bond2.add_target_atom(atomname=' O ', anyseqdist=True)
residue3 = antiparallel_beta_bridge_wide.add_residue(sequence_move=1,
index='o')
bond3 = residue3.add_bond(required=True, src_atom=' O ', trg_index='j')
bond3.add_target_atom(atomname=' H ', anyseqdist=True)
bond4 = residue3.add_bond(required=True, src_atom=' H ', trg_index='j')
bond4.add_target_atom(atomname=' O ', anyseqdist=True)
residue4 = antiparallel_beta_bridge_wide.add_residue(sequence_move=1,
index='p')
residue5 = antiparallel_beta_bridge_wide.add_residue(bond_move='h', index='q')
bond5 = residue5.add_bond(required=True, src_atom=' O ', trg_index='h')
bond5.add_target_atom(atomname=' H ', anyseqdist=True)
bond6 = residue5.add_bond(required=True, src_atom=' H ', trg_index='h')
bond6.add_target_atom(atomname=' O ', anyseqdist=True)
residue6 = antiparallel_beta_bridge_wide.add_residue(sequence_move=1,
index='h')
bond7 = residue6.add_bond(required=True, src_atom=' O ', trg_index='q')
bond7.add_target_atom(atomname=' H ', anyseqdist=True)
bond8 = residue6.add_bond(required=True, src_atom=' H ', trg_index='q')
bond8.add_target_atom(atomname=' O ', anyseqdist=True)
residue7 = antiparallel_beta_bridge_wide.add_residue(end_of_motif=True,
index='i')
if __name__ == "__main__":
cablam_fingerprints.make_pickle(antiparallel_beta_bridge_close)
cablam_fingerprints.make_pickle(antiparallel_beta_bridge_wide)
bond3b = res3.add_bond( allow_bifurcated = True, src_atom = ' H ') bond3b.add_target_atom( atomname = ' O ', seqdist = -3) res4 = threeten_general.add_residue( sequence_move = 1, index = 'd') bond4 = res4.add_bond( src_atom = ' H ') bond4.add_target_atom( atomname = ' O ', seqdist = -3) res5 = threeten_general.add_residue( sequence_move = 1, index = 'e', end_of_motif = True) bond5 = res5.add_bond( src_atom = ' H ') bond5.add_target_atom( atomname = ' O ', seqdist = -3) if __name__ == "__main__": cablam_fingerprints.make_pickle(alpha_helix_3os) cablam_fingerprints.make_pickle(alpha_helix_3hs) cablam_fingerprints.make_pickle(alpha_helix_3_full) cablam_fingerprints.make_pickle(threeten_general)
bond_move = 'e', end_of_motif = False, index = 't') bond13 = residue10.add_bond( required = True, src_atom = ' H ', trg_index = 'e') bond13.add_target_atom( atomname = ' O ', anyseqdist = True) residue11 = antiparallel_beta_cwc.add_residue( sequence_move = 2, end_of_motif = False, index = 'e') bond14 = residue11.add_bond( required = True, src_atom = ' O ', trg_index = 't') bond14.add_target_atom( atomname = ' H ', anyseqdist = True) residue12 = antiparallel_beta_cwc.add_residue( end_of_motif = True, index = 'g') if __name__ == "__main__": cablam_fingerprints.make_pickle(antiparallel_beta_wcw) cablam_fingerprints.make_pickle(antiparallel_beta_cwc)
#One of either seqdist or anyseqdist is *required* #Any number of possible target atoms may be added for each bond. #Any number of bonds may be required or banned for each residue. #Any number of residues may be defined for each motif. # Order matters when defining residues. New residues are append()ed to a list, # and so have order. Cablam will search for them in the order they are added. # Movement instructions in the form of sequence_move or bond_move are required # to get from one residue in this list to the next. #When finished: #Check that the last residue has end_of_motif=True #Check that atom names use pdb-format 4-character names, including whitespace #Check that the motif_name defined at the top of the motif is non-redundant with # any existing motif in cctbx/mmtbx/cablam/fingerprints that you do not wish to # overwrite. #Add this to the bottom of the code: if __name__ == "__main__": cablam_fingerprints.make_pickle(replace_this_with_name_of_motif) #Multiple motifs can be stored in the same code, but each needs its own call # to cablam_fingerprints.make_pickle, like so: cablam_fingerprints.make_pickle(another_motif) #Place all make_pickle calls at the end in a if __name__==__main__ to prevent # spontaneous generation of pickle files if the definitions are imported #Run the code from the commandline using phenix.python. This will generate # motif files in cctbx/mmtbx/cablam/fingerprints for cablam to use. #If you make any changes to the motif definition, you must re-run the code to # regenerate the pickled motif files with updated information.
