,
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On 12/06/2013 07:55 PM, Greg Landrum wrote:
Hi Dimitri,
The correct invocation is:
from rdkit import rdBase
print rdBase.rdkitVersion
D'oh. Should've thought of that. It was Friday, that's my excuse.
It works, thanks
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On 12/12/2013 9:50 PM, Greg Landrum wrote:
If the numbers are being used for the interpretation of mass spec
results, you almost certainly should be using exact masses, not the
average molecular weight:
In [9]: Descriptors.ExactMolWt(m)
Out[9]: 46.041864812
The ExactMolWt calculation uses
suppose I should've
looked there as well...
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Rapidly troubleshoot
is the only
layer that's required. Everything else is optional. Let's say you read
in InChI=1/C2H6O and print out InChI=1/C2H6O/c1-2-3.
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On 4/16/2014 1:55 AM, Greg Landrum wrote:
On Wed, Apr 16, 2014 at 8:16 AM, paul.czodrow...@merckgroup.com
mailto:paul.czodrow...@merckgroup.com wrote:
I have used this citation:
RDKit, Open-Source Cheminformatics. http://www.rdkit.org.
There has not (yet) been an RDKit paper
current
rpms)?
And the follow-up question: can I renumber them from 1? -- I've no
problem with 0-based indexing but my users for some reason do.
TIA
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will be heterogeneous). I am wondering if anyone knows where
my leak might be.
Nitpick: it's only a leak if the process never terminates, otherwise
it's deferred cleanup. ;)
My first question would be are the other processes actually doing anything?
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like what is supposed to happen. I think that
it should just add coords for the Hs that it adds.
Unless your backbone is laid out so there's room around it for all those
protons, expect the result to not look good.
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: N
O2 : N
N3 : N
C4 : S
C5 : N
C6 : N
-- with or without calling rdkit.Chem.FindMolChiralCenters( mol )
Is this what's supposed to happen?
TIA
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Description: application/vnd.kinar
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and I can do a
longer (but still brief) description.
No, what I need is to read the fine manual more carefully. Specifically,
the part where Chem.FindMolChiralCenters(m) returns a list instead of
modifying its argument in place.
Thanks and apologies for the noise
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, then you
can have a different definition of unique as an English word. In this
version of English, go buy a dictionary.
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On 2015-02-19 05:58, Greg Landrum wrote:
On Thu, Feb 19, 2015 at 10:11 AM, Markus Sitzmann
markus.sitzm...@gmail.com mailto:markus.sitzm...@gmail.com wrote:
Well, at least you said something important: conversion of InChI to
molecules is something that's not in general guaranteed to
' faces and other disciplines have nothing to do with it.
(Note, however, the face recognition people actually get simplistic
integer numbers so their unique keys tend to be based on well-defined
metrics and factor in isometries and other fun math stuff. Unlike IUPAC
and InChI.)
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On 2015-02-19 07:27, Markus Sitzmann wrote:
No, a chemical structure must calculate a unique InChI, but a InChI
might cover more then one chemical structure
Heh. I could swear last time I read the description it specifically
mentioned databases. In the database context 'unique' has a specific
of applications. It's your database.
What you can't do is redefine unique to mean two things at once: it's
not your discrete math. Sorry.
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rdkit.Chem.AllChem.UFFOptimizeMolecule( m )
ValueError: Bad Conformer Id
on the attached molecule. I wonder if it's triggering a bug in RDKit
somewhere. (I did try RemoveHs() instead of add, it made no difference.)
It's not a nice molecule...
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On 2015-03-13 01:25, Greg Landrum wrote:
Github does offer the option of setting up a wiki for a project, I
haven't done this for the RDKit since it doesn't seem that necessary
(and it seems that the information in wikis has a tendency to rot) but
if anyone has strong opinion otherwise, we
of the same software...
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lexer can't decide what's what.
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- if a record contains forbidden values, stop writing to the file,
with an error.
With the reader it looks like you can't help it if someone makes a value
like 55 or . With that caveat, you should be able to find tags
and read everything in between as a value.
