transformato.system

Description

Classes

class transformato.system.SystemStructure(configuration, structure)

Parameters:

• configuration (dict)

• structure (str)

__init__(configuration, structure)

A class that contains all informations for a single small ligand in different environments. Everything is constructed automatically from the charmm-gui folder. :param configuration: the configuration dictionary obtained with utils.load_config_yaml :type configuration: dict :param structure: either ‘structure1’ or ‘structure2’ :type structure: str

Parameters:

• configuration (dict)

• structure (str)

__weakref__

list of weak references to the object

_create_sdf_from_pdb(psf)

This function creates a sdf file from the file provided in openmm/step3_input.pdb and reads in this sdf file. This should now have the same order as the psf topology object and is from now on used as the rdkit mol object.

Parameters:

psf (pm.topologyobjects) – a topology provided by parmed (either CHARMM type or AMBER)

Returns:

mol – mol object

Return type:

rdkit.Chem.rdchem.Mol

_determine_offset_and_set_possible_dummy_properties(psf)

Determines the offset and sets possible properties on the psf. :param psf: :type psf: pm.charmm.CharmmPsfFile :param env: waterbox,complex or vacuum :type env: str

Parameters:

psf (CharmmPsfFile)

Return type:

int

_generate_rdkit_mol(env, psf)

Generates the rdkit mol object. :param env: waterbox,complex or vacuum :type env: str :param psf: :type psf: pm.charmm.CharmmPsfFile

Returns:

mol

Return type:

rdkit.Chem.rdchem.Mol

Parameters:

• env (str)

• psf (CharmmPsfFile)

_initialize_system(configuration, env)

Generates the psf file and sets the coordinates from the CHARMM-GUI files. :param configuration: the configuration dictionary obtained with utils.load_config_yaml :type configuration: dict :param env: waterbox,complex or vacuum :type env: str

Returns:

psf

Return type:

pm.charmm.CharmmPsfFile

Parameters:

• configuration (dict)

• env (str)

_read_parameters(env)

Reads in topparameters from a toppar dir and ligand specific parameters. :param env: waterbox,complex or vacuum :type env: str

Returns:

parameter – parameters obtained from the CHARMM-GUI output dir.

Return type:

pm.charmm.CharmmParameterSet

Parameters:

env (str)

generate_atom_tables_from_psf(psf, mol)

Generate mapping dictionaries for a molecule in a psf. :param psf: :type psf: pm.charmm.CharmmPsfFile or parmed.amber._amberparm.AmberParm

Returns:

mol – mol object with atom name and type properties

Return type:

Chem.rdchem.Mol

Parameters:

• psf (CharmmPsfFile)

• mol (Mol)