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- builtins.object
-
- BTSB_SUBBIN_TYPE
- BT_PROPERTIES
- BinTransitionCalculator
- BinTransitionData
class BTSB_SUBBIN_TYPE(builtins.object) |
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Enum for the way in which bins will be divided into subbins.
Default is BTSB_NONE, which means that the bin has no subbins. As subbin types are
added, add them (1) here, and (2) to the get_subbin_type_name function, and (3) to the setup_subbin_type
function, then add a function called by the setup_subbin_type function.
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Methods defined here:
- __eq__(...) from builtins.PyCapsule
- __eq__(rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE, rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE) -> bool
- __hash__(...) from builtins.PyCapsule
- __hash__(rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE) -> int
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE, int) -> NoneType
2. __init__(rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE, int) -> NoneType
- __int__(...) from builtins.PyCapsule
- __int__(rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE) -> int
- __ne__(...) from builtins.PyCapsule
- __ne__(rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE, rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE) -> 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.scoring.bin_transitions.BTSB_SUBBIN_TYPE) -> str
Data and other attributes defined here:
- BTSB_D_AA = BTSB_SUBBIN_TYPE.BTSB_D_AA
- BTSB_D_PRO = BTSB_SUBBIN_TYPE.BTSB_D_PRO
- BTSB_END_OF_LIST = BTSB_SUBBIN_TYPE.BTSB_END_OF_LIST
- BTSB_GLY = BTSB_SUBBIN_TYPE.BTSB_GLY
- BTSB_L_AA = BTSB_SUBBIN_TYPE.BTSB_L_AA
- BTSB_L_PRO = BTSB_SUBBIN_TYPE.BTSB_L_PRO
- BTSB_NONE = BTSB_SUBBIN_TYPE.BTSB_NONE
- BTSB_UNKNOWN = BTSB_SUBBIN_TYPE.BTSB_UNKNOWN
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class BT_PROPERTIES(builtins.object) |
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Enum for the properties that can be required or prohibited at the i or i+1 position.
These reflect properties that residues can have. Whenever a property is added, add
it (1) here, (2) to the get_property_effect_name function, and (3) to the has_property function.
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Methods defined here:
- __eq__(...) from builtins.PyCapsule
- __eq__(rosetta.core.scoring.bin_transitions.BT_PROPERTIES, rosetta.core.scoring.bin_transitions.BT_PROPERTIES) -> bool
- __hash__(...) from builtins.PyCapsule
- __hash__(rosetta.core.scoring.bin_transitions.BT_PROPERTIES) -> int
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.core.scoring.bin_transitions.BT_PROPERTIES, int) -> NoneType
2. __init__(rosetta.core.scoring.bin_transitions.BT_PROPERTIES, int) -> NoneType
- __int__(...) from builtins.PyCapsule
- __int__(rosetta.core.scoring.bin_transitions.BT_PROPERTIES) -> int
- __ne__(...) from builtins.PyCapsule
- __ne__(rosetta.core.scoring.bin_transitions.BT_PROPERTIES, rosetta.core.scoring.bin_transitions.BT_PROPERTIES) -> 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.scoring.bin_transitions.BT_PROPERTIES) -> str
Data and other attributes defined here:
- BT_ALPHA_AA = BT_PROPERTIES.BT_ALPHA_AA
- BT_AROMATIC = BT_PROPERTIES.BT_AROMATIC
- BT_BETA_AA = BT_PROPERTIES.BT_BETA_AA
- BT_CHARGED = BT_PROPERTIES.BT_CHARGED
- BT_CYCLIC = BT_PROPERTIES.BT_CYCLIC
- BT_DISULFIDE_BONDED = BT_PROPERTIES.BT_DISULFIDE_BONDED
- BT_D_AA = BT_PROPERTIES.BT_D_AA
- BT_END_OF_LIST = BT_PROPERTIES.BT_END_OF_LIST
- BT_L_AA = BT_PROPERTIES.BT_L_AA
- BT_METALBINDING = BT_PROPERTIES.BT_METALBINDING
- BT_POLAR = BT_PROPERTIES.BT_POLAR
- BT_PROTEIN = BT_PROPERTIES.BT_PROTEIN
- BT_SIDECHAIN_THIOL = BT_PROPERTIES.BT_SIDECHAIN_THIOL
- BT_UNKNOWN_PROPERTY = BT_PROPERTIES.BT_UNKNOWN_PROPERTY
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class BinTransitionCalculator(builtins.object) |
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.core.scoring.bin_transitions.BinTransitionCalculator) -> NoneType
2. __init__(self : rosetta.core.scoring.bin_transitions.BinTransitionCalculator, src : rosetta.core.scoring.bin_transitions.BinTransitionCalculator) -> 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.scoring.bin_transitions.BinTransitionCalculator, : rosetta.core.scoring.bin_transitions.BinTransitionCalculator) -> rosetta.core.scoring.bin_transitions.BinTransitionCalculator
- bin_definition_exists(...) from builtins.PyCapsule
- bin_definition_exists(self : rosetta.core.scoring.bin_transitions.BinTransitionCalculator, name : str) -> bool
Is a particular bin defined for at least one residue type?
