helmkit 0.7.4__tar.gz → 0.7.6__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-0.7.4 → helmkit-0.7.6}/PKG-INFO +1 -1
- {helmkit-0.7.4 → helmkit-0.7.6}/pyproject.toml +8 -1
- helmkit-0.7.6/src/helmkit/__init__.py +6 -0
- {helmkit-0.7.4 → helmkit-0.7.6}/src/helmkit/molecule.py +7 -8
- {helmkit-0.7.4 → helmkit-0.7.6}/uv.lock +105 -83
- helmkit-0.7.4/src/helmkit/__init__.py +0 -6
- {helmkit-0.7.4 → helmkit-0.7.6}/.gitignore +0 -0
- {helmkit-0.7.4 → helmkit-0.7.6}/.python-version +0 -0
- {helmkit-0.7.4 → helmkit-0.7.6}/LICENSE +0 -0
- {helmkit-0.7.4 → helmkit-0.7.6}/README.md +0 -0
- {helmkit-0.7.4 → helmkit-0.7.6}/src/helmkit/data/monomers.sdf +0 -0
- {helmkit-0.7.4 → helmkit-0.7.6}/src/helmkit/py.typed +0 -0
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@@ -1,6 +1,6 @@
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[project]
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name = "helmkit"
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version = "0.7.
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version = "0.7.6"
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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"
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@@ -46,3 +46,10 @@ ignore = ["I001", "N999"]
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[tool.ruff.format]
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skip-magic-trailing-comma = true
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[tool.ty.src]
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include = ["src"]
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exclude = ["tests"]
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[tool.pyrefly]
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project-includes = ["src/**/*.py"]
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@@ -15,8 +15,7 @@ from rdkit import Chem
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from rdkit import rdBase
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max_rgroups: int = 4
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MAX_RGROUPS = 4
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def get_molecule_property(
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@@ -183,13 +182,13 @@ def _create_missing_monomer(monomer_name: str, m_type: str = "aa") -> MonomerDat
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r_group_idx = [idx for _, idx in sorted_r]
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mol = Chem.RenumberAtoms(mol, main_atoms + r_group_idx)
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rgroup_idx_full: list[int | None] = [None] *
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rgroup_idx_full: list[int | None] = [None] * MAX_RGROUPS
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for i, (r_num, _) in enumerate(sorted_r):
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if 1 <= r_num <=
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if 1 <= r_num <= MAX_RGROUPS:
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rgroup_idx_full[r_num - 1] = len(main_atoms) + i
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attachment_points = infer_attachment_points(mol, rgroup_idx_full)
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rgroup_vals = [None] *
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rgroup_vals: list[str | None] = [None] * MAX_RGROUPS
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if m_type == "aa" and "_R1" not in monomer_name:
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matches = {
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@@ -335,7 +334,7 @@ class Molecule:
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def _extract_chain_id(self, chain_str: str) -> tuple[str, str]:
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"""Extract chain ID and return (chain_id, polymer_type)."""
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match = re.
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match = re.fullmatch(r"([A-Z]+)(\d+)", chain_str)
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if not match:
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raise ValueError(f"Invalid chain format: {chain_str}")
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@@ -660,7 +659,7 @@ class Molecule:
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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),
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for i in range(min(len(rgroups), 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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@@ -672,7 +671,7 @@ class Molecule:
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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),
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for i in range(min(len(rgroups), 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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@@ -15,39 +15,39 @@ resolution-markers = [
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[[package]]
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name = "biopython"
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version = "1.
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version = "1.88"
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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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{ name = "numpy", version = "2.5.
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]
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{ name = "numpy", version = "2.5.2", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.12'" },
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