all | End-to-end (extract → MEP → tsopt → irc → freq → dft) | pdb2reaction all -i 1.R.pdb 3.P.pdb --tsopt --thermo -o out | out/segments/seg_NN/{reactant,ts,product}.pdb + out/summary.json |
all (scan-list) | Single reactant + staged scans | pdb2reaction all -i 1.R.pdb -s '[(a,b,1.6)]' --tsopt -o out | as above |
all (ts-only) | Pre-existing TS candidate | pdb2reaction all -i ts.xyz -q 0 -m 1 --tsopt --thermo -o out | out/segments/seg_01/{ts,irc,freq}/... + out/segments/seg_01/structures/*.pdb |
extract | Active-site cluster cut | pdb2reaction extract -i raw.pdb -c 'SAM,GPP' -l 'SAM:1,GPP:-3' -r 2.6 -o cluster.pdb | cluster.pdb (-o is the output file path, not a directory) |
path-search | Recursive MEP w/ bond-change segmentation | pdb2reaction path-search -i 1.R.pdb 3.P.pdb -o out | out/hei_seg_NN.xyz + out/summary.json |
path-opt | Single-segment MEP refinement | pdb2reaction path-opt -i 1.R.pdb 2.P.pdb -o out | out/final_geometries_trj.xyz |
opt | Geometry minimization (LBFGS / RFO) | pdb2reaction opt -i geom.pdb -o out | out/final_geometry.xyz |
tsopt | TS optimization (RS-P-RFO / Dimer) | pdb2reaction tsopt -i ts.xyz -q 0 -m 1 -o out | out/final_geometry.xyz; result.json.n_imaginary_modes==1 for true TS |
freq | Hessian + QRRHO thermo | pdb2reaction freq -i geom.xyz -q 0 -m 1 -o out | out/frequencies_cm-1.txt, out/thermoanalysis.yaml |
sp | Single-point MLIP energy + forces (+optional Hessian) | pdb2reaction sp -i geom.pdb -q 0 -m 1 -o out | out/forces.npy (+ out/hessian.npy with --hess); energy printed to stdout; out/result.json + out/summary.json only with --out-json |
irc | IRC from a TS | pdb2reaction irc -i ts.xyz -q 0 -m 1 -o out | out/{forward,backward,finished}_irc_trj.xyz |
dft | Single-point DFT (PySCF / GPU4PySCF) | pdb2reaction dft -i geom.pdb --func-basis 'wb97m-v/def2-tzvpd' -o out | out/result.yaml always (energy.hartree, energy.engine); out/result.json with --out-json |
scan | 1D distance scan w/ restraints | pdb2reaction scan -i 1.R.pdb -s '[(a,b,1.6)]' -o out | out/scan_trj.xyz, per-stage stage_NN/result.xyz |
scan2d | 2D distance grid scan | pdb2reaction scan2d -i 1.R.pdb -s '[(a,b,1.3,3.1),(c,d,1.2,3.2)]' -o out | out/surface.csv + out/grid/point_i<d1Å>_j<d2Å>.xyz + out/scan2d_map.png |
scan3d | 3D distance grid scan | pdb2reaction scan3d -i 1.R.pdb -s '[(a,b,L,H),(c,d,L,H),(e,f,L,H)]' -o out | out/surface.csv + out/grid/point_i<d1Å>_j<d2Å>_k<d3Å>.xyz + out/scan3d_density.html |
trj2fig | Energy profile from XYZ trj | pdb2reaction trj2fig -i trj.xyz | energy.png (default when no -o) |
energy-diagram | Diagram from energy values | pdb2reaction energy-diagram -i "[0.0, 21.5, -0.7]" --label-x "['R','TS','P']" | energy_diagram.png |
add-elem-info | Add PDB element column (cols 77-78) | pdb2reaction add-elem-info -i raw.pdb -o fixed.pdb | fixed.pdb |
fix-altloc | Resolve PDB alternate locations | pdb2reaction fix-altloc -i raw.pdb -o fixed.pdb | fixed.pdb (single conformation per residue) |
bond-summary | Diff bonds between consecutive structures | pdb2reaction bond-summary -i reactant.pdb -i product.pdb (or positional R.pdb P.pdb) | stdout text by default; JSON to stdout with --json |
