def setVector(self, vector=None):
self.__vector__ = None
if vector is None:
try:
self.__vector__ = list(\
array(self.__atoms__[1].position) - \
array(self.__atoms__[0].position)\
)
except AttributeError, msg:
loki.debug('Bond.setVector(): ' + repr(msg))
def setVector(self, vector=None):
self.__vector__ = None
if vector is None:
try:
self.__vector__ = list(\
array(self.__atoms__[1].position) - \
array(self.__atoms__[0].position)\
)
except AttributeError, msg:
loki.debug('Bond.setVector(): ' + repr(msg))
def getAverage(self, normalise=False):
r = zeros((3), float)
for bond in self.__bonds__:
v = bond.getVector()
if v:
loki.debug('v=' + repr(v))
r += array(v)
if normalise:
r /= sqrt(sum(r**2))
else:
r /= float(len(self))
return r
def getAverage(self, normalise=False):
r = zeros((3), float)
for bond in self.__bonds__:
v = bond.getVector()
if v:
loki.debug('v=' + repr(v))
r += array(v)
if normalise:
r /= sqrt(sum(r**2))
else:
r /= float(len(self))
return r
def parse_option_hash(hash, translator=None, default_keys=None, \
default_value=None, default_function=None, translator_target='mara'):
"""
Parse and fix/append an option hash.
Arguments:
hash -- an unformatted option hash or a default value
translator -- a translator to format hash keys
(default: as is)
default_keys -- a list of keys to include
(default: keys of the original hash)
default_value -- a default value to use in the absense of a
proper input hash
default_function -- a default function to apply to values
(default: as is)
Returns:
out -- a formatted option hash
"""
loki.debug('hash(in)=%s' % repr(hash))
# a do-nothing translator will be used if none given
if not translator:
translator = lambda x, y: x
# a do-nothing function will be used if none given
if not default_function:
default_function = lambda x: x
# translate each key & apply default function to the value
if isinstance(hash, dict):
out = {}
for key in hash.keys():
if translator_target is not None:
k = translator(key, translator_target)
else:
k = translator(key)
out[k] = default_function(hash[key])
# or create a hash from the default keys & the given value
elif hash in [int, float, str]:
out = {}.fromkeys(default_keys, default_function(hash))
# or create a hash from the default keys & the default value
else:
loki.info('Incomprehensible hash -> using %s' % repr(default_value))
out = {}.fromkeys(default_keys, default_value)
loki.debug('hash(out)=%s' % repr(out))
return out
def getDCouplingVectors(self, dcouplings, include='all', exclude=[]):
if include == 'all':
inc = range(1, len(self) + 1)
else:
inc = []
for i in include:
if type(i) is int:
inc.append(i)
else:
loki.warn("discarding invalid residue '%s'", repr(i))
inc = intersection(inc, range(1, len(self) + 1))
exc = []
for i in exclude:
if type(i) is int:
exc.append(i)
else:
loki.warn("discarding invalid residue '%s'", repr(i))
include = sublist(inc, exc)
loki.debug('include=' + repr(include))
dcouplings = deepcopy(dcouplings)
loki.debug('dcouplings=' + repr(dcouplings)) # REMOVE
record = {}
for i in range(len(dcouplings)):
if type(dcouplings[i]) == str:
dcouplings[i] = DCouplings[dcouplings[i]]
dc = dcouplings[i]
record.setdefault(dc.atoms[0], {})
record.setdefault(dc.atoms[1], {})
if 'HN' in record.keys():
record.setdefault('H', {})
wanted = record.keys()
for i in include:
for atom in self[i - 1]:
if str(atom) in wanted:
record[str(atom)][int(self[i - 1])] = atom.position
if 'H' in wanted and len(record['H'].keys()):
for k in record['H'].keys():
if not record['HN'].has_key(k):
record['HN'][k] = record['H'][k]
loki.info('using H for HN in residue %d.', k)
loki.debug('record=%s', repr(record))
table = {}
for dc in dcouplings:
x, y = dc.atoms
residues = intersection(record[x].keys(), record[y].keys())
for i in residues:
tag = (i, str(dc))
table[tag] = [
m - n for m, n in zip(record[x][i], record[y][i])
]
tags = table.keys()
tags.sort()
vectors = [table[x] for x in tags]
return tags, vectors
def getDCouplingVectors(self, dcouplings, include='all', exclude=[]):