- bin_params_loaded(...) from builtins.PyCapsule
- bin_params_loaded(rosetta.core.scoring.bin_transitions.BinTransitionCalculator) -> bool
Return whether the bin params file has been loaded.
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.scoring.bin_transitions.BinTransitionCalculator) -> rosetta.core.scoring.bin_transitions.BinTransitionCalculator
Clone operation for BinTransitionCalculator.
Returns an owning pointer to a copy of this object.
- find_data(...) from builtins.PyCapsule
- find_data(self : rosetta.core.scoring.bin_transitions.BinTransitionCalculator, res_i : rosetta.core.conformation.Residue, res_iplus1 : rosetta.core.conformation.Residue, data_index : int) -> bool
Given residues at positions i and iplus1, find a bin transition probability data object that
describes the pair.
Inputs are res_i and res_iplus1. Outputs are data_i and data_iplus1 (BinTransitionData
indices). Function returns true if data are found successfully, false if no BinTransitionData object
could be found describing the residues in question.
- find_data_and_bin(...) from builtins.PyCapsule
- find_data_and_bin(self : rosetta.core.scoring.bin_transitions.BinTransitionCalculator, bin_name : str, res : rosetta.core.conformation.Residue, data_index : int, bin_index : int, use_iplus1 : bool) -> NoneType
Given a bin name and a residue, find a BinTransitionsData object describing that residue,
and the index of the bin within that object.
data_index and bin_index are outputs. Both are set to 0 if the search fails. Everything
else is const input. If bin_name is set to "", then the bin index that is returned is the index
corresponding to the residue's mainchain torsion vector.
- is_in_bin(...) from builtins.PyCapsule
- is_in_bin(*args, **kwargs)
Overloaded function.
1. is_in_bin(self : rosetta.core.scoring.bin_transitions.BinTransitionCalculator, res : rosetta.core.conformation.Residue, bin_name : str) -> bool
Is the given residue in the given bin?
For the bin definitions, this uses the first BinTransitionsData object that it finds where residue i matches the properties of the given
residue. Checks the i+1 definitions if nothing is found for the i transitions. Fails if no bin definitions for the given residue type are found.
2. is_in_bin(self : rosetta.core.scoring.bin_transitions.BinTransitionCalculator, res : rosetta.core.conformation.Residue, data_index : int, bin_index : int, use_iplus1 : bool) -> bool
Is the given residue in the bin given by a data object index and a bin index?
- load_bin_params(...) from builtins.PyCapsule
- load_bin_params(self : rosetta.core.scoring.bin_transitions.BinTransitionCalculator, filename : str) -> NoneType
Set the bin params file, and load all the bin params and transition probabilities.
- load_bin_params_from_file_contents(...) from builtins.PyCapsule
- load_bin_params_from_file_contents(self : rosetta.core.scoring.bin_transitions.BinTransitionCalculator, filecontents : str) -> NoneType
Loads all bin params from a string representing file contents.
Provided as an alternative to direct load from disk.
- n_bin_transition_data(...) from builtins.PyCapsule
- n_bin_transition_data(rosetta.core.scoring.bin_transitions.BinTransitionCalculator) -> int
Number of BinTransitionData objects stored (i.e. number of transition probability matrices stored).
- p_i_given_iplus1(...) from builtins.PyCapsule
- p_i_given_iplus1(self : rosetta.core.scoring.bin_transitions.BinTransitionCalculator, rsd_i : rosetta.core.conformation.Residue, rsd_iplus1 : rosetta.core.conformation.Residue, probability : float) -> bool
Given two residues (rsd_i and rsd_iplus1 at positions i and i+1, respectively), give me the
probability of seeing rsd_i in its bin given that rsd_iplus1 is in its bin.
