| | |
- builtins.object
-
- AtomInformation
- CisPeptideInformation
- CrystInfo
- HeaderInformation
- LinkInformation
- ModifiedResidueInformation
- RemarkInfo
- ResidueInformation
- SSBondInformation
- StructFileRep
- rosetta.basic.resource_manager.ResourceOptions(builtins.object)
-
- StructFileRepOptions
-
- StructFileReaderOptions
- rosetta.std.vector_core_io_RemarkInfo(builtins.object)
-
- Remarks
- rosetta.utility.SingletonBase_core_io_NomenclatureManager_t(builtins.object)
-
- NomenclatureManager
class CrystInfo(builtins.object) |
| | |
Methods defined here:
- A(...) from builtins.PyCapsule
- A(*args, **kwargs)
Overloaded function.
1. A(rosetta.core.io.CrystInfo) -> float
2. A(self : rosetta.core.io.CrystInfo, Ain : float) -> NoneType
- B(...) from builtins.PyCapsule
- B(*args, **kwargs)
Overloaded function.
1. B(rosetta.core.io.CrystInfo) -> float
2. B(self : rosetta.core.io.CrystInfo, Bin : float) -> NoneType
- C(...) from builtins.PyCapsule
- C(*args, **kwargs)
Overloaded function.
1. C(rosetta.core.io.CrystInfo) -> float
2. C(self : rosetta.core.io.CrystInfo, Cin : float) -> NoneType
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.core.io.CrystInfo) -> NoneType
2. __init__(self : rosetta.core.io.CrystInfo, : rosetta.core.io.CrystInfo) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.core.io.CrystInfo) -> str
- alpha(...) from builtins.PyCapsule
- alpha(*args, **kwargs)
Overloaded function.
1. alpha(rosetta.core.io.CrystInfo) -> float
2. alpha(self : rosetta.core.io.CrystInfo, alphain : float) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.io.CrystInfo, : rosetta.core.io.CrystInfo) -> rosetta.core.io.CrystInfo
- beta(...) from builtins.PyCapsule
- beta(*args, **kwargs)
Overloaded function.
1. beta(rosetta.core.io.CrystInfo) -> float
2. beta(self : rosetta.core.io.CrystInfo, betain : float) -> NoneType
- gamma(...) from builtins.PyCapsule
- gamma(*args, **kwargs)
Overloaded function.
1. gamma(rosetta.core.io.CrystInfo) -> float
2. gamma(self : rosetta.core.io.CrystInfo, gammain : float) -> NoneType
- spacegroup(...) from builtins.PyCapsule
- spacegroup(*args, **kwargs)
Overloaded function.
1. spacegroup(rosetta.core.io.CrystInfo) -> str
2. spacegroup(self : rosetta.core.io.CrystInfo, spacegroupin : str) -> NoneType
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class HeaderInformation(builtins.object) |
| |
Information stored in the header records
http://www.wwpdb.org/documentation/format32/sect2.html
HEADER PEPTIDASE 13-JAN-98 1A2Z
|
| |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.core.io.HeaderInformation) -> NoneType
2. __init__(self : rosetta.core.io.HeaderInformation, src : rosetta.core.io.HeaderInformation) -> 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.io.HeaderInformation, : rosetta.core.io.HeaderInformation) -> rosetta.core.io.HeaderInformation
- classification(...) from builtins.PyCapsule
- classification(rosetta.core.io.HeaderInformation) -> str
- clear_compounds(...) from builtins.PyCapsule
- clear_compounds(rosetta.core.io.HeaderInformation) -> NoneType
- clear_experimental_techniques(...) from builtins.PyCapsule
- clear_experimental_techniques(rosetta.core.io.HeaderInformation) -> NoneType
- clear_keywords(...) from builtins.PyCapsule
- clear_keywords(rosetta.core.io.HeaderInformation) -> NoneType
- clear_title(...) from builtins.PyCapsule
- clear_title(rosetta.core.io.HeaderInformation) -> NoneType
- compound_in_progress(...) from builtins.PyCapsule
- compound_in_progress(rosetta.core.io.HeaderInformation) -> bool
- compound_token_to_string(...) from builtins.PyCapsule
- compound_token_to_string(token : rosetta.core.io.CompoundToken) -> str
- compounds(...) from builtins.PyCapsule
- compounds(rosetta.core.io.HeaderInformation) -> rosetta.utility.vector1_std_pair_core_io_HeaderInformation_CompoundToken_std_string_t
- deposition_date(...) from builtins.PyCapsule
- deposition_date(*args, **kwargs)
Overloaded function.
1. deposition_date(rosetta.core.io.HeaderInformation) -> str
2. deposition_date(self : rosetta.core.io.HeaderInformation, yy : int, mm : int, dd : int) -> NoneType
get the deposition date using the format of two digit numbers
for the year, month and day of the month
- experimental_technique_in_progress(...) from builtins.PyCapsule
- experimental_technique_in_progress(rosetta.core.io.HeaderInformation) -> bool
- experimental_technique_to_string(...) from builtins.PyCapsule
- experimental_technique_to_string(technique : rosetta.core.io.ExperimentalTechnique) -> str
- experimental_techniques(...) from builtins.PyCapsule
- experimental_techniques(rosetta.core.io.HeaderInformation) -> rosetta.std.list_core_io_HeaderInformation_ExperimentalTechnique_std_allocator_core_io_HeaderInformation_ExperimentalTechnique_t
- finalize_compound_records(...) from builtins.PyCapsule
- finalize_compound_records(rosetta.core.io.HeaderInformation) -> NoneType
- finalize_experimental_technique_records(...) from builtins.PyCapsule
- finalize_experimental_technique_records(rosetta.core.io.HeaderInformation) -> NoneType
- finalize_keyword_records(...) from builtins.PyCapsule
- finalize_keyword_records(rosetta.core.io.HeaderInformation) -> NoneType
- finalize_parse(...) from builtins.PyCapsule
- finalize_parse(rosetta.core.io.HeaderInformation) -> NoneType
- idCode(...) from builtins.PyCapsule
- idCode(rosetta.core.io.HeaderInformation) -> str
- is_experimental_technique(...) from builtins.PyCapsule
- is_experimental_technique(self : rosetta.core.io.HeaderInformation, technique : rosetta.core.io.ExperimentalTechnique) -> bool
- keyword_in_progress(...) from builtins.PyCapsule
- keyword_in_progress(rosetta.core.io.HeaderInformation) -> bool
- keywords(...) from builtins.PyCapsule
- keywords(rosetta.core.io.HeaderInformation) -> rosetta.std.list_std_string_std_allocator_std_string_t
- parse_in_progress(...) from builtins.PyCapsule
- parse_in_progress(rosetta.core.io.HeaderInformation) -> bool
- store_classification(...) from builtins.PyCapsule
- store_classification(self : rosetta.core.io.HeaderInformation, classification : str) -> NoneType
- store_compound(...) from builtins.PyCapsule
- store_compound(*args, **kwargs)
Overloaded function.
1. store_compound(self : rosetta.core.io.HeaderInformation, compound : str) -> NoneType
2. store_compound(self : rosetta.core.io.HeaderInformation, token : rosetta.core.io.CompoundToken, value : str) -> NoneType
- store_deposition_date(...) from builtins.PyCapsule
- store_deposition_date(*args, **kwargs)
Overloaded function.
1. store_deposition_date(self : rosetta.core.io.HeaderInformation, deposition_date : str) -> NoneType
Store the deposition date using the format like "84-DEC-18"
2. store_deposition_date(self : rosetta.core.io.HeaderInformation, yy : int, mm : int, dd : int) -> NoneType
Store the deposition date using the format of two digit numbers
for the year, month and day of the month.
