adjusted migration

Initial bayer app

Show Pack Classification

Adjusted docker compose to bayer specifics

Adjusted Dockerfile for Bayer

Adding secret flags to group, add secret pools to packages

Adjusted View for Package creation

Prep configs, added Package Create Modal

wip

More on PES

wip

wip

Wip

minor

PW interactions

API PES

wip

Make Select Widget reflect required

make required generallay available

Update UI if pathway mode is set to build

Added ais

circle adjustments

Initial Zoom, fix AD Creation

wip

auth log, bb4g fix

missing import

Added viz hint if PES is part of reaction

Add Edge check for pes

flip boolean

...

pes

Added extra

...

In / Out Edges Viz, Submitting Button Text

...

.pre-commit-config.yaml

@@ -7,10 +7,10 @@ repos:
       - id: trailing-whitespace
         exclude: epiuclid/schemas/
       - id: end-of-file-fixer
-        exclude: ^epiuclid/schemas/|^static/js/ketcher3/
+        exclude: epiuclid/schemas/
       - id: check-yaml
       - id: check-added-large-files
-        exclude: ^static/images/|^epiuclid/schemas/|^fixtures/|^static/js/ketcher3/
+        exclude: ^static/images/|^epiuclid/schemas/|^fixtures/
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.13.3

bayer/models.py

@@ -185,7 +185,7 @@ class PESStructure(CompoundStructure):
     def create(
             compound: Compound,
             pes_link: str,
-            molfile: str,
+            mol_file: str,
             smiles: str,
             name: str = None,
             description: str = None,
@@ -204,7 +204,7 @@ class PESStructure(CompoundStructure):
             cs.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
 
         cs.smiles = smiles
-        cs.molfile = molfile
+        cs.mol_file = mol_file
         cs.pes_link = pes_link
         cs.compound = compound
 

bayer/templates/objects/compound_structure_viz.html

@@ -3,11 +3,7 @@
   <div class="collapse-arrow bg-base-200 collapse">
     <input type="checkbox" checked />
     <div class="collapse-title text-xl font-medium">Link to PES</div>
-    <div class="collapse-content">
-      <p>
-        <a href="{{ compound_structure.pes_link }}" class="hover:bg-base-200">{{ compound_structure.pes_link }}</a>
-      </p>
-    </div>
+    <div class="collapse-content">{{ compound_structure.pes_link }}</div>
   </div>
 
   <!-- Image Representation -->

bayer/templates/objects/compound_viz.html

@@ -3,11 +3,7 @@
   <div class="collapse-arrow bg-base-200 collapse">
     <input type="checkbox" checked />
     <div class="collapse-title text-xl font-medium">Link to PES</div>
-    <div class="collapse-content">
-      <p>
-        <a href="{{ compound.default_structure.pes_link }}" class="hover:bg-base-200">{{ compound.default_structure.pes_link }}</a>
-      </p>
-    </div>
+    <div class="collapse-content">{{ compound.default_structure.pes_link }}</div>
   </div>
 
   <!-- Image Representation -->

bayer/templates/objects/node_viz.html

@@ -3,11 +3,7 @@
   <div class="collapse-arrow bg-base-200 collapse">
     <input type="checkbox" checked />
     <div class="collapse-title text-xl font-medium">Link to PES</div>
-    <div class="collapse-content">
-      <p>
-        <a href="{{ node.default_node_label.pes_link }}" class="hover:bg-base-200">{{ node.default_node_label.pes_link }}</a>
-      </p>
-    </div>
+    <div class="collapse-content">{{ node.default_node_label.pes_link }}</div>
   </div>
 
