mmtf

Bindings for core::io::mmtf namespace

class pyrosetta.rosetta.core.io.mmtf.ExtraDataEnum

Bases: pybind11_builtins.pybind11_object

Enum definitions for pose extra data we will be storing/retrieving.

ALL Enums must also have their string equivalents defined in mmtf/ExtraDataEnumManager.cc

Members:

pose_cache_string_data

pose_cache_real_data

pdb_comments

simple_metric_string_data

simple_metric_real_data

simple_metric_composite_string_data

simple_metric_composite_real_data

simple_metric_per_residue_string_data

simple_metric_per_residue_real_data

simple_metric_per_residue_string_output

simple_metric_per_residue_real_output

ExtraDataEnum_total

ExtraDataEnum_total = <ExtraDataEnum.simple_metric_per_residue_real_output: 11>
property name
pdb_comments = <ExtraDataEnum.pdb_comments: 3>
pose_cache_real_data = <ExtraDataEnum.pose_cache_real_data: 2>
pose_cache_string_data = <ExtraDataEnum.pose_cache_string_data: 1>
simple_metric_composite_real_data = <ExtraDataEnum.simple_metric_composite_real_data: 7>
simple_metric_composite_string_data = <ExtraDataEnum.simple_metric_composite_string_data: 6>
simple_metric_per_residue_real_data = <ExtraDataEnum.simple_metric_per_residue_real_data: 9>
simple_metric_per_residue_real_output = <ExtraDataEnum.simple_metric_per_residue_real_output: 11>
simple_metric_per_residue_string_data = <ExtraDataEnum.simple_metric_per_residue_string_data: 8>
simple_metric_per_residue_string_output = <ExtraDataEnum.simple_metric_per_residue_string_output: 10>
simple_metric_real_data = <ExtraDataEnum.simple_metric_real_data: 5>
simple_metric_string_data = <ExtraDataEnum.simple_metric_string_data: 4>
class pyrosetta.rosetta.core.io.mmtf.ExtraDataEnumManager

Bases: pybind11_builtins.pybind11_object

Enum string/enum functions for pose extra data we will be storing/retrieving. ALL enums must be defined in mmtf/ExtraDataEnum.hh

assign(self: pyrosetta.rosetta.core.io.mmtf.ExtraDataEnumManager, : pyrosetta.rosetta.core.io.mmtf.ExtraDataEnumManager) pyrosetta.rosetta.core.io.mmtf.ExtraDataEnumManager

C++: core::io::mmtf::ExtraDataEnumManager::operator=(const class core::io::mmtf::ExtraDataEnumManager &) –> class core::io::mmtf::ExtraDataEnumManager &

enum_to_string(self: pyrosetta.rosetta.core.io.mmtf.ExtraDataEnumManager, data_name: pyrosetta.rosetta.core.io.mmtf.ExtraDataEnum) str

C++: core::io::mmtf::ExtraDataEnumManager::enum_to_string(const enum core::io::mmtf::ExtraDataEnum) const –> std::string

is_data_type(self: pyrosetta.rosetta.core.io.mmtf.ExtraDataEnumManager, data_name: str) bool

C++: core::io::mmtf::ExtraDataEnumManager::is_data_type(const std::string &) const –> bool

string_to_enum(self: pyrosetta.rosetta.core.io.mmtf.ExtraDataEnumManager, data_name: str) pyrosetta.rosetta.core.io.mmtf.ExtraDataEnum

C++: core::io::mmtf::ExtraDataEnumManager::string_to_enum(const std::string &) const –> enum core::io::mmtf::ExtraDataEnum

pyrosetta.rosetta.core.io.mmtf.add_ters_via_bonds(all_AIs: pyrosetta.rosetta.std.vector_core_io_AtomInformation, ai_to_model: pyrosetta.rosetta.std.vector_unsigned_long) None

This adds TERs based on what is bound to the C of each AA.

C++: core::io::mmtf::add_ters_via_bonds(class std::vector<struct core::io::AtomInformation, class std::allocator<struct core::io::AtomInformation> > &, const class std::vector<unsigned long, class std::allocator<unsigned long> > &) –> void

class pyrosetta.rosetta.core.io.mmtf.ai_cmp

Bases: pybind11_builtins.pybind11_object

simple comparator for AtomInformation when grouping by residue/grp

pyrosetta.rosetta.core.io.mmtf.create_sfr_from_mmtf_filename(mmtf_filename: str, options: pyrosetta.rosetta.core.io.StructFileReaderOptions) pyrosetta.rosetta.core.io.StructFileRep

create sfr from create_sfrs_from_mmtf_filename

C++: core::io::mmtf::create_sfr_from_mmtf_filename(const std::string &, const class core::io::StructFileReaderOptions &) –> class std::shared_ptr<class core::io::StructFileRep>

pyrosetta.rosetta.core.io.mmtf.dump_mmtf(*args, **kwargs)

Overloaded function.

