Secondary structure database

Under the hood, pmlbeta maintains a database of secondary structures, which is essentially a bunch of backbone dihedral angle triplets with labels. This is stored in the form of a Python dict, mapping string labels to tuples of floating point numbers.

By default the following are defined:

DEFAULT_HELIXTYPES = {
    'Z6M': (126.7, 62.6, 152.7),
    'Z6P': (-126.7, -62.6, -152.7),
    'Z8M': (47.5, 53.5, -104.3),
    'Z8P': (-47.5, -53.5, 104.3),
    'H8M': (76.8, -120.6, 52.7),
    'H8P': (-76.8, 120.6, -52.7),
    'H10M': (-77.5, -51.8, -75.1),
    'H10P': (77.5, 51.8, 75.1),
    'H12M': (92.3, -90.0, 104.6),
    'H12P': (-92.3, 90.0, -104.6),
    'H14M': (-140.3, 66.5, -136.8),
    'H14P': (140.3, -66.5, 136.8),
    'SM': (70.5, 176.2, 168.9),
    'SP': (-70.5, -176.2, -168.9),
    'Straight': (180, 180, 180),
    'Straight alpha': (180, None, 180),
    'Alpha-helix': (-57, None, -47),
    '3_10-helix': (-49, None, -26),
    'P-beta-sheet': (-119, None, 113),
    'AP-beta-sheet': (-139, None, 135),
}

Corresponding to the following:

Abbreviation	phi	theta	psi	Comments
Z6M	126.7°	62.6°	152.7°	from Beke et. al.(2006)
Z6P	-126.7°	-62.6°	-152.7°
Z8M	47.5°	53.5°	-104.3°
Z8P	-47.5°	-53.5°	104.3°
H8M	76.8°	-120.6°	52.7°
H8P	-76.8°	120.6°	-52.7°
H10M	-77.5°	-51.8°	-75.1°
H10P	77.5°	51.8°	75.1°
H12M	92.3°	-90.0°	104.6°
H12P	-92.3°	90.0°	-104.6°
H14M	-140.3°	66.5°	-136.8°
H14P	140.3°	-66.5°	136.8°
SM	70.5°	176.2°	168.9°
SP	-70.5°	-176.2°	-168.9°
Straight	180°	180°	180°
Straight alpha	180°	—	180°
Alpha-helix	-57°	—	-47°	from PyMOL
P-beta-sheet	-119°	—	113°
AP-beta-sheet	-139°	—	135°
3_10-helix	-49°	—	-26°

Editing this list is possible by the corresponding GUI utility, or by the ssdb_* commands.

Changes to the secondary structure database are remembered in the next PyMOL session.

Python API documentation

Implement a database of secondary structures using the plugin preference store of PyMOL

class pmlbeta.secstructdb.SecondaryStructureDB

A database of the known secondary structures and the corresponding dihedral angles

classmethod add(name: str, phi: float, theta: float, psi: float)

Add or edit an entry in the secondary structure torsion angle database

Parameters:

• name (str) – the name of the secondary structure
• phi (float) – the first torsion angle
• theta (float or None) – the second torsion angle (None for alpha-amino acid secondary structures)
• psi (float) – the third torsion angle

classmethod addDefaults()

Add the default secondary structure types to the list

classmethod dihedrals(name: str) → Tuple[float, Optional[float], float]

Get the dihedral angles corresponding to a secondary structure.

Parameters:name (str) – the name of the secondary structure Returns:the dihedral angles corresponding to that secondary structure, in degrees Return type:a tuple of three floats, the central one can be None Raises:KeyError – if the named entry does not exist

classmethod find(phi: float, theta: Optional[float], psi: float, tolerance: float = 0.5) → Optional[str]

Try to find a secondary structure in the database which matches the given torsion angles

Parameters:

• phi (float) – the first torsion angle
• theta (float or None) – the second torsion angle (None for alpha-amino acids)
• psi (float) – the third torsion angle
• tolerance (float) – absolute tolerance in each angle

Returns:

the name of the closest matching secondary structure or None if no match

Return type:

str or None

classmethod getAll(alpha: bool = True, beta: bool = True) → Dict[str, Tuple[float, float, float]]

Get the list of secondary structures from the PyMOL plugin preferences

Parameters:

• alpha (bool) – if secondary structures for alpha-peptides are requested
• beta (bool) – if secondary structures for beta-peptides are requested

Returns:

the known secondary structures and their backbone torsion angles

Return type:

a dict mapping names to triplets of floats

classmethod remove(name: str)

Remove an entry in the secondary structure torsion angle database

Parameters:name (str) – the name of the secondary structure

pmlbeta.secstructdb.ssdb_add(entryname: str, phi: Union[str, float], theta: Union[str, float], psi: Union[str, float, None] = None, _self=None)

DESCRIPTION

Add/modify an entry in the secondary structure database

USAGE

ssdb_add entryname, phi, theta, psi # for beta-amino acids

or

ssdb_add entryname, phi, psi # for alpha-amino acids

ARGUMENTS

entryname = string: the name of the entry

phi = float: the first (N-terminal) backbone dihedral angle: (C-, N, CA, C) for alpha-amino acids and

(C-, N, CB, CA) for beta-amino acids

theta = float: the middle backbone dihedral angle for beta-amino acids: (N, CB, CA, C)

psi = float: the last (C-terminal) backbone dihedral angle: (N, CA, C, N+) for alpha-amino acids and

(CB, CA, C, N+) for beta-amino acids

NOTES

changes are automatically saved for further PyMOL sessions.

SEE ALSO

ssdb_del, ssdb_list, ssdb_resetdefaults, ssdb_dihedrals

pmlbeta.secstructdb.ssdb_del(entryname: str, _self=None)

DESCRIPTION

Remove an entry from the secondary structure database

USAGE

ssdb_del entryname

ARGUMENTS

entryname = string: the name of the entry

NOTES

changes are automatically saved for further PyMOL sessions.

SEE ALSO

ssdb_add, ssdb_list, ssdb_resetdefaults, ssdb_dihedrals

pmlbeta.secstructdb.ssdb_dihedrals(entryname: str, _self=None)

DESCRIPTION

Print the dihedral angles corresponding to a given entry

secondary structure database

USAGE

ssdb_dihedrals entryname

ARGUMENTS

entryname = string: the name of the entry

SEE ALSO

ssdb_add, ssdb_del, ssdb_list, ssdb_resetdefaults

pmlbeta.secstructdb.ssdb_list(_self=None)

DESCRIPTION

Lists the entries in the secondary structure database

USAGE

ssdb_list

SEE ALSO

ssdb_add, ssdb_del, ssdb_resetdefaults, ssdb_dihedrals

pmlbeta.secstructdb.ssdb_resetdefaults(_self=None)

DESCRIPTION

Add back the default entries to the secondary structure database

USAGE

ssdb_resetdefaults

NOTES

changes are automatically saved for further PyMOL sessions.

SEE ALSO

ssdb_add, ssdb_del, ssdb_list, ssdb_dihedrals