def shutdown(self):
"""
Perform a clean exit by deleting all temporary files.
"""
loki.info('Removing temporary files.')
cmd = "rm -f %s*" % self.name
os.system(cmd)
def run(self, size):
"""
Run CYANA using a macro created earlier.
"""
loki.info('A new Cyana round started for %d structures.'%size)
# if no Rg check, point to something always true
if self.rg_limits:
check_rg = self.checkRg
else:
check_rg = len
# run cyana as many time as needed until it completes succesfully
run_cyana = "cyana < %s.cmd" % self.name
todo = size
while todo:
# check if a new macro is needed
if todo != self.__last_macro_size__:
self.writeMacro(todo)
self.writeScript()
os.system(run_cyana)
for i in range(1,todo+1):
name = '%s-%03d.pdb'%(self.name, i)
if os.path.exists(name) and check_rg(name):
todo -= 1
self.tally += 1
os.system('mv -f %s %s%s.pdb'%(name, self.output,
str(self.tally).zfill(self.tally_digits)))
else:
os.system('rm -f %s'%name)
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 checkRg(self, filename):
"""
Check whether a given conformation is within the limits set for radius
of gyration.
"""
rg = calculate_rg(filename)
loki.info('Rg(%s) = %f)'%(filename, rg))
if (self.rg_limits[0] != None and rg < self.rg_limits[0]) or \
(self.rg_limits[1] != None and rg > self.rg_limits[1]):
return False
return True
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 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 getSequence(self, unknown='???'):
mapping = {}
for coupling in self:
shift1, shift2 = coupling.getType().shift
if not mapping.has_key(int(coupling) + shift1):
mapping[int(coupling) + shift1] = coupling.residues[0]
if not mapping.has_key(int(coupling) + shift2):
mapping[int(coupling) + shift2] = coupling.residues[1]
keys = mapping.keys()
if unknown != None:
missing = 0
for i in range(min(keys) + 1, max(keys)):
if not mapping.has_key(i):
mapping[i] = unknown
missing += 1
if missing:
loki.info('Missing %d residue(s) in the sequence.' % missing)
sequence = []
for i in range(min(keys), max(keys) + 1):
if mapping.has_key(i):
sequence.append(mapping[i])
return sequence
def getSequence(self, unknown='???'):
mapping = {}
for coupling in self:
shift1, shift2 = coupling.getType().shift
if not mapping.has_key(int(coupling) + shift1):
mapping[int(coupling) + shift1] = coupling.residues[0]
if not mapping.has_key(int(coupling) + shift2):
mapping[int(coupling) + shift2] = coupling.residues[1]
keys = mapping.keys()
if unknown != None:
missing = 0
for i in range(min(keys) + 1, max(keys)):
if not mapping.has_key(i):
mapping[i] = unknown
missing += 1
if missing:
loki.info('Missing %d residue(s) in the sequence.' % missing)
sequence = []
for i in range(min(keys), max(keys) + 1):
if mapping.has_key(i):
sequence.append(mapping[i])
return sequence
def writeMacro(self, size):
"""
Write all the required CYANA-commands into a macro.
"""
loki.info('A new Cyana macro required for %d structures.'%size)
outf = open(self.name+'.cya', 'w')
outf.write('cyanalib\n')
outf.write('readdata %s\n'%self.name)
# all angles in given amino acids as well as all omegas should be fixed
if self.fixed_angles:
outf.write('angle select *\n')
outf.write('angle fix\n')
outf.write('angle select -OMEGA\n')
for fix in self.fixed_angles:
outf.write('angle select -%s\n' % fix)
outf.write('angle free\n')
outf.write('read pdb %s\n' % self.name)
outf.write('calc_all %d %s\n'% (size, self.__calc_end__))
outf.write('write_all %s- pdb\n'%self.name)
# this could be used to find out the end seed
# outf.write('system echo $seed > %s.seed'%self.name)
outf.close()
self.__last_macro_size__ = size
def anneal(self, amount, snippets=None, max_temp=4.0, min_temp=0.9,
steps=5000):
"""
Anneal.