   <!-- Image Representation -->

bayer/templates/objects/package.html

@@ -4,7 +4,6 @@
 
   {% block action_modals %}
     {% include "modals/objects/edit_package_modal.html" %}
-    {% include "modals/objects/view_package_permissions_modal.html" %}
     {% include "modals/objects/edit_package_permissions_modal.html" %}
     {% include "modals/objects/publish_package_modal.html" %}
     {% include "modals/objects/set_license_modal.html" %}

bayer/views.py

@@ -1,23 +1,20 @@
 import base64
-import logging
 
 import requests
 from django.conf import settings as s
-from django.http import HttpResponse, HttpResponseBadRequest, HttpResponseNotAllowed
+from django.core.exceptions import BadRequest
+from django.http import HttpResponse
 from django.shortcuts import redirect
 
 from bayer.models import PESCompound
 from epdb.logic import PackageManager
 from epdb.models import Pathway, Node
-from epdb.views import _anonymous_or_real, error
+from epdb.views import _anonymous_or_real
 from utilities.decorators import package_permission_required
 
 Package = s.GET_PACKAGE_MODEL()
 
 
-logger = logging.getLogger(__name__)
-
-
 @package_permission_required()
 def create_pes(request, package_uuid):
     current_user = _anonymous_or_real(request)
@@ -26,11 +23,7 @@ def create_pes(request, package_uuid):
     if request.method == "POST":
 
         if current_package.classification_level == Package.Classification.INTERNAL:
-            return error(
-                request,
-                f'Creation of PESs for package {current_package.name} failed!',
-                "Creating PESs for internal packages is not allowed.",
-            )
+            raise BadRequest("Cannot create PESs for internal packages.")
 
         compound_name = request.POST.get('compound-name')
         compound_description = request.POST.get('compound-description')
@@ -40,41 +33,27 @@ def create_pes(request, package_uuid):
             try:
                 pes_data = fetch_pes(request, pes_link)
             except ValueError as e:
-                return error(
-                    request,
-                    "Could not fetch PES",
-                    f"Could not fetch PES data for {pes_link}"
-                )
+                return BadRequest(f"Could not fetch PES data for {pes_link}")
 
             classification = pes_data.get("classificationLevel", "")
             if "secret" == classification.lower():
 
                 if current_package.classification_level != Package.Classification.SECRET:
-                    return error(
-                        request,
-                        "Classification Mismatch!",
-                        "Cannot create secret PESs in non-secret packages."
-                    )
+                    return BadRequest("Cannot create PESs for non-secret packages.")
 
-                if not current_package.data_pool or not current_package.data_pool.secret:
-                    logger.info(f"The current package does not have a secret data pool.")
-                    return error(
-                        request,
-                        "The current package does not have a secret data pool.",
-                        "Cannot create secret PESs in package without a secret data pool."
-                    )
+                data_pools = pes_data.get("dataPools")
+                if data_pools:
+                    if s.DATA_POOL_MAPPING[current_package.data_pool.name] not in data_pools:
+                        return BadRequest(
+                            f"PES data pool {s.DATA_POOL_MAPPING[current_package.data_pool.name]} not found in PES data")
 
             pes = PESCompound.create(current_package, pes_data, compound_name, compound_description)
 
             return redirect(pes.url)
         else:
-            return error(
-                request,
-                "No PES link received",
-                "Please provide a PES link."
-            )
+            return BadRequest("Please provide a PES link.")
     else:
-        return HttpResponseNotAllowed(["POST"])
+        pass
 
 
 @package_permission_required()
@@ -86,11 +65,7 @@ def create_pes_node(request, package_uuid, pathway_uuid):
     if request.method == "POST":
 
         if current_package.classification_level == Package.Classification.INTERNAL:
-            return error(
-                request,
-                f'Creation of PESs for package {current_package.name} failed!',
-                "Creating PESs for internal packages is not allowed.",
-            )
+            raise BadRequest("Cannot create PESs for internal packages.")
 
         compound_name = request.POST.get('compound-name')
         compound_description = request.POST.get('compound-description')
@@ -100,37 +75,23 @@ def create_pes_node(request, package_uuid, pathway_uuid):
             try:
                 pes_data = fetch_pes(request, pes_link)
             except ValueError as e:
-                return error(
-                    request,
-                    "Could not fetch PES",
-                    f"Could not fetch PES data for {pes_link}"
-                )
+                return BadRequest(f"Could not fetch PES data for {pes_link}")
 
             classification = pes_data.get("classificationLevel", "")
             if "secret" == classification.lower():
 
                 if current_package.classification_level != Package.Classification.SECRET:
-                    return error(
-                        request,
-                        "Classification Mismatch!",
-                        "Cannot create secret PESs in non-secret packages."
-                    )
+                    return BadRequest("Cannot create PESs for non-secret packages.")
 
