Python API

This page indexes the Python interfaces for the subsystems currently included in the apoCHARMM documentation build.

Public objects are available from the top-level package:

import apocharmm as apo

Select a Python object below to open its class and method reference. Select the corresponding subsystem page for cross-language behavior, ownership, lifetime, units, errors, limitations, and implementation details.

Errors and Enumerations

• apocharmm.ApoCharmmError reports nonzero native status results as an owned Python exception. See the ApoCharmmError subsystem.
• apocharmm.DistanceRestraintCondition selects no gate, exact D >= 0 activation, or exact D <= 0 activation for one distance-restraint term. See the DistanceRestraintForce subsystem.
• apocharmm.PeriodicBoundaryCondition selects the periodic boundary model used by contexts and force managers. See the CharmmContext subsystem and ForceManager subsystem.
• apocharmm.CrystalType selects the supported crystal symmetry and Langevin-piston degree-of-freedom layout. See the CUDA Integrators subsystem.
• apocharmm.VdwType selects the native van der Waals model. See the ForceManager subsystem.

The top-level package also exports the following status constants:

APO_STATUS_OK
APO_STATUS_INVALID_ARGUMENT
APO_STATUS_RUNTIME_ERROR
APO_STATUS_CUDA_ERROR
APO_STATUS_NOT_INITIALIZED
APO_STATUS_NOT_IMPLEMENTED

Their meanings and Python exception mapping are documented in the ApoCharmmError subsystem.

Molecular Input and Topology

• apocharmm.CharmmPsf reads and owns molecular topology. See the CharmmPSF subsystem.
• apocharmm.CharmmParameters reads and owns CHARMM force-field parameters. See the CharmmParameters subsystem.
• apocharmm.CharmmCrd reads CHARMM coordinate files. See the Coordinates subsystem.

Simulation State and Force Configuration

• apocharmm.CharmmContext owns mutable molecular state and coordinates force evaluation. See the CharmmContext subsystem.
• apocharmm.DistanceRestraintForce configures CHARMM RESDistance/RESD terms made from one or more weighted AtomReference endpoint pairs. Raw integer endpoint pairs are not accepted. See the DistanceRestraintForce subsystem.
• apocharmm.ForceManager configures and owns native force backends. See the ForceManager subsystem.
• apocharmm.HarmonicCenterOfMassRestraintForce configures periodic geometric-center or mass-weighted-center restraints. See the HarmonicCenterOfMassRestraintForce subsystem.
• apocharmm.HarmonicRestraintForce configures absolute mass-weighted harmonic restraints. See the HarmonicRestraintForce subsystem.

CUDA Integrators

• apocharmm.CudaIntegrator provides the shared lifecycle, context, subscriber, restart, and propagation interface.
• apocharmm.CudaNoseHooverIntegrator provides deterministic Nose-Hoover temperature control (NVT).
• apocharmm.CudaLangevinThermostatIntegrator provides stochastic Langevin temperature control (NVT).
• apocharmm.CudaLangevinPistonIntegrator provides pressure control with optional Nose-Hoover temperature control (NPH/NPT).

See the CUDA Integrators subsystem for construction, call order, state, ownership, units, restart behavior, and cross-language errors.

Atom Selection

• apocharmm.AtomReference owns one validated, topology-aware, zero-based atom identity. Native PSF object identity defines topology identity, and equality also requires an equal atom index.
• apocharmm.AtomSelection owns a set-valued bitset result containing zero or more atom indices.
• apocharmm.AtomSelector evaluates CHARMM-style expressions. select() returns AtomSelection; selectAtom() requires exactly one match and returns AtomReference.

See the Atom Selection and Atom References subsystem for construction, expression syntax, pointer-identity topology semantics, shared native PSF ownership, equality, lifetime, exact-one errors, and cross-language behavior.

Output Subscribers

• apocharmm.Subscriber provides the common operations inherited by concrete subscriber wrappers.
• apocharmm.DcdSubscriber writes coordinate trajectories in DCD format.
• apocharmm.RestartSubscriber writes CHARMM-style restart state.

See the Subscriber subsystem for scheduling, lifetime, synchronization, and file-format behavior.

Documentation Scope

This index includes only Python wrappers whose subsystem pages and wrapper sources are part of the curated documentation build. Additional public Python objects will be added when their corresponding subsystem documentation is included.