TorsionIndexer

pydantic model openff.qcsubmit.workflow_components.TorsionIndexer[source]

A class to keep track of the torsions highlighted for scanning, with methods for combining and deduplication.

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{
   "title": "TorsionIndexer",
   "description": "A class to keep track of the torsions highlighted for scanning, with methods for combining and deduplication.",
   "type": "object",
   "properties": {
      "torsions": {
         "title": "Torsions",
         "description": "A dictionary of the torsions to be scanned grouped by the central bond in the torsion.",
         "default": {},
         "type": "object",
         "additionalProperties": {
            "$ref": "#/definitions/SingleTorsion"
         }
      },
      "double_torsions": {
         "title": "Double Torsions",
         "description": "A dictionary of the 2D torsions to be scanned grouped by the sorted combination of the central bonds.",
         "default": {},
         "type": "object",
         "additionalProperties": {
            "$ref": "#/definitions/DoubleTorsion"
         }
      },
      "impropers": {
         "title": "Impropers",
         "description": "A dictionary of the improper torsions to be scanned grouped by the central atom in the torsion.",
         "default": {},
         "type": "object",
         "additionalProperties": {
            "$ref": "#/definitions/ImproperTorsion"
         }
      }
   },
   "definitions": {
      "SingleTorsion": {
         "title": "SingleTorsion",
         "description": "A class used to mark torsions that will be driven for torsiondrive datasets.\n\nNote:\n    This is only for 1D torsiondrives.",
         "type": "object",
         "properties": {
            "torsion1": {
               "title": "Torsion1",
               "description": "The torsion which is to be driven.",
               "type": "array",
               "minItems": 4,
               "maxItems": 4,
               "items": [
                  {
                     "type": "integer"
                  },
                  {
                     "type": "integer"
                  },
                  {
                     "type": "integer"
                  },
                  {
                     "type": "integer"
                  }
               ]
            },
            "scan_range1": {
               "title": "Scan Range1",
               "description": "The scan range used in the torsion drive",
               "type": "array",
               "minItems": 2,
               "maxItems": 2,
               "items": [
                  {
                     "type": "integer"
                  },
                  {
                     "type": "integer"
                  }
               ]
            },
            "scan_increment": {
               "title": "Scan Increment",
               "description": "The value in degrees between each grid point in the scan.",
               "default": [
                  15
               ],
               "type": "array",
               "items": {
                  "type": "integer"
               }
            },
            "symmetry_group1": {
               "title": "Symmetry Group1",
               "description": "The symmetry of the central atoms in the torsion used to deduplicate symmetrical torsions.",
               "type": "array",
               "minItems": 2,
               "maxItems": 2,
               "items": [
                  {
                     "type": "integer"
                  },
                  {
                     "type": "integer"
                  }
               ]
            }
         },
         "required": [
            "torsion1",
            "symmetry_group1"
         ]
      },
      "DoubleTorsion": {
         "title": "DoubleTorsion",
         "description": "A class used to mark coupled torsions which should be scanned.",
         "type": "object",
         "properties": {
            "torsion1": {
               "title": "Torsion1",
               "description": "The torsion which is to be driven.",
               "type": "array",
               "minItems": 4,
               "maxItems": 4,
               "items": [
                  {
                     "type": "integer"
                  },
                  {
                     "type": "integer"
                  },
                  {
                     "type": "integer"
                  },
                  {
                     "type": "integer"
                  }
               ]
            },
            "scan_range1": {
               "title": "Scan Range1",
               "description": "The scan range used in the torsion drive",
               "type": "array",
               "minItems": 2,
               "maxItems": 2,
               "items": [
                  {
                     "type": "integer"
                  },
                  {
                     "type": "integer"
                  }
               ]
            },
            "scan_increment": {
               "title": "Scan Increment",
               "default": [