-                if not current_package.data_pool or not current_package.data_pool.secret:
-                    logger.info(f"The current package does not have a secret data pool.")
-                    return error(
-                        request,
-                        "The current package does not have a secret data pool.",
-                        "Cannot create secret PESs in package without a secret data pool."
-                    )
+                data_pools = pes_data.get("dataPools")
+                if data_pools:
+                    if s.DATA_POOL_MAPPING[current_package.data_pool.name] not in data_pools:
+                        return BadRequest(
+                            f"PES data pool {s.DATA_POOL_MAPPING[current_package.data_pool.name]} not found in PES data")
 
             pes = PESCompound.create(current_package, pes_data, compound_name, compound_description)
 
-            node_qs = Node.objects.filter(
-                pathway=current_pathway,
-                default_node_label=pes.default_structure
-            )
-
+            node_qs = Node.objects.filter(pathway=current_pathway, default_node_label=pes.default_structure)
             if node_qs.exists():
                 return redirect(current_pathway.url)
 
@@ -148,13 +109,9 @@ def create_pes_node(request, package_uuid, pathway_uuid):
             return redirect(current_pathway.url)
 
         else:
-            return error(
-                request,
-                "No PES link received",
-                "Please provide a PES link."
-            )
+            return BadRequest("Please provide a PES link.")
     else:
-        return HttpResponseNotAllowed(["POST"])
+        pass
 
 
 def fetch_pes(request, pes_url) -> dict:

epapi/tests/v1/test_api_permissions.py

@@ -117,28 +117,25 @@ class APIPermissionTestBase(TestCase):
 
         # Create test compounds in each package
         cls.reviewed_compound = Compound.create(
-            cls.reviewed_package, "C", name="Reviewed Compound", description="Test compound"
+            cls.reviewed_package, "C", "Reviewed Compound", "Test compound"
         )
         cls.owned_compound = Compound.create(
-            cls.unreviewed_package_owned, "CC", name="Owned Compound", description="Test compound"
+            cls.unreviewed_package_owned, "CC", "Owned Compound", "Test compound"
         )
         cls.read_compound = Compound.create(
-            cls.unreviewed_package_read, "CCC", name="Read Compound", description="Test compound"
+            cls.unreviewed_package_read, "CCC", "Read Compound", "Test compound"
         )
         cls.write_compound = Compound.create(
-            cls.unreviewed_package_write, "CCCC", name="Write Compound", description="Test compound"
+            cls.unreviewed_package_write, "CCCC", "Write Compound", "Test compound"
         )
         cls.all_compound = Compound.create(
-            cls.unreviewed_package_all, "CCCCC", name="All Compound", description="Test compound"
+            cls.unreviewed_package_all, "CCCCC", "All Compound", "Test compound"
         )
         cls.no_access_compound = Compound.create(
-            cls.unreviewed_package_no_access,
-            "CCCCCC",
-            name="No Access Compound",
-            description="Test compound",
+            cls.unreviewed_package_no_access, "CCCCCC", "No Access Compound", "Test compound"
         )
         cls.group_compound = Compound.create(
-            cls.group_package, "CCCCCCC", name="Group Compound", description="Test compound"
+            cls.group_package, "CCCCCCC", "Group Compound", "Test compound"
         )
 
 

epapi/tests/v1/test_contract_get_entities.py

@@ -294,8 +294,8 @@ class CompoundPaginationAPITest(BaseTestAPIGetPaginated, TestCase):
         return Compound.create(
             package,
             smiles,
-            name=f"Reviewed Compound {idx:03d}",
-            description="Compound for pagination tests",
+            f"Reviewed Compound {idx:03d}",
+            "Compound for pagination tests",
         )
 
