Re: [Rdkit-discuss] Highlighting atoms with different colors in a molecule

[Greg Landrum]

On Tue, Jun 4, 2019 at 4:32 PM Omar H94  wrote:

> I wonder if it is possible to highlight different atoms with different
> colors in a one molecule. For example, to highlight atom 1 in red and atom
> 3 in blue in the same image of the molecule. If there’s a way to do this, I
> would like to know how.
>

Yep, there are some examples here:
http://rdkit.blogspot.com/2015/02/new-drawing-code.html

-greg
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[Rdkit-discuss] Highlighting atoms with different colors in a molecule

[Omar H94]

Dear RDKit users,
I wonder if it is possible to highlight different atoms with different
colors in a one molecule. For example, to highlight atom 1 in red and atom
3 in blue in the same image of the molecule. If there’s a way to do this, I
would like to know how.

Thanks,
Omar
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Re: [Rdkit-discuss] Catching errors in SMILES files

[Paolo Tosco]

Hi David,

I think I already have a fix for this bug, I'll submit a PR later. If 
you can create a ?GitHub issue it would be great so I can link my PR to 
the bug.


Thanks, cheers
p.


On 06/04/19 12:10, David Cosgrove wrote:

Hi Paolo,
Many thanks for the speedy reply.  I'll do as you suggest for now.  Do 
you want me to file an issue on github, or even, maybe, see if I can 
fix it myself?

Cheers,
Dave


On Mon, Jun 3, 2019 at 5:32 PM Paolo Tosco > wrote:


Hi David,

a workaround could be adding a final check after the for loop:

#!/usr/bin/env python

from rdkit import Chem

suppl1 = Chem.SmilesMolSupplier('test1.smi', titleLine=False,
nameColumn=1)
rec_num = 0
print("len(suppl1) = {0:d}".format(len(suppl1)))
for mol in suppl1:
    rec_num += 1
    if not mol:
    print('Record {} not read.'.format(rec_num))
    else:
    print('Record {} read ok.'.format(rec_num))
if (rec_num == len(suppl1) - 1):
    rec_num += 1
    print('Record {} not read.'.format(rec_num))


suppl2 = Chem.SmilesMolSupplier('test2.smi', titleLine=False,
nameColumn=1)
rec_num = 0
print("len(suppl2) = {0:d}".format(len(suppl2)))
for mol in suppl2:
    rec_num += 1
    if not mol:
    print('Record {} not read.'.format(rec_num))
    else:
    print('Record {} read ok.'.format(rec_num))
if (rec_num == len(suppl2) - 1):
    rec_num += 1
    print('Record {} not read.'.format(rec_num))

This should work until what seems to be an issue in the
SmilesSupplier is fixed.

Cheers,
p.

On 06/03/19 16:49, David Cosgrove wrote:

Hi,

I'm trying to catch the line numbers of lines in a SMILES file
that aren't parsed by the SmilesMolSupplier.  Example code is
attached, along with 2 SMILES files.  When there is a bad SMILES
string on the last line, the error is not reported, as in
test2.smi.  I've tried iterating through the file in a loop using
next(suppl1) and catching the StopIteration exception, but I have
the same issue. Is there a way to spot a last bad record in a file?

Thanks,
Dave

-- 
David Cosgrove

Freelance computational chemistry and chemoinformatics developer
http://cozchemix.co.uk





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--
David Cosgrove
Freelance computational chemistry and chemoinformatics developer
http://cozchemix.co.uk



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Re: [Rdkit-discuss] Catching errors in SMILES files

[David Cosgrove]

Hi Paolo,
Many thanks for the speedy reply.  I'll do as you suggest for now.  Do you
want me to file an issue on github, or even, maybe, see if I can fix it
myself?
Cheers,
Dave


On Mon, Jun 3, 2019 at 5:32 PM Paolo Tosco 
wrote:

> Hi David,
>
> a workaround could be adding a final check after the for loop:
>
> #!/usr/bin/env python
>
> from rdkit import Chem
>
> suppl1 = Chem.SmilesMolSupplier('test1.smi', titleLine=False, nameColumn=1)
> rec_num = 0
> print("len(suppl1) = {0:d}".format(len(suppl1)))
> for mol in suppl1:
> rec_num += 1
> if not mol:
> print('Record {} not read.'.format(rec_num))
> else:
> print('Record {} read ok.'.format(rec_num))
> if (rec_num == len(suppl1) - 1):
> rec_num += 1
> print('Record {} not read.'.format(rec_num))
>
>
> suppl2 = Chem.SmilesMolSupplier('test2.smi', titleLine=False, nameColumn=1)
> rec_num = 0
> print("len(suppl2) = {0:d}".format(len(suppl2)))
> for mol in suppl2:
> rec_num += 1
> if not mol:
> print('Record {} not read.'.format(rec_num))
> else:
> print('Record {} read ok.'.format(rec_num))
> if (rec_num == len(suppl2) - 1):
> rec_num += 1
> print('Record {} not read.'.format(rec_num))
>
> This should work until what seems to be an issue in the SmilesSupplier is
> fixed.
>
> Cheers,
> p.
>
> On 06/03/19 16:49, David Cosgrove wrote:
>
> Hi,
>
> I'm trying to catch the line numbers of lines in a SMILES file that aren't
> parsed by the SmilesMolSupplier.  Example code is attached, along with 2
> SMILES files.  When there is a bad SMILES string on the last line, the
> error is not reported, as in test2.smi.  I've tried iterating through the
> file in a loop using next(suppl1) and catching the StopIteration exception,
> but I have the same issue.  Is there a way to spot a last bad record in a
> file?
>
> Thanks,
> Dave
>
> --
> David Cosgrove
> Freelance computational chemistry and chemoinformatics developer
> http://cozchemix.co.uk
>
>
>
>
>
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>

-- 
David Cosgrove
Freelance computational chemistry and chemoinformatics developer
http://cozchemix.co.uk
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