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On 2015-04-29 23:08, Greg Landrum wrote:
Here are my thoughts on this:
The RDKit is usually strict while parsing molecules from SDF, SMILES, or
other formats.
My point was that given
'''
my_property2
1234
my_property3
'''
a lexer shouldn't have a problem recognizing the 2 tags. A
. Without a valid mol block you don't have a
molecule and you shouldn't be making one up. As in conservative in what
you produce.
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On 2015-05-03 15:06, Michael Reutlinger wrote:
Well... I think my proposal should enable us to put more strict, robust
QC in place, but I guess you are missing this point.
My definition of strict and robust is if the input is bad, what comes
out does is an out of band error signal. Such that
On 04/29/2015 05:32 PM, Andrew Dalke wrote:
On Apr 29, 2015, at 9:19 PM, Dimitri Maziuk wrote:
There is a difference between ACM members writing network protocols and
domain people writing junk.
I think that you are saying that the MDL connection table
file formats are junk. I do
in a
binary computer, you'll have to have 2 distinctly different canonical
benzenes. That's just how a binary computer works.
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RDKit does it
because Greg said so.
HTH
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and you only intend to run it a handful of times, N^2
is not worth worrying about. Otherwise try to split into smaller batches
that you can run in parallel on a cluster of computers.
FWIW
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e left trying to guess whether a given "CA" stands
for C-alpha or calcium.
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-
d busted PDB format gone, they
are not offering a usable alternative that I know of.
That's exactly what we've been doing at BMRB, too, and then complaining
about low rate of adoption of NMR-STAR by the NMR community.
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On 01/20/2016 04:57 PM, Peter S. Shenkin wrote:
> On Wed, Jan 20, 2016 at 5:33 PM, Dimitri Maziuk <dmaz...@bmrb.wisc.edu>
> wrote:
>> JSON encodes a single string. That is a problem for sending larger files
>> over the net, say, an NMR structure of a larger molecule with 1
?
TIA
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).GetSymbol() + str ((i+1))
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hat that layout might look better with all the Hs and
numbers added, than the one I get (the other 3 pictures).
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signature.
ike someone will
sit in front of Marvin and play with options until they get a perfect
picture for their paper.
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hat's what I expected and "removeHs = False" works, thanks. And I was
kidding about histidine of course.
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> and I'm sure he would appreciate the help.
GitHub does have a wiki. One has to become a "collaborator" to get edit
permissions, AFAIK it doesn't do fine-grained, but what it does should
be good enough.
The wiki is a git repo itself so it could be pulled and integrated into
relea
On 09/14/2016 02:23 PM, Dimitri Maziuk wrote:
> lbl=mol.GetAtomWithIdx(s[0]).GetSymbol() + str(s[0]+1)
> print label, ":", s[1]
^^^
Should be lbl
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Desc
;DL-Alanine" describing *either* D- or L-Alanine.
In this case "unspecified" is the correct value for chirality tag.
(And in the case of "2D" SDF it will be; unfortunately PubChem software
will generate a "3D" SDF for CID 602 and it will have a single
conformer: L-Alanine.
s in the source file. Which might matter in
the case of e.g. stereospecifically assigned methylene protons. (Or so
they tell me ;)
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Oops. AssignAtomChiralTagsFromStructure() does indeed work.
>> If your file has 3D coordinates, AssignAtomChrialTagsFromStructure
Good to see I'm not the only one with lysdexic fnigers. Apologies for
the noise:
;)
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do
have atom parity set even though there's no 3D coordinates. So I'll
probably go with your solution instead of TagsFromStructure b/c it'll
work for both 2D and 3D MOL files.
(elif p == 3 -> rdkit.Chem.rdchem.ChiralType.CHI_UNSPECIFIED, of course)
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ore, if the MOL file lacks the bond stereo information chirality
>> won't be set.
GetProp( "molParity" ) does work, thank you, but as I understand it's
based on atom ordering in the CTAB and not on CIP rules. So it's just as
good as OB's stereo "feature" for my purposes: e
On 09/10/2016 04:34 PM, David Cosgrove wrote:
...
