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- add_covalent_linkage(...) method of builtins.PyCapsule instance
- add_covalent_linkage(pose : rosetta.core.pose.Pose, resA_pos : int, resB_pos : int, resA_At : int, resB_At : int, remove_hydrogens : bool) -> NoneType
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
: Adds an arbitrary covalent linkage between two atoms (resA_At and resB_At) in two residues (at positions resA_pos and resB_pos).
: This is useful for adding covalent linkages between metal-binding side-chains and metal atoms. This code was shamelessly
stolen from Florian's EnzConstraintParameters.cc in protocols/toolbox/match_enzdes_utils, and was modified to permit deletion of
unnecessary protons. NOTE: THIS CODE MODIFIES THE RESIDUE TYPE LIST, AND IS CURRENTLY NOT THREADSAFE.
: Vikram K. Mulligan (vmullig.edu), Florian Richter (flosopher.com)
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
- add_covalent_linkages_to_metal(...) method of builtins.PyCapsule instance
- add_covalent_linkages_to_metal(*args, **kwargs)
Overloaded function.
1. add_covalent_linkages_to_metal(pose : rosetta.core.pose.Pose, metal_position : int, liganding_atomids : rosetta.utility.vector1_core_id_AtomID) -> NoneType
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
Function to add covalent linkages between a metal atom and all the liganding atoms provided in a vector of AtomIDs.
The inputs are:
pose (The pose to be modified)
metal_position (The residue number of the metal in the pose)
liganding_atomids (A list of AtomIDs on other residues that will be covalently linked to the metal)
remove_hydrogens (Should hydrogens on the liganding atoms be removed automatically? Default true.)
This function uses core::pose::add_covalent_linkage, which can strip off extraneous hydrogens.
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
2. add_covalent_linkages_to_metal(pose : rosetta.core.pose.Pose, metal_position : int, liganding_atomids : rosetta.utility.vector1_core_id_AtomID, remove_hydrogens : bool) -> NoneType
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
Function to add covalent linkages between a metal atom and all the liganding atoms provided in a vector of AtomIDs.
The inputs are:
pose (The pose to be modified)
metal_position (The residue number of the metal in the pose)
liganding_atomids (A list of AtomIDs on other residues that will be covalently linked to the metal)
remove_hydrogens (Should hydrogens on the liganding atoms be removed automatically? Default true.)
This function uses core::pose::add_covalent_linkage, which can strip off extraneous hydrogens.
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
- auto_setup_all_metal_bonds(...) method of builtins.PyCapsule instance
- auto_setup_all_metal_bonds(*args, **kwargs)
Overloaded function.
1. auto_setup_all_metal_bonds(pose : rosetta.core.pose.Pose) -> NoneType
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
Function to auto-detect and add covalent connections to all metal ions in a pose.
This function iteratively calls auto_setup_metal_bonds.
Inputs:
pose (The pose that we'll operate on, changed by operation)
dist_cutoff_multiplier (A float for the distance cutoff multiplier; the cutoff is the sum of the Lennard-Jones radii times the multiplier)
remove_hydrogesn (Should hydrogens on the liganding atoms be auto-removed? Default true.)
Vikram K. Mulligan (vmulligan.edu)
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
2. auto_setup_all_metal_bonds(pose : rosetta.core.pose.Pose, dist_cutoff_multiplier : float) -> NoneType
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
Function to auto-detect and add covalent connections to all metal ions in a pose.
This function iteratively calls auto_setup_metal_bonds.
Inputs:
pose (The pose that we'll operate on, changed by operation)
dist_cutoff_multiplier (A float for the distance cutoff multiplier; the cutoff is the sum of the Lennard-Jones radii times the multiplier)
remove_hydrogesn (Should hydrogens on the liganding atoms be auto-removed? Default true.)
Vikram K. Mulligan (vmulligan.edu)
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
3. auto_setup_all_metal_bonds(pose : rosetta.core.pose.Pose, dist_cutoff_multiplier : float, remove_hydrogens : bool) -> NoneType
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
Function to auto-detect and add covalent connections to all metal ions in a pose.
This function iteratively calls auto_setup_metal_bonds.
Inputs:
pose (The pose that we'll operate on, changed by operation)
dist_cutoff_multiplier (A float for the distance cutoff multiplier; the cutoff is the sum of the Lennard-Jones radii times the multiplier)
remove_hydrogesn (Should hydrogens on the liganding atoms be auto-removed? Default true.)
Vikram K. Mulligan (vmulligan.edu)
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
- auto_setup_all_metal_constraints(...) method of builtins.PyCapsule instance
- auto_setup_all_metal_constraints(*args, **kwargs)
Overloaded function.
