stjames 0.0.77__py3-none-any.whl → 0.0.78__py3-none-any.whl

stjames/atomium_stjames/pdb.py

@@ -3,7 +3,7 @@
 import re
 from datetime import datetime
 from itertools import chain, groupby
-from typing import Any, Callable
+from typing import Any, Callable, TypedDict
 
 from .data import CODES
 from .mmcif import add_secondary_structure_to_polymers
@@ -476,15 +476,17 @@ def add_atom_to_polymer(line: str, model: dict[Any, Any], chain_id: str, res_id:
     :param str res_id: the molecule ID to add to.
     :param dict aniso_dict: lookup dictionary for anisotropy information."""
 
+    atom = atom_line_to_dict(line, aniso_dict)
+
     try:
-        model["polymer"][chain_id]["residues"][res_id]["atoms"][int(line[6:11])] = atom_line_to_dict(line, aniso_dict)
+        model["polymer"][chain_id]["residues"][res_id]["atoms"][int(line[6:11])] = atom
     except Exception:
         name = line[17:20].strip()
         try:
             model["polymer"][chain_id]["residues"][res_id] = {
                 "name": name,
                 "full_name": full_names.get(name),
-                "atoms": {int(line[6:11]): atom_line_to_dict(line, aniso_dict)},
+                "atoms": {int(line[6:11]): atom},
                 "number": len(model["polymer"][chain_id]["residues"]) + 1,
             }
         except Exception:
@@ -495,7 +497,7 @@ def add_atom_to_polymer(line: str, model: dict[Any, Any], chain_id: str, res_id:
                 "residues": {
                     res_id: {
                         "name": line[17:20].strip(),
-                        "atoms": {int(line[6:11]): atom_line_to_dict(line, aniso_dict)},
+                        "atoms": {int(line[6:11]): atom},
                         "number": 1,
                         "full_name": None,
                     }
@@ -511,10 +513,11 @@ def add_atom_to_non_polymer(line: str, model: dict[Any, Any], res_id: str, aniso
     :param dict model: the model to update.
     :param str res_id: the molecule ID to add to.
     :param dict aniso_dict: lookup dictionary for anisotropy information."""
+    atom = atom_line_to_dict(line, aniso_dict)
 
     key = "water" if line[17:20] in ["HOH", "DOD"] else "non_polymer"
     try:
-        model[key][res_id]["atoms"][int(line[6:11])] = atom_line_to_dict(line, aniso_dict)
+        model[key][res_id]["atoms"][int(line[6:11])] = atom
     except Exception:
         name = line[17:20].strip()
         model[key][res_id] = {
@@ -522,7 +525,7 @@ def add_atom_to_non_polymer(line: str, model: dict[Any, Any], res_id: str, aniso
             "full_name": full_names.get(name),
             "internal_id": line[21],
             "polymer": line[21],
-            "atoms": {int(line[6:11]): atom_line_to_dict(line, aniso_dict)},
+            "atoms": {int(line[6:11]): atom},
         }
 
 
@@ -545,14 +548,32 @@ def guess_element_from_name(atom_name: str) -> str | None:
     return atom_name[0].upper()
 
 
-def atom_line_to_dict(line: str, aniso_dict: dict[Any, Any]) -> dict[str, Any]:
-    """Converts an ATOM or HETATM record to an atom dictionary.
+class AtomDict(TypedDict, total=False):
+    """A dictionary representing an atom in a PDB file."""
+
+    occupancy: float | None
+    bvalue: float | None
+    charge: int | None
+    anisotropy: float | None
+    is_hetatm: bool | None
+    name: str | None
+    alt_loc: str | None
+    x: float
+    y: float
+    z: float
+    element: str | None
+
+
+def atom_line_to_dict(line: str, aniso_dict: dict[Any, Any]) -> AtomDict:
+    """
+    Converts an ATOM or HETATM record to an atom dictionary.
 
