Molecule

Details

Base class for all flowerMD molecules, Polymers, and CoPolymers.

class flowermd.base.molecule.Molecule(num_mols, force_field=None, smiles=None, file=None, compound=None)

Base class for all flowerMD molecules.

The Molecule class generates molecules from the provided input and can be used to initialize a molecular structure. This class also provides information about the molecule topology, such as the number of particles, bonds, angles, etc.

Parameters:

  • num_mols (int, required) – Number of molecules to generate.

  • force_field (flowermd.ForceField or a list of) – hoomd.md.force.Force objects, default=None The forcefield to be applied to the molecule for parameterization. Note that setting force_field does not actually apply the forcefield to the molecule. The forcefield in this step is mainly used for validation purposes.

  • smiles (str, default None) – The smiles string of the molecule to generate.

  • file (str, default None) – The file path to the molecule to generate. Supported file types are: .mol2, .pdb, .sdf

  • compound (mbuild Compound or GMSO Topology, default None) – The mbuild Compound or GMSO Topology of the molecule to generate.

Notes

The molecule can be generated from either a smiles string, a file path, or a mbuild Compound or GMSO Topology.

coarse_grain(beads=None)

Coarse grain the molecule.

Parameters:

beads (dict, default None) – A dictionary of bead names and their corresponding SMILES string.

Examples

Coarse grain atomistic benzene molecules into a single bead type called “A”.

>>> from flowermd import Molecule
>>> benzene = Molecule(num_mols=10, smiles="c1ccccc1")
>>> benzene.coarse_grain(beads={"A": "c1ccccc1"})

Warning

The changes applied by coarse grain are in-place. All molecule properties will be modified after coarse graining based on the bead mapping.

property mapping

Dictionary of particle index to coarse grained bead mapping.

property molecules

List of all instances of the molecule.

property n_bonds

Total number of bonds in all of the molecules.

property n_particles

Total number of particles in all of the molecules.

property topology_information

Dictionary of topology information for the molecule.

The dictionary contains the following keys:

  • particle_types: list of all particle types.

  • hydrogen_types: list of all hydrogen types.

  • particle_charge: list of all particle charges.

  • particle_typeid: list of all particle type indices.

  • pair_types: list of all unique particle pairs.

  • bond_types: list of all unique bond types.

  • angle_types: list of all unique angle types.

  • dihedral_types: list of all unique dihedral types.

  • improper_types: list of all unique improper types.

class flowermd.base.molecule.Polymer(lengths, num_mols, smiles=None, file=None, force_field=None, bond_indices=None, bond_length=None, bond_orientation=None, **kwargs)

Bases: Molecule

Builds a polymer from a monomer.

Parameters:

  • lengths (int, required) – The total number of monomers in each chain.

  • num_mols (int, required) – Number of chains to generate.

  • smiles (str, default None) – The smiles string of the monomer to generate.

  • file (str, default None) – The file path to the monomer to generate.

  • force_field (flowermd.ForceField or a list of) – hoomd.md.force.Force objects, default=None The forcefield to be applied to the molecule for parameterization. Note that setting force_field does not actually apply the forcefield to the molecule. The forcefield in this step is mainly used for validation purposes.

  • bond_indices (list, default None) – The indices of the atoms to bond.

  • bond_length (float, default None) – The bond length between connected atoms (units: nm)

  • bond_orientation (list, default None) – The orientation of the bond between connected atoms.

property monomer

The monomer of the polymer.

class flowermd.base.molecule.CoPolymer(monomer_A, monomer_B, lengths, num_mols, force_field=None, sequence=None, AB_ratio=0.5, seed=24)

Bases: Molecule

Builds a polymer consisting of two monomer types.

Parameters:

  • monomer_A (flowermd.molecules.Polymer, required) – Class of the A-type monomer

  • monomer_B (flowermd.molecules.Polymer, required) – Class of the B-type monomer

  • length (int, required) – The total number of monomers in the molecule

  • num_mols (int, required) – Number of chains to generate.

  • sequence (str, default None) – Manually define the sequence of ‘A’ and ‘B’ monomers. Leave as None if generating random sequences. Example: sequence = “AABAABAAB”

  • AB_ratio (float, default 0.50) – The relative weight of A to B monomer types. Used when generating random sequences.

  • force_field (flowermd.ForceField or a list of) – hoomd.md.force.Force objects, default=None The forcefield to be applied to the molecule for parameterization. Note that setting force_field does not actually apply the forcefield to the molecule. The forcefield in this step is mainly used for validation purposes.

  • seed (int, default 24) – Set the seed used when generating random sequences

property A_ratio

The ratio of A monomers to B monomers in the CoPolymer.

property B_ratio

The ratio of B monomers to A monomers in the CoPolymer.