Hi folks
it seems that the “easiest” way to get my coords if I know the ChEBI identifier
is to do something like this in Python3 (note this snippet has no error
checking!):
> import sys # only needed to parse the command-line arguments
> chebi = sys.argv[1] # expect ChEBI identifier without the leading “CHEBI:"
> import pubchempy # have to pip install or conda install, whatever for your
> environment
> pubchempy.download("SDF", f“ChEBI_{chebi}.sdf", f”CHEBI:{chebi}", "name",
> record_type="3d", overwrite=True)
and running that with “64119” as the argument gives me a file ChEBI_64119.sdf
with 3D coords.
Many thanks to all who got me out of my hole!
Harry
> On 6 Dec 2022, at 12:19, Harry Powell <hrp-ccp...@virginmedia.com> wrote:
>
> Hi Julie
>
> Ta.
>
> Do you know if there’s an API (pref. Python 3.9 or later) for downloading the
> 3D coordinates from ChemSpider?
>
> Harry
>
>> On 6 Dec 2022, at 12:04, Julie Tucker
>> <000020908adb55d7-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>> Chemspider can also provide you with a .mol file amongst other things.
>> http://www.chemspider.com/Chemical-Structure.2424.html?rid=281bd645-a2c9-4d07-af08-c3148b323194
>> Best wishes
>> Julie
>>
>> On Tue, 6 Dec 2022 at 11:55, Oliver Smart <oliver.s.sm...@gmail.com> wrote:
>> Hi Harry,
>>
>> The SDF found at ChEBI is a 2D SDF with the coordinates used for the
>> diagram. I do not think that ChEBI has
>> 3D coordinates. Why not use PubChem instead as this does provide 3D sdf
>> files?
>>
>> For your caffeine example:
>>
>> https://pubchem.ncbi.nlm.nih.gov/compound/64119
>>
>> There
>>
>> https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/CID/2519/record/SDF/?record_type=3d&response_type=save&response_basename=Conformer3D_CID_2519
>>
>>
>> Provides a SDF file.
>>
>> Hope this helps
>>
>> Oliver
>>
>> p.s. I you are stuck with ChEBI identifiers it would be possible to
>> programatically find the equivalent PubChem CID.
>>
>>
>>
>>
>>> On 6 Dec 2022, at 11:31, Harry Powell
>>> <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>>>
>>> Hi folks
>>>
>>> Can anyone help with this?
>>>
>>> I must have missed something in the documentation, because I don’t
>>> understand why the .mol and .sdf files downloaded from
>>>
>>> https://www.ebi.ac.uk/chebi
>>>
>>> seem to have aromatic C-C bonds that are 0.825 Å long (it’s a few decades
>>> now since I solved any small molecule structures, but something around
>>> 1.395Å rings a faint bell).
>>>
>>> I need to have ligands that have realistic sizes, and while I’m perfectly
>>> at ease scaling the models to what I think are sensible sizes, I can’t help
>>> but think that this isn’t necessary and I’ve missed something somewhere.
>>>
>>> Here’s an example of a molecule that I used this morning -
>>>
>>>
>>> https://www.ebi.ac.uk/chebi/saveStructure.do?defaultImage=true&chebiId=31332&imageId=0
>>>
>>> contents of downloaded file -
>>>>
>>>> Marvin 01140911122D
>>>>
>>>> 15 15 0 0 0 0 999 V2000
>>>> -0.7145 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>>> -0.7145 0.4125 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
>>>> 0.7145 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>>> 0.7145 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>>> 0.0000 -0.8250 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
>>>> 0.0000 0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>>> 1.4992 0.6674 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
>>>> 1.4992 -0.6675 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
>>>> 1.9841 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>>> -1.4289 -0.8250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>>>> 0.0001 1.6500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>>>> 0.0001 -1.6500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>>> 1.7541 1.4520 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>>> -1.4289 0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>>> 2.0809 -1.5365 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>>>> 10 1 2 0 0 0 0
>>>> 1 2 1 0 0 0 0
>>>> 14 2 1 0 0 0 0
>>>> 8 3 1 0 0 0 0
>>>> 4 3 2 0 0 0 0
>>>> 7 4 1 0 0 0 0
>>>> 1 5 1 0 0 0 0
>>>> 5 3 1 0 0 0 0
>>>> 12 5 1 0 0 0 0
>>>> 6 2 1 0 0 0 0
>>>> 6 4 1 0 0 0 0
>>>> 11 6 2 0 0 0 0
>>>> 9 7 1 0 0 0 0
>>>> 13 7 1 0 0 0 0
>>>> 9 8 2 0 0 0 0
>>>> M END
>>>>
>>>
>>> Harry
>>>
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>>
>> --
>> Julie Tucker
>> York Biomedical Research Institute
>> Department of Biology and HYMS
>> University of York
>>
>> My normal working days are Monday-Tuesday and Thursday-Friday. Please be
>> patient if you do not hear from me promptly. I choose to work flexibly;
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