propka.ligand_pka_values

Ligand pKa values from Marvin

Ligand pKa values can be obtained from the commercial Marvin software (namely, the cxcalc and molconvert programs are required).

Classes

LigandPkaValues(parameters)

Ligand pKa value class.
class propka.ligand_pka_values.LigandPkaValues(parameters: Parameters)[source]

Ligand pKa value class.

static extract_pkas(output)[source]

Extract pKa value from output.

Parameters:

output – output string to parse

Returns:

  1. Indices

  2. Values

  3. Types

static find_in_path(program)[source]

Find a program in the system path.

Parameters:

program – program to find

Returns:

location of program

get_marvin_pkas_for_atoms(atoms, name='temp', reuse=False, num_pkas=10, min_ph=-10.0, max_ph=20.0)[source]

Use Marvin executables to calculate pKas for a list of atoms.

Parameters:

  • atoms – list of atoms

  • name – filename

  • reuse – flag to reuse the structure files

  • num_pkas – number of pKas to calculate

  • min_ph – minimum pH value

  • max_ph – maximum pH value

get_marvin_pkas_for_conformation_container(conformation, name='temp', reuse=False, num_pkas=10, min_ph=-10.0, max_ph=20.0)[source]

Use Marvin executables to calculate pKas for a conformation container.

Parameters:

  • conformation – conformation container

  • name – filename

  • reuse – flag to reuse the structure files

  • num_pkas – number of pKas to calculate

  • min_ph – minimum pH value

  • max_ph – maximum pH value

get_marvin_pkas_for_molecular_container(molecule: MolecularContainer, num_pkas=10, min_ph=-10.0, max_ph=20.0)[source]

Use Marvin executables to calculate pKas for a molecular container.

Parameters:

  • molecule – molecular container

  • num_pkas – number of pKas to calculate

  • min_ph – minimum pH value

  • max_ph – maximum pH value

get_marvin_pkas_for_molecule(atoms, filename='__tmp_ligand.mol2', reuse=False, num_pkas=10, min_ph=-10.0, max_ph=20.0)[source]

Use Marvin executables to calculate pKas for a molecule.

Parameters:

  • molecule – the molecule

  • name – filename

  • reuse – flag to reuse the structure files

  • num_pkas – number of pKas to calculate

  • min_ph – minimum pH value

  • max_ph – maximum pH value

get_marvin_pkas_for_pdb_file(molecule: MolecularContainer, parameters: NoReturn, num_pkas=10, min_ph=-10.0, max_ph=20.0)[source]

Use Marvin executables to get pKas for a PDB file.

Parameters:

  • pdbfile – PDB file

  • molecule – MolecularContainer object

  • num_pkas – number of pKas to get

  • min_ph – minimum pH value

  • max_ph – maximum pH value