Re: [Rdkit-discuss] PMI API

2017-01-16 Thread Chris Earnshaw
is impossible to say. 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 their reference). Best regards, Chris Dr Chris Earnshaw

Re: [Rdkit-discuss] PMI API

2017-01-16 Thread 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

Re: [Rdkit-discuss] PMI API

2017-01-17 Thread Chris Earnshaw
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> > wrote: > >> 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

Re: [Rdkit-discuss] PMI API

2017-01-17 Thread Chris Earnshaw
confusion. Chris 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

Re: [Rdkit-discuss] PMI API

2017-01-15 Thread Chris Earnshaw
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> > wrote: > >> 4) The big one! The returned results look very odd. They app

Re: [Rdkit-discuss] PMI API

2017-01-13 Thread Chris Earnshaw
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 >>

[Rdkit-discuss] PMI API

2017-01-08 Thread Chris Earnshaw
Hi 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 descriptors are

Re: [Rdkit-discuss] PMI API

2017-01-08 Thread Chris Earnshaw
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. > > Cheers, > Dave > > On Sun, 8 Jan 2017 at 10:19, Chris E

Re: [Rdkit-discuss] PMI API

2017-01-08 Thread Chris Earnshaw
any more information from me. Chris Earnshaw 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

Re: [Rdkit-discuss] mass replacement of External R-groups with many substituents

2017-03-16 Thread Chris Earnshaw
Hi Brian 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

Re: [Rdkit-discuss] SMARTS substructure queries with SQL conjunctions

2017-03-21 Thread Chris Earnshaw
Hi Akos 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

Re: [Rdkit-discuss] single SMARTS for two patterns with Boolean OR

2017-09-19 Thread Chris Earnshaw
) as required, but if you have a specific need for the 'single SMARTS' approach that's not much use. Sorry not to be more helpful... Chris Earnshaw On 19 September 2017 at 16:50, James T. Metz <jamestm...@aol.com> wrote: > Chris, > > Thank you for your interesting

Re: [Rdkit-discuss] Returning Z-matrix coordinates for a molecule in rdkit?

2017-09-19 Thread Chris Earnshaw
Hi 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). Regards, Chris Earnshaw

Re: [Rdkit-discuss] single SMARTS for two patterns with Boolean OR

2017-09-19 Thread Chris Earnshaw
Hi 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'. Regards, Chris Earnshaw On 19 September 2017 at 15:01

Re: [Rdkit-discuss] nitrogen valence issues

2017-10-05 Thread Chris Earnshaw
Hi 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 wrong. What's the provenance of your SD file? It isn't the same as as a fresh

Re: [Rdkit-discuss] Reaction changing bonds but not charges

2017-10-09 Thread Chris Earnshaw
- [#8-:2]-[#7+:1]=[O:3]>>[O+0:2]=[N+0:1]=[O:3] Chris Earnshaw On 9 October 2017 at 15:57, Chris Murphy <chris.mur...@schrodinger.com> wrote: > Hi, > > I am using rdChemReactions to perform substructure transformations as > defined by configurable reaction smarts. When I cre

Re: [Rdkit-discuss] nitrogen valence issues

2017-10-05 Thread Chris Earnshaw
____ > From: Chris Earnshaw <cgearns...@gmail.com> > Sent: Thursday, October 5, 2017 12:04:02 AM > To: Bennion, Brian; RDKit Discuss (rdkit-discuss@lists.sourceforge.net) > Subject: Re: [Rdkit-discuss] nitrogen valence issues > > Hi > > Be aware t

Re: [Rdkit-discuss] HasSubstructMatch doesn't work as expected

2017-09-13 Thread Chris Earnshaw
Hi 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 match

Re: [Rdkit-discuss] need SMARTS query with a specific exclusion

2017-09-24 Thread Chris Earnshaw
Hi 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. Regards, Chris Earnshaw On 24 Sep 2017 16:54, "

Re: [Rdkit-discuss] need SMARTS query with a specific exclusion

2017-09-24 Thread Chris Earnshaw
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! Chris Earnshaw On 24 September 2017

Re: [Rdkit-discuss] need SMARTS query with a specific exclusion

2017-09-24 Thread Chris Earnshaw
-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. Regards, Chris Earnshaw On 24 September 2017 at 05:04, James T. Metz via Rdkit-discuss <rdkit-discuss@lists.sourceforge.net>

Re: [Rdkit-discuss] nitrogen valence issues

2017-10-07 Thread Chris Earnshaw
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. > > Bran > > -Original Message- > From: Chris Earnshaw [mailto:c

Re: [Rdkit-discuss] Hypervalent halogen structures - chlorate etc.

