Computational data (Views)¶

The models that these views work on can be found in Computational data (Models)

Where the views are used (frontend)¶

Note: For the Diamond instance of fragalysis, authentication is handled by api.security.ISpyBSafeQuerySet, a version of the standard DRF (see RESTful API (Views)) viewsets.ReadOnlyModelViewSet.

viewer.views.ComputedSetView: This view is used to generate a list of all of the computed sets that exist for a specific target, so that the drop-down list for the third tab on the right-hand side (RHS) can be generated for each target-specific page
viewer.views.ComputedMolAndScoreView: This view is used to get all information about 3D molecules in a given computed set for a given target (computed sets obtained from viewer.views.ComputedSetView). The smiles string is used to generate the 2D image shown on each molecule in the RHS computed set tab using viewer.views.img_from_smiles. The scores for each molecule are displayed on the respective molecule card.
viewer.views.cset_key: This view is used to generate a computed set upload key at <root>/viewer/cset_key , and email it to the user to allow them to upload new computed sets at <root>/viewer/upload_cset
viewer.views.UploadCSet: This view is used to generate the form found at <root>/viewer/upload_cset, and to pass the values to the celery tasks controlled through viewer.views.ValidateTaskView and viewer.views.UploadTaskView that validate and process the uploaded data, saving it into the relevant models (see Computational data (Models))so that the data can be displayed on the RHS of a target specific page.

Other views listed below are currently not in use by the front-end.

View details¶

class viewer.views.ComputedSetView(**kwargs)¶

DjagnoRF view to retrieve information about computed sets

url:: api/compound-sets

queryset:: viewer.models.ComputedSet.objects.filter()

filter fields:

viewer.models.ComputedSet.target - ?target=<int>

returns: JSON

name: name of the computed set
submitted_sdf: link to the uploaded sdf file
spec_version: version of the upload specification used to generate the computed set sdf
method_url: link to url describing the methodology used to create the computed set
unique_name: auto-generated human-readable name for the computed set
target: id for the associated target
submitter: id for the associated submitter

example output:

"results": [
    {
        "name": "100threehop2020-07-27S8vv3vx",
        "submitted_sdf": "http://fragalysis.diamond.ac.uk/media/code/media/compound_sets/Top_100_three_hop_2020-07-27_S8vv3vx.sdf",
        "spec_version": 1.2,
        "method_url": "https://github.com/Waztom/xchem-xCOS",
        "unique_name": "WT-xCOS2-ThreeHop",
        "target": 62,
        "submitter": 13
    },]

serializer_class¶: alias of viewer.serializers.ComputedSetSerializer

class viewer.views.ComputedMoleculesView(**kwargs)¶

DjagnoRF view to retrieve information about computed molecules - 3D info

url:: api/compound-molecules

queryset:: viewer.models.ComputedMolecule.objects.filter()

filter fields:

viewer.models.ComputedMolecule.computed_set - ?computed_set=<int>

returns: JSON

id: id of the molecule
sdf_info: 3D coordinates of the molecule in MDL format
name: a name for the molecule
smiles: SMILES string
pdb_info: link to the associated pdb file (apo)
compound: id for the associated 2D compound
computed_set: name for the associated computed set
computed_inspirations: list of ids for the inspirations used in the design/computation of the molecule

example output:

"results": [
    {
        "id": 1997,
        "sdf_info": "FRA-DIA-8640f307-1    RDKit          3D 38 42  0  0  0  0  0  0  0  0999 V2000..."
        "name": "FRA-DIA-8640f307-1",
        "smiles": "CC(=O)NCCc1c[nH]c2c([C@H](CN(Cc3cc(C)on3)C(=O)NC3CC3)c3nnc(C)s3)cc(F)cc12",
        "pdb_info": "http://fragalysis.diamond.ac.uk/media/pdbs/Fragmenstein_J6Sfvrs.pdb",
        "compound": 4030,
        "computed_set": "100XCOS2Teo2020-07-23yuZJZFY",
        "computed_inspirations": []
    },]

serializer_class¶: alias of viewer.serializers.ComputedMoleculeSerializer

class viewer.views.NumericalScoresView(**kwargs)¶

DjagnoRF view to retrieve information about numerical computed molecule scores

url:: api/numerical-scores

queryset:: viewer.models.NumericalScoreValues.objects.filter()

filter fields:

viewer.models.NumericalScoreValues.compound - ?compound=<int>
viewer.models.NumericalScoreValues.score - ?score=<int>

returns: JSON

id: id of the score
score: dict of the score info:
- id: id of the score description
- name: name of the score
- description: description of the score
- computed_set: name of the computed set that the score is associated to
value: numerical value of the score
compound: id of the associated compound object

example output:

