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(
