def build_multifasta(file_name, sequenceList, force=False):
newFasta = File(file_name, 'w', overwrite=force)
file_dsc = newFasta.descriptor
for sequence in sequenceList:
file_dsc.write(sequence.format('FASTA') + "\n")
newFasta.close()
return Fasta(fasta_file=newFasta.full)
def build(file_name, sequenceID, sequence, force=False):
newFasta = File(file_name, 'w', overwrite=force)
newSeq = Sequence(seqID=sequenceID, sequence=sequence)
file_dsc = newFasta.descriptor
file_dsc.write(newSeq.format('FASTA'))
newFasta.close()
return Fasta(fasta_file=newFasta.full)
def format2file(self, filename, extension='pdb', center=False):
if extension not in ('pdb', 'js'):
raise AttributeError('Not accepted extension')
structure = File('.'.join([filename, extension]), 'w')
if extension == 'pdb': structure.write(self.pdb_format(center=center))
elif extension == 'js': structure.write(self.js_format(center=center))
structure.close()
def pdb_file(self, value):
"""
Sets a PDB file if none has been given
@raise UsedAttributeError
"""
if self._pdb_file is not None:
raise AttributeError(
"The PDB object is loaded from file {0}. To load the new file {1} create a new PDB object"
.format(self._pdb_file.full, value))
if isinstance(value, File):
self._pdb_file = value
else:
self._pdb_file = File(file_name=value, type='r')
def __init__(self, cif_file):
self._file = File(file_name=cif_file, action='r')
self.__name__ = 'databases.PDBeChem' # This must be included in every class for the SBIglobals.alert()
self._id = None
self._name = None
self._type = None
self._formula = None
self._parent = None
self._weight = None
self._fcharge = None
self._code1l = None
self._flformula = {}
self._parse()
self._decompose_formula()
def __init__(self, database, search_type = 'prot'):
#Search Type Check
if search_type not in set(['prot','nucl']):
raise BE(-10)
self._search_type = search_type
#Blast executable configuration
self._configurator = ConfigParser.RawConfigParser(allow_no_value=True)
self._configurator.read(os.getenv('SBI_CONFIG_FILE',default_configuration_file))
self._exe = Executable(executable = self._configurator.get('blast','executable'),
path = self._configurator.get('blast','path'),
variable_path = self._configurator.get('blast','variable_path'))
#Database Configuration
self._database = self._check_database(os.path.abspath(database))
if os.path.isfile(self._database.file.full + ".idx"):
self._idx = File(file_name = self._database.file.full + ".idx", action = 'r')
else:
self._idx = None
#Adding fixed blast parameters
self._exe.add_attribute(self._database.file.full, '-db')
self._exe.add_attribute('5', '-outfmt')
self._exe.add_parameter('-lcase_masking')
SBIglobals.alert('debug', self, 'New Blast Executable created.\nBlast executable at {0}\n'.format(self._exe.full_executable))
self._selfHit = False
self._hitIDformat = 'single'
self._overwritte = False
self._clean_files = True
def make_PDBseq(self, log_file, resolution_threshold=None):
if not self.has_local:
raise NameError(
'A local PDB database must be defined to do create a PDBseq database.'
)
outdir = self.PDBseq if self.PDBseq is not None else os.curdir
Path.mkdir(self.PDBseq)
fasta_file = File(file_name=os.path.join(outdir, 'PDBseq.fa'),
action='w',
overwrite=True)
fasta_fd = fasta_file.descriptor
idx_file = File(file_name=os.path.join(outdir, 'PDBseq.fa.idx'),
action='w',
overwrite=True)
idx_fd = idx_file.descriptor
# if resolution_threshold is not None:
# filtered_file_name = self.get_PDBseq_filtered(resolution_threshold)
# filtered_file = File(file_name = filtered_file_name, action = 'w', overwrite = True)
# filtered_fd = filtered_file.descriptor
# resolutions = self.get_resolutions(resolution_threshold = resolution_threshold)
log_file = File(file_name=log_file, action='w', overwrite=True)
log_idx = log_file.descriptor
for pdb_file in self.localPDBs:
log_idx.write("Reading File: {0}\n".format(pdb_file))
newPDB = PDB(pdb_file=pdb_file, dehydrate=True)
fasta_idx = newPDB.FASTA_IDX(nucleotide=False)
if len(fasta_idx['FASTA']) != len(fasta_idx['IDX']):
log_idx.write(
'ERROR!!!!! Number of fastas and indexes are different for pdb {0}!!\n'
.format(newPDB.id))
if len(fasta_idx['FASTA']) > 0:
log_idx.write('\tPrinting FASTA and IDX...\n')
else:
log_idx.write('\tProblably just a nucleotide PDB...\n')
for c in range(len(fasta_idx['FASTA'])):
sequence = fasta_idx['FASTA'][c].split('\n')[1]
sequence = sequence.replace('X', '').replace('x', '')
if len(sequence) > 0:
fasta_fd.write(fasta_idx['FASTA'][c] + "\n")
if resolution_threshold is not None and newPDB.id in resolutions and not newPDB.is_all_ca:
filtered_fd.write(fasta_idx['FASTA'][c] + "\n")
idx_fd.write(fasta_idx['IDX'][c] + "\n")
del (newPDB)
#CLOSE & END
fasta_file.close()
idx_file.close()
if resolution_threshold is not None:
filtered_fd.close()
def _process(self):
go_dic = {}
parseFile = File(os.path.join(self.local, self._gfile), 'r')
go = None
for line in parseFile.descriptor:
line = re.sub('\'', '\\\'', line)
if line.startswith('[Term]'):
if go is not None:
go_dic[go.id] = go
if line.startswith('id:'):
go = GOterm(id=line.split()[1].strip())
continue
if line.startswith('name:'):
go.name = " ".join(line.split()[1:]).strip()
continue
if line.startswith('namespace:'):
go.namespace = line.split()[1].strip()
continue
if line.startswith('alt_id:'):
go.alt_id.append(line.split()[1].strip())
continue
if line.startswith('is_obsolete:'):
go.obsolete = True
continue
if line.startswith('is_a:'):
go.parents.add(line.split()[1].strip())
continue
if line.startswith('relationship:'):
go.relations.append(
(line.split()[1].strip(), line.split()[2].strip()))
continue
if line.startswith('[Typedef]'):
go_dic[go.id] = go
break
parseFile.close()
for go in go_dic:
go_dic[go].parents = self._search_parents(go_dic, go)
goFile = File(self._gofile, 'w', True)
for go in go_dic:
go_dic[go].parents.add(go)
goFile.write(str(go_dic[go]) + "\n")
goFile.close()
def __init__(self,
pdb_file=None,
dehydrate=False,
header=False,
onlyheader=False,
biomolecule=False):
"""
@type pdb_file: String
@param pdb_file: PDB formated file to read
@raise IOError if pdb_file does not exist and it is not an empty object
"""
if biomolecule or onlyheader:
header = True
self._pdb_file = pdb_file
self._chains = []
self._NMR = False
self._NMR_chains = []
self._chain_id = set()
self._biomol_id = -1 # -1 -> original
# 0 -> symmetry
# >0 -> biomolecule
self._header = None
self._has_prot = False
self._has_nucl = False
self._COMPND = None
if self.pdb_file is not None:
self._pdb_file = File(file_name=self._pdb_file, action='r')
self._read_PDB_file(header=header,
onlyheader=onlyheader,
biomolecule=biomolecule)
if dehydrate:
self.dehydrate()
def _process(self):
tmoFile = File(self._pdbtmfile,'w', True)
for xmlfile in Path.list_files(os.path.join(self._local,'pdbtm/database/'), '*.xml'):
xmldata = TM(pdb = os.path.splitext(os.path.split(xmlfile)[1])[0].upper())
skip_chains = set()
read = False
fdxml = open(xmlfile)
for line in fdxml:
if line.startswith(' <TMRES>'): xmldata.tmres = line
elif line.startswith(' <TMTYPE'): xmldata.tmtype = line
elif line.startswith(' <PDBKWRES'): xmldata.kwres = line
elif line.startswith(' <SIDEDEFINITION'):
m = re.search('Side1="(\S+)"', line)
xmldata.side = m.group(1)
elif line.startswith(' <APPLY_TO_CHAIN'):
m = re.search('NEW_CHAINID=\"(\S{1})\"', line)
if m: skip_chains.add(m.group(1))
elif line.startswith(' <CHAIN '):
m = re.search('CHAINID=\"(\S{1})\" NUM_TM=\"(\d{1})\" TYPE=\"(\S+)\"', line)
if m:
chain, num, tmtype = m.group(1), m.group(2), m.group(3)
if not chain in skip_chains:
cdata = tuple([chain, num, tmtype])
xmldata.set_chain(cdata)
read = True
elif line.startswith(' <REGION ') and read:
m = re.search('pdb_beg=\"(\-*\d+\w*)\"[\s\S]+pdb_end=\"(\-*\d+\w*)\"\s+type=\"(\w{1})\"', line)
ini, end, tmtype = m.group(1), m.group(2), m.group(3)
xmldata.set_chain(cdata, tuple([ini, end, tmtype]))
elif line.startswith(' </CHAIN>'): read = False
fdxml.close()
if len(xmldata.chains) > 0:
tmoFile.write(str(xmldata)+"\n")
tmoFile.close()
def write(self, output_file=None, format='PDB', force=False, clean=False):
"""
Writes the object in a specific format
@type output_file: String
@param output_file: File to write
@type format: String
@param format: Format of the file to print
"""
outfile = File(file_name=output_file, action='w', overwrite=force)
if format == 'PDB':
self._write_PDB_file(pdb_file=outfile, clean=clean)
def _process(self):
enzymes = self._parse_enzclass() + self._parse_enzymedat()
enzymes.sort()
enzFile = File(self._enzfile, 'w', True)
for e in enzymes:
enzFile.write(repr(e) + "\n")
enzFile.close()
def __init__(self, fasta_file):
if isinstance(fasta_file, basestring):
self._file = File(file_name=fasta_file, action='r')
elif isinstance(fasta_file, File):
self._file = fasta_file
self._file.action = 'r'
else:
raise AttributeError('Check the input of the Fasta object')
self._is_multifasta = self._check_multifasta()
self._sequences = []
self._seqfinder = {}
def _process(self):
targets = self._process_targets()
drugs = self._process_drugs(targets)
drugFile = File(self._drugfile, 'w', True)
for d in drugs:
drugFile.write(repr(d) + "\n")
drugFile.close()
def get_PDBeChem(self, chemID):
if self.has_local:
for chem_file in self.localPDBeChems:
newfile = File(file_name=chem_file, action='r')
if newfile.prefix.upper() == chemID.upper():
return chem_file
#If we do not find it in local (or we do not have a local) we search it on the FTP
chem_file = chemID.upper() + '.cif'
source = PDBeChemftp['single'] + chem_file
try:
urllib.urlretrieve(source, chem_file)
except:
return False
return os.path.abspath(chem_file)
def get_PDBs(self, pdbIDset):
if isintance(pdbIDset, str):
warnings.warn(
'For single PDB search the get_PDB function is recomended.')
yield self.get_PDB(pdbIDset)
else:
pdbIDset = set([x.upper() for x in pdbIDset])
if self.has_local:
for pdb_file in self.localPDBs:
newfile = File(file_name=pdb_file, action='r')
if newfile.prefix.lstrip('pdb').upper() in pdbIDset:
yield pdb_file
else:
for pdbID in pdbIDset:
yield self.get_PDB(pdbID)
def get_PDB(self, pdbID):
if self.has_local:
rootdir = os.path.join(self.local, pdbID.lower()[1:3])
for pdb_file in Path.list_files(root=rootdir, pattern='*.ent.gz'):
newfile = File(file_name=pdb_file, action='r')
if newfile.prefix.lstrip('pdb').upper() == pdbID.upper():
return pdb_file
#If we do not find it in local (or we do not have a local) we search it on the FTP
pdb_file = 'pdb' + pdbID.lower() + '.ent.gz'
source = 'ftp://' + PDBftp['address'] + os.path.join(
PDBftp['structures'], pdbID[1:3].lower(), pdb_file)
try:
urllib.urlretrieve(source, pdb_file)
except:
return False
return os.path.abspath(pdb_file)
def get_PDBeChems(self, chemIDset):
if isintance(chemIDset, str):
warnings.warn(
'For single PDBeChem search the get_PDBeChem function is recomended.'
)
yield self.get_PDBeChem(chemIDset)
else:
chemIDset = set([x.upper() for x in chemIDset])
if self.has_local:
for chem_file in self.localPDBeChems:
newfile = File(file_name=chem_file, action='r')
if newfile.prefix.lstrip('pdb').upper() in chemIDset:
yield chem_file
else:
for chemID in chemIDset:
yield self.get_PDBeChem(chemID)
def get_resolutions(self):
# resolutions (-1) are for methods that do not define resolution
resolutions = {}
ftp = ftplib.FTP(PDBftp['address'])
ftp.login()
ftp.cwd(PDBftp['derived'])
resoluIDX = []
ftp.retrlines('RETR ' + PDBftp['resolution'], resoluIDX.append)
ftp.quit()
SBIglobals.alert('debug', self,
'Retrieving resolution data from PDB FTP...')
