helmkit 0.7.3__tar.gz → 0.7.4__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: helmkit
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- Version: 0.7.3
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+ Version: 0.7.4
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  Summary: Parse HELM strings into RDKit molecules
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  License-File: LICENSE
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  Requires-Python: >=3.11
@@ -1,6 +1,6 @@
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  [project]
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  name = "helmkit"
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- version = "0.7.3"
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+ version = "0.7.4"
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  description = "Parse HELM strings into RDKit molecules"
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  readme = "README.md"
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  requires-python = ">=3.11"
@@ -253,7 +253,7 @@ class Molecule:
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  def __init__(self, helm: str, monomer_df: MonomerLibrary | None = None):
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  """Initialize a Molecule object from a HELM string."""
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- self.mol = None
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+ self._mol = None
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  self.offset = []
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  self.bondlist = []
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  self.monomers = []
@@ -270,9 +270,14 @@ class Molecule:
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  self._parse_helm_string(helm)
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  self._build_molecule()
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- if not isinstance(self.mol, Chem.rdchem.Mol):
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+ if not isinstance(self._mol, Chem.rdchem.Mol):
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  raise TypeError("Failed to initialize RDKit Mol object")
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+ @property
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+ def mol(self) -> Chem.Mol:
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+ assert self._mol is not None
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+ return self._mol
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+
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  def _parse_helm_string(self, helm: str) -> None:
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  """Parse a HELM string into molecular components."""
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  polymer_sections, connection_sections, hydrogen_bonds_sections, _, _ = (
@@ -342,7 +347,7 @@ class Molecule:
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  def _process_monomer(
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  self, monomer_name: str, chain_id: str, residue_idx: int, polymer_type: str
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- ) -> MonomerData | None:
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+ ) -> MonomerData:
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  """Process a single monomer."""
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  monomer_name = (
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  monomer_name[1:-1]
@@ -373,14 +378,10 @@ class Molecule:
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  if m_type in self.monomer_df and monomer_name in self.monomer_df[m_type]:
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  monomer_info = self.monomer_df[m_type][monomer_name]
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  else:
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- try:
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- monomer_info = _create_missing_monomer(monomer_name, m_type)
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- if m_type not in self.monomer_df:
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- self.monomer_df[m_type] = {}
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- self.monomer_df[m_type][monomer_name] = monomer_info
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- except ValueError as e:
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- warnings.warn(str(e))
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- return None
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+ monomer_info = _create_missing_monomer(monomer_name, m_type)
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+ if m_type not in self.monomer_df:
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+ self.monomer_df[m_type] = {}
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+ self.monomer_df[m_type][monomer_name] = monomer_info
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  return {
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  "m_romol": monomer_info["m_romol"],
@@ -651,30 +652,30 @@ class Molecule:
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  def _build_molecule(self) -> None:
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  """Build the RDKit molecule from parsed monomer and bond data."""
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  if not self.monomers:
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- self.mol = Chem.RWMol()
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+ self._mol = Chem.RWMol()
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  return
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  monomer = self.monomers[0]
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- self.mol = Chem.RWMol(monomer["m_romol"])
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+ self._mol = Chem.RWMol(monomer["m_romol"])
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  rgroups = monomer["m_Rgroups"]
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  rgroup_idx = monomer["m_RgroupIdx"]
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  for i in range(min(len(rgroups), SequenceConstants.max_rgroups)):
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  if rgroups[i] is not None:
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- self._replace_rgroup(self.mol, 0, rgroup_idx[i], rgroups[i])
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+ self._replace_rgroup(self._mol, 0, rgroup_idx[i], rgroups[i])
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- current_offset = self.mol.GetNumAtoms()
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+ current_offset = self._mol.GetNumAtoms()
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  self.offset = [0, current_offset]
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  for monomer in self.monomers[1:]:
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- self.mol.InsertMol(monomer["m_romol"])
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+ self._mol.InsertMol(monomer["m_romol"])
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  rgroups = monomer["m_Rgroups"]
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  rgroup_idx = monomer["m_RgroupIdx"]
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  for i in range(min(len(rgroups), SequenceConstants.max_rgroups)):
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  if rgroups[i] is not None:
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  self._replace_rgroup(
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- self.mol, current_offset, rgroup_idx[i], rgroups[i]
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+ self._mol, current_offset, rgroup_idx[i], rgroups[i]
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  )
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  atom_count = monomer["m_romol"].GetNumAtoms()
@@ -714,7 +715,7 @@ class Molecule:
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  pattern = Chem.MolFromSmarts("[#0]")
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  matches = self.mol.GetSubstructMatches(pattern)
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  atoms_to_delete = sorted({idx for match in matches for idx in match})
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- self.mol = Chem.DeleteSubstructs(self.mol, pattern)
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+ self._mol = Chem.DeleteSubstructs(self._mol, pattern)
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  def correction(offset: int, idx: int) -> int:
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  return bisect.bisect_left(atoms_to_delete, idx) - bisect.bisect_left(
@@ -165,7 +165,7 @@ wheels = [
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  [[package]]
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  name = "helmkit"
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- version = "0.7.3"
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+ version = "0.7.4"
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  source = { editable = "." }
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  dependencies = [
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  { name = "rdkit" },
@@ -553,54 +553,54 @@ wheels = [
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  [[package]]
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  name = "polars"
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- version = "1.43.1"
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+ version = "1.43.2"
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  source = { registry = "https://pypi.org/simple" }
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  dependencies = [
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  { name = "polars-runtime-32" },
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  ]
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  [[package]]
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  name = "polars-runtime-32"
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- version = "1.43.1"
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+ version = "1.43.2"
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  source = { registry = "https://pypi.org/simple" }
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581
581
 
582
582
  [[package]]
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583
  name = "prek"
584
- version = "0.4.11"
584
+ version = "0.4.12"
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  [[package]]
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669
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670
670
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