chython 3.2__tar.gz → 3.3.1__tar.gz

{chython-3.2/chython.egg-info → chython-3.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: chython
-Version: 3.2
+Version: 3.3.1
 Summary: Library for processing molecules and reactions in python way
 Author-email: Ramil Nugmanov <nougmanoff@protonmail.com>
 License-Expression: LGPL-3.0-or-later

{chython-3.2 → chython-3.3.1}/chython/chemistry/__init__.py

@@ -45,15 +45,15 @@ from ._qed import alert_count, qed, qed_properties
 from ._residues import (RESIDUE_KINDS, ResidueTemplate, normalize_atom_name, residue_template,
                         residue_templates)
 from ._resonance import fix_resonance
-from ._salts import SaltComposition, decompose_salts, split_salts
+from ._salts import ComponentRow, DEFAULT_STABILIZER_CLASSES, SaltComposition, decompose_salts, split_salts
 from ._saturate import saturate
 from ._smarts import SmartsSyntaxError, compile_smarts
 from ._standardize import LogRecord, standardize
-from ._tables import (ACID_ROLES, AbbreviationRow, AcidRow, Endpoint, RESONANCE_ROLES, Rule, SALT_ROLES,
-                      SaltRow, abbreviation_row, abbreviations_rows, acids_rules, acids_rules_by_role,
-                      acids_table_text, groups_rules,
+from ._tables import (ACID_ROLES, AbbreviationRow, AcidRow, Endpoint, RESONANCE_ROLES, Rule,
+                      SALT_CLASSES, SALT_MATCHES, SaltRow, abbreviation_row, abbreviations_rows,
+                      acids_rules, acids_rules_by_role, acids_table_text, groups_rules,
                       metals_rules, read_table, resonance_rules, resonance_rules_by_role,
-                      resonance_table_text, salts_rows, salts_rows_by_role, salts_species_keys,
+                      resonance_table_text, salts_rows, salts_rows_by_klass, salts_species_keys,
                       salts_table_text, standardize_rules)
 from ._tpsa import tpsa
 from ..core._core import (_set_canonicalize_fn, _set_featurizer_fns, _set_hydrogens_fns,
@@ -62,7 +62,8 @@ from ..core._core import (_set_canonicalize_fn, _set_featurizer_fns, _set_hydrog
                           _set_valence_fn)
 
 
-__all__ = ['ACID_ROLES', 'AbbreviationRow', 'LogRecord', 'SALT_ROLES', 'SaltComposition',
+__all__ = ['ACID_ROLES', 'AbbreviationRow', 'ComponentRow', 'DEFAULT_STABILIZER_CLASSES',
+           'LogRecord', 'SALT_CLASSES', 'SALT_MATCHES', 'SaltComposition',
            'abbreviation_row', 'abbreviations_rows', 'alert_count',
            'calc_implicit', 'canonicalize', 'check_valence', 'crippen_logp', 'crippen_mr',
            'decompose_salts', 'expand_abbreviations', 'explicify_hydrogens', 'fix_resonance',

{chython-3.2 → chython-3.3.1}/chython/chemistry/_canonicalize.py

@@ -68,9 +68,12 @@ def canonicalize(molecule: MoleculeContainer, *, fix_tautomers: bool = True,
     sodium acetate stays sodium acetate -- there is no proton in it to move -- while ammonium acetate
     becomes acetic acid and ammonia, both drawings of one salt.
 
-    One stage does move the net charge, `standardize()`'s organometallic completion: a zinc or magnesium
-    holding one carbon and no halide is charged rather than left as a neutral one-coordinate metal.  It
-    is the only place in the pipeline where the total changes, and it says so in the log.
+    `standardize()` moves the net charge wherever a drawing omitted one: the organometallic completion
+    charges a metal nobody drew a halide for; `fix_salt_charges()` pairs each free metal with the acid
+    that belongs to it, deprotonating the acid and charging the metal only when it arrives neutral -- a
+    metal already drawn charged takes the proton and the total falls.  Both say so in the log, and
+    `neutralize()` two steps later leaves the repair alone: `acids.tsv`'s rows are charged sites only,
+    so a sodium cation is no donor to any of them.
     """
     # A refusal at the answer boundary, which is the only place one belongs.  `smiles()` returns
     # whichever container its string describes, so a `>>` in a structure column arrives here as a

{chython-3.2 → chython-3.3.1}/chython/chemistry/_organometallics.py

@@ -38,10 +38,10 @@ Ties are left tied.  Two candidates of equal rank are automorphic, so which one
 observable in the result, and the sort being stable makes the arbitrary half of the choice cheap.
 Charging needs no order at all, being one atom's charge and nothing else's.
 
-NET CHARGE MOVES HERE, which no other `standardize()` stage does, and every spelling that moves it is
-accepted: a lone `[Zn+]` beside a neutral halogen sits at `+1`, a neutral metal beside `[Cl-]` at `-1`,
-and a charged metal with no halide leaves `0` for `+1`.  A dropped sign is the premise of the stage, so
-the record states which way the total went rather than the pass declining to move it.
+NET CHARGE MOVES HERE, and every spelling that moves it is accepted: a lone `[Zn+]` beside a neutral
+halogen sits at `+1`, a neutral metal beside `[Cl-]` at `-1`, and a charged metal with no halide
+leaves `0` for `+1`.  A dropped sign is the premise of the stage, so the record states which way the
+total went rather than the pass declining to move it.
 """
 from collections.abc import MutableSequence
 from ..core import LogRecord, MoleculeContainer