active = False
for line in resoluIDX:
if line.startswith('-'):
active = True
continue
if active and len(line.strip()) > 0:
data = [x.strip() for x in line.split(';')]
if len(data[1]) > 0:
SBIglobals.alert(
'debug', self,
'\tResolution for {0[0]} is {0[1]}...'.format(data))
# if resolution_threshold is None:
resolutions[data[0]] = data[1]
#rsync is accumulative, we might have structures that are not in the residu.idx anymore.. must check
for pdb_file in self.localPDBs:
newfile = File(file_name=pdb_file, action='r')
pdbid = newfile.prefix.lstrip('pdb').upper()
if pdbid not in resolutions:
pdbobj = PDB(pdb_file=pdb_file, header=True, onlyheader=True)
SBIglobals.alert(
'debug', self,
'\tGrabbing Resolution for {0} is {1}...'.format(
pdbid, pdbobj.header.resolution))
resolutions[pdbid] = pdbobj.header.resolution
return resolutions
class PDBeChem(object):
"""
"""
def __init__(self, cif_file):
self._file = File(file_name=cif_file, action='r')
self.__name__ = 'databases.PDBeChem' # This must be included in every class for the SBIglobals.alert()
self._id = None
self._name = None
self._type = None
self._formula = None
self._parent = None
self._weight = None
self._fcharge = None
self._code1l = None
self._flformula = {}
self._parse()
self._decompose_formula()
"""ATTRIBUTES"""
@property
def id(self):
return self._id
@property
def name(self):
return self._name
@property
def type(self):
return self._type
@property
def formula(self):
return self._formula
@property
def full_formula(self):
return self._flformula
@property
def parent(self):
return self._parent
@property
def weight(self):
return self._weight
@property
def formal_charge(self):
return self._fcharge
@property
def code1(self):
return self._code1l
@property
def code3(self):
return self._id
"""PRIVATE METHODS"""
def _parse(self):
for line in self._file.descriptor:
if line.startswith('_chem_comp.'):
line = line.replace('_chem_comp.', '')
value = line[35:].strip().strip('"')
value = value.replace(' (NON-PREFERRED NAME)', '')
value = value if value != '?' else None
if line.startswith('id'): self._id = value
if line.startswith('pdbx_type'): self._type = value
if line.startswith('formula '): self._formula = value
if line.startswith('formula_weight'): self._weight = value
if line.startswith('pdbx_formal_charge'): self._fcharge = value
if line.startswith('one_letter_code'): self._code1l = value
if line.startswith('name'): self._name = value.upper()
if line.startswith('mon_nstd_parent_comp_id'):
self._parent = set([x.strip() for x in value.split(',')
]) if value is not None else None
if line.startswith(';') and self._name == '':
self._name += line.strip().lstrip(';').upper()
self._file.close()
def _decompose_formula(self):
if self.formula is not None:
data = self.formula.split()
atregex = re.compile('(\D+)(\d*)')
for atom in data:
m = atregex.search(atom)
if m.group(1) in element_dic:
self._flformula[m.group(1)] = m.group(
2) if m.group(2) != '' else 1
"""OVERWRITE INHERITED FUNCTIONS"""
def __str__(self):
if self.code1 is not None and self.parent is not None:
return "[{0.id} - {0.code1} from {0.parent}: {0.weight} - {0.formula} - {0.formal_charge}] {0.name} - {0.type}".format(
self)
elif self.code1 is not None:
return "[{0.id} - {0.code1}: {0.weight} - {0.formula} - {0.formal_charge}] {0.name} - {0.type}".format(
self)
elif self.parent is not None:
return "[{0.id} from {0.parent}: {0.weight} - {0.formula} - {0.formal_charge}] {0.name} - {0.type}".format(
self)
else:
return "[{0.id}: {0.weight} - {0.formula} - {0.formal_charge}] {0.name} - {0.type}".format(
self)
def localTM(self):
tmoFile = File(self._pdbtmfile, 'r')
for tm_line in tmoFile.descriptor:
yield tm_line
def localEnzymes(self):
enzFile = File(self._enzfile, 'r')
for enz_line in enzFile.descriptor:
yield enz_line
def localTrembls(self):
tblFile = File(self._trbfile, 'r')
for uni_line in tblFile.descriptor:
yield uni_line
def descriptions(self):
dscFile = File(self._desc, 'r')
for dsc_line in dscFile.descriptor:
if not dsc_line.startswith('#'):
yield dsc_line
def localGOs(self):
goFile = File(self._gofile, 'r')
for go_line in goFile.descriptor:
yield go_line
def relations(self):
relFile = File(self._rel, 'r')
for rel_line in relFile.descriptor:
if not rel_line.startswith('#'):
yield rel_line
class PDB(StorableObject):
"""
A {PDB} is a collection of {Chain}
