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- builtins.object
-
- AssignOrbitals
- ICoorOrbitalData
- OrbitalType
- OrbitalTypeMapper
- OrbitalTypeSet
- orbital_type_enum
class AssignOrbitals(builtins.object) |
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Methods defined here:
- Coordinates_Tetrahedral_bondedto3atoms_helper(...) from builtins.PyCapsule
- Coordinates_Tetrahedral_bondedto3atoms_helper(self : rosetta.core.chemical.orbitals.AssignOrbitals, atm_index1 : int, atm_index2 : int, atm_index3 : int, atm_index4 : int, dist : float) -> rosetta.utility.vector1_numeric_xyzVector_double_t
- Coordinates_TriganolPlanar_bondedto1atom_helper(...) from builtins.PyCapsule
- Coordinates_TriganolPlanar_bondedto1atom_helper(self : rosetta.core.chemical.orbitals.AssignOrbitals, atm_index1 : int, atm_index2 : int, atm_index3 : int, dist : float) -> rosetta.utility.vector1_numeric_xyzVector_double_t
- __init__(...) from builtins.PyCapsule
- __init__(self : rosetta.core.chemical.orbitals.AssignOrbitals, restype : rosetta.core.chemical.ResidueType) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_orbitals_to_restype(...) from builtins.PyCapsule
- add_orbitals_to_restype(self : rosetta.core.chemical.orbitals.AssignOrbitals, atm_index2 : int, atm_index3 : int, atmtype : rosetta.core.chemical.AtomType, atom_hybridization : str, orbital_xyz_vectors : rosetta.utility.vector1_numeric_xyzVector_double_t) -> NoneType
- assign_only_pi_orbitals_to_atom(...) from builtins.PyCapsule
- assign_only_pi_orbitals_to_atom(self : rosetta.core.chemical.orbitals.AssignOrbitals, atmtype : rosetta.core.chemical.AtomType) -> NoneType
- assign_orbitals(...) from builtins.PyCapsule
- assign_orbitals(rosetta.core.chemical.orbitals.AssignOrbitals) -> NoneType
- assign_sp2_orbitals_to_one_bonded_atom(...) from builtins.PyCapsule
- assign_sp2_orbitals_to_one_bonded_atom(self : rosetta.core.chemical.orbitals.AssignOrbitals, atmtype : rosetta.core.chemical.AtomType) -> NoneType
- assign_sp2_sp_orbitals_to_one_bonded_atom(...) from builtins.PyCapsule
- assign_sp2_sp_orbitals_to_one_bonded_atom(self : rosetta.core.chemical.orbitals.AssignOrbitals, atmtype : rosetta.core.chemical.AtomType) -> NoneType
- calculate_orbital_icoor(...) from builtins.PyCapsule
- calculate_orbital_icoor(self : rosetta.core.chemical.orbitals.AssignOrbitals, orbital_xyz : rosetta.numeric.xyzVector_double_t, atm_index1 : int, atm_index2 : int, atm_index3 : int, orbital_element_name : str) -> NoneType
- cross_product_helper(...) from builtins.PyCapsule
- cross_product_helper(self : rosetta.core.chemical.orbitals.AssignOrbitals, atm_index1 : int, atm_index2 : int, atm_index3 : int, dist : float) -> rosetta.utility.vector1_numeric_xyzVector_double_t
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class ICoorOrbitalData(builtins.object) |
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.core.chemical.orbitals.ICoorOrbitalData) -> NoneType
2. __init__(self : rosetta.core.chemical.orbitals.ICoorOrbitalData, phi : float, theata : float, distance : float, stub1 : int, stub2 : int, stub3 : int, capsule, capsule, capsule) -> NoneType
3. __init__(self : rosetta.core.chemical.orbitals.ICoorOrbitalData, : rosetta.core.chemical.orbitals.ICoorOrbitalData) -> 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.chemical.orbitals.ICoorOrbitalData, : rosetta.core.chemical.orbitals.ICoorOrbitalData) -> rosetta.core.chemical.orbitals.ICoorOrbitalData
- build(...) from builtins.PyCapsule
- build(self : rosetta.core.chemical.orbitals.ICoorOrbitalData, stub1_xyz : rosetta.numeric.xyzVector_double_t, stub2_xyz : rosetta.numeric.xyzVector_double_t, stub3_xyz : rosetta.numeric.xyzVector_double_t) -> rosetta.numeric.xyzVector_double_t
- distance(...) from builtins.PyCapsule
- distance(rosetta.core.chemical.orbitals.ICoorOrbitalData) -> float
- get_stub1(...) from builtins.PyCapsule
- get_stub1(rosetta.core.chemical.orbitals.ICoorOrbitalData) -> int
- get_stub2(...) from builtins.PyCapsule
- get_stub2(rosetta.core.chemical.orbitals.ICoorOrbitalData) -> int
- get_stub3(...) from builtins.PyCapsule
- get_stub3(rosetta.core.chemical.orbitals.ICoorOrbitalData) -> int
- phi(...) from builtins.PyCapsule
- phi(rosetta.core.chemical.orbitals.ICoorOrbitalData) -> float
- replace_stub1(...) from builtins.PyCapsule
- replace_stub1(self : rosetta.core.chemical.orbitals.ICoorOrbitalData, atom1 : int) -> NoneType
- replace_stub2(...) from builtins.PyCapsule
- replace_stub2(self : rosetta.core.chemical.orbitals.ICoorOrbitalData, atom2 : int) -> NoneType
- replace_stub3(...) from builtins.PyCapsule
- replace_stub3(self : rosetta.core.chemical.orbitals.ICoorOrbitalData, atom3 : int) -> NoneType
- theta(...) from builtins.PyCapsule
- theta(rosetta.core.chemical.orbitals.ICoorOrbitalData) -> float
- vertex1(...) from builtins.PyCapsule
- vertex1(*args, **kwargs)
Overloaded function.
