Amide

mbuild_polybuild.aa_functional_groups.amide.Amide

class mbuild_polybuild.aa_functional_groups.amide.Amide

Bases: Compound

An amide group (-C(=O)N(H)-).

This class initializes an amide functional group by loading its structure from a PDB file and setting up its ports for molecular assembly.

Ports

• port[0]: Connection to the carbon atom.

• port[1]: Connection to the nitrogen atom.

Examples

>>> from mbuild_polybuild.aa_functional_groups.amide import Amide
>>> amide = Amide()

Amide.box	Get the box of the Compound.
Amide.center	Get the cartesian center of the Compound based on its Particles.
Amide.charge	Return the total charge of a compound.
Amide.element	Get the element of the Compound.
Amide.mass	Return the total mass of a compound.
Amide.maxs	Return the maximum x, y, z coordinate of any particle in this compound.
Amide.mins	Return the mimimum x, y, z coordinate of any particle in this compound.
Amide.n_bonds	Return the total number of bonds in the Compound.
Amide.n_direct_bonds	Return the number of bonds a particle is directly involved in.
Amide.n_particles	Return the number of Particles in the Compound.
Amide.periodicity	Get the periodicity of the Compound.
Amide.pos	Get the position of the Compound.
Amide.root	Get the Compound at the top of self's hierarchy.
Amide.xyz	Return all particle coordinates in this compound.
Amide.xyz_with_ports	Return all particle coordinates in this compound including ports.

Amide.add(new_child[, label, containment, ...])	Add a part to the Compound.
Amide.add_bond(particle_pair[, bond_order])	Add a bond between two Particles.
Amide.all_ports()	Return all Ports referenced by this Compound and its successors.
Amide.ancestors()	Generate all ancestors of the Compound recursively.
Amide.available_ports()	Return all unoccupied Ports referenced by this Compound.
Amide.bonds([return_bond_order])	Return all bonds in the Compound and sub-Compounds.
Amide.check_for_overlap(excluded_bond_depth)	Check if a compound contains overlapping particles.
Amide.condense([inplace])	Condense the hierarchical structure of the Compound to the level of molecules.
Amide.direct_bonds([graph_depth])	Return a list of particles that this particle bonds to.
Amide.energy_minimize([forcefield, steps, ...])	Perform an energy minimization on a Compound.
Amide.flatten([inplace])	Flatten the hierarchical structure of the Compound.
Amide.freud_generate_bonds(name_a, name_b, ...)	Add Bonds between all pairs of types a/b within [dmin, dmax].
Amide.from_gmso(topology[, coords_only, ...])	Convert a GMSO Topology to mBuild Compound.
Amide.from_parmed(structure[, coords_only, ...])	Extract atoms and bonds from a pmd.Structure.
Amide.from_pybel(pybel_mol[, use_element, ...])	Create a Compound from a Pybel.Molecule.
Amide.from_trajectory(traj[, frame, ...])	Extract atoms and bonds from a md.Trajectory.
Amide.generate_bonds(name_a, name_b, dmin, dmax)	Add Bonds between all pairs of types a/b within [dmin, dmax].
Amide.get_boundingbox([pad_box])	Compute the bounding box of the compound.
Amide.get_smiles()	Get SMILES string for compound.
Amide.is_independent()	Return True if there is no bond between particles of the Compound to an external Compound.
Amide.min_periodic_distance(xyz0, xyz1)	Vectorized distance calculation considering minimum image.
Amide.particles([include_ports])	Return all Particles of the Compound.
Amide.particles_by_element(element)	Return all Particles of the Compound with a specific element.
Amide.particles_by_name(name)	Return all Particles of the Compound with a specific name.
Amide.particles_in_range(compound, dmax[, ...])	Find particles within a specified range of another particle.
Amide.print_hierarchy([print_full, index, ...])	Print the hierarchy of the Compound.
Amide.referenced_ports()	Return all Ports referenced by this Compound.
Amide.remove(objs_to_remove[, reset_labels])	Remove children from the Compound cleanly.
Amide.remove_bond(particle_pair)	Delete a bond between a pair of Particles.
Amide.reset_labels()	Reset Compound labels so that substituents and ports are renumbered, indexed from port[0] to port[N], where N-1 is the number of ports.
Amide.rotate(theta, around)	Rotate Compound around an arbitrary vector.
Amide.rotate_dihedral(bond, phi)	Rotate a dihedral about a central bond.
Amide.save(filename[, include_ports, box, ...])	Save the Compound to a file.
Amide.spin(theta, around[, anchor])	Rotate Compound in place around an arbitrary vector.
Amide.successors()	Yield Compounds below self in the hierarchy.
Amide.to_freud()
Amide.to_gmso(**kwargs)	Create a GMSO Topology from a mBuild Compound.
Amide.to_hoomdsnapshot(**kwargs)	Create a HOOMD-Blue snapshot from an mBuild Compound.
Amide.to_intermol([molecule_types])	Create an InterMol system from a Compound.
Amide.to_networkx([names_only])	Create a NetworkX graph representing the hierarchy of a Compound.
Amide.to_parmed([box, title, residues, ...])	Create a ParmEd Structure from a Compound.
Amide.to_pybel([box, title, residues, ...])	Create a pybel.Molecule from a Compound.
Amide.to_rdkit()	Create an RDKit RWMol from an mBuild Compound.
Amide.to_smiles([backend])	Create a SMILES string from an mbuild compound.
Amide.to_trajectory([include_ports, chains, ...])	Convert to an md.Trajectory and flatten the compound.
Amide.translate(by)	Translate the Compound by a vector.
Amide.translate_to(pos)	Translate the Compound to a specific position.
Amide.update_coordinates(filename[, ...])	Update the coordinates of this Compound from a file.
Amide.visualize([show_ports, backend, ...])	Visualize the Compound using py3dmol (default) or nglview.