"""
def __init__(self,
pdb_file=None,
dehydrate=False,
header=False,
onlyheader=False,
biomolecule=False):
"""
@type pdb_file: String
@param pdb_file: PDB formated file to read
@raise IOError if pdb_file does not exist and it is not an empty object
"""
if biomolecule or onlyheader:
header = True
self._pdb_file = pdb_file
self._chains = []
self._NMR = False
self._NMR_chains = []
self._chain_id = set()
self._biomol_id = -1 # -1 -> original
# 0 -> symmetry
# >0 -> biomolecule
self._header = None
self._has_prot = False
self._has_nucl = False
self._COMPND = None
if self.pdb_file is not None:
self._pdb_file = File(file_name=self._pdb_file, action='r')
self._read_PDB_file(header=header,
onlyheader=onlyheader,
biomolecule=biomolecule)
if dehydrate:
self.dehydrate()
#
# ATTRIBUTES
#
@property
def pdb_file(self):
"""
PDB file name
@rtype: String
"""
return self._pdb_file
@pdb_file.setter
def pdb_file(self, value):
"""
Sets a PDB file if none has been given
@raise UsedAttributeError
"""
if self._pdb_file is not None:
raise AttributeError(
"The PDB object is loaded from file {0}. To load the new file {1} create a new PDB object"
.format(self._pdb_file.full, value))
if isinstance(value, File):
self._pdb_file = value
else:
self._pdb_file = File(file_name=value, type='r')
@property
def chain_identifiers(self):
return self._chain_id
@property
def id(self):
return self._chains[0].pdb
@property
def chains(self):
"""
List of {Chain} contained in the PDB w/out NMR replicas
@rtype: List of {Chain}
"""
return self._chains
@property
def proteins(self):
"""
List of {ProteinChain} contained in the PDB w/out NMR replicas
@rtype: List of {ProteinChain} (iterator)
"""
for chain in self.chains:
if isinstance(chain, ChainOfProtein):
yield chain
@property
def nucleotides(self):
"""
List of {NucleotideChain} contained in the PDB w/out NMR replicas
@rtype: List of {NucleotideChain} (iterator)
"""
for chain in self.chains:
if isinstance(chain, ChainOfNucleotide):
yield chain
@property
def non_standard_chains(self):
"""
List of non {NucleotideChain}/ non {ProteinChain} contained in the PDB w/out NMR replicas
@rtype: List of non {NucleotideChain}/ non {ProteinChain} (iterator)
"""
for chain in self.chains:
if not isinstance(chain, ChainOfNucleotide) and not isinstance(
chain, ChainOfProtein):
yield chain
@property
def all_models(self):
"""
List of {Chain} contained in the PDB w/ NMR replicas
@rtype: List of {Chain}
"""
return self._chains + self._NMR_chains
@property
def header(self):
if self._header is None:
return ''
else:
return self._header
@property
def biomolecule_identifier(self):
return self._biomol_id
#
# COMPLEX GETTERS & SETTERS
#
def get_chain_by_id(self, id):
"""
Returns a chain according to its id or None if no chain with that id is found
@rtype: {Chain}
"""
for chain in self._chains:
if chain.chain == id:
return chain
return None
def add_chain(self, chain, NMR=False):
"""
Adds a new chain to the PDB
"""
if not NMR:
self._chains.append(chain)
elif NMR and self._NMR:
self._NMR_chains.append(chain)
self._chain_id.add(chain.chain)
def add_chains(self, chains, NMR=False):
"""
Adds a new chains to the PDB
"""
for chain in chains:
self.add_chain(chain=chain, NMR=NMR)
def _get_chain_position_by_id(self, id):
"""
Returns the position in the chain array where the chain is
@rtype: Integer
"""
for x in range(len(self._chains)):
if self._chains[x].chain == id:
return x
return None
#
# BOOLEANS
#
@property
def is_NMR(self):
"""
Identifies if the PDB contains NMRs
@rtype: Boolean
"""
return self._NMR
def chain_exists(self, chain):
"""
Confirms if a given chain exists in the PDB
@rtype: Boolean
"""
return chain in self._chain_id
@property
def has_protein(self):
"""
Checks if the PDB contains a protein (not only)
@rtype: Boolean
"""
return self._has_prot
@property
def has_nucleotide(self):
"""
Checks if the PDB contains a nucleotide chain (not only)
@rtype: Boolean
"""
return self._has_nucl
@property
def repeated_chain_ids(self):
"""
Checks if more than one {Chain} has the same assigned ID
@rtype: Boolean
"""
return len(self._chain_id) < len(self._chains)
@property
def is_all_ca(self):
for p in self.proteins:
if p.is_only_ca():
return True
return False
#
# METHODS
#
def dehydrate(self):
recheck_chains = False
for c in self.chains:
c.dehydrate()
if c.is_empty:
recheck_chains = True
if recheck_chains:
c = []
for ch in self.chains:
if not ch.is_empty:
c.append(ch)
else:
self._chain_id.remove(ch.chain)
self._chains = c
def duplicate(self, hetero=True, water=False, NMR=False):
"""
Returns a {PDB} identical to the original but as a new object
@rtype: {PDB}
"""
new_PDB = PDB()
new_PDB.pdb_file = self.pdb_file
for chain in self.chains:
new_PDB.add_chain(
chain=chain.duplicate(hetero=hetero, water=water))
if NMR:
for chain in self._NMR_chains:
new_PDB.add_chain(chain=chain.duplicate(hetero=hetero,
water=water),
NMR=True)
new_PDB._NMR = self._NMR
new_PDB._has_prot = self._has_prot
new_PDB._has_nucl = self._has_nucl
return new_PDB
def apply_symmetry_matrices(self):
"""
Only works if the PDB file is an original PDB file
or the matrices have been added in the correct PDB format
@rtype: {PDB}
"""
if self._header is None:
self._read_PDB_file(header=True, onlyheader=True)
return self._apply_matrix(matrix=self.header.symmetry_matrix)
def apply_biomolecule_matrices(self, keepchains=False, water=True):
"""
Only works if the PDB file is an original PDB file or
the matrices have been added in the correct PDB format
@rtype: {PDB}
"""
if self._header is None:
self._read_PDB_file(header=True, onlyheader=True)
PDB_list = []
for matrix in self.header.biomolecules:
PDB_list.append(
self._apply_matrix(matrix=matrix,
keepchains=keepchains,
water=water))
return PDB_list
def _apply_matrix(self, matrix, keepchains=False, water=True):
new_PDB = PDB()
new_PDB._biomol_id = matrix.identifier
for chain in self.chains:
if chain.chain in matrix.chains:
for mat in matrix.matrices:
new_chain = chain.duplicate(water=water)
new_chain.reposition(matrix=mat.matrix, vector=mat.vector)
if len(new_chain) >= 1:
new_PDB.add_chain(chain=new_chain)
if not keepchains:
new_PDB.tmpclean(cluster_by_alternative_id=True)
return new_PDB
def clean(self):
first_atom = 1
for c in self.chains:
c.clean(initatom=first_atom)
first_atom = c.last_residue.last_atom_number + 1
def tmpclean(self, cluster_by_alternative_id=False):
"""
Makes a clean version of the PDB, rechaining in order and renumerating atoms.
Renumbering residues is optional
"""
pchainsIDs = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz1234567890"
chainsIDs = ""
chainsNIDs = ""
chainID = 0
atom_count = 1
for x in range(len(pchainsIDs)):
if not self.chain_exists(chain=pchainsIDs[x]):
chainsIDs += pchainsIDs[x]
else:
chainsNIDs += pchainsIDs[x]
chain_change = len(self) <= len(chainsIDs)
for chain in self.chains:
if (not chain.chain in chainsNIDs) and chain_change:
self._chain_id.add(chain.chain)
chain.chain = chainsIDs[chainID]
chainID += 1
self._chain_id.add(chain.chain)
if cluster_by_alternative_id:
if self._COMPND is None:
self._COMPND = {}
if not self._COMPND.has_key(chain.alternative_id):
self._COMPND.setdefault(chain.alternative_id,
[]).append(
chain.alternative_id)
self._COMPND[chain.alternative_id].append(chain.chain)
else:
chainsNIDs = chainsNIDs.replace(chain.chain, '')
chain.renumerate_atoms(init=atom_count)
atom_count += (chain.atom_length)
def fuse_chains(self, chains_ids):
"""
Fuses several chains into the first one.
It will not allow to fuse different structural chains.
It does not alter the {PDB}, but provides a new one
@rtype: {Chain}
@raise AttributeError if:
a) A given chain ID is not present
b) Try to fuse different structural chains
"""
if len(self._chain_id.intersection(set(chains_ids))) < len(chains_ids):
raise AttributeError(
"Some of the given chains to fues do not exist")
error_counter = 0
error_control = [False, False]
new_PDB = PDB()
for c in chains_ids:
chain = self.get_chain_by_id(id=c)
new_PDB.add_chain(chain=chain.duplicate())
if isinstance(chain, ChainOfProtein) and not error_control[0]:
error_counter += 1
error_control[0] = True
elif isinstance(chain, ChainOfNucleotide) and not error_control[1]:
error_counter += 1
error_control[1] = True
if error_counter == 2:
raise AttributeError(
"Fuse different kinds of structural chain is not possible\n"
)
init_chain_num = new_PDB.chains[0].last_residue.number
for x in range(1, len(new_PDB.chains)):
new_PDB.chains[x].renumerate_residues(init=init_chain_num + 1)
init_chain_num = new_PDB.chains[0].last_residue.number
new_PDB.chains[0].fuse(chain=new_PDB.chains[x])
return_PDB = PDB()
return_PDB.add_chain(chain=new_PDB.chains[0])
