is impossible to
Either way, it makes it rather hard to trust their derivations generally -
especially as there appear to be other errors (e.g. the denominator in eq.
16 should be the square root of the given sum of squares, according to
Dr Chris Earnshaw
f a planar molecule like benzene
>>> should be zero. The eigenvalues of the inertia matrix for benzene, however,
>>> are definitely not zero (and not close enough that it's likely to be
>>> round-off error).
>>> It would be very nice if you could run the three files I
y but it does appear
> to match the moe PMI's.
> On Tue, Jan 17, 2017 at 4:55 AM, Chris Earnshaw <cgearns...@gmail.com>
>> The new version looks good to me as far as I can test it. PMI and NPR are
>> still fine, the radius of gyration is right (fo
On 16 January 2017 at 09:30, Greg Landrum <greg.land...@gmail.com> wrote:
> On Mon, Jan 16, 2017 at 10:22 AM, Chris Earnshaw <ch...@cge-compchem.co.uk
> > wrote:
>> Either way, it makes it rather hard to trust their derivations ge
e to look into this this weekend and I've found
> a bug and something I don't understand. Hopefully the community can help
> out here.
> On Sun, Jan 8, 2017 at 11:17 AM, Chris Earnshaw <cgearns...@gmail.com>
>> 4) The big one! The returned results look very odd. They app
gt;> W.r.t. efficiency: you do need to call the functions individually, but
>> the expensive calculation of the moments will only be done once, so it
>> doesn't end up doing repeated work.
>> And, finally, on the values themselves: I will have to take a look at
A while ago I had a project which needed PMI descriptors (specifically NPR1
and NPR2) which were not available in the main branch of RDKit at the time.
At the time I used the fork by 'hahnda6' which provided the
calcPMIDescriptors() function, and this worked well. Now that PMI
tidied it up (having just looked at it to get the
> link above, I see there's a typo on the first sentence, for example!) and
> sent in an interim Pull Request as for people starting out it might already
> be of value.
> On Sun, 8 Jan 2017 at 10:19, Chris E
any more information from me.
On 8 Jan 2017 18:17, "Brian Kelley" <fustiga...@gmail.com> wrote:
I think the relevant issue is that if you are using an existing build, we
don't yet have the capability for you to know what was built and what was
not. I.e. You need
I'm by no means an expert in RDKit with Python, but until someone else
comes along, here are a few thoughts.
Your reaction SMARTS specifically defines aromatic carbons joined by single
bonds which won't match an incoming benzene ring, and it's a bit redundant
to specify that aromatic
Very strange behaviour. I don't see anything wrong with your SQL syntax.
I've tried equivalent searches in my 2.6M compound database and they give
the expected results. I used iodine rather than gold, for which there are
19504 structures. Adding the qualifying SQL clauses singly and in
) as required, but if you have a specific need
for the 'single SMARTS' approach that's not much use. Sorry not to be more
On 19 September 2017 at 16:50, James T. Metz <jamestm...@aol.com> wrote:
> Thank you for your interesting
Open Babel will convert a wide range of structure formats and can produce
at least a couple of different flavours of Z-matrix, including MOPAC and
Gaussian. I'm not aware of any way to get a Z-matrix directly from RDKit
(but would be happy to find out I'm wrong).
Will the recursive SMARTS [$(C-C),$(N-N)] not do the job?
I'd parse this in English as 'an atom which is EITHER an aliphatic carbon
singly bonded to an aliphatic carbon OR an aliphatic nitrogen singly bonded
to an aliphatic nitrogen'.
On 19 September 2017 at 15:01
Be aware that there is a problem with one of the azide groups in
CHEMBL592333 - in SMILES it's '-N=[NH+]-[NH-]' rather than '-N=[N+]=[N-].
This doesn't render the structure chemically invalid but it's probably
What's the provenance of your SD file? It isn't the same as as a fresh
On 9 October 2017 at 15:57, Chris Murphy <chris.mur...@schrodinger.com> wrote:
> I am using rdChemReactions to perform substructure transformations as
> defined by configurable reaction smarts. When I cre
> From: Chris Earnshaw <cgearns...@gmail.com>
> Sent: Thursday, October 5, 2017 12:04:02 AM
> To: Bennion, Brian; RDKit Discuss (email@example.com)
> Subject: Re: [Rdkit-discuss] nitrogen valence issues
> Be aware t
The problem is due to RDkit perceiving the embedded pyranone in
CHEMBL1999443 as an aromatic system, which is probably correct. However, in
the structure of aspirin the carboxyl carbon and singly bonded oxygen are
non-aromatic, so if you just use the SMILES of aspirin as a query it won't
It amounts to the same thing - either do all tests on one atom, or one test
on all atoms.