'e': 'threeten_gen_c_end'
})
res1 = threeten_general.add_residue(sequence_move=1, index='a')
bond1 = res1.add_bond(src_atom=' O ')
bond1.add_target_atom(atomname=' H ', seqdist=3)
res2 = threeten_general.add_residue(sequence_move=1, index='b')
bond2 = res2.add_bond(src_atom=' O ')
bond2.add_target_atom(atomname=' H ', seqdist=3)
res3 = threeten_general.add_residue(sequence_move=1, index='c')
bond3a = res3.add_bond(allow_bifurcated=True, src_atom=' O ')
bond3a.add_target_atom(atomname=' H ', seqdist=3)
bond3b = res3.add_bond(allow_bifurcated=True, src_atom=' H ')
bond3b.add_target_atom(atomname=' O ', seqdist=-3)
res4 = threeten_general.add_residue(sequence_move=1, index='d')
bond4 = res4.add_bond(src_atom=' H ')
bond4.add_target_atom(atomname=' O ', seqdist=-3)
res5 = threeten_general.add_residue(sequence_move=1,
index='e',
end_of_motif=True)
bond5 = res5.add_bond(src_atom=' H ')
bond5.add_target_atom(atomname=' O ', seqdist=-3)
if __name__ == "__main__":
cablam_fingerprints.make_pickle(alpha_helix_3os)
cablam_fingerprints.make_pickle(alpha_helix_3hs)
cablam_fingerprints.make_pickle(alpha_helix_3_full)
cablam_fingerprints.make_pickle(threeten_general)
bond2 = residue1.add_bond(required=True, src_atom=' H ', trg_index='o')
bond2.add_target_atom(atomname=' O ', anyseqdist=True)
residue2 = parallel_beta_bridge.add_residue(bond_move='q', index='k')
bond3 = residue2.add_bond(required=True, src_atom=' H ', trg_index='q')
bond3.add_target_atom(atomname=' O ', anyseqdist=True)
residue3 = parallel_beta_bridge.add_residue(sequence_move=-1, index='q')
bond4 = residue3.add_bond(required=True, src_atom=' O ', trg_index='k')
bond4.add_target_atom(atomname=' H ', anyseqdist=True)
bond5 = residue3.add_bond(required=True, src_atom=' H ', trg_index='i')
bond5.add_target_atom(atomname=' O ', anyseqdist=True)
residue4 = parallel_beta_bridge.add_residue(sequence_move=-1, index='p')
residue5 = parallel_beta_bridge.add_residue(bond_move='g', index='o')
bond6 = residue5.add_bond(required=True, src_atom=' O ', trg_index='i')
bond6.add_target_atom(atomname=' H ', anyseqdist=True)
bond7 = residue5.add_bond(required=True, src_atom=' H ', trg_index='g')
bond7.add_target_atom(atomname=' O ', anyseqdist=True)
residue6 = parallel_beta_bridge.add_residue(sequence_move=2, index='g')
bond8 = residue6.add_bond(required=True, src_atom=' O ', trg_index='o')
bond8.add_target_atom(atomname=' H ', anyseqdist=True)
residue7 = parallel_beta_bridge.add_residue(end_of_motif=True, index='i')
if __name__ == "__main__":
cablam_fingerprints.make_pickle(parallel_beta)
cablam_fingerprints.make_pickle(parallel_beta_bridge)
trg_index = 'i') bond6.add_target_atom( atomname = ' H ', anyseqdist = True) bond7 = residue5.add_bond( required = True, src_atom = ' H ', trg_index = 'g') bond7.add_target_atom( atomname = ' O ', anyseqdist = True) residue6 = parallel_beta_bridge.add_residue( sequence_move = 2, index = 'g') bond8 = residue6.add_bond( required = True, src_atom = ' O ', trg_index = 'o') bond8.add_target_atom( atomname = ' H ', anyseqdist = True) residue7 = parallel_beta_bridge.add_residue( end_of_motif = True, index = 'i') if __name__ == "__main__": cablam_fingerprints.make_pickle(parallel_beta) cablam_fingerprints.make_pickle(parallel_beta_bridge)
residue8 = antiparallel_beta_cwc.add_residue(bond_move='n',
