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Pydoc: module dssp

dssp

index

DSSP based classification for protein secondary structure. The DSSP algorithm (see references below) provides a description of the secondary structure components in a protein biomolecule, based on backbone hydrogen bonding and the topology of beta-sheets. The most widely used feature of this algorithm is the per-residue classification of secondary structure using the following single character codes: H = alpha-helix B = residue in isolated beta-bridge E = extended strand, participates in beta-ladder G = 3-10-helix I = Pi-helix P = poly-proline II helix T = hydrogen-bonded turn S = bend <blank or ' '> = loops See Original paper: Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983. Current implementation: Joosten RP, te Beek TAH, Krieger E, Hekkelman ML, Hooft RWW, Schneider R, Sander C, Vriend A series of PDB related databases for everyday needs. Nuc. Acids Res. 2010. DSSP website: https://pdb-redo.eu/dssp/about constructor: DSSP(atomSel, min_poly_proline_stretch_length) atomSel is a string or atomSel.AtomSel min_poly_proline_stretch_length minimal number of residues having phi/psi in range for a PP helix; default value in current implementation is 2. To match the default used by the mkdssp program, use 3. methods: getResInfo(segid, resid) = returns the secondary structure classification (single character codes tabulated above) corresponding to per-residue segid (or chain ID) and residue number. getStatistics() = not tested # This file was automatically generated by SWIG (http://www.swig.org). # Version 4.0.2 # # Do not make changes to this file unless you know what you are doing--modify # the SWIG interface file instead.

Classes

builtins.object

DSSP
DSSP_ResidueInfo
DSSP_Statistics

class DSSP(builtins.object)

DSSP(*args, **kwargs)

Methods defined here:

__init__(self, *args, **kwargs): Initialize self. See help(type(self)) for accurate signature.

__repr__ = _swig_repr(self)

getResInfo(self, *args, **kwargs) -> 'DSSP_ResidueInfo'

getStatistics(self, *args, **kwargs) -> 'DSSP_Statistics'

pyXplorHelp(self, *args, **kwargs) -> 'String'

Static methods defined here:

__swig_destroy__ = delete_DSSP(...)

Data descriptors defined here:

__dict__: dictionary for instance variables (if defined)

__weakref__: list of weak references to the object (if defined)

thisown: The membership flag

class DSSP_ResidueInfo(builtins.object)

DSSP_ResidueInfo(*args)

Methods defined here:

__bool__ = __nonzero__(self)

__eq__(self, *args, **kwargs) -> 'bool': Return self==value.

__init__(self, *args): Initialize self. See help(type(self)) for accurate signature.

__nonzero__(self)

__repr__ = _swig_repr(self)

acceptor(self, *args, **kwargs) -> 'Pair< DSSP_ResidueInfo,double >'

alpha(self, *args, **kwargs) -> 'float_type const'

bend(self, *args, **kwargs) -> 'bool'

bridge_partner(self, *args, **kwargs) -> 'std::tuple< DSSP_ResidueInfo,int,bool >'

donor(self, *args, **kwargs) -> 'Pair< DSSP_ResidueInfo,double >'

empty(self, *args, **kwargs) -> 'bool'

helix(self, *args, **kwargs) -> 'DSSP_helix_position'

kappa(self, *args, **kwargs) -> 'float_type const'

next(self, *args, **kwargs) -> 'DSSP_ResidueInfo'

nr(self, *args, **kwargs) -> 'int'

omega(self, *args, **kwargs) -> 'float_type const'

phi(self, *args, **kwargs) -> 'float_type const'

psi(self, *args, **kwargs) -> 'float_type const'

residueName(self, *args, **kwargs) -> 'String'

residueNum(self, *args, **kwargs) -> 'int'

segmentName(self, *args, **kwargs) -> 'String'

setAlpha(self, *args, **kwargs) -> 'void'

setKappa(self, *args, **kwargs) -> 'void'

setOmega(self, *args, **kwargs) -> 'void'

setPhi(self, *args, **kwargs) -> 'void'

setPsi(self, *args, **kwargs) -> 'void'

setTco(self, *args, **kwargs) -> 'void'

sheet(self, *args, **kwargs) -> 'int'

strand(self, *args, **kwargs) -> 'int'

tco(self, *args, **kwargs) -> 'float_type const'

type(self, *args, **kwargs) -> 'DSSP_structure'

Static methods defined here:

__swig_destroy__ = delete_DSSP_ResidueInfo(...)

Data descriptors defined here:

__dict__: dictionary for instance variables (if defined)

__weakref__: list of weak references to the object (if defined)

thisown: The membership flag

Data and other attributes defined here:

__hash__ = None

class DSSP_Statistics(builtins.object)

DSSP_Statistics(*args, **kwargs)

Methods defined here:

__init__(self, *args, **kwargs): Initialize self. See help(type(self)) for accurate signature.

__repr__ = _swig_repr(self)

Static methods defined here:

__swig_destroy__ = delete_DSSP_Statistics(...)

Data descriptors defined here:

H_Bonds_per_distance

H_bonds

H_bonds_in_antiparallel_bridges

H_bonds_in_parallel_bridges

SS_bridges

__dict__: dictionary for instance variables (if defined)

__weakref__: list of weak references to the object (if defined)

antiparallel_bridges_per_ladder

chains

intra_chain_SS_bridges

ladders_per_sheet

parallel_bridges_per_ladder

residues

residues_per_alpha_helix

thisown: The membership flag

Functions
		pyXplorHelp(*args) -> 'String'

Data
		DSSP_helix__3_10 = 0 DSSP_helix_alpha = 1 DSSP_helix_pi = 2 DSSP_helix_position_End = 2 DSSP_helix_position_Middle = 4 DSSP_helix_position_Start = 1 DSSP_helix_position_StartAndEnd = 3 DSSP_helix_position__None = 0 DSSP_helix_pp = 3 DSSP_kHistogramSize = 30 DSSP_structure_Alphahelix = 'H' DSSP_structure_Bend = 'S' DSSP_structure_Betabridge = 'B' DSSP_structure_Helix_3 = 'G' DSSP_structure_Helix_5 = 'I' DSSP_structure_Helix_PPII = 'P' DSSP_structure_Loop = ' ' DSSP_structure_Strand = 'E' DSSP_structure_Turn = 'T' cvar = <Swig global variables>