2017-11-22 Thread Chris Earnshaw
Note that this way of doing things disables all "unreasonable" valence > checking. > > -greg > > > On Tue, Nov 21, 2017 at 10:12 AM, Chris Earnshaw <cgearns...@gmail.com> > wrote: >> >> Hi >> >> Sometime between 2014 and now there appears to

[Rdkit-discuss] Hypervalent 2nd row element (and higher) representation / sanitization

2017-11-23 Thread Chris Earnshaw
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... Chris

Re: [Rdkit-discuss] Hypervalent 2nd row element (and higher) representation / sanitization

2017-11-23 Thread Chris Earnshaw
h those, but it would be worth > incorporating them into any solution / test set? > > Yours, > > Steve > > On Thu, Nov 23, 2017 at 5:27 PM, Chris Earnshaw <cgearns...@gmail.com> > wrote: > >> Following a recent brief discussion about hypervalent halogen salt >>

Re: [Rdkit-discuss] Having trouble getting RDKIT to recognize LiAsF6

2017-11-25 Thread Chris Earnshaw
e Kim > > On Tue, Nov 21, 2017 at 8:22 AM, Chris Earnshaw <cgearns...@gmail.com> > wrote: > >> Hi >> >> 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

Re: [Rdkit-discuss] Having trouble getting RDKIT to recognize LiAsF6

2017-11-21 Thread Chris Earnshaw
values > 1, so by default it's not possible to construct e.g. > chlorates, or bromates, and no perhalates are allowed. > > Regards, > Chris Earnshaw > > On 20 November 2017 at 23:03, Yoolhee Kim <yoolh...@andrew.cmu.edu> wrote: >> Hello, >> >> I'm trying to get

Re: [Rdkit-discuss] Hypervalent halogen structures - chlorate etc.

2017-11-21 Thread Chris Earnshaw
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. > > Cheers, > p. > > > > On 11/21/17 09:12, Chris Earnsh

[Rdkit-discuss] Hypervalent halogen structures - chlorate etc.

2017-11-21 Thread Chris Earnshaw
this to happen! Does anyone know a way to restore the old behaviour for chlorites, bromates, periodates etc.? Best regards, Chris Earnshaw -- Check out the vibrant tech community on one of the world's most engaging tech sites

Re: [Rdkit-discuss] RDKit appears to be parsing SMILES stereochemistry differently

2017-11-09 Thread Chris Earnshaw
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

Re: [Rdkit-discuss] RDKit appears to be parsing SMILES stereochemistry differently

2017-11-08 Thread Chris Earnshaw
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... Best regards, Chris Earnshaw On 9 November 2017 at 07

Re: [Rdkit-discuss] edge matrix

2018-01-17 Thread Chris Earnshaw
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]]) b =

Re: [Rdkit-discuss] changing atomic charges with ReactionFromSmarts

2018-01-25 Thread Chris Earnshaw
Hi Jan 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. Best regards, Chris On 25 January

Re: [Rdkit-discuss] remove salts + neutralize

2018-03-14 Thread Chris Earnshaw
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

Re: [Rdkit-discuss] MolFromMol2Block changes carboxylic group representation

2018-03-28 Thread Chris Earnshaw
Hi Maria 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

Re: [Rdkit-discuss] generate conformes with a restrained core

2018-03-24 Thread Chris Earnshaw
Hi Felipe You're doing something similar to the problem Paolo addressed. ConstrainedEmbed (see http://www.rdkit.org/Python_Docs/rdkit.Chem.AllChem-module.html#ConstrainedEmbed) requires a mol object as the first parameter, but you are passing it an integer cid value, not a molecule. Your code