pose_from_sfr

Bindings for core::io::pose_from_sfr namespace

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

Bases: 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 MergeAndSplitBehaviorManager. 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.

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(std::string, std::string) –> 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 std::string &, const std::string &, const std::string &, const std::string &) –> 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 std::string &, const std::string &, const std::string &) –> 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 std::string &, const std::string &) –> 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 std::string &) –> 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 std::string &, const std::string &) –> 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