>>   ff = AllChem.MMFFGetMoleculeForceField(mh, mp)
>>>   ff.CalcEnergy()

This gives the 'raw' energy.

>>>   for atom in mh.GetAtoms():
>>>   if not atom.GetAtomicNum() == 1:
>>>   idx = atom.GetIdx()
>>>   ff.MMFFAddPositionConstraint(idx, maxDispl=0.5, forceConstant=100)
>>>   ff.Minimize(maxIts=1)
>>>   ff.CalcEnergy()

And this gives the energy after applying a moderate restraint (100 kcal/mol, 
with a maximum displacement of 0.5 A).

So I think this is ok(?), and I can compare the two energies and inspect the 
conformations visually.
What I was wondering was whether there is a way of obtaining the individual 
energy terms (ie each bonded and non-bonded term, angle, and torsion)?
Because what I'd really like to do is identify the areas of the molecule that 
contribute the most to the pre- and post- minimisation energy difference.

Any suggestions would be greatly appreciated!

Kind regards

James

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[Rdkit-discuss] Open3DAlign scoring of existing alignment?

[James Davidson]

Dear All (especially Paolo!),

I have a strong suspicion I have already asked this at some point in the past - 
so apologies in advance (but I can't seem to find the answer)...
I am interested in taking an existing overlay of two RDKit molecules in 3D and 
scoring the overlay using Open3DAlign scoring scheme (eg with MMFF atom-types), 
but *without* trying to optimise the alignment or score.

I thought setting maxIters=0 in the call to AllChem.GetO3A() would do the trick 
(I even tried setting options=3 to "trigger local optimization").  Eg

o3a = AllChem.GetO3A(prb_mol, ref_mol, maxIters=0, options=3)
o3a.Matches()  # Show the matches

But while the options setting certainly changes the matching atoms (and the 
score), the matches don't seem to correspond well to my starting alignment...
Any advice is greatly appreciated (including, of course, simply pointing me to 
the old answer that I am likely missing!)

Kind regards

James

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[Rdkit-discuss] A couple of questions regarding ReactionFromSmarts

[James Davidson]

Hi,
 
First of all, I'd like to start by saying how much I've been enjoying
exploring the functionality of RDKit - great job, Greg!
I have a couple of questions regarding
'rdkit.Chem.AllChem.ReactionFromSmarts':
 
(1)  I see that the reaction objects can be created from MDL Reaction
Files/Blocks - is there a way to do the reverse, and save a reaction
object in MDL .rxn format?  I tried using investigating the
rxn.ToBinary() attribute, but didn't get very far...  The reason I
wanted to do this, is that I was trying to figure-out how to generate a
form of the reaction object (generated from reaction SMARTS) that was
suitable for converting into a 2D depiction of the transformation.
 
(2) I know that reaction SMARTS isn't SMIRKS, but I have noticed some
behaviour that I would not expect - however, this could be down to my
SMARTS-naivety; my SMIRKS-naivety; or both!  I initially tried the
following:
 
from rdkit import Chem
from rdkit.Chem import AllChem
rxn_smarts =
'[!#1:1]-[NH:2]-[C:3](=[O:4])-[C,c:5]>>[!#1:1]-[C:3](=[O:4])-[NH:2]-[C,c
:5]'
sm = Chem.MolFromSmiles('CC(=O)NC')
rxn = AllChem.ReactionFromSmarts(rxn_smarts)
prods = rxn.RunReactants((sm,))
prod = Chem.MolToSmiles(prod[0][0])
 
 
This gives me prod = '[H]C(=O)NC'
 
If I replace with <>[!H:1]-[C:3](=[O:4])-[NH:2]-[C,c:5
]'>>, I get the behaviour I want - with prod = 'CNC(=O)C'.  So I think I
can get the behaviour I want, but was curious if I am using the SMARTS !
operator incorrectly in conjunction with atomic numbers, or whether this
may be a bug?
 
Kind regards
 
James

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Re: [Rdkit-discuss] A couple of questions regarding ReactionFromSmarts

[James Davidson]

Thanks for the help, Greg - my reaction SMARTS are now behaving themselves!  I 
must confess, I had not actually realised that the documentation from install 
(ie the 'Book') was different to the 'Getting Started' one that I had linked 
from the website.

Kind regards,

James 


-Original Message-
From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: Fri 04/06/2010 05:13
To: James Davidson
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] A couple of questions regarding ReactionFromSmarts
 
Dear James,

On Thu, Jun 3, 2010 at 7:51 PM, James Davidson  wrote:
>
> First of all, I'd like to start by saying how much I've been enjoying
> exploring the functionality of RDKit - great job, Greg!

Thanks!

> I have a couple of questions regarding
> 'rdkit.Chem.AllChem.ReactionFromSmarts':
>
> (1)  I see that the reaction objects can be created from MDL Reaction
> Files/Blocks - is there a way to do the reverse, and save a reaction object
> in MDL .rxn format?  I tried using investigating the rxn.ToBinary()
> attribute, but didn't get very far...  The reason I wanted to do this, is
> that I was trying to figure-out how to generate a form of the reaction
> object (generated from reaction SMARTS) that was suitable for converting
> into a 2D depiction of the transformation.

At the moment the reactions are essentially input-only. There's really
no way to get them out in any format that could be used elsewhere.
This is a sadly missing feature: it would be really nice to be able to
generate either .rxn files (or at least reaction smarts) from
reactions. I will add a feature request for this, but it may take a
while to happen.[1]

A workaround that kind of works is to paste the reaction smarts into
something like Marvin Sketch. It will normally display something that
at least gives some idea of what the reaction is.

> (2) I know that reaction SMARTS isn't SMIRKS, but I have noticed some
> behaviour that I would not expect - however, this could be down to my
> SMARTS-naivety; my SMIRKS-naivety; or both!

Anytime reactions behave in ways you don't expect, it's probably best
to just blame me for coming up with yet another way of expressing them
that is slightly incompatible with the existing ones. :-)

> I initially tried the
> following:
>
> from rdkit import Chem
> from rdkit.Chem import AllChem
> rxn_smarts =
> '[!#1:1]-[NH:2]-[C:3](=[O:4])-[C,c:5]>>[!#1:1]-[C:3](=[O:4])-[NH:2]-[C,c:5]'
> sm = Chem.MolFromSmiles('CC(=O)NC')
> rxn = AllChem.ReactionFromSmarts(rxn_smarts)
> prods = rxn.RunReactants((sm,))
> prod = Chem.MolToSmiles(prod[0][0])
>
>
> This gives me prod = '[H]C(=O)NC'

There's a discussion of this kind of case in the "RDKit Book"
($RDBASE/Docs/Book/RDKit_Book.pdf) starting on page 3. The short
answer is that if you have a query feature (atom list, recursive
smarts, etc.) in the reactants and you would like the matching atom to
be copied into the products you should include a dummy for that atom
in the products. A working form of your example is then:

[11]>>> rxn_smarts =
'[!#1:1]-[NH:2]-[C:3](=[O:4])-[C,c:5]>>[*:1]-[C:3](=[O:4])-[NH:2]-[*:5]'

[12]>>> rxn = AllChem.ReactionFromSmarts(rxn_smarts)

[13]>>> prods = rxn.RunReactants((Chem.MolFromSmiles('c1c1C(=O)NCC1CC1'),))

[14]>>> Chem.MolToSmiles(prods[0][0])
Out[14] 'O=C(CC1CC1)Nc1c1'

As an aside, in SMARTS it's shorter (and I think clearer) to write
[C,c] as [#6]. It also produces a query that runs a bit quicker, but
you probably won't notice that difference in most cases.

> If I replace with < '[!H:1]-[NH:2]-[C:3](=[O:4])-[C,c:5]>>[!H:1]-[C:3](=[O:4])-[NH:2]-[C,c:5]'>>,
> I get the behaviour I want - with prod = 'CNC(=O)C'.  So I think I can get
> the behaviour I want, but was curious if I am using the SMARTS ! operator
> incorrectly in conjunction with atomic numbers, or whether this may be a
> bug?

Not really a bug. The behavior when you have queries in the products
is undocumented: depending on the details of the query it will
sometimes do the right thing, sometimes not. It's much safer to just
use "*". What I probably should do is add a warning message if the
reaction contains a query in the products, I will think about this.

Best Regards,
-greg

[1] The underlying problem isn't actually generating the rxn files
themselves, they are just a collection of mol blocks with a bit of
extra verbiage sprinkled around. The problem is generating reasonable
mol blocks for molecules with query features. I already have a feature
request in for that one
(http://sourceforge.net/tracker/?group_id=160139&atid=814653), but it
turns out to not be quite as easy as it sou

[Rdkit-discuss] Number of Aromatic Rings

[James Davidson]

Dear Greg,
 
I have been trying figure-out how to return the count of aromatic rings
for molecules (in Python), and am going to have to admit defeat!  I saw
in an earlier message
(http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg0015
3.html) a similar query, but I'm afraid it didn't help me very much.  I
also read the section on Aromaticity in the rdkit book, and realised
that maybe this isn't a trivial exercise!
 
I would like the count to count aromatic ring-systems such that bicyclic
(eg indole or naphthalene) would only count as 1.  For reference, this
appears to be the behaviour of the OpenEye
OEDetermineAromaticRingSystems function - where the molecule derived
from the smiles "C(O)(=O)c12c1[nH]c(C3CCCc4c34)c2" (which
contains an indole and a tetrahydronaphthalene) gives a count of 2.
 
Any help would be greatly appreciated.
 
Thanks
 
James

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Re: [Rdkit-discuss] Number of Aromatic Rings

[James Davidson]

Thanks for the suggestion, Cedric.
 
I think something like this could work - but it would not get around the
issue of bicyclic aromatics, unless more advanced string parsing were
used.  For example, indole can be represented as [nH]1ccc2c12 in
SMILES, so would give two aromatic rings from your suggestion.  However,
it does occur to me that for bicyclic systems the 'a12' motif would
always be present(?), so maybe...
 
James



From: Cedric MORETTI [mailto:cedric.more...@firmenich.com] 
Sent: 10 June 2010 15:04
To: James Davidson; rdkit-discuss@lists.sourceforge.net
Subject: RE: Number of Aromatic Rings



I propose something; it's not a true approach

If you've a aromatic you've a smile c1c1 for example.

So if you count the number of "1" and divide by 2 you're the number of
aromatic 

If you've lot of cycle in your structure, you're count the number of 1,
the number of 2, 3 4 5 6 and you're sum and divide by 2.

No ?

C

 

 

 

From: James Davidson [mailto:j.david...@vernalis.com] 
Sent: jeudi, 10. juin 2010 14:35
To: rdkit-discuss@lists.sourceforge.net
Subject: [Rdkit-discuss] Number of Aromatic Rings

 

Dear Greg,

 

I have been trying figure-out how to return the count of aromatic rings
for molecules (in Python), and am going to have to admit defeat!  I saw
in an earlier message
(http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg0015
3.html) a similar query, but I'm afraid it didn't help me very much.  I
also read the section on Aromaticity in the rdkit book, and realised
that maybe this isn't a trivial exercise!

 

I would like the count to count aromatic ring-systems such that bicyclic
(eg indole or naphthalene) would only count as 1.  For reference, this
appears to be the behaviour of the OpenEye
OEDetermineAromaticRingSystems function - where the molecule derived
from the smiles "C(O)(=O)c12c1[nH]c(C3CCCc4c34)c2" (which
contains an indole and a tetrahydronaphthalene) gives a count of 2.

 

Any help would be greatly appreciated.

 

Thanks

 

James


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Re: [Rdkit-discuss] Number of Aromatic Rings

[James Davidson]

Thanks Greg,

The code looks pretty shiny to me!  I hope I can find time over the weekend to 
look at doing the post-processing, and will let you know how I get on.

Kind regards

James

 

-Original Message-
From: Greg Landrum [mailto:greg.land...@gmail.com] 
Sent: 11 June 2010 06:02
To: James Davidson
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] Number of Aromatic Rings

Dear James,

On Thu, Jun 10, 2010 at 2:35 PM, James Davidson  wrote:
>
> I have been trying figure-out how to return the count of aromatic 
> rings for molecules (in Python), and am going to have to admit defeat!  
> I saw in an earlier message
> (http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg00
> 153.html) a similar query, but I'm afraid it didn't help me very much.  
> I also read the section on Aromaticity in the rdkit book, and realised 
> that maybe this isn't a trivial exercise!

Correct. Counting the number of non-fused rings that are aromatic, like the 
post you reference does, is pretty easy; including the fused rings that are 
aromatic is more challenging.

> I would like the count to count aromatic ring-systems such that 
> bicyclic (eg indole or naphthalene) would only count as 1.  For 
> reference, this appears to be the behaviour of the OpenEye 
> OEDetermineAromaticRingSystems function - where the molecule derived 
> from the smiles "C(O)(=O)c12c1[nH]c(C3CCCc4c34)c2" (which 
> contains an indole and a
> tetrahydronaphthalene) gives a count of 2.
>
> Any help would be greatly appreciated.

I've attached a script that's not quite what you want, but it gets you almost 
there: it finds all aromatic ring systems, including fused ones. Anthracene, 
for example, gives 6 rings. The modifications to this to get what you're 
looking for aren't a straightforward post-processing step, but shouldn't be too 
bad. If there's not enough here, let me know and I will take a look at adding 
the extra code.

This code isn't perfectly polished and could certainly be faster, but it does 
seem mostly functional.

-greg

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Re: [Rdkit-discuss] Number of Aromatic Rings

[James Davidson]

Hi Greg

Well, I managed to have a go at this earlier than I expected.  So first some 
apologies, provisos, and caveats to warn you, and other readers, that your eyes 
will soon experience things inelegant and unpythonic, but it's the best I could 
come up with, with my limited faculties and experience!

On the plus side - I think it is doing what I wanted - ie giving a count of the 
number of aromatic systems (if you always want count a fused aromatic as 1 
aromatic system).  The downside is that the way I have done this now makes your 
script eg output (6,1) for anthracene - where the 1 is the count of aromatic 
systems (fused or otherwise).  It would be most generic if it maybe returned 
(6,3,1) as (all unique aromatic substructures, unique mono-cyclic 
substructures, aromatic systems).  I'm sure this is fairly straightforward, but 
for another day!

So what I added was:



def GetOuterSet(rings):
# Initialise a counter for parent aromatic 'super' rings 
result = 0

# Set-up a dictionary so that items can be referenced and deleted
ring_set = {}
for k, v in enumerate(rings):
ring_set[k] = v

# While there is something to process
while len(ring_set):
# Set the ring to be checked as the last in the list - should be the 
biggest
reference = sorted(ring_set)[-1]

for k,v in sorted(ring_set.iteritems()):
# if current item is contained in last item - remove current from 
dictionary
if v&ring_set[reference]:
ring_set.pop(k)
# If we are at the reference, then we have found our 'super' 
ring
if k == reference:
result += 1
break

return result



and I passed in the aromaticRings list from your script, then returned both the 
length of the aromaticRings list (as before) plus the output of GetOuterSet().  
ie:


superRings = GetOuterSet(aromaticRings)

return len(aromaticRings), superRings


So once again, thanks for the help, and I would welcome any pointers from 
anyone on tidying-up and improving this modification!  (or corrections if 
anyone spots them - I have only briefly tested this)


Kind regards

James


-Original Message-
From: Greg Landrum [mailto:greg.land...@gmail.com] 
Sent: 11 June 2010 06:02
To: James Davidson
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] Number of Aromatic Rings

Dear James,

On Thu, Jun 10, 2010 at 2:35 PM, James Davidson  wrote:
>
> I have been trying figure-out how to return the count of aromatic 
> rings for molecules (in Python), and am going to have to admit defeat!  
> I saw in an earlier message
> (http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg00
> 153.html) a similar query, but I'm afraid it didn't help me very much.  
> I also read the section on Aromaticity in the rdkit book, and realised 
> that maybe this isn't a trivial exercise!

Correct. Counting the number of non-fused rings that are aromatic, like the 
post you reference does, is pretty easy; including the fused rings that are 
aromatic is more challenging.

> I would like the count to count aromatic ring-systems such that 
> bicyclic (eg indole or naphthalene) would only count as 1.  For 
> reference, this appears to be the behaviour of the OpenEye 
> OEDetermineAromaticRingSystems function - where the molecule derived 
> from the smiles "C(O)(=O)c12c1[nH]c(C3CCCc4c34)c2" (which 
> contains an indole and a
> tetrahydronaphthalene) gives a count of 2.
>
> Any help would be greatly appreciated.

I've attached a script that's not quite what you want, but it gets you almost 
there: it finds all aromatic ring systems, including fused ones. Anthracene, 
for example, gives 6 rings. The modifications to this to get what you're 
looking for aren't a straightforward post-processing step, but shouldn't be too 
bad. If there's not enough here, let me know and I will take a look at adding 
the extra code.

This code isn't perfectly polished and could certainly be faster, but it does 
seem mostly functional.

-greg

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Re: [Rdkit-discuss] A couple of questions regarding ReactionFromSmarts

[James Davidson]

Thanks Greg - this is great!  I must confess, I was eager to try this out asap 
- but have not built rdkit before.  I did start having a go over the weekend on 
my home PC (Windows MCE2005) but ran into a couple of unexpected issues with 
the software installs that made me think I would wait and retry on my work PC.

[not really relevant, but for interest - I think the problems may have been 
related to the Visual Studio 2010 Express installation.  The result was an 
infuriating clicking in the audio when streaming live or recorded TV to an 
extender!!  Not an issue that I felt was easy to troubleshoot... I reinstalled 
my system from a drive image backup and the problem was gone... That's when I 
decided to leave well alone, as my family may not have seen the benefit of 
up-to-the-minute builds at home at the expense of TV enjoyment : ) ]

I will get my PC at work setup to build from SVN snapshots - but I was very 
pleased to see your post 
(http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg01097.html) 
saying that Q2 binaries should be available next week - great news!

Kind regards

James

-Original Message-
From: Greg Landrum [mailto:greg.land...@gmail.com] 
Sent: 18 June 2010 06:08
To: rdkit-discuss@lists.sourceforge.net
Cc: James Davidson
Subject: Re: [Rdkit-discuss] A couple of questions regarding ReactionFromSmarts

Dear all,

A followup/update on a request from a couple weeks ago:

On Fri, Jun 4, 2010 at 6:13 AM, Greg Landrum  wrote:
> On Thu, Jun 3, 2010 at 7:51 PM, James Davidson  
> wrote:
>>
>> (1)  I see that the reaction objects can be created from MDL Reaction 
>> Files/Blocks - is there a way to do the reverse, and save a reaction 
>> object in MDL .rxn format?  I tried using investigating the 
>> rxn.ToBinary() attribute, but didn't get very far...  The reason I 
>> wanted to do this, is that I was trying to figure-out how to generate 
>> a form of the reaction object (generated from reaction SMARTS) that 
>> was suitable for converting into a 2D depiction of the transformation.
>
> At the moment the reactions are essentially input-only. There's really 
> no way to get them out in any format that could be used elsewhere.
> This is a sadly missing feature: it would be really nice to be able to 
> generate either .rxn files (or at least reaction smarts) from 
> reactions. I will add a feature request for this, but it may take a 
> while to happen.[1]

I've added a partial solution to this that at least provides some help with 
visualizing reactions.

Here's my reaction:
[12]>>> rxn = 
AllChem.ReactionFromSmarts('[C:1](=[O:2])-[O;-,H].[N;!$(N-C=[O,N,S]);!$(N=*):3]>>[C:1](=[O:2])-[N:3]')


You can now output reaction smarts:
[13]>>> AllChem.ReactionToSmarts(rxn)
Out[13] 
'[C:1](=[O:2])-[O;-,H1].[N;!$(N-C=[O,N,S]);!$(N=*):3]>>[C:1](=[O:2])-[N:3]'

You can also generate coordinates for a reaction and the create an rxn file:
[14]>>> AllChem.Compute2DCoordsForReaction(rxn)
[15]>>> print AllChem.ReactionToRxnBlock(rxn)
--> print(AllChem.ReactionToRxnBlock(rxn))
$RXN

  RDKit

  2  1
$MOL

 RDKit  2D

  3  2  0  0  0  0  0  0  0  0999 V2000
   -0.0.0. C   0  0  0  0  0  0  0  0  0  1  0  0
   -0.   -1.50000. O   0  0  0  0  0  0  0  0  0  2  0  0
   -0.1.50000. *   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  1  3  1  0
V3 [O;-,H1]
M  END
$MOL

 RDKit  2D

  1  0  0  0  0  0  0  0  0  0999 V2000
0.50000.0. *   0  0  0  0  0  0  0  0  0  3  0  0
V1 [N;!$(N-C=[O,N,S]);!$(N=*):3]
M  END
$MOL

 RDKit  2D

  3  2  0  0  0  0  0  0  0  0999 V2000
1.50000.0. C   0  0  0  0  0  0  0  0  0  1  0  0
1.5000   -1.50000. O   0  0  0  0  0  0  0  0  0  2  0  0
1.50001.50000. N   0  0  0  0  0  0  0  0  0  3  0  0
  1  2  2  0
  1  3  1  0
M  END

#

Notice that query features on atoms in the rxn blocks are not output as 
property ctab query features. Instead I use the atom-value feature of ctabs and 
output the SMARTS query for the atoms. This has the marked disadvantage that it 
won't actually generate reactions that do sensible things in other tools, but 
at least you can do some debugging of reactions. At some point in the future it 
would be nice to have ctab queries handled correctly, but this is at least 
something.