1. auto_setup_all_metal_constraints(pose : rosetta.core.pose.Pose, distance_constraint_multiplier : float, angle_constraint_multiplier : float) -> NoneType
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
Function to set up distance and angle constraints between metals and the residues that bind them.
This function constrains the distances to be whatever they are in the input pose. This version
does not set the weights for the constraints terms in the scorefunction.
Inputs:
pose (The pose that we'll operate on, changed by operation)
distance_constraint_multiplier (A float for the strength of the metal - binding atom distance constraint. A value of 2.0 doubles
it, for example.)
angle_constraint_multiplier (A float for the strength of the metal - binding atom - binding atom parent angle constraint.)
Vikram K. Mulligan (vmulligan.edu)
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
2. auto_setup_all_metal_constraints(pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, distance_constraint_multiplier : float, angle_constraint_multiplie : float) -> NoneType
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
Function to set up distance and angle constraints between metals and the residues that bind them.
This function constrains the distances to be whatever they are in the input pose. This version
sets the weights for the constraints terms in the scorefunction to 1.0 if they're off, or scales the
constraints themselves appropriately if they're already on.
Inputs:
pose (The pose that we'll operate on, changed by operation)
sfxn (An owning pointer to the scorefunction, changed by operation)
distance_constraint_multiplier (A float for the strength of the metal - binding atom distance constraint. A value of 2.0 doubles
it, for example.)
angle_constraint_multiplier (A float for the strength of the metal - binding atom - binding atom parent angle constraint.)
Vikram K. Mulligan (vmulligan.edu)
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
- find_metalbinding_atoms(...) method of builtins.PyCapsule instance
- find_metalbinding_atoms(*args, **kwargs)
Overloaded function.
1. find_metalbinding_atoms(pose : rosetta.core.pose.Pose, metal_position : int) -> rosetta.utility.vector1_core_id_AtomID
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
Function that generates a list of metal-binding atoms that coordinate a metal in a protein.
This function generates the list by looping through all residues and checking all metal-binding atoms of all
metal-binding residues, so it's not super speedy.
Inputs:
pose (The pose that we'll operate on, unchanged by operation)
metal_postion (The residue number of the metal)
dist_cutoff_multiplier (A float for the distance cutoff multiplier; the cutoff is the sum of the Lennard-Jones radii times the multiplier)
Vikram K. Mulligan (vmulligan.edu)
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
2. find_metalbinding_atoms(pose : rosetta.core.pose.Pose, metal_position : int, dist_cutoff_multiplier : float) -> rosetta.utility.vector1_core_id_AtomID
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
Function that generates a list of metal-binding atoms that coordinate a metal in a protein.
This function generates the list by looping through all residues and checking all metal-binding atoms of all
metal-binding residues, so it's not super speedy.
Inputs:
pose (The pose that we'll operate on, unchanged by operation)
metal_postion (The residue number of the metal)
dist_cutoff_multiplier (A float for the distance cutoff multiplier; the cutoff is the sum of the Lennard-Jones radii times the multiplier)
Vikram K. Mulligan (vmulligan.edu)
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
- getMLweight(...) method of builtins.PyCapsule instance
- getMLweight(*args, **kwargs)
Overloaded function.
1. getMLweight(scorefxn : rosetta.core.scoring.ScoreFunction, : rosetta.core.pose.Pose) -> float
get the optimal weight on the xtal ML energy
2. getMLweight(scorefxn : rosetta.core.scoring.ScoreFunction, : rosetta.core.pose.Pose, : rosetta.core.kinematics.MoveMap) -> float
get the optimal weight on the xtal ML energy considering only movable DOFs
- getMLweight_cart(...) method of builtins.PyCapsule instance
- getMLweight_cart(*args, **kwargs)
Overloaded function.
1. getMLweight_cart(scorefxn : rosetta.core.scoring.ScoreFunction, : rosetta.core.pose.Pose) -> float
get the optimal weight on the xtal ML energy
2. getMLweight_cart(scorefxn : rosetta.core.scoring.ScoreFunction, : rosetta.core.pose.Pose, : rosetta.core.kinematics.MoveMap) -> float
get the optimal weight on the xtal ML energy considering only movable DOFs
- rebuild_disulfide(...) method of builtins.PyCapsule instance
- rebuild_disulfide(*args, **kwargs)
Overloaded function.
1. rebuild_disulfide(pose : rosetta.core.pose.Pose, lower_res : int, upper_res : int) -> NoneType
Rebuild a pair of cysteines (and possibly surrounding residues) so
that they form a near-ideal disulfide bond. Supports symmetric poses.
