def _parse_h_layer(self, layer):
chunks = self._split_h_layer(layer)
for chunk in chunks:
try:
head, tail = chunk.split('H')
except Exception, e:
raise oasa_inchi_error(
"error in hydrogen layer - missing H symbol")
num_h = tail and int(tail) or 1
vertices = []
for p in head.split(","):
if "-" in p:
try:
a, b = map(int, p.split("-"))
except Exception, e:
raise oasa_inchi_error(
"error in hydrogen layer - non-number character(s) present in atom range specification"
)
vertices.extend(range(a, b + 1))
else:
try:
vertices.append(int(p))
except Exception, e:
raise oasa_inchi_error(
"error in hydrogen layer - non-number character(s) present in atom specification"
)
def generate_inchi_and_inchikey(m,
program=None,
fixed_hs=True,
ignore_key_error=False):
"""ignore the case when InChIKey cannot be generated for some reason
(no mhash library and old InChI program)"""
if not program:
import config
program = config.Config.inchi_binary_path
mf = molfile.mol_to_text(m)
if os.name == 'nt':
options = "/AUXNONE /STDIO /Key" + (fixed_hs and " /FixedH" or "")
else:
options = "-AUXNONE -STDIO -Key" + (fixed_hs and " -FixedH" or "")
#print options
command = [os.path.abspath(program)] + options.split()
text = _run_command(command, mf)
inchi = ""
key = ""
warnings = []
for line in text.splitlines():
if line.startswith("Warning"):
warnings.append(line.strip() + "\n")
elif line.startswith("End of file detected"):
pass
elif line.startswith("InChIKey="):
key = line.strip()[9:]
break
elif line.startswith("InChI="):
inchi = inchi + line.strip()
elif line.startswith("Error"):
break
if not inchi:
raise oasa_inchi_error("InChI program did not create any output InChI")
if not key:
# probably old version of the InChI software
try:
import inchi_key
except ImportError:
if ignore_key_error:
key = None
else:
raise oasa_inchi_error(
"InChIKey could not be generated - inchi_key module failed to load properly."
)
else:
key = inchi_key.key_from_inchi(inchi)
return inchi, key, warnings
def read_inchi( self, text):
try:
self._read_inchi( text)
except AssertionError:
raise oasa_inchi_error( "Localization of bonds, charges or movable hydrogens failed")
except:
raise
def read_inchi(self, text):
try:
self._read_inchi(text)
except AssertionError:
raise oasa_inchi_error(
"Localization of bonds, charges or movable hydrogens failed")
except:
raise
def generate_inchi_and_inchikey( m, program=None, fixed_hs=True, ignore_key_error=False):
"""ignore the case when InChIKey cannot be generated for some reason
(no mhash library and old InChI program)"""
if not program:
import config
program = config.Config.inchi_binary_path
mf = molfile.mol_to_text( m)
if os.name == 'nt':
options = "/AUXNONE /STDIO /Key" + (fixed_hs and " /FixedH" or "")
else:
options = "-AUXNONE -STDIO -Key" + (fixed_hs and " -FixedH" or "")
#print options
command = [os.path.abspath( program)] + options.split()
text = _run_command( command, mf)
inchi = ""
key = ""
warnings = []
for line in text.splitlines():
if line.startswith( "Warning"):
warnings.append(line.strip() + "\n")
elif line.startswith( "End of file detected"):
pass
elif line.startswith( "InChIKey="):
key = line.strip()[9:]
break
elif line.startswith( "InChI="):
inchi = inchi + line.strip()
elif line.startswith( "Error"):
break
if not inchi:
raise oasa_inchi_error( "InChI program did not create any output InChI")
if not key:
# probably old version of the InChI software
try:
import inchi_key
except ImportError:
if ignore_key_error:
key = None
else:
raise oasa_inchi_error( "InChIKey could not be generated - inchi_key module failed to load properly.")
else:
key = inchi_key.key_from_inchi( inchi)
return inchi, key, warnings
def _parse_h_layer( self, layer):
chunks = self._split_h_layer( layer)
for chunk in chunks:
try:
head, tail = chunk.split( 'H')
except Exception, e:
raise oasa_inchi_error( "error in hydrogen layer - missing H symbol")
num_h = tail and int( tail) or 1
vertices = []
for p in head.split( ","):
if "-" in p:
try:
a, b = map( int, p.split("-"))
except Exception, e:
raise oasa_inchi_error( "error in hydrogen layer - non-number character(s) present in atom range specification")
vertices.extend( range( a, b+1))
else:
try:
vertices.append( int( p))
except Exception, e:
raise oasa_inchi_error( "error in hydrogen layer - non-number character(s) present in atom specification")
def get_lowest_numbered_neighbor( atom, verbotten_atom):
neighs = [(n.properties_.get('inchi_number',1000000), n)
for n in atom.neighbors
if n is not verbotten_atom and "inchi_number" in n.properties_]
if neighs:
neighs.sort( reverse=True)
return neighs[0][1]
else:
# we take the only one that is there (if any)
neighs = [n for n in atom.neighbors if n is not verbotten_atom]
if neighs:
return neighs[0]
else:
raise oasa_inchi_error( "No neigbors on atom with stereo information!")
