fairmd.idp.settings.molecules module

module:: settings/molecules.py
description:: Module file with definition of different global-level dictionaries.

There is a dictionary of lipids, ions, etc. If you add a lipid which is not yet in the databank, you have to add it here!

class fairmd.idp.settings.molecules.Molecule(name: str)[source]

Bases: ABC

Abstract base class representing a molecule and its related operations.

This class is designed to provide an interface for interacting with molecule-related files, which are stored in a molecule-related folder. It serves as a base for concrete implementations that need to define specific operations for handling molecule data.

register_mapping(fname: str) → None[source]

Register mapping dictionary for the Molecule object

Parameters:: fname – mapping filename (without path)
Returns:

property mapping_dict: dict

property name: str

Molecule name.

Type:: return

class fairmd.idp.settings.molecules.Lipid(name: str)[source]

Bases: Molecule

Lipid class inherited from Molecule base. Contains all the molecules which belongs to the bilayer.

class fairmd.idp.settings.molecules.NonLipid(name: str)[source]

Bases: Molecule

Class for non-bilayer molecules: solvent, ions, etc.

class fairmd.idp.settings.molecules.MoleculeSet(*args)[source]

Bases: MutableSet[Molecule], ABC

MoleculeSet is a Set (repeating normal set functionality) but with some additional molecule-specific things.

add(item: Molecule)[source]

Add a lipid to the set.

Parameters:: item – Can add either Molecule or str (then Molecule constructor will be called)

discard(item)[source]: Remove a lipid from the set without raising an error if it does not exist.

property names: set[str]

class fairmd.idp.settings.molecules.LipidSet(*args)[source]

Bases: MoleculeSet

MoleculeSet specialization for Lipid.

static load_from_data()[source]

Loads lipid data from the designated directory and returns a set of lipids.

Return type:: LipidSet
Returns:: An instance of loaded LipidSet.

class fairmd.idp.settings.molecules.NonLipidSet(*args)[source]

Bases: MoleculeSet

MoleculeSet specialization for NonLipid.

static load_from_data()[source]

Loads Nonlipid data from the designated directory and returns a set of lipids.

Return type:: NonLipidSet
Returns:: An instance of loaded NonLipidSet.

fairmd.idp.settings.molecules.lipids_set: LipidSet = LipidSet[{'BOG', 'TLCL_0H', 'DEPC', 'DHMDMAB', 'DSPC', 'TLCL', 'PAZEPCPROT', 'SAPI', 'SDG', 'DCHOL', 'SLPI', 'POPE', 'DPPG', 'SAPC', 'CHOL', 'DPPE', 'GM1', 'DYPC', 'DOPC', 'DMTAP', 'DLPC', 'TMCL', 'SOPC', 'DMPC', 'DPPGK', 'GB3', 'PAZEPCDEPROT', 'SAPI24', 'DPPC', 'POPS', 'POPG', 'DOPE', 'SDPE', 'DRPC', 'C30', 'DAPC', 'CER180', 'TOCL', 'SLIPC', 'PYPC', 'CER', 'SAPI25', 'SM16', 'SM18', 'DOPS', 'DOG', 'DLIPC', 'POPC', 'POPI', 'DDOPC'}]: Dictionary of possible lipids

fairmd.idp.settings.molecules.lipids_dict = LipidSet[{'BOG', 'TLCL_0H', 'DEPC', 'DHMDMAB', 'DSPC', 'TLCL', 'PAZEPCPROT', 'SAPI', 'SDG', 'DCHOL', 'SLPI', 'POPE', 'DPPG', 'SAPC', 'CHOL', 'DPPE', 'GM1', 'DYPC', 'DOPC', 'DMTAP', 'DLPC', 'TMCL', 'SOPC', 'DMPC', 'DPPGK', 'GB3', 'PAZEPCDEPROT', 'SAPI24', 'DPPC', 'POPS', 'POPG', 'DOPE', 'SDPE', 'DRPC', 'C30', 'DAPC', 'CER180', 'TOCL', 'SLIPC', 'PYPC', 'CER', 'SAPI25', 'SM16', 'SM18', 'DOPS', 'DOG', 'DLIPC', 'POPC', 'POPI', 'DDOPC'}]

Use lipids_set instead.

Type:: @deprecated

fairmd.idp.settings.molecules.molecules_set: NonLipidSet = NonLipidSet[{'LIG', 'CES', 'C20', 'TRIS', 'SOD', 'CLA', 'TMA', 'CAL', 'HPO4', 'POT', 'H2PO4', 'SOL'}]: Dictionary of other than lipid molecules.

fairmd.idp.settings.molecules.molecules_dict = NonLipidSet[{'LIG', 'CES', 'C20', 'TRIS', 'SOD', 'CLA', 'TMA', 'CAL', 'HPO4', 'POT', 'H2PO4', 'SOL'}]

Use molecules_set instead

Type:: @deprecated

fairmd.idp.settings.molecules.molecule_ff_set = {'FFBOG', 'FFC20', 'FFC30', 'FFCAL', 'FFCER', 'FFCER180', 'FFCES', 'FFCHOL', 'FFCLA', 'FFDAPC', 'FFDCHOL', 'FFDDOPC', 'FFDEPC', 'FFDHMDMAB', 'FFDLIPC', 'FFDLPC', 'FFDMPC', 'FFDMTAP', 'FFDOG', 'FFDOPC', 'FFDOPE', 'FFDOPS', 'FFDPPC', 'FFDPPE', 'FFDPPG', 'FFDPPGK', 'FFDRPC', 'FFDSPC', 'FFDYPC', 'FFGB3', 'FFGM1', 'FFH2PO4', 'FFHPO4', 'FFLIG', 'FFPAZEPCDEPROT', 'FFPAZEPCPROT', 'FFPOPC', 'FFPOPE', 'FFPOPG', 'FFPOPI', 'FFPOPS', 'FFPOT', 'FFPYPC', 'FFSAPC', 'FFSAPI', 'FFSAPI24', 'FFSAPI25', 'FFSDG', 'FFSDPE', 'FFSLIPC', 'FFSLPI', 'FFSM16', 'FFSM18', 'FFSOD', 'FFSOL', 'FFSOPC', 'FFTLCL', 'FFTLCL_0H', 'FFTMA', 'FFTMCL', 'FFTOCL', 'FFTRIS'}: Dictionary containing possible force-field labels for molecules given by the contributor (used for README/info fields validation)