                  15,
                  15
               ],
               "type": "array",
               "items": {
                  "type": "integer"
               }
            },
            "symmetry_group1": {
               "title": "Symmetry Group1",
               "description": "The symmetry of the central atoms in the torsion used to deduplicate symmetrical torsions.",
               "type": "array",
               "minItems": 2,
               "maxItems": 2,
               "items": [
                  {
                     "type": "integer"
                  },
                  {
                     "type": "integer"
                  }
               ]
            },
            "torsion2": {
               "title": "Torsion2",
               "description": "The torsion tuple of the second dihedral to be drive at the same time as the first.",
               "type": "array",
               "minItems": 4,
               "maxItems": 4,
               "items": [
                  {
                     "type": "integer"
                  },
                  {
                     "type": "integer"
                  },
                  {
                     "type": "integer"
                  },
                  {
                     "type": "integer"
                  }
               ]
            },
            "scan_range2": {
               "title": "Scan Range2",
               "description": "The separate scan range that should be used for the second dihedral.",
               "type": "array",
               "minItems": 2,
               "maxItems": 2,
               "items": [
                  {
                     "type": "integer"
                  },
                  {
                     "type": "integer"
                  }
               ]
            },
            "symmetry_group2": {
               "title": "Symmetry Group2",
               "description": "The symmetry group of the second torsion, used to deduplicate torsions.",
               "type": "array",
               "minItems": 2,
               "maxItems": 2,
               "items": [
                  {
                     "type": "integer"
                  },
                  {
                     "type": "integer"
                  }
               ]
            }
         },
         "required": [
            "torsion1",
            "symmetry_group1",
            "torsion2",
            "symmetry_group2"
         ]
      },
      "ImproperTorsion": {
         "title": "ImproperTorsion",
         "description": "A class to keep track of improper torsions being scanned.",
         "type": "object",
         "properties": {
            "central_atom": {
               "title": "Central Atom",
               "description": "The index of the central atom of an improper torsion.",
               "type": "integer"
            },
            "improper": {
               "title": "Improper",
               "description": "The tuple of the atoms in the improper torsion.",
               "type": "array",
               "minItems": 4,
               "maxItems": 4,
               "items": [
                  {
                     "type": "integer"
                  },
                  {
                     "type": "integer"
                  },
                  {
                     "type": "integer"
                  },
                  {
                     "type": "integer"
                  }
               ]
            },
            "scan_range": {
               "title": "Scan Range",
               "description": "The scan range of the improper dihedral which should normally be limited.",
               "type": "array",
               "minItems": 2,
               "maxItems": 2,
               "items": [
                  {
                     "type": "integer"
                  },
                  {
                     "type": "integer"
                  }
               ]
            },
            "scan_increment": {
               "title": "Scan Increment",
               "description": "The value in degrees between each grid point in the scan.",
               "default": [
                  15
               ],
               "type": "array",
               "items": {
                  "type": "integer"
               }
            },
            "symmetry_group": {
               "title": "Symmetry Group",
               "description": "The symmetry group of the improper used to deduplicate improper torsions.",
               "type": "array",
               "minItems": 4,
               "maxItems": 4,
               "items": [
                  {
                     "type": "integer"
                  },
                  {
                     "type": "integer"
                  },
                  {
                     "type": "integer"
                  },
                  {
                     "type": "integer"
                  }
               ]
            }
         },
         "required": [
            "central_atom",
            "improper",
            "symmetry_group"
         ]
      }
   }
}