- store_experimental_technique(...) from builtins.PyCapsule
- store_experimental_technique(self : rosetta.core.io.HeaderInformation, technique : rosetta.core.io.ExperimentalTechnique) -> NoneType
- store_experimental_techniques(...) from builtins.PyCapsule
- store_experimental_techniques(self : rosetta.core.io.HeaderInformation, exp : str) -> NoneType
the list of techniques string following the technqiue
field in the EXPDTA record of the pdb format and store the techniques
- store_idCode(...) from builtins.PyCapsule
- store_idCode(self : rosetta.core.io.HeaderInformation, id_code : str) -> NoneType
- store_keywords(...) from builtins.PyCapsule
- store_keywords(self : rosetta.core.io.HeaderInformation, keywords : str) -> NoneType
- store_title(...) from builtins.PyCapsule
- store_title(self : rosetta.core.io.HeaderInformation, title : str) -> NoneType
Append title record onto current title string
- string_to_compound_token(...) from builtins.PyCapsule
- string_to_compound_token(token : str) -> rosetta.core.io.CompoundToken
- string_to_experimental_technique(...) from builtins.PyCapsule
- string_to_experimental_technique(technique : str) -> rosetta.core.io.ExperimentalTechnique
- title(...) from builtins.PyCapsule
- title(rosetta.core.io.HeaderInformation) -> str
Data and other attributes defined here:
- BIOLOGICAL_UNIT = CompoundToken.BIOLOGICAL_UNIT
- CHAIN = CompoundToken.CHAIN
- CRYO_ELECTRON_MICROSCOPY = ExperimentalTechnique.CRYO_ELECTRON_MICROSCOPY
- CompoundToken = <class 'rosetta.core.io.HeaderInformation.CompoundToken'>
- CompoundToken_max = CompoundToken.CompoundToken_max
- EC = CompoundToken.EC
- ELECTRON_CRYSTALLOGRAPHY = ExperimentalTechnique.ELECTRON_CRYSTALLOGRAPHY
- ELECTRON_DEFRACTION = ExperimentalTechnique.ELECTRON_DEFRACTION
- ELECTRON_MICROSCOPY = ExperimentalTechnique.ELECTRON_MICROSCOPY
- ENGINEERED = CompoundToken.ENGINEERED
- ExperimentalTechnique = <class 'rosetta.core.io.HeaderInformation.ExperimentalTechnique'>
- Fields for the EXPDTA Record
- ExperimentalTechnique_max = ExperimentalTechnique.ExperimentalTechnique_max
- ExperimentalTechnique_max_current = ExperimentalTechnique.ExperimentalTechnique_max_current
- FIBER_DIFFRACTION = ExperimentalTechnique.FIBER_DIFFRACTION
- FLORECENCE_TRANSFER = ExperimentalTechnique.FLORECENCE_TRANSFER
- FRAGMENT = CompoundToken.FRAGMENT
- MOLECULE = CompoundToken.MOLECULE
- MOL_ID = CompoundToken.MOL_ID
- MUTATION = CompoundToken.MUTATION
- NEUTRON_DIFFRACTION = ExperimentalTechnique.NEUTRON_DIFFRACTION
- NMR = ExperimentalTechnique.ExperimentalTechnique_max
- OTHER_DETAILS = CompoundToken.CompoundToken_max
- SOLID_STATE_NMR = ExperimentalTechnique.SOLID_STATE_NMR
- SOLUTION_NMR = ExperimentalTechnique.SOLUTION_NMR
- SOLUTION_SCATTERING = ExperimentalTechnique.SOLUTION_SCATTERING
- SOLUTION_SCATTERING_THEORETICAL_MODEL = ExperimentalTechnique.SOLUTION_SCATTERING_THEORETICAL_MODEL
- SYNONYM = CompoundToken.SYNONYM
- THEORETICAL_MODEL = ExperimentalTechnique.ExperimentalTechnique_max_current
- X_RAY_DIFFRACTION = ExperimentalTechnique.X_RAY_DIFFRACTION
|
class Remarks(rosetta.std.vector_core_io_RemarkInfo) |
| | |
- Method resolution order:
- Remarks
- rosetta.std.vector_core_io_RemarkInfo
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(rosetta.core.io.Remarks) -> 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.io.Remarks, : rosetta.core.io.Remarks) -> rosetta.core.io.Remarks
Methods inherited from rosetta.std.vector_core_io_RemarkInfo:
- __bool__(...) from builtins.PyCapsule
- __bool__(rosetta.std.vector_core_io_RemarkInfo) -> bool
Check whether the list is nonempty
- __delitem__(...) from builtins.PyCapsule
- __delitem__(*args, **kwargs)
Overloaded function.
1. __delitem__(rosetta.std.vector_core_io_RemarkInfo, int) -> NoneType
Delete list elements using a slice object
2. __delitem__(rosetta.std.vector_core_io_RemarkInfo, slice) -> NoneType
Delete list elements using a slice object
- __getitem__(...) from builtins.PyCapsule
- __getitem__(*args, **kwargs)
Overloaded function.
1. __getitem__(rosetta.std.vector_core_io_RemarkInfo, int) -> core::io::RemarkInfo
2. __getitem__(self : rosetta.std.vector_core_io_RemarkInfo, s : slice) -> rosetta.std.vector_core_io_RemarkInfo
Retrieve list elements using a slice object
- __iter__(...) from builtins.PyCapsule
- __iter__(rosetta.std.vector_core_io_RemarkInfo) -> iterator
- __len__(...) from builtins.PyCapsule
- __len__(rosetta.std.vector_core_io_RemarkInfo) -> int
- __repr__(...) from builtins.PyCapsule
- __repr__(rosetta.std.vector_core_io_RemarkInfo) -> str
Return the canonical string representation of this list.
- __setitem__(...) from builtins.PyCapsule
- __setitem__(*args, **kwargs)
Overloaded function.
1. __setitem__(rosetta.std.vector_core_io_RemarkInfo, int, core::io::RemarkInfo) -> NoneType
2. __setitem__(rosetta.std.vector_core_io_RemarkInfo, slice, rosetta.std.vector_core_io_RemarkInfo) -> NoneType
Assign list elements using a slice object
- append(...) from builtins.PyCapsule
- append(self : rosetta.std.vector_core_io_RemarkInfo, x : core::io::RemarkInfo) -> NoneType
Add an item to the end of the list
- capacity(...) from builtins.PyCapsule
- capacity(rosetta.std.vector_core_io_RemarkInfo) -> int
returns the number of elements that can be held in currently allocated storage
- clear(...) from builtins.PyCapsule
- clear(rosetta.std.vector_core_io_RemarkInfo) -> NoneType
clears the contents
- empty(...) from builtins.PyCapsule
- empty(rosetta.std.vector_core_io_RemarkInfo) -> bool
checks whether the container is empty
- extend(...) from builtins.PyCapsule
- extend(self : rosetta.std.vector_core_io_RemarkInfo, L : rosetta.std.vector_core_io_RemarkInfo) -> NoneType
Extend the list by appending all the items in the given list
- insert(...) from builtins.PyCapsule
- insert(self : rosetta.std.vector_core_io_RemarkInfo, i : int, x : core::io::RemarkInfo) -> NoneType
Insert an item at a given position.
