Glossary

This page provides definitions for abbreviations and technical terms used throughout the pdb2reaction documentation.

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Reaction Path & Optimization

Term	Full Name	Description
MEP	Minimum Energy Path	The lowest-energy pathway connecting reactants to products through a transition state (on a potential energy surface).
TS	Transition State	A first-order saddle point on the potential energy surface, typically the highest-energy point along the reaction coordinate.
IRC	Intrinsic Reaction Coordinate	A mass-weighted steepest-descent path from a TS toward reactants and products. Often used to validate TS connectivity.
GSM	Growing String Method	A string-based method that grows images from endpoints and optimizes them to approximate an MEP.
DMF	Direct Max Flux	A chain-of-states method for optimizing an MEP by maximizing flux along the pathway. In pdb2reaction it is selected with --mep-mode dmf.
NEB	Nudged Elastic Band	A chain-of-states method that uses spring forces to maintain image spacing along a reaction path.
HEI	Highest-Energy Image	The image along an MEP with maximum energy; often used as a TS guess.
Image	—	A single geometry (one “node”) along a chain-of-states path.
Segment	—	An MEP between two adjacent endpoints (e.g., R → I1, I1 → I2, …).

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Optimization Algorithms

Term	Full Name	Description
L-BFGS	Limited-memory BFGS	A quasi-Newton optimization algorithm that approximates the Hessian using a limited history of gradients. Used in --opt-mode light.
RFO	Rational Function Optimization	A trust-region optimization method that uses explicit Hessian information. Used in --opt-mode heavy.
RS-I-RFO	Restricted-Step Image-RFO	A variant of RFO for saddle point (TS) optimization that follows one negative eigenvalue.
Dimer	Dimer Method	A TS optimization method that estimates the lowest curvature mode without computing the full Hessian. Used in --opt-mode light for TSOPT.

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Machine Learning & Calculators

Term	Full Name	Description
MLIP	Machine Learning Interatomic Potential	A model (often neural-network-based) that predicts energies and forces from atomic structures, trained on quantum-mechanical data.
UMA	Universal Machine-learning potential for Atoms	Meta’s family of pretrained MLIPs used as the default calculator backend in pdb2reaction.
Analytical Hessian	—	Computing the exact second derivatives of energy; faster but requires more VRAM.
Finite Difference	—	Approximating derivatives by small displacements; slower but more memory-efficient.

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Quantum Chemistry

Term	Full Name	Description
QM	Quantum Mechanics	First-principles electronic structure calculations (DFT, HF, post-HF, etc.).
DFT	Density Functional Theory	A quantum-mechanical method that models electronic structure via electron density functionals.
Hessian	—	The matrix of second derivatives of energy with respect to atomic coordinates; used for vibrational analysis and TS optimization.
SP	Single Point	A calculation at a fixed geometry (no optimization); often used for higher-level energy refinement.
Spin Multiplicity	—	2S+1, where S is total spin. Singlet = 1, doublet = 2, triplet = 3, etc.

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Structural Biology & Pocket Extraction

Term	Full Name	Description
PDB	Protein Data Bank	A file format and database for macromolecular 3D structures.
XYZ	—	A simple text format listing atomic symbols and Cartesian coordinates.
GJF	Gaussian Job File	An input format for Gaussian; pdb2reaction reads charge/multiplicity and coordinates from these files.
Pocket	Active-site Pocket	A truncated structure around the substrate(s) used to reduce system size for MEP/TS search. Also called “cluster model”.
Cluster Model	—	Synonym for pocket; a computationally tractable subset of the full enzyme–substrate complex.
Link Hydrogen	—	A hydrogen atom added to cap severed bonds when extracting a pocket from a larger structure.
Backbone	—	The main chain of a protein (N–Cα–C–O atoms). Can be excluded during pocket extraction with --exclude-backbone True.

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Thermochemistry

Term	Full Name	Description
ZPE	Zero-Point Energy	The vibrational energy at 0 K; a quantum correction to the electronic energy.
Gibbs Energy	Free Energy (G)	G = H − TS; includes thermal and entropic contributions.
Enthalpy	(H)	H = E + PV; total heat content at constant pressure.
Entropy	(S)	A measure of disorder; contributes −TS to Gibbs energy.

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Units & Constants

Term	Description
Hartree	Atomic unit of energy; 1 Hartree ≈ 627.5 kcal/mol ≈ 27.21 eV.
kcal/mol	Kilocalories per mole; a common unit for reaction energetics.
kJ/mol	Kilojoules per mole; 1 kcal/mol ≈ 4.184 kJ/mol.
eV	Electron volt; 1 eV ≈ 23.06 kcal/mol.
Bohr	Atomic unit of length; 1 Bohr ≈ 0.529 Å.
Angstrom (Å)	10⁻¹⁰ meters; standard unit for atomic distances.

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CLI Conventions

Term	Description
Boolean option	CLI flags that take True or False (capitalized). Example: --tsopt True.
Residue selector	A specification like 'SAM,GPP' (names) or 'A:123,B:456' (chain:ID).
Atom selector	A specification like 'TYR,285,CA' identifying a specific atom by residue name, number, and atom name.

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See Also

• Getting Started — installation and a first run

• Concepts & Workflow — how pocket extraction, MEP search, and post-processing fit together

• Troubleshooting — common errors and fixes

• YAML Reference — configuration file format

• UMA Calculator — machine learning potential details