[chimerax-users] Select ring atoms of ligand using python in chimerax

[Dr. Vijay Masand]

Thank you, Eric. The above commands are very helpful.
Using following command, I am getting sasa for all Carbon atoms:
from chimerax.core.commands import run as rc
from chimerax.atomic import all_atoms
atoms = all_atoms(session)
        ring_atoms = [a for a in atoms if a.rings()]
        ringC = [a for a in ring_atoms if a.element.name == "C"]
       for a in ringC:
        SASA = rc(session, 'measure sasa all sum %s'%a)
        print(SASA)
But I am not getting the expected result. I am now looking for a better
pythonic way to calculate sasa for ring carbon atoms of ligand only.
Thanks in advance for the help.

With Warm Regards
*Dr. Vijay H. Masand*
Department of Chemistry,
Vidya Bharati College, Amravati, 444 602
Maharashtra, India.
Phone number- +91-9403312628
https://sites.google.com/site/vijaymasand/



On Thu, Jan 19, 2023 at 12:39 AM Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Hi Vijay,
> Atom objects have an 'element' attribute which in turn has 'name' and
> 'number' attributes.  The 'name' attribute is actually the atomic symbol,
> *e.g.* H for hydrogen.
> You can use normal Python operations, such as 'not', to find these things,
> so the non-ring ligand atoms are: [a for a in ligand_atoms if not a.rings()]
>
> --Eric
>
> On Jan 17, 2023, at 6:26 PM, Dr. Vijay Masand via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
>
> Thank you for the details and nice solution, Eric.
> How can I extend the above code to select ring nitrogen and oxygen atoms
> and to sum charges on different atoms (ring/non-ring)?
> Thanks in advance.
>
> With Warm Regards
> *Dr. Vijay H. Masand*
> Department of Chemistry,
> Vidya Bharati College, Amravati, 444 602
> Maharashtra, India.
> Phone number- +91-9403312628
> https://sites.google.com/site/vijaymasand/
>
>
>
> On Wed, Jan 18, 2023 at 1:36 AM Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>
>> Hi Vijay,
>> I don't know exactly how efficient you need things to be, but here is
>> some info...
>>
>> *Get all atoms*:
>> from chimerax.atomic import all_atoms
>> atoms = all_atoms(session)
>>
>> *Filter down to just ligand atoms*:
>> ligand_atoms = atoms.filter(atoms.structure_categories == "ligand")
>>
>> *Ligand ring atoms*:
>> ring_atoms = [a for a in ligand_atoms if a.rings()]
>>
>> *Assign charges to ligand residues*:
>> from chimerax.add_charge import add_charges
>> add_charges(session, ligand_atoms.unique_residues)
>>
>> *Sum the charges*:
>> charge_sum = sum([a.charge for a in ligand_atoms])
>>
>> This all assumes the structure has hydrogens.  In particular, the charge
>> sum will be massively negative if hydrogens are missing!  Some of the calls
>> above are covered in the ChimeraX programmer's guide (
>> https://www.rbvi.ucsf.edu/chimerax/docs/devel/index.html, also included
>> in the app under Help), particularly the "API Reference" link.
>> When you said "select ring atoms" I don't know if you meant just find
>> them (which the above does) or actually select them in the graphics
>> window.  This would do that:
>>
>> session.selection.clear()
>> for a in ring_atoms:
>> a.selected = True
>>
>> --Eric
>>
>> Eric Pettersen
>> UCSF Computer Graphics Lab
>>
>>
>> On Jan 16, 2023, at 11:03 PM, Dr. Vijay Masand via ChimeraX-users <
>> chimerax-users at cgl.ucsf.edu> wrote:
>>
>> Dear all
>> I am looking for an efficient method to select ring atoms of ligands
>> using python in chimeraX. Also, is there any python code/method to get the
>> sum of charges on ligand atoms only?
>> Thanks in advance.
>> From
>> Vijay
>>
>> With Warm Regards
>> *Dr. Vijay H. Masand*
>> Department of Chemistry,
>> Vidya Bharati College, Amravati, 444 602
>> Maharashtra, India.
>> Phone number- +91-9403312628
>> https://sites.google.com/site/vijaymasand/
>>
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