These changes are checked into subversion and will be in the next release.

Best Regards,
-greg

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Re: [Rdkit-discuss] [Rdkit-announce] Q2 2010 Release

[James Davidson]

Congratulations on the release, Greg!

I am really a very recent adopter of RDKit, but even in the short time I have 
been using it I have been amazed at the quality and depth of functionality!  
Please keep up the good work, and I hope I can continue to help a tiny amount 
in the only way I know how - by selfishly requesting new features :)

Kind regards

James


-Original Message-
From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: Wed 30/06/2010 21:16
To: RDKit Discuss; RDKit Developers List; rdkit-annou...@lists.sourceforge.net
Subject: [Rdkit-announce] Q2 2010 Release
 
Dear all,

I'm very happy to announce that the next version of the RDKit --
Q22010_1 -- is released.

The release notes are below.

The source release and windows binaries (python 2.6 only this time,
please let me know if anyone needs a python 2.5 release) will be on
the sourceforge downloads page:
http://sourceforge.net/projects/rdkit/files/rdkit/Q2_2010/
The files can also be downloaded from the google project page:
http://code.google.com/p/rdkit/downloads/list

I have also updated the online documentation.

Thanks to the everyone who submitted bug reports and suggestions for
this release!

Please let me know if you find any problems with the release or have
suggestions for the next one.

-greg

**  Release_Q22010_1 ***
(Changes relative to Release_Q12010_1)

!! IMPORTANT !!
 - There are a couple of refactoring changes that affect people using
   the RDKit from C++. Please look in the Other section below for a list.
 - If you are building the RDKit yourself, changes made in this
   release require that you use a reasonably up-to-date version of
   flex to build it. Please look in the Other section below for more
   information.

Acknowledgements:
 - Andrew Dalke, James Davidson, Kirk DeLisle, Thomas Heller, Peter Gedeck,
   Greg Magoon, Noel O'Boyle, Nik Stiefl,

Bug Fixes:
 - The depictor no longer generates NaNs for some molecules on
   windows (issue 2995724)
 - [X] query features work correctly with chiral atoms. (issue
   3000399)
 - mols will no longer be deleted by python when atoms/bonds returned
   from mol.Get{Atom,Bond}WithIdx() are still active. (issue 3007178)
 - a problem with force-field construction for five-coordinate atoms
   was fixed. (issue 3009337)
 - double bonds to terminal atoms are no longer marked as "any" bonds
   when writing mol blocks. (issue 3009756)
 - a problem with stereochemistry of double bonds linking rings was
   fixed. (issue 3009836)
 - a problem with R/S assignment was fixed. (issue 3009911)
 - error and warning messages are now properly displayed when cmake
   builds are used on windows.
 - a canonicalization problem with double bonds incident onto aromatic
   rings was fixed. (issue 3018558)
 - a problem with embedding fused small ring systems was fixed.
   (issue 3019283)

New Features:
 - RXN files can now be written. (issue 3011399)
 - reaction smarts can now be written.
 - v3000 RXN files can now be read. (issue 3009807)
 - better support for query information in mol blocks is present.
   (issue 2942501)
 - Depictions of reactions can now be generated.
 - Morgan fingerprints can now be calculated as bit vectors (as
   opposed to count vectors.
 - the method GetFeatureDefs() has been added to
   MolChemicalFeatureFactory
 - repeated recursive SMARTS queries in a single SMARTS will now be
   recognized and matched much faster.
 - the SMILES and SMARTS parsers can now be run safely in
   multi-threaded code.

Deprecated modules (to be removed in next release):
 - rdkit/qtGui
 - Projects/SDView

Removed modules:
 - SVD code: External/svdlibc External/svdpackc rdkit/PySVD
 - rdkit/Chem/CDXMLWriter.py

Other:
 - The large scale changes in the handling of stereochemistry were
   made for this release. These should make the code more robust.
 - If you are building the RDKit yourself, changes made in this
   release require that you use a reasonably up-to-date version of
   flex to build it. This is likely to be a problem on Redhat, and
   redhat-derived systems. Specifically: if your version of flex is
   something like 2.5.4 (as opposed to something like 2.5.33, 2.5.34,
   etc.), you will need to get a newer version from
   http://flex.sourceforge.net in order to build the RDKit.

 - Changes only affecting C++ programmers:
   - The code for calculating topological-torsion and atom-pair
 fingerprints has been moved from $RDBASE/Code/GraphMol/Descriptors
 to $RDBASE/Code/GraphMol/Fingerprints.
   - The naming convention for methods of ExplicitBitVect and
 SparseBitVect have been changed to make it more consistent with
 the rest of the RDKit.
   - the bjam-based build system should be considered
 deprecated. This is the last release it will be actively
 maintained.

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[Rdkit-discuss] Interacting with molecules in PyMOL

[James Davidson]

Dear All,
 
I am trying to work out the best way to accomplish some tasks involving
RDKit, using PyMOL as an interface, and would appreciate some help.  I
would like to be able to start from a PDB file of a ligand-bound crystal
structure loaded in PyMOL and be able to 'virtually' build some
analogues - initially just simple substitutions - and visually inspect
the results.
 
(1)  So my first question is - having started PyMOL with the -R option,
is there an easy or recommended way of transferring molecules from PyMOL
to RDKit?  I can accomplish this by writing molfiles to a temporary
file, but wondered if I am creating work, if eg RDKit could
automatically create Mol objects from non-biopolymer atoms in PyMol(?).
ie it would be nice if:
 
from rdkit import Chem
from rdkit.Chem import PyMol
v = PyMol.MolViewer()
 
# Invented function to create an RDKit mol object
mol = v.GetAtomsAsMol(selection)
 
(2)  Once the ligand is converted to an RDKit mol object (by whatever
means) I want to enumrate some libraries of virtual products - eg
choosing an atom in PyMol as the attachment point, then running a set of
reactions to get products with a set of substituents added.  In
principle I think this is quite straightforward; however, what I am
struggling with is a mechanism to 'freeze' the 3D coordintes of the
original ligand atoms, but still be able to use RDKit to generate
sensible 3D positions for the newly added atoms so that the products can
be passed back to PyMOL and minimised in situ (if required) using
'mengine.exe'.  Am I looking at this the wrong way, and should I
actually try aligning the virtual products back on the starting ligand
conformation?
 
(3)  Apologies that this last point is maybe a bit off-topic, but I
wondered if anyone has an opinion as to whether MMTK is the way to go
for 'simple' minimisations of modified ligands bound to proteins? (I
don't have any real experience with MMTK...
 
Kind regards
 
James

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Re: [Rdkit-discuss] Interacting with molecules in PyMOL

[James Davidson]

Dear Greg,

Thanks for your very rapid response - 'AllChem.ConstrainedEmbed' was
just what I was looking for!


Kind regards

James

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Re: [Rdkit-discuss] Interacting with molecules in PyMOL

[James Davidson]

I just wanted to quickly update the List on how I've got on with this,
in case it is of use / interest to others.  I followed Greg's advice and
did the following:
 
1.  Exported molfile from PyMOL
2.  Read into RDKit
3.  Read in an SDF of already-constructed molecules based on the core
(could have built the products in RDKit, but the SDF was already
available!)
4.  Iterated over the objects in the supplier to do the
AllChem.ConstrainedEmbed as discussed, then load the results into PyMOL
 
NOTE - Because the molecules weren't built in RDKit, I couldn't rely on
the atom numbering when read into PyMOL (maybe this can't be relied on
anyway?).  So I ran mol.GetSubstructMatch(core) for each molecule to get
the aligned product atom IDs that matched the core.  I then flagged
these in PyMOL with flag 3 [Fixed Atoms (no movement allowed)] (flag 2 -
harmonically constrained may be better..?) so that I could subsequently
run the mengine 'clean' command in PyMOL to tidy-up the UFF output
without allowing the template to move:
 
from rdkit import Chem
core = Chem.MolFromMolFile(mol_filepath)
supplier = Chem.SDMolSupplier(sdf_filepath)
for n,mol in enumerate(supplier):
mol = Chem.AddHs(mol)
newMol = AllChem.ConstrainedEmbed(mol, core, True)
name = "mol"+str(n)
fix = ','.join([str(n) for n in mol.GetSubstructMatch(core)])
v.ShowMol(newMol, name=name, showOnly=False)
selection = '('+name+' and (id '+fix+'))'
v.server.do('flag 3, '+selection+', set')
 
 
Kind regards
 
James

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[Rdkit-discuss] Reading Molfiles with 'ambiguous' 5-membered aromatics

[James Davidson]

Dear All,
 
I have been exploring some interactivity between PyMOL and RDKit
recently, and at the moment am ferrying molecules between the two in MOL
format.  However, I have come up against a bit of a problem that I
wondered if anyone could help with?
 
PyMOL does a pretty good job of setting bond valences automatically for
ligands read-in as part of PDB files, and most of the time these ligands
exported in MOL format are recognised fine by RDKit (a little bit of
parsing is necessary to change things like 'Cl' being capitalised in
some PDB files, etc!).  However, it seems that when there is ambiguity
about how to tautomerise 5-membered heteroaromatics, RDKit fails to
create a mol object from the molfile.  I have included an example
Molfile below (a pyrazolopyrimidine).
 
Ideally (from my point of view at least!) it would be great if in these
situations RDKit yielded an arbitrary explicit H to 'mend' the problem.
However, I am definitely open to workaround suggestions (including "go
post on the PyMOL lists" :-)  ).  Maybe this is something that is
relatively trivial to tackle using PyMOL's ChemPy module? (which I know
very little about!).
 
 
untitled
  ChemPy3D 0
 
  9 10  0  0  1  0  0  0  0  0999 V2000
   16.6400   15.1940   18.3320 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.6190   14.6050   17.0520 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.7200   15.3750   15.9600 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.8570   16.7060   16.1150 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.8760   17.3110   17.3320 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.7640   16.5880   18.4530 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.4970   14.1830   19.1960 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.3960   13.0610   18.4470 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.4690   13.2930   17.2130 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  4  0  0  0  0
  2  1  4  0  0  0  0
  2  9  4  0  0  0  0
  3  2  4  0  0  0  0
  4  3  4  0  0  0  0
  4  5  4  0  0  0  0
  5  6  4  0  0  0  0
  7  1  4  0  0  0  0
  8  7  4  0  0  0  0
  9  8  4  0  0  0  0
M  END
 
 
Kind regards
 
James

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Re: [Rdkit-discuss] Reading Molfiles with \'ambiguous\' 5-membered aromatics

[James Davidson]

Dear All,
 
It's been a couple of weeks since Greg first helped me with this, and
after some further help I agreed that I would do my best to summarise
things for the benefit of the Group.
 
The attached file 'sanifix3.py' was provided to me by Greg, and
essentially does exactly what I (thought I) wanted - ie if required,
'cleans' up an input molecule by modifying aromatic nitrogen-containing
ring systems until a 'sanitizable' form is generated.
 
However, having tested this a bit further, I found that N-containing
heteroaromatics (which I originally posted the question about) are only
one of many possible issues when dealing with automated atom- and
bond-typing from PDB files!  So taking this approach would require a
significantly larger set of 'rules' to cover all possible problems (I'm
sure many people more experienced than me will have been aware of this
for a long time!).  As Greg said:
 
> Figuring out the correct chemistry for a pdb ligand is one of 
> those challenges at I wouldn't dream of attempting. Between 
> the various sources of ligand structures out there you can 
> probably find omsething at least halfway acceptable. For in 
> house stuff, I would assume that you can use the registry 
> number to get a smiles or mol block, right?
> You could use that with the rdkit substructure matching code 
> to test the pymol-assigned structures.

And indeed, this is the way that I ended-up going for in-house
structures - a script that extracts our corporate ID from the PDB file
and searches our database to return the SMILES.  Then (again, thanks to
Greg for more help here, and steering me away from some clumsy usage of
ConstrainedEmbed!) a substructure match is conducted between an RDKit
mol from the SMILES (refered to as 'db_mol' in the function below), and
the original ligand.

The main point here is to convert the original ligand structure to a set
of non-aromatic atoms joined by 'unspecified' bond-types.  Below is the
excerpt from what I am using with PyMOL: 'molfile3D' is a temporary
molfile that has been created using the PyMOL 'save' command, that gets
converted to the required 'connectivity substructure' that carries the
3D coordinates we will need later:


def make3DTemplate(molfile3D):

mol = Chem.MolFromMolFile(molfile3D, False)
for atom in mol.GetAtoms():
atom.SetIsAromatic(False)
for bond in mol.GetBonds():
bond.SetBondType(rdkit.Chem.rdchem.BondType.UNSPECIFIED)

return mol


Then once we have this '3D template', the substructure match can be
conducted for the molecule built from the database SMILES string
(db_mol).  If the match is successful, the original 3D coordinates for
the atoms in the 'template' are then applied back to a conformer of our
new molecule.  Finally, this new molecule + conformation is returned as
the molblock, which I then read back in PyMOL to give a 'sanitized'
version of the bound ligand for any in-house crystal structure:


def outputMolBlock(db_mol, template_mol):

matches = db_mol.GetSubstructMatches(template_mol)
if not matches:
raise ValueError,"no substruct match"
if len(matches)>1:
print "warning! more than one isomorphism found!"

db_conf = db_mol.GetConformer()
template_conf = template_mol.GetConformer()

match = matches[0]

# This sets the 3D coordinates for 
for i,mIdx in enumerate(match):
db_conf.SetAtomPosition(mIdx,
template_conf.GetAtomPosition(i))

db_conf.Set3D(True)

return Chem.MolToMolBlock(db_mol)


It wouldn't now be too much of a leap(?) to extend the same methodology
to public PDB structures - using the LigandExpo SDF.  See this post from
Noel on Blue Obelisk for background:

http://blueobelisk.shapado.com/questions/how-to-get-an-experimental-liga
nd-structure-from-the-pdb


Also, just for interest - I am using cx_Oracle to connect to our
corporate database from Python, which is now allowing me to add a few
extra bits - like flagging up to people if the in-house structure they
have just opened has been previously crystallised in any other targets,
etc, etc.  If anybody is trying to do similar, but has not used
cx_Oracle, then give me a shout and I will see if I can help (although
SQL is definitely also on the list of things I know only barely enough
about!).

Kind regards

James

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[Rdkit-discuss] Align SDF to user-supplied template coordinates (2D)

[James Davidson]

Dear All,
 
I am currently struggling with something that I expect is very easy to
solve (I have just got back from holiday, so I think my brain isn't
quite in the zone!)
 
I am trying to read in an SDF and align each molecule to a template
scaffold provided in molfile format.  I want to supply a tool that
allows a user to sketch in a template and view their SDF entries in 2D
all aligned (where there is a match) to the supplied template.
 
I have essentially followed this entry in the Chemistry Toolkit Rosetta
-
http://ctr.wikia.com/wiki/Align_the_depiction_using_a_fixed_substructure
 , which in essence is pretty-much the same as the info in the RDKit
documentation.
 
However, when I am using pre-supplied 2D coordinates for the template,
rather than generating them from the first substructure match (as in the
CTR example), I find that the alignment proceeds as required, but there
is a mis-match between the scaling of the bond-lengths in the aligned
substructure compared with the rest of the molecule...
 
Is there a way to 'scale' the molecules according to the template mol
(or alternatively scale the template according to the RDKit default)?
Or is it that I am tackling this in the wrong way?
 
Kind regards
 
James

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Re: [Rdkit-discuss] Align SDF to user-supplied template coordinates (2D)

[James Davidson]

Thanks Greg,

Greg wrote:
> Ah yes, the depictions that you get look rather silly, no?

Yes they do!

> You're doing it correctly; no worries there. The problem is 
> that most pieces of chemical drawing software generate 2D 
> coordinates for molecules such that a C-C single bond is 1.0A 
> long. The RDKit, on the other hand, sets the C-C single bond 
> to be 1.5A long. The consequence is a depiction with a core 
> that's smaller than it should be.

I was using ISISDraw for sketching the core motif.  It seems that the
single-bond length (from the Origdraw settings) is ~ 0.825 A (!)

So I modified the scalar to 1.818 (1.5/0.825) in your code and it works
beautifully!
 
> It should be possible to specify the scale used in the RDKit 
> depictions so that these contortions are not necessary. I 
> will put a feature request in for this and get it in the next version.

Thanks for this - I certainly think this would be a worthwhile feature.
What I may implement in the meantime is running through all the bonds of
type SINGLE in the core molecule, taking the average, then using
1.5/(average) as the scalar to protect against differing user settings!

Kind regards

James

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[Rdkit-discuss] Cleaning SD files

[James Davidson]

Dear All,
 
Today I have spent some time processing a freely-available SDF that
contains many compounds and melting-points / ranges (
http://www.mdpi.org/molmall/mdpi1-51sd.zip).  The reason for doing this
is that I wanted to implement a melting-point predictor following the
work of Andreas Bender (J. Chem. Inf. Model. 2005, 45, 581-590) and more
recently Reifeng Liu at AZ (J. Chem. Inf. Model. 2008, 48, 981-987).
 
I have attached the python-script that I have at the moment (a) in case
it is of some use to anybody else, (b) in the hope that I can improve my
python and rdkit abilities through any suggested alterations (I'm sure
there are many!), and (c) to form the basis of a couple of questions.
At the moment, the script is just running through each compound;
checking if the molecule is valid; and if so, noting how many
components, and whether any of the atoms are outside of the desired
list.  These two results are then written out to a new SDF.  I am then
using this to make sure my data-set contains only compounds that I would
say are 'reasonable' to build a melting-point model with.  Now for the
questions:
 
1.  In RDKit, has the 'cleaning / washing / salt-stripping' of molecules
already been formalised based on a set of rules, etc?
2.  When identifying compounds that contain a non-allowed atom-type, why
do I find the SMARTS def [!H;!C;!N;!O;!F;!S;!Cl;!Br;!I] gives unexpected
results, but [!#1;!#6;!#7;!#8;!#9;!#16;!#17;!#35;!#53] works as I would
expect?
 
Kind regards
 
James

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Re: [Rdkit-discuss] Cleaning SD files

[James Davidson]

Hi Greg,

Thanks for the reply.

> > 1.  In RDKit, has the 'cleaning / washing / salt-stripping' of 
> > molecules already been formalised based on a set of rules, etc?
> 
> Not that I'm aware of on the open-source side of things. All 
> of the functionality required to do this is, I believe, 
> present in the RDKit though.

Great - I certainly found all the functionality I was looking for, but just 
wanted to make sure I wasn't missing any short-cuts!

> > 2.  When identifying compounds that contain a non-allowed 
> atom-type, 
> > why do I find the SMARTS def [!H;!C;!N;!O;!F;!S;!Cl;!Br;!I] gives 
> > unexpected results, but [!#1;!#6;!#7;!#8;!#9;!#16;!#17;!#35;!#53] 
> > works as I would expect?
> 
> This is a fairly common SMARTS "gotcha": in SMARTS the query "[C]"
> means "aliphatic C". This leads to the following behavior:
> [3]>>> 
> Chem.MolFromSmiles('c1c1').GetSubstructMatches(Chem.MolFro
> mSmarts('[!C]'))
> Out[3] ((0,), (1,), (2,), (3,), (4,), (5,)) If you want to be 
> sure that your SMARTS will capture aliphatic or aromatic 
> atoms, you need to provide the atomic numbers, as in your 
> second query:
> [4]>>> 
> Chem.MolFromSmiles('c1c1').GetSubstructMatches(Chem.MolFro
> mSmarts('[!#6]'))
> Out[4] ()

Wow - I really was having some sort of mental block yesterday! (goes-off to 
look for some sort of embarrassed + dunce smiley...)

Kind regards

James

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[Rdkit-discuss] Identifying isotopes of hydrogen?

