Supported molecules

HADDOCK 3 supported residues.

The HADDOCK3 supported residues are defined by the different .top files in the cns/toppar source folder. This module will automatically retrieve any new residue added to the .top defined in the folder and add it to the variables here.

If a new .top file is added in the folder, that must be added here inside the read_supported_residues() function, because file retrieve is not done automatically on purpose.

.top files considered here:

• carbohydrate.top

• dna-rna-CG-MARTINI-2-1p.top

• dna-rna-allatom-hj-opls-1.3.top

• fragment_probes.top

• hemes-allhdg.top

• ion.top

• protein-CG-Martini-2-2.top

• protein-CG-Martini.top

• protein-allhdg5-4.top

• solvent-allhdg5-4.top

• shape.top

DNA-related files are all concatenated into a single DNA-supported residues datastructure. The same occurs for protein residues (natural or modified).

You can import from this module the different sets containing the supported residue names:

• supported_aminoacids_resnames

• supported_carbo_resnames

• supported_fragments_resnames

• supported_hemes_resnames

• supported_single_ions_resnames

• supported_single_ions_elements

• supported_single_ions_atoms

• supported_multiatom_ions_resnames

• supported_nucleic_resnames

• supported_solvents_resnames

• supported_shape

• supported_ATOM (contains residues and nucleic acids)

• supported_HETATM (everything not contained in ATOM)

class haddock.core.supported_molecules.CNSTopologyResidue(resname: str, charge: float, atoms: Iterable[str])

Bases: object

CNS topology residue.

property atoms: tuple[str, ...]

Tuple of residue atoms.

property charge: float

Residue total charge.

property elements: tuple[str, ...]

List of elements for all atoms composing the molecule.

This list is ordered the same as atoms.

By default elements is not defined and must be injected manually.

See also

• get_ion_element_from_atoms()

property resname: str

Residue name.

haddock.core.supported_molecules.get_ion_element_from_atoms(atoms: Iterable[str]) → tuple[str, ...]

Generate the element name from the atom name for single atom ions.

Examples

>>> get_ion_element_from_atoms(["ZN+2", "CU+2", "NI"])
("ZN", "CU", "NI")

Parameters:

atom (list) – A list of atom names.

haddock.core.supported_molecules.get_resnames(group: Iterable[CNSTopologyResidue]) → dict[str, haddock.core.supported_molecules.CNSTopologyResidue]

Make a set of residue names.

Elements of the group must have a resname attribute.

Parameters:

group (list of CNSTopologyResidue)

Returns:

dict – Dict of residue name and residue pairs.

haddock.core.supported_molecules.read_residues_from_top_file(topfile: str | Path) → list[haddock.core.supported_molecules.CNSTopologyResidue]

Read the residues defined in CNS topology file.

This is a general implementation to read the basic information from the CNS topology files. This basic information is the information needed to help the the haddock.gear.preprocessing step in identifying the supported residues and correctly format their PDB lines.

Parameters:

topfile (str or pathlib.Path) – Path to the topology file.

Returns:

list – List of CNSTopologyResidue objects. Each object has information on the residue name, the atoms, and the total charge of the residue.

See also

• haddock.gear.preprocessing.read_additional_residues()

haddock.core.supported_molecules.read_supported_residues(source_path: str | Path) → tuple[dict[str, haddock.core.supported_molecules.CNSTopologyResidue], ...]

Read supported residues from a folder containing .top files.

The function expects the source_path to have the required files.

Expected files are:

• carbohydrate.top

• dna-rna-CG-MARTINI-2-1p.top

• dna-rna-allatom-hj-opls-1.3.top

• fragment_probes.top

• hemes-allhdg.top

• ion.top

• protein-CG-Martini-2-2.top

• protein-CG-Martini.top

• protein-allhdg5-4.top

• solvent-allhdg5-4.top

• shape.top

You need to edit this function to account for any additional .top file that is added to the source_path on top of the above ones. Otherwise, read the residues manually using read_residues_from_top_file() and get_resnames() and add them to the relevant set, or have them as a new set.