The probability value is set to a number from 0 to 1. Inputs are rsd_i and rsd_iplus1.
Function returns true if data are found successfully, false if no BinTransitionData object
could be found describing the residues in question.
- p_iplus1_given_i(...) from builtins.PyCapsule
- p_iplus1_given_i(self : rosetta.core.scoring.bin_transitions.BinTransitionCalculator, rsd_i : rosetta.core.conformation.Residue, rsd_iplus1 : rosetta.core.conformation.Residue, probability : float) -> bool
Given two residues (rsd_i and rsd_iplus1 at positions i and i+1, respectively), give me the
probability of seeing rsd_iplus1 in its bin given that rsd_i is in its bin.
The probability value is set to a number from 0 to 1. Inputs are rsd_i and rsd_iplus1.
Function returns true if data are found successfully, false if no BinTransitionData object
could be found describing the residues in question.
- random_bin(...) from builtins.PyCapsule
- random_bin(self : rosetta.core.scoring.bin_transitions.BinTransitionCalculator, res : rosetta.core.conformation.Residue, iplus1 : bool, data_index : int) -> int
Randomly pick a bin, given an input residue.
The residue's properties and name are used to find the first BinTransitionData object matching the properties and name.
A random bin is then picked based on the frequency with which that bin is observed for that class of residues. If the bin ends
up being from the i+1st residue, iplus1 is set to "true"; otherwise, it remains "false". The data_index variable is set by this
function to the index of the BinTransitionData object that provides the transition probability data.
- random_bin_based_on_prev_and_next(...) from builtins.PyCapsule
- random_bin_based_on_prev_and_next(self : rosetta.core.scoring.bin_transitions.BinTransitionCalculator, conformation : rosetta.core.conformation.Conformation, res_index : int, must_switch_bins : bool, data_index_i : int, data_index_iplus1 : int) -> int
Given the current residue and its conformation, pick a bin for the current residue based on the bins of the previous and
next residues, and the bin transition probabilities.
Bin transition probabilities are assumed to be independent. That is, P(ABC) = P(B | A & C) = P (B | A ) * P(B | C).
This function also finds and returns the indices of the BinTransitionData objects that describe the AB transition (data_index_iplus1)
and the BC transition (data_index_i). So conformation and res_index are const inputs, and data_index_i and data_index_iplus1 are outputs.
If must_switch_bins is true, then the current bin for the current residue is never chosen; otherwise, it is in the pool to be picked.
- random_bin_based_on_previous(...) from builtins.PyCapsule
- random_bin_based_on_previous(self : rosetta.core.scoring.bin_transitions.BinTransitionCalculator, thisres : rosetta.core.conformation.Residue, prevres : rosetta.core.conformation.Residue, prev_torsions : rosetta.utility.vector1_double, data_index : int) -> int
Given the current residue and the previous residue, as well as the mainchain torsion values for the previous residue,
pick a bin for the current residue based on bin transition probabilities.
This function takes thisres (the current residue) and prevres (the previous residue) as inputs, using them for their
properties and identities to find a BinTransitionData object that matches the criteria at the i and i+1st residues. It then
sets data_index to the index of that BinTransitionData object before returning the index of a bin chosen for the current (i+1st)
residue at random, based on the relative probabilities of bins given the previous (ith) residue.
- random_mainchain_torsions_from_bin(...) from builtins.PyCapsule
- random_mainchain_torsions_from_bin(*args, **kwargs)
Overloaded function.
1. random_mainchain_torsions_from_bin(self : rosetta.core.scoring.bin_transitions.BinTransitionCalculator, bin_name : str, conformation : rosetta.core.conformation.Conformation, res_indices : rosetta.utility.vector1_unsigned_long, mainchain_torsions : rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) -> NoneType
Draw random mainchain torsion values for a set of residues, given a bin from which the values should be drawn.
Takes a bin name, a const conformation, and a const list of residue indices as input; the conformation is just for checking residues types, numbers of mainchain
torsions, etc. Output is the mainchain_torsions vector of vectors (reset and replaced by this operation). The distribution WITHIN the bin depends on the BinTransitionData
object and what was specified in the bin_params file. Default is uniform within each bin, though Ramachandran-biased distributions are also permitted for alpha-amino acids.
Note that this function uses bins for residue i, and only checks i+1 if no suitable data are found for i.