2. rebuild_disulfide(pose : rosetta.core.pose.Pose, lower_res : int, upper_res : int, packer_task : rosetta.core.pack.task.PackerTask) -> NoneType
Rebuild a pair of cysteines (and possibly surrounding residues) so
that they form a near-ideal disulfide bond. Supports symmetric poses.
3. rebuild_disulfide(pose : rosetta.core.pose.Pose, lower_res : int, upper_res : int, packer_task : rosetta.core.pack.task.PackerTask, packer_score : rosetta.core.scoring.ScoreFunction) -> NoneType
Rebuild a pair of cysteines (and possibly surrounding residues) so
that they form a near-ideal disulfide bond. Supports symmetric poses.
4. rebuild_disulfide(pose : rosetta.core.pose.Pose, lower_res : int, upper_res : int, packer_task : rosetta.core.pack.task.PackerTask, packer_score : rosetta.core.scoring.ScoreFunction, mm : rosetta.core.kinematics.MoveMap) -> NoneType
Rebuild a pair of cysteines (and possibly surrounding residues) so
that they form a near-ideal disulfide bond. Supports symmetric poses.
5. rebuild_disulfide(pose : rosetta.core.pose.Pose, lower_res : int, upper_res : int, packer_task : rosetta.core.pack.task.PackerTask, packer_score : rosetta.core.scoring.ScoreFunction, mm : rosetta.core.kinematics.MoveMap, minimizer_score : rosetta.core.scoring.ScoreFunction) -> NoneType
Rebuild a pair of cysteines (and possibly surrounding residues) so
that they form a near-ideal disulfide bond. Supports symmetric poses.
6. rebuild_disulfide(pose : rosetta.core.pose.Pose, disulfides : rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) -> NoneType
Rebuild a number of pairs of cysteines (and possibly surrounding
residues) so that they form near-ideal disulfide bonds
7. rebuild_disulfide(pose : rosetta.core.pose.Pose, disulfides : rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t, packer_task : rosetta.core.pack.task.PackerTask) -> NoneType
Rebuild a number of pairs of cysteines (and possibly surrounding
residues) so that they form near-ideal disulfide bonds
8. rebuild_disulfide(pose : rosetta.core.pose.Pose, disulfides : rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t, packer_task : rosetta.core.pack.task.PackerTask, packer_score : rosetta.core.scoring.ScoreFunction) -> NoneType
Rebuild a number of pairs of cysteines (and possibly surrounding
residues) so that they form near-ideal disulfide bonds
9. rebuild_disulfide(pose : rosetta.core.pose.Pose, disulfides : rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t, packer_task : rosetta.core.pack.task.PackerTask, packer_score : rosetta.core.scoring.ScoreFunction, mm : rosetta.core.kinematics.MoveMap) -> NoneType
Rebuild a number of pairs of cysteines (and possibly surrounding
residues) so that they form near-ideal disulfide bonds
10. rebuild_disulfide(pose : rosetta.core.pose.Pose, disulfides : rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t, packer_task : rosetta.core.pack.task.PackerTask, packer_score : rosetta.core.scoring.ScoreFunction, mm : rosetta.core.kinematics.MoveMap, minimizer_score : rosetta.core.scoring.ScoreFunction) -> NoneType
Rebuild a number of pairs of cysteines (and possibly surrounding
residues) so that they form near-ideal disulfide bonds
- remove_cutpoint_variants(...) method of builtins.PyCapsule instance
- remove_cutpoint_variants(pose : rosetta.core.pose.Pose) -> NoneType
Removes cutpoint variants from `pose` by scanning the fold tree
- switch_to_residue_type_set(...) method of builtins.PyCapsule instance
- switch_to_residue_type_set(*args, **kwargs)
Overloaded function.
1. switch_to_residue_type_set(pose : rosetta.core.pose.Pose, type_set_name : str) -> NoneType
the function allows a pose to use a different residue_type_set to
represent all its residues, such as from fullatom residues to centroid
residues, or vice versa. During the switch, corresponding atoms will be
copied. Redundant atoms will be removed (in case from fullatom to centroid)
and missing atoms will be built by ideal geometry (in the case from centroid
to fullatom).
2. switch_to_residue_type_set(pose : rosetta.core.pose.Pose, type_set_name : str, allow_sloppy_match : bool) -> NoneType
the function allows a pose to use a different residue_type_set to
represent all its residues, such as from fullatom residues to centroid
residues, or vice versa. During the switch, corresponding atoms will be
copied. Redundant atoms will be removed (in case from fullatom to centroid)
and missing atoms will be built by ideal geometry (in the case from centroid
to fullatom).
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