if include == 'all':
inc = range(1, len(self) + 1)
else:
inc = []
for i in include:
if type(i) is int:
inc.append(i)
else:
loki.warn("discarding invalid residue '%s'", repr(i))
inc = intersection(inc, range(1, len(self) + 1))
exc = []
for i in exclude:
if type(i) is int:
exc.append(i)
else:
loki.warn("discarding invalid residue '%s'", repr(i))
include = sublist(inc, exc)
loki.debug('include=' + repr(include))
dcouplings = deepcopy(dcouplings)
loki.debug('dcouplings=' + repr(dcouplings)) # REMOVE
record = {}
for i in range(len(dcouplings)):
if type(dcouplings[i]) == str:
dcouplings[i] = DCouplings[dcouplings[i]]
dc = dcouplings[i]
record.setdefault(dc.atoms[0], {})
record.setdefault(dc.atoms[1], {})
if 'HN' in record.keys():
record.setdefault('H', {})
wanted = record.keys()
for i in include:
for atom in self[i-1]:
if str(atom) in wanted:
record[str(atom)][int(self[i-1])] = atom.position
if 'H' in wanted and len(record['H'].keys()):
for k in record['H'].keys():
if not record['HN'].has_key(k):
record['HN'][k] = record['H'][k]
loki.info('using H for HN in residue %d.', k)
loki.debug('record=%s', repr(record))
table = {}
for dc in dcouplings:
x, y = dc.atoms
residues = intersection(record[x].keys(), record[y].keys())
for i in residues:
tag = (i, str(dc))
table[tag] = [m-n for m,n in zip(record[x][i], record[y][i])]
tags = table.keys()
tags.sort()
vectors = [table[x] for x in tags]
return tags, vectors
def __call__(self, word, target=None, attributes=None, find_best=True):
"""
Translate a word into a target language matching desired attributes.
arguments:
word -- word of interest
target -- target language (default: None == self.default)
attributes -- list of desired attributes (default: [])
find_best -- whether to actually search for a best match
(default: True)
TODO: find_best redundant, remove print statements etc.
"""
if target == None:
target = self.default
if attributes is None:
attributes = []
elif type(attributes) is str:
attributes = [attributes]
loki.debug('attributes=%s', attributes)
loki.debug('word=%s' % repr(word))
if not self.__dictionaries__.has_key(target):
raise ArgumentError, "Unknown target language '%s'." % target
if not self.__links__.has_key(target):
raise ArgumentError, "No known links to target language '%s'." \
% target
if word in self.__dictionaries__[target]:
return word
else:
name = None
original = None
for dictionary in self.__dictionaries__.values():
if word in dictionary:
name = str(dictionary)
original = dictionary[word]
for a in original.attributes:
if a not in attributes:
attributes.append(a)
break
loki.debug('original=%s' % repr(original))
loki.debug('attributes=%s', attributes)
loki.debug('name=%s' % repr(name))
if name != None:
path = self.__paths__[name][target]
loki.debug('path=%s' % repr(path))
if path != None:
# start from the base form
if original.base:
word = original.base
loki.debug('word=%s' % repr(word))
# traverse through the links to find the target word
for p in path:
word = str(self.__links__[name][p][word])
loki.debug('word=%s @ %s' % (repr(word), repr(p)))
name = p
# find the best match for the original form
if find_best:
new = self.__dictionaries__[target][word]
loki.debug('new=%s' % repr(new))
matches, mismatches = self.__match_attributes__(
attributes, new.attributes)
loki.debug('matches=%s', matches)
loki.debug('mismatches=%s', mismatches)
if mismatches:
alt = [word] + new.synonyms + new.conjugates
loki.debug('alt=%s' % repr(alt))
record = []
best = None
for a in alt:
m, mm = self.__match_attributes__( \
attributes, \
self.__dictionaries__\
[target][a].attributes)
record.append((m,mm))
if best == None or m > record[best][0] or \
(m == record[best][0] and \
mm < record[best][1]):
best = len(record)-1
loki.debug('record=%s', record)
loki.debug('best=%s', best)
if record[best][0] > matches or \
(record[best][0] == matches and \
record[best][1] < mismatches):
return alt[best]
return word
return self.unknown
def parse_sequence(args):
"""
Parse an amino acid sequence.