[James Davidson]

Dear All,
 
I have been struggling with a substructure search to remove compounds
containing isotopes of hydrogen other than 1H...  I had hoped that the
following would work: patt = Chem.MolFromSmarts('[2H,3H]') but this does
not give a valid mol.
 
I then tried patt = Chem.MolFromSmarts('[2#1,3#1]').  This at leasts
gives a mol object, but when used for substructure querying does not
behave as I would like (ie mol.HasSubstructMatch(patt) is false even for
molecules containing 2H or 3H)
 
Finally, I thought that I could run them one at a time with eg patt =
Chem.MolFromSmiles('[2H]', True) for the deuteriums.  This does work for
me (sort of), but identifies molecules containing 3H as well as 2H -
which I guess is great, as this is originally what I wanted!  However,
I'm not sure why it works - and what I should be doing to make it behave
as expected.
 
Any help/advice much appreciated!  And apologies for my high percentage
of questions revolving around a lack of SMARTS experience!
 
 
Kind regards
 
James

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Re: [Rdkit-discuss] Identifying isotopes of hydrogen?

[James Davidson]

Thanks for the VERY rapid response, Greg (it makes me think you have a
pro-forma to answer SMARTS-related questions)! 

Greg wrote:
> If you see anything different, I would certainly like to know 
> about it. In that case, please let me know which version of 
> the RDKit on which platform.

I see the same (as you probably expected!).  However, what I probably
should have said to start with is that I am bringing my molecules in
using an SD supplier.  So:

p = Chem.MolFromSmarts('[2#1,3#1]')
suppl = Chem.SDMolSupplier(myfile)
for mol in suppl:
  mol.HasSubstructMatch(p)

Gives me a long list of 'False's.  But your reply got me thinking, so
doing the following actually gives the matching as expected:


p = Chem.MolFromSmarts('[2#1,3#1]')
suppl = Chem.SDMolSupplier(myfile)
for mol in suppl:
  newMol = Chem.MolToSmiles(mol, True)
  newMol = Chem.MolFromSmiles(newMol)
  newMol.HasSubstructMatch(p)


The SDF I am using was generated by RDKit via reaction enumeration.  I'm
confused!

James


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Re: [Rdkit-discuss] Identifying isotopes of hydrogen?

[James Davidson]

Greg wrote:
> hmm, here I don't understand what's going on. It *should* 
> make no difference if the molecule comes from an CTAB or a 
> smiles. Would it be possible to send a small version of the 
> SDF showing the problem that contains only non-proprietary structures?

I repeated my workflow using just two selected amines (one with
deuteriums, and one without), and benzaldehyde - instead of a
proprietary aldehyde.  The resultant SDF (which I believe behaves as the
one described previously) is attached.  Having spent some time trying to
'repair' the CTAB format by hand, I am still none the wiser - so, good
luck!

Kind regards

James

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Re: [Rdkit-discuss] Beta of Q3 2010 release up

[James Davidson]

> And now the python2.6 windows binary is up on google code:
>
http://code.google.com/p/rdkit/downloads/detail?name=RDKit_Q32010_1beta1
.win32.py26.zip

> Please let me know if you encounter any problems with the new binary.

I have unzipped the binary, but don't seem to see any dll files in the
bin folder... Have paths changed, or am I doing something wrong?
 
Kind regards
 
James

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Re: [Rdkit-discuss] Beta of Q3 2010 release up

[James Davidson]

Hi Greg,

Greg wrote: 
> I just uploaded a new version of the zip file that contains the
> relevant boost dlls. The filename is in the same place (with the same
> name):
>
http://code.google.com/p/rdkit/downloads/detail?name=RDKit_Q32010_1beta1
.win32.py26.zip
> 
> Note that the install instructions have changed with this release and
> that you should add $RDBASE/lib to your path instead of $RDBASE/bin.
> 
> hopefully this fixes the problems some of you were having and sorry
> again for the mistake,

Thanks for the updated binary installer - that sorted things out!

I had a very quick look to see if some things that I have depending on
RDKit still play nice.  So far, they certainly seem to - they just don't
look as nice while doing it!  I'm sure it will be a trivial fix, but on
Q22010_1 the following gives nicely anti-aliased(?) images:

from rdkit import Chem
from rdkit.Chem import Draw
mol = Chem.MolFromSmiles('n1c1CCCOC')
Draw.MolToImageFile(mol, r'C:\Q2_test.png')

whereas the corresponding in Q32010_1beta1 gives a rather
raggedy-looking molecule (example PNGs attached).  For info, I have
PIL(1.1.7) and aggdraw(1.2a3) installed under Python 2.6; and also have
a set of DLLs in a cairo folder in python26\Lib\site-packages - but get
an error if I try 'import cairo' (and can't remember why I put them
there!)

Kind regards

James

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Re: [Rdkit-discuss] How can I escape to this error

[James Davidson]

Hi Greg,

Apologies for resurrecting a rather old thread, but I have been
investigating the Q32010_1beta1 release on a set of commercial amines
(from ACD) and came across the 'hypervalent P' issue as well.

Greg wrote:
> To continue and try to answer Christian's question: it is currently
> impossible to really work with this hypervalent molecule in the RDKit.
> The only real solution is to tell the RDKit that P is allowed to have
> 7 substituents. If you really want to do this you can edit the file
> $RDBASE/Code/GraphMol/atomic_data.cpp and change the allowed valence
> list for P from "3 5" to "3 5 7". After you do this, you will need to
> rebuild the code.

With the new release currently in beta, I wondered whether this would be
a good time to consider if the change you suggest above for P should
make it into the release code(?)  Having said that, I am expecting that
your comment "it is currently impossible to really work with this
hypervalent molecule in the RDKit" suggests that a robust solution is
not as simple as just changing the allowed valence list...

Anyway, what I was finding from my list of amines was that the
hexafluorophosphate counterion  [PF6]-  was triggering the error.  Not a
particularly common counterion - so I can certainly live without(!) -
but not particularly esoteric either :-)

Kind regards

James

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[Rdkit-discuss] Beta of RDKit knime nodes available

[James Davidson]

Dear Greg (and, of course, Thorsten and Bernd!)
 
Great job on the Knime nodes!  I have been giving these a go and am
impressed (and excited about the future development!).  A couple of
observations / comments / questions:
 
1.  I have observed that sometimes the FP node seems to generate blank
fingerprints (doesn't appear to just be the rendering - eg blank if I
swap to 'Bit Scratch' render as well.  I have mainly been trying the
default Morgan FPs, and find that if I reset the node and re-run, the FP
is still blank.  If, however, I swap the node to eg atompair, run, then
swap back to Morgan - it seems to work...  I am running on knime 2.2.2
on Windows 32-bit.
 
2.  The next point is probably down to cheminformatics / knime naivety,
but I must confess I am struggling a little to cluster compounds based
on the FP...   I have used the 'Distance Matrix Calculate' node (with
Tanimoto similarity) to get a matrix that can be used by the
'Heirarchical Clustering (DistMatrix)' or 'k-Medoids' nodes.  However,
both of these appear to perform VERY slowly for a set of ~ 4000
compounds.  I also attempted to cluster on the fingerprints directly,
using the Neighborgrams nodes - but must confess I am some way off
understanding what I am doing!  My limited experience of using the RDKit
functionality to cluster compounds and eg select a representative set
(based on the FP Tanimoto distances and the Murtagh clustering) was that
it performed rather rapidly.  Is there the intention to expose this
functionality in knime (or is the functionality already there and I just
don't know how?)
 
3.  Any plans for Windows 64-bit support?
 
4.  I would be interested to know what the team views as the next
priorities - property calcs, 3D conformations, pharmacophores,
rendering?  So much great stuff to choose from!  :-)
 
Kind regards
 
James

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[Rdkit-discuss] Handling certain sterochemistry in reactions

[James Davidson]

Dear All,
 
I wonder if anybody can help with the following?  I am trying to
figure-out how to handle double-bond stereochemistry in reactions when
the stereochemistry is involved with the making / breaking bond.
Hopefully this example will explain better than that sentence(!):
 
rxn = AllChem.ReactionFromSmarts('[c:1][Cl,Br,I].[#6:2][B]>>[*:1][*:2]')
mol1 = Chem.MolFromSmiles('c1c1Br')
mol2 = Chem.MolFromSmiles('C\C=C\B(O)O')
ps = rxn.RunReactants((mol1, mol2))
Chem.MolToSmiles(ps[0][0], True)
 
--->  'CC=Cc1c1' (stereochemical information lost)
 
whereas using mol2 = Chem.MolFromSmiles('C\C=C\c1c1B(O)O') gives
 
--->  'C/C=C/c1c(-c2c2)1' (stereochemical information retained)
 
Not quite the same, but I have read through some related SMIRKS info
here: http://www.daylight.com/dayhtml/doc/theory/theory.smirks.html
 .
However, this explains how to handle stereo centres and stereo bonds in
reactions when they are explicitly defined on both sides of the
reaction.  I guess what I am looking for is a shortcut for saying
'retain' or 'invert' stereochemistry at reacting centre (sp3) or bond
attached to reacting centre (sp2)...
 
Having got to the end of explaining that, I am thinking that the way I
should handle this is to check for 'problem' reactants and pass to a
more specific rSMARTS when required!
 
Kind regards
 
James

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Re: [Rdkit-discuss] Beta of RDKit knime nodes available

[James Davidson]

Hi Greg and Thorsten,


> Greg:
>
>> Thorsten:
>> On the other hand, 4000 rows should not take that long in KNIME. How
>> much times does it currently take?
>
> I just did 1000 rows on my macbook. Assuming I'm reading the knime log
> correctly, that took about a minute.


Thanks for testing this out, Greg.  I must confess, I didn't wait for
the hierarchical clustering to finish for the 4000!  Going back and
selecting a random 1000 molecule subset, I reproduce your result of ~ 1
min (I get 67 secs).  If I then go to 2000, it takes 520 secs - so to me
this looks like cubic complexity - which is what the documentation for
the node states (this would mean > 1 hr for my original 4000...)

For completeness - this result was with the Hierarchical
Clustering(DistMatrix) node set with 'Tanimoto' similarity and 'Complete
Linkage' for cluster comparison.  Changing the comparison to 'Single
Linkage' did not reduce the time.

Interestingly, the documentation for the 'standard' Hierarchical
Clustering' (ie non-distance matrix) node states that it operates with
"n-squared complexity".  I guess other clustering algorithms available
in knime must scale better than cubicly as well (k-means, fuzzy
c-means?) - but as far as I can see they don't currently operate on
distance matrices (or directly on bit vectors).  If they could, then
this may be a solution; or implementing the Murtagh algorithm (I am
guessing the scaling is below cubic from my recollection of the speeds
observed in rdkit).

Kind regards

James

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Re: [Rdkit-discuss] Handling certain sterochemistry in reactions

[James Davidson]

Hi Greg,

Greg wrote:
> yeah. Here's an even shorter illustration of correct behavior:
>
> In [11]: mol2 = Chem.MolFromSmiles(r'C\C=C\CB(O)O')
>
> In [12]: ps = rxn.RunReactants((mol1, mol2))
>
> In [13]: Chem.MolToSmiles(ps[0][0], True)
> Out[13]: 'C/C=C/Cc1c1'

Yes, this was the first example that I went for as well - but then
chemically I didn't like the idea of using allyl boronic acids in Suzuki
reactions - because I couldn't recollect ever trying this, and if they
did couple I would be worried about double-bond migrations; ironically
making the question of stereochemistry rather mute!  So my medchemist
conscience won-out over clarity - and I concocted an example that I
would happily test with 'wet' experiment! :-)

>> Having got to the end of explaining that, I am thinking that the way
I
>> should handle this is to check for 'problem' reactants and pass to a
more
>> specific rSMARTS when required!
>
> I don't think that will help. Unfortunately the problem is in the way
> stereochemical information is handled in the reaction code. My gut
> feeling is that this is not going to be a quick one to fix, but I will
> take a look.

Thanks for looking into it!

Kind regards

James

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[Rdkit-discuss] Canonical smiles for medium and large rings?

[James Davidson]

Dear All,
 
I have been investigating an issue that a colleague of mine identified.
He was working with the RDKit Canon Smiles node in Knime, and found that
for the natural product, Geldanamycin, the double-bond geometry
information was being lost during canonicalisation.  I repeated this
result outside of knime:
 
from rdkit import Chem
from rdkit.Chem import AllChem

>>> smi =
r'NC(=O)o...@h]1c(/C)=C/[...@h](C)[C@@H](O)[C@@H](OC)c...@h](C)C\C2=C(/OC)C(
=O)\C=C(\NC(=O)C(\C)=C\C=C/[C@@H]1OC)C2=O'
>>> AllChem.CanonSmiles(smi)

'COC1=C2C[C@@H](C)c...@h](OC)[...@h](O)[C@@H](C)C=C(C)[...@h](OC(N)=O)[C@@H](
OC)C=CC=C(C)C(=O)NC(=CC1=O)C2=O'


The simpler example below may be better:

>>> smi1 = r'O1CC/C=C\1' # cyclic ether
>>> smi2 = r'OCC/C=C\' # corresponding acyclic alcohol

>>> AllChem.CanonSmiles(smi1)
'C1C=CCCOCCC1' -> stereochemistry lost
>>> AllChem.CanonSmiles(smi2)
'/C=C\\CCO' -> stereochemistry retained


So, I am guessing that double-bonds in rings are being 'ignored'(?) by
the canonicaliser?  For 'classic' aliphatic systems, double-bonds in
3-7-membered rings can only sensibly exist in the cis orientation, so
'ignoring' them would be ok.  However, for 8-membered and above, cis or
trans are certainly both possible, so it becomes more important to keep
track - particularly if canonical smiles are being used to check for
unique structures, as my colleague was doing with the geldanamycin
example above.
 
Any thoughts / suggestions are much appreciated as always!

Kind regards

James

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Re: [Rdkit-discuss] Canonical smiles for medium and large rings?

[James Davidson]

Hi Greg,

> On Sat, Dec 18, 2010 at 6:27 AM, Greg Landrum 
>  wrote:
> 
> I just checked in a set of changes that should get this 
> (mostly) working correctly. Here's a demonstration with Geldanamycin:
> 
> In [7]: 
> smi=r'NC(=O)o...@h]1c(/C)=C/[...@h](C)[C@@H](O)[C@@H](OC)c...@h](C
> )C\C2=C(/OC)C(=O)\C=C(\NC(=O)C(\C)=C\C=C/[C@@H]1OC)C2=O'
> 
> In [8]: print Chem.CanonSmiles(smi)
> COC1=C2C[C@@H](C)c...@h](OC)[...@h](O)[C@@H](C)/C=C(\C)[...@h](OC(N
> )=O)[C@@H](OC)/C=C\C=C(/C)C(=O)NC(=CC1=O)C2=O

Thanks for looking into this so quickly!

> It would be *really* useful to have some more real-world 
> cases like this one to use as tests. So if you happen to have 
> others you can send I would be quite happy to have them.

On that note, I have added a comment to the bug tracker
(https://sourceforge.net/tracker/?func=detail&aid=3139534&group_id=16013
9&atid=814650) - but was not sure how to attach a file (eg sdf) there,
so apologies for it ending up on more lines than I intended...  Also, I
logged in with my google account, but it looks like it may not be clear
who it is!

The first two examples are two marine natural products that only differ
in the geometry of the double bond in the medium ring.  The final
example is a cis- analogue that I synthesised during my PhD for which a
crystal structure was also obtained.  The stereochemistry in these
systems is 'challenging' to say the least, so I thought they would make
reasonable test cases.  I should say that even for the cis- double bond
cases, RDKit does a rather ugly job of the 2D depiction - but I am not
sure if other depictors will perform much better...

On a related note, I was keen to manually double-check the
stereochemistry that had been assigned to each of the chiral centres
(particularly the ones involving the 9-5 ring connections - as these are
potentially troublesome), and found myself wishing there was a way to
easily label a 2D depiction of the molecules with the atom ID.  What I
ended-up doing was the following:

1.  Getting the R/S info + atomIdx back from RDKit (example output):
>>> Chem.FindMolChiralCenters(mol)
[(3, 'R'), (7, 'R'), (8, 'S'), (9, 'R'), (11, 'R'), (18, 'R'), (24,
'R')]
2.  Opening the molfile in a program where I know how to label with atom
IDs (pymol)
3.  Check which atom is which manually (had to add 1 to the RDKit
atomIdx values as they start at 0) then double-check with reference
values.

RDKit performed admirably - but I presume this is dependant on the
quality of the wedge info coming in from the SDF(?)

Kind regards

James

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[Rdkit-discuss] Beta of Q4 2010 release up

[James Davidson]

Hi Greg,

> Greg wrote:
> If there's demand for it, I will also put up a windows binary.
> 
> As usual: if no show-stopper bugs appear, I will do the release itself
> in about a week.

I would appreciate a Windows binary to check out the beta release - but
if it is just me, I can obviously wait for the full release (presuming a
windows binary would be available at that point?)

Kind regards

James

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[Rdkit-discuss] Change to GenerateDepictionMatching3DStructure?

[James Davidson]

Hi Greg,

I have some code that relies on the GenerateDepictionMatching3DStructure
function, that I have found no longer plays nicely with 2010_12_1.

In 2010_09_1, the following works fine:


>>> from rdkit import Chem
>>> from rdkit.Chem import AllChem, Draw
>>> mol = Chem.MolFromSmiles("CCOCCNC")
>>> AllChem.EmbedMolecule(mol)
>>> AllChem.UFFOptimizeMolecule(mol)
>>> AllChem.GenerateDepictionMatching3DStructure(mol, 0)
>>> Draw.MolToImageFile(mol, "C:\\test.png")


However, with 2010_12_1, I get the following at the point of calling
GenerateDepictionMatching3DStructure:

Traceback (most recent call last):
  File "", line 1, in 
AllChem.GenerateDepictionMatching3DStructure(mol, 0)
  File "C:\RDKit_2010_12_1\rdkit\Chem\AllChem.py", line 149, in
GenerateDepictionMatching3DStructure
conf = reference.GetConformer(confId)
AttributeError: 'int' object has no attribute 'GetConformer'


I am guessing that something has changed that means a reference
structure is now a requirement(?)  Previously I had been just passing in
0 - which I had assumed meant "don't bother trying to align to anything;
just try and make a tidy 2D representation that looks like the 3D
arrangement".

I must confess I was not 100% sure what the reference option was, but
was fairly happy in my ignorance while I could successfully pass 0 in!
However, now I find that I have to pass a mol type in - I think now
doing:

>>> AllChem.GenerateDepictionMatching3DStructure(mol, mol)

is giving the same results as the previous
"AllChem.GenerateDepictionMatching3DStructure(mol, 0)"...  Am I doing
this correctly, and is the changed behaviour deliberate?

Kind regards

James

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[Rdkit-discuss] Problems importing rdkit on Windows

[James Davidson]

Hi Noel,
 
Recently I had issues with RDKit_2010_12_1 py2.6 binary on two machines
running XP (not 7).  I was getting a crash each time I tried to "from
rdkit import Chem".  After a fair bit of messing around, my rather
heavy-handed 'mend' was to delete the Python26 directory and reinstall
Python and the modules I needed!
 
It then ocurred to me that it could have been an incompatibility with an
earlier Numpy version(?)  Would this be involved at the point of import?
The version I reinstalled was 1.5.1rc1.
 
Probably not going to be of help to you, but I thought I would share
just on the off-chance!  : )
 
Kind regards
 
James

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Re: [Rdkit-discuss] Beta of Q1 2011 Release Available

[James Davidson]

Hi Greg - great news about the beta / new functionality!

> Greg wrote:
> This morning I tagged the beta for the Q1 2011 (2011.03 in the new
> numbering) release in svn:
> http://rdkit.svn.sourceforge.net/viewvc/rdkit/tags/Release_201
> 1_03_1beta1/
> 
> and uploaded a source distribution to the google code site:
> http://code.google.com/p/rdkit/downloads/detail?name=RDKit_201
> 1_03_1beta1.tgz
> If there's demand for it, I will also put up a windows binary.