- max_size(...) from builtins.PyCapsule
- max_size(rosetta.std.vector_core_io_RemarkInfo) -> int
returns the maximum possible number of elements
- pop(...) from builtins.PyCapsule
- pop(*args, **kwargs)
Overloaded function.
1. pop(rosetta.std.vector_core_io_RemarkInfo) -> core::io::RemarkInfo
Remove and return the last item
2. pop(self : rosetta.std.vector_core_io_RemarkInfo, i : int) -> core::io::RemarkInfo
Remove and return the item at index ``i``
- reserve(...) from builtins.PyCapsule
- reserve(rosetta.std.vector_core_io_RemarkInfo, int) -> NoneType
reserves storage
- shrink_to_fit(...) from builtins.PyCapsule
- shrink_to_fit(rosetta.std.vector_core_io_RemarkInfo) -> NoneType
reduces memory usage by freeing unused memory
- swap(...) from builtins.PyCapsule
- swap(rosetta.std.vector_core_io_RemarkInfo, rosetta.std.vector_core_io_RemarkInfo) -> NoneType
swaps the contents
|
class ResidueInformation(builtins.object) |
| |
Subset of data from "ATOM" lines that is shared by all atoms in a
residue.
This class is used for temporary storage of information during Pose building
and "unbuilding".
|
| |
Methods defined here:
- __eq__(...) from builtins.PyCapsule
- __eq__(self : rosetta.core.io.ResidueInformation, that : rosetta.core.io.ResidueInformation) -> bool
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.core.io.ResidueInformation) -> NoneType
2. __init__(self : rosetta.core.io.ResidueInformation, ai : rosetta.core.io.AtomInformation) -> NoneType
3. __init__(self : rosetta.core.io.ResidueInformation, : rosetta.core.io.ResidueInformation) -> NoneType
- __ne__(...) from builtins.PyCapsule
- __ne__(self : rosetta.core.io.ResidueInformation, that : rosetta.core.io.ResidueInformation) -> bool
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- append_atom(...) from builtins.PyCapsule
- append_atom(self : rosetta.core.io.ResidueInformation, atoms : rosetta.core.io.AtomInformation) -> NoneType
- append_atoms(...) from builtins.PyCapsule
- append_atoms(self : rosetta.core.io.ResidueInformation, source : rosetta.core.io.ResidueInformation) -> NoneType
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.io.ResidueInformation, : rosetta.core.io.ResidueInformation) -> rosetta.core.io.ResidueInformation
- atoms(...) from builtins.PyCapsule
- atoms(rosetta.core.io.ResidueInformation) -> rosetta.utility.vector1_core_io_AtomInformation
- chainID(...) from builtins.PyCapsule
- chainID(*args, **kwargs)
Overloaded function.
1. chainID(rosetta.core.io.ResidueInformation) -> str
2. chainID(self : rosetta.core.io.ResidueInformation, setting : str) -> NoneType
- iCode(...) from builtins.PyCapsule
- iCode(*args, **kwargs)
Overloaded function.
1. iCode(rosetta.core.io.ResidueInformation) -> str
2. iCode(self : rosetta.core.io.ResidueInformation, setting : str) -> NoneType
- rename_atom(...) from builtins.PyCapsule
- rename_atom(self : rosetta.core.io.ResidueInformation, orig_name : str, new_name : str) -> NoneType
- resName(...) from builtins.PyCapsule
- resName(*args, **kwargs)
Overloaded function.
1. resName(rosetta.core.io.ResidueInformation) -> str
2. resName(self : rosetta.core.io.ResidueInformation, setting : str) -> NoneType
- resSeq(...) from builtins.PyCapsule
- resSeq(*args, **kwargs)
Overloaded function.
1. resSeq(rosetta.core.io.ResidueInformation) -> int
2. resSeq(self : rosetta.core.io.ResidueInformation, setting : int) -> NoneType
- resid(...) from builtins.PyCapsule
- resid(rosetta.core.io.ResidueInformation) -> str
Returns a short, printable designation for this residue.
- segmentID(...) from builtins.PyCapsule
- segmentID(*args, **kwargs)
Overloaded function.
1. segmentID(rosetta.core.io.ResidueInformation) -> str
2. segmentID(self : rosetta.core.io.ResidueInformation, setting : str) -> NoneType
- set_temp(...) from builtins.PyCapsule
- set_temp(self : rosetta.core.io.ResidueInformation, atomname : str, val : float) -> NoneType
- set_xyz(...) from builtins.PyCapsule
- set_xyz(self : rosetta.core.io.ResidueInformation, atomname : str, vect : rosetta.numeric.xyzVector_double_t) -> NoneType
- temps(...) from builtins.PyCapsule
- temps(rosetta.core.io.ResidueInformation) -> rosetta.std.map_std_string_double
- terCount(...) from builtins.PyCapsule
- terCount(*args, **kwargs)
Overloaded function.
1. terCount(rosetta.core.io.ResidueInformation) -> int
2. terCount(self : rosetta.core.io.ResidueInformation, setting : int) -> NoneType
- xyz(...) from builtins.PyCapsule
- xyz(rosetta.core.io.ResidueInformation) -> rosetta.std.map_std_string_numeric_xyzVector_double_t
A convenience accessor for the coordinates.
|
class StructFileReaderOptions(StructFileRepOptions) |
| | |
- Method resolution order:
- StructFileReaderOptions
- StructFileRepOptions
- rosetta.basic.resource_manager.ResourceOptions
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, options : rosetta.utility.options.OptionCollection) -> NoneType
3. __init__(handle, rosetta.core.io.StructFileReaderOptions) -> 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.io.StructFileReaderOptions, : rosetta.core.io.StructFileReaderOptions) -> rosetta.core.io.StructFileReaderOptions
- glycam_pdb_format(...) from builtins.PyCapsule
- glycam_pdb_format(rosetta.core.io.StructFileReaderOptions) -> bool
- list_options_read(...) from builtins.PyCapsule
- list_options_read(*args, **kwargs)
Overloaded function.
1. list_options_read(read_options : rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_std_allocator_utility_keys_VariantKey_utility_options_OptionKey_t) -> NoneType
Declare the list of options that are read in the process of reading a PDB (or SDF) and converting
it into a Pose.
2. list_options_read(read_options : rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_std_allocator_utility_keys_VariantKey_utility_options_OptionKey_t) -> NoneType
Declare the list of options that are read in the process of reading a PDB (or SDF) and converting
it into a Pose.
3. list_options_read(read_options : rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_std_allocator_utility_keys_VariantKey_utility_options_OptionKey_t) -> NoneType
- new_chain_order(...) from builtins.PyCapsule
- new_chain_order(rosetta.core.io.StructFileReaderOptions) -> bool
- obey_ENDMDL(...) from builtins.PyCapsule
- obey_ENDMDL(rosetta.core.io.StructFileReaderOptions) -> bool
- parse_my_tag(...) from builtins.PyCapsule
- parse_my_tag(self : rosetta.core.io.StructFileReaderOptions, tag : utility::tag::Tag) -> NoneType
- read_pdb_header(...) from builtins.PyCapsule
- read_pdb_header(rosetta.core.io.StructFileReaderOptions) -> bool
- set_glycam_pdb_format(...) from builtins.PyCapsule
- set_glycam_pdb_format(self : rosetta.core.io.StructFileReaderOptions, setting : bool) -> NoneType
- set_new_chain_order(...) from builtins.PyCapsule
- set_new_chain_order(self : rosetta.core.io.StructFileReaderOptions, setting : bool) -> NoneType
- set_obey_ENDMDL(...) from builtins.PyCapsule
- set_obey_ENDMDL(self : rosetta.core.io.StructFileReaderOptions, setting : bool) -> NoneType
- set_read_pdb_header(...) from builtins.PyCapsule
- set_read_pdb_header(self : rosetta.core.io.StructFileReaderOptions, setting : bool) -> NoneType
- type(...) from builtins.PyCapsule
- type(rosetta.core.io.StructFileReaderOptions) -> str
Methods inherited from StructFileRepOptions:
- chains_whose_residues_are_separate_chemical_entities(...) from builtins.PyCapsule
- chains_whose_residues_are_separate_chemical_entities(rosetta.core.io.StructFileRepOptions) -> str
- check_if_residues_are_Ctermini(...) from builtins.PyCapsule
- check_if_residues_are_Ctermini(rosetta.core.io.StructFileRepOptions) -> str
- check_if_residues_are_Ntermini(...) from builtins.PyCapsule
- check_if_residues_are_Ntermini(rosetta.core.io.StructFileRepOptions) -> str
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.io.StructFileRepOptions) -> rosetta.core.io.StructFileRepOptions
Copy this object and return an owning pointer to the copy.
