pose_from_sfr

Bindings for core::io::pose_from_sfr namespace

class pyrosetta.rosetta.core.io.pose_from_sfr.PoseFromSFRBuilder

Bases: pybind11_builtins.pybind11_object

The %PoseFromSFRBuilder is responsible for taking a partially-processed representation of a structure file, a structure-file repersentation or StructFileRep, and it constructs a Pose from it. Its primary output is a Pose, but it also keeps track of the “missing atoms:” the set of atoms in the Pose whose coordinates were not given in the original file.

The construction involves renaming some atoms, for example, the O2* atom in RNA would be renamed O2’, and resolving the chain- and branch-connectivity. It uses the ResidueTypeFinder to select the best-fit ResidueType for each residue.

This code handles n-terminal acetylation, and some other similar chemical modifications, by merging the atoms in the “ACE” residue with the next residue. Instructions of what residue types to merge and how to rename the atoms to avoid naming collisions are read in from the database by the MergeBehaviorManager. After the atoms are merged and renamed, the appropriate AcetylatedNtermProteinFull is applied to that next residue.

The process of building a pose is handled in four passes.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.core.io.pose_from_sfr.PoseFromSFRBuilder, rts: pyrosetta.rosetta.core.chemical.ResidueTypeSet, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> None
2. __init__(self: pyrosetta.rosetta.core.io.pose_from_sfr.PoseFromSFRBuilder, arg0: pyrosetta.rosetta.core.io.pose_from_sfr.PoseFromSFRBuilder) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

assign(self: pyrosetta.rosetta.core.io.pose_from_sfr.PoseFromSFRBuilder, : pyrosetta.rosetta.core.io.pose_from_sfr.PoseFromSFRBuilder) → pyrosetta.rosetta.core.io.pose_from_sfr.PoseFromSFRBuilder

C++: core::io::pose_from_sfr::PoseFromSFRBuilder::operator=(const class core::io::pose_from_sfr::PoseFromSFRBuilder &) –> class core::io::pose_from_sfr::PoseFromSFRBuilder &

build_pose(self: pyrosetta.rosetta.core.io.pose_from_sfr.PoseFromSFRBuilder, sfr: pyrosetta.rosetta.core.io.StructFileRep, pose: pyrosetta.rosetta.core.pose.Pose) → None

Build a Pose from an SFR using the ResidueTypeSet and the StructFileReaderOptions

object that were passed in to the %Builder in it’s constructor.

C++: core::io::pose_from_sfr::PoseFromSFRBuilder::build_pose(const class core::io::StructFileRep &, class core::pose::Pose &) –> void

missing_atoms(self: pyrosetta.rosetta.core.io.pose_from_sfr.PoseFromSFRBuilder) → pyrosetta.rosetta.core.id.AtomID_Map_bool_t

not present in the SFR

C++: core::io::pose_from_sfr::PoseFromSFRBuilder::missing_atoms() const –> const class core::id::AtomID_Map<bool> &

pyrosetta.rosetta.core.io.pose_from_sfr.bonding_distance_threshold(element1: str, element2: str) → float

Get theshold distance below which two atoms are considered bonded. (1.2*covalent)

C++: core::io::pose_from_sfr::bonding_distance_threshold(class std::basic_string<char>, class std::basic_string<char>) –> double

pyrosetta.rosetta.core.io.pose_from_sfr.check_and_correct_sister_atom_based_on_chirality(rsd: pyrosetta.rosetta.core.conformation.Residue, sister1_name: str, sister2_name: str, parent_name: str, outer_ref_name: str) → None

C++: core::io::pose_from_sfr::check_and_correct_sister_atom_based_on_chirality(class std::shared_ptr<class core::conformation::Residue> &, const class std::basic_string<char> &, const class std::basic_string<char> &, const class std::basic_string<char> &, const class std::basic_string<char> &) –> void

pyrosetta.rosetta.core.io.pose_from_sfr.check_and_correct_sister_atom_based_on_outgroup(rsd: pyrosetta.rosetta.core.conformation.Residue, sister1_name: str, sister2_name: str, outgroup_name: str) → None

