def _load_struct(self):
parser = PDBParser()
self._struct = parser.get_structure("struct", self._pdb_file)
if (len(self._struct) > 1):
msgs.show(
"WARNING", "%d models found. Only the first will be used!" %
(len(self._struct)))
self._res_list = []
self._res_seq = []
self._res_index = {}
# gets only the first model
model = self._struct[0]
count = 0
for chain in model.child_list:
for res in chain.child_list:
new_residue = Residue(chain.id, res.id[1], res.resname.strip(),
res)
self._res_list.append(new_residue)
self._res_seq.append(count)
self._res_index[new_residue.key()] = [count, None]
count += 1
return (True)
def _get_atoms_residue(self, atom_list, src_res, trg_res):
src_atom_list = []
trg_atom_list = []
src_atom_list_tmp = filter(lambda a: a.get_name() in atom_list,
src_res)
trg_atom_list_tmp = filter(lambda a: a.get_name() in atom_list,
trg_res)
# for each atom in reference
for src_atom in src_atom_list_tmp:
found = False
src_name = src_atom.get_full_id()[4][0]
# search for an atom with the same name in the comparison
for trg_atom in trg_atom_list_tmp:
trg_name = trg_atom.get_full_id()[4][0]
# if the atom was found keep it and jump to the next
if (src_name == trg_name):
src_atom_list.append(src_atom)
trg_atom_list.append(trg_atom)
found = True
break
if (not found):
msgs.show(
"WARNING",
"Atom %s from residue %s not found in target atom list" %
(src_name, src_res.id))
return (src_atom_list, trg_atom_list)
def parse_endmdl(self, row):
if (not self._in_model):
msgs.show("Warning", "Missing 'MODEL' declaration.")
#~ self.show_err( "Missing 'MODEL' declaration." )
if (self._in_atom):
msgs.show("Warning", "Missing 'TER' declaration.")
#~ self.show_err( "Missing 'TER' declaration." )
self._in_model = False
self._in_atom = False
return ("ENDMDL")
def get_index_file( pdb_file, pdb_result_file="" ):
index_file = "%s.%s.index" %(pdb_file.replace( ".pdb", "" ), pdb_result_file.replace( ".pdb", "" ))
if (pdb_result_file is "") or (not os.path.isfile( index_file )):
index_file = pdb_file.replace( ".pdb", ".index" )
if( not os.path.isfile( index_file ) ):
msgs.show( "INFO", "INDEX SKIPPED! '%s' skipped for '%s'." %(index_file, pdb_file) )
index_file= None
else:
msgs.show( "INFO", "INDEX FOUND! '%s' for '%s'." %(index_file, pdb_file) )
return( index_file )
def _get_atoms_struct(self, atom_list, src_residues, trg_residues):
src_atoms = []
trg_atoms = []
if (len(src_residues) != len(trg_residues)):
msgs.show("ERROR", "Different number of residues!")
return (None)
for (src_res, trg_res) in zip(src_residues, trg_residues):
(sa, ta) = self._get_atoms_residue(atom_list, src_res, trg_res)
src_atoms.extend(sa)
trg_atoms.extend(ta)
return (src_atoms, trg_atoms)
def get_interactions(self, type="ALL"):
if (type == "ALL"):
# "ALL": returns all interactions
return self._interactions
elif (type in ("PAIR")):
# "PAIR": returns all pairs irrespective of their type
return filter(lambda x: x[0] in ("PAIR_2D", "PAIR_3D"),
self._interactions)
elif (type in ("PAIR_2D", "PAIR_3D", "STACK")):
# "PAIR_2D", "PAIR_3D", "STAK": returns the interactions of the specified type
return filter(lambda x: x[0] == type, self._interactions)
else:
msgs.show(
"FATAL",
"Wrong interaction type '%s' expected: 'ALL', 'PAIR', 'PAIR_2D', 'PAIR_3D' or 'STACK'"
% type)
def pvalue(self, m, N, param):
if (param == "+"):
a = 5.1
b = 15.8
elif (param == "-"):
a = 6.4
b = 12.7
else:
msgs.show(
"FATAL",
"Wrong p-value parameter '%s'. Expected '+' or '-'" % param)
RMSD = a * (N**0.41) - b
Z = (m - RMSD) / 1.8
pv = (1.0 + erf(Z / (2**0.5))) / 2.0
return (pv)
def set_rank(self, attr, rank):
if( attr == "rmsd" ):
self.rmsd_rank = rank
elif( attr == "pvalue" ):
self.pvalue_rank = rank
elif( attr == "DI_ALL" ):
self.DI_ALL_rank = rank
elif( attr == "INF_ALL" ):
self.INF_ALL_rank = rank
elif( attr == "INF_WC" ):
self.INF_WC_rank = rank
elif( attr == "INF_NWC" ):
self.INF_NWC_rank = rank
elif( attr == "INF_STACK" ):
self.INF_STACK_rank = rank
elif( attr == "clashscore" ):
self.clashscore_rank = rank
elif( attr == "mcq" ):
self.mcq_rank = rank
elif( attr == "gdt" ):
self.gdt_rank = rank
else:
msgs.show( "FATAL", "Can't set attribute '%s' in class 'Eval'" %(attr) )
def _load_index(self, index_name):
self._res_seq = []
entries = []
for row in open(index_name).read().split("\n"):
row = row.strip()
if ((not row.startswith("#")) and (row != "")):
entries.extend(map(lambda row: row.split(":"), row.split(",")))
for entry in entries:
if (len(entry) != 3):
msgs.show("ERROR", "Bad index entry: '%s'" % entry)
return (False)
chain = entry[0]
pos = int(entry[1])
count = int(entry[2])
# get the index position
ndx = self._get_index(chain, pos, 0)
if (ndx is None):
return (False)
# get the positions
for i in range(ndx, ndx + count):
if (i >= len(self._res_list)):
msgs.show(
"ERROR",
"Bad count %d in index entry: '%s'" % (count, entry))
return (False)
if (self._res_list[i].chain != chain):
msgs.show(
"ERROR",
"Position %d in index entry: '%s' is outside the chain"
% (i, entry))
return (False)
self._res_seq.append(i)
# update the index with the rank of the residue
self._res_index[self._res_list[i].key()][1] = (
len(self._res_seq) - 1)
return (True)
def show_err(self, msg):
msgs.show("ERROR", "Line %d: %s\n" % (self._row_count, msg))
self._ok = False