- connect_info_cutoff(...) from builtins.PyCapsule
- connect_info_cutoff(rosetta.core.io.StructFileRepOptions) -> float
- constraints_from_link_records(...) from builtins.PyCapsule
- constraints_from_link_records(rosetta.core.io.StructFileRepOptions) -> bool
- exit_if_missing_heavy_atoms(...) from builtins.PyCapsule
- exit_if_missing_heavy_atoms(rosetta.core.io.StructFileRepOptions) -> bool
- fold_tree_io(...) from builtins.PyCapsule
- fold_tree_io(rosetta.core.io.StructFileRepOptions) -> bool
- ignore_sugars(...) from builtins.PyCapsule
- ignore_sugars(rosetta.core.io.StructFileRepOptions) -> bool
- ignore_unrecognized_res(...) from builtins.PyCapsule
- ignore_unrecognized_res(rosetta.core.io.StructFileRepOptions) -> bool
- ignore_waters(...) from builtins.PyCapsule
- ignore_waters(rosetta.core.io.StructFileRepOptions) -> bool
- ignore_zero_occupancy(...) from builtins.PyCapsule
- ignore_zero_occupancy(rosetta.core.io.StructFileRepOptions) -> bool
- keep_input_protonation_state(...) from builtins.PyCapsule
- keep_input_protonation_state(rosetta.core.io.StructFileRepOptions) -> bool
- missing_dens_as_jump(...) from builtins.PyCapsule
- missing_dens_as_jump(rosetta.core.io.StructFileRepOptions) -> bool
- no_chainend_ter(...) from builtins.PyCapsule
- no_chainend_ter(rosetta.core.io.StructFileRepOptions) -> bool
- no_output_cen(...) from builtins.PyCapsule
- no_output_cen(rosetta.core.io.StructFileRepOptions) -> bool
- normalize_to_thk(...) from builtins.PyCapsule
- normalize_to_thk(rosetta.core.io.StructFileRepOptions) -> bool
- output_torsions(...) from builtins.PyCapsule
- output_torsions(rosetta.core.io.StructFileRepOptions) -> bool
- output_virtual(...) from builtins.PyCapsule
- output_virtual(rosetta.core.io.StructFileRepOptions) -> bool
- output_virtual_zero_occ(...) from builtins.PyCapsule
- output_virtual_zero_occ(rosetta.core.io.StructFileRepOptions) -> bool
- pdb_comments(...) from builtins.PyCapsule
- pdb_comments(rosetta.core.io.StructFileRepOptions) -> bool
- pdb_parents(...) from builtins.PyCapsule
- pdb_parents(rosetta.core.io.StructFileRepOptions) -> bool
- per_chain_renumbering(...) from builtins.PyCapsule
- per_chain_renumbering(rosetta.core.io.StructFileRepOptions) -> bool
- preserve_crystinfo(...) from builtins.PyCapsule
- preserve_crystinfo(rosetta.core.io.StructFileRepOptions) -> bool
- preserve_header(...) from builtins.PyCapsule
- preserve_header(rosetta.core.io.StructFileRepOptions) -> bool
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : utility::tag::XMLSchemaDefinition) -> NoneType
Describe the XML Schema for this ResourceOption object
- randomize_missing_coords(...) from builtins.PyCapsule
- randomize_missing_coords(rosetta.core.io.StructFileRepOptions) -> bool
- remember_unrecognized_res(...) from builtins.PyCapsule
- remember_unrecognized_res(rosetta.core.io.StructFileRepOptions) -> bool
- remember_unrecognized_water(...) from builtins.PyCapsule
- remember_unrecognized_water(rosetta.core.io.StructFileRepOptions) -> bool
- renumber_pdb(...) from builtins.PyCapsule
- renumber_pdb(rosetta.core.io.StructFileRepOptions) -> bool
- residues_for_atom_name_remapping(...) from builtins.PyCapsule
- residues_for_atom_name_remapping(rosetta.core.io.StructFileRepOptions) -> rosetta.utility.vector1_std_string
- set_chains_whose_residues_are_separate_chemical_entities(...) from builtins.PyCapsule
- set_chains_whose_residues_are_separate_chemical_entities(self : rosetta.core.io.StructFileRepOptions, setting : str) -> NoneType
- set_check_if_residues_are_Ctermini(...) from builtins.PyCapsule
- set_check_if_residues_are_Ctermini(self : rosetta.core.io.StructFileRepOptions, check_if_residues_are_Ctermini : str) -> NoneType
- set_check_if_residues_are_Ntermini(...) from builtins.PyCapsule
- set_check_if_residues_are_Ntermini(self : rosetta.core.io.StructFileRepOptions, check_if_residues_are_Ntermini : str) -> NoneType
- set_connect_info_cutoff(...) from builtins.PyCapsule
- set_connect_info_cutoff(self : rosetta.core.io.StructFileRepOptions, connect_info_cutoff : float) -> NoneType
- set_constraints_from_link_records(...) from builtins.PyCapsule
- set_constraints_from_link_records(self : rosetta.core.io.StructFileRepOptions, setting : bool) -> NoneType
- set_exit_if_missing_heavy_atoms(...) from builtins.PyCapsule
- set_exit_if_missing_heavy_atoms(self : rosetta.core.io.StructFileRepOptions, exit_if_missing_heavy_atoms : bool) -> NoneType
- set_fold_tree_io(...) from builtins.PyCapsule
- set_fold_tree_io(self : rosetta.core.io.StructFileRepOptions, fold_tree_io : bool) -> NoneType
- set_ignore_sugars(...) from builtins.PyCapsule
- set_ignore_sugars(self : rosetta.core.io.StructFileRepOptions, setting : bool) -> NoneType
- set_ignore_unrecognized_res(...) from builtins.PyCapsule
- set_ignore_unrecognized_res(self : rosetta.core.io.StructFileRepOptions, ignore_unrecognized_res : bool) -> NoneType
- set_ignore_waters(...) from builtins.PyCapsule
- set_ignore_waters(self : rosetta.core.io.StructFileRepOptions, ignore_waters : bool) -> NoneType
- set_ignore_zero_occupancy(...) from builtins.PyCapsule
- set_ignore_zero_occupancy(self : rosetta.core.io.StructFileRepOptions, ignore_zero_occupancy : bool) -> NoneType
- set_keep_input_protonation_state(...) from builtins.PyCapsule
- set_keep_input_protonation_state(self : rosetta.core.io.StructFileRepOptions, keep_input_protonation_state : bool) -> NoneType
- set_missing_dens_as_jump(...) from builtins.PyCapsule
- set_missing_dens_as_jump(self : rosetta.core.io.StructFileRepOptions, missing_dens_as_jump : bool) -> NoneType
- set_no_chainend_ter(...) from builtins.PyCapsule
- set_no_chainend_ter(self : rosetta.core.io.StructFileRepOptions, no_chainend_ter : bool) -> NoneType
- set_no_output_cen(...) from builtins.PyCapsule
- set_no_output_cen(self : rosetta.core.io.StructFileRepOptions, no_output_cen : bool) -> NoneType
- set_normalize_to_thk(...) from builtins.PyCapsule
- set_normalize_to_thk(self : rosetta.core.io.StructFileRepOptions, normalize_to_thk : bool) -> NoneType
- set_output_torsions(...) from builtins.PyCapsule