As usual, "yes, please" for a python 2.6 windows binary if possible  : )

Kind regards

James

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[Rdkit-discuss] Problem with ConstrainedEmbed()

[James Davidson]

Dear All,

I am currently having some problems using the AllChem.ConstrainedEmbed() -
which I have previously used successfully in version 2010_09_1 (Windows py26
binary).  The following example demonstrates the issue:

>>> from rdkit import Chem
>>> from rdkit.Chem import AllChem
>>> template = Chem.MolFromSmiles("c1cnn(Cc2c2)c1")
>>> mol = Chem.MolFromSmiles("c1ccc(Cn2ncc(-c3c3)c2)cc1")

Now I give the template some 3D coordinates:

>>> AllChem.EmbedMolecule(template)
>>> AllChem.UFFOptimizeMolecule(template)

and finally, try to force an overlay of 'mol' onto 'template'

>>> AllChem.ConstrainedEmbed(mol, template, True)

Traceback (most recent call last):
  File "", line 1, in 
AllChem.ConstrainedEmbed(mol, template, True)
  File "C:\RDKit_2010_12_1\rdkit\Chem\AllChem.py", line 294, in
ConstrainedEmbed
rms = AlignMol(mol,core,atomMap=algMap)
RuntimeError: Range Error


I am not getting a ValueError - so I think this shows the substructure match
is ok, but wasn't sure where to go to dig into the AlignMol() function...

As the error message above shows, this is running 2010_12_1.  I have just
tried with 2011_03_1beta1 and 2011_03_2 and get the same thing.  In
2010_09_1 the ConstrainedEmbed() passes back an RDKit molecule fine.

Kind regards

James
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Re: [Rdkit-discuss] Sample RD Files?

[James Davidson]

Hi Greg,

Thanks for the python-full reply!

> # let's test the reaction to make sure it works.
> # due to a (already reported) bug in the way atom properties 
> are handled, nrxn cannot be directly used, # so we use a hack 
> and reparse it:
> >>> nrxn = AllChem.ReactionFromSmarts(AllChem.ReactionToSmarts(nrxn))
> >>> nrxn.Validate()
> # now we can run a molecule through to make sure it works:
> >>> nmol = Chem.MolFromSmiles('c1c1C') nps = 
> >>> nrxn.RunReactants((nmol,)) print Chem.MolToSmiles(nps[0][0])
> # output is: BrCc1c1
> 
> Is that what you're looking for?

It certainly allows me to do what I want - which is get a mapped RXN
out.  And this can even be done with coordinates - which I have added
below as a reminder to anyone (which included me until about 10 mins
ago!) who had forgotten:

AllChem.Compute2DCoordsForReaction(nrxn)
rxnBlock = AllChem.ReactionToRxnBlock(nrxn)


So Thanks very much!  : )

 - and thanks for the reminder about sanitizing products from
reactions...

> The molecules that come back from reactions have not been 
> sanitized, so all you need to do is add a call to 
> Chem.SanitizeMol first:
> 
> >>> Chem.SanitizeMol(prod)

Kind regards

James

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[Rdkit-discuss] rdkit.Chem.Draw.spingCanvas.py (and py27 aggdraw / cairo help?)

[James Davidson]

Dear All,
 
I am in the process of upgrading to python 2.7 under Windows, and part
of this has included moving to the RDKit_2011_03_2 (py27) build.  I had
previously done most work with earlier versions of RDKit under python
2.6, but have found a problem with calling Draw.MolToImage() with the
latest RDKit binary for both py26 and py27:
 
Traceback (innermost last):
  File "C:\Python26\lib\site-packages\Pmw\Pmw_1_3\lib\PmwBase.py", line
1747, in __call__
return apply(self.func, args)
  File "C:\Python26\lib\site-packages\pmg_tk\startup\VerMOL.py", line
1188, in 
command=lambda
s=self:s.draw_ligand(self.modelling_chainlist.listbox, self.ligcanvas,
self.smiles, '3D',200,200, 'modelling_lig_image'))
  File "C:\Python26\lib\site-packages\pmg_tk\startup\VerMOL.py", line
2871, in draw_ligand
im = Draw.MolToImage(mol, size=(x,y))
  File "C:\Python26\RDKit_2011_03_2\rdkit\Chem\Draw\__init__.py", line
71, in MolToImage
drawer.AddMol(mol,**kwargs)
  File "C:\Python26\RDKit_2011_03_2\rdkit\Chem\Draw\MolDrawing.py", line
361, in AddMol
color=color,width=width,color2=color2)
  File "C:\Python26\RDKit_2011_03_2\rdkit\Chem\Draw\MolDrawing.py", line
190, in _drawBond
dash=self.dash)
  File "C:\Python26\RDKit_2011_03_2\rdkit\Chem\Draw\MolDrawing.py", line
169, in _drawWedgedBond
 
self.canvas.addCanvasDashedWedge(poly[0],poly[1],poly[2],color=color)
  File "C:\Python26\RDKit_2011_03_2\rdkit\Chem\Draw\spingCanvas.py",
line 104, in addCanvasDashedWedge
pts1 = _getLinePoints(p1,p2,dash)
: global name '_getLinePoints' is not
defined
 
 
Not a big problem to sort - I think spingCanvas.addCanvasDashedWedge()
should read:
 
pts1 = self._getLinePoints(p1,p2,dash)
pts2 = self._getLinePoints(p1,p3,dash)
 
on lines 104, 105 instead of:
 
pts1 = _getLinePoints(p1,p2,dash)
pts2 = _getLinePoints(p1,p3,dash)
 
 
Anyway, this is only a problem if spingCanvas is being called - which I
think only happens as a last resort if aggdraw or cairo aren't found.
So on that note, the reason I was calling spingCanvas was that I don't
have a build of aggdraw for python 2.7, and I have found that when
cairo/pycairo are available to python 2.7 I get a pythonw.exe
Application Error at the point of calling Draw.MolToImage().  Under
python 2.6 I thought I would see what would happen if I removed aggdraw
to force cairo into play (different version of PIL, different version of
cairo - not an ideal comparison!):
 
File "C:\Python26\RDKit_2011_03_2\rdkit\Chem\Draw\__init__.py", line 54,
in MolToImage
canvas = Canvas(img)
  File "C:\Python26\RDKit_2011_03_2\rdkit\Chem\Draw\cairoCanvas.py",
line 38, in __init__
imgd = image.tostring("raw","BGRA")
  File "C:\Python26\lib\site-packages\PIL\Image.py", line 516, in
tostring
e = _getencoder(self.mode, encoder_name, args)
  File "C:\Python26\lib\site-packages\PIL\Image.py", line 389, in
_getencoder
return apply(encoder, (mode,) + args + extra)
: unknown raw mode
 
 
If it helps, I can follow-up with more details on exact versions of
DLLs, etc; but for now wondered if:
 
(a) anybody had a version of aggdraw for windows, built with python 2.7?
(b) or any recommendations for reliable PIL / cairo / pycairo
combinations for python 2.7 / windows?
 
Kind regards
 
 
James

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Re: [Rdkit-discuss] rdkit.Chem.Draw.spingCanvas.py (and py27 aggdraw / cairo help?)

[James Davidson]

Dear Greg, Riccardo, et al.


> Riccardo wrote:
> I don't know exactly about the other problems, but this one 
> should be related to the version of the installed PIL. If I 
> remember correctly, BGRA raw mode requires PIL 1.1.7.

@Riccardo - 
Thanks for the advice, Riccardo.  I think I was already on 1.1.7 - but
maybe an alpha release(?)  Anyway, I have now standardised across Python
2.6 and 2.7 with the latest PIL installers from
http://www.pythonware.com/products/pil/.


> Greg wrote: 
> I will try to do an aggdraw build for 2.7. If I succeed, I'll 
> post something.

@Greg -
Thanks for the kind offer.  I for one would be very pleased to be using
aggdraw again (as I think the image quality seems the best).  I am
pleased to say, however, that it is less critical now that I have worked
through my cairo issues!  : )


Previously I was getting:

Python 2.7.1 (r271:86832, Nov 27 2010, 18:30:46) [MSC v.1500 32 bit
(Intel)] on win32
Type "copyright", "credits" or "license()" for more information.
>>> from rdkit import Chem
>>> from rdkit.Chem import AllChem, Draw
>>> mol = Chem.MolFromSmiles("c1c1")
>>> AllChem.Compute2DCoords(mol)
>>> im = Draw.MolToImage(mol)
!!!PYTHONW.EXE CRASH!!!


Finally, after a morning of going round in circles (and following
red-herring Dependency Walker trails(!)), things are running well; with
RDKit now happily calling cairo!  I thought it might be useful for
others to list the versions of software / DLLs that I finally found to
work:

Windows XP Pro. SP3 (32-bit)
Python 2.7.1 (http://www.python.org/ftp/python/2.7.1/python-2.7.1.msi)
PIL 1.1.7 (installer -
http://effbot.org/downloads/PIL-1.1.7.win32-py2.7.exe)
Pycairo-1.8.10.win32-py2.7 (installer -
http://ftp.gnome.org/pub/GNOME/binaries/win32/pycairo/1.8/pycairo-1.8.10
.win32-py2.7.exe)
Libcairo-2.dll (get from the following archive:
http://wxpython.org/cairo/cairo_1.8.6-1_win32.zip)
libpng12-0.dll (get from the following archive:
http://wxpython.org/cairo/libpng_1.2.34-1_win32.zip)
Zlib1.dll (get from the following archive:
http://wxpython.org/cairo/zlib123-dll.zip)

I then put the 3 DLLs into the C:\Python27\Lib\site-packages\cairo\
folder, and made sure that this is on the system path.  The use of the
wxPython DLLs seemed to be the key to sorting things out (I certainly
tried a few other versions!) - thanks to Alex Matan's blog-post for the
instructions
(http://electromagnetictelegraph.com/install-cairo-wxpyton-pycairo-pytho
n-windows)

The setup under 2.6 was exactly the same - except I used the
corresponding 2.6 installer for PIL, and used the
Pycairo-1.8.4.win32-py26 from the wxPython site
(http://wxpython.org/cairo/pycairo-1.8.4.win32-py2.6.exe) as detailed in
Alex's blog.


I can add these instructions to to the wiki if you like(?)

Kind regards

James

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Re: [Rdkit-discuss] rdkit.Chem.Draw.spingCanvas.py (and py27 aggdraw / cairo help?)

[James Davidson]

Hi Greg,

> Greg wrote: 
> The attached .pyd is 32-bit aggdraw build for python2.7 on 
> windows. I tested it very briefly and it seems to work; let 
> me know if you have problems with it.

It works a treat - very much appreciated!  My molecules have never
looked better  : )

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[Rdkit-discuss] Beta of Q2 2011 Release Available

[James Davidson]

Hi Greg,

 

Thanks for the update - looks exciting!  I for one would appreciate a
windows binary (py27, please  : )  )

 

Kind regards

 

James


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Re: [Rdkit-discuss] Beta of Q2 2011 Release Available

[James Davidson]

Hi Greg, 

> > windows binary (py27, please  : )  )
> 
> It's up on the google download page; hopefully I remembered 
> all the DLLs this time. :-S
> 
> -greg


The binary works a treat - no sign of missing DLLs - thanks!

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[Rdkit-discuss] Lipinski HBD count

[James Davidson]

Dear All,
 
Apologies for posting on a rather well-trodden (and tedious?) topic...
I have just spent some time counting H-bond donors in a variety of ways
for a 4000 compound data set - to see how our calculations could best
match the results coming from a collaborator (it's as fun as it sounds).
 
As it turns-out, Descriptors.NumHDonors is pretty much on the money! (ie
counting the number or N and O atoms that have at least one H attached)
However, during this process I ended-up going back to a (the?) Lipinski
paper - 

Christopher A Lipinski, Franco Lombardo, Beryl W Dominy, Paul J Feeney,
Experimental and computational approaches to estimate solubility and
permeability in drug discovery and development settings, Advanced Drug
Delivery Reviews, Volume 46, Issues 1-3, 1 March 2001, Pages 3-26, ISSN
0169-409X, 10.1016/S0169-409X(00)00129-0.

- to see what the Lipinski definition of Hydrogen Bond Donors was.  I
read the following:

"We found that simply adding the number of NH bonds and OH bonds does
remarkably well as an index of H bond donor character. Importantly, this
parameter has direct structural relevance to the chemist."


As far as I can tell, this would require explicit addition of Hs to the
molecule, followed by counting the number of matches for an NH or OH
BOND; something like the following:

>>> from rdkit import Chem
>>> from rdkit.Chem import Descriptors

>>> smarts = Chem.MolFromSmarts("[#7,#8]-[#1]")
>>> mol = Chem.MolFromSmiles("CC(=O)N")
>>> mol = Chem.AddHs(mol)
>>> matches = mol.GetSubstructMatches(smarts)
>>> print len(matches)
2

The MOE descriptor lip_don seems to exactly reproduce these 'bond count'
numbers for my set of compounds.  So I guess my question is - shouldn't
we be counting the NH and OH bonds for Lipinski-like counting? (and I
guess this is what MOE's lip_don is for)

Kind regards

James


 
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Re: [Rdkit-discuss] Lipinski HBD count

[James Davidson]

Hi Greg,

Greg wrote: 
> You actually don't need to add the Hs:
> >>> p1 = Chem.MolFromSmarts('[#7,#8;H1]')
> >>> p2 = Chem.MolFromSmarts('[#7,#8;H2]')
> >>> p3 = Chem.MolFromSmarts('[#7,#8;H3]') m = 
> >>> Chem.MolFromSmiles('CC(=O)N')
> >>> m2 = Chem.MolFromSmiles('OCC(=O)N')
> >>> def NHOHCount(mol): return 
> >>> 
> len(mol.GetSubstructMatches(p1))+2*len(mol.GetSubstructMatches(p2))+
> >>> 3*len(mol.GetSubstructMatches(p3))
> ...
> >>> NHOHCount(m)
> 2
> >>> NHOHCount(m2)
> 3

I think this system works well in almost all cases : )  However, I had a
nagging concern over a couple of 'edge' cases - namely water, and
ammonia (and for that matter, the oxonium and ammonium ions).

I guess the simple inclusion of P4 = Chem.MolFromSmarts('[#8;H4]') would
make sure all cases were covered(?).

Out of interest, I decided to compile a small list of 'normal' and
'edge' case SMILES, and ran it through the MOE descriptor node in KNIME.
For all these cases, lip_don behaves as I would expect (tab-separated
output included below)

Kind regards

James

"SMILES""a_acc" "a_don" "lip_acc"   "lip_don"
"CO"1.0 1.0 1.0 1.0
"C(=O)N"1.0 1.0 2.0 2.0
"O" 1.0 1.0 1.0 2.0
"CN"1.0 1.0 1.0 2.0
"[O+]"  1.0 0.0 1.0 3.0
"C[O+]" 1.0 0.0 1.0 2.0
"[N+]"  0.0 0.0 1.0 4.0
"C[N+]" 0.0 0.0 1.0 3.0
"[N-]"  0.0 1.0 1.0 2.0
"[O-]"  0.0 1.0 1.0 1.0
"C(=O)[N-]" 0.0 1.0 2.0 1.0

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Re: [Rdkit-discuss] Lipinski HBD count

[James Davidson]

Hi Greg,

Greg wrote: 
> For what it's worth: the results here are definitely not 
> correct for the SMILES as provided. Atoms in SMILES that are 
> in square brackets have no implicit Hs, so [N+] actually has 
> zero hydrogens. I guess you actually provided the molecules 
> to MOE in some other form.

Oops - you're quite right - I converted them to MOL format with ChemAxon
MolConverter.  However, the point about implicit hydrogens for atoms in
square brackets had completely passed me by - thanks!

> Output with the SVN version of the RDKit:
> 
> #--
> Smiles NOCount NHOHCount
> CO 1 1
> C(=O)N 2 2
> O 1 2
> CN 1 2
> [OH3+] 1 3
> C[OH2+] 1 2
> [NH4+] 1 4
> C[NH3+] 1 3
> [NH2-] 1 2
> [OH-] 1 1
> C(=O)[NH-] 2 1
> #-


Looks great!

Kind regards

James

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Re: [Rdkit-discuss] Beta of Q3 2011 Release Available

[James Davidson]

Hi Greg,

> If there's demand for it, I will also put up a windows binary.

As usual, I'd appreciate a Windows build against python 2.7  : )

Thanks

James

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Re: [Rdkit-discuss] 2011.09 (Q3 2011) RDKit release

[James Davidson]

Hi Greg,
 
I probably should have picked this up in the beta (but didn't...)  When
I try to import AllChem, I see the following:
 
>>> from rdkit import Chem
>>> from rdkit.Chem import AllChem
 
Traceback (most recent call last):
  File "", line 1, in 
from rdkit.Chem import AllChem
  File "C:\Python27\RDKit_2011_09_1\rdkit\Chem\AllChem.py", line 28, in

from rdkit.Chem.rdSLNParse import *
ImportError: DLL load failed: The specified module could not be found.
 
Any advice?
 
Kind regards
 
James

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Re: [Rdkit-discuss] 2011.09 (Q3 2011) RDKit release

[James Davidson]

Thanks Greg, and George.
 
I have not tested the new win-py27 binary fully - but it does at least
behave itself when importing AllChem!
 
Kind regards
 
James

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[Rdkit-discuss] Polymers, S-Groups, and molblock-parsing (oh my!)

[James Davidson]

Dear All,
 
I just wanted to raise an observation about the behaviour of the
molblock parser.  I was running some SMARTS-based substructure queries
in KNIME, and happened to be looking for aromatic N-oxides - the query
was just "nO" - which should maybe be the answer as well!  : )
 
Anyway, I was actually searching DrugBank (via the SDF -
http://www.drugbank.ca/system/downloads/current/structures/small_molecul
e.sdf.zip) and found Heparin was a hit for my query - which I thought
was a bit funny as there are no aromatic nitrogens.  It seems, however,
that the match is due to the * atoms in the molblock (see below) that
are representing the polymer repeat points (leading to *-O, which is
matching n-O).  As I understand it, the rest of the info about the
polymer is stored as S-Group data - and I am presuming that RDKit is not
currently interpreting this(?)
 
So I guess the simple question is - should polymers, etc be handled by
the parser (maybe if not fully, just partially - eg by deleting the *
atoms if the S-Group data are found)?
 
Kind regards
 
James
 
 
 
  Mrv0541 09201117322D  
 
14  0  0  1  0999 V2000
   12.8725  -11.15210. C   0  0  1  0  0  0  0  0  0  0  0  0
   13.5903  -11.56670. C   0  0  1  0  0  0  0  0  0  0  0  0
   12.8725  -10.32720. C   0  0  2  0  0  0  0  0  0  0  0  0
   11.8517  -11.74930. O   0  0  0  0  0  0  0  0  0  0  0  0
   14.2992  -11.15210. C   0  0  2  0  0  0  0  0  0  0  0  0
   13.5903  -12.39140. O   0  0  0  0  0  0  0  0  0  0  0  0
   13.5903   -9.91720. O   0  0  0  0  0  0  0  0  0  0  0  0
   12.1547   -9.91720. C   0  0  0  0  0  0  0  0  0  0  0  0
   10.8307  -12.33350. C   0  0  1  0  0  0  0  0  0  0  0  0
   14.2992  -10.32720. C   0  0  2  0  0  0  0  0  0  0  0  0
   14.9729  -11.91850. N   0  0  0  0  0  0  0  0  0  0  0  0
   11.4415  -10.32720. O   0  0  0  0  0  0  0  0  0  0  0  0
   10.8307  -13.15820. C   0  0  1  0  0  0  0  0  0  0  0  0
   10.1175  -11.92320. O   0  0  0  0  0  0  0  0  0  0  0  0
   15.3200   -9.74330. O   0  0  0  0  0  0  0  0  0  0  0  0
   16.1934  -11.91390. S   0  0  0  0  0  0  0  0  0  0  0  0
   10.1175  -13.57280. C   0  0  2  0  0  0  0  0  0  0  0  0
   11.7684  -14.14450. O   0  0  0  0  0  0  0  0  0  0  0  0
9.3996  -12.33350. C   0  0  2  0  0  0  0  0  0  0  0  0
   16.3409   -9.15040. C   0  0  2  0  0  0  0  0  0  0  0  0
   16.1889  -12.73870. O   0  0  0  0  0  0  0  0  0  0  0  0
   16.1889  -11.08920. O   0  0  0  0  0  0  0  0  0  0  0  0
   17.0225  -11.91390. O   0  0  0  0  0  0  0  0  0  0  0  0
9.3996  -13.15820. C   0  0  1  0  0  0  0  0  0  0  0  0
   10.1175  -14.39750. O   0  0  0  0  0  0  0  0  0  0  0  0
8.6864  -11.92320. C   0  0  0  0  0  0  0  0  0  0  0  0
   16.3409   -8.32570. C   0  0  2  0  0  0  0  0  0  0  0  0
   17.0586   -9.56500. C   0  0  1  0  0  0  0  0  0  0  0  0
8.6819  -13.56830. O   0  0  0  0  0  0  0  0  0  0  0  0
7.9730  -12.33350. O   0  0  0  0  0  0  0  0  0  0  0  0
8.6864  -11.09850. O   0  0  0  0  0  0  0  0  0  0  0  0
   17.0586   -7.91540. O   0  0  0  0  0  0  0  0  0  0  0  0
   15.6276   -7.91540. C   0  0  0  0  0  0  0  0  0  0  0  0
   17.7720   -9.15040. C   0  0  2  0  0  0  0  0  0  0  0  0
   17.0586  -10.39420. O   0  0  0  0  0  0  0  0  0  0  0  0
6.9121  -13.55940. *   0  0  0  0  0  0  0  0  0  0  0  0
   17.7720   -8.32570. C   0  0  2  0  0  0  0  0  0  0  0  0
   14.9099   -8.32570. O   0  0  0  0  0  0  0  0  0  0  0  0
   15.6276   -7.09070. O   0  0  0  0  0  0  0  0  0  0  0  0
   19.3208  -10.04870. O   0  0  0  0  0  0  0  0  0  0  0  0
   18.7974   -7.73260. O   0  0  0  0  0  0  0  0  0  0  0  0
   19.8138   -7.14420. C   0  0  2  0  0  0  0  0  0  0  0  0
   19.8138   -6.31940. C   0  0  2  0  0  0  0  0  0  0  0  0
   20.5314   -7.55890. C   0  0  1  0  0  0  0  0  0  0  0  0
   20.5314   -5.90930. O   0  0  0  0  0  0  0  0  0  0  0  0
   19.1005   -5.90930. C   0  0  0  0  0  0  0  0  0  0  0  0
   21.2449   -7.14420. C   0  0  2  0  0  0  0  0  0  0  0  0
   20.5314   -8.38800. O   0  0  0  0  0  0  0  0  0  0  0  0
   21.2449   -6.31940. C   0  0  0  0  0  0  0  0  0  0  0  0
   18.2713   -5.90040. O   0  0  0  0  0  0  0  0  0  0  0  0
   22.5298   -7.73480. N   0  0  0  0  0  0  0  0  0  0  0  0
   22.7828   -5.43680. *   0  0  0  0  0  0  0  0  0  0  0  0
   17.4465   -5.89590. S   0  0  0  0  0  0  0  0  0  0  0  0
   22.5342   -8.56390. C   0  0  0  0  0  0  0  0  0  0  0  0
   17.4421   -6.72070. O   0  0  0  0  0  0  0  0  0  0  0  

Re: [Rdkit-discuss] Polymers, S-Groups, and molblock-parsing (oh my!)

