extract

Overview

Summary: Extract a cluster model (active-site pocket) from a protein–ligand PDB. Specify substrates with -c by residue name, residue ID, or a PDB path. Link hydrogens are added to cap cut bonds. Use --ligand-charge for non-standard residue charges.

At a glance

• Input: One or more complex PDBs with consistent atom ordering (ensemble mode supported).

• Substrate selection (-c): residue IDs (A:123A), residue names (GPP,SAM), or a substrate PDB that matches the complex coordinates.

• Selection logic: distance cutoff (--radius) plus optional hetero–hetero proximity (--radius-het2het) and peptide/disulfide/PRO safeguards.

• Truncation & capping: trims residues/segments and optionally adds link hydrogens (--add-linkH True by default).

• Charges: unknown residues default to 0 unless --ligand-charge supplies a total charge or per-resname mapping.

pdb2reaction extract creates an active-site pocket (cluster model) from a protein–ligand PDB. It selects residues near the substrate, truncates the model according to backbone/side-chain rules, optionally caps severed bonds with link hydrogens, and can process single structures or ensembles.

If you run into misclassification (e.g., unusual residue/atom naming), see the appendix below on naming requirements and the internal reference lists.

Usage

pdb2reaction extract -i COMPLEX.pdb [COMPLEX2.pdb ...]
                     -c SUBSTRATE_SPEC
                     [-o POCKET.pdb [POCKET2.pdb ...]]
                     [--radius Å] [--radius-het2het Å]
                     [--include-H2O {True\|False}]
                     [--exclude-backbone {True\|False}]
                     [--add-linkH {True\|False}]
                     [--selected-resn LIST]
                     [--ligand-charge MAP_OR_NUMBER]
                     [--verbose {True\|False}]

Examples

# Minimal (ID-based substrate) with explicit total ligand charge
pdb2reaction extract -i complex.pdb -c '123' -o pocket.pdb --ligand-charge -3

# Substrate provided as a PDB; per-resname charge mapping (others remain 0)
pdb2reaction extract -i complex.pdb -c substrate.pdb -o pocket.pdb --ligand-charge 'GPP:-3,SAM:1'

# Name-based substrate selection including all matches (WARNING is logged)
pdb2reaction extract -i complex.pdb -c 'GPP,SAM' -o pocket.pdb --ligand-charge 'GPP:-3,SAM:1'

# Multi-structure to single multi-MODEL output with hetero-hetero proximity enabled
pdb2reaction extract -i complex1.pdb complex2.pdb -c 'GPP,SAM' -o pocket_multi.pdb --radius-het2het 2.6 --ligand-charge 'GPP:-3,SAM:1'

# Multi-structure to multiple outputs with hetero-hetero proximity enabled
pdb2reaction extract -i complex1.pdb complex2.pdb -c 'GPP,SAM' -o pocket1.pdb pocket2.pdb --radius-het2het 2.6 --ligand-charge 'GPP:-3,SAM:1'

Workflow

Residue inclusion

• Always include the substrate residues from -c/--center.

• Standard cutoff (--radius, default 2.6 Å):

  • When --exclude-backbone False, any atom within the cutoff qualifies a residue.

  • When --exclude-backbone True, amino-acid residues must contact the substrate with a non-backbone atom (not N/H*/CA/HA*/C/O). Non-amino acids use any atom.

• Independent hetero–hetero cutoff (--radius-het2het): adds residues when a substrate hetero atom (non C/H) lies within the specified Å of a protein hetero atom. With backbone exclusion enabled the protein atom must be non-backbone.

• Water handling: HOH/WAT/H2O/DOD/TIP/TIP3/SOL are included by default (--include-H2O True).

• Forced inclusion: --selected-resn accepts IDs with chains/insertion codes (e.g., A:123A).

• Neighbor safeguards:

  • When backbone exclusion is off and a residue contacts the substrate with a backbone atom, auto-include the peptide-adjacent N/C neighbors (C–N ≤ 1.9 Å). Termini keep caps (N/H* or C/O/OXT).

  • Disulfide bonds (SG–SG ≤ 2.5 Å) bring both cysteines.

  • Non-terminal PRO residues always pull in the N-side amino acid; CA is preserved even if backbone atoms are removed, and when --exclude-backbone True, the neighbor’s C/O/OXT remain to maintain the peptide bond.

Truncation/capping

• Isolated residues retain only side-chain atoms; amino-acid backbone atoms (N, CA, C, O, OXT plus N/CA hydrogens) are removed except for PRO/HYP safeguards.