Returns:

tuple – A tuple of the residue names supported by HADDOCK3.

haddock.core.supported_molecules.supported_ATOM = {'A', 'ACE', 'ALA', 'ALY', 'ARG', 'ASH', 'ASN', 'ASP', 'C', 'CFE', 'CHX', 'CSP', 'CTN', 'CYC', 'CYF', 'CYM', 'CYS', 'DA', 'DC', 'DDZ', 'DG', 'DJ', 'DT', 'DUM', 'G', 'GLH', 'GLN', 'GLU', 'GLY', 'HIS', 'HLY', 'HY3', 'HYP', 'ILE', 'LEU', 'LYS', 'M3L', 'MET', 'MLY', 'MLZ', 'MSE', 'NEP', 'NME', 'PHE', 'PNS', 'PRO', 'PTR', 'QSR', 'SEC', 'SEP', 'SER', 'SHA', 'THR', 'TOP', 'TRP', 'TYP', 'TYR', 'TYS', 'U', 'VAL'}

Supported ATOM residues.

These residues must be defined as ATOM records in PDB files for HADDOCK3.

haddock.core.supported_molecules.supported_HETATM = {'A2G', 'ACD', 'ACN', 'ACT', 'ADY', 'AG', 'AG1', 'AL', 'AL3', 'AMN', 'AR', 'AS', 'AU', 'AU1', 'AU3', 'BDY', 'BEN', 'BGC', 'BMA', 'BR', 'BR1', 'BUT', 'CA', 'CA2', 'CD', 'CD2', 'CHE', 'CL', 'CL1', 'CO', 'CO2', 'CO3', 'COH', 'COM', 'CR', 'CR2', 'CR3', 'CS', 'CS1', 'CU', 'CU1', 'CU2', 'CYA', 'DFO', 'DME', 'DMS', 'DOD', 'EOL', 'ETA', 'ETH', 'F', 'F1', 'FCA', 'FCB', 'FE', 'FE2', 'FE3', 'FUC', 'FUL', 'GAL', 'GLA', 'GLC', 'GXL', 'HEB', 'HEC', 'HG', 'HG1', 'HG2', 'HO', 'HO3', 'HOH', 'I', 'I1', 'IMI', 'IR', 'IR3', 'K', 'K1', 'KR', 'LI1', 'MAG', 'MAN', 'MER', 'MG', 'MG2', 'MIY', 'MN', 'MN2', 'MN3', 'MO', 'MO3', 'NA', 'NA1', 'NAG', 'NDG', 'NGA', 'NI', 'NI2', 'O2', 'OS', 'OS4', 'PB', 'PB2', 'PHN', 'PO4', 'PT', 'PT2', 'RAM', 'SIA', 'SIB', 'SO4', 'SR', 'SR2', 'THS', 'TIP', 'TIP3', 'U3', 'U4', 'URE', 'V', 'V2', 'V3', 'WAT', 'WO4', 'XE', 'XYP', 'YB', 'YB2', 'YB3', 'ZN', 'ZN2'}

Supported HETATM residues.

These residues must be defined as HETATM records in PDB files for HADDOCK3.

haddock.core.supported_molecules.supported_aminoacids_resnames = {'ACE', 'ALA', 'ALY', 'ARG', 'ASH', 'ASN', 'ASP', 'CFE', 'CHX', 'CSP', 'CTN', 'CYC', 'CYF', 'CYM', 'CYS', 'DDZ', 'DUM', 'GLH', 'GLN', 'GLU', 'GLY', 'HIS', 'HLY', 'HY3', 'HYP', 'ILE', 'LEU', 'LYS', 'M3L', 'MET', 'MLY', 'MLZ', 'MSE', 'NEP', 'NME', 'PHE', 'PNS', 'PRO', 'PTR', 'QSR', 'SEC', 'SEP', 'SER', 'THR', 'TOP', 'TRP', 'TYP', 'TYR', 'TYS', 'VAL'}

