Hi Greg, I am using 32-bit python27 and anaconda (with 64-bit windows 10).
So I cannot update to latest version and test as you proposed several days ago.
Since it did not trouble me, I plan to upgrade all this environment in the
future.
BTW, is it necessary to upgrade python into 3.6
)
#drawer.DrawMolecule(mol,highlightAtoms=mol.GetSubstructMatch(p))
drawer.DrawMolecule(tm,highlightAtoms=tm.GetSubstructMatch(smarts))
drawer.FinishDrawing() svg = drawer.GetDrawingText().replace('svg:','')
Hongbin Yang
From: Greg LandrumDate: 2017-02-18 12:59To: 杨弘宾CC: rdkit-discussSubject: Re
Hi, everyone,? ??I want to draw two molecules in a svg file with rdMolDraw2D.
When I executed the following code, the jupyter cracked without any error or
warning.```drawer = rdMolDraw2D.MolDraw2DSVG(400,400)
i=0
for mol in mols:
? if mol.HasSubstructMatch(smarts):
? ?
/Install.html#frequently-encountered-problems
Hope it is helpful.
Hongbin Yang 杨弘宾
Research: Toxicophore and Chemoinformatics
Pharmaceutical Science, School of Pharmacy
East China University of Science and Technology
From: Menaka JayawardenaDate: 2016-09-06 00:05To: rdkit-discussSubject:
[Rdkit
read by OpenBabel. But I have no idea why it didnot work.
Hongbin Yang 杨弘宾
Research: Toxicophore and Chemoinformatics
Pharmaceutical Science, School of Pharmacy
East China University of Scie
LandrumDate: 2016-09-19 12:08To: 杨弘宾CC: rdkit-discussSubject: Re:
[Rdkit-discuss] a SMILES that rdkit cannot readHi,
On Mon, Sep 19, 2016 at 5:33 AM, 杨弘宾 <yanyangh...@163.com> wrote:
When I used rdkit to parse a smi file, I found that there was a SMILES that
rdkit cannot parse, and no any
1[N+](=O)[O-]')
>>> s.findall(a)
[(6, 7, 8, 9)]
It is a pity that rdkit can calculate the topological distance between two
atoms while it cannot match the fragments... Is there any better API which I
didn't find?
Hongbin Yang 杨弘宾
Research: Toxicophore and Chemoinformatics
Pharmaceutical Scien
Thanks, it works! I appreciate that Rdkit is so strict in representation of
the the molecules and the substructures. I learned a lot in the mail list.
Hongbin Yang
From: Paolo ToscoDate: 2016-10-27 17:19To: 杨弘宾; rdkit-discussSubject: Re:
[Rdkit-discuss] The fragmentMatcher
Hi，Peter S. Shenkin, I think this blog may help you draw molecule with
labels and it told more about drawing with rdMolDraw2D.
http://rdkit.blogspot.com/2015/02/new-drawing-code.html
Hongbin Yang From: Peter S. ShenkinDate: 2016-10-24 10:18To: Dimitri Maziuk;
RDKit DiscussSubject:
Hi, Peter, I don't know whether it can help you since I did not repeat your
code. But it acturally works in my computer: change the extended name
from .svg into .html and open it via chrome. It should be valid with
svg2.svg (the namespace of svg were removed).
Hongbin Yang
e to
manually initiate the compounds?
Hongbin Yang 杨弘宾
Research: Toxicophore and Chemoinformatics
Pharmaceutical Science, School of Pharmacy
East China University of Science and Technology?
--
Developer Access Program
: 2016-11-01 19:56To: 杨弘宾CC: rdkit-discussSubject: Re:
[Rdkit-discuss] Is there a way to init the conformations of smiles supplier to
improve the performance for substructure matching.I'll make two more points (
thanks to Greg Landrum for pointing this out )
1). In your code each call to suppl[i
he
name of each compoundBTW, I tried to use suppl[0].GetPropNames() but only to
get ",class std::allocator > at 0x7402e90>" that seemed
tell nothing. I wondered that is there any way to make it readable in python?
Hongbin Yang 杨弘宾
Research: Toxicophore and Chemoinformatics
ot
find this property_name untill he read the source code, or define the
property_name through adding headers.
Hongbin Yang 杨弘宾
?From:?Paolo ToscoDate:?2016-10-13?18:56To:?杨弘宾; rdkit-discussSubject:?Re:
[Rdkit-discuss] property of name in smilesMolSupplier
Hi Hongbi
Hi, rdkiters,
? ? Have you tried install rdkit from source? It's ok when I installed rdkit by
conda in my PC. But when I tried installing it in a server in which I am only a
user who cannot use "sudo" and the "python" is in a read-only directory.
Here is my cmake
iles('[$(Oc)]')) >>> ((10,),)
Then only atom 10 will be matched and it won't interfere with other counts.
Reference: http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html 4.4
Hongbin Yang
From: Chenyang ShiDate: 2017-03-09 01:32To: Greg LandrumCC: rdkit-discuss;
杨弘宾Subject
t; ((3,),)m.GetSubstructMatchs(COOH)>> ((1, 3, 2),)
Since atom "3" has been already matched, it should be ignored. So you can
create a "set" to record the matched atoms to avoid repetitive count.
Hongbin Yang 杨弘宾
From: Chenyang ShiDate: 2017-03-06 14:04To: Greg LandrumCC: R
Hi, Alexis,
Why don’t you output the molecule as “Smiles” format since the “Smarts” you
wanted to output was really a molecule.
And it is possible to remove the dummy atom via mol object. For example:
In [26]: x = Chem.MolFromSmiles('CC*')
In [27]: x.GetSubstructMatch(Chem.MolFromSmiles('*'))
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