OpenFF QCSubmit documentation

ScanEnumerator

pydantic model openff.qcsubmit.workflow_components.ScanEnumerator

This module will tag any matching substructures for scanning, useful for torsiondrive datasets.

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{
   "title": "ScanEnumerator",
   "description": "This module will tag any matching substructures for scanning, useful for torsiondrive datasets.",
   "type": "object",
   "properties": {
      "type": {
         "title": "Type",
         "default": "ScanEnumerator",
         "enum": [
            "ScanEnumerator"
         ],
         "type": "string"
      },
      "torsion_scans": {
         "title": "Torsion Scans",
         "description": "A list of scan objects which describes the scan range and scan incrementthat should be used with the associated smarts pattern.",
         "default": [],
         "type": "array",
         "items": {
            "$ref": "#/definitions/Scan1D"
         }
      },
      "double_torsion_scans": {
         "title": "Double Torsion Scans",
         "description": "A list of double scan objects which describes the scan ranges and scan increments,that should be used with each of the smarts patterns.",
         "default": [],
         "type": "array",
         "items": {
            "$ref": "#/definitions/Scan2D"
         }
      },
      "improper_scans": {
         "title": "Improper Scans",
         "description": "A list of improper scan objects which describes the scan range and scan incrementthat should be used with the smarts pattern.",
         "default": [],
         "type": "array",
         "items": {
            "$ref": "#/definitions/ImproperScan"
         }
      }
   },
   "definitions": {
      "Scan1D": {
         "title": "Scan1D",
         "description": "A class to hold information on 1D scans to be computed.",
         "type": "object",
         "properties": {
            "smarts1": {
               "title": "Smarts1",
               "description": "The numerically tagged SMARTs pattern used to select the torsion.",
               "type": "string"
            },
            "scan_range1": {
               "title": "Scan Range1",
               "description": "The scan range that should be given to this torsion drive.",
               "type": "array",
               "minItems": 2,
               "maxItems": 2,
               "items": [
                  {
                     "type": "integer"
                  },
                  {
                     "type": "integer"
                  }
               ]
            },
            "scan_increment": {
               "title": "Scan Increment",
               "description": "The angle in degrees between each grid point in the scan.",
               "default": 15,
               "type": "array",
               "items": {
                  "type": "integer"
               }
            }
         },
         "required": [
            "smarts1"
         ]
      },
      "Scan2D": {
         "title": "Scan2D",
         "description": "A class to hold information on 2D scans to be computed.",
         "type": "object",
         "properties": {
            "smarts1": {
               "title": "Smarts1",
               "description": "The numerically tagged SMARTs pattern used to select the torsion.",
               "type": "string"
            },
            "scan_range1": {
               "title": "Scan Range1",
               "description": "The scan range that should be given to this 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"
               }
            },
            "smarts2": {
               "title": "Smarts2",
               "description": "The second numerically tagged SMARTs pattern used to select a torsion.",
               "type": "string"
            },
            "scan_range2": {
               "title": "Scan Range2",
               "description": "The scan range which should be given to the second torsion drive.",
               "type": "array",
               "minItems": 2,
               "maxItems": 2,
               "items": [
                  {
                     "type": "integer"
                  },
                  {
                     "type": "integer"
                  }
               ]
            }
         },
         "required": [
            "smarts1",
            "smarts2"
         ]
      },
      "ImproperScan": {
         "title": "ImproperScan",
         "description": "A class to hold information on Improper scans to be computed.",
         "type": "object",
         "properties": {
            "smarts": {
               "title": "Smarts",
               "description": "The numerically tagged SMARTs pattern used to select the improper torsion.",
               "type": "string"
            },
            "central_smarts": {
               "title": "Central Smarts",
               "description": "The numerically tagged SMARTSs pattern used to select the centralof the improper torsion.",
               "type": "string"
            },
            "scan_range": {
               "title": "Scan Range",
               "description": "The scan range which should be used for the improper.",
               "type": "array",
               "minItems": 2,
               "maxItems": 2,
               "items": [
                  {
                     "type": "integer"
                  },
                  {
                     "type": "integer"
                  }
               ]
            },
            "scan_increment": {
               "title": "Scan Increment",
               "description": "The angle in degrees between each grid point in the scan.",
               "default": 15,
               "type": "array",
               "items": {
                  "type": "integer"
               }
            }
         },
         "required": [
            "smarts",
            "central_smarts"
         ]
      }
   }
}

Config

• allow_mutation: bool = True

• validate_assignment: bool = True

Fields

• double_torsion_scans (List[openff.qcsubmit.workflow_components.utils.Scan2D])

• improper_scans (List[openff.qcsubmit.workflow_components.utils.ImproperScan])

• torsion_scans (List[openff.qcsubmit.workflow_components.utils.Scan1D])

• type (Literal['ScanEnumerator'])

field type: Literal['ScanEnumerator'] = 'ScanEnumerator'

field torsion_scans: List[openff.qcsubmit.workflow_components.utils.Scan1D] = []

A list of scan objects which describes the scan range and scan incrementthat should be used with the associated smarts pattern.

field double_torsion_scans: List[openff.qcsubmit.workflow_components.utils.Scan2D] = []

A list of double scan objects which describes the scan ranges and scan increments,that should be used with each of the smarts patterns.

field improper_scans: List[openff.qcsubmit.workflow_components.utils.ImproperScan] = []

A list of improper scan objects which describes the scan range and scan incrementthat should be used with the smarts pattern.

classmethod description()

Returns a friendly description of the workflow component.

Return type

str

classmethod fail_reason()

Returns a friendly description of why a molecule would fail to pass the component.

Return type

str

classmethod properties()

Returns the runtime properties of the component such as parallel safe.

Return type

openff.qcsubmit.common_structures.ComponentProperties

add_torsion_scan(smarts, scan_rage=None, scan_increment=15)

Add a targeted 1D torsion scan to the scan enumerator.

Parameters

• smarts (str) – The numerically tagged SMARTs pattern that should be used to identify the torsion atoms.

• scan_rage (Optional[Tuple[int, int]]) – The angle in degrees the torsion should be scanned between, from low to high

• scan_increment (int) – The value in degrees between each grid point in the scan.

Return type

None

add_double_torsion(smarts1, smarts2, scan_range1=None, scan_range2=None, scan_increments=(15, 15))

Add a targeted 2D torsion scan to the scan enumerator.

Parameters

• smarts1 (str) – The numerically tagged SMARTs pattern that should be used to identify the first torsion atoms.

• smarts2 (str) – The numerically tagged SMARTs pattern that should be used to identify the second torsion atoms.

• scan_range1 (Optional[Tuple[int, int]]) – The angle in degrees the first torsion should be scanned between, from low to high

• scan_range2 (Optional[Tuple[int, int]]) – The angle in degrees the second torsion should be scanned between, from low to high

• scan_increments (List[int]) – A list of the values in degrees between each grid point in the scans.

Return type

None

add_improper_torsion(smarts, central_smarts, scan_range=None, scan_increment=15)

Add a targeted Improper torsion to the scan enumerator.

Parameters

• smarts (str) – The numerically tagged SMARTs pattern which describes the entire improper.

• central_smarts (str) – The numerically tagged SMARTs pattern which identifies the central atom in the improper.

• scan_range (Optional[Tuple[int, int]]) – The angles in degrees the improper should be scanned between, from low to high.

• scan_increment (int) – The value in degrees between each grid point in the scan.

Return type

None