Usage: pdb2reaction dft [OPTIONS]
Single-point DFT using GPU4PySCF (CPU PySCF backend).
Options:
--help-advanced Show all options (including advanced settings)
and exit.
-i, --input FILE Input structure file (.pdb, .xyz, _trj.xyz,
etc.). [required]
-q, --charge INTEGER Total charge. Required for non-.gjf inputs
unless --ligand-charge is provided (PDB inputs
or XYZ/GJF with --ref-pdb).
-l, --ligand-charge TEXT Total charge or per-resname mapping (e.g.,
GPP:-3,SAM:1) used to derive charge when -q is
omitted (requires PDB input or --ref-pdb).
-m, --multiplicity INTEGER Spin multiplicity (2S+1; inherits from .gjf
when available; otherwise defaults to 1).
--convert-files / --no-convert-files
Accepted for interface consistency; dft does
not emit PDB/GJF outputs. [default: convert-
files]
--ref-pdb FILE Reference PDB topology to use when the input
is XYZ/GJF (keeps XYZ coordinates).
--func-basis TEXT Exchange–correlation functional and basis set
as 'FUNC/BASIS' (e.g., 'wb97m-v/6-31g**',
'wb97m-v/def2-tzvpd'). [default:
wb97m-v/def2-tzvpd]
--max-cycle INTEGER Maximum SCF iterations. [default: 100]
--conv-tol FLOAT SCF convergence tolerance (Eh). [default:
1e-09]
--grid-level INTEGER Numerical integration grid level (PySCF
grids.level). [default: 3]
-o, --out-dir TEXT Output directory. [default: ./result_dft/]
--engine [gpu|cpu] SCF backend: gpu (GPU4PySCF, raises error if
unavailable) or cpu (PySCF). [default: gpu]
--config FILE Base YAML configuration file applied before
explicit CLI options.
--show-config / --no-show-config
Print resolved configuration and continue
execution. [default: no-show-config]
--out-json / --no-out-json Write machine-readable result.json to out_dir.
[default: no-out-json]
--dry-run / --no-dry-run Validate options and print the execution plan
without running DFT. [default: no-dry-run]
-h, --help Show this message and exit.