2. random_mainchain_torsions_from_bin(self : rosetta.core.scoring.bin_transitions.BinTransitionCalculator, bin_index : int, iplus1 : bool, data_index : int, mainchain_torsions : rosetta.utility.vector1_double) -> NoneType
Randomly pick mainchain torsion values from within a bin
The residue's properties and name are used to find the first BinTransitionData object matching the properties and name.
Mainchain torsion values are then picked randomly from within the bin. The distribution WITHIN the bin depends on the BinTransitionData
object and what was specified in the bin_params file. Default is uniform within each bin, though Ramachandran-biased distributions are
also permitted for alpha-amino acids. If iplus1 is true, we draw from the bins for the i+1st residue; otherwise, we draw from the bins
for the ith residue. The data_index value tells this function which BinTransitionData object to use.
- random_mainchain_torsions_from_bins(...) from builtins.PyCapsule
- random_mainchain_torsions_from_bins(self : rosetta.core.scoring.bin_transitions.BinTransitionCalculator, conformation : rosetta.core.conformation.Conformation, res_indices : rosetta.utility.vector1_unsigned_long, mainchain_torsions : rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) -> NoneType
Initialize a string of residues to a bunch of random bins, based on bin transition probabilities; then draw random mainchain torsion angles from those bins.
Takes a const conformation and a const list of residue indices as input; the conformation is just for checking residues types, numbers of mainchain torsions, etc.
The residue indices must be in order, defining a contiguous chain (running backwards or forwards). Output is the mainchain_torsions vector of vectors (reset and
replaced by this operation). The distribution WITHIN the bin depends on the BinTransitionData object and what was specified in the bin_params file. Default is uniform
within each bin, though Ramachandran-biased distributions are also permitted for alpha-amino acids.
- random_mainchain_torsions_using_adjacent_bins(...) from builtins.PyCapsule
- random_mainchain_torsions_using_adjacent_bins(self : rosetta.core.scoring.bin_transitions.BinTransitionCalculator, conformation : rosetta.core.conformation.Conformation, res_index : int, must_switch_bins : bool, mainchain_torsions : rosetta.utility.vector1_double) -> NoneType
Randomly pick mainchain torsions for a residue based on the torsion bins of its i+1 and i-1 neighbours.
Takes a const conformatoin, a const residue index, and a boolean valueas input. The conformation is for checking residue
types, numbers of mainchain torsions, etc. The boolean determines whether this residue should be allowed to stay in its own bin
or be required to switch to another bin. Output is the mainchain_torsions vector of Reals, with one entry for each mainchain torsion
of the residue.
- summarize_stored_data(...) from builtins.PyCapsule
- summarize_stored_data(self : rosetta.core.scoring.bin_transitions.BinTransitionCalculator, verbose : bool) -> str
Prints a report summarizing the data stored in this object, including
all of the BinTransitionData objects.
If verbose is true, the full sub-bin information is printed, too.
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class BinTransitionData(builtins.object) |
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.core.scoring.bin_transitions.BinTransitionData) -> NoneType
2. __init__(self : rosetta.core.scoring.bin_transitions.BinTransitionData, src : rosetta.core.scoring.bin_transitions.BinTransitionData) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_property_i(...) from builtins.PyCapsule
- add_property_i(self : rosetta.core.scoring.bin_transitions.BinTransitionData, property : str) -> NoneType
Add a property to the list of properties that the ith residue MUST have.
- add_property_iplus1(...) from builtins.PyCapsule
- add_property_iplus1(self : rosetta.core.scoring.bin_transitions.BinTransitionData, property : str) -> NoneType
Add a property to the list of properties that the i+1st residue MUST have.
- add_res_identity_i(...) from builtins.PyCapsule
- add_res_identity_i(self : rosetta.core.scoring.bin_transitions.BinTransitionData, resname : str) -> NoneType
Add a residue identity to the list of residue identities that the ith residue MUST have.
If the list is left empty, the residue identities can be anything. Residue names are
provided as three-letter codes.
- add_res_identity_iplus1(...) from builtins.PyCapsule
- add_res_identity_iplus1(self : rosetta.core.scoring.bin_transitions.BinTransitionData, resname : str) -> NoneType
Add a residue identity to the list of residue identities that the i+1st residue MUST have.