     @classmethod
@@ -305,8 +305,8 @@ class CompoundPaginationAPITest(BaseTestAPIGetPaginated, TestCase):
         return Compound.create(
             package,
             smiles,
-            name=f"Draft Compound {idx:03d}",
-            description="Compound for pagination tests",
+            f"Draft Compound {idx:03d}",
+            "Compound for pagination tests",
         )
 
 

epapi/v1/endpoints/additional_information.py

@@ -9,8 +9,8 @@ from envipy_additional_information import registry
 from envipy_additional_information.groups import GroupEnum
 from epapi.utils.schema_transformers import build_rjsf_output
 from epapi.utils.validation_errors import handle_validation_error
-from epdb.models import AdditionalInformation, Scenario, Node
-from ..dal import get_scenario_for_read, get_scenario_for_write, get_package_for_write
+from epdb.models import AdditionalInformation
+from ..dal import get_scenario_for_read, get_scenario_for_write
 
 logger = logging.getLogger(__name__)
 
@@ -58,61 +58,6 @@ def list_scenario_info(request, scenario_uuid: UUID):
     return result
 
 
-@router.post("/information/{model_name}/")
-def add_object_info(request, model_name: str, payload: Dict[str, Any] = Body(...)):
-    from epdb.views import EPDBURLParser
-
-    cls = registry.get_model(model_name.lower())
-    if not cls:
-        raise HttpError(404, f"Unknown model: {model_name}")
-
-    try:
-        instance = cls(**payload)  # Pydantic validates
-    except ValidationError as e:
-        handle_validation_error(e)
-
-    if "attach_obj_url" in payload:
-        url_parser = EPDBURLParser(payload["attach_obj_url"])
-
-        if url_parser.contains_package_url():
-            package = get_package_for_write(request.user, url_parser.get_objects()[0].uuid)
-            attach_obj = url_parser.get_object()
-
-            if "scenario_uuid" in payload:
-                scenario = get_scenario_for_read(request.user, payload["scenario_uuid"])
-            else:
-                scenario = Scenario.create(
-                    package,
-                    name=f"Scenario {Scenario.objects.filter(package=package).count() + 1}",
-                    description="no description",
-                    scenario_date=None,
-                    scenario_type=None,
-                    additional_information=[],
-                )
-
-            if isinstance(attach_obj, Node):
-                ai = add_info_to_node(package, instance, scenario, attach_obj)
-            else:
-                raise HttpError(404, f"Bad request - Not implemented for {type(attach_obj)}!")
-
-            return {"status": "created", "uuid": ai.uuid}
-
-    raise HttpError(404, "Bad request!")
-
-
-def add_info_to_node(package, add_inf, scenario, node):
-    ai = AdditionalInformation.create(
-        package,
-        add_inf,
-        scenario=scenario,
-        content_object=node,
-    )
-
-    node.pathway.scenarios.add(scenario)
-
-    return ai
-
-
 @router.post("/scenario/{uuid:scenario_uuid}/information/{model_name}/")
 def add_scenario_info(
     request, scenario_uuid: UUID, model_name: str, payload: Dict[str, Any] = Body(...)

epdb/exceptions.py

@@ -1,10 +1,2 @@
 class InvalidSMILESException(Exception):
     pass
-
-
-class InvalidMolfileException(Exception):
-    pass
-
-
-class PackageImportException(Exception):
-    pass

epdb/legacy_api.py

@@ -15,7 +15,6 @@ from ninja.security import HttpBearer
 
 from utilities.chem import FormatConverter
 from utilities.misc import PackageExporter
-
 from .logic import (
     EPDBURLParser,
     GroupManager,
@@ -634,14 +633,9 @@ class CompoundSchema(Schema):
     reviewStatus: str = Field(False, alias="review_status")
     scenarios: List["SimpleScenario"] = Field([], alias="scenarios")
     structures: List["CompoundStructureSchema"] = []
-    pesLink: str | None = Field(None, alias="pes_link")
 
