molbuilder 1.0.0__py3-none-any.whl → 1.1.0__py3-none-any.whl

molbuilder/__init__.py

@@ -5,4 +5,4 @@ Build, analyze, and plan synthesis of molecules from atoms up through
 industrial-scale manufacturing processes.
 """
 
-__version__ = "1.0.0"
+__version__ = "1.1.0"

molbuilder/cli/demos.py

@@ -465,7 +465,7 @@ def demo_visualization():
             print(f"  Rendering gallery of {len(mols)} molecules...")
             visualize_gallery(mols)
     else:
-        print("  Skipped.")
+        print("  Skipped visualization.")
     print()
 
 
@@ -514,3 +514,75 @@ def demo_quantum_visualization():
     else:
         print("  Skipped.")
     print()
+
+
+def demo_slowmo_interaction():
+    """Extreme slow-motion atomic interaction visualization."""
+    try:
+        import matplotlib
+    except ImportError:
+        print("  matplotlib is not installed. Skipping visualization.")
+        return
+
+    print("=" * 60)
+    print("  EXTREME SLOW-MOTION ATOMIC INTERACTIONS")
+    print("=" * 60)
+    print()
+
+    print("  This demo visualizes atomic interactions at sub-femtosecond")
+    print("  time resolution using molecular dynamics simulation.")
+    print()
+
+    choice = input(
+        "  Show: [1] Ethane MD vibration  [2] SN2 mechanism\n"
+        "        [3] Bond formation        [4] Skip: ").strip()
+
+    if choice == "1":
+        from molbuilder.molecule.builders import build_ethane
+        from molbuilder.visualization.interaction_viz import (
+            visualize_md_trajectory, PlaybackConfig,
+        )
+        print("  Building ethane and running MD at 300 K...")
+        mol = build_ethane(60.0)
+        config = PlaybackConfig(
+            show_electron_density=False,
+            slowmo_factor=1e15,
+        )
+        visualize_md_trajectory(mol, n_steps=500, config=config)
+
+    elif choice == "2":
+        from molbuilder.molecule.builders import build_ethane
+        from molbuilder.dynamics.mechanisms import sn2_mechanism
+        from molbuilder.visualization.interaction_viz import (
+            visualize_reaction, PlaybackConfig,
+        )
+        print("  Setting up SN2 mechanism demonstration...")
+        mol = build_ethane(60.0)
+        mechanism = sn2_mechanism(
+            substrate_C=0, nucleophile=1, leaving_group=2)
+        config = PlaybackConfig(
+            show_electron_density=True,
+            show_electron_flows=True,
+        )
+        visualize_reaction(
+            mol, mechanism,
+            n_steps_per_stage=150, config=config)
+
+    elif choice == "3":
+        from molbuilder.molecule.graph import Molecule, Hybridization
+        from molbuilder.visualization.interaction_viz import (
+            visualize_bond_formation, PlaybackConfig,
+        )
+        print("  Setting up bond formation between two carbon atoms...")
+        mol = Molecule("C...C bond formation")
+        c0 = mol.add_atom("C", [0.0, 0.0, 0.0], Hybridization.SP3)
+        c1 = mol.add_atom("C", [3.0, 0.0, 0.0], Hybridization.SP3)
+        config = PlaybackConfig(
+            show_electron_density=True,
+            show_electron_flows=True,
+        )
+        visualize_bond_formation(mol, c0, c1, config=config)
+
+    else:
+        print("  Skipped.")
+    print()

molbuilder/cli/menu.py

@@ -19,6 +19,7 @@ from molbuilder.cli.demos import (
     demo_amino_acids,
     demo_visualization,
     demo_quantum_visualization,
+    demo_slowmo_interaction,
 )
 from molbuilder.cli.wizard import wizard_main
 
@@ -38,6 +39,7 @@ DEMOS = [
     ("Amino Acids & Functional Groups",     demo_amino_acids),
     ("3D Molecule Visualization",           demo_visualization),
     ("Quantum Orbital Visualization",       demo_quantum_visualization),
+    ("Slow-Motion Atomic Interactions",     demo_slowmo_interaction),
     ("Molecule Builder Wizard",             wizard_main),
 ]
 

molbuilder/dynamics/__init__.py

@@ -0,0 +1,49 @@
+"""Molecular dynamics engine for atomic interaction visualization.
+
+Provides a force field, Velocity Verlet integrator, trajectory storage
+with sub-femtosecond interpolation, reaction mechanism templates, and
+steered-MD choreography for animating bond formation/breaking events.
+
+Public API
+----------
+ForceField, ForceFieldParams, ForceResult
+    Vectorized force computation (LJ + Coulomb + harmonic bond/angle +
+    OPLS-AA torsion).
+
+VelocityVerletIntegrator, IntegratorState, BerendsenThermostat
+    Symplectic integration and temperature control.
+
+Trajectory, TrajectoryFrame
+    Frame storage with CubicSpline interpolation for sub-fs resolution.
+
+MDSimulation
+    High-level orchestrator: build from a ``Molecule``, run plain or
+    steered MD, and record trajectories.
+
+MechanismType, ReactionMechanism, MechanismStage, ElectronFlow
+    Reaction mechanism data model and predefined templates.
+
+MechanismChoreographer
+    Converts mechanism stages into time-varying restraint forces.
+"""
+
+from molbuilder.dynamics.forcefield import ForceField, ForceFieldParams, ForceResult
+from molbuilder.dynamics.integrator import (
+    VelocityVerletIntegrator,
+    IntegratorState,
+    BerendsenThermostat,
+)
+from molbuilder.dynamics.trajectory import Trajectory, TrajectoryFrame
+from molbuilder.dynamics.simulation import MDSimulation
+from molbuilder.dynamics.mechanisms import (
+    MechanismType,
+    ReactionMechanism,
+    MechanismStage,
+    ElectronFlow,
+    FlowType,
+    sn2_mechanism,
+    e2_mechanism,
+    radical_substitution_mechanism,
+    nucleophilic_addition_mechanism,
+)
+from molbuilder.dynamics.mechanism_choreography import MechanismChoreographer