Supported amino acids residue names.

haddock.core.supported_molecules.supported_carbo_resnames = {'A2G', 'BGC', 'BMA', 'FCA', 'FCB', 'FUC', 'FUL', 'GAL', 'GLA', 'GLC', 'GXL', 'MAG', 'MAN', 'NAG', 'NDG', 'NGA', 'RAM', 'SIA', 'SIB', 'XYP'}

Supported carbohydrate residues names.

haddock.core.supported_molecules.supported_fragments_resnames = {'ACD', 'ACN', 'ACT', 'ADY', 'AMN', 'BDY', 'BEN', 'BUT', 'CHE', 'DFO', 'DME', 'EOL', 'ETA', 'IMI', 'MER', 'MIY', 'PHN', 'THS', 'URE'}

Supported fragments residue names.

haddock.core.supported_molecules.supported_hemes_resnames = {'CYA', 'HEB', 'HEC'}

Supported Hemes.

haddock.core.supported_molecules.supported_multiatom_ions_resnames = {'PO4', 'SO4', 'WO4'}

Supported multiatom ions residue names.

haddock.core.supported_molecules.supported_nucleic_resnames = {'A', 'C', 'DA', 'DC', 'DG', 'DJ', 'DT', 'G', 'U'}

Supported nucleic acid residue names.

haddock.core.supported_molecules.supported_residues = {'A', 'A2G', 'ACD', 'ACE', 'ACN', 'ACT', 'ADY', 'AG', 'AG1', 'AL', 'AL3', 'ALA', 'ALY', 'AMN', 'AR', 'ARG', 'AS', 'ASH', 'ASN', 'ASP', 'AU', 'AU1', 'AU3', 'BDY', 'BEN', 'BGC', 'BMA', 'BR', 'BR1', 'BUT', 'C', 'CA', 'CA2', 'CD', 'CD2', 'CFE', 'CHE', 'CHX', 'CL', 'CL1', 'CO', 'CO2', 'CO3', 'COH', 'COM', 'CR', 'CR2', 'CR3', 'CS', 'CS1', 'CSP', 'CTN', 'CU', 'CU1', 'CU2', 'CYA', 'CYC', 'CYF', 'CYM', 'CYS', 'DA', 'DC', 'DDZ', 'DFO', 'DG', 'DJ', 'DME', 'DMS', 'DOD', 'DT', 'DUM', 'EOL', 'ETA', 'ETH', 'F', 'F1', 'FCA', 'FCB', 'FE', 'FE2', 'FE3', 'FUC', 'FUL', 'G', 'GAL', 'GLA', 'GLC', 'GLH', 'GLN', 'GLU', 'GLY', 'GXL', 'HEB', 'HEC', 'HG', 'HG1', 'HG2', 'HIS', 'HLY', 'HO', 'HO3', 'HOH', 'HY3', 'HYP', 'I', 'I1', 'ILE', 'IMI', 'IR', 'IR3', 'K', 'K1', 'KR', 'LEU', 'LI1', 'LYS', 'M3L', 'MAG', 'MAN', 'MER', 'MET', 'MG', 'MG2', 'MIY', 'MLY', 'MLZ', 'MN', 'MN2', 'MN3', 'MO', 'MO3', 'MSE', 'NA', 'NA1', 'NAG', 'NDG', 'NEP', 'NGA', 'NI', 'NI2', 'NME', 'O2', 'OS', 'OS4', 'PB', 'PB2', 'PHE', 'PHN', 'PNS', 'PO4', 'PRO', 'PT', 'PT2', 'PTR', 'QSR', 'RAM', 'SEC', 'SEP', 'SER', 'SHA', 'SIA', 'SIB', 'SO4', 'SR', 'SR2', 'THR', 'THS', 'TIP', 'TIP3', 'TOP', 'TRP', 'TYP', 'TYR', 'TYS', 'U', 'U3', 'U4', 'URE', 'V', 'V2', 'V3', 'VAL', 'WAT', 'WO4', 'XE', 'XYP', 'YB', 'YB2', 'YB3', 'ZN', 'ZN2'}