     :param str line: the record to convert.
     :param dict aniso_dict: the anisotropy dictionary to use.
-    :rtype: ``dict``"""
+    :return: atom dictionary
+    """
 
-    a = {"occupancy": 1, "bvalue": None, "charge": 0, "anisotropy": aniso_dict.get(int(line[6:11].strip()), None)}
+    a: AtomDict = {"occupancy": 1, "bvalue": None, "charge": 0, "anisotropy": aniso_dict.get(int(line[6:11].strip()), None)}
     a["is_hetatm"] = line[:6] == "HETATM"
     a["name"] = line[12:16].strip() or None
     a["alt_loc"] = line[16].strip() or None
@@ -565,6 +586,9 @@ def atom_line_to_dict(line: str, aniso_dict: dict[Any, Any]) -> dict[str, Any]:
         a["bvalue"] = float(line[60:66].strip())
     a["element"] = line[76:78].strip() or None
     if not a["element"]:
+        if not a["name"]:
+            raise ValueError("Cannot guess element from empty name.")
+        assert isinstance(a["name"], str)
         a["element"] = guess_element_from_name(a["name"])
     if line[78:80].strip():
         try:
@@ -582,6 +606,7 @@ def atom_line_to_dict(line: str, aniso_dict: dict[Any, Any]) -> dict[str, Any]:
         a["occupancy"] = None
     if a["name"] == a["element"]:
         a["name"] = None
+
     return a
 
 

stjames/molecule.py

@@ -90,20 +90,27 @@ class Molecule(Base):
         r"""
         Calculate the angle between three atoms.
 
-        >>> Molecule.from_xyz("H 0 0 0\nO 0 0 1\nH 0 1 1").angle(0, 1, 2)
+        >>> Molecule.from_xyz("H 0 0 0\nO 0 0 1\nH 0 1 1").angle(1, 2, 3)
         90.0
         """
 
-        return angle(self.coordinates[i], self.coordinates[j], self.coordinates[k], degrees=degrees)
+        return angle(self.coordinates[i - 1], self.coordinates[j - 1], self.coordinates[k - 1], degrees=degrees)
 
     def dihedral(self, i: int, j: int, k: int, l: int, degrees: bool = True, positive_domain: bool = True) -> float:
         r"""
         Calculate the dihedral angle between four atoms.
 
-        >>> Molecule.from_xyz("H 0 0 0\nO 0 0 1\nO 0 1 1\nH 1 1 1").dihedral(0, 1, 2, 3)
+        >>> Molecule.from_xyz("H 0 0 0\nO 0 0 1\nO 0 1 1\nH 1 1 1").dihedral(1, 2, 3, 4)
         270.0
         """
-        return dihedral(self.coordinates[i], self.coordinates[j], self.coordinates[k], self.coordinates[l], degrees=degrees, positive_domain=positive_domain)
+        return dihedral(
+            self.coordinates[i - 1],
+            self.coordinates[j - 1],
+            self.coordinates[k - 1],
+            self.coordinates[l - 1],
+            degrees=degrees,
+            positive_domain=positive_domain,
+        )
 
     @property
     def coordinates(self) -> Vector3DPerAtom:
@@ -365,19 +372,17 @@ class Molecule(Base):
         return cls(atoms=atoms, cell=cell, charge=charge, multiplicity=multiplicity, energy=energy, gradient=gradients)
 
     @classmethod
-    def from_rdkit(cls: type[Self], rdkm: RdkitMol, cid: int = 0) -> Self:
+    def from_rdkit(cls: type[Self], rdkm: RdkitMol, cid: int = 0, multiplicity: int = 1) -> Self:
         if len(rdkm.GetConformers()) == 0:
             rdkm = _embed_rdkit_mol(rdkm)
 