Arguments:
args -- a list of sequence items or a name of a file containing
them, e.g. 'GLU PRO GLU CYS' or 'EPEC GLK C EEK'
Returns:
sequence -- a list of 3-letter amino acid symbols
"""
loki.debug('parse_sequence < %s' % repr(args))
if isinstance(args, str) and os.path.isfile(args):
fname = args
elif len(args) == 1 and isinstance(args[0], str):
if os.path.isfile(args[0]):
fname = args[0]
else:
if args[0].count(' '):
args = args[0].split()
else:
args = args[0]
fname = None
else:
fname = None
if fname:
f = open(fname)
seq = f.read()
f.close()
loki.info("Read sequence from file '%s'." % fname)
args = seq.strip().split()
loki.debug('args=%s' % repr(args))
# sequence = []
# for aa in seq.strip().split():
# try:
# sequence.append(omniTranslator(aa.capitalize(), \
# '3-letter-aminoacids'))
# except KeyError:
# loki.warn("Discarding unknown aminoacid '%s'." % repr(aa))
# else:
# check whether all the sequence items are separated from each other
args = [x.capitalize() for x in args]
separated = True
for a in args:
if not (a in libLingua.dictionaryAmino1 or \
a in libLingua.dictionaryAmino3):
separated = False
loki.debug('separated=%s' % repr(separated))
sequence = []
if separated:
# append each item after converting it to a 3-letter symbol
for a in args:
try:
sequence.append(omniTranslator(a.capitalize(), \
'3-letter-aminoacids'))
except KeyError:
loki.warn("Discarding unknown aminoacid '%s'." % repr(a))
else:
# jam all symbols together (hope they are all 1-letter symbols)
aa = ''
for a in args:
aa += str(a)
aa = aa.replace(' ', '')
loki.debug('aa=%s' % repr(aa))
# append each item after converting it to a 3-letter symbol
for a in list(aa):
try:
sequence.append(omniTranslator(a, '3-letter-aminoacids'))
except KeyError:
loki.warn("Discarding unknown aminoacid '%s'." % repr(a))
loki.debug('parse_sequence > %s' % repr(sequence))
return sequence
def parse_sequence(args):
"""
Parse an amino acid sequence.