All HADDOCK3 supported residues.

haddock.core.supported_molecules.supported_shape_resnames = {'SHA'}

Supported shape.

haddock.core.supported_molecules.supported_single_ions_atoms = {'AG', 'AG+1', 'AL', 'AL+3', 'AR', 'AS', 'AU', 'AU+1', 'AU+3', 'BR', 'BR-1', 'CA', 'CA+2', 'CD', 'CD+2', 'CL', 'CL-1', 'CO', 'CO+2', 'CO+3', 'CR', 'CR+2', 'CR+3', 'CS', 'CS+1', 'CU', 'CU+1', 'CU+2', 'F', 'F-1', 'FE', 'FE+2', 'FE+3', 'HG', 'HG+1', 'HG+2', 'HO', 'HO+3', 'I', 'I-1', 'IR', 'IR+3', 'K', 'K+1', 'KR', 'LI+1', 'MG', 'MG+2', 'MN', 'MN+2', 'MN+3', 'MO', 'MO+3', 'NA', 'NA+1', 'NI', 'NI+2', 'OS', 'OS+4', 'P', 'PB', 'PB+2', 'PT', 'PT+2', 'S', 'SR', 'SR+2', 'U+3', 'U+4', 'V', 'V+2', 'V+3', 'W', 'XE', 'YB', 'YB+2', 'YB+3', 'ZN', 'ZN+2'}

Supported single ion atom names.

