pysoftk.topologies package

Submodules

pysoftk.topologies.branched module

class pysoftk.topologies.branched.Bd(core, arm, atom)

Bases: object

A class for creating a branched polymer from given RDKit molecules.

Examples

Note

RDKit package must be installed.

arm

atom

branched_polymer(iter_ff=100, FF='MMFF', swap_H=True)

Function to create branched polymers

Parameters:

• FF (str) – Selected FF between MMFF or UFF

• relax_iterations (int) –

  Number of iterations used for relaxing a molecular object.

  swap_H: bool

  Indicates if the user defined atomic place holder is changed to a Hydrogen atom or remain as the used species.

Returns:

newMol_H – RDKit Mol object

Return type:

rdkit.Chem.rdchem.Mol

core

merge_arms(core, arm, atom)

Function to attach user defined molecules to a

provided molecular core using a placeholder.

Parameters:

• core (rdkit.Chem.rdchem.Mol) – RDKit Mol object

• arm (rdkit.Chem.rdchem.Mol) – RDKit Mol object.

• atom (str) – The placeholder atom to combine the molecules and form a new monomer.

Returns:

mol – RDKit Mol object.

Return type:

rdkit.Chem.rdchem.Mol

pysoftk.topologies.diblock module

class pysoftk.topologies.diblock.Db(ma, mb, atom)

Bases: object

A class for creating a diblock copolymers from

given RDKit molecules.

Examples

Note

RDKit package must be installed.

atom

diblock_copolymer(len_block_A, len_block_B, FF='MMFF', relax_iterations=100)

Function to create a diblock copolymer

Parameters:

• len_block_A (int) – Length of the molecular block A

• len_block_B (int) – Length of the molecular block B

• FF (str) – Selected FF between MMFF or UFF

• relax_iterations (int) – Number of iterations used for relaxing a molecular object.

Returns:

diblock – RDKit Mol object

Return type:

rdkit.Chem.rdchem.Mol

ma

mb

class pysoftk.topologies.diblock.Pt(pattern, mols, atom)

Bases: object

A class for creating a Patterned polymers from a list of RDKit molecules.

Examples

Note

RDKit package must be installed.

atom

mols

pattern

pattern_block_poly(relax_iterations=100, FF='MMFF', swap_H=True)

Function to create a polymer based on an alphabetic ordered pattern.

Parameters:

• relax_iterations (int) – Number of iterations used for relaxing a molecular object.

• FF (str) – Selected FF between MMFF or UFF

• swap_H (bool) – Indicates if the user defined atomic place holder is changed to a Hydrogen atom or remain as the used species.

Returns:

return – A molecular pysoftk object.

Return type:

mol

pysoftk.topologies.ranpol module

class pysoftk.topologies.ranpol.Rnp(ma, mb, atom)

Bases: object

A class for creating a random copolymer from given RDKit molecules.

Examples

Note

RDKit package must be installed.

atom

ma

mb

random_ab_copolymer(len_polymer, pA, relax_iterations=100, FF='MMFF', swap_H=True)

Function to build a random copolymer using an user provided

probability (pA) for merging the monomer ma and imposing the condition pB=1-pA.

Parameters:

• len_polymer (int) – User defined length of the polymer.

• pA (float) – User defined attaching probability of ma.

• iter_ff (int) – User defined iterations for a FF.

• FF (str) –

  User selected FF between “MMFF” or “UFF”.

  swap_H: bool

  Indicates if the user defined atomic place holder is changed to a Hydrogen atom or remain as the used species.

Returns:

mol – RDKit Mol object

Return type:

rdkit.Chem.rdchem.Mol

random_abc_copolymer(mc, len_polymer, pA, pB, relax_iterations=100, FF='MMFF', swap_H=True)

Function to build a random copolymer based on an user defined

probability (pA) of merging mA, pB for monomer mb, and the condition pC=1-pA-pB.

Parameters:

• mc (rdkit.Chem.rdchem.Mol) – RDKit Mol object #

• len_polymer (float) – User defined length of the polymer.

• pA (float) – User defined attaching probability of ma.

• pB (float) – User defined attaching porbability of mb.

• atom (str) – User defined atom used as place-holder.

• iter_ff (int) – User defined iterations for a FF.

• FF (str) – User selected FF.

• swap_H (bool) – Indicates if the user defined atomic place holder is changed to a Hydrogen atom or remain as the used species.

Returns:

mol – RDKit Mol object

Return type:

rdkit.Chem.rdchem.Mol

pysoftk.topologies.ring module

class pysoftk.topologies.ring.Rn(mol, atom)

Bases: object

A class for creating a circular (ring-shaped) polymer

from given RDKit molecules.

Examples

Note

RDKit package must be installed.

atom

check_proto(mol, FF='MMFF', iter_ff=100)

Function to check the proto polymer creation.

Parameters:

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

• FF (str) – Selected FF to perform a relaxation

• iter (int) – Number of iterations to perform a FF geometry optimisation.

Returns:

newMol_H – RDKit Mol object

Return type:

rdkit.Chem.rdchem.Mol

create_ring(mol, atom)

Function to create a circular polymer based on a RDKit

molecular object.

Parameters:

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

• atom (str) – The placeholder atom to combine the molecules and form a new monomer

Returns:

final – RDKit Mol object

Return type:

rdkit.Chem.rdchem.Mol

mol

pol_ring(len_polymer=2, FF='MMFF', iter_ff=100, shift=1.25)

Function to create a polymer with ring structure (circular)

Parameters:

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

• atom (str) – The placeholder atom to combine the molecules and form a new monomer

• len_polymer (int) – Extension of the polymer

• FF (str) – Selected FF to perform a relaxation

• iter_ff (int) – Number of iterations to perform a FF geometry optimisation.

• shift (float) – User defined shift for spacing the monomers using the LP function.

Returns:

pol_ring – RDKit Mol object

Return type:

rdkit.Chem.rdchem.Mol

Module contents