"results": [
    "results": [
        {
            "id": 8145,
            "score": {
                "id": 48,
                "name": "Score_1",
                "description": "The score is scaled by the number of bit atoms",
                "computed_set": "100XCOS2Teo2020-07-23yuZJZFY"
            },
            "value": 19.8653,
            "compound": 1997
        },

serializer_class¶: alias of viewer.serializers.NumericalScoreSerializer

class viewer.views.TextScoresView(**kwargs)¶

DjagnoRF view to retrieve information about text computed molecule scores

url:: api/text-scores

queryset:: viewer.models.TextScoreValues.objects.filter()

filter fields:

viewer.models.TextScoreValues.compound - ?compound=<int>
viewer.models.TextScoreValues.score - ?score=<int>

returns: JSON

id: id of the score
score: dict of the score info:
- id: id of the score description
- name: name of the score
- description: description of the score
- computed_set: name of the computed set that the score is associated to
value: text value of the score
compound: id of the associated compound object

example output:

"results": [
    "results": [
        {
            "id": 8145,
            "score": {
                "id": 48,
                "name": "Score_1",
                "description": "Desctription",
                "computed_set": "100XCOS2Teo2020-07-23yuZJZFY"
            },
            "value": "Yes",
            "compound": 1997
        },

serializer_class¶: alias of viewer.serializers.TextScoreSerializer

class viewer.views.CompoundScoresView(**kwargs)¶

DjagnoRF view to retrieve descriptions of scores for a given name or computed set

url:: api/compound-scores

queryset:: viewer.models.ScoreDescription.objects.filter()

filter fields:

viewer.models.ScoreDescription.computed_set - ?computed_set=<int>
viewer.models..ScoreDescription.name - ?name=<str>

returns: JSON

id: id of the score
score: dict of the score info:
- id: id of the score description
- name: name of the score
- description: description of the score
- computed_set: name of the computed set that the score is associated to

example output:

"results": [
    {
        "id": 22,
        "name": "FeatureSteinScore",
        "description": "FeatureStein Score",
        "computed_set": "top26062020axX6Vqt"
    },]

serializer_class¶: alias of viewer.serializers.ScoreDescriptionSerializer

class viewer.views.ComputedMolAndScoreView(**kwargs)¶

DjagnoRF view to retrieve all information about molecules from a computed set, along with all of their scores

url:: api/compound-mols-scores

queryset:: viewer.models.ComputedMolecule.objects.filter()

filter fields:

viewer.models.ComputedMolecule.computed_set - ?computed_set=<int>

returns: JSON

id: id of the molecule
sdf_info: 3D coordinates of the molecule in MDL format
name: a name for the molecule
smiles: SMILES string
pdb_info: link to the associated pdb file (apo)
compound: id for the associated 2D compound
computed_set: name for the associated computed set
computed_inspirations: list of ids for the inspirations used in the design/computation of the molecule
numerical_scores: dict of numerical scores, where each key is a score name, and each value is the associated score
text_scores: dict of text scores, where each key is a score name, and each value is the associated score

example output:

"results": [
    {
        "id": 1997,
        "sdf_info": "FRA-DIA-8640f307-1     RDKit          3D 38 42  0  0  0  0  0  0  0"
        "name": "FRA-DIA-8640f307-1",
        "smiles": "CC(=O)NCCc1c[nH]c2c([C@H](CN(Cc3cc(C)on3)C(=O)NC3CC3)c3nnc(C)s3)cc(F)cc12",
        "pdb_info": "http://fragalysis.diamond.ac.uk/media/pdbs/Fragmenstein_J6Sfvrs.pdb",
        "compound": 4030,
        "computed_set": "100XCOS2Teo2020-07-23yuZJZFY",
        "computed_inspirations": [],
        "numerical_scores": {
            "Score_1": 19.8653,
            "N_hits": 4.0
        },
        "text_scores": {}
    },]

serializer_class¶: alias of viewer.serializers.ComputedMolAndScoreSerializer

class viewer.views.cset_key(request)¶

View to render and control viewer/generate-key.html - a page allowing an upload key to be generated for a user allowing upload of computed sets

allowed requests:

GET: renders form
POST: generates an upload key, emails it to the user, and informs the user that this will happen

url:: viewer/cset_key

template:: viewer/generate-key.html

request params:

contact_email (django.forms.FormField): user contact email

context:

form (django.Forms.form): instance of viewer.forms.UploadKeyForm
message (str): A message rendered in the template. Informs the user that their upload key will be emailed

class viewer.views.UploadCSet(**kwargs)¶

View to render and control viewer/upload-cset.html - a page allowing upload of computed sets. Validation and upload tasks are defined in viewer.compound_set_upload, viewer.sdf_check and viewer.tasks and the task response handling is done by viewer.views.ValidateTaskView and viewer.views.UploadTaskView

allowed requests:

GET: renders form
POST: validates and optionally uploads the computed set that the user provides via the template form

url:: viewer/upload_cset

template:: viewer/upload-cset.html

request params:

target_name (django.forms.CharField): Name of the existing fragalysis target to add the computed set to
sdf_file (django.forms.FileField): SDF file of all computed molecules to upload for the computed set
pdb_zip (django.forms.FileField): zip file of apo pdb files referenced in the ref_pdb field for molecules in sdf_file (optional)
submit_choice (django.forms.CharField): 0 to validate, 1 to validate and upload
upload_key (django.forms.CharField): users unique upload key, generated by viewer.views.cset_key

context:

form (django.Forms.form): instance of viewer.forms.CSetForm
validate_task_id (str): celery task id for validation step
validate_task_status (str): celery task status for validation step
upload_task_id (str): celery task id for upload step
upload_task_status (str): celery task status for upload step

class viewer.views.ValidateTaskView(**kwargs)¶

View to handle dynamic loading of validation results from viewer.tasks.validate - the validation of files uploaded to viewer/upload_cset

allowed requests:

GET: takes a task id, checks it’s status and returns the status, and result if the task is complete

url:: validate_task/<validate_task_id>

template:: viewer/upload-cset.html

get(request, validate_task_id)¶

Get method for ValidateTaskView. Takes a validate task id, checks it’s status and returns the status, and result if the task is complete

Parameters

request (request) – Context sent by UploadCSet
validate_task_id (str) – task id provided by UploadCSet

Returns

response_data –

response data (dict) in JSON format:

if status = ‘RUNNING’:
- validate_task_status (str): task.status
- validate_task_id (str): task.id
if status = ‘FAILURE’:
- validate_task_status (str): task.status
- validate_task_id (str): task.id
- validate_traceback (str): task.traceback
if status = ‘SUCCESS’:
- validate_task_status (str): task.status
- validate_task_id (str): task.id
- html (str): html of task outcome - success message or html table of errors & fail message

Return type

JSON

class viewer.views.UploadTaskView(**kwargs)¶

View to handle dynamic loading of upload results from viewer.tasks.process_compound_set - the upload of files for a computed set by a user at viewer/upload_cset

allowed requests:

GET: takes a task id, checks it’s status and returns the status, and result if the task is complete

url:: upload_task/<uploads_task_id>

template:: viewer/upload-cset.html

get(request, upload_task_id)¶

Get method for UploadTaskView. Takes an upload task id, checks it’s status and returns the status, and result if the task is complete

Parameters

request (request) – Context sent by UploadCSet
upload_task_id (str) – task id provided by UploadCSet

Returns

response_data –

response data (dict) in JSON format:

if status = ‘RUNNING’:
- upload_task_status (str): task.status
- upload_task_id (str): task.id
if status = ‘FAILURE’:
- upload_task_status (str): task.status
- upload_task_id (str): task.id
- upload_traceback (str): task.traceback
if status = ‘SUCCESS’:
- upload_task_status (str): task.status
- upload_task_id (str): task.id
- if results are a list (data was not validated):
  
  validated (str): ‘Not validated’
  
  html (str): html table of validation errors
- if results are a string (data was validated and uploaded:
  
  validated (str): ‘Validated’
  
  results (dict): results
  
  results[‘cset_download_url’] (str): download url for computed set sdf file
  
  results[‘pset_download_url’] (str): download url for computed set pdb files (zip)
- if results are not string or list:
  
  processed (str): ‘None’
  
  html (str): message to tell the user their data was not processed

Return type

JSON

class viewer.views.cset_download(request, name)¶

View to download an SDF file of a computed set by name

allowed requests:

GET: return the SDF file as a download

url:: viewer/compound_set/(<name>)

request params:

name (str): the name of the computed set to download

Returns

<name>.sdf: sdf file for the computed set

Return type

Response (attachment; text/plain)

class viewer.views.pset_download(request, name)¶

View to download a zip file of all protein structures (apo) for a computed set

allowed requests:

GET: return the zip file as a download

url:: viewer/compound_set/(<name>)

request params:

name (str): the name of the computed set to download

Returns

<name>.zip: zip file for the computed set

Return type

Response (attachment; application/zip)

Computational data (Views)¶

Where the views are used (frontend)¶

View details¶

Fragalysis-Backend

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