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.
- {helmkit-0.7.3 → helmkit-0.7.4}/PKG-INFO +1 -1
- {helmkit-0.7.3 → helmkit-0.7.4}/pyproject.toml +1 -1
- {helmkit-0.7.3 → helmkit-0.7.4}/src/helmkit/molecule.py +19 -18
- {helmkit-0.7.3 → helmkit-0.7.4}/uv.lock +49 -49
- {helmkit-0.7.3 → helmkit-0.7.4}/.gitignore +0 -0
- {helmkit-0.7.3 → helmkit-0.7.4}/.python-version +0 -0
- {helmkit-0.7.3 → helmkit-0.7.4}/LICENSE +0 -0
- {helmkit-0.7.3 → helmkit-0.7.4}/README.md +0 -0
- {helmkit-0.7.3 → helmkit-0.7.4}/src/helmkit/__init__.py +0 -0
- {helmkit-0.7.3 → helmkit-0.7.4}/src/helmkit/data/monomers.sdf +0 -0
- {helmkit-0.7.3 → helmkit-0.7.4}/src/helmkit/py.typed +0 -0
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@@ -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.
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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 = []
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@@ -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.
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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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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, _, _ = (
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@@ -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
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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]
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@@ -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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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"],
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@@ -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.
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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.
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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.
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self._replace_rgroup(self._mol, 0, rgroup_idx[i], rgroups[i])
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current_offset = self.
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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.
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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.
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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()
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@@ -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.
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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(
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@@ -165,7 +165,7 @@ wheels = [
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[[package]]
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name = "helmkit"
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version = "0.7.
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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" },
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@@ -553,54 +553,54 @@ wheels = [
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[[package]]
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name = "polars"
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version = "1.43.
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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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sdist = { url = "https://files.pythonhosted.org/packages/
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sdist = { url = "https://files.pythonhosted.org/packages/89/13/3873f213304bcbaaf39e63c8b905ceb460a0524448d57f86a829f6d4d0fd/polars-1.43.2.tar.gz", hash = "sha256:c699671b99eb71ff53334d237917aaa3db5ad4dda480abcb6c80e0eaee7b677b", size = 750312, upload-time = "2026-08-01T06:28:30.872Z" }
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wheels = [
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{ url = "https://files.pythonhosted.org/packages/
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]
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[[package]]
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name = "polars-runtime-32"
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version = "1.43.
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version = "1.43.2"
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source = { registry = "https://pypi.org/simple" }
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sdist = { url = "https://files.pythonhosted.org/packages/
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wheels = [
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]
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[[package]]
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name = "prek"
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version = "0.4.
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version = "0.4.12"
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source = { registry = "https://pypi.org/simple" }
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{ url = "https://files.pythonhosted.org/packages/68/94/95942bcc20a6a91ec2989aa30fdeb00ad095be736ec48b4bbcf0376166b1/prek-0.4.12-py3-none-musllinux_1_1_i686.whl", hash = "sha256:3d0208370da73e8b5bc97f2492dc3975f8dd2c22f4bf6e1f2cf3342503764b52", size = 5975030, upload-time = "2026-08-03T11:28:25.683Z" },
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{ url = "https://files.pythonhosted.org/packages/ef/6d/26e6497198d81cf9aa82495400aef46adea8df3e4a4efc5f00e3b6ab3292/prek-0.4.12-py3-none-musllinux_1_1_x86_64.whl", hash = "sha256:b1005f42920111bec1403c25e8f2f12ec7af0be06686cc3b8dcf85429af908a8", size = 6458532, upload-time = "2026-08-03T11:28:27.121Z" },
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{ url = "https://files.pythonhosted.org/packages/e5/7b/744cff84def48c1ce38c0b4f643a3553c66976c5bb7869ab7317044870e4/prek-0.4.12-py3-none-win_amd64.whl", hash = "sha256:fdd27bad8adafea8fe77606950ca09200d59296a47ab131cfb88718d460949d7", size = 5868065, upload-time = "2026-08-03T11:28:30.377Z" },
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{ url = "https://files.pythonhosted.org/packages/46/1d/e2c0fc222904ef73df1739b11a83edc29e38bc4bc61259f2ca6d2f15abb0/prek-0.4.12-py3-none-win_arm64.whl", hash = "sha256:45e34a24fba4a4e4568682477158591698efc2375b8d1d418ae424691c4bd01b", size = 5632819, upload-time = "2026-08-03T11:28:31.743Z" },
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name = "rdkit"
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version = "2026.3.
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+
version = "2026.3.5"
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source = { registry = "https://pypi.org/simple" }
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dependencies = [
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{ name = "numpy", version = "2.4.6", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.12'" },
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@@ -676,22 +676,22 @@ dependencies = [
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{ name = "pillow" },
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wheels = [
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{ url = "https://files.pythonhosted.org/packages/
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{ url = "https://files.pythonhosted.org/packages/
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{ url = "https://files.pythonhosted.org/packages/
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680
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681
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682
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683
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684
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685
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686
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687
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688
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689
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690
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691
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692
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693
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694
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[[package]]
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