iphasimulator.parameterization_gaff2

GAFF2 parameterisation workflow using AmberTools.

Exceptions

AmberToolsError

Raised when AmberTools is unavailable or a command fails.

Classes

Gaff2Outputs

Files produced by the GAFF2/AmberTools workflow.

Functions

ambertools_available(→ bool)	Return True when the required AmberTools executables are on PATH.
require_ambertools(→ None)	Raise a clear error if AmberTools executables are not available.
parameterize_gaff2(→ Gaff2Outputs)	Create GAFF2 AMBER topology files from an input SDF.

Module Contents

class iphasimulator.parameterization_gaff2.Gaff2Outputs

Files produced by the GAFF2/AmberTools workflow.

output_dir: pathlib.Path

mol2_path: pathlib.Path

frcmod_path: pathlib.Path

tleap_input_path: pathlib.Path

prmtop_path: pathlib.Path

inpcrd_path: pathlib.Path

pdb_path: pathlib.Path

antechamber_log: pathlib.Path

raw_antechamber_log: pathlib.Path

sqm_log: pathlib.Path

parmchk2_log: pathlib.Path

tleap_log: pathlib.Path

timing_log: pathlib.Path

antechamber_seconds: float

parmchk2_seconds: float

tleap_seconds: float

exception iphasimulator.parameterization_gaff2.AmberToolsError

Raised when AmberTools is unavailable or a command fails.

iphasimulator.parameterization_gaff2.ambertools_available() → bool

Return True when the required AmberTools executables are on PATH.

iphasimulator.parameterization_gaff2.require_ambertools() → None

Raise a clear error if AmberTools executables are not available.

iphasimulator.parameterization_gaff2.parameterize_gaff2(input_sdf: str | pathlib.Path, output_dir: str | pathlib.Path, *, name: str | None = None, net_charge: int = 0, residue_name: str = 'MOL', charge_method: str = 'abcg2', atom_count_warning_threshold: int | None = 120, verbose: bool = False, runner=subprocess.run, check_tools: bool = True) → Gaff2Outputs

Create GAFF2 AMBER topology files from an input SDF.

The workflow runs AmberTools in three steps: antechamber -> parmchk2 -> tleap.