haddock.core.supported_molecules.supported_single_ions_atoms_map = {'AG': CNSTopologyResidue('AG', 0.0, ('AG',)), 'AG+1': CNSTopologyResidue('AG1', 1.0, ('AG+1',)), 'AL': CNSTopologyResidue('AL', 0.0, ('AL',)), 'AL+3': CNSTopologyResidue('AL3', 3.0, ('AL+3',)), 'AR': CNSTopologyResidue('AR', 0.0, ('AR',)), 'AS': CNSTopologyResidue('AS', 0.0, ('AS',)), 'AU': CNSTopologyResidue('AU', 0.0, ('AU',)), 'AU+1': CNSTopologyResidue('AU1', 1.0, ('AU+1',)), 'AU+3': CNSTopologyResidue('AU3', 3.0, ('AU+3',)), 'BR': CNSTopologyResidue('BR', 0.0, ('BR',)), 'BR-1': CNSTopologyResidue('BR1', -1.0, ('BR-1',)), 'CA': CNSTopologyResidue('CA', 0.0, ('CA',)), 'CA+2': CNSTopologyResidue('CA2', 2.0, ('CA+2',)), 'CD': CNSTopologyResidue('CD', 0.0, ('CD',)), 'CD+2': CNSTopologyResidue('CD2', 2.0, ('CD+2',)), 'CL': CNSTopologyResidue('CL', 0.0, ('CL',)), 'CL-1': CNSTopologyResidue('CL1', -1.0, ('CL-1',)), 'CO': CNSTopologyResidue('CO', 0.0, ('CO',)), 'CO+2': CNSTopologyResidue('CO2', 2.0, ('CO+2',)), 'CO+3': CNSTopologyResidue('CO3', 3.0, ('CO+3',)), 'CR': CNSTopologyResidue('CR', 0.0, ('CR',)), 'CR+2': CNSTopologyResidue('CR2', 2.0, ('CR+2',)), 'CR+3': CNSTopologyResidue('CR3', 3.0, ('CR+3',)), 'CS': CNSTopologyResidue('CS', 0.0, ('CS',)), 'CS+1': CNSTopologyResidue('CS1', 1.0, ('CS+1',)), 'CU': CNSTopologyResidue('CU', 0.0, ('CU',)), 'CU+1': CNSTopologyResidue('CU1', 1.0, ('CU+1',)), 'CU+2': CNSTopologyResidue('CU2', 2.0, ('CU+2',)), 'F': CNSTopologyResidue('F', 0.0, ('F',)), 'F-1': CNSTopologyResidue('F1', -1.0, ('F-1',)), 'FE': CNSTopologyResidue('FE', 0.0, ('FE',)), 'FE+2': CNSTopologyResidue('FE2', 2.0, ('FE+2',)), 'FE+3': CNSTopologyResidue('FE3', 3.0, ('FE+3',)), 'HG': CNSTopologyResidue('HG', 0.0, ('HG',)), 'HG+1': CNSTopologyResidue('HG1', 1.0, ('HG+1',)), 'HG+2': CNSTopologyResidue('HG2', 2.0, ('HG+2',)), 'HO': CNSTopologyResidue('HO', 0.0, ('HO',)), 'HO+3': CNSTopologyResidue('HO3', 3.0, ('HO+3',)), 'I': CNSTopologyResidue('I', 0.0, ('I',)), 'I-1': CNSTopologyResidue('I1', -1.0, ('I-1',)), 'IR': CNSTopologyResidue('IR', 0.0, ('IR',)), 'IR+3': CNSTopologyResidue('IR3', 3.0, ('IR+3',)), 'K': CNSTopologyResidue('K', 0.0, ('K',)), 'K+1': CNSTopologyResidue('K1', 1.0, ('K+1',)), 'KR': CNSTopologyResidue('KR', 0.0, ('KR',)), 'LI+1': CNSTopologyResidue('LI1', 1.0, ('LI+1',)), 'MG': CNSTopologyResidue('MG', 0.0, ('MG',)), 'MG+2': CNSTopologyResidue('MG2', 2.0, ('MG+2',)), 'MN': CNSTopologyResidue('MN', 0.0, ('MN',)), 'MN+2': CNSTopologyResidue('MN2', 2.0, ('MN+2',)), 'MN+3': CNSTopologyResidue('MN3', 3.0, ('MN+3',)), 'MO': CNSTopologyResidue('MO', 0.0, ('MO',)), 'MO+3': CNSTopologyResidue('MO3', 3.0, ('MO+3',)), 'NA': CNSTopologyResidue('NA', 0.0, ('NA',)), 'NA+1': CNSTopologyResidue('NA1', 1.0, ('NA+1',)), 'NI': CNSTopologyResidue('NI', 0.0, ('NI',)), 'NI+2': CNSTopologyResidue('NI2', 2.0, ('NI+2',)), 'OS': CNSTopologyResidue('OS', 0.0, ('OS',)), 'OS+4': CNSTopologyResidue('OS4', 4.0, ('OS+4',)), 'P': CNSTopologyResidue('PO4', -2.0, ('P', 'O1', 'O2', 'O3', 'O4')), 'PB': CNSTopologyResidue('PB', 0.0, ('PB',)), 'PB+2': CNSTopologyResidue('PB2', 2.0, ('PB+2',)), 'PT': CNSTopologyResidue('PT', 0.0, ('PT',)), 'PT+2': CNSTopologyResidue('PT2', 2.0, ('PT+2',)), 'S': CNSTopologyResidue('SO4', -2.0, ('S', 'O1', 'O2', 'O3', 'O4')), 'SR': CNSTopologyResidue('SR', 0.0, ('SR',)), 'SR+2': CNSTopologyResidue('SR2', 2.0, ('SR+2',)), 'U+3': CNSTopologyResidue('U3', 3.0, ('U+3',)), 'U+4': CNSTopologyResidue('U4', 4.0, ('U+4',)), 'V': CNSTopologyResidue('V', 0.0, ('V',)), 'V+2': CNSTopologyResidue('V2', 2.0, ('V+2',)), 'V+3': CNSTopologyResidue('V3', 3.0, ('V+3',)), 'W': CNSTopologyResidue('WO4', -2.0, ('W', 'O1', 'O2', 'O3', 'O4')), 'XE': CNSTopologyResidue('XE', 0.0, ('XE',)), 'YB': CNSTopologyResidue('YB', 0.0, ('YB',)), 'YB+2': CNSTopologyResidue('YB2', 2.0, ('YB+2',)), 'YB+3': CNSTopologyResidue('YB3', 3.0, ('YB+3',)), 'ZN': CNSTopologyResidue('ZN', 0.0, ('ZN',)), 'ZN+2': CNSTopologyResidue('ZN2', 0.96, ('ZN+2',))}