• Continuous peptide stretches keep internal backbone atoms; only terminal caps (N/H* or C/O/OXT) are removed. TER awareness prevents capping across chain breaks.

• With --exclude-backbone True, main-chain atoms on all non-substrate amino acids are stripped (subject to PRO/HYP safeguards and PRO neighbor retention).

• Non-amino-acid residues never lose atoms named like backbone (N/CA/HA/H/H1/H2/H3).

Link hydrogens (--add-linkH True)

• Adds carbon-only link hydrogens at 1.09 Å along severed bond vectors (CB–CA, CA–N, CA–C; PRO/HYP use CA–C only).

• Inserted after a TER as contiguous HETATM records named HL in residue LKH (chain L). Serial numbers continue from the main block.

• In multi-structure mode the same bonds are capped across all models; coordinates remain model-specific.

Charge summary (--ligand-charge)

• Amino acids and common ions draw charges from internal dictionaries; waters are zero.

• Unknown residues default to 0 unless --ligand-charge supplies either a total charge (distributed across unknown substrate residues, or all unknowns when no unknown substrate) or a per-resname mapping like GPP:-3,SAM:1.

• Summaries (protein/ligand/ion/total) are logged for the first input when verbose mode is enabled.

Multi-structure ensembles

• Accepts multiple input PDBs (identical atom ordering is validated at the head/tail of each file). Each structure is processed independently and the union of selected residues is applied to every model so that outputs remain consistent.

• Output policy:

  • No -o, multiple inputs → per-file pocket_<original_basename>.pdb.

  • One -o path → single multi-MODEL PDB.

  • N outputs where N == number of inputs → N individual PDBs.

• Diagnostics echo raw vs. kept atom counts per model along with residue IDs.

Substrate specification (-c/--center)

• PDB path: the coordinates must match the first input exactly (tolerance 1e-3 Å); residue IDs propagate to other structures.

• Residue IDs: '123,124', 'A:123,B:456', '123A', 'A:123A' (insertion codes supported).

• Residue names: comma-separated list (case insensitive). If multiple residues share a name, all matches are included and a warning is logged.

CLI options

Note: Default values shown are used when the option is not specified.

Option	Description	Default
-i, --input PATH...	One or more protein–ligand PDB files (identical atom ordering required).	Required
-c, --center SPEC	Substrate specification (PDB path, residue IDs, or residue names).	Required
-o, --output PATH...	Pocket PDB output(s). One path ⇒ multi-MODEL, N paths ⇒ per input.	Auto (pocket.pdb or pocket_<input>.pdb)
-r, --radius FLOAT	Atom–atom distance cutoff (Å) for inclusion.	2.6
--radius-het2het FLOAT	Independent hetero–hetero cutoff (Å, non C/H).	0.0 (internally 0.001 Å when zero)
--include-H2O {True|False}	Include HOH/WAT/H2O/DOD/TIP/TIP3/SOL waters.	True
--exclude-backbone {True|False}	Remove backbone atoms on non-substrate amino acids (PRO/HYP safeguards).	True
--add-linkH {True|False}	Add carbon-only link hydrogens at 1.09 Å along severed bonds.	True
--selected-resn TEXT	Force-include residues (IDs with optional chains/insertion codes).	""
--ligand-charge TEXT	Total charge or per-resname mapping (e.g., GPP:-3,SAM:1).	None
-v, --verbose {True|False}	Emit INFO-level logging (True) or keep warnings only (False).	True

Outputs

<output>.pdb  # Pocket PDB(s) with optional link hydrogens after a TER record
               # Single input → pocket.pdb by default
               # Multiple inputs without -o → pocket_<original_basename>.pdb per structure
               # One -o path with multiple inputs → single multi-MODEL PDB
               # Output directories are not created automatically; ensure they exist

• Charge summary (protein/ligand/ion/total) is logged for model #1 when verbose mode is enabled.

• Programmatic use (extract_api) returns {"outputs": [...], "counts": [...], "charge_summary": {...}}.

Appendix: PDB naming requirements and reference lists

This appendix is mainly for debugging cases where extract misclassifies residues due to non-standard residue/atom naming. If your inputs follow standard PDB conventions, you can usually skip it.

Important

For extract to work correctly, residue names and atom names in the input PDB must conform to standard PDB naming conventions. The tool relies on internal dictionaries to recognize amino acids, ions, water molecules, and backbone atoms. Non-standard naming will cause residues to be misclassified or charges to be incorrectly assigned.