-        atoms = []
         atomic_numbers = [atom.GetAtomicNum() for atom in rdkm.GetAtoms()]  # type: ignore [no-untyped-call, unused-ignore]
-        geom = rdkm.GetConformers()[cid].GetPositions()
-
-        for i in range(len(atomic_numbers)):
-            atoms.append(Atom(atomic_number=atomic_numbers[i], position=geom[i]))
+        atoms = [
+            Atom(atomic_number=atom, position=xyz)  # keep open
+            for atom, xyz in zip(atomic_numbers, rdkm.GetConformers()[cid].GetPositions(), strict=True)
+        ]
 
         charge = Chem.GetFormalCharge(rdkm)
-        multiplicity = 1
 
         return cls(atoms=atoms, charge=charge, multiplicity=multiplicity)
 

stjames/workflows/hydrogen_bond_basicity.py

@@ -7,10 +7,10 @@ from .workflow import MoleculeWorkflow
 
 class HydrogenBondAcceptorSite(Base):
     """
-    A hydrogen bond acceptor site.
+    A hydrogen-bond-acceptor site.
 
     :param atom_idx: index of the atom
-    :param pkbhx: Hydrogen bond basicity
+    :param pkbhx: Hydrogen-bond basicity
     :param position: position of the atom
     :param name: name of the atom
     """
@@ -21,9 +21,23 @@ class HydrogenBondAcceptorSite(Base):
     name: str | None = None
 
 
+class HydrogenBondDonorSite(Base):
+    """
+    A hydrogen-bond-donor site.
+
+    :param atom_idx: index of the atom
+    :param pk_alpha: Hydrogen-bond acidity
+    :param position: position of the atom
+    """
+
+    atom_idx: int  # zero-indexed
+    pk_alpha: float
+    position: tuple[float, float, float]
+
+
 class HydrogenBondBasicityWorkflow(MoleculeWorkflow):
     """
-    Workflow for calculating hydrogen bond basicity.
+    Workflow for calculating hydrogen-bond basicity and acidity.
 
     Inherited:
     :param initial_molecule: Molecule of interest
@@ -36,6 +50,7 @@ class HydrogenBondBasicityWorkflow(MoleculeWorkflow):
     Results:
     :param optimization: UUID of optimization
     :param hba_sites: hydrogen-bond-acceptor sites
+    :param hbd_sites: hydrogen-bond-donor sites
     """
 
     do_csearch: bool = True
@@ -43,3 +58,4 @@ class HydrogenBondBasicityWorkflow(MoleculeWorkflow):
 
     optimization: UUID | None = None
     hba_sites: list[HydrogenBondAcceptorSite] = []  # noqa: RUF012
+    hbd_sites: list[HydrogenBondDonorSite] = []  # noqa: RUF012

stjames/workflows/multistage_opt.py

@@ -1,15 +1,19 @@
 """Multi-stage optimization workflow."""
 
+import re
 from typing import Self, Sequence
 
+import more_itertools as mit
 from pydantic import BaseModel, Field, model_validator
 
+from stjames.correction import Correction
+
 from ..constraint import Constraint
 from ..method import XTB_METHODS, Method
 from ..mode import Mode
 from ..opt_settings import OptimizationSettings
 from ..settings import Settings
-from ..solvent import Solvent, SolventSettings
+from ..solvent import Solvent, SolventModel, SolventSettings
 from ..task import Task
 from ..types import UUID
 from .workflow import MoleculeWorkflow
@@ -264,6 +268,73 @@ class MultiStageOptMixin(BaseModel):
         return self
 