1. vertex1(rosetta.core.chemical.orbitals.ICoorOrbitalData) -> capsule
2. vertex1(self : rosetta.core.chemical.orbitals.ICoorOrbitalData, capsule) -> NoneType
- vertex2(...) from builtins.PyCapsule
- vertex2(*args, **kwargs)
Overloaded function.
1. vertex2(rosetta.core.chemical.orbitals.ICoorOrbitalData) -> capsule
2. vertex2(self : rosetta.core.chemical.orbitals.ICoorOrbitalData, capsule) -> NoneType
- vertex3(...) from builtins.PyCapsule
- vertex3(*args, **kwargs)
Overloaded function.
1. vertex3(rosetta.core.chemical.orbitals.ICoorOrbitalData) -> capsule
2. vertex3(self : rosetta.core.chemical.orbitals.ICoorOrbitalData, capsule) -> NoneType
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class OrbitalType(builtins.object) |
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : rosetta.core.chemical.orbitals.OrbitalType, orbital_name : str, atom_type_name : str) -> NoneType
2. __init__(self : rosetta.core.chemical.orbitals.OrbitalType, : rosetta.core.chemical.orbitals.OrbitalType) -> 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.chemical.orbitals.OrbitalType, : rosetta.core.chemical.orbitals.OrbitalType) -> rosetta.core.chemical.orbitals.OrbitalType
- atom_type_name(...) from builtins.PyCapsule
- atom_type_name(rosetta.core.chemical.orbitals.OrbitalType) -> rosetta.utility.vector1_std_string
returns the atom_types associated with the orbital type. defined in orbital_properties.txt
- distance(...) from builtins.PyCapsule
- distance(rosetta.core.chemical.orbitals.OrbitalType) -> float
returns the distance from the atom the orbital comes off. defined in orbital_properties.txt
- hybridization(...) from builtins.PyCapsule
- hybridization(rosetta.core.chemical.orbitals.OrbitalType) -> str
returns hybrdiziation of atom the orbital is attached to
- name(...) from builtins.PyCapsule
- name(rosetta.core.chemical.orbitals.OrbitalType) -> str
returns the name of the orbital type. defined in orbital_properties.txt
- orbital_enum(...) from builtins.PyCapsule
- orbital_enum(rosetta.core.chemical.orbitals.OrbitalType) -> rosetta.core.chemical.orbitals.orbital_type_enum
- orbital_name(...) from builtins.PyCapsule
- orbital_name(rosetta.core.chemical.orbitals.OrbitalType) -> str
returns the orbital associated with the type
- set_parameter(...) from builtins.PyCapsule
- set_parameter(self : rosetta.core.chemical.orbitals.OrbitalType, param : str, setting : float) -> NoneType
The parameters are the actual headings in the orbital_properties.txt. If you want to add more paramters,
you must edit orbital_properties.txt and add another heading. You also need to edit AtomTypeSet.txt so that
it recognizes that parameter and parses it. The parameters are different form the properties in that they
are Reals/Size and properties are strings.
- set_property(...) from builtins.PyCapsule
- set_property(self : rosetta.core.chemical.orbitals.OrbitalType, property : str, setting : bool) -> NoneType
Currently, these properties are not actually in the orbital_properties.txt. I have them here
as an example on how to add properties. This is also a place holder as the ligand code will
soon be using these properties. The Acceptor/Donor could refer to orbitals that have a lone pair
and are donating to a hydrogen, or an electron defficient region. In order to add properties, one
must add the properties to the last line of orbital_properties.txt and make a private member variable
for that property in the header file. Then do a string match comparision, like seen below. These properties
are set via OrbitalTypeSet.hh
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class OrbitalTypeSet(builtins.object) |
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Methods defined here:
- __getitem__(...) from builtins.PyCapsule
- __getitem__(self : rosetta.core.chemical.orbitals.OrbitalTypeSet, index : int) -> rosetta.core.chemical.orbitals.OrbitalType
[ ] operator, simulating vector index behavior
look up an OrbitalTypeSet by 1-based indexing
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : rosetta.core.chemical.orbitals.OrbitalTypeSet, directory : str) -> NoneType
2. __init__(self : rosetta.core.chemical.orbitals.OrbitalTypeSet, : rosetta.core.chemical.orbitals.OrbitalTypeSet) -> 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.chemical.orbitals.OrbitalTypeSet, : rosetta.core.chemical.orbitals.OrbitalTypeSet) -> rosetta.core.chemical.orbitals.OrbitalTypeSet
- orbital_type_index(...) from builtins.PyCapsule
- orbital_type_index(*args, **kwargs)
Overloaded function.
1. orbital_type_index(self : rosetta.core.chemical.orbitals.OrbitalTypeSet, orbital_type_name : str) -> int
lookup the orbital type by the orbital type name string
2. orbital_type_index(self : rosetta.core.chemical.orbitals.OrbitalTypeSet, orbital_type_name : str) -> int
lookup the orbital type by the orbital type name string
- read_file(...) from builtins.PyCapsule
- read_file(self : rosetta.core.chemical.orbitals.OrbitalTypeSet, filename : str) -> NoneType
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