Build

For explicit topology construction, use molsysmt.MolSysBuilder. Declare atoms and groups first, add bonds with optional metadata such as builder.add_bond(atom_0, atom_1, bond_order=2, bond_type="covalent"), assign coordinates with set_coordinates(), and call build() to materialize a native system. Before materialization, molsysmt.get(builder, ...) reads the complete declared attribute union of the builder’s chemical/topological and structural components. A builder does not store molecular-mechanics attributes or per-structure chemical-state associations. The four course paths include complete builder examples.

Conversions among molsysmt.MolSys, molsysmt.MolSysBuilder, and molsysmt.MolSysDict provide exhaustive fidelity reports. The reduced dictionary conversion canonicalizes atom selections, preserves the requested structure_indices order, and rejects detected loss when strict=True.

bond_order is the formal numeric order; bond_type describes the chemical relationship and accepts covalent, dative, or explicitly unknown. Aromaticity, fractional order, and force-field parameter classes are distinct concepts and are not encoded as arbitrary bond_type labels.

Add bonds	Adding new covalent bonds between atoms in a molecular system
Add missing bonds	Adding the missing bonds in a molecular system
Add missing heavy atoms	Adding the missing heavy atoms in a molecular system
Add missing hydrogens	Adding the missing hydrogen atoms in a molecular system
Add missing terminal_cappings	Adding the missing terminal cappings in a molecular system
Build peptide	Building a peptide
Define new chain	Define a new chain with new id and name attributes
Get disulfide bonds	Getting the disulfide bonds of a molecular system
Get missing bonds	Getting the missing bonds of a molecular system
Get missing heavy_atoms	Getting the missing heavy atoms of a molecular system
Get missing residues	Getting the missing residues of a molecular system
Get missing terminal_cappings	Getting the missing terminal cappings of a molecular system
Get non standard residues	Getting the non standard residues of a molecular system
Has hydrogens	Checking if a molecular system has hydrogen atoms
Is solvated	Checking if a molecular system is solvated
Make bioassembly	Making a bioassembly of a molecular system
Make water box	Making a water box system
Mutate	Mutating residues in a molecular system
Remove overlapping molecules	Removing overlapping molecules in a molecular system
Solvate	Solvating of a molecular system
Solve atoms with alternate location	Solving the coordinates of atoms with alternate locations in a molecular system