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better logging added.
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@stsouko
stsouko committed Jan 20, 2021
1 parent 78ce928 commit bdd3674
Showing 1 changed file with 79 additions and 27 deletions.
106 changes: 79 additions & 27 deletions CGRtools/algorithms/standardize.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@
from CachedMethods import class_cached_property
from collections import defaultdict
from itertools import count
from typing import List, TYPE_CHECKING, Union
from typing import List, TYPE_CHECKING, Union, Tuple
from ..containers import query # cyclic imports resolve
from ..containers.bonds import Bond
from ..exceptions import ValenceError
Expand All @@ -34,23 +34,35 @@
class Standardize:
__slots__ = ()

def canonicalize(self: 'MoleculeContainer') -> bool:
def canonicalize(self: 'MoleculeContainer', *,
logging=False) -> Union[bool, List[Tuple[Tuple[int, ...], int, str]]]:
"""
Convert molecule to canonical forms of functional groups and aromatic rings without explicit hydrogens.
:param logging: return log.
"""
k = self.kekule()
s = self.standardize(fix_stereo=False)
s = self.standardize(fix_stereo=False, logging=logging)
h = self.implicify_hydrogens(fix_stereo=False)
t = self.thiele()
if logging:
if k:
s.insert(0, ((), -1, 'kekulized'))
if h:
s.append(((), -1, 'implicified'))
if t:
s.append(((), -1, 'aromatized'))
return s
return k or s or h or t

def standardize(self: Union['MoleculeContainer', 'Standardize'], *, fix_stereo=True, logging=False) -> bool:
def standardize(self: Union['MoleculeContainer', 'Standardize'], *, fix_stereo=True,
logging=False) -> Union[bool, List[Tuple[Tuple[int, ...], int, str]]]:
"""
Standardize functional groups. Return True if any non-canonical group found.
:param logging: return list of fixed atoms with matched rules.
"""
neutralized = self.neutralize(fix_stereo=False)
neutralized = self.neutralize(fix_stereo=False, logging=logging)
hs, log = self.__standardize()
if hs:
if not neutralized:
Expand All @@ -66,23 +78,26 @@ def standardize(self: Union['MoleculeContainer', 'Standardize'], *, fix_stereo=T
self._fix_stereo()
if logging:
if neutralized:
log.append(((), -1, 'neutralized'))
log.append((tuple(neutralized), -1, 'neutralized'))
return log
return True
if neutralized:
if fix_stereo:
self._fix_stereo()
if logging:
log.append(((), -1, 'neutralized'))
log.append((tuple(neutralized), -1, 'neutralized'))
return log
return True
if logging:
return log
return False

def neutralize(self: Union['MoleculeContainer', 'Standardize'], *, fix_stereo=True) -> bool:
def neutralize(self: Union['MoleculeContainer', 'Standardize'], *, fix_stereo=True,
logging=False) -> Union[bool, List[int]]:
"""
Transform biradical or dipole resonance structures into neutral form. Return True if structure form changed.
:param logging: return list of changed atoms.
"""
atoms = self._atoms
charges = self._charges
Expand Down Expand Up @@ -130,7 +145,11 @@ def neutralize(self: Union['MoleculeContainer', 'Standardize'], *, fix_stereo=Tr
self._calc_hybridization(n)
if fix_stereo:
self._fix_stereo()
if logging:
return list(hs)
return True
if logging:
return []
return False

def remove_hydrogen_bonds(self: 'MoleculeContainer', *, keep_to_terminal=True, fix_stereo=True) -> int:
Expand Down Expand Up @@ -1344,61 +1363,94 @@ class StandardizeReaction:
__slots__ = ()
__class_cache__ = {}

def canonicalize(self: 'ReactionContainer', fix_mapping: bool = True) -> bool:
def canonicalize(self: 'ReactionContainer', fix_mapping: bool = True, *,
logging=False) -> Union[bool, Tuple[int, Tuple[int, ...], int, str]]:
"""
Convert molecules to canonical forms of functional groups and aromatic rings without explicit hydrogens.
Works only for Molecules.
Return True if in any molecule found not canonical group.
:param fix_mapping: Search AAM errors of functional groups.
:param logging: return log from molecules with index of molecule at first position.
Otherwise return True if these groups found in any molecule.
"""
total = False
for m in self.molecules():
if logging:
total = []
else:
total = False
for n, m in enumerate(self.molecules()):
if not isinstance(m, Standardize):
raise TypeError('Only Molecules supported')
if m.canonicalize() and not total:
total = True
out = m.canonicalize(logging=logging)
if out:
if logging:
total.extend((n, *x) for x in out)
else:
total = True

if fix_mapping and self.fix_mapping():
if logging:
total.append((-1, (), -1, 'mapping fixed'))
return total
return True

if total:
self.flush_cache()
return total

def standardize(self: 'ReactionContainer', fix_mapping: bool = True) -> bool:
def standardize(self: 'ReactionContainer', fix_mapping: bool = True, *,
logging=False) -> Union[bool, Tuple[int, Tuple[int, ...], int, str]]:
"""
Standardize functional groups. Works only for Molecules.
Return True if in any molecule found not canonical group.
:param fix_mapping: Search AAM errors of functional groups.
:param logging: return log from molecules with index of molecule at first position.
Otherwise return True if these groups found in any molecule.
"""
total = False
for m in self.molecules():
if logging:
total = []
else:
total = False
for n, m in enumerate(self.molecules()):
if not isinstance(m, Standardize):
raise TypeError('Only Molecules supported')
if m.standardize() and not total:
total = True
out = m.standardize(logging=logging)
if out:
if logging:
total.extend((n, *x) for x in out)
else:
total = True

if fix_mapping and self.fix_mapping():
if logging:
total.append((-1, (), -1, 'mapping fixed'))
return total
return True

if total:
self.flush_cache()
return total

def neutralize(self: 'ReactionContainer') -> bool:
def neutralize(self: 'ReactionContainer', *, logging=False) -> Union[bool, Tuple[int, Tuple[int, ...]]]:
"""
Transform biradical or dipole resonance structures into neutral form.
Works only for Molecules.
Return True if these groups found in any molecule.
Transform biradical or dipole resonance structures into neutral form. Works only for Molecules.
:param logging: return log from molecules with index of molecule at first position.
Otherwise return True if these groups found in any molecule.
"""
total = False
for m in self.molecules():
if logging:
total = []
else:
total = False
for n, m in enumerate(self.molecules()):
if not isinstance(m, Standardize):
raise TypeError('Only Molecules supported')
if m.neutralize() and not total:
total = True
out = m.neutralize(logging=logging)
if out:
if logging:
total.extend((n, tuple(x)) for x in out)
else:
total = True
if total:
self.flush_cache()
return total
Expand Down

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