If the list is left empty, the residue identities can be anything. Residue names are
provided as three-letter codes.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.scoring.bin_transitions.BinTransitionData, : rosetta.core.scoring.bin_transitions.BinTransitionData) -> rosetta.core.scoring.bin_transitions.BinTransitionData
- bin_boundaries_i(...) from builtins.PyCapsule
- bin_boundaries_i(self : rosetta.core.scoring.bin_transitions.BinTransitionData, n : int, m : int) -> (float, float)
Get the bin start and end boundaries, in degrees, for the nth bin and the mth mainchain torsion for residue i.
If the end is less than the start, it means that the bin runs through 180 degrees and wraps around.
- bin_boundaries_iplus1(...) from builtins.PyCapsule
- bin_boundaries_iplus1(self : rosetta.core.scoring.bin_transitions.BinTransitionData, n : int, m : int) -> (float, float)
Get the bin start and end boundaries, in degrees, for the nth bin and the mth mainchain torsion for residue i+1.
If the end is less than the start, it means that the bin runs through 180 degrees and wraps around.
- bin_exists(...) from builtins.PyCapsule
- bin_exists(self : rosetta.core.scoring.bin_transitions.BinTransitionData, name : str) -> bool
Does a bin with the specified name exist?
- bin_exists_i(...) from builtins.PyCapsule
- bin_exists_i(self : rosetta.core.scoring.bin_transitions.BinTransitionData, name : str) -> bool
Does a bin with the specified name exist, defined for the ith residue?
- bin_exists_iplus1(...) from builtins.PyCapsule
- bin_exists_iplus1(self : rosetta.core.scoring.bin_transitions.BinTransitionData, name : str) -> bool
Does a bin with the specified name exist, defined for the i+1st residue?
- binname_index_from_string_i(...) from builtins.PyCapsule
- binname_index_from_string_i(self : rosetta.core.scoring.bin_transitions.BinTransitionData, bin_name : str) -> int
Given a bin name, get the bin index.
Returns 0 if the name is not found. Checks the list of bin names
for the ith residue.
- binname_index_from_string_iplus1(...) from builtins.PyCapsule
- binname_index_from_string_iplus1(self : rosetta.core.scoring.bin_transitions.BinTransitionData, bin_name : str) -> int
Given a bin name, get the bin index.
Returns 0 if the name is not found. Checks the list of bin names
for the i+1st residue.
- binsums_i(...) from builtins.PyCapsule
- binsums_i(self : rosetta.core.scoring.bin_transitions.BinTransitionData, bin_index_i : int) -> float
Get the sum of a row of the probability matrix.
This is the sum of all counts(bin_i, bin_iplus1), summed across all bin_iplus1. This is pre-calculated and stored,
so this is a fast lookup.
- binsums_iplus1(...) from builtins.PyCapsule
- binsums_iplus1(self : rosetta.core.scoring.bin_transitions.BinTransitionData, bin_index_iplus1 : int) -> float
Get the sum of a column of the probability matrix.
This is the sum of all counts(bin_i, bin_iplus1), summed across all bin_i. This is pre-calculated and stored,
so this is a fast lookup.
- check_property_overlap(...) from builtins.PyCapsule
- check_property_overlap(rosetta.core.scoring.bin_transitions.BinTransitionData) -> NoneType
Checks through the required and prohibited properties lists, and asserts that there is no overlap.
Throws an error if there is overlap.
- check_residentity_overlap(...) from builtins.PyCapsule
- check_residentity_overlap(rosetta.core.scoring.bin_transitions.BinTransitionData) -> NoneType
Checks through the required and prohibited residue identities lists, and asserts that there is no overlap.
Throws an error if there is overlap.
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.scoring.bin_transitions.BinTransitionData) -> rosetta.core.scoring.bin_transitions.BinTransitionData
Clone operation for BinTransitionData.
Returns an owning pointer to a copy of this object.
- copy_i_bins_to_iplus1(...) from builtins.PyCapsule
- copy_i_bins_to_iplus1(rosetta.core.scoring.bin_transitions.BinTransitionData) -> NoneType
Copy the bin names and torsion ranges for residue i to those for residue i+1.
- criteria_match_i(...) from builtins.PyCapsule
- criteria_match_i(self : rosetta.core.scoring.bin_transitions.BinTransitionData, rsd : rosetta.core.conformation.Residue) -> bool
Given a residue, check whether its properties match the required and prohibited properties lists for residue i,
and whether its name matches the required and prohibited names list for residue i.