> Also, the atoms in a molecule should have the property _CIPRank set, you
> might be able to do something with that.
Possibly, but since the non-typo'ed function seems to do the trick,
that's good enough for me.
Thanks
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a single conformer with ID 0, with the coordinates
from the file. `Conformer`s have a `Is3D` method, which *should* do what
you want.
It does. "There's conformer[0]" is the bit I was missing. It seems to be
there for 2D MOLs as well with Is3D() -> False.
Thank you.
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t's one or
the other?
TIA,
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_
s( 'C[C@@H](C(=O)O)N' )
instead, the output is
C2 : S
(this is L-ALA from the same PubChem record as the SDF).
So it looks like MOL reader ignores chirality, is that the case?
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D
On 2016-09-24 01:25, Greg Landrum wrote:
> https://medium.com/@greg.landrum_t5/the-rdkit-and-modern-c-48206b966218?source=linkShare-d698b3fa9f7-1474698147
>
> This is a big and important change and I'd love to hear whatever
> feedback members of the community may have. Please comment either on
On the plus side, when drawing PubChem CID 5057 from a 3D SDF before and
after our canonicalization, RDKit draws a mirror image, but otherwise
the same 2D structure. OB's "after" version is attached: enjoy the
7-bond carbon in the ring.
;)
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On 2016-09-29 00:57, Markus Sitzmann wrote:
> I get the feeling, RH/Centos 6 becomes the next XP kind of story - to
> many legacies that make the update impossible or very hard. Also docker,
> a great technology that could mitigate this problem, is very painful
> under RH/Centos 6.
systemd,
c++-14 code with
c++-03 compilers.
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should have.
For reference, CID260719.ob.svg is the other toolkit's rendering of the
same file with (atom indexes changed to green from OB's default red).
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alatis_output_Structure3D_CID_260719.sdf
Description
On 2016-09-26 18:19, Peter S. Shenkin wrote:
> 2D drawing code is tough. The 90/10 rule applies: the last 10% of
> I think for the present purposes what we need is something correct,
> robust and legible, and of course the example shown does not exhibit
> that. (But I don't know what the starting
one(s) with least clashes/overlaps.
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it either way,
unfortunately my target viewer is firefox (it's a web application and
the user's default browser is firefox) and firefox isn't one of them.
Without svg:'s it'll show the file as xml text instead of the image.
HTH
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On 2016-10-24 19:04, Peter S. Shenkin wrote:
> My second conclusion (based on the .svg-file experiments) is that it's
> not an iPython problem and, since you see the same thing on Firefox,
> it's unlikely to be a Chrome problem.
Well, what I got it from (Greg's I think) tutorial that if you
On 10/25/2016 11:21 AM, Peter S. Shenkin wrote:
> Hi, Hongbin,
>
> Thanks. Indeed. svg2.svg, when renamed to svg2.html, shows the correct
> image in Chrome. svg.html shows garbage.
>
> Still, it would be good to be able to create a real .svg file from RDKit.
OK, you made me look and I learned
=rdkit.Chem.Draw.rdMolDraw2D.MolDraw2DSVG(800,800)
dr.SetFontSize(0.3)
op = dr.drawOptions()
for i in range(mol.GetNumAtoms()) :
op.atomLabels[i]=mol.GetAtomWithIdx(i).GetSymbol() + str((i+1))
rdkit.Chem.AllChem.Compute2DCoords(mol)
dr.DrawMolecule(mol)
dr.FinishDrawing()
svg=dr.GetDrawingText()
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We have no proof
that it's 100% correct, but all duplicates it found in the PDB ligand
expo at the time were genuine.
Enjoy,
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537 comes close.
Marvin doesn't do much better on this one even if you don't turn on all
the labels.
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On 2016-10-26 23:39, Peter S. Shenkin wrote:
> Hey, by the way, my agenda is trying to understand all this.
(Using python syntax instead of ML)
Recommended by TFM:
from "http://www.w3.org/2000/svg; import *
All svg names should work with or without package qualifier: point(),
line(), etc., as
ere all hydrogens are explicitly present and indexed. I
wonder if they stay that way throughout the steps leading to (and past)
the smarts match.