[James Davidson]

Hi Greg:

James wrote:
>> So I guess the simple question is - should polymers, etc be handled by the
>> parser (maybe if not fully, just partially - eg by deleting the * atoms if
>> the S-Group data are found)?

Greg wrote:
> I'm reluctant to do this since I don't understand the semantics of
> Sgroups well enough to be able to tell if this modification only makes
> sense in this one case or if it's general. In the cases of polymers I
> would tend to say that the correct thing to do is to reject the
> molecule completely since the RDKit is incapable of correctly storing
> what the user intended with the mol block.

> I will try to find the time to grok the CTFile documentation for
> Sgroups, but I would be happy to get input on this from others.


I found some time to have a look into this a bit more myself, and would be 
inclined to agree that the best thing to do would be to reject polymers.  From 
my reading of the CTFILE spec, and the (extremely useful) Gushurst paper (J. 
Chem. Inf. Comput. Sci. 1991, 31, 447-454) I would suggest rejecting any 
molecule with "polymer" or "components, mixtures, and formulations" Sgroup data 
in the molblock; and ignoring or handling the "drawing and displaying 
shortcuts" Sgroup data (if there are no Sgroup data in the previous two 
categories).

I have copied below my understanding of the categories:

Sgroup types for "polymers":

SRU - structural repeating unit (for structure-based representation)
MON - monomer type (for source-based representation)
COP - copolymer
CRO - cross-link across two polymers
GRA - graft (eg terminally-attached) polymer2 on repeat unit of polymer1
MOD - for representing incomplete(?) modifications
MER - used when monomer repeat is 1 - ie alternating copolymers
ANY - (query) for posing more general polymer search queries


Sgroup types for "components, mixtures, and formulations":

COM - components (members of mixtures/formulations)
MIX - mixtures (order is not important)
FOR - formulations (order is important)


Sgroup types for "drawing and display shortcuts"

SUP - superatoms (can be contracted/expanded for representation purposes)
MUL - multiple groups (like a repeating superatom, but can only have 0 or 2 
crossing bonds)
GEN - generic bracketing (does not affect structure)


Rejecting based on the first two categories should be straightforward(?), and 
equally applicable to V2000 and V3000.  Ignoring the SUP and MUL types will 
only (I think...) cause issues in 2D layout - so 'handling' could maybe be to 
force the expansion of these groups, then get rid of them and regenerate 
coordinates?

Kind regards

James


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Re: [Rdkit-discuss] windows binary install

[James Davidson]

Hi Alan,

 

My guess is that your problem is missing DLLs, available in the MS C++
Redistributable package - solution described by George for a very
similar problem:
http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg02381
.html.

 

I now tend to explicitly just put a copy of these two DLLs into the
RDKit lib folder when installing for others, and I can reproduce your
error if I remove one of these DLLs from there on my system.

 

Cheers

 

James

 


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Re: [Rdkit-discuss] windows binary install

[James Davidson]

Hi again, Alan.

 

Apologies - I rather jumped the gun with the last suggestion regarding
the C++ redistributable...  It may be a solution, but actually the only
reason that I thought I reproduced your error when I did a quick test of
removing the DLLs was that I had inadvertently started-up 64-bit Python
(I have both installed on my system).  I could not reproduce when using
32-bit python.

 

Regards

 

James


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[Rdkit-discuss] rSMARTS and "zero-level parentheses"

[James Davidson]

Dear All,

 

One of my colleagues has been trying to use the RDKit to process some
intramolecular reactions (ring-closing metatheses).  It seems, however,
that what Daylight would refer to as "zero-level parentheses" are not
supported in RDKit reaction SMARTS(?)

 


---

ValueErrorTraceback (most recent call
last)

C:\Users\j.davidson\ in ()

  1 from rdkit import Chem

  2 from rdkit.Chem import AllChem, Draw

> 3 rxn1 =
AllChem.ReactionFromSmarts("([C:1]=[C;H2].[C:2]=[C;H2])>>[*:1]=[*:2]")

  4 rxn1

  5 

 

ValueError: ChemicalReactionParserException: Problems constructing
reactant from SMARTS: ([C:1]=[C;H2]

 

 

To explain a little further by example (from the Daylight manual) - here
is how intra-molecular vs inter-molecular reactions can be specified /
distinguished with zero-level parentheses:

 

C(=O)O.OCC>>C(=O)OCC.O  Matches esterifications

(C(=O)O).(OCC)>>C(=O)OCC.O Matches intermolecular esterifications

(C(=O)O.OCC)>>C(=O)OCC.O   Matches intramolecular esterifications
(lactonizations)

 

 

Is there a workaround to this, and if not is this reaction behaviour
something that should be added in the future?

 

Kind regards

 

James


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Re: [Rdkit-discuss] rSMARTS and "zero-level parentheses"

[James Davidson]

Hi Greg,

> Correct. They are not currently supported in either SMARTS or reaction
> SMARTS.

D'oh!  With hindsight this would have been a good one for the "What's
missing" session at the UGM!  : )

> I have to think about it a bit more, but I believe that getting the
correct
> behavior in the SMARTS matcher is going to be difficult (this is why
it's not
> already supported).

> However, modifying the Reaction SMARTS parser so that
> it allows you to do intra-molecular reactions is certainly doable for
the next
> release. It won't be perfect (if you have two components in the single
> reactant, the matches in that reactant won't be limited to a single
> component), but it should handle most cases.

That would be a good start!

But I guess this means that enumeration would be fairly well sorted, but
full control in searching mixtures / reactions would rely on the
'difficult' support in the SMARTS matcher(?)

Kind regards

James

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[Rdkit-discuss] fdef files

[James Davidson]

Dear All,

 

At the UGM I promised to send a reminder (mainly for Greg, but possibly
also Nik?) about the potential use of two fdef files - one with and one
without explicit hydrogens.  During the demo of the PyMOL interactivity
with 3D ligand + pharmacophoric features (showfeats.py script), it was
clear that explicitly 'protonated' nitrogens (eg in a specific tautomer
of pyrrazole) were being flagged as possible hydrogen-bond acceptors, as
well as donors, due to the fdef being used recognising the potential for
a 1,2-H shift.  I made the comment at the time that in cases where the
molecule had hydrogens specifically added (perhaps a docking result),
then it would probably be best to flag 'specific' rather than
'potential' Ph4 features - hence the use of separate fdef files.

 

My recollection (from Nik?) was that this was perhaps already the case
in NIBR user of RDKit(?)

 

Kind regards

 

James

 

_____

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Re: [Rdkit-discuss] Crippen pKa model in RDKit

[James Davidson]

Hi Paul,

 

Thanks for the comments!

 

I may have jumped in a bit too enthusiastically with this - having
tested with the single "walk through" example from the paper.  Having
now seen rather strange predictions for a lot of in-house molecules, I
have started to do what I should have done at the start - actually
reproduce the full test set (also in the supporting info
http://pubs.acs.org/doi/suppl/10.1021/ci8001815) - something is clearly
up, because most don't agree(!)

 

At the moment, I am presuming this is down to the SMARTS modifications
that I made.  I will look into this further when I have some more time -
for now, here are the changes I think I made - roughly in the order that
I found them (I found the piece of paper where I had scrawled them
down!)

 

#G6 = #8,#16,#34,#52,#84

i = $(*!-*)

#X = !#1;!#6

!#G4 = !#6;!#14;!#32;!#50;!#82

#G7 = #9,#17,#35,#53,#85

#N = #8,#7,#9,#17,#35

!#N = !#8;!#7;!#9;!#17;!#35

!i = !$(*!-*)

q3 = $(*(@*)(@*)@*)

 

 

But there is also maybe an additional, more fundamental, issue - the
SMILES in the supporting test-set suggest that the molecules need
pre-'washing'.  More precisely - bases appear in the list as their
conjugate acids - which means there still needs to be a 'gross'
assessment of possible basic centres (SMARTS), then a corresponding
mono-protonation prior to pKa calculation.

 

Kind regards

 

James


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Re: [Rdkit-discuss] Handling reaction stereochemistry

[James Davidson]

Hi Greg,

 

> I've got a question for the community about how chirality should be
handled in reactions.

> This morning I managed to fix one of the outstanding reaction
stereochemistry problems in the RDKit: the loss of chirality when one
bond to a stereocenter is to an unmapped atom. Here's a quick demo of
the new behavior (not yet checked in; there are still a couple things to
be cleaned up):

> 

> In [7]: rxn = AllChem.ReactionFromSmarts('[C:1]-O>>[C:1]-S')

> In [8]: ps = rxn.RunReactants((Chem.MolFromSmiles('F[C@H](O)Cl'),))

> In [9]: Chem.MolToSmiles(ps[0][0],True)

> Out[9]: 'F[C@H](S)Cl'

> 

> It seems nice to be able to preserve chirality in these cases.

> The question that comes up is: "*Should* we be preserving chirality in
these cases?". The change makes it impossible to indicate a reaction
that scrambles stereochemistry. That doesn't seem right.

> So... the question to you guys: How should stereochemistry
inversion/retention/loss be indicated in Reaction SMARTS?

 

 

Good question - and let me be the first to jump in, feet first, without
thinking enough!  : )

Instinctively, I would say it would be good to (a) scramble
stereochemistry if not otherwise specified - at least this way we
default to losing information rather than risking keeping incorrect
information; (b) use a flag at each centre if we want to retain
stereochemistry (what about '@'?); (c) use another flag if we want to
invert (and, inventive I know, what about '@@'?).

 

So in the above example, let's say I want to always invert (eg to
represent an SN2 reaction) - the rSMARTS could then be something like
[C:1]-O>>[C:1@@]-S, and the example input above would give F[C@@H](S)Cl
out.

The same output with no specification could give FC(H)(S)Cl and, of
course, achiral input would always give achiral output - regardless of
the flag in the rSMARTS.

 

 

> Bonus points to anyone who can explain to me how the
inversion/retention flags in RXN files should be handled. At the moment
the RDKit uses what's in the products and ignores them in the reactants.

 

Something like the above? (I told you I hadn't thought about it enough!)

 

Kind regards

 

James


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Re: [Rdkit-discuss] Handling reaction stereochemistry

[James Davidson]

Hi Greg

> 
> I should have provided a bit more context around what the current
behavior
> is, or at least what it's supposed to be. Sorry I forgot that.

My fault - I should have (re)read the manual (I thought it seemed a bit
familiar..!)


> Currently, when creating a reaction from rxnSMARTS,
inversion/retention is
> handled by looking at the relative stereochemistry of atoms in the
reactants
> and products.
> 
> If they're different you get inversion (apologies for the extremely
bogus
> example "reaction"):
> 
> In [13]: rxn = AllChem.ReactionFromSmarts("[C@:1]>>[C@@:1]")
> 
> In [14]: ps =
rxn.RunReactants((Chem.MolFromSmiles('F[C@](Cl)(Br)I'),))
> 
> In [15]: Chem.MolToSmiles(ps[0][0],True)
> Out[15]: 'F[C@@](Cl)(Br)I'
> 
> In [16]: ps =
rxn.RunReactants((Chem.MolFromSmiles('F[C@@](Cl)(Br)I'),))
> 
> In [17]: Chem.MolToSmiles(ps[0][0],True)
> Out[17]: 'F[C@](Cl)(Br)I'
> 
> and if they're the same you get retention:
> 
> In [7]: rxn2 = AllChem.ReactionFromSmarts("[C@:1]>>[C@:1]")
> 
> In [8]: ps =
rxn2.RunReactants((Chem.MolFromSmiles('F[C@](Cl)(Br)I'),))
> 
> In [9]: Chem.MolToSmiles(ps[0][0],True)
> Out[9]: 'F[C@](Cl)(Br)I'
> 
> In [10]: rxn3 = AllChem.ReactionFromSmarts("[C@@:1]>>[C@@:1]")
> 
> In [11]: ps =
rxn3.RunReactants((Chem.MolFromSmiles('F[C@](Cl)(Br)I'),))
> 
> In [12]: Chem.MolToSmiles(ps[0][0],True)
> Out[12]: 'F[C@](Cl)(Br)I'
> 
> 
> This much feels logical to me, though of course it can be changed if
there's
> disagreement.

It sort of does to me too, but I can't shift the sensation that there
might be a can of worms here - more on that in a moment...


> If you call the reaction with non-chiral starting material, you get
non-chiral
> ouput:
> 
> In [20]: rxn3 = AllChem.ReactionFromSmarts("[C@@:1]>>[C@@:1]")
> 
> In [21]: ps = rxn3.RunReactants((Chem.MolFromSmiles('FC(Cl)(Br)I'),))
> 
> In [22]: Chem.MolToSmiles(ps[0][0],True)
> Out[22]: 'FC(Cl)(Br)I'
> 
> This is probably also ok; it certainly reflects what would happen in
the lab (er,
> at least I think it does).

Just to be a pedant for a moment (but actually, this could be important
later) - this is actually calling the reaction with *chiral* (albeit
presumably racemic) starting material


> So far so good. We've got inversion of stereochemistry and retention
of
> stereochemistry. There are two cases left: resolution/creation and
> scrambling.
> 
> One obvious thing to do here would be:
> 
>   [C@:1]>>[C:1]   scrambling
>   [C:1]>>[C@:1]   resolution/induction
> 
> This is where my extremely bogus example starts to make things more
> difficult to understand, so here's a more real example of the
induction case:
>[#6:1]/[C:2]=[C:3](/[#6:4])>>[#6:1][C@H:2](Br)[C@H:3](Br)[#6:4]
> 
> Seem right?

<>  At first sight this seems perfectly ok(?) -
as long as we accept that we know what we mean by the (R) flags on the
carbons (by my reckoning we probably mean syn addition of Br2 across a
double-bond?).  But - problems of symmetry and atom priorities aside(!)
- what do I do if I want to employ the same transformation but with no
absolute stereo-control (ie if I don't have the same wonder-catalyst)?
At the moment I guess there is no way to represent relative
stereochemistry in the absence of an enhanced stereochemistry model?

This brings me on to the main can of worms sensation - and I think it
may revolve trying to service both real and 'virtual/fake' reactions in
the same system, as well as some obvious concerns about enhanced
stereochemistry.  So some examples / questions:

1.  I have a super-useful enzyme that will only hydrolyse (R)-esters (or
more precisely I should say it won't hydrolyse (S)-esters).  So:

CC[C@H](C)C(=O)OC>>CC[C@H](C)C(=O)O ## R gets hydrolysed
CC[C@@H](C)C(=O)OC>>CC[C@@H](C)C(=O)OC  ## S doesn't
CCC(C)C(=O)OC>> ## Oh dear, what do we want to happen here?  I know what
my enzyme will do - but we do have to assume that we are implying a
racemic mix (it gets more worrying if we might mean a single, but
unknown, enantiomer, or we might know nothing at all - we're back to
enhanced stereochemistry again!)
CCC(C)C(=O)OC>>CC[C@H](C)C(=O)O.CC[C@@H](C)C(=O)OC  ## So this is
what the enzyme would do - because we have treated the chiral centre as
a racemic mix - essentially expanding out to:
CC[C@H](C)C(=O)OC.CC[C@@H](C)C(=O)OC>>CC[C@H](C)C(=O)O.CC[C@@H](C)C(=O)O
C

The problem with this is that it doesn't fit with the existing rSMARTS
nomenclature for retention and inversion, because the absolute
stereochemistry of the starting material affects the outcome of the
reaction!  But I guess my enzyme reaction above would be represented as
something like

[C@:1][C:2](=[O:3])[O:4]C>>[C@:1][C:2](=[O:3])[O:4]H

But we would have to (a) assume now that '@' in the starting material
only matched (R), and (b) treat incoming racemates intrinsically as
two-component mixtures of (R) and (S) to then apply the transformation
to just the (R) and add the (S) starting material to the products...


2.  I am a database admin, and I want to

Re: [Rdkit-discuss] Handling reaction stereochemistry

[James Davidson]

Hi Greg,

> Correct, relative (or other forms of enhanced) stereochemistry is not
> possible. It's worth talking about how to deal with this, but it's
going to be
> "more than a little bit" of work, I suspect.

I suspect so, too!


> The conversation about representation of and handling of enhanced
> stereochemistry, and what the actual use cases are, would be a good
one to
> have. I think it's probably going to be difficult via email though.
Maybe a topic
> for the UGM...

I agree re: email.  A topic for discussion at the UGM sounds like a very
good idea - that gives everybody 6 months to mull it over!


Kind regards

James

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Re: [Rdkit-discuss] Chemistry 101 question...

[James Davidson]

Hi JP, Nik, Greg, RDKitters

The question about the lipophilicity (or otherwise) of nitro groups was 
interesting to me...  I came from a CNS background, where there was, of course, 
a stricter requirement for molecules to be suitably lipophilic to cross the 
blood-brain barrier.  My recollection was that the observed lipophilicity of 
nitro groups was dependent on their local environments (ie electron rich / +m 
gave more polar character, and electron poor / -m gave more polar character)... 
 But rather than rely on my hazy recollections, I decided to have a quick look 
back at some historical reverse-phase analytical LC data.

What I did was took all retention times (in mins) under one well-used gradient 
method, and generated the matched-molecular pairs using George's KNIME node.  I 
was then only interested in *[H] >> [*][N+](=O)[O-] transformations, so 
filtered-down to just those changes involving 5 atoms in the transformation 
(because this was quicker than chemically searching!).  I then grouped across 
the examples of transformations to give some average changes in retention time, 
plus n, range, sd:

Transformation

Mean RT change (min)

RT range (min)

SD

n

*[H]>>[*]CCC

2.5

3.3

0.999

28

*[H]>>[*]C(C)C

2.19

5.47

1.09

37

*[H]>>[*]CCCl

1.91

1.5

1.06

2

*[H]>>[*]C(F)F

1.22

1.36

0.748

3

*[H]>>[*]C1CC1

1.18

1.04

0.436

4

*[H]>>[*]N(C)C

1.08

1.21

0.472

6

*[H]>>[*]CSC

0.67

0

0

1

*[H]>>[*]OCC

0.479

4.67

1.17

15

*[H]>>[*][N+](=O)[O-]

0.169

2.82

0.645

35

*[H]>>[*]NCC

0.0625

0.045

0.0318

2

*[H]>>[*]CCO

0.06

0.04

0.0283

2

*[H]>>[*]COC

-0.001

2.46

0.62

14

*[H]>>[*]CC=C

-0.357

0

0

1

*[H]>>[*]C(C)=O

-0.397

1.21

0.696

3

*[H]>>[*]C(=O)O

-0.848

4.3

2.17

3

*[H]>>[*]CC#N

-1.3

2.35

1.66

2

*[H]>>[*]C(N)=O

-2.72

0

0

1

*[H]>>[*]CCN

-2.77

0

0

1



So on average over the 35 examples of H --> NO2 the change made the molecules 
slightly more lipophilic (or, at least, they were retained slightly longer on a 
C18 column).
I expect there is much more data-digging that could be done - particularly with 
larger data sets, and (maybe) with proper logP / logD measurements; but for now 
I am going to stick to thinking NO2 groups can be lipophilic additions(!)