- criteria_match_iplus1(...) from builtins.PyCapsule
- criteria_match_iplus1(self : rosetta.core.scoring.bin_transitions.BinTransitionData, rsd : rosetta.core.conformation.Residue) -> bool
Given a residue, check whether its properties match the required and prohibited properties lists for residue i+1,
and whether its name matches the required and prohibited names list for residue i+1.
- finalize(...) from builtins.PyCapsule
- finalize(rosetta.core.scoring.bin_transitions.BinTransitionData) -> NoneType
Do final post-load calculations (e.g. precomputing the sum of the transition probability matrix entries,
the sum of the columns, the sum of the rows, etc.)
- get_property_effect_name(...) from builtins.PyCapsule
- get_property_effect_name(self : rosetta.core.scoring.bin_transitions.BinTransitionData, property : rosetta.core.scoring.bin_transitions.BT_PROPERTIES) -> str
Given a property enum value, return the property name as it would appear in a
residue params file.
- get_property_from_name(...) from builtins.PyCapsule
- get_property_from_name(self : rosetta.core.scoring.bin_transitions.BinTransitionData, name : str) -> rosetta.core.scoring.bin_transitions.BT_PROPERTIES
Given a property name, return the property enum value.
Returns BT_UNKNOWN_PROPERTY if not identifiable.
- get_subbin_type_from_name(...) from builtins.PyCapsule
- get_subbin_type_from_name(self : rosetta.core.scoring.bin_transitions.BinTransitionData, name : str) -> rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE
Given a sub-bin type name, return the sub-bin type enum value.
Returns BTSB_UNKNOWN if not identifiable.
- get_subbin_type_name(...) from builtins.PyCapsule
- get_subbin_type_name(self : rosetta.core.scoring.bin_transitions.BinTransitionData, type : rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE) -> str
Given a sub-bin type enum, return its name as it would appear in
a residue params file.
- has_property(...) from builtins.PyCapsule
- has_property(self : rosetta.core.scoring.bin_transitions.BinTransitionData, property : rosetta.core.scoring.bin_transitions.BT_PROPERTIES, rsd : rosetta.core.conformation.Residue) -> bool
Given a property, check whether a residue has that property.
This function provides the link to the suitable property lookup function in ResidueType.
- in_bin_i(...) from builtins.PyCapsule
- in_bin_i(self : rosetta.core.scoring.bin_transitions.BinTransitionData, bin_index : int, rsd : rosetta.core.conformation.Residue) -> bool
Is a given residue within the bounds of a given bin?
Uses bin definitions for the ith residue.
- in_bin_iplus1(...) from builtins.PyCapsule
- in_bin_iplus1(self : rosetta.core.scoring.bin_transitions.BinTransitionData, bin_index : int, rsd : rosetta.core.conformation.Residue) -> bool
Is a given residue within the bounds of a given bin?
Uses bin definitions for the i+1st residue.
- matrix_finalized(...) from builtins.PyCapsule
- matrix_finalized(rosetta.core.scoring.bin_transitions.BinTransitionData) -> bool
Have final calculations been done after initializing the probability matrix?
- matrix_initialized(...) from builtins.PyCapsule
- matrix_initialized(rosetta.core.scoring.bin_transitions.BinTransitionData) -> bool
Have the n_bins_i_ and n_bins_iplus1_ variables been set, so that the
transition probability matrix could be initialized?
- n_bins_i(...) from builtins.PyCapsule
- n_bins_i(rosetta.core.scoring.bin_transitions.BinTransitionData) -> int
Get the number of bins for the ith residue.
- n_bins_iplus1(...) from builtins.PyCapsule
- n_bins_iplus1(rosetta.core.scoring.bin_transitions.BinTransitionData) -> int
Get the number of bins for the i+1st residue.
- n_mainchain_torsions_i(...) from builtins.PyCapsule
- n_mainchain_torsions_i(rosetta.core.scoring.bin_transitions.BinTransitionData) -> int
Get the number of mainchain torsions for the ith residue.
- n_mainchain_torsions_iplus1(...) from builtins.PyCapsule
- n_mainchain_torsions_iplus1(rosetta.core.scoring.bin_transitions.BinTransitionData) -> int
Get the number of mainchain torsions for the i+1st residue.
- probability_matrix(...) from builtins.PyCapsule
- probability_matrix(self : rosetta.core.scoring.bin_transitions.BinTransitionData, n : int, m : int) -> float
Get an entry in the transition probability matrix.
[n][m] = bin of ith residue, bin of i+1st residue.
