Usage: pdb2reaction dft [OPTIONS]
Single-point DFT using GPU4PySCF or CPU PySCF.
Options:
-v, --verbose LEVEL Console verbosity 0-3 (default 2). 0=silent;
1=milestones only; 2=+detailed step logging
and deliverable paths; 3=everything (full
config blocks, per-file paths, DEBUG logging).
[0<=x<=3]
--help-advanced Show all options (including advanced settings)
and exit.
-i, --input FILE Input structure file (.pdb, .cif, .mmcif,
.xyz, .gjf, _trj.xyz, etc.). [required]
-q, --charge INTEGER Total charge. Required for non-.gjf inputs
unless --ligand-charge is provided (PDB/mmCIF
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/mmCIF input or --ref-
pdb).
-m, --multiplicity INTEGER Spin multiplicity (2S+1; inherits from .gjf
when available). [default: (1)]
--ref-pdb FILE Reference PDB/mmCIF 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 RANGE Maximum SCF iterations. [default: 100; x>=1]
--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]
--lowmem / --no-lowmem Use gpu4pyscf rks_lowmem.RKS for closed-shell
GPU runs (memory-efficient direct JK; mutually
exclusive with density fitting). Open-shell,
CPU, or pre-rks_lowmem GPU4PySCF installs
auto-fall back to standard RKS/UKS with
density fitting. [default: lowmem]
--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]
--allow-charge-mult-mismatch Skip the cluster charge/multiplicity electron-
parity check (logs that it was skipped). Open-
shell clusters need a matching multiplicity
instead; use this only for an intentionally
nonstandard electron count.
-h, --help Show this message and exit.