def __init__(self, fasta_align, m1, m2, si=0, sj=1):
"""
fasta_align --- Alignment object
m1, m2 --- two models
si, sj --- the sequences in the Alignment object that
correspond to the structures
"""
l=fasta_align.get_alignment_length()
# Get the residues in the models
rl1=Selection.unfold_entities(m1, 'R')
rl2=Selection.unfold_entities(m2, 'R')
# Residue positions
p1=0
p2=0
# Map equivalent residues to each other
map12={}
map21={}
# List of residue pairs (None if -)
duos=[]
for i in range(0, l):
column=fasta_align.get_column(i)
aa1=column[si]
aa2=column[sj]
if aa1!="-":
# Position in seq1 is not -
while True:
# Loop until an aa is found
r1=rl1[p1]
p1=p1+1
if is_aa(r1):
break
self._test_equivalence(r1, aa1)
else:
r1=None
if aa2!="-":
# Position in seq2 is not -
while True:
# Loop until an aa is found
r2=rl2[p2]
p2=p2+1
if is_aa(r2):
break
self._test_equivalence(r2, aa2)
else:
r2=None
if r1:
# Map residue in seq1 to its equivalent in seq2
map12[r1]=r2
if r2:
# Map residue in seq2 to its equivalent in seq1
map21[r2]=r1
# Append aligned pair (r is None if gap)
duos.append((r1, r2))
self.map12=map12
self.map21=map21
self.duos=duos
def __init__(self, fasta_align, m1, m2, si=0, sj=1):
"""
fasta_align --- Alignment object
m1, m2 --- two models
si, sj --- the sequences in the Alignment object that
correspond to the structures
"""
l = fasta_align.get_alignment_length()
# Get the residues in the models
rl1 = Selection.unfold_entities(m1, 'R')
rl2 = Selection.unfold_entities(m2, 'R')
# Residue positions
p1 = 0
p2 = 0
# Map equivalent residues to each other
map12 = {}
map21 = {}
# List of residue pairs (None if -)
duos = []
for i in range(0, l):
column = fasta_align.get_column(i)
aa1 = column[si]
aa2 = column[sj]
if aa1 != "-":
# Position in seq1 is not -
while True:
# Loop until an aa is found
r1 = rl1[p1]
p1 = p1 + 1
if is_aa(r1):
break
self._test_equivalence(r1, aa1)
else:
r1 = None
if aa2 != "-":
# Position in seq2 is not -
while True:
# Loop until an aa is found
r2 = rl2[p2]
p2 = p2 + 1
if is_aa(r2):
break
self._test_equivalence(r2, aa2)
else:
r2 = None
if r1:
# Map residue in seq1 to its equivalent in seq2
map12[r1] = r2
if r2:
# Map residue in seq2 to its equivalent in seq1
map21[r2] = r1
# Append aligned pair (r is None if gap)
duos.append((r1, r2))
self.map12 = map12
self.map21 = map21
self.duos = duos
def __init__(self, model, pdb_file):
depth_dict={}
depth_list=[]
depth_keys=[]
# get_residue
residue_list=Selection.unfold_entities(model, 'R')
# make surface from PDB file
surface=get_surface(pdb_file)
# calculate rdepth for each residue
for residue in residue_list:
if not is_aa(residue):
continue
rd=residue_depth(residue, surface)
ca_rd=ca_depth(residue, surface)
# Get the key
res_id=residue.get_id()
chain_id=residue.get_parent().get_id()
depth_dict[(chain_id, res_id)]=(rd, ca_rd)
depth_list.append((residue, (rd, ca_rd)))
depth_keys.append((chain_id, res_id))
# Update xtra information
residue.xtra['EXP_RD']=rd
residue.xtra['EXP_RD_CA']=ca_rd
AbstractPropertyMap.__init__(self, depth_dict, depth_keys, depth_list)
def __init__(self, model, pdb_file):
depth_dict = {}
depth_list = []
depth_keys = []
# get_residue
residue_list = Selection.unfold_entities(model, 'R')
# make surface from PDB file
surface = get_surface(pdb_file)
# calculate rdepth for each residue
for residue in residue_list:
if not is_aa(residue):
continue
rd = residue_depth(residue, surface)
ca_rd = ca_depth(residue, surface)
# Get the key
res_id = residue.get_id()
chain_id = residue.get_parent().get_id()
depth_dict[(chain_id, res_id)] = (rd, ca_rd)
depth_list.append((residue, (rd, ca_rd)))
depth_keys.append((chain_id, res_id))
# Update xtra information
residue.xtra['EXP_RD'] = rd
residue.xtra['EXP_RD_CA'] = ca_rd
AbstractPropertyMap.__init__(self, depth_dict, depth_keys, depth_list)
def __contains__(self, res):
"""True if the given residue is in any of the mapped fragments.
@type res: L{Residue}
"""
return (res in self.fd)
def __getitem__(self, res):
"""
@type res: L{Residue}
@return: fragment classification
@rtype: L{Fragment}
"""
return self.fd[res]
if __name__ == "__main__":
import sys
p = PDBParser()
s = p.get_structure("X", sys.argv[1])
m = s[0]
fm = FragmentMapper(m, 10, 5, "levitt_data")
for r in Selection.unfold_entities(m, "R"):
print("%s:" % r)
if r in fm:
print(fm[r])
raise PDBException("No transformation has been calculated yet")
rot, tran=self.rotran
rot=rot.astype('f')
tran=tran.astype('f')
for atom in atom_list:
atom.transform(rot, tran)
if __name__=="__main__":
import sys
from SAP.Bio.PDB import PDBParser, Selection
p=PDBParser()
s1=p.get_structure("FIXED", sys.argv[1])
fixed=Selection.unfold_entities(s1, "A")
s2=p.get_structure("MOVING", sys.argv[1])
moving=Selection.unfold_entities(s2, "A")
rot=numpy.identity(3).astype('f')
tran=numpy.array((1.0, 2.0, 3.0), 'f')
for atom in moving:
atom.transform(rot, tran)
sup=Superimposer()
sup.set_atoms(fixed, moving)
print(sup.rotran)
def __contains__(self, res):
"""True if the given residue is in any of the mapped fragments.
@type res: L{Residue}
"""
return (res in self.fd)
def __getitem__(self, res):
"""
@type res: L{Residue}
@return: fragment classification
@rtype: L{Fragment}
"""
return self.fd[res]
if __name__=="__main__":
import sys
p = PDBParser()
s = p.get_structure("X", sys.argv[1])
m = s[0]
fm = FragmentMapper(m, 10, 5, "levitt_data")
for r in Selection.unfold_entities(m, "R"):
print("%s:" % r)
if r in fm:
print(fm[r])
raise PDBException("No transformation has been calculated yet")
rot, tran = self.rotran
rot = rot.astype('f')
tran = tran.astype('f')
for atom in atom_list:
atom.transform(rot, tran)
if __name__ == "__main__":
import sys
from SAP.Bio.PDB import PDBParser, Selection
p = PDBParser()
s1 = p.get_structure("FIXED", sys.argv[1])
fixed = Selection.unfold_entities(s1, "A")
s2 = p.get_structure("MOVING", sys.argv[1])
moving = Selection.unfold_entities(s2, "A")
rot = numpy.identity(3).astype('f')
tran = numpy.array((1.0, 2.0, 3.0), 'f')
for atom in moving:
atom.transform(rot, tran)
sup = Superimposer()
sup.set_atoms(fixed, moving)
print(sup.rotran)