Dear colleagues,
I got two conformers of a molecule. It looks like they have the same chirality
(S, I believe). But RDKit perceives them as different. Is it a bug, or did I
miss anything?
Thank you.
Ling
mol = Chem.MolFromMolFile(input.sdf, removeHs=False)
Hello Dimitrios,
You may also take a look at an earlier entry for a somewhat more sophisticated
discussion.
http://www.mail-archive.com/rdkit-discuss%40lists.sourceforge.net/msg03671.html
You may like to read the whole thread too.
Ling
From: Dimitrios Spiliotopoulos
Dear colleagues,
I am trying to fix a molecule (originally in PDB format - what can you expect?)
which is a fluro-chloro-benzene with a hydrogen missing. I have somehow already
converted it into MDL MOL format (see attached). The carbon atom with the
missing hydrogen was set to have a formal
Dear Sergio,
The lactam ring (atoms 1 2 4 6 8 10) is not really aromatic. The bonds 4-6,
6-8, 8-10 should all be single rather than aromatic in the mol2 file. The
remaining three bonds in the ring should be double or single rather than
aromatic.
Ling
From: Wong, Sergio E. wong...@llnl.gov
Hello Jan,
Thank you for your work to simulate the ROCS volume overlap. It looks
interesting, so I have been following your web page. I am running
RDKit_2014_03. There is no rdShape module. Do I need to get it from github? If
so, where is it? Or can I just wait for 2014_09?
I am also comparing
Hello Jan,
This has been discussed not long ago:
http://www.mail-archive.com/rdkit-discuss%40lists.sourceforge.net/msg03671.html
Your second Smarts string is the Chemaxon Smarts in this discussion.
There may not be an easy way out. You may need to do it in two steps and
add back the non-amide
Good evening,
I have some molecules with neutral amidine heads. I would like to
make them positively charged. So I do:
mol = Chem.MolFromMolFile('input.mol', removeHs=False)
q = Chem.MolFromSmarts('[NH]=C[NH2]')
for mat in mol.GetSubstructMatches(q):
- Forwarded Message -
From: S.L. Chan slch...@yahoo.com
To: JP jeanpaul.ebe...@inhibox.com
Sent: Tuesday, January 14, 2014 10:03 PM
Subject: Re: [Rdkit-discuss] Add a charge to an atom and modify Hs accordingly
(protonation)
Hello JP,
You need to bear in mind that by default
Hello Greg,
Multiple bonds from metal ions (Ca, Mg, etc.) are not unusual in the PDB. And
from what I remember, it is not even consistent in the sense that metal ions do
not always have multiple bonds.
Do forcefields have parameters for bonds involving metal ions? If not, perhaps
you could
Yep, this is what I think I need. Many thanks Greg!
And thank Toby for the tips too.
Ling
From: Greg Landrum greg.land...@gmail.com
To: S.L. Chan slch...@yahoo.com
Cc: rdkit-discuss@lists.sourceforge.net
rdkit-discuss@lists.sourceforge.net
Sent: Wednesday
Good evening,
I would like to get an exhaustive substructure matching of a molecule onto
itself. Generally I could use the GetSubstructMatches function with the
uniquify=False option. However, if there is a carboxylate or a guanidinium
head around, this would give only one side of the match
Hello Greg,
By 3D similarity of aligned molecules based on molecular shape do you mean
ShapeTanimotoDist ?
Also are there any integrated examples on how to use the pharmacophore packages
like Chem.FeatMap, Chem.Pharm2D, Chem.Pharm3D etc. ? I found the manual pages
but some more guidance would
Indeed with the latest release there is no problem any more.
Ling
From: Greg Landrum greg.land...@gmail.com
To: S.L. Chan slch...@yahoo.com
Cc: rdkit-discuss@lists.sourceforge.net
rdkit-discuss@lists.sourceforge.net
Sent: Thursday, August 22, 2013 6:57 PM
Good afternoon folks,
I would imagine that if you remove the hydrogens, the
resulting molecule would be a substructure of the
original molecule. However, when I do the following
to the attached MDL mol file, there is no matches.
from rdkit import Chem
mol = Chem.MolFromMolFile('temp.mol',
Hello folks,
In a way this is a continuation of a previous discussion.
My question is: so is there a simple way to obtain the original
indexing with all hydrogen atoms included? Do I have to write
my own function?
Thank you.
Ling
Re: [Rdkit-discuss] SMILES and atom indexing
greg landrum
Dear Greg and others,
I am looking for a function that returns all the atom
keys of a molecule. I thought GetAtoms was it. But then
it does not seem to give a stable list of atom keys.
For example:
mol = Chem.MolFromSmiles('')
for c in mol.GetAtoms():
... print c
...
16 matches
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