def parse(self, line):
line = chomp(line)
self.line = line
fields = line.split('\t')
try:
self.domainid = fields[0]
self.pdbid = fields[1]
self.chainidField = fields[2]
self.scopfamily = fields[3]
self.scopid = fields[4]
self.scopinfoField = fields[5]
self.chainids = []
self.chainrange = {}
for chainid in self.chainidField.split(','):
chainfields = chainid.split(':')
if len(chainfields) == 1:
if chainfields[0] == '-':
chainfields = ['', '']
else:
chainfields = ['', chainfields[0]]
self.chainids.append(chainfields[0])
self.chainrange[chainfields[0]] = chainfields[1]
except:
return
self.isinit = True
def Load(self, filename):
infh = file(filename)
for line in infh:
if line[0] == '#':
fields = chomp(line).split('\t')
self.cutoff = float(fields[1])
self.specificity = float(fields[2])
self.sensitivity = float(fields[3])
else:
self.falseNegatives.append(ScoresEntry(line))
def Parse(self, line):
fields = chomp(line).split('#', 1)
data = fields[0].strip()
if len(fields) > 1:
self.comments = fields[1].strip()
fields = data.split('\t')
self.label = fields[0]
self.values = map(float, fields[1:])
subfields = self.label.split('_')
self.pdbid = '_'.join(subfields[1:-1])
self.index = int(subfields[-1])
def Parse(self, line):
fields = chomp(line).split('\t')
name = fields[1]
value = fields[2]
if name not in self.SPECIAL_PARAMETERS:
return None
name, func = self.SPECIAL_PARAMETERS[name]
self.name = name
self.value = func(value)
return self
def parse(self, line):
line = chomp(line)
self.line = line
fields = line.split('\t')
self.pdbid = fields[0].lower()
self.chainid = ''
self.comment = fields[-1]
match = COMMENT_RE.search(self.comment)
if match:
self.chainid = match.group('chainid')
if self.chainid:
self.chainid = self.chainid.lower()
def Parse(self, line):
self.line = line
fields = chomp(line).split('\t')
self.label = fields[0]
subfields = fields[0].split('_')
self.pdbid = '_'.join(subfields[1:-1])
self.index = int(subfields[-1])
self.score = float(fields[1])
self.x = float(fields[2])
self.y = float(fields[3])
self.z = float(fields[4])
self.description = '\t'.join(fields[5:])
def advance(snake, direction, food):
""" Takes a list of positions (snake) and returns a snake advanced in the
direction given of type Direction. Snake "grows" if it eats food
snake must be a list """
return \
apply(
lambda x:
chain(
[x],
chomp(iter(snake)) if not x == food else iter(snake)),
tuple(
map(
add,
snake[0],
direction.value)))
def Parse(self, line):
self.line = line
fields = chomp(line).split('\t')
self.name = fields[0]
subfields = self.name.split('-')
self.property = '-'.join(subfields[:-1])
self.volume = int(subfields[-1])
self.pvalue = float(fields[1])
self.minval = float(fields[2])
self.binsize = float(fields[3])
self.scores = map(float, fields[4:4 + self.NUM_BINS])
extendedFields = fields[4 + self.NUM_BINS:]
if extendedFields and extendedFields[0] == '#':
for idx, value in enumerate(extendedFields[1:]):
if not idx < len(self.EXTENDED_FIELDNAMES):
warning('Too many extended fields')
break
name, func = self.EXTENDED_FIELDNAMES[idx]
setattr(self, name, func(value))