- set_output_torsions(self : rosetta.core.io.StructFileRepOptions, output_torsions : bool) -> NoneType
- set_output_virtual(...) from builtins.PyCapsule
- set_output_virtual(self : rosetta.core.io.StructFileRepOptions, output_virtual : bool) -> NoneType
- set_output_virtual_zero_occ(...) from builtins.PyCapsule
- set_output_virtual_zero_occ(self : rosetta.core.io.StructFileRepOptions, output_virtual_zero_occ : bool) -> NoneType
- set_pdb_comments(...) from builtins.PyCapsule
- set_pdb_comments(self : rosetta.core.io.StructFileRepOptions, pdb_comments : bool) -> NoneType
- set_pdb_parents(...) from builtins.PyCapsule
- set_pdb_parents(self : rosetta.core.io.StructFileRepOptions, pdb_parents : bool) -> NoneType
- set_per_chain_renumbering(...) from builtins.PyCapsule
- set_per_chain_renumbering(self : rosetta.core.io.StructFileRepOptions, per_chain_renumbering : bool) -> NoneType
- set_preserve_crystinfo(...) from builtins.PyCapsule
- set_preserve_crystinfo(self : rosetta.core.io.StructFileRepOptions, preserve_crystinfo : bool) -> NoneType
- set_preserve_header(...) from builtins.PyCapsule
- set_preserve_header(self : rosetta.core.io.StructFileRepOptions, preserve_header : bool) -> NoneType
- set_randomize_missing_coords(...) from builtins.PyCapsule
- set_randomize_missing_coords(self : rosetta.core.io.StructFileRepOptions, randomize_missing_coords : bool) -> NoneType
- set_remember_unrecognized_res(...) from builtins.PyCapsule
- set_remember_unrecognized_res(self : rosetta.core.io.StructFileRepOptions, remember_unrecognized_res : bool) -> NoneType
- set_remember_unrecognized_water(...) from builtins.PyCapsule
- set_remember_unrecognized_water(self : rosetta.core.io.StructFileRepOptions, remember_unrecognized_water : bool) -> NoneType
- set_renumber_pdb(...) from builtins.PyCapsule
- set_renumber_pdb(self : rosetta.core.io.StructFileRepOptions, setting : bool) -> NoneType
- set_residues_for_atom_name_remapping(...) from builtins.PyCapsule
- set_residues_for_atom_name_remapping(self : rosetta.core.io.StructFileRepOptions, setting : rosetta.utility.vector1_std_string) -> NoneType
- set_show_all_fixes(...) from builtins.PyCapsule
- set_show_all_fixes(self : rosetta.core.io.StructFileRepOptions, setting : bool) -> NoneType
- set_skip_connect_info(...) from builtins.PyCapsule
- set_skip_connect_info(self : rosetta.core.io.StructFileRepOptions, skip_connect_info : bool) -> NoneType
- set_suppress_zero_occ_pdb_output(...) from builtins.PyCapsule
- set_suppress_zero_occ_pdb_output(self : rosetta.core.io.StructFileRepOptions, setting : bool) -> NoneType
- set_use_pdb_format_HETNAM_records(...) from builtins.PyCapsule
- set_use_pdb_format_HETNAM_records(self : rosetta.core.io.StructFileRepOptions, setting : bool) -> NoneType
- set_write_all_connect_info(...) from builtins.PyCapsule
- set_write_all_connect_info(self : rosetta.core.io.StructFileRepOptions, setting : bool) -> NoneType
- set_write_pdb_link_records(...) from builtins.PyCapsule
- set_write_pdb_link_records(self : rosetta.core.io.StructFileRepOptions, setting : bool) -> NoneType
- set_write_pdb_parametric_info(...) from builtins.PyCapsule
- set_write_pdb_parametric_info(self : rosetta.core.io.StructFileRepOptions, setting : bool) -> NoneType
- show_all_fixes(...) from builtins.PyCapsule
- show_all_fixes(rosetta.core.io.StructFileRepOptions) -> bool
- skip_connect_info(...) from builtins.PyCapsule
- skip_connect_info(rosetta.core.io.StructFileRepOptions) -> bool
- suppress_zero_occ_pdb_output(...) from builtins.PyCapsule
- suppress_zero_occ_pdb_output(rosetta.core.io.StructFileRepOptions) -> bool
- use_pdb_format_HETNAM_records(...) from builtins.PyCapsule
- use_pdb_format_HETNAM_records(rosetta.core.io.StructFileRepOptions) -> bool
- write_all_connect_info(...) from builtins.PyCapsule
- write_all_connect_info(rosetta.core.io.StructFileRepOptions) -> bool
- write_pdb_link_records(...) from builtins.PyCapsule
- write_pdb_link_records(rosetta.core.io.StructFileRepOptions) -> bool
- write_pdb_parametric_info(...) from builtins.PyCapsule
- write_pdb_parametric_info(rosetta.core.io.StructFileRepOptions) -> bool
Methods inherited from rosetta.basic.resource_manager.ResourceOptions:
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.basic.resource_manager.ResourceOptions) -> str
- name(...) from builtins.PyCapsule
- name(*args, **kwargs)
Overloaded function.
1. name(rosetta.basic.resource_manager.ResourceOptions) -> str
A name given to a particular ResourceOptions instance.
This function allows for better error message delivery.
2. name(self : rosetta.basic.resource_manager.ResourceOptions, setting : str) -> NoneType
Set the name for this %ResoureOptions instance.
|
class StructFileRep(builtins.object) |
| |
This class is designed to store information about a structure in a
"non-Rosetta" way, such that it can serve as an intermediary between
various file formats and a Pose.
This class is intended to be light, consisting primarily of simple
accessors.
|
| |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.core.io.StructFileRep) -> NoneType
2. __init__(self : rosetta.core.io.StructFileRep, : rosetta.core.io.StructFileRep) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.core.io.StructFileRep) -> str
- additional_string_output(...) from builtins.PyCapsule
- additional_string_output(*args, **kwargs)
Overloaded function.
1. additional_string_output(rosetta.core.io.StructFileRep) -> str
Access a catch-all place to store additional data for output.
Each file outputter must figure out how to write this out in
its output format.
2. additional_string_output(rosetta.core.io.StructFileRep) -> str
- append_to_additional_string_output(...) from builtins.PyCapsule
- append_to_additional_string_output(self : rosetta.core.io.StructFileRep, input_string : str) -> NoneType
Append more string data to the additional_string_output_ string in the SFR.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.io.StructFileRep, : rosetta.core.io.StructFileRep) -> rosetta.core.io.StructFileRep
- chain_sequences(...) from builtins.PyCapsule
- chain_sequences(*args, **kwargs)
Overloaded function.