The syntax is shorter for the latter if you can use the vector bindings but
may not be otherwise, especially if multiple exclusions are needed.
On 24 Sep 2017 16:54, "
atoms have been matched - for example, do you want to match quinoline
because it contains a benzene ring, or exclude it because it contains
a pyridine? If the former you'll have to check that the atoms matched
by your two patterns are different.
Hope this helps!
On 24 September 2017
-ring aromatic pattern a:1:a:a:a:a:a:1,
with recursive SMARTS applied to the first atom to ensure that this
can't match any of the 6 ring atoms in your undesired system.
On 24 September 2017 at 05:04, James T. Metz via Rdkit-discuss
are only a dozen problem cases out of 1.5 million compounds, I
> just removed them from my main file and downloaded the mol files from
> chembl and double check the structures.
> -Original Message-
> From: Chris Earnshaw [mailto:c
Note that this way of doing things disables all "unreasonable" valence
> On Tue, Nov 21, 2017 at 10:12 AM, Chris Earnshaw <cgearns...@gmail.com>
>> Sometime between 2014 and now there appears to
checks on dative bond forms which
presumably now get converted)
- graphmolMolOpsTest (builds perchlorates etc. and expects the result to be
in dative bond form)
- pythonTestDirChem (not sure what's wrong with this one - I can't find
what it does!)
Apologies for the length of all this...
h those, but it would be worth
> incorporating them into any solution / test set?
> On Thu, Nov 23, 2017 at 5:27 PM, Chris Earnshaw <cgearns...@gmail.com>
>> Following a recent brief discussion about hypervalent halogen salt
> On Tue, Nov 21, 2017 at 8:22 AM, Chris Earnshaw <cgearns...@gmail.com>
>> The entries for P and As in RDKit's atomic_data.cpp are -
>> 15 P 0.750.892.0830.974 5 31
>> 30.97376163 3
values > 1, so by default it's not possible to construct e.g.
> chlorates, or bromates, and no perhalates are allowed.
> Chris Earnshaw
> On 20 November 2017 at 23:03, Yoolhee Kim <yoolh...@andrew.cmu.edu> wrote:
>> I'm trying to get
one you report
> chlorate [O-][Cl2+]([O+])[O-]
> perchlorate [O-][Cl3+]([O-])([O+])[O-]
> it looks wrong to me as there is an overall formal charge of +1. All O's
> should bear a -1 charge.
> On 11/21/17 09:12, Chris Earnsh
this to happen!
Does anyone know a way to restore the old behaviour for chlorites,
bromates, periodates etc.?
Check out the vibrant tech community on one of the world's most
engaging tech sites
Trouble is, you're mixing chemical operations and lexical ones. It
might be handy if this 'just worked' but in practice it's not going to
produce valid SMILES without more work.
I've written code in the past to do this kind of thing for virtual
library building, using dummy atoms to mark link
change the behaviour - or get RDKit
to issue a warning that the SMILES isn't 'strict' in these cases.
I think the safest approach is to stick to SMILES which are unequivocally
valid, unless RDKit is going to create its own definition of SMILES...
On 9 November 2017 at 07
I don't think there's a way to do this using RDKit itself, but it appears
to be straightforward using Python with numpy and networkx, e.g.
import numpy as np
import networkx as nx
a = np.matrix([[0, 1, 0, 0, 0],[1, 0, 1, 1, 0],[0, 1, 0, 0, 0],[0, 1, 0, 0,
1],[0, 0, 0, 1, 0]])
Your code doesn't change the charges because the reaction SMARTS doesn't
tell it to. If you say -
rxn_smarts = ['[N+:1]=[*:2]-[O-:3]>>[N+0:1]-[*:2]=[O+0:3]']
- the charges in the product are explicitly defined and you should get the
result you expect.
On 25 January
The minuses are right. These are the single bonds between the individual
aromatic rings and this representation is strictly correct. The OpenBabel
representation doesn't mark these bonds as explicitly single and, as
they're between two aromatic atoms, the bond type could be inferred to be
I would say that the behaviour of RDKit with your MOL2 file is right.
SMILES notation doesn't have a way to represent the delocalised form of a
carboxylate anion, so the O=C[O-] form is the correct SMILES for this
structure. RDKit does a good job in recognising that it's the anion based
You're doing something similar to the problem Paolo addressed.
requires a mol object as the first parameter, but you are passing it an
integer cid value, not a molecule. Your code
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