end_of_motif=False,
index='k')
bond11 = residue8.add_bond(required=True, src_atom=' H ', trg_index='n')
bond11.add_target_atom(atomname=' O ', anyseqdist=True)
residue9 = antiparallel_beta_cwc.add_residue(sequence_move=6,
end_of_motif=False,
index='n')
bond12 = residue9.add_bond(required=True, src_atom=' O ', trg_index='k')
bond12.add_target_atom(atomname=' H ', anyseqdist=True)
residue10 = antiparallel_beta_cwc.add_residue(bond_move='e',
end_of_motif=False,
index='t')
bond13 = residue10.add_bond(required=True, src_atom=' H ', trg_index='e')
bond13.add_target_atom(atomname=' O ', anyseqdist=True)
residue11 = antiparallel_beta_cwc.add_residue(sequence_move=2,
end_of_motif=False,
index='e')
bond14 = residue11.add_bond(required=True, src_atom=' O ', trg_index='t')
bond14.add_target_atom(atomname=' H ', anyseqdist=True)
residue12 = antiparallel_beta_cwc.add_residue(end_of_motif=True, index='g')
if __name__ == "__main__":
cablam_fingerprints.make_pickle(antiparallel_beta_wcw)
cablam_fingerprints.make_pickle(antiparallel_beta_cwc)
#One of either seqdist or anyseqdist is *required*
#Any number of possible target atoms may be added for each bond.
#Any number of bonds may be required or banned for each residue.
#Any number of residues may be defined for each motif.
# Order matters when defining residues. New residues are append()ed to a list,
# and so have order. Cablam will search for them in the order they are added.
# Movement instructions in the form of sequence_move or bond_move are required
# to get from one residue in this list to the next.
#When finished:
#Check that the last residue has end_of_motif=True
#Check that atom names use pdb-format 4-character names, including whitespace
#Check that the motif_name defined at the top of the motif is non-redundant with
# any existing motif in cctbx/mmtbx/cablam/fingerprints that you do not wish to
# overwrite.
#Add this to the bottom of the code:
if __name__ == "__main__":
cablam_fingerprints.make_pickle(replace_this_with_name_of_motif)
#Multiple motifs can be stored in the same code, but each needs its own call
# to cablam_fingerprints.make_pickle, like so:
cablam_fingerprints.make_pickle(another_motif)
#Place all make_pickle calls at the end in a if __name__==__main__ to prevent
# spontaneous generation of pickle files if the definitions are imported
#Run the code from the commandline using phenix.python. This will generate
# motif files in cctbx/mmtbx/cablam/fingerprints for cablam to use.
#If you make any changes to the motif definition, you must re-run the code to
# regenerate the pickled motif files with updated information.
src_atom = ' H ', trg_index = 'h') bond6.add_target_atom( atomname = ' O ', anyseqdist = True) residue6 = antiparallel_beta_bridge_wide.add_residue( sequence_move = 1, index = 'h') bond7 = residue6.add_bond( required = True, src_atom = ' O ', trg_index = 'q') bond7.add_target_atom( atomname = ' H ', anyseqdist = True) bond8 = residue6.add_bond( required = True, src_atom = ' H ', trg_index = 'q') bond8.add_target_atom( atomname = ' O ', anyseqdist = True) residue7 = antiparallel_beta_bridge_wide.add_residue( end_of_motif = True, index = 'i') if __name__ == "__main__": cablam_fingerprints.make_pickle(antiparallel_beta_bridge_close) cablam_fingerprints.make_pickle(antiparallel_beta_bridge_wide)
