ViennaPTM package

• Introduction
• Installation
• Tutorial
• List of PTMs
• Entrypoint
• API
• Citation

Datastructures —

AnnotatedStructure(id)

Extension of Bio.PDB.Structure.Structure with annotation support.

Modifier —

Modifier([library])	Applies residue-level chemical modifications to a biomolecular structure.
AddBranch(*, anchor_atoms, weights, add_atoms)	Definition of an application branch for residue transformation.
Modification(*, ...)	Definition of a residue application.
ModificationLibraryMetadata(*[, date, ...])	Container for library metadata such as the date it was created.
ModificationLibrary([library_path, ...])	Container and loader for residue modifications and template structures.
ModifierParameters(*, config, input, modify, ...)	Configuration model for a ViennaPTM command-line run.

GROMACS —

EditConf(input_gro, output_gro, **kwargs)	Wrapper for the GROMACS editconf command.
GromacsCommand([gmx_bin, mpi, workdir, ...])	Abstract base class for all GROMACS command wrappers.
Grompp(mdp, structure, topology, tpr, **kwargs)	Wrapper for the GROMACS grompp preprocessor command.
PDB2GMXParameters(*, input[, output_gro, ...])	Parameter model for the GROMACS pdb2gmx command.
PDB2GMX(params[, mpi, workdir, stdin, ...])	Wrapper for the GROMACS pdb2gmx topology generation command.
Mdrun(deffnm, **kwargs)	Wrapper for the GROMACS mdrun execution command.
Trjconv(structure, tpr, output_pdb, **kwargs)	Wrapper for the GROMACS trjconv trajectory conversion command.

Miscellaneous —

compute_alignment_transform(coord_reference, ...)	Compute the roto-translational transform (with weights!) that aligns coord_template to coord_reference.
apply_transform(coords, M_rotation, ...)	Apply a roto-translational transform to a set of points, i.e. the atomic positions of atoms that are to be added from the template to the original reference frame.
minimize_and_write_pdb(conf_gro, topology, ...)	Run an energy minimization workflow and write a minimized PDB file.
Visualizer(*, structure[, name, cartoon_color])	Interactive 3D visualization wrapper for biomolecular structures.