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- builtins.object
-
- LipidAccInfo
- MEM
- MembraneInfo
- Span
- SpanningTopology
- rosetta.utility.excn.EXCN_Msg_Exception(rosetta.utility.excn.EXCN_Exception)
-
- EXCN_Membrane
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- EXCN_Illegal_Arguments
- EXCN_MembraneFoldTree
- EXCN_Membrane_Bounds
- EXCN_NonMembrane
- EXCN_Resource_Definition
- EXCN_VirtualRsd
class MEM(builtins.object) |
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Methods defined here:
- __eq__(...) from builtins.PyCapsule
- __eq__(rosetta.core.conformation.membrane.MEM, rosetta.core.conformation.membrane.MEM) -> bool
- __hash__(...) from builtins.PyCapsule
- __hash__(rosetta.core.conformation.membrane.MEM) -> int
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.core.conformation.membrane.MEM, int) -> NoneType
2. __init__(rosetta.core.conformation.membrane.MEM, int) -> NoneType
- __int__(...) from builtins.PyCapsule
- __int__(rosetta.core.conformation.membrane.MEM) -> int
- __ne__(...) from builtins.PyCapsule
- __ne__(rosetta.core.conformation.membrane.MEM, rosetta.core.conformation.membrane.MEM) -> bool
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __repr__(...) from builtins.PyCapsule
- __repr__(rosetta.core.conformation.membrane.MEM) -> str
Data and other attributes defined here:
- center = MEM.center
- normal = MEM.normal
- thickness = MEM.thickness
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class MembraneInfo(builtins.object) |
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MembraneInfo describes the membrane bilayer and its relationship with the protein
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : handle, membrane_pos : int, membrane_jump : int, topology : core::conformation::membrane::SpanningTopology) -> NoneType
2. __init__(self : handle, membrane_pos : int, membrane_jump : int, lips : rosetta.core.conformation.membrane.LipidAccInfo, topology : core::conformation::membrane::SpanningTopology) -> NoneType
3. __init__(handle, rosetta.core.conformation.membrane.MembraneInfo) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.core.conformation.membrane.MembraneInfo) -> str
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.conformation.membrane.MembraneInfo, src : rosetta.core.conformation.membrane.MembraneInfo) -> rosetta.core.conformation.membrane.MembraneInfo
create a deep copy of all data in thsi object upon assignment
- atom_z_position(...) from builtins.PyCapsule
- atom_z_position(self : rosetta.core.conformation.membrane.MembraneInfo, conf : rosetta.core.conformation.Conformation, resnum : int, atomnum : int) -> float
Compute atom position relative to membrane normal
Calculate the z coordinate of the atom, projected onto
the membrane normal axis. Objective is to maintain correct coordinates
in relative coordinate frame.
- check_membrane_fold_tree(...) from builtins.PyCapsule
- check_membrane_fold_tree(self : rosetta.core.conformation.membrane.MembraneInfo, ft_in : rosetta.core.kinematics.FoldTree) -> bool
Somewhat weak check that a membrane foldtree is valid. Use checks in
protocols/membrane/util.hh instead!
- in_membrane(...) from builtins.PyCapsule
- in_membrane(self : rosetta.core.conformation.membrane.MembraneInfo, conf : rosetta.core.conformation.Conformation, resnum : int) -> bool
Is residue in the membrane? Takes CA coordinate
Uses the thickness stored in MembraneInfon and the residue_z_position
- include_lips(...) from builtins.PyCapsule
- include_lips(rosetta.core.conformation.membrane.MembraneInfo) -> bool
Does this MembraneInfo includes lipophilicity information?
- lipid_acc_data(...) from builtins.PyCapsule
- lipid_acc_data(rosetta.core.conformation.membrane.MembraneInfo) -> rosetta.core.conformation.membrane.LipidAccInfo
Per-residue lipophilicity (probability of exposure to lipid)
Returns a LipidAccInfo describing per residue probability
of exposure to lipid. Data calcualted via the run_lips.pl script
and provided by the user on the commandline if applicable
- membrane_center(...) from builtins.PyCapsule
- membrane_center(self : rosetta.core.conformation.membrane.MembraneInfo, conf : rosetta.core.conformation.Conformation) -> rosetta.numeric.xyzVector_double_t
Membrane center
Returns the xyzVector describing the center of the membrane
This is the same as the MPct atom of the membrane (MEM) residue.
