from __future__ import absolute_import, division, print_function from mmtbx.cablam import cablam_fingerprints #Antiparallel Beta Bridge/loose definitions, uses 4 bonds #Original by Christopher Williams, converted to new format by Danny Oh #Two strands: # g (h) i (j) k # r (q) p (o) n antiparallel_beta_bridge_close = cablam_fingerprints.motif( motif_name="antiparallel_beta_bridge_close", residue_names={ "i": "antiparallel_beta_bridge_close", "p": "antiparallel_beta_bridge_close" }) residue1 = antiparallel_beta_bridge_close.add_residue(bond_move='p', index='i') bond1 = residue1.add_bond(required=True, src_atom=' O ', trg_index='p') bond1.add_target_atom(atomname=' H ', anyseqdist=True) bond2 = residue1.add_bond(required=True, src_atom=' H ', trg_index='p') bond2.add_target_atom(atomname=' O ', anyseqdist=True) residue2 = antiparallel_beta_bridge_close.add_residue(sequence_move=2, index='p') bond3 = residue2.add_bond(required=True, src_atom=' O ', trg_index='i') bond3.add_target_atom(atomname=' H ', anyseqdist=True) bond4 = residue2.add_bond(required=True, src_atom=' H ', trg_index='i') bond4.add_target_atom(atomname=' O ', anyseqdist=True) residue3 = antiparallel_beta_bridge_close.add_residue(bond_move='g', index='r') bond5 = residue3.add_bond(required=True, src_atom=' H ', trg_index='g') bond5.add_target_atom(atomname=' O ', anyseqdist=True)
from __future__ import division from mmtbx.cablam import cablam_fingerprints #Loose helix definitions, n-terminal end alpha_helix_3os = cablam_fingerprints.motif( motif_name = 'alpha_helix_3os', residue_names = {'b':'alpha_helix_3os'}) res1 = alpha_helix_3os.add_residue( sequence_move = 1) bond1 = res1.add_bond( src_atom = ' O ') bond1.add_target_atom( atomname = ' H ', seqdist = 4) res2 = alpha_helix_3os.add_residue( sequence_move = 1, index = 'b') bond2 = res2.add_bond( src_atom = ' O ') bond2.add_target_atom( atomname = ' H ', seqdist = 4) res3 = alpha_helix_3os.add_residue( end_of_motif = True) bond3 = res3.add_bond( src_atom = ' O ') bond3.add_target_atom( atomname = ' H ',
from __future__ import division from mmtbx.cablam import cablam_fingerprints #Antiparallel beta, close #Original by Christopher Williams, converted to new format by Danny Oh #Two strands: # g (h)* i* (j)* k # r (q)* p* (o)* n antiparallel_beta_wcw = cablam_fingerprints.motif( motif_name = "antiparallel_beta_wcw", residue_names = {"i":"antiparallel_beta_close", "p":"antiparallel_beta_close"}) residue1 = antiparallel_beta_wcw.add_residue( bond_move = 'p', end_of_motif = False, index = 'i') bond1 = residue1.add_bond( required = True, src_atom = ' O ', trg_index = 'p') bond1.add_target_atom( atomname = ' H ', anyseqdist = True) bond2 = residue1.add_bond( required = True, src_atom = ' H ', trg_index = 'p') bond2.add_target_atom( atomname = ' O ', anyseqdist = True)
from __future__ import division from mmtbx.cablam import cablam_fingerprints #How to write and format a motif fingerprint for cablam #Put "from __future__ import division" at the top of file (see above) #Import the cablam_fingerprints module (see above) #Write a short description of the motif being coded. #Create an instance of the motif class replace_this_with_name_of_motif = cablam_fingerprints.motif( motif_name = "replace_this_with_name_of_motif", residue_names = {"a":"residue1","b":"residue"}, superpose_order = {"b":["CA","N"],"c":["CA"],"d":["CA"],"e":["CA","OH"]}) #Pass the class a name for the motif (as a string). This will be used in # printing, filenameing, etc. #motif_name is an attribute