Supported single ion atom names mapping.

haddock.core.supported_molecules.supported_single_ions_elements = {'AG', 'AL', 'AR', 'AS', 'AU', 'BR', 'CA', 'CD', 'CL', 'CO', 'CR', 'CS', 'CU', 'F', 'FE', 'HG', 'HO', 'I', 'IR', 'K', 'KR', 'LI', 'MG', 'MN', 'MO', 'NA', 'NI', 'OS', 'PB', 'PT', 'SR', 'U', 'V', 'XE', 'YB', 'ZN'}

Supported single ions elements.

haddock.core.supported_molecules.supported_single_ions_elements_map = {'AG': CNSTopologyResidue('AG1', 1.0, ('AG+1',)), 'AL': CNSTopologyResidue('AL3', 3.0, ('AL+3',)), 'AR': CNSTopologyResidue('AR', 0.0, ('AR',)), 'AS': CNSTopologyResidue('AS', 0.0, ('AS',)), 'AU': CNSTopologyResidue('AU3', 3.0, ('AU+3',)), 'BR': CNSTopologyResidue('BR1', -1.0, ('BR-1',)), 'CA': CNSTopologyResidue('CA2', 2.0, ('CA+2',)), 'CD': CNSTopologyResidue('CD2', 2.0, ('CD+2',)), 'CL': CNSTopologyResidue('CL1', -1.0, ('CL-1',)), 'CO': CNSTopologyResidue('CO3', 3.0, ('CO+3',)), 'CR': CNSTopologyResidue('CR3', 3.0, ('CR+3',)), 'CS': CNSTopologyResidue('CS1', 1.0, ('CS+1',)), 'CU': CNSTopologyResidue('CU2', 2.0, ('CU+2',)), 'F': CNSTopologyResidue('F1', -1.0, ('F-1',)), 'FE': CNSTopologyResidue('FE3', 3.0, ('FE+3',)), 'HG': CNSTopologyResidue('HG2', 2.0, ('HG+2',)), 'HO': CNSTopologyResidue('HO3', 3.0, ('HO+3',)), 'I': CNSTopologyResidue('I1', -1.0, ('I-1',)), 'IR': CNSTopologyResidue('IR3', 3.0, ('IR+3',)), 'K': CNSTopologyResidue('K1', 1.0, ('K+1',)), 'KR': CNSTopologyResidue('KR', 0.0, ('KR',)), 'LI': CNSTopologyResidue('LI1', 1.0, ('LI+1',)), 'MG': CNSTopologyResidue('MG2', 2.0, ('MG+2',)), 'MN': CNSTopologyResidue('MN3', 3.0, ('MN+3',)), 'MO': CNSTopologyResidue('MO3', 3.0, ('MO+3',)), 'NA': CNSTopologyResidue('NA1', 1.0, ('NA+1',)), 'NI': CNSTopologyResidue('NI2', 2.0, ('NI+2',)), 'OS': CNSTopologyResidue('OS4', 4.0, ('OS+4',)), 'PB': CNSTopologyResidue('PB2', 2.0, ('PB+2',)), 'PT': CNSTopologyResidue('PT2', 2.0, ('PT+2',)), 'SR': CNSTopologyResidue('SR2', 2.0, ('SR+2',)), 'U': CNSTopologyResidue('U4', 4.0, ('U+4',)), 'V': CNSTopologyResidue('V3', 3.0, ('V+3',)), 'XE': CNSTopologyResidue('XE', 0.0, ('XE',)), 'YB': CNSTopologyResidue('YB3', 3.0, ('YB+3',)), 'ZN': CNSTopologyResidue('ZN2', 0.96, ('ZN+2',))}