return return_PDB
# def calculate_dssp(self, out_dir = None, store = True):
# """
# Executes DSSP and assigns the prediction to each chain
# @param out_dir: directory to save the output
# @defaut out_dir: None
# @param store: Save the dssp output(?)
# """
# for chain in self.proteins:
# if out_dir is None:
# pdb_file = chain.globalID + ".pdb2dssp"
# dssp_file = chain.globalID + ".dssp"
# else:
# Path.mkdir(newdir = out_dir)
# pdb_file = os.path.join(os.path.abspath(out_dir), chain.globalID + ".pdb2dssp")
# dssp_file = os.path.join(os.path.abspath(out_dir), chain.globalID + ".dssp")
# pdb_fd = open(pdb_file, 'w')
# pdb_fd.write(chain.PDB_format())
# pdb_fd.close()
# dssp_calc = DSSPexec(pdb_file = pdb_file, dssp_file = dssp_file,
# chain = chain, store = store)
def rotate(self, matrix=None):
"""
Rotates each {Chain} according to a given matrix
@type matrix: numpy.matrix
"""
if matrix is None:
matrix = numpy.identity(3, float)
for chain in self.all_models:
chain.rotate(matrix=matrix)
def translate(self, vector=None):
"""
Translates each {Chain} according to a translational vector
@type vector: numpy.array
"""
if vector is None:
vector = numpy.zeros(3, float)
for chain in self.all_models:
chain.translate(vector=vector)
def reposition(self, matrix=None, vector=None):
"""
Rotates and Translates each {Chain} according to a matrix and a translational vector
@type matrix: numpy.matrix
@type vector: numpy.array
"""
if matrix is None:
matrix = numpy.identity(3, float)
if vector is None:
vector = numpy.zeros(3, float)
for chain in self.all_models:
chain.reposition(matrix=matrix, vector=vector)
# def calculate_protein_heteroatom_contacts(self, distance = 6):
# """
# Returns a {HeteroatomContacts} list with the contacts between a protein and its heteroatoms
# at a maximum given distance
# @type distance: Integer
# @rtype: list of {HeteroatomContacts}
# """
# data = []
# for protein in self.proteins:
# data.append(HeteroatomContacts(chain = protein, max_distance = distance))
# return data
#
# OVERRIDE PARENT'S FUNCTIONS
#
@staticmethod
def read(input_file, format='PDB'):
"""
Reads a file of data in a specific format and returns the object
@type input_file: String
@param input_file: File to read
@type format: String
@param format: Format of the file to read
"""
if format == 'PDB':
pdb = PDB(pdb_file=input_file)
return pdb
def write(self, output_file=None, format='PDB', force=False, clean=False):
"""
Writes the object in a specific format
@type output_file: String
@param output_file: File to write
@type format: String
@param format: Format of the file to print
"""
outfile = File(file_name=output_file, action='w', overwrite=force)
if format == 'PDB':
self._write_PDB_file(pdb_file=outfile, clean=clean)
#
# IO
#
def _read_PDB_file(self,
header=False,
onlyheader=False,
biomolecule=False):
"""
Process and load crystal data from a PDB formated file
"""
from parse_pdb import read_PDB_file, read_PDB_header
if header:
read_PDB_header(self)
self._pdb_file.close()
if not onlyheader:
# read_PDB_file(self, biomolecule=biomolecule)
read_PDB_file(self)
self._pdb_file.close()
# def _represent_COMPND(self):
# if self._COMPND is None: return ''
# data = []
# mol_counter = 1
# for chain in self._COMPND:
# data.append("COMPND MOL_ID: %d;" %mol_counter)
# data.append("COMPND 2 CHAIN: " + ",".join(self._COMPND[chain]) + ";")
# if len(self._biomolecA) > 0:
# matrices = []
# for mat in self._biomolecA:
# if mat[1] == chain: matrices.append(str(mat[0]))
# data.append("COMPND 3 MATRICES: " + ",".join(sorted(matrices)))
# mol_counter += 1
# return "\n".join(data) + "\n"
def _write_PDB_file(self, pdb_file, clean=False):
"""
Print a crystal into a PDB formated file
"""
out_fd = pdb_file.descriptor
# out_fd.write(self._represent_COMPND())
out_fd.write(self.PDB_format(clean=clean) + "\n")
pdb_file.close()
def PDB_format(self, clean=False, terminal=True):
"""
Strings a {PDB} in PDB format
@rtype: String
"""
lines = []
if clean:
self.clean()
