pysoftk.linear_polymer package

Submodules

pysoftk.linear_polymer.calculators module

class pysoftk.linear_polymer.calculators.Opt(xyz_file)

Bases: object

Geometrical optimization tools using GFN-XTB2 and PySCF as engines.

Note

This class requires a GFN-XTB executable and/or a PYSCF semiempirical installation to be used.

pyscf_semi(steps)

Function invoking PYSCF semiempirical implementation for geometry optimization.

Parameters:

steps (int, optional) – Number of steps which PYSCF code will perform the optimization routine.

Returns:

Print the file pyscf_final.xyz reporting the results from a PYSCF calculation.

Return type:

None

class pysoftk.linear_polymer.calculators.Pyscf_print

Bases: object

Print a PYSCF object into cartesian coordinates.

xyz(mol)

Function to print a file with Cartesian coordinates from a PYSCF geometry optimization calculation.

Parameters:

mol (pyscf.gto.mole.Mole) – A PySCF gto mole Mole object.

Returns:

pysfc_final – An xyz file containing the optimized coordinates of the provided PYSCF Mole object.

Return type:

str

pysoftk.linear_polymer.linear_polymer module

class pysoftk.linear_polymer.linear_polymer.Lp(mol, atom, n_copies, shift)

Bases: object

A class for creating a linear polymer from given RdKit molecules.

Examples

Note

RDKit package must be installed.

atom

bond_conn(outmol)

Function to peruse the bonds and connections of place-hold atom within a super_monomer object.

Parameters:

outmol (rdkit.Chem.rdchem.Mol) – RDKit Mol object

Returns:

Tuple – A tuple of lists containing connections and neighbours of the place-holder atom.

Return type:

list

copy_mol()

Function to replicate super_monomers.

Parameters:

mol (rdkit.Chem.rdchem.Mol) – RDKit Mol object

Returns:

fragments – List of RDKit Mol objects

Return type:

list

linear_polymer(force_field='MMFF', relax_iterations=350, rot_steps=125, no_att=True)

Function to create a linear polymer from a given super_monomer object.

Parameters:

• force_field (str) – Selected Force-Field from RDKit options, i.e., UFF, MMFF, or MMFF94.

• relax_iterations (int) – The maximum number of iterations used for the FF.

• rot_steps (int) – Number of steps for rotor optimization.

• no_att (bool, optional) – If True, remove placeholder atoms. Defaults to True.

Returns:

newMol_H – RDKit Mol object

Return type:

rdkit.Chem.rdchem.Mol

max_dist_mol()

Returns the maximum distance between atoms from an RDKit Mol Object.

Returns:

maximum value from a Molecule Bound Matrix

Return type:

np.float

mol

n_copies

polimerisation(fragments)

Function to produce a polymer in a recursive manner.

Parameters:

fragments (list) – A list of RDKit objects.

Returns:

outmol – RDKit Mol object

Return type:

rdkit.Chem.rdchem.Mol

proto_polymer()

Function to create a linear polymer from a given

super_monomer object.

Returns:

newMol_H – RDKit Mol object

Return type:

rdkit.Chem.rdchem.Mol

shift

x_shift()

Re-calibrate distance between monomers

Returns:

shift_final – Value to translates the unit repetitions

Return type:

‘float’

pysoftk.linear_polymer.mol_conformer module

class pysoftk.linear_polymer.mol_conformer.Mcon(mol, num_conf)

Bases: object

Calculates molecular conformers

Example

Note

This class requires RDKit to be installed.

conformer(output_name)

Calculate a molecular conformer for a given molecule. If enabled the highest-energy conformer is returned.

Returns:

list of molecules – SDWriter Mol object

Return type:

rdkit.Chem.Mol

mol

num_conf

pysoftk.linear_polymer.super_monomer module

class pysoftk.linear_polymer.super_monomer.Emb

Bases: object

Class created to use the ETKDGV3 method provided in RDKit for 3D Geometry embedding.

etkdgv3(mol)

Function to perform Geometry embedding.

Parameters:

mol (rdkit.Chem.rdchem.Mol) – The resulting combined molecule as RDKit Mol Object.

Returns:

mol – The resulting embedded molecule as RDKit Mol Object.

Return type:

rdkit.Chem.rdchem.Mol

class pysoftk.linear_polymer.super_monomer.Sm(mol_1, mol_2, atom)

Bases: object

Class to create a new combined molecule from two provided RDKit Mol objects.

Example

Note

This class requires RDKit to be installed.

atom

constructor()

Function to combine two molecules using an atom placeholder.

Returns:

mol_4 – The resulting combined molecule as RDKit Mol Object.

Return type:

rdkit.Chem.rdchem.Mol

mol_1

mol_2

mon_to_poly()

Function to create a RDKit Mol object to prepare for x-axis translation.

Returns:

mol – The resulting combined molecule as RDKit Mol Object.

Return type:

rdkit.Chem.rdchem.Mol

monomer()

Function to produce a single polymer unit as an RDKit Mol Object.

Returns:

• mol (rdkit.Chem.rdchem.Mol)

• The resulting combined molecule as RDKit Mol Object.

Module contents