Supported single ions elements mapping.

haddock.core.supported_molecules.supported_single_ions_resnames = {'AG', 'AG1', 'AL', 'AL3', 'AR', 'AS', 'AU', 'AU1', 'AU3', 'BR', 'BR1', 'CA', 'CA2', 'CD', 'CD2', 'CL', 'CL1', 'CO', 'CO2', 'CO3', 'CR', 'CR2', 'CR3', 'CS', 'CS1', 'CU', 'CU1', 'CU2', 'F', 'F1', 'FE', 'FE2', 'FE3', 'HG', 'HG1', 'HG2', 'HO', 'HO3', 'I', 'I1', 'IR', 'IR3', 'K', 'K1', 'KR', 'LI1', 'MG', 'MG2', 'MN', 'MN2', 'MN3', 'MO', 'MO3', 'NA', 'NA1', 'NI', 'NI2', 'OS', 'OS4', 'PB', 'PB2', 'PT', 'PT2', 'SR', 'SR2', 'U3', 'U4', 'V', 'V2', 'V3', 'XE', 'YB', 'YB2', 'YB3', 'ZN', 'ZN2'}

Supported single residue names.

haddock.core.supported_molecules.supported_single_ions_resnames_map = {'AG': CNSTopologyResidue('AG', 0.0, ('AG',)), 'AG1': CNSTopologyResidue('AG1', 1.0, ('AG+1',)), 'AL': CNSTopologyResidue('AL', 0.0, ('AL',)), 'AL3': CNSTopologyResidue('AL3', 3.0, ('AL+3',)), 'AR': CNSTopologyResidue('AR', 0.0, ('AR',)), 'AS': CNSTopologyResidue('AS', 0.0, ('AS',)), 'AU': CNSTopologyResidue('AU', 0.0, ('AU',)), 'AU1': CNSTopologyResidue('AU1', 1.0, ('AU+1',)), 'AU3': CNSTopologyResidue('AU3', 3.0, ('AU+3',)), 'BR': CNSTopologyResidue('BR', 0.0, ('BR',)), 'BR1': CNSTopologyResidue('BR1', -1.0, ('BR-1',)), 'CA': CNSTopologyResidue('CA', 0.0, ('CA',)), 'CA2': CNSTopologyResidue('CA2', 2.0, ('CA+2',)), 'CD': CNSTopologyResidue('CD', 0.0, ('CD',)), 'CD2': CNSTopologyResidue('CD2', 2.0, ('CD+2',)), 'CL': CNSTopologyResidue('CL', 0.0, ('CL',)), 'CL1': CNSTopologyResidue('CL1', -1.0, ('CL-1',)), 'CO': CNSTopologyResidue('CO', 0.0, ('CO',)), 'CO2': CNSTopologyResidue('CO2', 2.0, ('CO+2',)), 'CO3': CNSTopologyResidue('CO3', 3.0, ('CO+3',)), 'CR': CNSTopologyResidue('CR', 0.0, ('CR',)), 'CR2': CNSTopologyResidue('CR2', 2.0, ('CR+2',)), 'CR3': CNSTopologyResidue('CR3', 3.0, ('CR+3',)), 'CS': CNSTopologyResidue('CS', 0.0, ('CS',)), 'CS1': CNSTopologyResidue('CS1', 1.0, ('CS+1',)), 'CU': CNSTopologyResidue('CU', 0.0, ('CU',)), 'CU1': CNSTopologyResidue('CU1', 1.0, ('CU+1',)), 'CU2': CNSTopologyResidue('CU2', 2.0, ('CU+2',)), 'F': CNSTopologyResidue('F', 0.0, ('F',)), 'F1': CNSTopologyResidue('F1', -1.0, ('F-1',)), 'FE': CNSTopologyResidue('FE', 0.0, ('FE',)), 'FE2': CNSTopologyResidue('FE2', 2.0, ('FE+2',)), 'FE3': CNSTopologyResidue('FE3', 