Add missing terminal cappings#

Adding terminal cappings to peptides and proteins.

Capping the termini of peptides and proteins is often required in molecular modeling to ensure charge neutrality, stability, or to match specific biological conditions. The function molsysmt.build.add_missing_terminal_cappings() adds chemical capping groups (such as ACE for N-terminus and NME for C-terminus) or completes uncapped terminal residues.

Added in version 1.0.0.

API documentation

Follow this link for a detailed description of the input arguments, raised errors, and returned objects of this function: molsysmt.build.add_missing_terminal_cappings().

Basic usage#

Let’s show how this function works using a tripeptide example (AlaValPro):

import molsysmt as msm

molsys = msm.build.build_peptide('AlaValPro', to_form='molsysmt.MolSys')

msm.info(molsys, element='group')

index	id	name	type	n atoms	molecule type	entity name
0	1	ALA	amino acid	10	peptide	peptide 0
1	2	VAL	amino acid	16	peptide	peptide 0
2	3	PRO	amino acid	14	peptide	peptide 0

As shown, the termini of the peptide are currently incomplete. We now add the atoms required to complete the terminal amino acids without capping groups, producing a charged version of the peptide:

molsys_charged = msm.build.add_missing_terminal_cappings(molsys, N_terminal=None, C_terminal=None)

msm.info(molsys_charged, element='group')

index	id	name	type	n atoms	molecule type	entity name
0	1	ALA	amino acid	12	peptide	peptide 0
1	2	VAL	amino acid	16	peptide	peptide 0
2	3	PRO	amino acid	15	peptide	peptide 0

Let’s check the group charges under these conditions using molsysmt.physchem.get_charge():

msm.physchem.get_charge(molsys_charged, element='group')

Magnitude	[0.0 0.0 0.0]
Units	elementary_charge

To neutralize terminal charges, we can cap the N-terminus with an acetyl group (ACE) and the C-terminus with an N-methyl amide group (NME):

molsys_uncharged = msm.build.add_missing_terminal_cappings(molsys, N_terminal='ACE', C_terminal='NME')

msm.info(molsys_uncharged, element='group')

index	id	name	type	n atoms	molecule type	entity name
0	0	ACE	terminal capping	6	peptide	peptide 0
1	1	ALA	amino acid	10	peptide	peptide 0
2	2	VAL	amino acid	16	peptide	peptide 0
3	3	PRO	amino acid	14	peptide	peptide 0
4	4	NME	terminal capping	6	peptide	peptide 0

We inspect the group charges again to confirm that the capped peptide is now neutral:

msm.physchem.get_charge(molsys_uncharged, element='group')

Magnitude	[0.0 0.0 0.0 0.0 0.0]
Units	elementary_charge

Native domain preservation#

Native insertion of terminal atoms or ACE/NME requires one chemical state. Existing atom IDs, chemical assignments, state identity/provenance and coordinates survive. Inserted groups can change atom/group indices. New chemical values remain unknown and connectivity is partial: a modeled capping geometry does not declare or validate all terminal chemistry. Assign the intended chemical state separately.

Named interaction analyses retain their definitions and remapped source axes; occurrences and evaluated coverage are cleared for recalculation. Structural attributes or force-field atom parameters without values for new atoms are dropped with a diagnostic. Observe these diagnostics in preparation workflows. The strict attribute-loss option belongs to the separate heavy-atom repair tool; this terminal tool keeps its existing intersection behavior.

Inspecting nonterminal gaps#

The native engine also calls bounded heavy-atom repair. Unsupported side-chain gaps remain missing with a warning even when OXT or ACE/NME insertion succeeds. Inspect both msm.build.get_missing_terminal_cappings(molsys_charged) and msm.build.get_missing_heavy_atoms(molsys_charged). PDBFixer can choose wider heavy-atom reconstruction, so whole-system counts need not match between engines. Matching terminal inventories do not certify all side-chain coordinates.