 
+def mso_settings_from_method_string(
+    methods: str,
+    solvent: Solvent | None = None,
+    use_solvent_for_opt: bool = False,
+    constraints: list[Constraint] | None = None,
+    transition_state: bool = False,
+    frequencies: bool = False,
+) -> MultiStageOptSettings:
+    """
+    Helper function to construct multi-stage opt settings objects from a method string.
+
+    >>> mso_settings_from_method_string("r2SCAN-3c/CPCM(Water)//B3LYP-D3/6-31G(d)/ALPB(Water)//GFN2-xTB/CPCM(Water)//GFN0-xTB").level_of_theory
+    'r2scan_3c/cpcm(water)//b3lyp-d3/6-31g(d)/alpb(water)//gfn2_xtb/cpcm(water)//gfn0_xtb'
+    """
+    solvent_models = "|".join(model.name for model in SolventModel)
+
+    pattern = rf"""
+        (?P<method>[^/()]+)                                 # Method + optional corrections
+        (?:/(?P<basis_set>(?!{solvent_models})[^/]+?))?     # Optional basis_set, not starting with solvent model name
+        (?:/(?P<solvent_model>{solvent_models})             # Optional solvent model
+            \((?P<solvent>[^()]+)\))?                       # Solvent name in parentheses
+        (?:\/\/|$)                                          # End or separator
+"""
+    constraints = constraints or []
+    opt_settings = OptimizationSettings(constraints=constraints, transition_state=transition_state)
+    OPT = [Task.OPTIMIZE if not transition_state else Task.OPTIMIZE_TS]
+
+    valid_corrections = {c.name.lower() for c in Correction}  # Python3.11 hack
+
+    def process(match: re.Match[str]) -> Settings:
+        data = match.groupdict()
+
+        method, corrections = mit.partition(lambda x: x.lower() in valid_corrections, data["method"].split("-"))
+        solvent_settings = SolventSettings(solvent=data["solvent"], model=data["solvent_model"]) if data["solvent"] else None
+
+        return Settings(
+            method="-".join(method),
+            basis_set=data["basis_set"],
+            tasks=OPT,
+            solvent_settings=solvent_settings,
+            opt_settings=opt_settings,
+            corrections=list(corrections),
+        )
+
+    optimization_settings = [process(match) for match in re.finditer(pattern, methods, re.VERBOSE | re.IGNORECASE)]
+    if len(optimization_settings) > 1:
+        sp_settings = optimization_settings.pop(0)
+        sp_settings.tasks = [Task.ENERGY]
+    else:
+        sp_settings = None
+
+    optimization_settings = optimization_settings[::-1]
+    if frequencies:
+        optimization_settings[-1].tasks.append(Task.FREQUENCIES)
+
+    return MultiStageOptSettings(
+        mode=Mode.MANUAL,
+        optimization_settings=optimization_settings,
+        singlepoint_settings=sp_settings,
+        solvent=solvent,
+        xtb_preopt=False,
+        constraints=constraints,
+        transition_state=transition_state,
+        frequencies=frequencies,
+    )
+
+
 def build_mso_settings(
     sp_method: Method,
     sp_basis_set: str | None,

stjames/workflows/protein_cofolding.py

@@ -12,6 +12,7 @@ class CofoldingModel(LowercaseStrEnum):
 
     CHAI_1R = "chai_1r"
     BOLTZ_1 = "boltz_1"
+    BOLTZ_2 = "boltz_2"
 
 
 class CofoldingScores(BaseModel):
@@ -20,6 +21,15 @@ class CofoldingScores(BaseModel):
     iptm: float  # interface predicted template modeling score
 
 
+class AffinityScore(BaseModel):
+    pred_value: float
+    probability_binary: float
+    pred_value1: float
+    probability_binary1: float
+    pred_value2: float
+    probability_binary2: float
+
+
 class ProteinCofoldingWorkflow(FASTAWorkflow):
     """
     A workflow for predicting structures. Especially protein structures.
@@ -38,4 +48,5 @@ class ProteinCofoldingWorkflow(FASTAWorkflow):
     use_templates_server: bool = False
     predicted_structure_uuid: UUID | None = None
     scores: CofoldingScores | None = None
-    model: CofoldingModel = CofoldingModel.CHAI_1R
+    model: CofoldingModel = CofoldingModel.BOLTZ_2
+    affinity_score: AffinityScore | None = None

stjames/workflows/workflow.py

@@ -32,6 +32,7 @@ class FASTAWorkflow(Workflow):
 
     initial_protein_sequences: list[str]
     initial_smiles_list: list[str] | None = None
+    ligand_binding_affinity_index: int | None = None
 
     def __repr__(self) -> str:
         return f"<{type(self).__name__} {self.initial_protein_sequences} {self.initial_smiles_list}>"

