Classes

class cgbind.Linker(arch_name, smiles=None, name='linker', charge=0, n_confs=300, filename=None, use_etdg_confs=False)

__init__(arch_name, smiles=None, name='linker', charge=0, n_confs=300, filename=None, use_etdg_confs=False)

Metallocage Linker. Inherits from cgbind.molecule.Molecule

Parameters:

• arch_name – (str) Name of the architecture

• smiles – (str) SMILES string

• name – (str) Linker name

• charge – (int)

• n_confs – (int) Number of initial conformers to search through

• filename – (str)

• use_etdg_confs – (bool) Use a different, sometimes better, conformer generation algorithm

arch

(Arch object) Metallocage architecture

cage_template

(Template object) Metallocage template

dr

(float) Template shift distance

get_xmotif_coordinates()

Return a numpy array of all the coordinates in the Xmotifs

set_ranked_linker_possibilities(metal=None, n=0)

For this linker, return a list of Linker objects with appropriate .xyzs, .dr and .x_motifs attributes ordered by their cost function low -> high i.e. good to bad. This will loop through all the possibilities and the possible combinations of x motifs in the linker. Linker.dr controls how large the template needs to be to make the best fit

Parameters:

• metal – (str) Atomic symbol of the metal

• n – (int) linker number in the template

Returns:

(list(Linker))

x_atoms

(list(int)) List of donor atom ids

x_motifs

(list(Xmotif object))

class cgbind.Cage(linker=None, metal='M', metal_charge=0, linkers=None, solvent=None, mult=1, name='cage', max_cost=5)

__init__(linker=None, metal='M', metal_charge=0, linkers=None, solvent=None, mult=1, name='cage', max_cost=5)

Metallocage object. Inherits from cgbind.molecule.BaseStruct

Variables:

• self.metal – (str)

• self.linkers – (list(Linker object))

• self.dr – (float)

• self.arch – (Arch object)

• self.cage_template – (Template object)

• self.m_ids – (list(int))

• self.metal_charge – (int)

Parameters:

• name – (str) Name of the cage

• solvent – (str)

• linker – (Linker object) Linker to initialise a homoleptic metallocage

• linkers – (list(Linker object)) List of Linkers to inialise a metallocage

• metal – (str) Atomic symbol of the metal

• metal_charge – (int) Formal charge on the metal atom/ion

• mult – (int) Total spin multiplicity of the cage

• max_cost – (float) Acceptable ligand-ligand repulsion to accommodate in metallocage construction

get_cavity_vol()

For a cage extract the cavity volume defined as the volume of the largest sphere, centered on the cage centroid that may be constructed while r < r(midpoint–closest atom)

Returns:

(float) Cavity volume in Å^3

get_centroid()

Get the centroid of a metallocage. Defined as the midpoint between all self.metal atoms in the structure

Returns:

(np.ndarray) Centroid coordinate (x, y, z)

get_charges(estimate=False)

Get the partial atomic charges on the cage either using XTB or estimate using no polarisation i.e. the metals retain their full charge and the linker charges are estimated using the Gasteiger scheme in RDKit

Parameters:

• estimate – (bool)

• guess – (bool) Guess the charges based on the electronegativity

Returns:

(function) calculations.get_charges(self)

get_esp_cube(return_min_max=False)

Get the electrostatic potential (ESP) in a Gaussian .cube format by calculating partial atomic charges using XTB (tested with v. 6.2). Calls self.get_charges() and depends on self.xyzs

Parameters:

return_min_max – (bool) Return the minimum and maximum of the ESP along with the cube file lines evaluated roughly on the VdW surface

Returns:

(list) .cube file lines

get_m_m_dist()

For a cage calculate the average M-M distance

Returns:

(float) Distance in Å

get_max_escape_sphere(basinh=False, max_dist_from_metals=10)

Get the maximum radius of a sphere that can escape from the centroid of the cage – will iterate through all theta/phi

Parameters:

• basinh – (bool) Find the true maximum escape sphere by basin hopping on the surface

• max_dist_from_metals –

  (float) Distance in Å on top of the

  average M-M distance that will be used for

  the search for the maximum escape sphere

Returns:

(float) Volume of the maximum escape sphere in Å^3

get_metal_atom_ids()

Get the atom ids of the self.metal atoms in the xyzs

Returns:

(list(int))

get_num_h_bond_acceptors()

Get the number of hydrogen bond acceptors in a metallocage

Returns:

(int)

get_num_h_bond_donors()

Get the number of hydrogen bond donors in a metallocage

Returns:

(int)

get_num_rot_bonds()

Get the number of rotatable bonds in a metallocage

Returns:

(int)

print_esp_cube_file()

Print an electrostatic potential (ESP) .cube file. Prints the lines from self.get_esp_cube()

Returns:

None

class cgbind.Substrate(smiles=None, name='substrate', n_confs=1, charge=0, mult=1, filename=None, solvent=None)

__init__(smiles=None, name='substrate', n_confs=1, charge=0, mult=1, filename=None, solvent=None)

Substrate. Inherits from cgbind.molecule.Molecule

Parameters:

• smiles – (str) SMILES string

• name – (str) Molecule name

• n_confs – (int) Number of conformers to initialise with

• charge – (int) Charge on the molecule

• mult – (int) Spin multiplicity on the molecule

• filename – (str)

gen_confs(n_confs=1)

Populate self.conf_xyzs by calling RDKit

class cgbind.CageSubstrateComplex(cage, substrate, solvent=None, mult=1, n_subst_confs=1, n_init_geom=50, energy_method='repulsion')

__init__(cage, substrate, solvent=None, mult=1, n_subst_confs=1, n_init_geom=50, energy_method='repulsion')

Cage-substrate complex. Generated by minimising the energy given an energy method. Inherits from cgbind.molecule.BaseStruct

Variables:

• self.energy_func – (function)

• self.binding_energy_kcal – (float) Binding energy of the substrate in kcal mol-1

• self.n_subst_confs – (int)

• self.n_init_geom – (int)

• self.name – (str) cage.name + ‘_’ + substrate.name

• self.cage – (Cage object)

• self.substrate – (Substrate object)

Parameters:

• cage – (Cage object)

• substrate – (Substrate object)

• solvent – (str)

• mult – (int) Spin multiplicity of the cage-substrate complex

• n_subst_confs – (int) Number of substrate conformations to iterate over while minimising the energy

• n_init_geom – (int) Number of initial geometries to minimise the energy from (generated by random rotation)

• energy_method – (str) Name of the energy method to build the structure from

class cgbind.molecule.BaseStruct(name='molecule', charge=0, mult=1, filename=None, solvent=None)

__init__(name='molecule', charge=0, mult=1, filename=None, solvent=None)

Base structure class

Parameters:

• name – (str)

• charge – (int)

• mult – (int) Spin multiplicity

• filename – (str)

• solvent – (str)

atoms

(list(list)) Geometry of the structure

centre()

Centre the species at the centre of mass (i.e. so COM = origin)

charge

(int) Charge in e

com

(np.ndarray) Center of mass (x, y, z)

energy

(float) Energy in Hartrees (Ha)

mult

(int) Spin multiplicity 2S+1

n_atoms

(int) Number of atoms

name

(str) Name of the structure

optimise(method, keywords=None, n_cores=1, cartesian_constraints=None)

Perform a single-point energy evaluation using an electronic structure theory method e.g. XTB, ORCA, G09

Parameters:

• method – (autode.ElectronicStructureMethod)

• keywords – (list(str)) Keywords to use for the ESM e.g. [‘Opt’, ‘PBE’, ‘def2-SVP’]

• n_cores – (int) Number of cores for the calculation to use

• cartesian_constraints – (list(int)) List of atom ids to constrain to their current coordinates

Returns:

None

print_xyz_file(filename=None)

Print a .xyz file from self.xyzs provided self.reasonable_geometry is True

Parameters:

filename – (str) Override the default filename

Returns:

None

reasonable_geometry

(bool)

set_atoms(atoms=None, coords=None)

Set the xyzs of a molecular structure

Parameters:

• atoms – (list(cgbind.atoms.Atom))

• coords – (np.ndarray) n_atoms x 3 positions of the atoms

Returns:

None

singlepoint(method, keywords=None, n_cores=None)

Perform a single-point energy evaluation using an electronic structure theory method e.g. XTB, ORCA, G09

Parameters:

• method – (autode.ElectronicStructureMethod)

• keywords – (list(str)) Keywords to use for the ESM e.g. [‘SP’, ‘PBE’, ‘def2-SVP’]

• n_cores – (int) Number of cores for the calculation to use

Returns:

None

solvent

(str) Name of the solvent

class cgbind.molecule.Molecule(smiles=None, name='molecule', charge=0, mult=1, n_confs=1, filename=None, solvent=None, use_etdg_confs=False)

__init__(smiles=None, name='molecule', charge=0, mult=1, n_confs=1, filename=None, solvent=None, use_etdg_confs=False)

Molecule. Inherits from cgbind.molecule.BaseStruct

Parameters:

• smiles – (str) SMILES string

• name – (str) Molecule name

• n_confs – (int) Number of conformers to initialise with

• charge – (int) Charge on the molecule

• mult – (int) Spin multiplicity on the molecule

• filename – (str)

• use_etdg_confs – (bool) Use an alternate conformer generation algorithm

bonds

(list(tuple)) List of bonds defined by atom ids

conformers

(list(BaseStruct)) List of conformers

get_charges(estimate=False)

Get the partial atomic charges using either XTB or estimate with RDKit using the Gasteiger charge scheme

Parameters:

• estimate – (bool)

• guess – (bool)

Returns:

mol_obj

(RDKit.mol object)

n_confs

(int) Number of conformers initialised with

n_h_acceptors

(int) Number of H-bond acceptors

n_h_donors

(int) Number of H-bond donors

n_rot_bonds

(int) Number of rotatable bonds

smiles

(str) SMILES string

volume

(float) Molecular volume in Å^3