Cheers

James

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Re: [Rdkit-discuss] Chemistry 101 question...

[James Davidson]

Hi Nik,

Nik wrote:
> Interesting. I wonder if this is also dependent on the transport phase that 
> was used. Do you have any info on that? Was it a typical 10% MeOH or more 
> something with dichlormethane?

I dug-out the conditions:
LC retention time Method A refers to elution of a sample through an XTERRA RP18 
(50 mm x 4.6 mm) 5 µm column under gradient conditions.  The initial eluent 
comprises 50% Methanol (pump-A) and 50% of a 10 mM aqueous ammonium acetate 
solution containing 5% IPA (pump-B) at a flow rate of 2 mL/min.  After 1 min, a 
gradient is run over 5 min to an end point of 80% pump-A and 20% pump-B, which 
is isocratically maintained for a further 3 min.  UV peak detection is 
generally carried out at a wavelength of 220 nm.


I should also say that, in my experience, even under normal-phase conditions 
(ie silica column and organic eluent) nitro-aromatics tend to behave 
'greasily'.  Who in big pharma wants to mine some nitration reaction data to 
pull out TLC plate Rf data (normal phase) + LC retention (reverse phase)?  I 
think your DB may be bigger than ours!  : )

Cheers

James

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Re: [Rdkit-discuss] Beta of Q3 2013 release available

[James Davidson]

Hi Greg (et al.),

Thanks for the beta!  I have been going through some of the recently-added 
functionality, and had a couple of questions regarding the PDB reading / 
writing.


1.   Do I remember correctly that there was a proposal (from Roger) to add 
some auto bond-type perception to the PDB parser for ligands (or is that just 
wishful thinking!)?

2.   If not, I notice that there is an AssignBondOrdersFromTemplate() 
method - but the example in the doc-string only shows (I think) the case where 
the input PDB is just a single small molecule - so the matching is pretty easy! 
 I think a more real-World case is when one wants to set the bond orders for 
multiple ligands (HETATM residues) based on substructure matches - which will 
then return an atom index selection that can be used as a start point.  Is 
there any way to have the AssignBondOrdersFromTemplate() convenience function 
optionally accept a list of atom indexes to specify a substructure?

3.   Is there some explanation for what the 'flavor' option does for 
reading/writing PDB?

4.   Having read in a PDB file I see the correct atoms flagged as HETATM 
(from GetIsHeteroAtom()).  But when call Chem.MolToPDBBlock() these atoms get 
written as ATOM records...  Also, a Chem.MolToPDBFile() method would be nice 
for completeness / symmetry : )

5.   It seems to me that GetResidueNumber() and GetSerialNumber() may have 
got mixed-up at some point(?).  At least, when I call GetSerialNumber() I see 
what appears to be the residue number; and when I call GetResidueNumber() I get 
"0"!

6.   I also seem to be seeing all of the bonds (for all residues) being 
written out in CONECT records - such that they all appear as single bonds in eg 
PyMOL - is this expected behaviour at the moment?

Cheers

James



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Re: [Rdkit-discuss] Beta of Q3 2013 release available

[James Davidson]

Hi Roger,

Thanks for the response

> The use of an integer file format "flavor" argument allows the caller to
> customize the behavior of the readers and writers.  The semantics is that a
> reasonable default is zero (for all bits), but that new features may be added
> without changing the API/ABI.
> Most of the bits above (for the writer) control strict compliance with the PDB
> format specification.  For example, a flavor of 12 will write bond orders the
> way the RCSB expects them both throwing away bond orders and increasing
> the size of the PDB file.

As a test, I am using 2VCI, and am retrieving the PDB data from the RCSB using 
the following

import requests
url = 
"http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=2VCI";
response = requests.get(url)
pdb_block = response.content
response.close()


pdb_block shows CONECT records only for the HETATM records.
If I now read into RDKit, using the defaults, and write back out using the 
defaults, I see CONECT records for every atom (ie protein as well).  And I 
can't see any double-bonds rendered in PyMOL:

from rdkit import Chem
from rdkit.Chem import AllChem
pdb = Chem.MolFromPDBBlock(pdb_block)
pdb_block_out = Chem.MolToPDBBlock(pdb)

First 10 CONECT records of output:
CONECT12
CONECT235
CONECT344   10
CONECT56
CONECT67
CONECT7889
CONECT   10   11
CONECT   11   12   14
CONECT   12   13   13   17
CONECT   14   15   16


If I use Chem.MolToPDBBlock(pdb, flavor=12) I do, indeed see the ligand CONECT 
records in what looks like the original format (albeit now numbered 
differently), and I still see CONECT records for the protein - but this PDB 
*will* render double bonds in PyMOL.

First 10 CONECT records of output:
CONECT344
CONECT788
CONECT   12   13   13
CONECT   19   20   20
CONECT   23   24   24
CONECT   28   29   29
CONECT   35   36   36
CONECT   38   39   39
CONECT   40   42   42
CONECT   41   43   43


And even if I use Chem.MolToPDBBlock(pdb, flavor=2) I still see CONECT records 
for every protein residue (and, again, I also see double bonds in PyMOL).

First 10 CONECT records of output:
CONECT12
CONECT2135
CONECT324   10
CONECT43
CONECT526
CONECT657
CONECT7689
CONECT87
CONECT97
CONECT   103   11


Am I maybe doing something wrong with options in the reading step?  


> For the reader, the flavor argument controls whether alternate locations are
> read (for use by PDB power users), or whether a sensible subset of atoms is
> used for the RDKit::ROMol.

Can you (or Greg) post a list of what the current input flavors do?



> > 6.   I also seem to be seeing all of the bonds (for all
> > residues) being written out in CONECT records - such that they all
> > appear as single bonds in eg PyMOL - is this expected behaviour at the
> > moment?
> >
> > Another one for Roger.
> 
> I believe this should work fine.  RDKit's PDB file writer by default encodes 
> the
> bond orders, which should be interpreted by PyMol.  In the words of the late
> great Warren:
> http://www.phenix-online.org/pipermail/phenixbb/2008-April/012188.html
> 
> We need to check where the bond orders are getting lost.  If you read the
> PDB file back RDKit's PDB file reader and write out the SMILES does it have
> double bonds?

More weirdness here...  Reading the 3 flavours of output (pdb_block_out) from 
above back in and showing the kekulised SMILES gives the same SMILES - but not 
fully kekulised...

print Chem.MolToSmiles(Chem.MolFromPDBBlock(pdb_block_out), kekuleSmiles=True)

O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.CCNC(O)C1NOC(C2CC(C(C)C)C(O)CC2O)C1C1CCC(CN2CCOCC2)CC1.CCC(C)C(NC(=O)CNC(=O)C(NC(=O)C(CC(=O)O)NC(=O)C(NC(=O)C(NC(=O)C(NC(=O)C(CC(C)C)NC(=O)C(NC(=O)C(CCCNC(=N)N)NC(=O)C(CC(=O)O)NC(=O)C(CCC(N)=O)NC(=O)C(N)NC(=O)C(CC(N)=O)NC(=O)C1CCCN1C(=O)C(NC(=O)C(CC(C)C)NC(=O)C(CC(N)=O)NC(=O)C(NC(=O)C(CC1:C:[NH]:C:N:1)NC(=O)C(CC(C)C)NC(=O)C(CCC(=O)O)NC(=O)C(N)NC(=O)CNC(=O)C(CO)NC(=O)C(CC(=O)O)NC(=O)C(CC(C)C)NC(=O)C(N)NC(=O)C(CO)NC(=O)C1CCCN1C(=O)C(CC(=O)O)NC(=O)C(NC(=O)C(CC(C)C)NC(=O)C(CO)NC(=O)C(CCC(=O)O)NC(=O)C(CC1:C:C:C(O):C:C:1
 
)NC(=O)C(CCCNC(=N)N)NC(=O)C(NC(=O)C(N)NC(=O)C(CC(=O)O)NC(=O)C(CC(C)C)NC(=O)C(C)NC(=O)C(CC(=O)O)NC(=O)C(CO)NC(=O)C(CO)NC(=O)C(CC(N)=O)NC(=O)C(CO)NC(=O)C(NC(=O)C(CC(C)C)NC(=O)C(CCC(=O)O)NC(=O)C(CCCNC(=N)N)NC(=O)C(CC(C)C)NC(=O)C(CC1:C:C:C:C:C:1)NC(=O)C(NC(=O)C(CCC(=O)O)NC(=O)C(N)NC(=O)C(CC

Re: [Rdkit-discuss] Beta of Q3 2013 release available

[James Davidson]

Hi Sereina,

Sereina wrote:
> Regarding the AssignBondOrdersFromTemplate() method:
> As far as I understood, the PDB reader assigns bond orders to the amino acids 
> in a protein, but if a ligand is present it puts all bonds of it to SINGLE 
> bonds as auto bond-type perception is not trivial (see Roger's comments).
> However, usually one knows which ligand was crystallized (i.e. the SMILES is 
> available), so the AssignBondOrdersFromTemplate() method can be used to set 
> the bond orders based on the known ligand structure.
> This is the idea of the method. Now, to your real-world application. I'm 
> sorry but I don't think I understand it completely. Do you want to set only 
> the bond orders of a specific substructure?
> Or would you like to give the function a set of ligands and a set of 
> templates and it figures out which template belongs to which ligand and sets 
> the bonds orders accordingly? 

This is very likely to be me being stupid - so please bear with me!
If I read in a complex (pdb), and already have my reference ligand (lig), then 
AllChem.AssignBondOrdersFromTemplate(lig, pdb) fails because the reference 
ligand has not been matched to the ligand in the pdb 'complex' (dot-separated 
list of molecules).
The doc-string states that the method works on two molecules - but I want to 
work on a reference molecule (lig) and a *substructure* of the macromolecule 
(pdb).  How should I be getting the bound ligand out as a molecule object to 
then use the AssignBondOrdersFromTemplate() method?  Am I missing some new 
PDB-related methods, or have I forgotten some fundamental RDKit methods for 
dealing with multi-component molecules?

I guess a sensible process would be:
1. Identify any HETATM residues
2. For each residue (or at least those that have bonds!) extract or copy the 
mol (unless it can be addressed 'in place'?)
3. Use AssignBondOrdersFromTemplate() - relying on lookup be eg residue name, 
etc
4. Insert the molecule back into the complex (or update the info if it has been 
modified 'in place')

Is this how the method is intended to be used with complexes (and if so, do you 
have an example for steps 2 and 4?

Thanks

James

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Re: [Rdkit-discuss] Chemistry 101 question...

[James Davidson]

Greg wrote:
>  This is what it looks like the state of play at the moment is:
>  
>  - Adding nitro groups tends to make molecules more lipophilic, at least as 
> measured by retention time in chromatography.
>  - Nitro groups are H-bond acceptors, at least according to the papers I 
> found above and the evidence one finds in the CSD.
>  
>  This seems like an argument for having nitro groups in the default fdef file 
> as both lumped hydrophobes (the whole group) and acceptors (the Os).
>  
>  Make sense?


Makes sense to me!

Cheers

James

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[Rdkit-discuss] Minimising bits of molecules?

[James Davidson]

Dear All,

I think this is probably one for Paolo - I was looking at fixing certain atoms 
during MMFF minimisation, but couldn't find the option...  Then I re-read the 
UGM slides, and found the one titled "Force-field wish list", and "fixed atoms" 
were one of the listed items!

My intended use-case is the following:


1.   Load protein-ligand complex into PyMOL

2.   Make some changes to the bound ligand (using the Builder functionality)

3.   Select atoms that are allowed to move (manual selection, then use of 
PyMOL's 'flag' command)

4.   Pass the molecule over to RDKit (already incorporated in a plugin we 
use), to minimise and then pass back (either as a new object, or apply the new 
coordinates to the existing object in situ)

Actually, this process is already well-used by some of our chemists here - as a 
way of doing some simple modelling / idea exploration - but is currently using 
a much 'flakier' MMFF implementation.  So I would definitely like to move to 
RDKit for the minimisation - any idea when a 'fixed atoms' option is likely to 
be added?

Kind regards

James

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[Rdkit-discuss] Building RDKit on Windows

[James Davidson]

Dear All,

As part of a New Year's resolution, I decided I should try to enjoy the 
benefits of a cutting-edge version of RDKit built from source(!)  So far this 
has proven to be much more realistic than eg 'not drinking for January' - as I 
now have a working build to show for my efforts.

However, I wonder if I could quickly list the steps I took; and also ask a 
couple of questions (relating to InChi and Avalon)?  For reference I am running 
on Windows7 64-bit, but use python 2.7.6 32bit, so am building 32-bit RDKit.  I 
essentially followed the guide on the wiki 
(https://code.google.com/p/rdkit/wiki/BuildingOnWindows) but thought the 
version info of boost, etc may be of use to others, and the steps may help put 
my questions into context:


1.   Downloaded Visual Studio Express 2012 for Desktop, installed, and 
accepted the updates

2.   Downloaded matching version of Windows boost binaries 
(boost_1_55_0-msvc-11.0-32.exe) from 
http://sourceforge.net/projects/boost/files/boost-binaries/ and extracted to 
the default path

3.   Used TortoiseSVN to add a repository link to 
https://github.com/rdkit/rdkit.git/trunk (and not the SF path as currently 
shown in the wiki guide) in C:/RDKit

4.   Set the environment variables as described on the wiki.

5.   Downloaded the INCHI src as described in the wiki and set the 
RDK_BUILD_INCHI_SUPPORT option later in cmake.  Incidentally, the location for 
the downloads from IUPAC have changed (ie the info in the README is out of 
date): http://www.iupac.org/home/publications/e-resources/inchi/download.html

6.   Ran CMake configure (GUI) following the wiki, and based on the output, 
made some boost-related additions to environment variables

a.   Added C:\local\boost_1_55_0\lib32-msvc-11.0 to PATH

b.  Created BOOST_ROOT=C:\local\boost_1_55_0

c.   Created BOOST_LIBRARYDIR=C:\local\boost_1_55_0\lib32-msvc-11.0

7.   Re-ran configure, then generate, then followed the rest of the wiki 
instructions to build and test - all tests passed except the dbCli one.


So now for the questions:
I thought I did everything right for adding INCHI support.  However, I see the 
following:



In [1]: from rdkit import Chem

In [2]: Chem.inchi.INCHI_AVAILABLE

Out[2]: False



CMake shows:


Could NOT find InChI in system locations (missing:  INCHI_LIBRARY 
INCHI_INCLUDE_DIR)

Found InChI software locally



Do I also need to download the InChi binary and set these two variables 
appropriately in CMake?



Also, I am struggling to build with Avalon support...  Choosing the 
RDK_BUILD_AVALON_SUPPORT appears to configure fine, but when I try to 
'Generate' I see the following error:



CMake Error at Code/cmake/Modules/RDKitUtils.cmake:26 (add_library):
Cannot find source file:

/common/layout.c

Tried extensions .c .C .c++ .cc .cpp .cxx .m .M .mm .h .hh .h++ .hm .hpp
.hxx .in .txx
Call Stack (most recent call first):
External/AvalonTools/CMakeLists.txt:43 (rdkit_library)

Any thought on how to get around this?  Do I need to download the Avalon 
project src and put it somewhere?

And final question - can I happily ignore the CMake messages about not finding 
FLEX and BISON, or are these needed when incorporating any of the non-default 
entries (SWIG wrappers, etc)?


Kind regards

James

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Re: [Rdkit-discuss] Building RDKit on Windows

[James Davidson]

Hi Greg,

> > 5.   Downloaded the INCHI src as described in the wiki and set the
> > RDK_BUILD_INCHI_SUPPORT option later in cmake.  Incidentally, the 
> > location for the downloads from IUPAC have changed (ie the info in the 
> > README is out of date):
> > http://www.iupac.org/home/publications/e-resources/inchi/download.html
>
> The link that is in the README, which is to a  more recent version (1.04 
> instead of 1.03), does still work for me. Did you have problems with that?

I realised that in my first attempts I had mistakenly linked to the RDKit repo 
on SourceForge (following the wiki).  The README there points to 
http://www.iupac.org/inchi/download/version1.03/INCHI-1-API.zip which no longer 
exists.
I am now using the INCHI download link from the current README - thanks! 

> > 7.   Re-ran configure, then generate, then followed the rest of the
> > wiki instructions to build and test - all tests passed except the 
> > dbCli one.
> >
> What was the DbCLI test failure?

I just see " 76/82 Test #76: pythonTestDbCLI ..***Failed   
50.66 sec"

> > I thought I did everything right for adding INCHI support.  However, I 
> > see the following:
> >
> > In [1]: from rdkit import Chem
> > In [2]: Chem.inchi.INCHI_AVAILABLE
> > Out[2]: False
> >
> > Do I also need to download the InChi binary and set these two 
> > variables appropriately in CMake?
> >
> No; that should not be necessary.
> If you have the source in the right place (and that cmake message makes it 
> look like you do) and have RDK_BUILD_INCHI_SUPPORT set, run "generate",
> and then do a build and an install, it should produce the binaries you need 
> and update that file so that Chem.inchi.INCHI_AVAILABLE is True. Did you 
> re-run "generate" after installing the INCHI source?

I thought I had re-run 'generate'...  Perhaps it was an issue with using older 
INCHI source?


> > Also, I am struggling to build with Avalon support...  
> 
> 1) download the beta source distribution from sf.net; 
> http://sourceforge.net/projects/avalontoolkit/files/AvalonToolkit_1.1_beta/AvalonToolkit_1.1_beta.source.tar/download
> 2) extract that tar file somewhere. It's going to create SourceDistribution 
> and a StandardFiles directories
> 3) set the cmake variable AVALONTOOLS_DIR to point to the SourceDistribution 
> directory
> 3) set RDK_BUILD_AVALON_SUPPORT=ON in cmake
> 4) run a build and install.
> 
> Note: one or two of the avalontools tests may fail on windows. This is 
> currently expected.


I have now included the INCHI 1.04 source, and followed your Avalon steps 
above.  The AVALONTOOLS_DIR currently needs to be added manually in CMake (but 
that's ok).  I should also say that, just in case, I deleted the build folder 
and cleared the CMake cache before this build attempt.  I also *definitely* 
re-ran the 'generate' command (a few times!) before 'configure'.
Anyway, I now see more tests when running 'ctest' - which I think is due to the 
addition of testInchi, testAvalonLib1, and pyAvalonTools - all of which pass!  
I can also confirm that Chem.inchi.INCHI_AVAILABLE now returns "True".
(pythonTestDbCLI still fails as before.)


Thanks very much for the help!

Kind regards

James


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Re: [Rdkit-discuss] Building RDKit on Windows

[James Davidson]

Hi Greg,

> Try: ctest -V -R DbCLI
> that should run the test in Verbose mode so that you can see the failures.

Thanks - I have pasted the output below - looks like a file access issue (but I 
don't know why...).

