luster and/or are willing to pay for
spinning up a bunch of VMs on amazon etc. Otherwise the best you can
hope for is to run maybe two per CPU core.
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iles haven't been processed by
them, all bets are off.
And so on
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On 12/16/2019 10:07 AM, Illimar Hugo Rekand wrote:
Would it be viable to create a function where you could create a mol object
from specific lines within a pdb-file?
PDB file is simple text. There's any number of utilities to extract the
lines you want, incl. a plain text editor, why spend
On 10/5/2019 10:34 AM, Maciek Wójcikowski wrote:
Paolo and Chris,
There actually is Rdkit function to do this very task: SplitMolByPDBChainId
Why, though? -- It's a punch-card format with chain id in specific
column, you just read the lines and sort them into buckets on line[X].
Unless you
s with labels, I am
painfully aware of how crowded the image becomes. Perhaps some day I'll
manage to persuade my spectroscopist to use a 3D image instead -- her
argument is that having to move the mouse to the other screen to rotate
that thing all the time is too distracting.)
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PS I played with it a bit: the least ugly version is if you
MMFF94-optimize it after rdkit.Chem.rdCoordGen.AddCoords()
It's still far from perfect.
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algorithms.
Here's out latest one for example. The thing about this one is, the
molecule itself is not that bad, it not clear why the picture isn't any
better.
Enjoy. (Try it in OB if you think RDKit's pix is bad. ;)
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ut you're right: getting that to work in an
interactive display in a notebook would be a hassle.
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On 8/7/2019 7:20 PM, Wout Bittremieux wrote:
...
Unfortunately the quality of the molecule drawing is rather poor (see
attachment; nonsensical spectrum and molecule). This seems to be true
for non-SVG drawing in general, and unfortunately it's not really
possible to combine SVG output with
IA :
REMARK 210
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE :
"""
(the last one is the one I mentioned earlier)
You would typically have "lowest energy" as selection criteria and "best
reperesentative" is the minimized average of those submit
multiple conformers in one file, there is at
least one in PDB.
(It's been a while since I did this so I don't remember the remark
number, nor the multi-conormer entry id off the top of my head.)
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ific
version of another package that depends on... turtles all the way down.
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ide of
the try/catch block and ignore ones not followed by the warning message.
(And run with #!/usr/bin/python -u and/or flush sys.stdout/stderr on
every iteration for good measure.)
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ame 3D structure with the same atom
labels on round-trip, *as long as you don't removeH/addH/recalculate
conformers etc.*
(At least on all molecules they tried and I think that includes the
entire PubChem.)
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gh any cheminformatics program,
there's 50% chance you'll get a different molecule out.
That's how chemistry works when it meets compsci.
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les/sdata201773
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- boost -
swig - python is not something I'd want to ever become familiar with...
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On 11/02/2018 12:19 AM, Greg Landrum wrote:
> On Fri, Nov 2, 2018 at 12:32 AM Dimitri Maziuk via Rdkit-discuss <
> rdkit-discuss@lists.sourceforge.net> wrote:
>
>> Does anyone know where TH does
>>
>>
>>
>> come from? --
>
>
> assuming y
s draws atom labels:
op = dr.drawOptions()
for i in range( self._mol.GetNumAtoms() ) :
op.atomLabels[i] = self._mol.GetAtomWithIdx( i ).GetSymbol() +
str( (i + 1) )
HTH,
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not cp1252.
Any ideas?
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,
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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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rdkit container instead. I strongly recommend doing
that, or finding a singularity version of the same.
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__
"same
molecule" for your purposes, then it doesn't matter.
If it does mater, then alatis (the link I sent earlier) is the best
option that I know of.
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tion?
https://www.nature.com/articles/sdata201773
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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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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
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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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
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
the exact same
ligand*.
(It's the *substructure* bit that I'm not entirely sure about.)
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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
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
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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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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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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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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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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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
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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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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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 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
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
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
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 2017-06-09 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
;, "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
n a regular basis
is a realistic use case, either.
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Check out the vibrant te
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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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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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
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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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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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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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
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
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
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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=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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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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c++-14 code with
c++-03 compilers.
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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,
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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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 2016-09-24 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 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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;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.
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.
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t's one or
the other?
TIA,
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ull
> 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
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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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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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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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
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
hat's what I expected and "removeHs = False" works, thanks. And I was
kidding about histidine of course.
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Description: Ope
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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Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
signature.as
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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Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
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Description: OpenP
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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Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
alatis_output_Structure3D_CID_260719.sdf
Description
).GetSymbol() + str ((i+1))
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Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
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Description: OpenPGP digital signature
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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Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
signature.
?
TIA
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Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
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___
Rdkit-discuss mailing
e left trying to guess whether a given "CA" stands
for C-alpha or calcium.
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Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
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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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Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.b
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
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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Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
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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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Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
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RDKit does it
because Greg said so.
HTH
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Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
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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
. 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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Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
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