pysoftk.tools package
Submodules
pysoftk.tools.utils_func module
- pysoftk.tools.utils_func.atom_neigh(mol, atom)[source]
Find the neighbours from an atoms inside a molecule.
- Parameters:
mol (rdkit.Chem.rdchem.Mol) – RDKit Mol object
atom (str) – The placeholder atom
- Returns:
neigh – List of neighbors
- Return type:
list
- pysoftk.tools.utils_func.count_plholder(mol, atom)[source]
- Function to count the number of user defined
atomic placeholders.
- Parameters:
mol (rdkit.Chem.rdchem.Mol) – RDKit Mol object
atom (class.str) – The placeholder atom
- Returns:
num_br – Number of atomic place holders inside a molecule.
- Return type:
class.int
- pysoftk.tools.utils_func.create_pol(mol, atom, tpb)[source]
Function to create polymers.
- Parameters:
mol (rdkit.Chem.rdchem.Mol) – RDKit Mol object
atom (str) – The placeholder atom
- tpb: list
List of tuples with atoms to be connected
- Returns:
rmwol1 – RDKit Mol object
- Return type:
rdkit.Chem.rdchem.Mol
- pysoftk.tools.utils_func.get_file_extension(path)[source]
Gets the extension of a file.
- Parameters:
path (str) – The path to the file.
- Returns:
The extension of the file.
- Return type:
str
- pysoftk.tools.utils_func.pattern_mol_seq(mols, pattern)[source]
- Function to create a list of molecules based on a user
provided pattern.
- Parameters:
pattern (class.str) – A string value containing the desired pattern.
mols (class.list) – List containing the names of the molecules to form a polymer with a given pattern.
- Returns:
return – List with the correct sequence of molecular fragments to be merged.
- Return type:
class.list
- pysoftk.tools.utils_func.pattern_recon(pattern)[source]
Function to find unique values from a string pattern.
- Parameters:
pattern (str) – Variable containing the pattern written in a string.
- Returns:
result – Returns the unique values of the pattern in alphabetic order.
- Return type:
list
- pysoftk.tools.utils_func.pattern_repl(pattern, tup_repl)[source]
- Function to perform a pattern replacement using tuples generated
by pattern and molecular names.
- Parameters:
pattern (str) – Variable containing the pattern written in a string
- Returns:
return – Returns the names of the molecules as provided by the string pattern.
- Return type:
list
pysoftk.tools.utils_ob module
- pysoftk.tools.utils_ob.check_bond_order(file_name)[source]
Function to check and correct the bonds of a given file.
- Parameters:
file_name (class.str) – An user-provided file containing a molecule in an accepted openbabel format.
- Returns:
A new file containing checked bond and bond order molecular system.
- Return type:
None
- pysoftk.tools.utils_ob.ff_ob_relaxation(mol, FF='MMFF94', iter_ff=100, ff_thr=1e-06)[source]
- Setting up an openbabel FF for
geometry optimization.
- Parameters:
mol (OBabel.Mol) – An user-provided OpenBabel moelcule.
FF (class.str) – Selected Force Field. Options are MMFF94, UFF, GAFF.
iter (class.int) – Number of iterations to be used for the FF.
- Returns:
mol_new – Open Babel Molecule with optmised Geometry.
- Return type:
Mol.OBabel.Mol
- pysoftk.tools.utils_ob.rotor_opt(mol, FF='MMFF94', rot_steps=125)[source]
Setting up an openbabel FF for rotor optimization.
- Parameters:
mol (OBabel.Mol) – An user-provided OpenBabel moelcule.
FF (class.str) – Selected Force Field. Options are MMFF94, UFF, GAFF.
rot_steps (class.int) – Number of iterations to be used for the rotational optimization.
- Returns:
mol_new – Open Babel Molecule with optmised Geometry.
- Return type:
Mol.OBabel.Mol
pysoftk.tools.utils_rdkit module
- pysoftk.tools.utils_rdkit.MMFF_rel(mol, iter_ff, vdw_par=0.001)[source]
Function to employ a MMFF molecular mechanics FF.
- Parameters:
mol (rdkit.Chem.rdchem.Mol) – RDKit Mol object
iter_ff (int) – Number of iterations to perform a FF geometry optimization.
vdw_par (float) – Extension of the vdW interaction range.
- Returns:
mol – RDKit Mol object
- Return type:
rdkit.Chem.rdchem.Mol
- pysoftk.tools.utils_rdkit.UFF_rel(mol, iter_ff, vdw_par=0.001)[source]
Function to employ an UFF molecular mechanics FF.
- Parameters:
mol (rdkit.Chem.rdchem.Mol) – RDKit Mol object
iter_ff (int) – Number of iterations to perform a FF geometry optimization.
vdw_par (float) – Extension of the vdW interaction range.
- Returns:
mol – RDKit Mol object
- Return type:
rdkit.Chem.rdchem.Mol
- pysoftk.tools.utils_rdkit.etkdgv3_energies(mol, num_conf=1)[source]
Calculate molecular configurations using the RDKit-ETKDG3 method.
- Parameters:
mol (rdkit.Chem.Mol) – RDKit Mol object
num_conf (int) – The number of configurations requested to be computed.
- Returns:
datapoint – RDKit Mol object
- Return type:
rdkit.Chem.rdistGeom.EmbedMultipleConfs
- pysoftk.tools.utils_rdkit.no_swap(mol, iter_ff, FF='MMFF')[source]
- Function to sanitize a molecule with Hydrogens
and the user defined atomic place holder.
- Parameters:
mol (rdkit.Chem.rdchem.Mol) – RDKit Mol object
FF (str) – Selected FF to perform a relaxation
iter_ff (int) – Number of iterations to perform a FF geometry optimization.
- Returns:
newMol_H – RDKit Mol object
- Return type:
rdkit.Chem.rdchem.Mol
- pysoftk.tools.utils_rdkit.plc_holder(mol, atom)[source]
Function Seeking for a specific placeholder atom.
- Parameters:
mol (rdkit.Chem.rdchem.Mol) – RDKit Mol object
atom (str) – The placeholder atom
- Returns:
return – List of neighbors from the place holder atom.
- Return type:
list
- pysoftk.tools.utils_rdkit.remove_plcholder(mol, atom)[source]
Function that seeks for a place holder atom and replace it with a Hydrogen atom.
- Parameters:
mol (rdkit.Chem.Mol) – RDKit Mol object
- Returns:
RDKit Mol object
- Return type:
None
- pysoftk.tools.utils_rdkit.swap_hyd(mol, iter_ff, atom, FF='MMFF')[source]
Function to swap atomic place holders to Hydrogen atoms.
- Parameters:
mol (rdkit.Chem.rdchem.Mol) – RDKit Mol object
iter_ff (int) – Number of iterations to perform a FF geometry optimization.
atom (str) – The placeholder atom to combine the molecules and form a new monomer.
FF (str) – Selected FF to perform a geometry optimization.
- Returns:
newMol_H – RDKit Mol object
- Return type:
rdkit.Chem.rdchem.Mol