1. chain_sequences(rosetta.core.io.StructFileRep) -> rosetta.std.map_char_utility_vector1_std_string_std_allocator_std_string_t
Access the sequences for each chain.
2. chain_sequences(rosetta.core.io.StructFileRep) -> rosetta.std.map_char_utility_vector1_std_string_std_allocator_std_string_t
- chains(...) from builtins.PyCapsule
- chains(*args, **kwargs)
Overloaded function.
1. chains(rosetta.core.io.StructFileRep) -> rosetta.utility.vector0_utility_vector0_core_io_AtomInformation_std_allocator_core_io_AtomInformation_t
Access the actual atomic coordinates, stored as chains.
2. chains(rosetta.core.io.StructFileRep) -> rosetta.utility.vector0_utility_vector0_core_io_AtomInformation_std_allocator_core_io_AtomInformation_t
- cispep_map(...) from builtins.PyCapsule
- cispep_map(*args, **kwargs)
Overloaded function.
1. cispep_map(rosetta.core.io.StructFileRep) -> rosetta.std.map_std_string_core_io_CisPeptideInformation
Access map for storing CISPEP records.
Key is 6-character resID of 1st residue in the peptide bond.
2. cispep_map(rosetta.core.io.StructFileRep) -> rosetta.std.map_std_string_core_io_CisPeptideInformation
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.io.StructFileRep) -> rosetta.core.io.StructFileRep
Create a copy and return an owning pointer to the copy.
- crystinfo(...) from builtins.PyCapsule
- crystinfo(*args, **kwargs)
Overloaded function.
1. crystinfo(rosetta.core.io.StructFileRep) -> rosetta.core.io.CrystInfo
Access crystallographic information.
2. crystinfo(rosetta.core.io.StructFileRep) -> rosetta.core.io.CrystInfo
- filename(...) from builtins.PyCapsule
- filename(*args, **kwargs)
Overloaded function.
1. filename(rosetta.core.io.StructFileRep) -> str
Access the name of the input/output file, if any.
2. filename(rosetta.core.io.StructFileRep) -> str
Access the name of the input/output file, if any.
- foldtree_string(...) from builtins.PyCapsule
- foldtree_string(*args, **kwargs)
Overloaded function.
1. foldtree_string(rosetta.core.io.StructFileRep) -> str
Access the The foldtree, represented as a string.
Each file outputter must figure out how to write this out in
its output format.
2. foldtree_string(rosetta.core.io.StructFileRep) -> str
- header(...) from builtins.PyCapsule
- header(*args, **kwargs)
Overloaded function.
1. header(rosetta.core.io.StructFileRep) -> core::io::HeaderInformation
Access HEADER, TITLE, EXPDTA, KEYWDS, and COMPND records.
"header" is a misnomer, as it actually stores HEADER, TITLE,
EXPDTA, KEYWDS, and COMPND records.
2. header(rosetta.core.io.StructFileRep) -> core::io::HeaderInformation
- heterogen_formulae(...) from builtins.PyCapsule
- heterogen_formulae(*args, **kwargs)
Overloaded function.
1. heterogen_formulae(rosetta.core.io.StructFileRep) -> rosetta.std.map_std_string_std_string
Access map for storing FORMUL records.
key is hetID
value is the chemical formula, including a potential asterisk character
2. heterogen_formulae(rosetta.core.io.StructFileRep) -> rosetta.std.map_std_string_std_string
- heterogen_names(...) from builtins.PyCapsule
- heterogen_names(*args, **kwargs)
Overloaded function.
1. heterogen_names(rosetta.core.io.StructFileRep) -> rosetta.std.map_std_string_std_string
Access map for storing HETNAM records.
key is hetID
value is the chemical name field
2. heterogen_names(rosetta.core.io.StructFileRep) -> rosetta.std.map_std_string_std_string
- heterogen_synonyms(...) from builtins.PyCapsule
- heterogen_synonyms(*args, **kwargs)
Overloaded function.
1. heterogen_synonyms(rosetta.core.io.StructFileRep) -> rosetta.std.map_std_string_utility_vector1_std_string_std_allocator_std_string_t
Access map for storing HETSYN records.
key is hetID
value is the chemical synonym list field
2. heterogen_synonyms(rosetta.core.io.StructFileRep) -> rosetta.std.map_std_string_utility_vector1_std_string_std_allocator_std_string_t
- link_map(...) from builtins.PyCapsule
- link_map(*args, **kwargs)
Overloaded function.
1. link_map(rosetta.core.io.StructFileRep) -> rosetta.std.map_std_string_utility_vector1_core_io_LinkInformation_std_allocator_core_io_LinkInformation_t
Access map for storing LINK records.
Key is 6-character resID of 1st residue in link.
(A vector is needed because a single saccharide residue can
have multiple branches.)
2. link_map(rosetta.core.io.StructFileRep) -> rosetta.std.map_std_string_utility_vector1_core_io_LinkInformation_std_allocator_core_io_LinkInformation_t
- modeltag(...) from builtins.PyCapsule
- modeltag(*args, **kwargs)
Overloaded function.
1. modeltag(rosetta.core.io.StructFileRep) -> str
Access the model tag.
2. modeltag(rosetta.core.io.StructFileRep) -> str
Access the model tag.
- modres_map(...) from builtins.PyCapsule
- modres_map(*args, **kwargs)
Overloaded function.
1. modres_map(rosetta.core.io.StructFileRep) -> rosetta.std.map_std_string_core_io_ModifiedResidueInformation
Access map for storing MODRES records.
Key is 6-character resID of the modified residue.
2. modres_map(rosetta.core.io.StructFileRep) -> rosetta.std.map_std_string_core_io_ModifiedResidueInformation
- pdb_comments(...) from builtins.PyCapsule
- pdb_comments(*args, **kwargs)
Overloaded function.
1. pdb_comments(rosetta.core.io.StructFileRep) -> rosetta.std.map_std_string_std_string
Access The PDB comments, represented as a map of string->string.
Each file outputter must figure out how to write this out in
its output format.
2. pdb_comments(rosetta.core.io.StructFileRep) -> rosetta.std.map_std_string_std_string
- remarks(...) from builtins.PyCapsule
- remarks(*args, **kwargs)
Overloaded function.
1. remarks(rosetta.core.io.StructFileRep) -> core::io::Remarks
Access PDB remarks.
2. remarks(rosetta.core.io.StructFileRep) -> core::io::Remarks
- residue_type_base_names(...) from builtins.PyCapsule
- residue_type_base_names(*args, **kwargs)
Overloaded function.
1. residue_type_base_names(rosetta.core.io.StructFileRep) -> rosetta.std.map_std_string_std_pair_std_string_std_string_t
Access map for storing ResidueType base (non-variant) names; parsed from HETNAM records:
key is 6-character resID
first value of pair is 3-letter-code; second value of pair is the base_name.
2. residue_type_base_names(rosetta.core.io.StructFileRep) -> rosetta.std.map_std_string_std_pair_std_string_std_string_t
- ssbond_map(...) from builtins.PyCapsule
- ssbond_map(*args, **kwargs)
Overloaded function.
1. ssbond_map(rosetta.core.io.StructFileRep) -> rosetta.std.map_std_string_utility_vector1_core_io_SSBondInformation_std_allocator_core_io_SSBondInformation_t
Access map for storing SSBOND records.
key is 6-character resID of 1st residue in ssbond
(A vector is needed because to futureproof if we ever handle
weird disorder situations.)