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y, waiting 5 sec for a page refresh wouldn't be great.
Maybe not, but depending how the browser lays out the grid, it may take
5 seconds anyway.
My recommendation for that use case would be to pre-generate the images
and store the URLs in that database. Which is what we do here.
;)
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On 12/15/2016 02:53 PM, Peter S. Shenkin wrote:
> Looks good, but maybe too slow for production use... (?)
I wonder what kind of production use would require sub-second wall clock
time for this.
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rdized representation of all the
properties you consider relevant and produce a unique hash of that.
Doesn't matter if it's a SHA-1 string or some graph-based magic or a
matrix voodoo. (String comparison is of course easier.)
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On 12/02/2016 03:12 PM, George Papadatos wrote:
> Here's a pragmatic idea:
... would it not be safe to
> assume that *any *word containing more than 4 'C' or 'c' characters would
> only be a SMILES string?
pneumonoultramicroscopicsilicovolcanoconiosis
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can guarantee you that a)
it's much more than $20, and b) hiring a competent programmer will cost
you more than buying a "better computer" and is not guaranteed to result
in any appreciable speed-up.
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we need a billion depictions all at once" implies that
you have a billion users looking at them all at once. If you don't, then
rapid response is a very interesting academic exercise but its practical
usefulness might be somewhat questionable.
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On 2016-12-29 07:19, John M wrote:
> For why you need sub-second depiction consider these times for 92877507
> structures (current size PubChem Compound):
>
> 1s per structure = 1074 days (~3 years)
> 100 ms per structure = 107 days
> 1ms per structure = 25 hours
The Dilbert answer is buy a
n a regular basis
is a realistic use case, either.
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Check out the vibrant te
;, "on" )
cmd.png( outfile, width = 800, dpi = 300, ray = 1 )
while threading.active_count() > 2 :
time.sleep( 2 )
cmd.quit()
HTH,
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On 2017-03-02 04:37, Guillaume GODIN wrote:
> Based on the precision of the coordinates (in rdkit sdf files it's 4
> digits) can we infer the precision on the PBF value based on that ?
Only if you *know* the values are actually accurate to 4 digits and not
e.g. were printed as "%.4f" just
On 2017-06-22 01:36, Francois BERENGER wrote:
make deb # in rdkit source tree
Some people might ask for a make rpm target also.
You'd have to track any changes that redhat, canonical, suse, and
whoever else's out there might make to e.g. filesystem layout, linked
libraries, python and so
On 2017-06-09 08:12, Alexis Parenty wrote:
Dear Greg and Brian,
Many thanks for your response. I was also thinking of your streaming
approach! I think the RAM of most machine would deal with lists of 100K
mol so we could put the threshold higher than 1000. Actually, I was
thinking to monitor
t back up today, will output a MOL file with atoms
ordered as per the article.
The downside is it only works on 3D MOLs.
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vers doing
the crunching are currently down.
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Check out the vibra
On 2017-06-10 07:42, Chris Swain wrote:
This sounds like the situation where a database might be a better
option, tuned to store fingerprints in RAM?
The issue is how much programming time it will take, how much that time
is worth, and how many times the solution will be reused. A clever
On 2017-09-13 09:56, TJ O'Donnell wrote:
Let the database do the work for you. Create a canonical SMILES column
and/or InChI column and declare them to be unique. As you insert new
rows, postgres will let you know if there is already a row with the same
SMILES or InChI.
Here's some help on
eas you
want it represented as one.
Last I looked PDB Ligand Expo had two different benzenes. Their software
doesn't (didn't?) do the circle version so they don't have the third one.
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Descript
On 2017-09-13 10:17, Markus Sitzmann wrote:
Canonical SMILES are only a very rough approximation for "unique
molecule" as they usually don't work well for tautomeric forms of compound.
InChI or Standard InChI is much better although also not perfect.