def get_lowest_numbered_neighbor(atom, verbotten_atom):
neighs = [
(n.properties_.get('inchi_number', 1000000), n)
for n in atom.neighbors
if n is not verbotten_atom and "inchi_number" in n.properties_
]
if neighs:
neighs.sort(reverse=True)
return neighs[0][1]
else:
# we take the only one that is there (if any)
neighs = [n for n in atom.neighbors if n is not verbotten_atom]
if neighs:
return neighs[0]
else:
raise oasa_inchi_error(
"No neigbors on atom with stereo information!")
def _read_inchi( self, text):
if not text:
raise oasa_inchi_error( "No inchi was given")
self.structure = molecule()
self.layers = self.split_layers( text)
# version support (very crude)
self.version = self._check_version( self.layers[0])
if not self.version:
raise oasa_unsupported_inchi_version_error( self.layers[0])
elif str( self.version[0]) != '1' or str( self.version[1]) != '0':
raise oasa_unsupported_inchi_version_error( self.layers[0])
self.hs_in_hydrogen_layer = self.get_number_of_hydrogens_in_hydrogen_layer()
self.read_sum_layer()
self.read_connectivity_layer()
self._charge_mover = self._move_charge_somewhere_else()
repeat = True
run = 0
# we have to repeat this step in order to find the right positioning of movable hydrogens
while repeat and not self._no_possibility_to_improve:
# cleanup
for h in self._added_hs:
self.structure.remove_vertex( h)
for b in self.structure.edges:
b.order = 1
for v in self.structure.vertices:
v.symbol = v.symbol
v.charge = 0
self.cleanup()
# the code itself
run += 1
assert run < 50
self._deal_with_notorious_groups()
self.process_forced_charges()
self.read_hydrogen_layer( run=run)
self.read_charge_layer()
self.read_p_layer()
self.deal_with_da_bonds()
#self._deal_with_valencies()
self.compensate_for_forced_charges()
self.structure.add_missing_bond_orders()
#self.read_double_bond_stereo_layer()
# here we check out if the molecule seems ok
fvs = [v for v in self.structure.vertices if v.free_valency]
if not fvs and not filter( None, [not v.order for v in self.structure.edges]):
repeat = False
else:
if len( fvs) == 1:
a = fvs[0]
a.symbol = a.symbol # this resets the valency
a.raise_valency_to_senseful_value()
if not a.free_valency:
repeat = False
if repeat and self._no_possibility_to_improve and self.charge:
try:
self._charge_mover.next()
except StopIteration:
pass
else:
self._no_possibility_to_improve = False
run = 0
if repeat and self._no_possibility_to_improve:
## if len( filter( None, [v.free_valency for v in self.structure.vertices])) == 1:
## print
## print [(v.symbol, v.valency, v.free_valency) for v in self.structure.vertices if v.free_valency], filter( None, [not v.order for v in self.structure.edges]), text
## if sum( [v.charge for v in self.structure.vertices]) != self.charge:
## print "Charge problem", sum( [v.charge for v in self.structure.vertices]), self.charge
#pass
raise oasa_inchi_error( "Localization of bonds, charges or movable hydrogens failed")
def _read_inchi(self, text):
if not text:
raise oasa_inchi_error("No inchi was given")
self.structure = molecule()
self.layers = self.split_layers(text)
# version support (very crude)
self.version = self._check_version(self.layers[0])
if not self.version:
raise oasa_unsupported_inchi_version_error(self.layers[0])
elif str(self.version[0]) != '1' or str(self.version[1]) != '0':
raise oasa_unsupported_inchi_version_error(self.layers[0])
self.hs_in_hydrogen_layer = self.get_number_of_hydrogens_in_hydrogen_layer(
)
self.read_sum_layer()
self.read_connectivity_layer()
self._charge_mover = self._move_charge_somewhere_else()
repeat = True
run = 0
# we have to repeat this step in order to find the right positioning of movable hydrogens
while repeat and not self._no_possibility_to_improve:
# cleanup
for h in self._added_hs:
self.structure.remove_vertex(h)
for b in self.structure.edges:
b.order = 1
for v in self.structure.vertices:
v.symbol = v.symbol
v.charge = 0
self.cleanup()
# the code itself
run += 1
assert run < 50
self._deal_with_notorious_groups()
self.process_forced_charges()
self.read_hydrogen_layer(run=run)
self.read_charge_layer()
self.read_p_layer()
self.deal_with_da_bonds()
#self._deal_with_valencies()
self.compensate_for_forced_charges()
self.structure.add_missing_bond_orders()
#self.read_double_bond_stereo_layer()
# here we check out if the molecule seems ok
fvs = [v for v in self.structure.vertices if v.free_valency]
if not fvs and not filter(
None, [not v.order for v in self.structure.edges]):
repeat = False
else:
if len(fvs) == 1:
a = fvs[0]
a.symbol = a.symbol # this resets the valency
a.raise_valency_to_senseful_value()
if not a.free_valency:
repeat = False
if repeat and self._no_possibility_to_improve and self.charge:
try:
self._charge_mover.next()
except StopIteration:
pass
else:
self._no_possibility_to_improve = False
run = 0
if repeat and self._no_possibility_to_improve:
## if len( filter( None, [v.free_valency for v in self.structure.vertices])) == 1:
## print
## print [(v.symbol, v.valency, v.free_valency) for v in self.structure.vertices if v.free_valency], filter( None, [not v.order for v in self.structure.edges]), text
## if sum( [v.charge for v in self.structure.vertices]) != self.charge:
## print "Charge problem", sum( [v.charge for v in self.structure.vertices]), self.charge
#pass
raise oasa_inchi_error(
"Localization of bonds, charges or movable hydrogens failed")
