from SAP.Bio.PDB import PDBParser
if len(sys.argv) != 4:
print("Expects three arguments,")
print(" - FASTA alignment filename (expect two sequences)")
print(" - PDB file one")
print(" - PDB file two")
sys.exit()
# The alignment
fa=AlignIO.read(open(sys.argv[1]), "fasta", generic_protein)
pdb_file1=sys.argv[2]
pdb_file2=sys.argv[3]
# The structures
p=PDBParser()
s1=p.get_structure('1', pdb_file1)
p=PDBParser()
s2=p.get_structure('2', pdb_file2)
# Get the models
m1=s1[0]
m2=s2[0]
al=StructureAlignment(fa, m1, m2)
# Print aligned pairs (r is None if gap)
for (r1, r2) in al.get_iterator():
print("%s %s" % (r1, r2))
for i in range(0, L):
residues[i].xtra["SS_PSEA"] = ss_seq[i]
#os.system("rm "+fname)
class PSEA(object):
def __init__(self, model, filename):
ss_seq = psea(filename)
ss_seq = psea2HEC(ss_seq)
annotate(model, ss_seq)
self.ss_seq = ss_seq
def get_seq(self):
"""
Return secondary structure string.
"""
return self.ss_seq
if __name__ == "__main__":
import sys
from SAP.Bio.PDB import PDBParser
# Parse PDB file
p = PDBParser()
s = p.get_structure('X', sys.argv[1])
# Annotate structure with PSEA sceondary structure info
PSEA(s[0], sys.argv[1])
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)
if __name__=="__main__":
import sys
from SAP.Bio.PDB import PDBParser
p=PDBParser()
s=p.get_structure("X", sys.argv[1])
model=s[0]
rd=ResidueDepth(model, sys.argv[1])
for item in rd:
print(item)
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)
if __name__ == "__main__":
import sys
from SAP.Bio.PDB import PDBParser
p = PDBParser()
s = p.get_structure("X", sys.argv[1])
model = s[0]
rd = ResidueDepth(model, sys.argv[1])
for item in rd:
print(item)
from SAP.Bio.PDB import PDBParser
if len(sys.argv) != 4:
print("Expects three arguments,")
print(" - FASTA alignment filename (expect two sequences)")
print(" - PDB file one")
print(" - PDB file two")
sys.exit()
# The alignment
fa = AlignIO.read(open(sys.argv[1]), "fasta", generic_protein)
pdb_file1 = sys.argv[2]
pdb_file2 = sys.argv[3]
# The structures
p = PDBParser()
s1 = p.get_structure('1', pdb_file1)
p = PDBParser()
s2 = p.get_structure('2', pdb_file2)
# Get the models
m1 = s1[0]
m2 = s2[0]
al = StructureAlignment(fa, m1, m2)
# Print aligned pairs (r is None if gap)
for (r1, r2) in al.get_iterator():
print("%s %s" % (r1, r2))
if self.rotran is None:
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)
for i in range(0, L):
residues[i].xtra["SS_PSEA"]=ss_seq[i]
#os.system("rm "+fname)
class PSEA(object):
def __init__(self, model, filename):
ss_seq=psea(filename)
ss_seq=psea2HEC(ss_seq)
annotate(model, ss_seq)
self.ss_seq=ss_seq
def get_seq(self):
"""
Return secondary structure string.
"""
return self.ss_seq
if __name__=="__main__":
import sys
from SAP.Bio.PDB import PDBParser
# Parse PDB file
p=PDBParser()
s=p.get_structure('X', sys.argv[1])
# Annotate structure with PSEA sceondary structure info
PSEA(s[0], sys.argv[1])
if self.rotran is None:
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)