- prohibit_property_i(...) from builtins.PyCapsule
- prohibit_property_i(self : rosetta.core.scoring.bin_transitions.BinTransitionData, property : str) -> NoneType
Add a property to the list of properties that the ith residue MUST NOT have.
- prohibit_property_iplus1(...) from builtins.PyCapsule
- prohibit_property_iplus1(self : rosetta.core.scoring.bin_transitions.BinTransitionData, property : str) -> NoneType
Add a property to the list of properties that the i+1st residue MUST NOT have.
- prohibit_res_identity_i(...) from builtins.PyCapsule
- prohibit_res_identity_i(self : rosetta.core.scoring.bin_transitions.BinTransitionData, resname : str) -> NoneType
Add a residue identity to the list of residue identities that the ith residue MUST NOT have.
If the list is left empty, the residue identities can be anything. Residue names are
provided as three-letter codes.
- prohibit_res_identity_iplus1(...) from builtins.PyCapsule
- prohibit_res_identity_iplus1(self : rosetta.core.scoring.bin_transitions.BinTransitionData, resname : str) -> NoneType
Add a residue identity to the list of residue identities that the i+1st residue MUST NOT have.
If the list is left empty, the residue identities can be anything. Residue names are
provided as three-letter codes.
- random_bin_i(...) from builtins.PyCapsule
- random_bin_i(rosetta.core.scoring.bin_transitions.BinTransitionData) -> int
Select a random bin from the bins allowed for residue i, biased by the relative counts for that bin.
- random_bin_iplus1(...) from builtins.PyCapsule
- random_bin_iplus1(rosetta.core.scoring.bin_transitions.BinTransitionData) -> int
Select a random bin from the bins allowed for residue i+1, biased by the relative counts for that bin.
- random_bin_iplus1_given_i(...) from builtins.PyCapsule
- random_bin_iplus1_given_i(self : rosetta.core.scoring.bin_transitions.BinTransitionData, bin_i : int) -> int
Select a random bin from the bins allowed for residue i+1, biased by the relative counts for that bin given that residue i is in a particular bin.
- set_binname_i(...) from builtins.PyCapsule
- set_binname_i(self : rosetta.core.scoring.bin_transitions.BinTransitionData, bin : int, name : str) -> NoneType
Set the name of bin n for residue i.
This requires that the number of bins has already been set.
- set_binname_iplus1(...) from builtins.PyCapsule
- set_binname_iplus1(self : rosetta.core.scoring.bin_transitions.BinTransitionData, bin : int, name : str) -> NoneType
Set the name of bin n for residue i+1.
This requires that the number of bins has already been set.
- set_binrange_i(...) from builtins.PyCapsule
- set_binrange_i(self : rosetta.core.scoring.bin_transitions.BinTransitionData, bin : int, torsion : int, start : float, end : float) -> NoneType
Set the torsion ranges for bin n, mainchain torsion m of residue i.
This requires that the number of bins and the number of mainchain torsions have already been set.
- set_binrange_iplus1(...) from builtins.PyCapsule
- set_binrange_iplus1(self : rosetta.core.scoring.bin_transitions.BinTransitionData, bin : int, torsion : int, start : float, end : float) -> NoneType
Set the torsion ranges for bin n, mainchain torsion m of residue i+1.
This requires that the number of bins and the number of mainchain torsions have already been set.
- set_matrix_entry(...) from builtins.PyCapsule
- set_matrix_entry(self : rosetta.core.scoring.bin_transitions.BinTransitionData, n : int, m : int, val : float) -> NoneType
Set a value in the transition probability matrix.
- set_n_bins(...) from builtins.PyCapsule
- set_n_bins(self : rosetta.core.scoring.bin_transitions.BinTransitionData, n_bins_i : int, n_bins_iplus1 : int) -> NoneType
Set the number of bins for the ith and i+1st residues.
This also initializes the probability matrix (to all zeros), the binnames vectors
(to vectors of empty strings), and the binranges vectors (to all zeros).
- set_n_mainchain_torsions_i(...) from builtins.PyCapsule
- set_n_mainchain_torsions_i(self : rosetta.core.scoring.bin_transitions.BinTransitionData, val : int) -> NoneType
Set the number of mainchain torsions for residue i.
- set_n_mainchain_torsions_iplus1(...) from builtins.PyCapsule
- set_n_mainchain_torsions_iplus1(self : rosetta.core.scoring.bin_transitions.BinTransitionData, val : int) -> NoneType
Set the number of mainchain torsions for residue i+1.