"""
amount = int(amount)
if snippets is None:
snippets = amount
else:
snippets = int(snippets)
max_temp = float(max_temp)
min_temp = float(min_temp)
steps = int(steps)
if snippets > amount:
loki.warn('Snippet size larger than total amount. '
'Running in one go.')
snippets = amount
# Current version of Cyana (2.1?) seems to be broken as tend is not
# supported by anneal. FIXME when corrected.
# self.__calc_end__ = 'anneal thigh=%1.3f tend=%1.3f steps=%d'%( \
# max_temp, min_temp, steps)
self.__calc_end__ = 'anneal thigh=%1.3f steps=%d'%( \
max_temp, steps)
if len(str(amount)) > self.tally_digits:
self.tally_digits = len(str(amount))
loki.info('--- Anneal ---\nthigh=%1.3f tend=%1.3f steps=%d\n'%( \
max_temp, min_temp, steps) + '-'*14)
done = 0
while done < amount:
if amount-done > snippets:
batch = snippets
else:
batch = amount - done
self.run(batch)
done += batch
loki.info('%d structures ready'%done)
loki.info('all done. Thank you for all the fish.')
def __init__(self, input, output=None, fixed_angles=None, rg_limits=None,
use_limits=True, seed=None, state=None, jump=None, tally=0,
tally_digits=3, name=None, verbose=False, debug=False):
# store and/or process inputs
self.input = str(input)
self.rg_limits = rg_limits
self.use_limits = bool(use_limits)
self.tally = int(tally)
self.tally_digits = int(tally_digits)
if output != None:
self.output = str(output)
else:
self.output = self.input + '-'
self.fixed_angles = fixed_angles
if fixed_angles != None:
if type(fixed_angles) != list:
if type(fixed_angles) == tuple:
self.fixed_angles = list(fixed_angles)
else:
self.fixed_angles = [fixed_angles]
for i in range(len(self.fixed_angles)):
if type(self.fixed_angles[i]) in [list, tuple]:
lo, hi = str(self.fixed_angles[i][0]), \
str(self.fixed_angles[i][1])
elif re.search('([0-9]+).+([0-9]+)', str(self.fixed_angles[i])):
lo, hi = re.search('([0-9]+).+([0-9]+)', \
str(self.fixed_angles[i])).groups()
else:
lo = hi = str(self.fixed_angles[i])
self.fixed_angles[i] = '%s..%s'%(lo,hi)
if name is None:
self.name = 'temp-%d'%os.getpid()
else:
self.name = str(name)
if debug: loki.setLevel(logging.DEBUG)
elif verbose: loki.setLevel(logging.INFO)
# check that required input files exist
if not os.path.isfile(self.input+'.seq'):
raise ArgumentError, ('No sequence file found.', 'Cyana')
if self.fixed_angles and not os.path.isfile(self.input + '.pdb'):
raise ArgumentError, ('No model PDB file found for angle fixes.',
'Cyana')
# setup temporary files
os.system('cp -f %s.seq %s.seq'%(self.input, self.name))
loki.info('Readied the sequence file for further use.')
if self.use_limits:
for suffix in ['lol', 'upl', 'aco', 'xplor']:
if os.path.isfile(self.input + '.' + suffix):
os.system('cp -f %s.%s %s.%s'%(self.input, suffix,
self.name, suffix))
loki.info("Readied a '%s' file for further use."%suffix)
if self.fixed_angles:
os.system('cp -f %s.pdb %s.pdb'%(self.input, self.name))
# initialise the random generator
self.randgen = Random(seed)
if state == None:
if jump != None:
if sys.version < '2.2':
loki.warn('Python older than 2.2. Problems may arise.')
elif sys.version > '2.2' and sys.version < '2.3':
# this should provide enough room for each run to be in
# unique state space
self.randgen.jumpahead(jump*self.amount*1.1)
else:
self.randgen.jumpahead(jump)
else:
self.randgen.setstate(state)
self.__last_macro_size__ = None
def run(self, txt=''):
loki.info('arguments: %s'%txt)
os.system('%s %s'%(self.command, txt))
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