Arguments:
args -- a list of sequence items or a name of a file containing
them, e.g. 'GLU PRO GLU CYS' or 'EPEC GLK C EEK'
Returns:
sequence -- a list of 3-letter amino acid symbols
"""
loki.debug("parse_sequence < %s" % repr(args))
if isinstance(args, str) and os.path.isfile(args):
fname = args
elif len(args) == 1 and isinstance(args[0], str):
if os.path.isfile(args[0]):
fname = args[0]
else:
if args[0].count(" "):
args = args[0].split()
else:
args = args[0]
fname = None
else:
fname = None
if fname:
f = open(fname)
seq = f.read()
f.close()
loki.info("Read sequence from file '%s'." % fname)
args = seq.strip().split()
loki.debug("args=%s" % repr(args))
# sequence = []
# for aa in seq.strip().split():
# try:
# sequence.append(omniTranslator(aa.capitalize(), \
# '3-letter-aminoacids'))
# except KeyError:
# loki.warn("Discarding unknown aminoacid '%s'." % repr(aa))
# else:
# check whether all the sequence items are separated from each other
args = [x.capitalize() for x in args]
separated = True
for a in args:
if not (a in libLingua.dictionaryAmino1 or a in libLingua.dictionaryAmino3):
separated = False
loki.debug("separated=%s" % repr(separated))
sequence = []
if separated:
# append each item after converting it to a 3-letter symbol
for a in args:
try:
sequence.append(omniTranslator(a.capitalize(), "3-letter-aminoacids"))
except KeyError:
loki.warn("Discarding unknown aminoacid '%s'." % repr(a))
else:
# jam all symbols together (hope they are all 1-letter symbols)
aa = ""
for a in args:
aa += str(a)
aa = aa.replace(" ", "")
loki.debug("aa=%s" % repr(aa))
# append each item after converting it to a 3-letter symbol
for a in list(aa):
try:
sequence.append(omniTranslator(a, "3-letter-aminoacids"))
except KeyError:
loki.warn("Discarding unknown aminoacid '%s'." % repr(a))
loki.debug("parse_sequence > %s" % repr(sequence))
return sequence
def __call__(self, word, target=None, attributes=None, find_best=True):
"""
Translate a word into a target language matching desired attributes.
arguments:
word -- word of interest
target -- target language (default: None == self.default)
attributes -- list of desired attributes (default: [])
find_best -- whether to actually search for a best match
(default: True)
TODO: find_best redundant, remove print statements etc.
"""
if target == None:
target = self.default
if attributes is None:
attributes = []
elif type(attributes) is str:
attributes = [attributes]
loki.debug('attributes=%s', attributes)
loki.debug('word=%s' % repr(word))
if not self.__dictionaries__.has_key(target):
raise ArgumentError, "Unknown target language '%s'." % target
if not self.__links__.has_key(target):
raise ArgumentError, "No known links to target language '%s'." \
% target
if word in self.__dictionaries__[target]:
return word
else:
name = None
original = None
for dictionary in self.__dictionaries__.values():
if word in dictionary:
name = str(dictionary)
original = dictionary[word]
for a in original.attributes:
if a not in attributes:
attributes.append(a)
break
loki.debug('original=%s' % repr(original))
loki.debug('attributes=%s', attributes)
loki.debug('name=%s' % repr(name))
if name != None:
path = self.__paths__[name][target]
loki.debug('path=%s' % repr(path))
if path != None:
# start from the base form
if original.base:
word = original.base
loki.debug('word=%s' % repr(word))
# traverse through the links to find the target word
for p in path:
word = str(self.__links__[name][p][word])
loki.debug('word=%s @ %s' % (repr(word), repr(p)))
name = p
# find the best match for the original form
if find_best:
new = self.__dictionaries__[target][word]
loki.debug('new=%s' % repr(new))
matches, mismatches = self.__match_attributes__(
attributes, new.attributes)
loki.debug('matches=%s', matches)
loki.debug('mismatches=%s', mismatches)
if mismatches:
alt = [word] + new.synonyms + new.conjugates
loki.debug('alt=%s' % repr(alt))
record = []
best = None
for a in alt:
m, mm = self.__match_attributes__( \
attributes, \
self.__dictionaries__\
[target][a].attributes)
record.append((m, mm))
if best == None or m > record[best][0] or \
(m == record[best][0] and \
mm < record[best][1]):
best = len(record) - 1
loki.debug('record=%s', record)
loki.debug('best=%s', best)
if record[best][0] > matches or \
(record[best][0] == matches and \
record[best][1] < mismatches):
return alt[best]
return word
return self.unknown