{stjames-0.0.77.dist-info → stjames-0.0.78.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.77
+Version: 0.0.78
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames
@@ -12,6 +12,7 @@ Requires-Dist: pydantic>=2.4
 Requires-Dist: numpy
 Requires-Dist: requests
 Requires-Dist: rdkit
+Requires-Dist: more-itertools
 Dynamic: license-file
 
 # stjames

{stjames-0.0.77.dist-info → stjames-0.0.78.dist-info}/RECORD

@@ -13,7 +13,7 @@ stjames/int_settings.py,sha256=5HXp8opt5ZyY1UpmfaK7NVloWVLM5jkG0elEEqpVLUo,896
 stjames/message.py,sha256=Rq6QqmHZKecWxYH8fVyXmuoCCPZv8YinvgykSeorXSU,216
 stjames/method.py,sha256=k7WtNvD_0OyXWWDjukmVXFFYfIO-Wg4vY1W58o99-gQ,2821
 stjames/mode.py,sha256=xw46Cc7f3eTS8i35qECi-8DocAlANhayK3w4akD4HBU,496
-stjames/molecule.py,sha256=q1pgcfcae3Z6klTaiIqAVaE966GxhuRKP92O9TP1h3Y,20529
+stjames/molecule.py,sha256=l4S6prH1xflnZtbwidSF2THsiHaSJtRiy1rmUbH366Q,20631
 stjames/opt_settings.py,sha256=LEwGXUEKq5TfU5rr60Z4QQBhCqiw1Ch5w0M_lXawWo8,642
 stjames/pdb.py,sha256=_pIdJCMhIzS4t2HWQa_susDWjZEl0oLn4Njb1QoKvKw,26460
 stjames/periodic_cell.py,sha256=eV_mArsY_MPEFSrFEsTC-CyCc6V8ITAXdk7yhjjNI7M,1080
@@ -28,7 +28,7 @@ stjames/types.py,sha256=rs2CdpkruIfU-PS98rjr9HAJNFGdZDB_zl-u3wa5rAs,4092
 stjames/atomium_stjames/__init__.py,sha256=gZkzC7i9D_fmWUTN55gtygITo3-qvJUda5CXLR0jyCQ,306
 stjames/atomium_stjames/data.py,sha256=-hzwBpTHq5JetsOVyopUJswKnKAkMtJ_XkONxjXVupU,5675
 stjames/atomium_stjames/mmcif.py,sha256=em1fNt6577OaUjL7Pctru7aJp3ceZ9kEnj5w6BRWdVs,27090
-stjames/atomium_stjames/pdb.py,sha256=3cVvLsdK0_6m5Z5P0XlathoEvRXCv174MdmxecM4cis,23280
+stjames/atomium_stjames/pdb.py,sha256=hoEV1xmbkYkXW8A6YX5uspvSRvGlhzM1o_BiikQ6DiU,23734
 stjames/atomium_stjames/utilities.py,sha256=-YtM7sRMvMk0wWrC3svWUWH4CGI0NtY77nXsg9tjHfc,4964
 stjames/data/__init__.py,sha256=O59Ksp7AIqwOELCWymfCx7YeBzwNOGCMlGQi7tNLqiE,24
 stjames/data/bragg_radii.json,sha256=hhbn-xyZNSdmnULIjN2Cvq-_BGIZIqG243Ls_mey61w,1350
@@ -47,22 +47,22 @@ stjames/workflows/descriptors.py,sha256=T4tc7xdtBdxESGO86KR323jPQ2pgwxBqgV0khA6M
 stjames/workflows/docking.py,sha256=GCW_-JeEZcMXKZ9EQFOxWUYRo0jsbzwIv10aSz8KuaQ,3027
 stjames/workflows/electronic_properties.py,sha256=GT3-NC7w-dbcOJ-3AzJ7LgzH6frTbiH2Iyb9BCa-SvY,4112
 stjames/workflows/fukui.py,sha256=T6TDg-lcE-sfTDVpa3KFBenLe7PGUO2QrQ2jNuw_iiU,1756