Kind regards
James



C:\RDKit\build>ctest -V -R DbCLI
UpdateCTestConfiguration  from :C:/RDKit/build/DartConfiguration.tcl
UpdateCTestConfiguration  from :C:/RDKit/build/DartConfiguration.tcl
Test project C:/RDKit/build
Constructing a list of tests
Done constructing a list of tests
Checking test dependency graph...
Checking test dependency graph end
test 76
Start 76: pythonTestDbCLI

76: Test command: C:\Python27\python.exe "C:/RDKit/Projects/test_list.py" 
"--testDir" "C:/RDKit/Projects"
76: Test timeout computed to be: 9.99988e+006
76: [10:13:51] INFO: Reading molecules and constructing molecular database.
76: [10:13:51] INFO: Generating molecular database in file 
testData/bzr\Compounds.sqlt
76: [10:13:51] INFO:   Processing 10 molecules
76: [10:13:51] INFO: Generating fingerprints and descriptors:
76: [10:13:51] INFO: Finished.
76: [10:13:52] INFO: Reading molecules and constructing molecular database.
76: [10:13:52] INFO: Generating molecular database in file 
testData/bzr\Compounds.sqlt
76: [10:13:52] INFO:   Processing 163 molecules
76: [10:13:53] INFO:   done 100
76: [10:13:53] INFO: Generating fingerprints and descriptors:
76: [10:14:02] INFO: Finished.
76: [10:14:02] INFO: Reading query molecules and generating fingerprints
76: [10:14:03] INFO: Finding Neighbors
76: [10:14:04] INFO: The search took 0.6 seconds
76: [10:14:04] INFO: Creating output
76: [10:14:04] INFO: Done!
76: [10:14:05] INFO: Reading query molecules and generating fingerprints
76: [10:14:05] INFO: Finding Neighbors
76: [10:14:05] INFO: The search took 0.3 seconds
76: [10:14:05] INFO: Creating output
76: [10:14:05] INFO: Done!
76: [10:14:06] INFO: Reading query molecules and generating fingerprints
76: [10:14:06] INFO: Finding Neighbors
76: [10:14:06] INFO: The search took 0.1 seconds
76: [10:14:06] INFO: Creating output
76: [10:14:06] INFO: Done!
76: [10:14:07] INFO: Doing property query
76: [10:14:07] INFO: Found 30 molecules matching the query
76: [10:14:07] INFO: Creating output
76: [10:14:07] INFO: Done!
76: [10:14:08] INFO: Doing property query
76: [10:14:08] INFO: Found 30 molecules matching the query
76: [10:14:08] INFO: Creating output
76: [10:14:08] INFO: Done!
76: [10:14:08] INFO: Doing substructure query
76: [10:14:09] INFO:Fingerprint screenout rate: 112 of 163 (%68.71)
76: [10:14:09] INFO: Found 49 molecules matching the query
76: [10:14:09] INFO: Creating output
76: [10:14:09] INFO: Done!
76: [10:14:09] INFO: Doing substructure query
76: [10:14:09] INFO:Fingerprint screenout rate: 112 of 163 (%68.71)
76: [10:14:09] INFO: Found 49 molecules matching the query
76: [10:14:09] INFO: Creating output
76: [10:14:09] INFO: Done!
76: [10:14:10] INFO: Doing substructure query
76: [10:14:10] INFO: Found 114 molecules matching the query
76: [10:14:10] INFO: Creating output
76: [10:14:10] INFO: Done!
76: [10:14:11] INFO: Doing substructure query
76: [10:14:11] INFO:Fingerprint screenout rate: 23 of 30 (%76.67)
76: [10:14:11] INFO: Found 5 molecules matching the query
76: [10:14:11] INFO: Creating output
76: [10:14:11] INFO: Done!
76: [10:14:12] INFO: Doing substructure query
76: [10:14:12] INFO: Found 25 molecules matching the query
76: [10:14:12] INFO: Creating output
76: [10:14:12] INFO: Done!
76: [10:14:13] INFO: Reading query molecules and generating fingerprints
76: [10:14:18] INFO: Finding Neighbors
76: [10:14:19] INFO: The search took 0.9 seconds
76: [10:14:19] INFO: Creating output
76: [10:14:19] INFO: Done!
76: [10:14:20] INFO: Reading query molecules and generating fingerprints
76: [10:14:20] INFO: Finding Neighbors
76: [10:14:20] INFO: The search took 0.0 seconds
76: [10:14:20] INFO: Creating output
76: [10:14:20] INFO: Done!
76: [10:14:21] INFO: Reading molecules and constructing molecular database.
76: [10:14:21] INFO: Generating molecular database in file 
testData/bzr\Compounds.sqlt
76: [10:14:21] INFO:   Processing 10 molecules
76: [10:14:21] INFO: Generating fingerprints and descriptors:
76: [10:14:21] INFO: Finished.
76: [10:14:23] INFO: Reading molecules and constructing molecular database.
76: [10:14:23] INFO: Generating molecular database in file 
testData/bzr\Compounds.sqlt
76: [10:14:23] INFO:   Processing 10 molecules
76: [10:14:23] INFO: Generating fingerprints and descriptors:
76: [10:14:23] INFO: Finished.
76: .Traceback (most recent call last):
76:   File "CreateDb.py", line 460, in 
76: CreateDb(options,dataFilename)
76:   File "CreateDb.py", line 214, in CreateDb
76: startAnew=not options.updateDb
76:   File "C:\RDKit\rdkit\Chem\MolDb\Loader_sa.py", line 111, in LoadDb
76: os.unlink(dbName)
76: WindowsError: [Error 32] The process cannot access the file because it is 
being used by another process: 'testData/bzr\\Compounds.sqlt'
76: [10:14:24] INFO: R

Re: [Rdkit-discuss] Building RDKit on Windows

[James Davidson]

Hi All,

I have just rebuilt RDKit on Windows using the latest source, and am seeing a 
problem with smaTest1 failing (as well as still seeing the same DbCLI failure 
posted previously...)
The smaTest1 failure seems a little strange because it actually throws a 
Windows executable error  ("smaTest1.exe has stopped working", etc).
If I run ctest -V -R smaTest1 I see the output below.  Any thoughts?

Kind regards

James



C:\RDKit\build>ctest -V -R smaTest1
UpdateCTestConfiguration  from :C:/RDKit/build/DartConfiguration.tcl
UpdateCTestConfiguration  from :C:/RDKit/build/DartConfiguration.tcl
Test project C:/RDKit/build
Constructing a list of tests
Done constructing a list of tests
Checking test dependency graph...
Checking test dependency graph end
test 32
Start 32: smaTest1

32: Test command: C:\RDKit\build\Code\GraphMol\SmilesParse\Release\smaTest1.exe
32: Test timeout computed to be: 9.99988e+006
32: [17:42:57] -
32: [17:42:57] Testing patterns which should parse.
32: [17:42:57] SMARTS Parse Error: syntax error for input: c1b1
32: [17:42:57]
32:
32: 
32: Invariant Violation
32: c1b1
32: Violation occurred on line 90 in file 
..\..\..\..\Code\GraphMol\SmilesParse\smatest.cpp
32: Failed Expression: mol
32: 
32:
1/1 Test #32: smaTest1 .***Failed4.03 sec

0% tests passed, 1 tests failed out of 1

Total Test time (real) =   4.29 sec

The following tests FAILED:
 32 - smaTest1 (Failed)
Errors while running CTest

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Re: [Rdkit-discuss] Building RDKit on Windows

[James Davidson]

Hi Greg,

Before building yesterday, I updated RDKit to rev3060, then removed the 'build' 
directory and re-set / configured cmake.  I just checked the 'smarts.tab.cpp' 
file, and it is certainly dated with yesterday's date...  So I presume it was 
freshly regenerated at the time(?)

Kind regards

James

From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: 04 March 2014 04:12
To: James Davidson; RDKit Discuss
Subject: Re: [Rdkit-discuss] Building RDKit on Windows

Hi James,

On Mon, Mar 3, 2014 at 6:45 PM, James Davidson 
mailto:j.david...@vernalis.com>> wrote:

I have just rebuilt RDKit on Windows using the latest source, and am seeing a 
problem with smaTest1 failing (as well as still seeing the same DbCLI failure 
posted previously...)
The smaTest1 failure seems a little strange because it actually throws a 
Windows executable error  ("smaTest1.exe has stopped working", etc).
If I run ctest -V -R smaTest1 I see the output below.  Any thoughts?

I checked in some changes to allow the aromatic "b" in mid-February. When I did 
so, I added a test to make sure it's working. You've got the test (that's the 
one that is failing), but it looks like the build did not regenerate the parser 
files it needs to. You should be able to clear this up by re-configuring cmake 
and regenerating the build files. After you do this, check to see that 
$RDBASE/Code/GraphMol/SmilesParse/smarts.tab.cpp has been freshly re-created.

-greg


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Re: [Rdkit-discuss] Building RDKit on Windows

[James Davidson]

Thanks Greg - that did the trick!
(I still see pythonTestDbCLI - as previously posted)

Kind regards

James

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[Rdkit-discuss] RDKit cartridge similarity search speeds(?)

[James Davidson]

Dear All,

I have recently been spending a bit more time with the RDKit cartridge, and 
have what is probably a very naïve question...
Having built some RDKit fingerprints for ChEMBL_18, I see the following 
behaviour (for clarification - 'ecfp4_bv' is the column in my rdk.fps table 
that has been generated using morganbv_fp(mol, 2)):


chembl_18=# \timing on
Timing is on.

chembl_18=# set rdkit.tanimoto_threshold=0.5;
SET
Time: 0.167 ms

chembl_18=# select chembl_id from rdk.fps where ecfp4_bv % 
morganbv_fp('c1nnccc1'::mol,2);
  chembl_id
-
CHEMBL15719
(1 row)

Time: 2033.348 ms

chembl_18=# select chembl_id from rdk.fps where tanimoto_sml(ecfp4_bv, 
morganbv_fp('c1nnccc1'::mol, 2)) > 0.5;
  chembl_id
-
CHEMBL15719
(1 row)

Time: 6843.605 ms


I can see that the query plans are different in the two cases, but I don't 
fully understand why - see below:

QUERY 1 (with explain analyze)
chembl_18=# explain analyze select chembl_id from rdk.fps where ecfp4_bv % 
morganbv_fp('c1nnccc1'::mol,2);

 QUERY PLAN

Bitmap Heap Scan on fps  (cost=106.91..5298.31 rows=1352 width=13) (actual 
time=1774.986..1774.987 rows=1 loops=1)
   Recheck Cond: (ecfp4_bv % 
'\x0100084200048204'::bfp)
   ->  Bitmap Index Scan on fps_ecfp4bv_idx  (cost=0.00..106.57 rows=1352 
width=0) (actual time=1774.969..1774.969 rows=1 loops=1)
 Index Cond: (ecfp4_bv % 
'\x0100084200048204'::bfp)
Total runtime: 1775.035 ms
(5 rows)

Time: 1776.133 ms


QUERY 2 (with explain analyze)
chembl_18=# explain analyze select chembl_id from rdk.fps where 
tanimoto_sml(ecfp4_bv, morganbv_fp('c1nnccc1'::mol, 2)) > 0.5;

  QUERY PLAN
---
Seq Scan on fps  (cost=0.00..388808.17 rows=450793 width=13) (actual 
time=1278.115..6953.977 rows=1 loops=1)
   Filter: (tanimoto_sml(ecfp4_bv, 
'\x0100084200048204'::bfp)
 > 0.5::double precision)
   Rows Removed by Filter: 1352377
Total runtime: 6954.010 ms
(4 rows)

Time: 6955.103 ms


It seems conceptually 'easier' to add the similarity value as part of the 
query, rather than setting it as a variable ahead of the query; but clearly I 
should be doing it the latter way for performance reasons.  So even if I don't 
fully understand why at the moment, am I correct in thinking that queries of 
this sort should always be run with the similarity operators (%, #)?  And if 
so, is the rdkit.tanimoto_threshold variable set at the level of the session, 
the user, or the database?

Kind regards

James

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Re: [Rdkit-discuss] RDKit cartridge similarity search speeds(?)

[James Davidson]

Hi Greg,

> What these are telling you is that the second query is not using the index:
> it's a sequential scan, so it has to test all rows of the database. This
> happens because the index is defined for the operator %, but not for the
> function tanimoto_sml(). There may be an approach to get the index set up
> using that function, but there we reach the limits of my expertise.

Well, I will stick to the recommended operator use then!


> One final advanced topic: if you are planning on making regular use of the
> similarity features in the cartridge and are running on a linux system or
> Mac I would recommend recompiling the cartridge with some optimizations for
> tanimoto similarity. To do this, you need to edit the cartridge Makefile
> from:
> PG_CPPFLAGS = -I${BOOSTHOME} -I${RDKIT}/Code -DRDKITVER='"007200"'
> ${INCHIFLAGS} #-DUSE_BUILTIN_POPCOUNT -msse4.2
> 
> to:
> PG_CPPFLAGS = -I${BOOSTHOME} -I${RDKIT}/Code -DRDKITVER='"007200"'
> ${INCHIFLAGS} -DUSE_BUILTIN_POPCOUNT -msse4.2
> 
> (I just removed a comment character here). This speeds the Tanimoto
> calculation up a fair bit (it's still not nearly as fast as Andrew's
> chemfp, but it's better than the default behavior).

I'm on linux (Ubuntu), and have just re-built with the above recommendation.
I'll see what the speeds look like afterwards (out of interest, I presume the 
timings in your examples were with this optimisation in place?).

Does this also affect dice?

And final question - after rebuilding the cartridge, does the extension need to 
be dropped and then re-created in all databases; does postgreSQL server need 
restarting; or neither?


> Hope this helps,
> -greg

It does - thanks!

Kind regards

James

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[Rdkit-discuss] MMFF constraints question

[James Davidson]

Dear All (but mainly Paulo!),

I have really been appreciating the MMFF implementation in RDKit - particularly 
now with the ability to add position / distance / angle / torsional constraints!
I have a couple of naïve questions; and apologise in advance if I have missed 
answers to these in the documentation / method doc-strings...

1.  This is a simple one - but just to categorically confirm - 
ff.CalcEnergy() gives results in kcal/mol units, right?
2.  Now onto force constants...  I see from the unittest (aka documentation 
if you can't find anything else) 'testConstraints.py' that the value of 1.0e5 
is used in the tests.  1.0e5 what?  And should this be viewed as a strong, 
modest, or weak restraint?  Presuming this constant is somewhat like saying how 
springy a spring is(?), then what is a sensible value to give me a super-strong 
steel joist that would essentially resist everything (or is 1.0e5 it)?
3.  Final thing:  the problem with making something really good / useful is 
that people get used to it and then start wanting more!  How's the GBSA 
implicit solvation coming on?   : )

Kind regards

James


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Re: [Rdkit-discuss] MMFF constraints question

[James Davidson]

Hi Paolo,

First of all - please see this time my brain has engaged quicker than my 
English-biased touch-typing - and I have spelt your name correctly(!).
Thanks for the very clear explanation on force constants - this is really 
helpful!

And, regarding your new non-academic position vs continued 'forcefield tools' 
development in RDKit - I kind of suspected the answer before I asked!  Oh well, 
my non-academic position of course gives me access to commercial 
implementations of MMFF + implicit solvation...  It's just not nearly as fun!  
: (

Kind regards

James


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[Rdkit-discuss] Avalon test failing(?)

[James Davidson]

Hi Greg,

I wondered if you (or anyone else) have been seeing any issues with win64 build 
of the RDKit - with Avalon toolkit support - recently?
Yesterday I updated my local SVN copy of RDKit (to rev4274) and rebuilt.  
Everything seemed to go ok, but the testAvalonLib1 test is now failing (the 
pyAvalonTools test passes) - see below.
I can see that test1.cpp has changed recently, but my AvalonTools source 
hasn't...  Has a problem been introduced into the test?

Kind regards

James


C:\RDKit\build>ctest -R testAvalon -V
UpdateCTestConfiguration  from :C:/RDKit/build/DartConfiguration.tcl
UpdateCTestConfiguration  from :C:/RDKit/build/DartConfiguration.tcl
Test project C:/RDKit/build
Constructing a list of tests
Done constructing a list of tests
Checking test dependency graph...
Checking test dependency graph end
test 2
Start 2: testAvalonLib1

2: Test command: C:\RDKit\build\External\AvalonTools\Release\testAvalonLib1.exe
2: Test timeout computed to be: 9.99988e+006
2: [12:31:18] testing canonical smiles generation
2: [12:31:18] done
2: [12:31:18] testing coordinate generation
2: [12:31:18] done
2: [12:31:18] testing fingerprint generation
2: [12:31:18] c1n1 18
2:   returning
2: [12:31:18] c1n1 6
2: [12:31:18] c1nnccc1 28
2: [12:31:18] c1ncncc1 25
2: [12:31:18] c1cccnc1 18
2: [12:31:18] c1c1 6
2: [12:31:18] c1cccnc1 19
2: [12:31:18] c1cocc1 48
2: [12:31:18]
2:
2: 
2: Test Assert
2: Expression Failed:
2: Violation occurred on line 146 in file 
..\..\..\External\AvalonTools\test1.cpp
2: Failed Expression: bv.getNumOnBits()==53
2: 
2:
1/1 Test #2: testAvalonLib1 ...***Failed2.87 sec

0% tests passed, 1 tests failed out of 1

Total Test time (real) =   2.98 sec

The following tests FAILED:
  2 - testAvalonLib1 (Failed)
Errors while running CTest


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Re: [Rdkit-discuss] Avalon test failing(?)

[James Davidson]

Hi Greg,


> The new version of the test code is targeting the 1.2 avalon toolkit

> version.

> Here's the commit that did that.

> https://github.com/rdkit/rdkit/commit/42dab414ee6fbe5489078e5e52046608bbf785cb

>

> As an FYI, to make these tests pass on windows, you need to edit the code

> to fix a bug:

>

> you need to comment out line 1446 of reaccsio.c:

>//MyFree((char *)tempdir);

Following your advice, I downloaded the 1.2 source from Sourceforge 
(http://sourceforge.net/projects/avalontoolkit/files/AvalonToolkit_1.2/); 
commented-out the line in reaccsio.c; and then reconfigured in cmake and 
rebuilt in VS.  The tests pass now - thanks!

Kind regards

James

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Re: [Rdkit-discuss] Tests failing on Windows: more info

[James Davidson]

Hi Paolo, Greg, et al.

I have also been having some problems recently building (64-bit Windows) from 
recent github versions, but I don't know if this is related to what you see, 
Paolo...
My environment is Win 7 64-bit, CMake 3.0.0, boost_1_55_0-msvc-11.0-64, MS 
Visual Studio Express 2012.

I have done a bit of version rolling-back and forwards to see if I can pinpoint 
the last version that builds with no errors, and this is what I have found so 
far (sorted by revision, not by sequence of attempts!):

4577   - compiles fine, - passes all tests
4618   - as above
4649   - some errors during compile, -passes all tests except the molDraw2D 
bits (which are also involved in the errors)
4651   - as above
4743   - as above
4765   - as above
4780   - pyGraphMolWrap now fails test
4826   - this is where significant problems start (for me at least).  
pyGraphMolWrap still fails, but now with a segfault
4859   - same segfault as above.  Also pymolDraw2D test fails...


The errors I start to see for molDraw2D are this sort of thing (is this 
expected?):

Error  49   error C2668: 'boost::tuples::tie' : ambiguous call to 
overloaded function
C:\RDKit\Code\GraphMol\MolDraw2D\MolDraw2D.cpp   341 1  
MolDraw2D
Error  50   error C2668: 'boost::tuples::tie' : ambiguous call to 
overloaded function
C:\RDKit\Code\GraphMol\MolDraw2D\MolDraw2D.cpp   353 1  
MolDraw2D
Error  51   error C2668: 'boost::tuples::tie' : ambiguous call to 
overloaded function
C:\RDKit\Code\GraphMol\MolDraw2D\MolDraw2D.cpp   357 1  
MolDraw2D
Error  61   error C2668: 'boost::tuples::tie' : ambiguous call to 
overloaded function
C:\RDKit\Code\GraphMol\MolDraw2D\MolDraw2D.cpp   544 1  
MolDraw2D
Error  63   error C2668: 'boost::tuples::tie' : ambiguous call to 
overloaded function
C:\RDKit\Code\GraphMol\MolDraw2D\MolDraw2D.cpp   591 1  
MolDraw2D
Error  131 error LNK1181: cannot open input file 
'..\..\..\lib\Release\MolDraw2D.lib'
C:\RDKit\build\Code\GraphMol\MolDraw2D\LINK  moldraw2DTest1
Error  149 error LNK1181: cannot open input file 
'..\..\..\lib\Release\MolDraw2D.lib'
C:\RDKit\build\Code\GraphMol\Wrap\LINK   rdmolops


If I see the above errors when building 'ALL_BUILD', I also see the following 
error when building the 'INSTALL' section:

Error  41   error MSB3073: The command "setlocal
"C:\Program Files (x86)\CMake\bin\cmake.exe" -DBUILD_TYPE=Release -P 
cmake_install.cmake
if %errorlevel% neq 0 goto :cmEnd
:cmEnd
endlocal & call :cmErrorLevel %errorlevel% & goto :cmDone
:cmErrorLevel
exit /b %1
:cmDone
if %errorlevel% neq 0 goto :VCEnd
:VCEnd" exited with code 1.C:\Program Files 
(x86)\MSBuild\Microsoft.Cpp\v4.0\V110\Microsoft.CppCommon.targets   
 134 5  INSTALL



Anyway, 4618 is the latest revision that I have tested where I see no build 
errors, and 4765 is the latest revision I've found before I start to see 
pyGraphMolWrap tests failing (or segfaults).  For now, I have rolled-back my 
installation to 4618 (but would be very happy if anyone can figure-out what 
causes the problems with later revisions).