of the motif class, not something to replace with # the name of the motif #superpose_order defines the atoms from each indexed residue to be used for # automated superposition with superpose_pdbs. Optional unless that feature is # desired for the motif. #Pass the class a dictionary of names for the residues in the motif # The keys for this dictionary must correspond to the indices used to identify # residues later in the fingerprint. Some functions may .sort() these keys for # printing, so using alphabetization-friendly keys is advised #Add the first residue to the motif. The add_residue() method also returns the # new residue for easy access. Here it's named residue1. residue1 = replace_this_with_name_of_motif.add_residue( allowed_resname = [], banned_resname = [],
from __future__ import absolute_import, division, print_function from mmtbx.cablam import cablam_fingerprints #Loose helix definitions, n-terminal end alpha_helix_3os = cablam_fingerprints.motif( motif_name='alpha_helix_3os', residue_names={'b': 'alpha_helix_3os'}) res1 = alpha_helix_3os.add_residue(sequence_move=1) bond1 = res1.add_bond(src_atom=' O ') bond1.add_target_atom(atomname=' H ', seqdist=4) res2 = alpha_helix_3os.add_residue(sequence_move=1, index='b') bond2 = res2.add_bond(src_atom=' O ') bond2.add_target_atom(atomname=' H ', seqdist=4) res3 = alpha_helix_3os.add_residue(end_of_motif=True) bond3 = res3.add_bond(src_atom=' O ') bond3.add_target_atom(atomname=' H ', seqdist=4) #------------------------------------------------------------------------------- #Loose helix definitions, c-terminal end alpha_helix_3hs = cablam_fingerprints.motif( motif_name='alpha_helix_3hs', residue_names={'b': 'alpha_helix_3hs'}) res1 = alpha_helix_3hs.add_residue(sequence_move=1) bond1 = res1.add_bond(src_atom=' H ') bond1.add_target_atom(atomname=' O ', seqdist=-4) res2 = alpha_helix_3hs.add_residue(sequence_move=1, index='b') bond2 = res2.add_bond(src_atom=' H ')
from __future__ import division from mmtbx.cablam import cablam_fingerprints #Parallel beta #Original by Christopher Williams, converted to new format by Danny Oh #Two strands: # (g) h* i* j* (k) # m (n) o* p* q* (r) s parallel_beta = cablam_fingerprints.motif(motif_name="parallel_beta", residue_names={ "i": "parallel_beta_close", "p": "parallel_beta_wide" }) residue1 = parallel_beta.add_residue(sequence_move=1, index='i') bond1 = residue1.add_bond(required=True, src_atom=' O ', trg_index='q') bond1.add_target_atom(atomname=' H ', anyseqdist=True) bond2 = residue1.add_bond(required=True, src_atom=' H ', trg_index='o') bond2.add_target_atom(atomname=' O ', anyseqdist=True) residue2 = parallel_beta.add_residue(sequence_move=1, index='j') residue3 = parallel_beta.add_residue(bond_move='s', index='k') bond3 = residue3.add_bond(required=True, src_atom=' H ', trg_index='q') bond3.add_target_atom(atomname=' O ', anyseqdist=True) bond4 = residue3.add_bond(required=True, src_atom=' O ', trg_index='s') bond4.add_target_atom(atomname=' H ', anyseqdist=True) residue4 = parallel_beta.add_residue(sequence_move=-2, index='s') bond5 = residue4.add_bond(required=True, src_atom=' H ', trg_index='k')
from __future__ import division from mmtbx.cablam import cablam_fingerprints #Parallel beta #Original by Christopher Williams, converted to new format by Danny Oh #Two strands: # (g) h* i* j* (k) # m (n) o* p* q* (r) s parallel_beta = cablam_fingerprints.motif( motif_name = "parallel_beta", residue_names = {"i":"parallel_beta_close", "p":"parallel_beta_wide"}) residue1 = parallel_beta.add_residue( sequence_move = 1, index = 'i') bond1 = residue1.add_bond( required = True, src_atom = ' O ', trg_index = 'q') bond1.add_target_atom( atomname = ' H ', anyseqdist = True) bond2 = residue1.add_bond( required = True, src_atom = ' H ', trg_index = 'o') bond2.add_target_atom( atomname = ' O ', anyseqdist = True)