     @staticmethod
-    def resolve_pes_link(obj: Compound):
-        return getattr(obj.default_structure, "pes_link", None)
-
-    @staticmethod
-    def resolve_review_status(obj: Compound):
+    def resolve_review_status(obj: CompoundStructure):
         return "reviewed" if obj.package.reviewed else "unreviewed"
 
     @staticmethod
@@ -715,7 +709,6 @@ class CompoundStructureSchema(Schema):
     reviewStatus: str = Field(None, alias="review_status")
     scenarios: List["SimpleScenario"] = Field([], alias="scenarios")
     smiles: str = Field(None, alias="smiles")
-    pesLink: str | None = Field(None, alias="pes_link")
 
     @staticmethod
     def resolve_review_status(obj: CompoundStructure):
@@ -851,7 +844,6 @@ def get_package_compound_structure(request, package_uuid, compound_uuid, structu
 
 class CreateCompound(Schema):
     compoundSmiles: str
-    compoundMolFile: str | None = None
     compoundName: str | None = None
     compoundDescription: str | None = None
     inchi: str | None = None
@@ -881,21 +873,17 @@ def create_package_compound(
             if "secret" == classification.lower():
 
                 if p.classification_level != Package.Classification.SECRET:
-                    return 400, {"message": "Cannot create secret PESs in non-secret packages."}
-
-                if not p.data_pool or not p.data_pool.secret:
-                    return 400, {"message": "Cannot create secret PESs in package without a secret data pool."}
+                    return 400, {"Cannot create PESs for non-secret packages."}
 
+                data_pools = pes_data.get("dataPools")
+                if data_pools:
+                    if s.DATA_POOL_MAPPING[p.data_pool.name] not in data_pools:
+                        return 400, { "messsage": f"PES data pool {s.DATA_POOL_MAPPING[p.data_pool.name]} not found in PES data"}
 
             c = PESCompound.create(p, pes_data, c.compoundName, c.compoundDescription)
         else:
             c = Compound.create(
-                p,
-                c.compoundSmiles,
-                molfile=c.compoundMolFile,
-                name=c.compoundName,
-                description=c.compoundDescription,
-                inchi=c.inchi
+                p, c.compoundSmiles, c.compoundName, c.compoundDescription, inchi=c.inchi
             )
         return redirect(c.url)
     except ValueError as e:
@@ -1704,10 +1692,9 @@ class PathwayNode(Schema):
     image: str = Field(None, alias="image")
     imageSize: int = Field(None, alias="image_size")
     name: str = Field(None, alias="name")
-    proposed: List[Dict[str, Any]] = []
+    proposed: List[Dict[str, str]] = Field([], alias="proposed_intermediate")
     smiles: str = Field(None, alias="smiles")
     pseudo: bool = Field(False, alias="pseudo")
-    pesLink: str | None = Field(None, alias="pes_link")
 
     @staticmethod
     def resolve_atom_count(obj: Node):
@@ -1720,10 +1707,24 @@ class PathwayNode(Schema):
         # TODO
         return []
 
+    @staticmethod
+    def resolve_engineered_intermediate(obj: Node):
+        # TODO
+        return False
+
+    @staticmethod
+    def resolve_image(obj: Node):
+        return f"{obj.default_node_label.url}?image=svg"
+
     @staticmethod
     def resolve_image_size(obj: Node):
         return 400
 
+    @staticmethod
+    def resolve_proposed_intermediate(obj: Node):
+        # TODO
+        return []
+
 
 class PathwaySchema(Schema):
     aliases: List[str] = Field([], alias="aliases")
@@ -1974,8 +1975,7 @@ def get_package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
 
 
 class CreateNode(Schema):
-    nodeAsSmiles: str | None = None
-    nodeAsMolFile: str | None = None
+    nodeAsSmiles: str
     nodeName: str | None = None
     nodeReason: str | None = None
     nodeDepth: str | None = None
@@ -2006,10 +2006,14 @@ def add_pathway_node(request, package_uuid, pathway_uuid, n: Form[CreateNode]):
             if "secret" == classification.lower():
 
                 if p.classification_level != Package.Classification.SECRET:
-                    return 400, {"message": "Cannot create secret PESs in non-secret packages."}
+                    return 400, "Cannot create PESs for non-secret packages."
 