2. ssbond_map(rosetta.core.io.StructFileRep) -> rosetta.std.map_std_string_utility_vector1_core_io_SSBondInformation_std_allocator_core_io_SSBondInformation_t
|
class StructFileRepOptions(rosetta.basic.resource_manager.ResourceOptions) |
| | |
- Method resolution order:
- StructFileRepOptions
- rosetta.basic.resource_manager.ResourceOptions
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, options : rosetta.utility.options.OptionCollection) -> NoneType
3. __init__(handle, rosetta.core.io.StructFileRepOptions) -> 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.io.StructFileRepOptions, : rosetta.core.io.StructFileRepOptions) -> rosetta.core.io.StructFileRepOptions
- chains_whose_residues_are_separate_chemical_entities(...) from builtins.PyCapsule
- chains_whose_residues_are_separate_chemical_entities(rosetta.core.io.StructFileRepOptions) -> str
- check_if_residues_are_Ctermini(...) from builtins.PyCapsule
- check_if_residues_are_Ctermini(rosetta.core.io.StructFileRepOptions) -> str
- check_if_residues_are_Ntermini(...) from builtins.PyCapsule
- check_if_residues_are_Ntermini(rosetta.core.io.StructFileRepOptions) -> str
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.io.StructFileRepOptions) -> rosetta.core.io.StructFileRepOptions
Copy this object and return an owning pointer to the copy.
- connect_info_cutoff(...) from builtins.PyCapsule
- connect_info_cutoff(rosetta.core.io.StructFileRepOptions) -> float
- constraints_from_link_records(...) from builtins.PyCapsule
- constraints_from_link_records(rosetta.core.io.StructFileRepOptions) -> bool
- exit_if_missing_heavy_atoms(...) from builtins.PyCapsule
- exit_if_missing_heavy_atoms(rosetta.core.io.StructFileRepOptions) -> bool
- fold_tree_io(...) from builtins.PyCapsule
- fold_tree_io(rosetta.core.io.StructFileRepOptions) -> bool
- ignore_sugars(...) from builtins.PyCapsule
- ignore_sugars(rosetta.core.io.StructFileRepOptions) -> bool
- ignore_unrecognized_res(...) from builtins.PyCapsule
- ignore_unrecognized_res(rosetta.core.io.StructFileRepOptions) -> bool
- ignore_waters(...) from builtins.PyCapsule
- ignore_waters(rosetta.core.io.StructFileRepOptions) -> bool
- ignore_zero_occupancy(...) from builtins.PyCapsule
- ignore_zero_occupancy(rosetta.core.io.StructFileRepOptions) -> bool
- keep_input_protonation_state(...) from builtins.PyCapsule
- keep_input_protonation_state(rosetta.core.io.StructFileRepOptions) -> bool
- list_options_read(...) from builtins.PyCapsule
- list_options_read(*args, **kwargs)
Overloaded function.
1. list_options_read(read_options : rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_std_allocator_utility_keys_VariantKey_utility_options_OptionKey_t) -> NoneType
Declare the list of options that are read in the process of reading a PDB (or SDF) and converting
it into a Pose.
2. list_options_read(read_options : rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_std_allocator_utility_keys_VariantKey_utility_options_OptionKey_t) -> NoneType
Declare the list of options that are read in the process of reading a PDB (or SDF) and converting
it into a Pose.
3. list_options_read(read_options : rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_std_allocator_utility_keys_VariantKey_utility_options_OptionKey_t) -> NoneType
- missing_dens_as_jump(...) from builtins.PyCapsule
- missing_dens_as_jump(rosetta.core.io.StructFileRepOptions) -> bool
- no_chainend_ter(...) from builtins.PyCapsule
- no_chainend_ter(rosetta.core.io.StructFileRepOptions) -> bool
- no_output_cen(...) from builtins.PyCapsule
- no_output_cen(rosetta.core.io.StructFileRepOptions) -> bool
- normalize_to_thk(...) from builtins.PyCapsule
- normalize_to_thk(rosetta.core.io.StructFileRepOptions) -> bool
- output_torsions(...) from builtins.PyCapsule
- output_torsions(rosetta.core.io.StructFileRepOptions) -> bool
- output_virtual(...) from builtins.PyCapsule
- output_virtual(rosetta.core.io.StructFileRepOptions) -> bool
- output_virtual_zero_occ(...) from builtins.PyCapsule
- output_virtual_zero_occ(rosetta.core.io.StructFileRepOptions) -> bool
- parse_my_tag(...) from builtins.PyCapsule
- parse_my_tag(self : rosetta.core.io.StructFileRepOptions, tag : utility::tag::Tag) -> NoneType
- pdb_comments(...) from builtins.PyCapsule
- pdb_comments(rosetta.core.io.StructFileRepOptions) -> bool
- pdb_parents(...) from builtins.PyCapsule
- pdb_parents(rosetta.core.io.StructFileRepOptions) -> bool
- per_chain_renumbering(...) from builtins.PyCapsule
- per_chain_renumbering(rosetta.core.io.StructFileRepOptions) -> bool
- preserve_crystinfo(...) from builtins.PyCapsule
- preserve_crystinfo(rosetta.core.io.StructFileRepOptions) -> bool
- preserve_header(...) from builtins.PyCapsule
- preserve_header(rosetta.core.io.StructFileRepOptions) -> bool
- provide_xml_schema(...) from builtins.PyCapsule
- provide_xml_schema(xsd : utility::tag::XMLSchemaDefinition) -> NoneType
Describe the XML Schema for this ResourceOption object
- randomize_missing_coords(...) from builtins.PyCapsule
- randomize_missing_coords(rosetta.core.io.StructFileRepOptions) -> bool
- remember_unrecognized_res(...) from builtins.PyCapsule
- remember_unrecognized_res(rosetta.core.io.StructFileRepOptions) -> bool
- remember_unrecognized_water(...) from builtins.PyCapsule
- remember_unrecognized_water(rosetta.core.io.StructFileRepOptions) -> bool
- renumber_pdb(...) from builtins.PyCapsule
- renumber_pdb(rosetta.core.io.StructFileRepOptions) -> bool
- residues_for_atom_name_remapping(...) from builtins.PyCapsule
- residues_for_atom_name_remapping(rosetta.core.io.StructFileRepOptions) -> rosetta.utility.vector1_std_string
- set_chains_whose_residues_are_separate_chemical_entities(...) from builtins.PyCapsule
- set_chains_whose_residues_are_separate_chemical_entities(self : rosetta.core.io.StructFileRepOptions, setting : str) -> NoneType
- set_check_if_residues_are_Ctermini(...) from builtins.PyCapsule
- set_check_if_residues_are_Ctermini(self : rosetta.core.io.StructFileRepOptions, check_if_residues_are_Ctermini : str) -> NoneType
- set_check_if_residues_are_Ntermini(...) from builtins.PyCapsule
- set_check_if_residues_are_Ntermini(self : rosetta.core.io.StructFileRepOptions, check_if_residues_are_Ntermini : str) -> NoneType
- set_connect_info_cutoff(...) from builtins.PyCapsule
- set_connect_info_cutoff(self : rosetta.core.io.StructFileRepOptions, connect_info_cutoff : float) -> NoneType
- set_constraints_from_link_records(...) from builtins.PyCapsule
- set_constraints_from_link_records(self : rosetta.core.io.StructFileRepOptions, setting : bool) -> NoneType
- set_exit_if_missing_heavy_atoms(...) from builtins.PyCapsule