- set_subbin_type_i(...) from builtins.PyCapsule
- set_subbin_type_i(self : rosetta.core.scoring.bin_transitions.BinTransitionData, type : str) -> NoneType
Set the sub-bin type for residue i.
Each bin can be divided into sub-bins in one of several ways. For example,
phi/psi/omega bins (like the ABEGO bins) can be divided into 5x5x90 bins corresponding
to the bins used by the Rama scorefunction. This is useful for drawing random phi/psi
angles from within the bin.
- set_subbin_type_iplus1(...) from builtins.PyCapsule
- set_subbin_type_iplus1(self : rosetta.core.scoring.bin_transitions.BinTransitionData, type : str) -> NoneType
Set the sub-bin type for residue i+1.
Each bin can be divided into sub-bins in one of several ways. For example,
phi/psi/omega bins (like the ABEGO bins) can be divided into 5x5x90 bins corresponding
to the bins used by the Rama scorefunction. This is useful for drawing random phi/psi
angles from within the bin.
- subbin_cdf_i(...) from builtins.PyCapsule
- subbin_cdf_i(self : rosetta.core.scoring.bin_transitions.BinTransitionData, n : int) -> rosetta.utility.vector1_double
Get the sub-bin cumulative distribution function for bin n for the ith residue.
Const-access only.
- subbin_cdf_iplus1(...) from builtins.PyCapsule
- subbin_cdf_iplus1(self : rosetta.core.scoring.bin_transitions.BinTransitionData, n : int) -> rosetta.utility.vector1_double
Get the sub-bin cumulative distribution function for bin n for the i+1st residue.
Const-access only.
- subbin_end_i(...) from builtins.PyCapsule
- subbin_end_i(self : rosetta.core.scoring.bin_transitions.BinTransitionData, bin_i : int, subbin_j : int, mainchain_torsion_k : int) -> float
Get the end of the sub-bin torsion range for the ith bin, the jth sub-bin, and the kth mainchain torsion.
- subbin_end_iplus1(...) from builtins.PyCapsule
- subbin_end_iplus1(self : rosetta.core.scoring.bin_transitions.BinTransitionData, bin_i : int, subbin_j : int, mainchain_torsion_k : int) -> float
Get the end of the sub-bin torsion range for the ith bin, the jth sub-bin, and the kth mainchain torsion.
- subbin_start_i(...) from builtins.PyCapsule
- subbin_start_i(self : rosetta.core.scoring.bin_transitions.BinTransitionData, bin_i : int, subbin_j : int, mainchain_torsion_k : int) -> float
Get the start of the sub-bin torsion range for the ith bin, the jth sub-bin, and the kth mainchain torsion.
- subbin_start_iplus1(...) from builtins.PyCapsule
- subbin_start_iplus1(self : rosetta.core.scoring.bin_transitions.BinTransitionData, bin_i : int, subbin_j : int, mainchain_torsion_k : int) -> float
Get the start of the sub-bin torsion range for the ith bin, the jth sub-bin, and the kth mainchain torsion.
- subbin_type_i(...) from builtins.PyCapsule
- subbin_type_i(rosetta.core.scoring.bin_transitions.BinTransitionData) -> rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE
Get the sub-bin type enum for residue i.
- subbin_type_iplus1(...) from builtins.PyCapsule
- subbin_type_iplus1(rosetta.core.scoring.bin_transitions.BinTransitionData) -> rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE
Get the sub-bin type enum for residue i+1.
- summarize_data(...) from builtins.PyCapsule
- summarize_data(self : rosetta.core.scoring.bin_transitions.BinTransitionData, verbose : bool) -> str
Writes a report summarizing the data stored in this BinTransitionData object.
If verbose is true, the full set of sub-bins is written out, too.
- which_bin_i(...) from builtins.PyCapsule
- which_bin_i(self : rosetta.core.scoring.bin_transitions.BinTransitionData, mainchain_torsions : rosetta.utility.vector1_double) -> int
Given a vector of mainchain torsions for a particular residue (at position i), figure out which bin the torsions lie in.
- which_bin_iplus1(...) from builtins.PyCapsule
- which_bin_iplus1(self : rosetta.core.scoring.bin_transitions.BinTransitionData, mainchain_torsions : rosetta.utility.vector1_double) -> int
Given a vector of mainchain torsions for a particular residue (at position i+1), figure out which bin the torsions lie in.
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