def get_next_strand (self, sheet_id, strand_id, pdb_labels,
next_ladder=None) :
from iotbx.pdb import secondary_structure
start_i_res = end_i_res = None
next_ladder_i_start = sys.maxint
next_ladder_i_end = - sys.maxint
if (next_ladder is not None) :
next_ladder_i_start = min(next_ladder.bridges[0].i_res,
next_ladder.bridges[-1].i_res)
next_ladder_i_end = max(next_ladder.bridges[-1].i_res,
next_ladder.bridges[0].i_res)
j_res_start = min(self.bridges[0].j_res, self.bridges[-1].j_res)
j_res_end = max(self.bridges[-1].j_res, self.bridges[0].j_res)
start_i_res = min(j_res_start, next_ladder_i_start)
end_i_res = max(j_res_end, next_ladder_i_end)
if (start_i_res > end_i_res) :
out = cStringIO.StringIO()
self.show(out=out)
raise RuntimeError("start_i_res(%d) > end_i_res(%d):\n%s" %
(start_i_res, end_i_res, out.getvalue()))
start = pdb_labels[start_i_res]
end = pdb_labels[end_i_res]
strand = secondary_structure.pdb_strand(
sheet_id=sheet_id,
strand_id=strand_id,
start_resname=start.resname,
start_chain_id=start.chain_id,
start_resseq=start.resseq,
start_icode=start.icode,
end_resname=end.resname,
end_chain_id=end.chain_id,
end_resseq=end.resseq,
end_icode=end.icode,
sense=self.direction)
return strand
def get_next_strand(self, sheet_id, strand_id, pdb_labels,
next_ladder=None):
from iotbx.pdb import secondary_structure
start_i_res = end_i_res = None
next_ladder_i_start = sys.maxsize
next_ladder_i_end = - sys.maxsize
if (next_ladder is not None):
next_ladder_i_start = min(next_ladder.bridges[0].i_res,
next_ladder.bridges[-1].i_res)
next_ladder_i_end = max(next_ladder.bridges[-1].i_res,
next_ladder.bridges[0].i_res)
j_res_start = min(self.bridges[0].j_res, self.bridges[-1].j_res)
j_res_end = max(self.bridges[-1].j_res, self.bridges[0].j_res)
start_i_res = min(j_res_start, next_ladder_i_start)
end_i_res = max(j_res_end, next_ladder_i_end)
if (start_i_res > end_i_res):
out = StringIO()
self.show(out=out)
raise RuntimeError("start_i_res(%d) > end_i_res(%d):\n%s" %
(start_i_res, end_i_res, out.getvalue()))
start = pdb_labels[start_i_res]
end = pdb_labels[end_i_res]
strand = secondary_structure.pdb_strand(
sheet_id=sheet_id,
strand_id=strand_id,
start_resname=start.resname,
start_chain_id=start.chain_id,
start_resseq=start.resseq,
start_icode=start.icode,
end_resname=end.resname,
end_chain_id=end.chain_id,
end_resseq=end.resseq,
end_icode=end.icode,
sense=self.direction)
return strand
def get_initial_strand(self, sheet_id, pdb_labels):
from iotbx.pdb import secondary_structure
start_i_res = min(self.bridges[0].i_res, self.bridges[-1].i_res)
end_i_res = max(self.bridges[0].i_res, self.bridges[-1].i_res)
start = pdb_labels[start_i_res]
end = pdb_labels[end_i_res]
first_strand = secondary_structure.pdb_strand(
sheet_id=sheet_id,
strand_id=1,
start_resname=start.resname,
start_chain_id=start.chain_id,
start_resseq=start.resseq,
start_icode=start.icode,
end_resname=end.resname,
end_chain_id=end.chain_id,
end_resseq=end.resseq,
end_icode=end.icode,
sense=0)
return first_strand
def get_initial_strand (self, sheet_id, pdb_labels) :
from iotbx.pdb import secondary_structure
start_i_res = min(self.bridges[0].i_res, self.bridges[-1].i_res)
end_i_res = max(self.bridges[0].i_res, self.bridges[-1].i_res)
start = pdb_labels[start_i_res]
end = pdb_labels[end_i_res]
first_strand = secondary_structure.pdb_strand(
sheet_id=sheet_id,
strand_id=1,
start_resname=start.resname,
start_chain_id=start.chain_id,
start_resseq=start.resseq,
start_icode=start.icode,
end_resname=end.resname,
end_chain_id=end.chain_id,
end_resseq=end.resseq,
end_icode=end.icode,
sense=0)
return first_strand