- membrane_jump(...) from builtins.PyCapsule
- membrane_jump(rosetta.core.conformation.membrane.MembraneInfo) -> int
Indeitifier for the membrane jump
Returns an integer (core::Size) denoting the jump number in the foldtree
representing the jump relating the membrane residue to the rest of the molecule
- membrane_normal(...) from builtins.PyCapsule
- membrane_normal(self : rosetta.core.conformation.membrane.MembraneInfo, conf : rosetta.core.conformation.Conformation) -> rosetta.numeric.xyzVector_double_t
Membrane normal
Returns the membrane normal, which describes the membrane
orientation. This is the same as the xyzVector in the MPnm atom
in the membrane residue.
- membrane_rsd_num(...) from builtins.PyCapsule
- membrane_rsd_num(rosetta.core.conformation.membrane.MembraneInfo) -> int
Sequence position of the membrane residue
Return the residue number of MEM (rsd.seqpos()) in the pose
- membrane_steepness(...) from builtins.PyCapsule
- membrane_steepness(rosetta.core.conformation.membrane.MembraneInfo) -> float
Steepness of hydrophobic -> hydrophillic transition
For IMM - default is 10
- membrane_thickness(...) from builtins.PyCapsule
- membrane_thickness(rosetta.core.conformation.membrane.MembraneInfo) -> float
Effective thickness of the membrane
For IMM = default is 15.
- residue_z_position(...) from builtins.PyCapsule
- residue_z_position(self : rosetta.core.conformation.membrane.MembraneInfo, conf : rosetta.core.conformation.Conformation, resnum : int) -> float
Compute residue position relative to membrane normal
Calculate the z coordinate of the residue, projected onto
the membrane normal axis. Objective is to maintain correct coordinates
in relative coordinate frame.
- set_membrane_jump(...) from builtins.PyCapsule
- set_membrane_jump(self : rosetta.core.conformation.membrane.MembraneInfo, jumpnum : int) -> NoneType
Allow a protocol to set a new jump number for the membrane jump
Set the membrane jump number (core::SSize)
- show(...) from builtins.PyCapsule
- show(rosetta.core.conformation.membrane.MembraneInfo) -> NoneType
Generate a string representation of information represented by this MembraneInfo and send it to std::cout
- spanning_topology(...) from builtins.PyCapsule
- spanning_topology(rosetta.core.conformation.membrane.MembraneInfo) -> core::conformation::membrane::SpanningTopology
Transmembrane spaning topology
Return a SpanningTopology object, which includes a
list of Span objects, describing the start and end sequence
positions of each transmembrane span
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class Span(builtins.object) |
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.core.conformation.membrane.Span) -> NoneType
2. __init__(self : rosetta.core.conformation.membrane.Span, start : int, end : int) -> NoneType
3. __init__(self : rosetta.core.conformation.membrane.Span, src : rosetta.core.conformation.membrane.Span) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.conformation.membrane.Span, src : rosetta.core.conformation.membrane.Span) -> rosetta.core.conformation.membrane.Span
Assignment Operator
Make a deep copy of this object
- center(...) from builtins.PyCapsule
- center(rosetta.core.conformation.membrane.Span) -> int
Get residue closest to center
- end(...) from builtins.PyCapsule
- end(rosetta.core.conformation.membrane.Span) -> int
Get end position
Get the end position of a transmembrane span
- is_valid(...) from builtins.PyCapsule
- is_valid(rosetta.core.conformation.membrane.Span) -> bool
Check that this Span is Valid
Check that this span describes a consecutive transmembrane span
of nonzero length.