The following internal constants define the recognized names:

AMINO_ACIDS

A dictionary mapping residue names to their nominal integer charges. Membership in this dictionary determines whether a residue is treated as an amino acid for backbone handling, truncation, and charge calculation.

Standard 20 amino acids (charges reflect physiological pH):

• Neutral: ALA, ASN, CYS, GLN, GLY, HIS, ILE, LEU, MET, PHE, PRO, SER, THR, TRP, TYR, VAL

• Positive (+1): ARG, LYS

• Negative (−1): ASP, GLU

Canonical extras:

• SEC (selenocysteine, 0), PYL (pyrrolysine, +1)

Protonation/tautomer variants (Amber/CHARMM style):

• HIP (+1, fully protonated His), HID (0, Nδ-protonated His), HIE (0, Nε-protonated His)

• ASH (0, neutral Asp), GLH (0, neutral Glu), LYN (0, neutral Lys), ARN (0, neutral Arg)

• TYM (−1, deprotonated Tyr phenolate)

Phosphorylated residues:

• Dianionic (−2): SEP, TPO, PTR

• Monoanionic (−1): S1P, T1P, Y1P

• Phospho-His (phosaa19SB): H1D (0), H2D (−1), H1E (0), H2E (−1)

Cysteine variants:

• CYX (0, disulfide), CSO (0, sulfenic acid), CSD (−1, sulfinic acid), CSX (0, generic derivative)

• OCS (−1, cysteic acid), CYM (−1, deprotonated Cys)

Lysine variants / carboxylation:

• MLY (+1), LLP (+1), KCX (−1, Nz-carboxylic acid)

D-amino acids (19 residues):

• DAL, DAR, DSG, DAS, DCY, DGN, DGL, DHI, DIL, DLE, DLY, MED, DPN, DPR, DSN, DTH, DTR, DTY, DVA

Other modified residues:

• CGU (−2, gamma-carboxy-glutamate), CGA (−1), PCA (0, pyroglutamate), MSE (0, selenomethionine), OMT (0, methionine sulfone), HYP (0, hydroxyproline)

• Various others: ASA, CIR, FOR, MVA, IIL, AIB, HTN, SAR, NMC, PFF, NFA, ALY, AZF, CNX, CYF

N-terminal variants (prefix N): NALA (+1), NARG (+2), NASP (0), NGLU (0), NLYS (+2), etc., plus ACE (0), NTER (+1, generic)

C-terminal variants (prefix C): CALA (−1), CARG (0), CASP (−2), CGLU (−2), CLYS (0), etc., plus NHE (0), NME (0), CTER (−1, generic)

BACKBONE_ATOMS

A set of atom names considered backbone atoms for amino acids. These are used when --exclude-backbone True to determine which atoms to remove from non-substrate residues:

N, C, O, CA, OXT, H, H1, H2, H3, HN, HA, HA2, HA3

ION

A dictionary mapping ion residue names to their formal charges. Recognized ions are automatically assigned correct charges in the charge summary.

Charge	Residue Names
+1	LI, NA, K, RB, CS, TL, AG, CU1, Ag, K+, NA+, NH4, H3O+
+2	MG, CA, SR, BA, MN, FE2, CO, NI, CU, ZN, CD, HG, PB, BE, PD, PT, SN, RA, YB2, V2+
+3	FE, AU3, AL, GA, IN, CE, CR, DY, EU, EU3, ER, GD3, LA, LU, ND, PR, SM, TB, TM, Y, PU
+4	U4+, TH, HF, ZR
−1	F, CL, BR, I, CL-, IOD

WATER_RES

A set of residue names recognized as water molecules. Waters are included by default (--include-H2O True) and assigned zero charge:

HOH, WAT, H2O, DOD, TIP, TIP3, SOL

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Notes

• --radius defaults to 2.6 Å; 0 is nudged to 0.001 Å to avoid empty selections. --radius-het2het is off by default (also nudged to 0.001 Å when zero is provided).

• Waters can be excluded with --include-H2O False.

• Backbone trimming plus capping respect chain breaks and PRO/HYP safeguards as outlined above; non-amino residues never lose backbone-like atom names.

• Link hydrogens are inserted only on carbon cuts and reuse identical bonding patterns across models in ensemble mode.

• INFO logs summarize residue selection, truncation counts, and charge breakdowns.

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See Also

• all — End-to-end workflow that calls extract internally via -c/--center

• path-search — MEP search on extracted pockets

• scan — Staged scan on extracted pockets

• add-elem-info — Fix missing PDB element columns before extraction

• Troubleshooting — Common extraction errors

• Glossary — Definitions of Pocket, Cluster Model, Link Hydrogen