ALATIS I linked to above does impose a
On 09/14/2017 03:04 PM, Markus Sitzmann wrote:
> Not on Centos 6 - Docker requires Centos 7 for the host system.
You can't win... :(
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idea to update.
Just FYI: python 2.6 is the system python on (at least) RHEL-6 family of
linux distros that will be officially with us until June 30, 2024.
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centos-sclo-rh
> python27-python-pip.noarch 8.1.2-1.el6
> centos-sclo-rh
...
Any guesses as to how many things will break in my infrastructure
manglement setup (saltstack) if I enable Software Collections and some
On 09/14/2017 02:58 PM, Andrew Dalke wrote:
> If only Greg got as much money for long term RDKit support as Red Hat
> gets for long term RHEL support. :)
Yep. But an rdkit docker container might be feasible.
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On 2017-09-13 05:13, Wandré wrote:
Compare if the SMILES as already inserted is easy (text compare), but,
compare fingerprint of molecule...
Here's one option: http://alatis.nmrfam.wisc.edu/ -- you can use string
comparison on the resulting inchi string.
Dima
es, except where it doesn't.
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On 11/20/2017 04:45 PM, Markus Metz wrote:
> opts.clearBackground=False
>
> or
>
> opts.setBackgroundColour((1,1,0))
>
> are not working for me.
What's your output format?
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the exact same
ligand*.
(It's the *substructure* bit that I'm not entirely sure about.)
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PS the real question is why you're trying to run psql built with a newer
toolset when there's 2 perfectly good ones available: one from the
distro vendor and one from postgres repos.
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5
/usr/lib64/libpanel.so.5.9
/usr/lib64/libpanelw.so.5
/usr/lib64/libpanelw.so.5.9
/usr/lib64/libtic.so.5
/usr/lib64/libtic.so.5.9
/usr/lib64/libtinfo.so.5
/usr/lib64/libtinfo.so.5.9
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Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
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Desc
On 2018-01-16 22:46, Greg Landrum wrote:
It might be worth thinking about adding an option to the aromaticity
perception code to maintain the original bond types and just set the
"isAromatic" flag on the bonds.
This is how it's modeled in mmCIF chem. comp. It may or may not come
from
On 2018-01-17 10:25, Jason Biggs wrote:
For the case in question, I find that if I read in a mol file containing
2D coordinates, and I skip the sanitization step altogether, then the 3D
embedding algorithms fail.
Well, yes, as I mentioned in the other thread: the only way you can get
it to
n that I don't know if there's
anything that works on not proteins, or can predict disordered regions
well etc.
If anyone's counting votes, pretty 2D depictions get mine.
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Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
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On 5/23/2018 10:23 AM, Chenyang Shi wrote:
A separate
question is that is the converted molecular structure from SMILES the
same as that taken from a crystal structure?
Provided there's no undefined/different stereochemistry on SMILES side,
no quirks with added protons, and so on and so
On 6/13/2018 10:06 AM, Greg Landrum wrote:
Note that my answer assumes that there is a reason that you don't have
X11 installed on your linux box. If that's not the case, you should be
able to fix things "more easily" by installing X
Quite frankly, this is rapidly becoming unusable as a
er
container, but compiling it on my desktop is simply not worth my time.
(And our compute nodes are the same or older as my desktop, so if it
doesn't work on my box, we can't deploy it anywhere.)
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Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
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nows they're doing and watches
the whole ting very carefully.
No, it's not your problem, you're doing the best you can, and thank you
for that. But the end result is that ready-made builds are getting
increasingly too bloated to be of use, and custom builds are too
"non-trivial" to attemp
Also, it seems that SDMolSupplier.next() does not work anymore?
if sys.version_info[0] == 2 : next()
elif sys.version_info[0] == 3 : __next()__
else : raise Exception( "Go! is looking better every day" )
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Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.
rdkit container instead. I strongly recommend doing
that, or finding a singularity version of the same.
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Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
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__
On 10/24/2018 12:10 PM, Dimitri Maziuk via Rdkit-discuss wrote:
> Yes. I once spent a couple of hours trying and ended up installing docer
docker
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Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
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