- not_valid(...) from builtins.PyCapsule
- not_valid(rosetta.core.conformation.membrane.Span) -> NoneType
- shift(...) from builtins.PyCapsule
- shift(self : rosetta.core.conformation.membrane.Span, offset : int) -> NoneType
Shift by offset
Shift the transmembrane span by a user-provided offset
- show(...) from builtins.PyCapsule
- show(rosetta.core.conformation.membrane.Span) -> NoneType
Show This Span
Show the information in this span. TODO: Should override base method
- start(...) from builtins.PyCapsule
- start(rosetta.core.conformation.membrane.Span) -> int
Get start position
Get the Starting Position of a transmembrane span
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class SpanningTopology(builtins.object) |
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, str) -> NoneType
doc
3. __init__(self : handle, spanfile : str, total_residues : int) -> NoneType
4. __init__(self : handle, res_z_coord : rosetta.utility.vector1_double, chainID : rosetta.utility.vector1_unsigned_long, secstruct : rosetta.utility.vector1_char, thickness : float) -> NoneType
5. __init__(handle, rosetta.core.conformation.membrane.SpanningTopology) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.core.conformation.membrane.SpanningTopology) -> str
- add_span(...) from builtins.PyCapsule
- add_span(*args, **kwargs)
Overloaded function.
1. add_span(self : rosetta.core.conformation.membrane.SpanningTopology, span : rosetta.core.conformation.membrane.Span) -> NoneType
2. add_span(self : rosetta.core.conformation.membrane.SpanningTopology, span : rosetta.core.conformation.membrane.Span, offset : int) -> NoneType
3. add_span(self : rosetta.core.conformation.membrane.SpanningTopology, start : int, end : int) -> NoneType
4. add_span(self : rosetta.core.conformation.membrane.SpanningTopology, start : int, end : int, offset : int) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.conformation.membrane.SpanningTopology, src : rosetta.core.conformation.membrane.SpanningTopology) -> rosetta.core.conformation.membrane.SpanningTopology
Assignment Operator
Overload assignemnt operator - required Rosetta method
- concatenate_topology(...) from builtins.PyCapsule
- concatenate_topology(self : rosetta.core.conformation.membrane.SpanningTopology, topo : rosetta.core.conformation.membrane.SpanningTopology) -> rosetta.core.conformation.membrane.SpanningTopology
- fill_from_spanfile(...) from builtins.PyCapsule
- fill_from_spanfile(*args, **kwargs)
Overloaded function.
1. fill_from_spanfile(self : rosetta.core.conformation.membrane.SpanningTopology, spanfile : str) -> NoneType
2. fill_from_spanfile(self : rosetta.core.conformation.membrane.SpanningTopology, spanfile : str, total_residues : int) -> NoneType
- fill_from_structure(...) from builtins.PyCapsule
- fill_from_structure(self : rosetta.core.conformation.membrane.SpanningTopology, res_z_coord : rosetta.utility.vector1_double, chainID : rosetta.utility.vector1_unsigned_long, secstruct : rosetta.utility.vector1_char, thickness : float) -> NoneType
- get_spans(...) from builtins.PyCapsule
- get_spans(rosetta.core.conformation.membrane.SpanningTopology) -> rosetta.utility.vector1_std_shared_ptr_core_conformation_membrane_Span_t
//////////////////////
- in_span(...) from builtins.PyCapsule
- in_span(self : rosetta.core.conformation.membrane.SpanningTopology, residue : int) -> bool
///////////////
- is_valid(...) from builtins.PyCapsule
- is_valid(rosetta.core.conformation.membrane.SpanningTopology) -> bool
Determine if this Spanning Topology Object is Valid
Check that spans still span the membrane
- nres_topo(...) from builtins.PyCapsule
- nres_topo(rosetta.core.conformation.membrane.SpanningTopology) -> int
- nspans(...) from builtins.PyCapsule
- nspans(rosetta.core.conformation.membrane.SpanningTopology) -> int
- reorder_spans(...) from builtins.PyCapsule
- reorder_spans(rosetta.core.conformation.membrane.SpanningTopology) -> NoneType
- span(...) from builtins.PyCapsule
- span(self : rosetta.core.conformation.membrane.SpanningTopology, span_number : int) -> rosetta.core.conformation.membrane.Span
- spanning(...) from builtins.PyCapsule
- spanning(self : rosetta.core.conformation.membrane.SpanningTopology, res_z_coord : rosetta.utility.vector1_double, span : rosetta.core.conformation.membrane.Span) -> bool
- write_spanfile(...) from builtins.PyCapsule
- write_spanfile(self : rosetta.core.conformation.membrane.SpanningTopology, output_filename : str) -> NoneType
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