Config

allow_mutation: bool = True
arbitrary_types_allowed: bool = True
json_encoders: dict = {<class ‘numpy.ndarray’>: <function DatasetConfig.Config.<lambda> at 0x7f458c1c88b0>, <enum ‘Enum’>: <function DatasetConfig.Config.<lambda> at 0x7f458c1c8940>}
validate_assignment: bool = True

Fields

double_torsions (Dict[Tuple[Tuple[int, int], Tuple[int, int]], openff.qcsubmit.workflow_components.utils.DoubleTorsion])
impropers (Dict[int, openff.qcsubmit.workflow_components.utils.ImproperTorsion])
torsions (Dict[Tuple[int, int], openff.qcsubmit.workflow_components.utils.SingleTorsion])

field torsions: Dict[Tuple[int, int], openff.qcsubmit.workflow_components.utils.SingleTorsion] = {}: A dictionary of the torsions to be scanned grouped by the central bond in the torsion.

field double_torsions: Dict[Tuple[Tuple[int, int], Tuple[int, int]], openff.qcsubmit.workflow_components.utils.DoubleTorsion] = {}: A dictionary of the 2D torsions to be scanned grouped by the sorted combination of the central bonds.

field impropers: Dict[int, openff.qcsubmit.workflow_components.utils.ImproperTorsion] = {}: A dictionary of the improper torsions to be scanned grouped by the central atom in the torsion.

property get_dihedrals: List[Union[openff.qcsubmit.workflow_components.utils.SingleTorsion, openff.qcsubmit.workflow_components.utils.DoubleTorsion, openff.qcsubmit.workflow_components.utils.ImproperTorsion]]: Return a list of all of the dihedrals tagged making it easy to loop over.

property torsion_groups: List[Tuple[int, int]]: Return a list of all of the currently covered torsion symmetry groups. Note this only includes central bond atoms.

property double_torsion_groups: List[Tuple[Tuple[int, int], Tuple[int, int]]]: Return a list of all of the currently covered pairs of torsion symmetry groups.

property improper_groups: List[Tuple[int, int, int, int]]: Return a list of all of the currently covered improper torsion symmetry groups.

add_torsion(torsion, symmetry_group, scan_range=None, scan_increment=[15], overwrite=False)[source]

Add a single torsion to the torsion indexer if this central bond has not already been tagged and the torsion is symmetry unique.

Parameters

torsion (Tuple[int, int, int, int]) –
symmetry_group (Tuple[int, int]) –
scan_range (Optional[Tuple[int, int]]) –
scan_increment (List[int]) –
overwrite (bool) –

Return type

None

add_double_torsion(torsion1, torsion2, symmetry_group1, symmetry_group2, scan_range1=None, scan_range2=None, scan_increment=[15, 15], overwrite=False)[source]

Add a double torsion to the indexer if this central bond combination has not been tagged and the torsion pair are symmetry unique.

Parameters

torsion1 (Tuple[int, int, int, int]) –
torsion2 (Tuple[int, int, int, int]) –
symmetry_group1 (Tuple[int, int]) –
symmetry_group2 (Tuple[int, int]) –
scan_range1 (Optional[Tuple[int, int]]) –
scan_range2 (Optional[Tuple[int, int]]) –
scan_increment (List[int]) –
overwrite (bool) –

Return type

None

add_improper(central_atom, improper, symmetry_group, scan_range=None, scan_increment=[15], overwrite=False)[source]

Add an improper torsion to the indexer if its central atom is not already covered and the improper is symmetry unique.

Parameters

central_atom (int) –
improper (Tuple[int, int, int, int]) –
symmetry_group (Tuple[int, int, int, int]) –
scan_range (Optional[Tuple[int, int]]) –
scan_increment (List[int]) –
overwrite (bool) –

Return type

None

update(torsion_indexer, reorder_mapping=None)[source]

Update the current torsion indexer with another.

Parameters

torsion_indexer (openff.qcsubmit.workflow_components.utils.TorsionIndexer) – The other torsionindxer that should be used to update the current object.
reorder_mapping (Optional[Dict[int, int]]) – The mapping between the other and current molecule should the order need updating.

Return type

None

property n_torsions: int: Return the number of torsions highlighted.

property n_double_torsions: int: Return the number of double torsions highlighted.

property n_impropers: int: Return the number of imporpers highlighted.