from __future__ import absolute_import, division, print_function from mmtbx.cablam import cablam_fingerprints #Antiparallel beta, close #Original by Christopher Williams, converted to new format by Danny Oh #Two strands: # g (h)* i* (j)* k # r (q)* p* (o)* n antiparallel_beta_wcw = cablam_fingerprints.motif( motif_name="antiparallel_beta_wcw", residue_names={ "i": "antiparallel_beta_close", "p": "antiparallel_beta_close" }) residue1 = antiparallel_beta_wcw.add_residue(bond_move='p', end_of_motif=False, index='i') bond1 = residue1.add_bond(required=True, src_atom=' O ', trg_index='p') bond1.add_target_atom(atomname=' H ', anyseqdist=True) bond2 = residue1.add_bond(required=True, src_atom=' H ', trg_index='p') bond2.add_target_atom(atomname=' O ', anyseqdist=True) residue2 = antiparallel_beta_wcw.add_residue(sequence_move=1, end_of_motif=False, index='p') bond3 = residue2.add_bond(required=True, src_atom=' O ', trg_index='i') bond3.add_target_atom(atomname=' H ', anyseqdist=True) bond4 = residue2.add_bond(required=True, src_atom=' H ', trg_index='i') bond4.add_target_atom(atomname=' O ', anyseqdist=True)
from __future__ import division from mmtbx.cablam import cablam_fingerprints #How to write and format a motif fingerprint for cablam #Put "from __future__ import division" at the top of file (see above) #Import the cablam_fingerprints module (see above) #Write a short description of the motif being coded. #Create an instance of the motif class replace_this_with_name_of_motif = cablam_fingerprints.motif( motif_name="replace_this_with_name_of_motif", residue_names={ "a": "residue1", "b": "residue" }, superpose_order={ "b": ["CA", "N"], "c": ["CA"], "d": ["CA"], "e": ["CA", "OH"] }) #Pass the class a name for the motif (as a string). This will be used in # printing, filenameing, etc. #motif_name is an attribute of the motif class, not something to replace with # the name of the motif #superpose_order defines the atoms from each indexed residue to be used for # automated superposition with superpose_pdbs. Optional unless that feature is # desired for the motif. #Pass the class a dictionary of names for the residues in the motif # The keys for this dictionary must correspond to the indices used to identify # residues later in the fingerprint. Some functions may .sort() these keys for
from __future__ import division from mmtbx.cablam import cablam_fingerprints #Antiparallel Beta Bridge/loose definitions, uses 4 bonds #Original by Christopher Williams, converted to new format by Danny Oh #Two strands: # g (h) i (j) k # r (q) p (o) n antiparallel_beta_bridge_close = cablam_fingerprints.motif( motif_name = "antiparallel_beta_bridge_close", residue_names = {"i":"antiparallel_beta_bridge_close", "p":"antiparallel_beta_bridge_close"}) residue1 = antiparallel_beta_bridge_close.add_residue( bond_move = 'p', index = 'i') bond1 = residue1.add_bond( required = True, src_atom = ' O ', trg_index = 'p') bond1.add_target_atom( atomname = ' H ', anyseqdist = True) bond2 = residue1.add_bond( required = True, src_atom = ' H ', trg_index = 'p') bond2.add_target_atom( atomname = ' O ', anyseqdist = True) residue2 = antiparallel_beta_bridge_close.add_residue(