for chain in self._chains:
lines.append(chain.PDB_format(terminal=terminal))
lines.append("END")
return "\n".join(lines)
def FASTA_format(self, gapped=True, protein=True, nucleotide=False):
lines = []
for c in self.chains:
if isinstance(c, ChainOfProtein) and protein:
lines.append(">{0}\t{1}".format(c.globalID,
c.aminoacids[0].identifier))
if gapped:
lines.append("{0}".format(c.gapped_protein_sequence))
else:
lines.append("{0}".format(c.protein_sequence))
if isinstance(c, ChainOfNucleotide) and nucleotide:
lines.append(">{0}\t{1}".format(c.globalID,
c.nucleotides[0].identifier))
if gapped:
lines.append("{0}".format(c.gapped_nucleotide_sequence()))
else:
lines.append("{0}".format(c.nucleotide_sequence()))
if len(lines) == 0:
return ""
else:
return "\n".join(lines) + "\n"
def IDX_format(self, protein=True, nucleotide=False):
lines = []
for c in self.chains:
if isinstance(c, ChainOfProtein) and protein:
lines.append(">{0}\t{1}".format(c.globalID, c.protein_idx))
if isinstance(c, ChainOfNucleotide) and nucleotide:
lines.append(">{0}\t{1}".format(c.globalID,
c.nucleotide_idx()))
if len(lines) == 0:
return ""
else:
return "\n".join(lines) + "\n"
def FASTA_IDX(self, protein=True, nucleotide=False):
data = {}
data.setdefault('FASTA', [])
data.setdefault('IDX', [])
for c in self.chains:
if isinstance(c, ChainOfProtein) and protein:
data['FASTA'].append(">{0}\n{1}".format(
c.globalID, c.gapped_protein_sequence))
data['IDX'].append(">{0}\t{1}".format(c.globalID,
c.protein_idx))
if isinstance(c, ChainOfNucleotide) and nucleotide:
data['FASTA'].append(">{0}\n{1}".format(
c.globalID, c.gapped_nucleotide_sequence()))
data['IDX'].append(">{0}\t{1}".format(c.globalID,
c.nucleotide_idx()))
return data
#
# OVERRIDE DEFAULT METHODS
#
def __len__(self):
return len(self._chains)
def get_FASTA_IDX_by_names_to_file(self, names, outfile):
fastafile = Fasta(self.PDBseq)
selectedfasta = fastafile.retrieve(copy.deepcopy(names))
output_fasta = File(outfile, 'w')
for sequence in selectedfasta:
output_fasta.write(sequence.format('FASTA') + "\n")
output_fasta.close()
idxfile = self.PDBseq + '.idx'
output_idx = File(outfile + '.idx', 'w')
input_idx = File(idxfile, 'r')
for line in input_idx.descriptor:
info = line.split()
pdbname = info[0][1:]
if pdbname in names:
output_idx.write(line)
input_idx.close()
output_idx.close()
class CDhitList(StorableObject):
def __init__(self, cdhitfile):
self._clusters = []
self._allseqids = {}
self._file = File(file_name=cdhitfile)
self._parse_file()
@property
def clusters(self):
return self._clusters
def get_cluster4sequence(self, sequence):
if sequence in self._allseqids:
return self._clusters[self._allseqids[sequence]]
else:
return None
def is_in_cluster(self, sequence):
c = self.get_cluster4sequence(sequence)
if c is None: return 'N'
else: return 'M' if c.is_master(sequence) else 'H'
def add_cluster(self, cluster):
self._clusters.append(cluster)
def add_sequence2cluster(self, sequence, clusterid=None):
if clusterid is None:
self.clusters[-1].add_sequence(sequence)
self._allseqids[sequence.name] = len(self.clusters) - 1
else:
for x in range(len(self._clusters)):
if self._clusters[x].identifier == clusterid:
self._clusters[x].add_sequence(sequence)
self._allseqids[sequence.name] = x
break
def dictionary_role_summary(self):
data = {'master': [], 'homolog': []}
for c in self.clusters:
data['master'].append(c.master.name)
for s in c.sequences:
data['homolog'].append(s)
return data
def _parse_file(self):
for line in self._file.descriptor:
if line.startswith('>'):
c = CDhit(clusterid=line.split()[-1].strip())
self.add_cluster(c)
else:
data = line.split()[1:]
h = CDhitHomolog(name=data[1],
length=data[0],
homology=data[-1])
self.add_sequence2cluster(sequence=h)
self._file.close()
def __repr__(self):
text = []
for c in self.clusters:
text.append('{0}'.format(c))
return '\n'.join(text)
def __init__(self, cdhitfile):
self._clusters = []
self._allseqids = {}
self._file = File(file_name=cdhitfile)
self._parse_file()