[cctbxbb] Phi-Psi Angles

[Oleg Sobolev]

PS.

Please note, that for some of the features mentioned you will need the
latest cctbx version, preferably fresh check-out from svn.

Oleg.

On Mon, Sep 21, 2015 at 9:49 AM, Oleg Sobolev <osobolev at lbl.gov> wrote:

> Hi Nicholas,
>
> First, the most basic way to calculate torsion (dihedral) angle for 4
> given atoms is:
> from scitbx.math import dihedral_angle
> angle = dihedral_angle(sites=[(1,0,0), (0,0,0), (0,1,0), (1,1,0)],
> deg=True)
> where 'sites' contain atom coordinates.
>
> Second, here is more high-level way to get phi-psi angles:
>   from mmtbx.conformation_dependent_library import generate_protein_threes
>   pdb_h = iotbx.pdb.hierarchy.input(file_name=args[0]).hierarchy
>   sites_cart = pdb_h.atoms().extract_xyz()
>   # Note that this is a generator
>   for three in generate_protein_threes(
>           hierarchy=pdb_h,
>           geometry=None):
>     proxies = three.get_dummy_dihedral_proxies()
>     for p in proxies:
>       print "angle=", dihedral_angle(
>           sites=[sites_cart[x] for x in p.i_seqs],
>           deg=True)
>
> Third, to get all proxies, use this function with hierarchy:
>   from mmtbx.geometry_restraints.torsion_restraints.utils import \
>       get_complete_dihedral_proxies
>   dih_proxies = get_complete_dihedral_proxies(
>       pdb_hierarchy=pdb_h)
>
> Hope this helps, full script is below and attached (run with pdb file as
> the only argument).
>
> Best regards,
> Oleg Sobolev.
>
> import sys
> from scitbx.math import dihedral_angle
> import iotbx.pdb
> import os.path
>
> def basics():
>   print "Basics:"
>   angle = dihedral_angle(sites=[(1,0,0), (0,0,0), (0,1,0), (1,1,0)],
> deg=True)
>   print "Angle:", angle
>   angle = dihedral_angle(sites=[(2,1,1), (0,0,0), (0,1,0), (1,1,0)],
> deg=True)
>   print "Angle in degrees:", angle
>   angle = dihedral_angle(sites=[(2,1,1), (0,0,0), (0,1,0), (1,1,0)],
> deg=False)
>   print "Angle in radians:", angle
>   print "="*50
>
> def advanced(args):
>   print "Advanced phi-psi:"
>   if len(args) != 1 or not os.path.isfile(args[0]):
>     print "Bad argument"
>     return
>
>   # phi-psi angles
>   from mmtbx.conformation_dependent_library import generate_protein_threes
>   pdb_h = iotbx.pdb.hierarchy.input(file_name=args[0]).hierarchy
>   sites_cart = pdb_h.atoms().extract_xyz()
>   n_proxies = 0
>   # Note that this is a generator
>   for three in generate_protein_threes(
>           hierarchy=pdb_h,
>           geometry=None):
>     proxies = three.get_dummy_dihedral_proxies()
>     for p in proxies:
>       for i_seq in p.i_seqs:
>         print pdb_h.atoms()[i_seq].id_str(),
>       print "angle=", dihedral_angle(
>           sites=[sites_cart[x] for x in p.i_seqs],
>           deg=True)
>       n_proxies += 1
>   print "Total angles:", n_proxies
>
>
> def all_dihedral_proxies(args):
>   print "Advanced all:"
>   if len(args) != 1 or not os.path.isfile(args[0]):
>     print "Bad argument"
>     return
>   # all angles:
>   from mmtbx.geometry_restraints.torsion_restraints.utils import \
>       get_complete_dihedral_proxies
>
>   pdb_h = iotbx.pdb.hierarchy.input(file_name=args[0]).hierarchy
>   sites_cart = pdb_h.atoms().extract_xyz()
>   dih_proxies = get_complete_dihedral_proxies(
>       pdb_hierarchy=pdb_h)
>   for p in dih_proxies:
>     for i_seq in p.i_seqs:
>       print pdb_h.atoms()[i_seq].id_str(),
>     print "angle=", dihedral_angle(
>         sites=[sites_cart[x] for x in p.i_seqs],
>         deg=True)
>   print "Total angles:", dih_proxies.size()
>
> def run(args):
>   basics()
>   advanced(args)
>   all_dihedral_proxies(args)
>
> if (__name__ == "__main__"):
>   run(sys.argv[1:])
>
>
>
> On Sun, Sep 20, 2015 at 3:30 PM, Nicholas Pearce <
> nicholas.pearce at stx.ox.ac.uk> wrote:
>
>> Hi Everyone,
>>
>> Phenomenally stupid question, but is there an easy way to calculate
>> phi-psi angles for a protein using cctbx? And, following on from that,
>> Chi-1, Chi-2 etc angles?
>>
>> I’ve had a poke around, but couldn’t find any obvious (at least to me)
>> way that worked…
>>
>> I presume this must be implemented rigorously somewhere, and I didn’t
>> want to waste time reimplementing the wheel.
>>
>> Thanks,
>> Nick
>> _______________________________________________
>> cctbxbb mailing list
>> cctbxbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/cctbxbb
>>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/cctbxbb/attachments/20150921/0c6a0337/attachment-0001.htm>