  1. dump_mmtf(pose: pyrosetta.rosetta.core.pose.Pose, file_name: str) -> bool

  2. dump_mmtf(pose: pyrosetta.rosetta.core.pose.Pose, file_name: str, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> bool

Dump a MMTF from a pose to a file.

Return success or failure.

C++: core::io::mmtf::dump_mmtf(const class core::pose::Pose &, const std::string &, class std::shared_ptr<const class core::io::StructFileRepOptions>) –> bool

  1. dump_mmtf(pose: pyrosetta.rosetta.core.pose.Pose, out: pyrosetta.rosetta.std.ostream) -> pyrosetta.rosetta.core.io.StructFileRep

  2. dump_mmtf(pose: pyrosetta.rosetta.core.pose.Pose, out: pyrosetta.rosetta.std.ostream, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> pyrosetta.rosetta.core.io.StructFileRep

Dump mmtf to an outstream, optionally passing options and returning a StructFileRep for further processing

C++: core::io::mmtf::dump_mmtf(const class core::pose::Pose &, std::ostream &, class std::shared_ptr<const class core::io::StructFileRepOptions>) –> class std::shared_ptr<class core::io::StructFileRep>

  1. dump_mmtf(pose: pyrosetta.rosetta.core.pose.Pose, jd2_job_data: str, out: pyrosetta.rosetta.std.ostream) -> pyrosetta.rosetta.core.io.StructFileRep

Dump a MMTF from a pose, optionally extracting extra info.

NOTE: DEPRECATED. LEGACY JD2 function to use JOB data, which we no longer use in JD3

C++: core::io::mmtf::dump_mmtf(const class core::pose::Pose &, const std::string &, std::ostream &) –> class std::shared_ptr<class core::io::StructFileRep>

  1. dump_mmtf(file_name: str, sfr: pyrosetta.rosetta.core.io.StructFileRep, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> bool

dump_mmtf function.

Create the sfr from pose using the PoseToStructFileRepConverter class. Return success or failure.

The file name to write the mmtf to

The StructFileRepOP to build the mmtf from

The StructFileRepOptions used to build the sfr

C++: core::io::mmtf::dump_mmtf(const std::string &, class std::shared_ptr<class core::io::StructFileRep>, const class core::io::StructFileRepOptions &) –> bool

  1. dump_mmtf(out: pyrosetta.rosetta.std.ostream, sfr: pyrosetta.rosetta.core.io.StructFileRep, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> None

dump single mmtf function.

We sadly have to use this to call the function

that dumps a vector of SFRs due to the mmtf file format. It only makes sense because of the compression scheme used.

C++: core::io::mmtf::dump_mmtf(std::ostream &, class std::shared_ptr<class core::io::StructFileRep>, const class core::io::StructFileRepOptions &) –> void

pyrosetta.rosetta.core.io.mmtf.make_chain(chain_atoms: pyrosetta.rosetta.utility.vector0_core_io_AtomInformation) pyrosetta.rosetta.utility.vector0_utility_vector0_core_io_AtomInformation_std_allocator_core_io_AtomInformation_t

group chain_atoms into groups based on chain_id and resseq

C++: core::io::mmtf::make_chain(const class utility::vector0<struct core::io::AtomInformation, class std::allocator<struct core::io::AtomInformation> > &) –> class utility::vector0<utility::vector0<core::io::AtomInformation> >

class pyrosetta.rosetta.core.io.mmtf.sd_index

Bases: pybind11_builtins.pybind11_object

storage for indicies to something in a mmtf struct this makes it easier to iterate the struct in relation to AtomInformation vectors

property chain_index
property group_atom_index
property group_index
property model_index
to_string(self: pyrosetta.rosetta.core.io.mmtf.sd_index) str

C++: core::io::mmtf::sd_index::to_string() const –> std::string

pyrosetta.rosetta.core.io.mmtf.set_mmtf_default_options(options: pyrosetta.rosetta.core.io.StructFileRepOptions) None

Set StructFileRepOptions defauls for mmtf

options to modify for mmtf

C++: core::io::mmtf::set_mmtf_default_options(class core::io::StructFileRepOptions &) –> void