Kind regards

James

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Re: [Rdkit-discuss] Tests failing on Windows: more info

[James Davidson]

Hi Greg

Thanks for the fix – I can confirm that rev4861 builds and passes all the tests 
under my environment now.

Kind regards

James

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[Rdkit-discuss] Problem building recent revisions on Windows

[James Davidson]

Dear All,

I just tried building the latest RDKit build (rev. 5204) from the github 
repository, and hit a lot of link errors...  So (somewhat at random) I tried an 
older build (5042), and saw very similar things (errors for this attempt are 
below).
I am running on 64-bit Windows, and use cmake and Visual Studio 2012 - my build 
process hasn't changed since the last time I successfully built (rev. 4274 - 
and I can confirm that if I roll-back to this revision, the build is once again 
successful), so I wondered if anyone more skilled in the art than me could 
suggest what the problem might be from the errors below(?)


These are the errors when building the 'ALL_BUILD' project:

Error  2651   error LNK2005: "public: virtual __cdecl 
boost::detail::thread_data_base::~thread_data_base(void)" 
(??1thread_data_base@detail@boost@@UEAA@XZ) already defined in 
boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll)  
C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj)
   rdDistGeom
Error  2652   error LNK2005: "public: void __cdecl 
boost::thread::detach(void)" (?detach@thread@boost@@QEAAXXZ) already defined in 
boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll)
C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj)
rdDistGeom
Error  2653   error LNK2005: "class boost::thread::id __cdecl 
boost::this_thread::get_id(void)" 
(?get_id@this_thread@boost@@YA?AVid@thread@2@XZ) already defined in 
boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll)   
C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj)
   rdDistGeom
Error  2654   error LNK2005: "public: class boost::thread::id __cdecl 
boost::thread::get_id(void)const " (?get_id@thread@boost@@QEBA?AVid@12@XZ) 
already defined in 
boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll)   
C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj)
rdDistGeom
Error  2656   error LNK2005: "private: bool __cdecl 
boost::thread::join_noexcept(void)" (?join_noexcept@thread@boost@@AEAA_NXZ) 
already defined in 
boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll)   
C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj)
rdDistGeom
Error  2658   error LNK2005: "public: bool __cdecl 
boost::thread::joinable(void)const " (?joinable@thread@boost@@QEBA_NXZ) already 
defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll)   

C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj)
rdDistGeom
Error  2659   error LNK2005: "private: bool __cdecl 
boost::thread::start_thread_noexcept(void)" 
(?start_thread_noexcept@thread@boost@@AEAA_NXZ) already defined in 
boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll)   
C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj)
   rdDistGeom
Error  2660   error LNK1169: one or more multiply defined symbols found 
   C:\RDKit\build\rdkit\Chem\Release\rdDistGeom.pydrdDistGeom
Error  2675   error LNK2005: "public: virtual __cdecl 
boost::detail::thread_data_base::~thread_data_base(void)" 
(??1thread_data_base@detail@boost@@UEAA@XZ) already defined in 
boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll)  
C:\RDKit\build\Code\GraphMol\ForceFieldHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj)
   rdForceFieldHelpers
Error  2676   error LNK2005: "public: void __cdecl 
boost::thread::detach(void)" (?detach@thread@boost@@QEAAXXZ) already defined in 
boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll)
C:\RDKit\build\Code\GraphMol\ForceFieldHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj)
rdForceFieldHelpers
Error  2677   error LNK2005: "class boost::thread::id __cdecl 
boost::this_thread::get_id(void)" 
(?get_id@this_thread@boost@@YA?AVid@thread@2@XZ) already defined in 
boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll)   
C:\RDKit\build\Code\GraphMol\ForceFieldHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj)
   rdForceFieldHelpers
Error  2678   error LNK2005: "public: class boost::thread::id __cdecl 
boost::thread::get_id(void)const " (?get_id@thread@boost@@QEBA?AVid@12@XZ) 
already defined in 
boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll)   
C:\RDKit\build\Code\GraphMol\ForceFieldHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj)
rdForceFieldHelpers
Error  2679   error LNK2005: "private: bool __cdecl 
boost::thread::join_noexcept(void)" (?join_noexcept@thread@boost@@AEAA_NXZ) 
already defined in 

Re: [Rdkit-discuss] Problem building recent revisions on Windows

[James Davidson]

Hi Greg – thanks!
One extra piece:  as of a few minutes ago, I can confirm that revision 4947 
(last revision in Feb) builds, and passes all of the tests.

Kind regards

James

From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: 08 April 2015 15:14
To: James Davidson
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] Problem building recent revisions on Windows

I will fire up windows tomorrow morning and ensure that things can build. It's 
been a couple weeks since I last did that.

-greg


On Wed, Apr 8, 2015 at 3:43 PM, James Davidson 
mailto:j.david...@vernalis.com>> wrote:
Dear All,

I just tried building the latest RDKit build (rev. 5204) from the github 
repository, and hit a lot of link errors…  So (somewhat at random) I tried an 
older build (5042), and saw very similar things (errors for this attempt are 
below).
I am running on 64-bit Windows, and use cmake and Visual Studio 2012 – my build 
process hasn’t changed since the last time I successfully built (rev. 4274 – 
and I can confirm that if I roll-back to this revision, the build is once again 
successful), so I wondered if anyone more skilled in the art than me could 
suggest what the problem might be from the errors below(?)


These are the errors when building the ‘ALL_BUILD’ project:

Error  2651   error LNK2005: "public: virtual __cdecl 
boost::detail::thread_data_base::~thread_data_base(void)" 
(??1thread_data_base@detail@boost@@UEAA@XZ) already defined in 
boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll)  
C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj)
   rdDistGeom
Error  2652   error LNK2005: "public: void __cdecl 
boost::thread::detach(void)" (?detach@thread@boost@@QEAAXXZ) already defined in 
boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll)
C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj)
rdDistGeom
Error  2653   error LNK2005: "class boost::thread::id __cdecl 
boost::this_thread::get_id(void)" 
(?get_id@this_thread@boost@@YA?AVid@thread@2@XZ) already defined in 
boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll)   
C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj)
   rdDistGeom
Error  2654   error LNK2005: "public: class boost::thread::id __cdecl 
boost::thread::get_id(void)const " (?get_id@thread@boost@@QEBA?AVid@12@XZ) 
already defined in 
boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll)   
C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj)
rdDistGeom
Error  2656   error LNK2005: "private: bool __cdecl 
boost::thread::join_noexcept(void)" (?join_noexcept@thread@boost@@AEAA_NXZ) 
already defined in 
boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll)   
C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj)
rdDistGeom
Error  2658   error LNK2005: "public: bool __cdecl 
boost::thread::joinable(void)const " (?joinable@thread@boost@@QEBA_NXZ) already 
defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll)   

C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj)
rdDistGeom
Error  2659   error LNK2005: "private: bool __cdecl 
boost::thread::start_thread_noexcept(void)" 
(?start_thread_noexcept@thread@boost@@AEAA_NXZ) already defined in 
boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll)   
C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj)
   rdDistGeom
Error  2660   error LNK1169: one or more multiply defined symbols found 
   C:\RDKit\build\rdkit\Chem\Release\rdDistGeom.pydrdDistGeom
Error  2675   error LNK2005: "public: virtual __cdecl 
boost::detail::thread_data_base::~thread_data_base(void)" 
(??1thread_data_base@detail@boost@@UEAA@XZ) already defined in 
boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll)  
C:\RDKit\build\Code\GraphMol\ForceFieldHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj)
   rdForceFieldHelpers
Error  2676   error LNK2005: "public: void __cdecl 
boost::thread::detach(void)" (?detach@thread@boost@@QEAAXXZ) already defined in 
boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll)
C:\RDKit\build\Code\GraphMol\ForceFieldHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj)
rdForceFieldHelpers
Error  2677   error LNK2005: "class boost::thread::id __cdecl 
boost::this_thread::get_id(void)" 
(?get_id@this_thread@boost@@YA?AVid@thread@2@XZ) already defined in 
boost_thr

Re: [Rdkit-discuss] Problem building recent revisions on Windows

[James Davidson]

Hi Paolo,

> Unfortunately I have the impression that James' problem is related to
> neither of those. Might it be a boost/libboost naming issue?

Perhaps, but cmake seems happy (see below)...

> James, could it be that you have multiple version of boost on your Windows
> machine and CMake is not picking the correct one? You might try to explicitly
> define on the CMake command line both BOOST_ROOT and
> BOOST_LIBRARYDIR location as I do on my system:
> 
> "C:\Program Files (x86)\CMake\bin\cmake"
> -DBOOST_LIBRARYDIR=c:\32\boost_1_55_0_py34\lib32-msvc-12.0
> -DBOOST_ROOT=c:\32\boost_1_55_0_py34 ..

I do have multiple versions around, but I have the following set (from the 
cmake GUI):

BOOST_LIBRARYDIRC:/local/boost_1_55_0-msvc-11.0-64/lib64-msvc-11.0
BOOST_ROOT  C:/local/boost_1_55_0-msvc-11.0-64

and cmake reports that this version of boost is found:

Boost version: 1.55.0
Found the following Boost libraries:
  regex

So I am not sure what change is giving me the issue...  Let's wait and see what 
Greg finds as well(!)

Kind regards

James

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Re: [Rdkit-discuss] Problem building recent revisions on Windows

[James Davidson]

Hi Greg,

> James: one odd thing I notice about the error messages you posted is that 
> they are all referencing a boost library that seems to be present in your 
> build directory:
> 
> Error  2651   error LNK2005: "public: virtual __cdecl 
> boost::detail::thread_data_base::~thread_data_base(void)" 
> (??1thread_data_base@detail@boost@@UEAA
> @XZ) already defined in 
> boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll)  
> C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost
> _thread-vc110-mt-1_55.lib(thread.obj)   rdDistGeom
> 
> Is this just MSVC being odd about how it reports errors or is there really a 
> version of the boost threading library in your 
> build\Code\GraphMol\DistGeomHelpers\Wrap directory?

No boost threading library there...  And I clear-out the build folder between 
builds anyway.  So I guess it is a quirk of the reporting.
I will have another go at building the latest version and report back on 
success or otherwise(!)

Kind regards

James

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Re: [Rdkit-discuss] Problem building recent revisions on Windows

[James Davidson]

Here's an update:

Tried building rev5211, but saw similar linking errors (to do with Boost 
threading libraries).  The most recent build that I have successfully managed 
without the errors is rev5016.

It occurred to me that a couple of my cmake options relate to threading 
(RDK_BUILD_THREADSAFE=ON; RDK_TEST_MULTITHREADED=ON) - and perhaps other people 
(Greg, Paolo) with successful Windows builds had these set OFF (default)(?).  
Indeed, if I set both of these to OFF, I can successfully build rev5211, and 
all of the tests pass.
So this is good - but I still don't understand what has changed (in relation to 
Boost threading) that means that later versions don't build...

Threading aside, I was now feeling pretty confident that I would be ok to build 
the latest revision (rev5611).  Unfortunately this was not the case - I 
initially hit a problem with MolHash.cpp, which I thought was down to MSVC 
being stupid about snprintf() (line 265).  After a little stack-overflowing, I 
thought changing this to _snprintf() would solve the problem - which it appears 
to (at least MolHash.cpp now compiles), but then I get a couple of further 
errors down-stream (probably related to the change I made?):


Error  1  error LNK2019: unresolved external symbol "class 
std::basic_string,class std::allocator 
> __cdecl RDKit::Descriptors::calcMolFormula(class RDKit::ROMol const 
&,bool,bool)" 
(?calcMolFormula@Descriptors@RDKit@@YA?AV?$basic_string@DU?$char_traits@D@std@@V?$allocator@D@2@@std@@AEBVROMol@2@_N1@Z)
 referenced in function "void __cdecl 
RDKit::MolHash::generateMoleculeHashSet(class RDKit::ROMol const &,struct 
RDKit::MolHash::HashSet &,class std::vector > const *,class std::vector > const *)" 
(?generateMoleculeHashSet@MolHash@RDKit@@YAXAEBVROMol@2@AEAUHashSet@12@PEBV?$vector@IV?$allocator@I@std@@@std@@2@Z)
 C:\RDKit\build\Code\GraphMol\MolHash\Wrap\MolHash.lib(MolHash.obj) 
   rdMolHash

Error  2  error LNK1120: 1 unresolved externals   
C:\RDKit\build\rdkit\Chem\Release\rdMolHash.pyd  rdMolHash


So I guess it would still be good to understand the threading issue (or at 
least for someone else to be able to reproduce it); and perhaps the observed 
MolHash issue is an easier one to sort(?)

Kind regards

James

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Re: [Rdkit-discuss] Problem building recent revisions on Windows

[James Davidson]

Thanks Greg

I have now tried using boost 1.56 (the cmake configuration once BOOST_ROOT is 
set is a little different vs. 1.55…).  Either way I can’t seem to build with 
threadsafe/multithreaded support – but perhaps we should draw a line under it 
for now / follow-up ‘off-line’(?).

The good news is that (with the thread settings OFF) the changes you checked-in 
(rev5616) have indeed sorted the MolHash piece, and all tests pass – thanks!

Kind regards

James

From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: 14 April 2015 05:35
To: James Davidson
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] Problem building recent revisions on Windows

Hi James

Thanks for your patience here. I will invest the time in trying to get 
automated builds happening on this Windows side so that this stops happening.

I just pushed some changes that should clear up the MolHash-related build 
problems. I had forgotten that that bit of code still needed to be tested on 
Windows. I haven't tested building the cartridge on Windows (I'm not set up to 
do that), but the python wrappers definitely do build for me now with both 
RDK_BUILD_THREADSAFE_SSS and RDK_TEST_MULTITHREADED set to ON. I don't think it 
should make a difference, but just in case: I am doing this using boost 1.56.

Best,
-greg




On Mon, Apr 13, 2015 at 11:30 AM, James Davidson 
mailto:j.david...@vernalis.com>> wrote:
Here’s an update:

Tried building rev5211, but saw similar linking errors (to do with Boost 
threading libraries).  The most recent build that I have successfully managed 
without the errors is rev5016.

It occurred to me that a couple of my cmake options relate to threading 
(RDK_BUILD_THREADSAFE=ON; RDK_TEST_MULTITHREADED=ON) – and perhaps other people 
(Greg, Paolo) with successful Windows builds had these set OFF (default)(?).  
Indeed, if I set both of these to OFF, I can successfully build rev5211, and 
all of the tests pass.
So this is good – but I still don’t understand what has changed (in relation to 
Boost threading) that means that later versions don’t build…

Threading aside, I was now feeling pretty confident that I would be ok to build 
the latest revision (rev5611).  Unfortunately this was not the case – I 
initially hit a problem with MolHash.cpp, which I thought was down to MSVC 
being stupid about snprintf() (line 265).  After a little stack-overflowing, I 
thought changing this to _snprintf() would solve the problem – which it appears 
to (at least MolHash.cpp now compiles), but then I get a couple of further 
errors down-stream (probably related to the change I made?):


Error  1  error LNK2019: unresolved external symbol "class 
std::basic_string,class std::allocator 
> __cdecl RDKit::Descriptors::calcMolFormula(class RDKit::ROMol const 
&,bool,bool)" 
(?calcMolFormula@Descriptors@RDKit@@YA?AV?$basic_string@DU?$char_traits@D@std@@V?$allocator@D@2@@std@@AEBVROMol@2@_N1@Z)
 referenced in function "void __cdecl 
RDKit::MolHash::generateMoleculeHashSet(class RDKit::ROMol const &,struct 
RDKit::MolHash::HashSet &,class std::vector > const *,class std::vector > const *)" 
(?generateMoleculeHashSet@MolHash@RDKit@@YAXAEBVROMol@2@AEAUHashSet@12@PEBV?$vector@IV?$allocator@I@std@@@std@@2@Z)
 C:\RDKit\build\Code\GraphMol\MolHash\Wrap\MolHash.lib(MolHash.obj) 
   rdMolHash

Error  2  error LNK1120: 1 unresolved externals   
C:\RDKit\build\rdkit\Chem\Release\rdMolHash.pyd  rdMolHash


So I guess it would still be good to understand the threading issue (or at 
least for someone else to be able to reproduce it); and perhaps the observed 
MolHash issue is an easier one to sort(?)

Kind regards

James

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Vernal

[Rdkit-discuss] Python GetShortestPath()?

[James Davidson]

Dear All,

I might be having a 'moment' here, but for the life of me I can't seem to find 
the equivalent of RDKit::MolOps::getShortestPath exposed in python(?).
I want to pass in two atom ids, and get back a list of atom ids in the shortest 
path.  I could possibly try to roll my own by using GetDistanceMatrix() and 
GetAdjacencyMatrix(), but I think I may struggle(!).

So, any pointer to GetShortestPath() greatly appreciated!

Kind regards

James

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Re: [Rdkit-discuss] Python GetShortestPath()?

[James Davidson]

Hi Nick,

Well on the plus side I don't get a segfault(!)
On the minus side - unfortunately I think this approach only gives the length 
of the shortest path, rather than a list of the atom ids in the shortest path.

Kind regards

James

> -Original Message-
> From: Nicholas Firth [mailto:nicholas.fi...@icr.ac.uk]
> Sent: 21 April 2015 17:44
> To: James Davidson; rdkit-discuss@lists.sourceforge.net
> Subject: RE: Python GetShortestPath()?
> 
> Dear James,
> 
> I tried to be helpful and show you how I do it with GetAdjacencyMatrix,
> however I ran into my old friend the segmentation fault 11 as there is still
> some weird error with this function.
> 
> Here's what I have though, should work for you.
> 
> 
> >>> from rdkit import Chem
> >>> m =
> >>>
> Chem.MolFromSmiles('CC[C@H](CO)NC1=NC(=C2C(=N1)N(C=N2)C(C)C)NCC
> 3=CC=
> >>> CC=C3')
> >>> atomIdx1 = 0
> >>> atomIdx2 = 10
> >>> print(Chem.GetAdjacencyMatrix(m)[atomIdx1][atomIdx2])
> Segmentation fault: 11
> 
> 
> 
> Best,
> Nick
> 
> Nicholas C. Firth | PhD Student | Cancer Therapeutics The Institute of Cancer
> Research | 15 Cotswold Road | Belmont | Sutton | Surrey | SM2 5NG T 020
> 8722 4033 | E nicholas.fi...@icr.ac.uk | W www.icr.ac.uk | Twitter @ICRnews
> 
> 
> From: James Davidson [j.david...@vernalis.com]
> Sent: 21 April 2015 17:06
> To: rdkit-discuss@lists.sourceforge.net
> Subject: [Rdkit-discuss] Python GetShortestPath()?
> 
> Dear All,
> 
> I might be having a 'moment' here, but for the life of me I can't seem to find
> the equivalent of RDKit::MolOps::getShortestPath exposed in python(?).
> I want to pass in two atom ids, and get back a list of atom ids in the 
> shortest
> path.  I could possibly try to roll my own by using GetDistanceMatrix() and
> GetAdjacencyMatrix(), but I think I may struggle(!).
> 
> So, any pointer to GetShortestPath() greatly appreciated!
> 
> Kind regards
> 
> James
> 
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Re: [Rdkit-discuss] Python GetShortestPath()?

[James Davidson]

Hi Greg,

I just built the latest revision - and the functionality is exposed - thanks 
(and, of course, thanks Paolo!).

Kind regards

James

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[Rdkit-discuss] rev5771 and boost_chrono?

[James Davidson]

Dear All,

I recently rebuilt RDKit under 64bit Windows and things worked great for me.  
However, I found that when I shared the build with another user, things weren't 
so good -> "from rdkit.Chem import AllChem" gave a DLL error that pointed to 
rdForceFieldHelpers.pyd.

So I then ran Dependecy Walker and, as well as pointing at the usual boost 
libraries (python, system, thread), it also pointed at chrono.  This is the 
first time I had seen this.  Adding boost_chrono-vc110-mt-1_56.dll to the other 
user's rdkit/lib folder sorted the issue - which is great.

So this is a heads-up, in case it helps others; but also a question:  is there 
a good way to figure out all the boost dependencies ahead of deploying?

Kind regards

James

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