C++: core::io::pose_from_sfr::check_and_correct_sister_atom_based_on_outgroup(class std::shared_ptr<class core::conformation::Residue> &, const class std::basic_string<char> &, const class std::basic_string<char> &, const class std::basic_string<char> &) –> void

pyrosetta.rosetta.core.io.pose_from_sfr.check_and_correct_sister_atoms(rsd: pyrosetta.rosetta.core.conformation.Residue) → None

due to differences in different crystallography/NMR/modeling packages, labeling of sister atoms

(like OP1 <–> OP2, or H41 <–> H42) in PDBs is totally wacky. This is an attempt to regularize… and it can actually make a difference since sometimes partial charges on sister hydrogens can be different. Right now only set up for nucleic acids, but could probably generalize.

C++: core::io::pose_from_sfr::check_and_correct_sister_atoms(class std::shared_ptr<class core::conformation::Residue> &) –> void

pyrosetta.rosetta.core.io.pose_from_sfr.convert_atom_name(res_name: str, atom_name: str) → str

C++: core::io::pose_from_sfr::convert_atom_name(const class std::basic_string<char> &, const class std::basic_string<char> &) –> std::string

pyrosetta.rosetta.core.io.pose_from_sfr.convert_res_name(name: str) → str

C++: core::io::pose_from_sfr::convert_res_name(const class std::basic_string<char> &) –> std::string

pyrosetta.rosetta.core.io.pose_from_sfr.create_working_data(options: pyrosetta.rosetta.core.io.StructFileRepOptions, sfr: pyrosetta.rosetta.core.io.StructFileRep, rinfos: pyrosetta.rosetta.utility.vector1_core_io_ResidueInformation) → None

C++: core::io::pose_from_sfr::create_working_data(const class core::io::StructFileRepOptions &, const class core::io::StructFileRep &, class utility::vector1<class core::io::ResidueInformation, class std::allocator<class core::io::ResidueInformation> > &) –> void

pyrosetta.rosetta.core.io.pose_from_sfr.flip_atom_xyz(rsd: pyrosetta.rosetta.core.conformation.Residue, sister1_name: str, sister2_name: str) → None

C++: core::io::pose_from_sfr::flip_atom_xyz(class std::shared_ptr<class core::conformation::Residue> &, const class std::basic_string<char> &, const class std::basic_string<char> &) –> void

pyrosetta.rosetta.core.io.pose_from_sfr.get_chirality_sign(xyz_sister1: pyrosetta.rosetta.numeric.xyzVector_double_t, xyz_sister2: pyrosetta.rosetta.numeric.xyzVector_double_t, xyz_parent: pyrosetta.rosetta.numeric.xyzVector_double_t, xyz_outer_ref: pyrosetta.rosetta.numeric.xyzVector_double_t) → int

C++: core::io::pose_from_sfr::get_chirality_sign(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &) –> int

pyrosetta.rosetta.core.io.pose_from_sfr.get_closest_sister(xyz_sister1: pyrosetta.rosetta.numeric.xyzVector_double_t, xyz_sister2: pyrosetta.rosetta.numeric.xyzVector_double_t, xyz_outgroup: pyrosetta.rosetta.numeric.xyzVector_double_t) → int

C++: core::io::pose_from_sfr::get_closest_sister(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &) –> int

pyrosetta.rosetta.core.io.pose_from_sfr.randomize_missing_coords(ai: pyrosetta.rosetta.core.io.AtomInformation) → None

randomize missing density

C++: core::io::pose_from_sfr::randomize_missing_coords(struct core::io::AtomInformation &) –> void

pyrosetta.rosetta.core.io.pose_from_sfr.sgn(x: float) → int

C++: core::io::pose_from_sfr::sgn(const double &) –> int

pyrosetta.rosetta.core.io.pose_from_sfr.update_atom_information_based_on_occupancy(options: pyrosetta.rosetta.core.io.StructFileRepOptions, ai: pyrosetta.rosetta.core.io.AtomInformation) → bool

C++: core::io::pose_from_sfr::update_atom_information_based_on_occupancy(const class core::io::StructFileRepOptions &, struct core::io::AtomInformation &) –> bool