- set_exit_if_missing_heavy_atoms(self : rosetta.core.io.StructFileRepOptions, exit_if_missing_heavy_atoms : bool) -> NoneType
- set_fold_tree_io(...) from builtins.PyCapsule
- set_fold_tree_io(self : rosetta.core.io.StructFileRepOptions, fold_tree_io : bool) -> NoneType
- set_ignore_sugars(...) from builtins.PyCapsule
- set_ignore_sugars(self : rosetta.core.io.StructFileRepOptions, setting : bool) -> NoneType
- set_ignore_unrecognized_res(...) from builtins.PyCapsule
- set_ignore_unrecognized_res(self : rosetta.core.io.StructFileRepOptions, ignore_unrecognized_res : bool) -> NoneType
- set_ignore_waters(...) from builtins.PyCapsule
- set_ignore_waters(self : rosetta.core.io.StructFileRepOptions, ignore_waters : bool) -> NoneType
- set_ignore_zero_occupancy(...) from builtins.PyCapsule
- set_ignore_zero_occupancy(self : rosetta.core.io.StructFileRepOptions, ignore_zero_occupancy : bool) -> NoneType
- set_keep_input_protonation_state(...) from builtins.PyCapsule
- set_keep_input_protonation_state(self : rosetta.core.io.StructFileRepOptions, keep_input_protonation_state : bool) -> NoneType
- set_missing_dens_as_jump(...) from builtins.PyCapsule
- set_missing_dens_as_jump(self : rosetta.core.io.StructFileRepOptions, missing_dens_as_jump : bool) -> NoneType
- set_no_chainend_ter(...) from builtins.PyCapsule
- set_no_chainend_ter(self : rosetta.core.io.StructFileRepOptions, no_chainend_ter : bool) -> NoneType
- set_no_output_cen(...) from builtins.PyCapsule
- set_no_output_cen(self : rosetta.core.io.StructFileRepOptions, no_output_cen : bool) -> NoneType
- set_normalize_to_thk(...) from builtins.PyCapsule
- set_normalize_to_thk(self : rosetta.core.io.StructFileRepOptions, normalize_to_thk : bool) -> NoneType
- set_output_torsions(...) from builtins.PyCapsule
- set_output_torsions(self : rosetta.core.io.StructFileRepOptions, output_torsions : bool) -> NoneType
- set_output_virtual(...) from builtins.PyCapsule
- set_output_virtual(self : rosetta.core.io.StructFileRepOptions, output_virtual : bool) -> NoneType
- set_output_virtual_zero_occ(...) from builtins.PyCapsule
- set_output_virtual_zero_occ(self : rosetta.core.io.StructFileRepOptions, output_virtual_zero_occ : bool) -> NoneType
- set_pdb_comments(...) from builtins.PyCapsule
- set_pdb_comments(self : rosetta.core.io.StructFileRepOptions, pdb_comments : bool) -> NoneType
- set_pdb_parents(...) from builtins.PyCapsule
- set_pdb_parents(self : rosetta.core.io.StructFileRepOptions, pdb_parents : bool) -> NoneType
- set_per_chain_renumbering(...) from builtins.PyCapsule
- set_per_chain_renumbering(self : rosetta.core.io.StructFileRepOptions, per_chain_renumbering : bool) -> NoneType
- set_preserve_crystinfo(...) from builtins.PyCapsule
- set_preserve_crystinfo(self : rosetta.core.io.StructFileRepOptions, preserve_crystinfo : bool) -> NoneType
- set_preserve_header(...) from builtins.PyCapsule
- set_preserve_header(self : rosetta.core.io.StructFileRepOptions, preserve_header : bool) -> NoneType
- set_randomize_missing_coords(...) from builtins.PyCapsule
- set_randomize_missing_coords(self : rosetta.core.io.StructFileRepOptions, randomize_missing_coords : bool) -> NoneType
- set_remember_unrecognized_res(...) from builtins.PyCapsule
- set_remember_unrecognized_res(self : rosetta.core.io.StructFileRepOptions, remember_unrecognized_res : bool) -> NoneType
- set_remember_unrecognized_water(...) from builtins.PyCapsule
- set_remember_unrecognized_water(self : rosetta.core.io.StructFileRepOptions, remember_unrecognized_water : bool) -> NoneType
- set_renumber_pdb(...) from builtins.PyCapsule
- set_renumber_pdb(self : rosetta.core.io.StructFileRepOptions, setting : bool) -> NoneType
- set_residues_for_atom_name_remapping(...) from builtins.PyCapsule
- set_residues_for_atom_name_remapping(self : rosetta.core.io.StructFileRepOptions, setting : rosetta.utility.vector1_std_string) -> NoneType
- set_show_all_fixes(...) from builtins.PyCapsule
- set_show_all_fixes(self : rosetta.core.io.StructFileRepOptions, setting : bool) -> NoneType
- set_skip_connect_info(...) from builtins.PyCapsule
- set_skip_connect_info(self : rosetta.core.io.StructFileRepOptions, skip_connect_info : bool) -> NoneType
- set_suppress_zero_occ_pdb_output(...) from builtins.PyCapsule
- set_suppress_zero_occ_pdb_output(self : rosetta.core.io.StructFileRepOptions, setting : bool) -> NoneType
- set_use_pdb_format_HETNAM_records(...) from builtins.PyCapsule
- set_use_pdb_format_HETNAM_records(self : rosetta.core.io.StructFileRepOptions, setting : bool) -> NoneType
- set_write_all_connect_info(...) from builtins.PyCapsule
- set_write_all_connect_info(self : rosetta.core.io.StructFileRepOptions, setting : bool) -> NoneType
- set_write_pdb_link_records(...) from builtins.PyCapsule
- set_write_pdb_link_records(self : rosetta.core.io.StructFileRepOptions, setting : bool) -> NoneType
- set_write_pdb_parametric_info(...) from builtins.PyCapsule
- set_write_pdb_parametric_info(self : rosetta.core.io.StructFileRepOptions, setting : bool) -> NoneType
- show_all_fixes(...) from builtins.PyCapsule
- show_all_fixes(rosetta.core.io.StructFileRepOptions) -> bool
- skip_connect_info(...) from builtins.PyCapsule
- skip_connect_info(rosetta.core.io.StructFileRepOptions) -> bool
- suppress_zero_occ_pdb_output(...) from builtins.PyCapsule
- suppress_zero_occ_pdb_output(rosetta.core.io.StructFileRepOptions) -> bool
- type(...) from builtins.PyCapsule
- type(rosetta.core.io.StructFileRepOptions) -> str
- use_pdb_format_HETNAM_records(...) from builtins.PyCapsule
- use_pdb_format_HETNAM_records(rosetta.core.io.StructFileRepOptions) -> bool
- write_all_connect_info(...) from builtins.PyCapsule
- write_all_connect_info(rosetta.core.io.StructFileRepOptions) -> bool
- write_pdb_link_records(...) from builtins.PyCapsule
- write_pdb_link_records(rosetta.core.io.StructFileRepOptions) -> bool
- write_pdb_parametric_info(...) from builtins.PyCapsule
- write_pdb_parametric_info(rosetta.core.io.StructFileRepOptions) -> bool
Methods inherited from rosetta.basic.resource_manager.ResourceOptions:
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.basic.resource_manager.ResourceOptions) -> str
- name(...) from builtins.PyCapsule
- name(*args, **kwargs)
Overloaded function.
1. name(rosetta.basic.resource_manager.ResourceOptions) -> str
A name given to a particular ResourceOptions instance.
This function allows for better error message delivery.
2. name(self : rosetta.basic.resource_manager.ResourceOptions, setting : str) -> NoneType
Set the name for this %ResoureOptions instance.
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