3.0, ('FE+3',)), 'HG': CNSTopologyResidue('HG', 0.0, ('HG',)), 'HG1': CNSTopologyResidue('HG1', 1.0, ('HG+1',)), 'HG2': CNSTopologyResidue('HG2', 2.0, ('HG+2',)), 'HO': CNSTopologyResidue('HO', 0.0, ('HO',)), 'HO3': CNSTopologyResidue('HO3', 3.0, ('HO+3',)), 'I': CNSTopologyResidue('I', 0.0, ('I',)), 'I1': CNSTopologyResidue('I1', -1.0, ('I-1',)), 'IR': CNSTopologyResidue('IR', 0.0, ('IR',)), 'IR3': CNSTopologyResidue('IR3', 3.0, ('IR+3',)), 'K': CNSTopologyResidue('K', 0.0, ('K',)), 'K1': CNSTopologyResidue('K1', 1.0, ('K+1',)), 'KR': CNSTopologyResidue('KR', 0.0, ('KR',)), 'LI1': CNSTopologyResidue('LI1', 1.0, ('LI+1',)), 'MG': CNSTopologyResidue('MG', 0.0, ('MG',)), 'MG2': CNSTopologyResidue('MG2', 2.0, ('MG+2',)), 'MN': CNSTopologyResidue('MN', 0.0, ('MN',)), 'MN2': CNSTopologyResidue('MN2', 2.0, ('MN+2',)), 'MN3': CNSTopologyResidue('MN3', 3.0, ('MN+3',)), 'MO': CNSTopologyResidue('MO', 0.0, ('MO',)), 'MO3': CNSTopologyResidue('MO3', 3.0, ('MO+3',)), 'NA': CNSTopologyResidue('NA', 0.0, ('NA',)), 'NA1': CNSTopologyResidue('NA1', 1.0, ('NA+1',)), 'NI': CNSTopologyResidue('NI', 0.0, ('NI',)), 'NI2': CNSTopologyResidue('NI2', 2.0, ('NI+2',)), 'OS': CNSTopologyResidue('OS', 0.0, ('OS',)), 'OS4': CNSTopologyResidue('OS4', 4.0, ('OS+4',)), 'PB': CNSTopologyResidue('PB', 0.0, ('PB',)), 'PB2': CNSTopologyResidue('PB2', 2.0, ('PB+2',)), 'PT': CNSTopologyResidue('PT', 0.0, ('PT',)), 'PT2': CNSTopologyResidue('PT2', 2.0, ('PT+2',)), 'SR': CNSTopologyResidue('SR', 0.0, ('SR',)), 'SR2': CNSTopologyResidue('SR2', 2.0, ('SR+2',)), 'U3': CNSTopologyResidue('U3', 3.0, ('U+3',)), 'U4': CNSTopologyResidue('U4', 4.0, ('U+4',)), 'V': CNSTopologyResidue('V', 0.0, ('V',)), 'V2': CNSTopologyResidue('V2', 2.0, ('V+2',)), 'V3': CNSTopologyResidue('V3', 3.0, ('V+3',)), 'XE': CNSTopologyResidue('XE', 0.0, ('XE',)), 'YB': CNSTopologyResidue('YB', 0.0, ('YB',)), 'YB2': CNSTopologyResidue('YB2', 2.0, ('YB+2',)), 'YB3': CNSTopologyResidue('YB3', 3.0, ('YB+3',)), 'ZN': CNSTopologyResidue('ZN', 0.0, ('ZN',)), 'ZN2': CNSTopologyResidue('ZN2', 0.96, ('ZN+2',))}

Supported single ion resname mapping.

haddock.core.supported_molecules.supported_solvents_resnames = {'COH', 'COM', 'DMS', 'DOD', 'ETH', 'HOH', 'O2', 'TIP', 'TIP3', 'WAT'}

Supported solvents.