-stjames/workflows/hydrogen_bond_basicity.py,sha256=XDpHEluw6DQ9Zk5g2Je2a81HqIkqPglZ-6f2YZnd4Bc,1159
+stjames/workflows/hydrogen_bond_basicity.py,sha256=q9eXty68ZyCmrB6G_8bfeOT8Ui_IQquRPu6z-3rNreQ,1589
 stjames/workflows/ion_mobility.py,sha256=e6XSidrud5qSkrAcjzOzgHaf-G09JoP09V76myjdyjc,1097
 stjames/workflows/irc.py,sha256=ZP7icylW8rgo_Uh7h3bmyumn0ru1IyF-61nP5Jnmq3M,3402
 stjames/workflows/macropka.py,sha256=KRIyk4gsSYL3eqyzCDndStGLwjWSo60cgCAzvAoD1Nk,3754
 stjames/workflows/molecular_dynamics.py,sha256=kxugE73Ntzpj-xpJSoQ1EwGzXXdvi_NTyeP4913EVwE,3173
-stjames/workflows/multistage_opt.py,sha256=pPLAZDztHd37q8cxCUkdq8EzOFyrTzZJHNfDV5auiHs,13638
+stjames/workflows/multistage_opt.py,sha256=P8rxMUhKXMmDi7Id95IOTEmM0xN1ErsKcDJfgY08vjc,16538
 stjames/workflows/pka.py,sha256=j3vBh2YM3nJzJ1XJKPsmYahRCeaU9n3P-G-u9_moaFw,2065
-stjames/workflows/protein_cofolding.py,sha256=lHeAYRzELo5VMeZsVX-FHJteR9cXCAx_DznDwX7WwGg,1188
+stjames/workflows/protein_cofolding.py,sha256=y4egDFTVEmUPN4gVeivgO83IA3CG6AVbRtvU5Ng3iuE,1454
 stjames/workflows/redox_potential.py,sha256=7S18t9Y3eynSnA3lZbRlvLfdbgeBopdiigLzt1zxg5c,3871
 stjames/workflows/scan.py,sha256=DXQBpa2t2PowAtOwmdgpxaSLq--fEShljzAGSb8Nf5U,2993
 stjames/workflows/solubility.py,sha256=kGfVyPPGDLRpf2j6dSY7woCkfsoXSbUzdSImA4mcMpw,1898
 stjames/workflows/spin_states.py,sha256=0degmE-frovgoXweshZyjfjqL7nkbaFoO9YoJhvQnaI,4748
 stjames/workflows/tautomer.py,sha256=7eYKziGPg8Km6lfowTzSkgJfJ4SHUPrAmnTf8Bi-SB0,1164
-stjames/workflows/workflow.py,sha256=NA4H9W_47UQWnrsdB5UXFODMaZWrmULYqW1pud5ErO4,1900
-stjames-0.0.77.dist-info/licenses/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
-stjames-0.0.77.dist-info/METADATA,sha256=3Hheys7rszNhTmStDBl9Xk6rS1BmeNHS4h5SdjWrUXc,1694
-stjames-0.0.77.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-stjames-0.0.77.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
-stjames-0.0.77.dist-info/RECORD,,
+stjames/workflows/workflow.py,sha256=OE05pt2ZOd8TzTOlBngXCVg9wv_553ZR60VNRPlq0f8,1953
+stjames-0.0.78.dist-info/licenses/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
+stjames-0.0.78.dist-info/METADATA,sha256=F9H_rYG2dPbIsXty-Du4PnKs64_-k1f1VRt69dqZU9U,1724
+stjames-0.0.78.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+stjames-0.0.78.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
+stjames-0.0.78.dist-info/RECORD,,