-                if not p.data_pool or not p.data_pool.secret:
-                    return 400, {"message": "Cannot create secret PESs in package without a secret data pool."}
+                data_pools = pes_data.get("dataPools")
+                if data_pools:
+                    if s.DATA_POOL_MAPPING[p.data_pool.name] not in data_pools:
+                        return 400, {
+                            "messsage": f"PES data pool {s.DATA_POOL_MAPPING[p.data_pool.name]} not found in PES data"
+                        }
 
             c = PESCompound.create(p, pes_data, n.nodeName, n.nodeReason)
 
@@ -2033,14 +2037,7 @@ def add_pathway_node(request, package_uuid, pathway_uuid, n: Form[CreateNode]):
             else:
                 node_depth = -1
 
-            node = Node.create(
-                pw,
-                n.nodeAsSmiles,
-                node_depth,
-                molfile=n.nodeAsMolFile,
-                name=n.nodeName,
-                description=n.nodeReason,
-            )
+            node = Node.create(pw, n.nodeAsSmiles, node_depth, n.nodeName, n.nodeReason)
 
         return redirect(node.url)
     except ValueError:
@@ -2395,26 +2392,3 @@ def get_setting(request, setting_uuid):
         return 403, {
             "message": f"Getting Setting with id {setting_uuid} failed due to insufficient rights!"
         }
-
-
-########
-# Util #
-########
-class NonPersistent(Schema):
-    smiles: str
-    setting_url: str = Field(..., alias="settingUri")
-
-
-@router.post("/util", response={200: Any, 403: Error})
-def predict(request, np: Form[NonPersistent]):
-    try:
-        from epdb.logic import SPathway
-
-        setting = SettingManager.get_setting_by_url(request.user, np.setting_url)
-        spw = SPathway(prediction_setting=setting, root_nodes=[np.smiles])
-        spw.predict()
-        return spw.to_json()
-    except ValueError:
-        return 403, {
-            "message": f"Getting Setting with id {np.setting_url} failed due to insufficient rights!"
-        }

epdb/logic.py

@@ -1078,8 +1078,10 @@ class PackageManager(object):
         data: Dict[str, Any],
         owner: User,
         preserve_uuids=False,
+        add_import_timestamp=True,
+        trust_reviewed=False,
     ) -> Package:
-        importer = PackageImporter(data, preserve_uuids)
+        importer = PackageImporter(data, preserve_uuids, add_import_timestamp, trust_reviewed)
         imported_package = importer.do_import()
 
         up = UserPackagePermission()
@@ -1896,12 +1898,6 @@ class SPathway(object):
                 "to": to_indices,
             }
 
-            if edge.rule:
-                e["rule"] = edge.rule.simple_json()
-
-            if edge.probability:
-                e["probability"] = edge.probability
-
             edges.append(e)
 
         return {

epdb/models.py

@@ -31,10 +31,7 @@ from sklearn.model_selection import ShuffleSplit
 
 from bridge.contracts import Property
 from bridge.dto import RunResult, PropertyPrediction
-from epdb.exceptions import (
-    InvalidMolfileException,
-    InvalidSMILESException,
-)
+from epdb.exceptions import InvalidSMILESException
 from utilities.chem import FormatConverter, IndigoUtils, PredictionResult, ProductSet
 from utilities.ml import (
     ApplicabilityDomainPCA,
@@ -797,13 +794,6 @@ class Compound(
 
     external_identifiers = GenericRelation("ExternalIdentifier")
 
-    def get_structure_by_smiles(self, smiles: str) -> "CompoundStructure":
-        for struct in self.structures.all():
-            if struct.smiles == smiles:
-                return struct
-
-        raise ValueError(f"No structure with SMILES {smiles} found for {self.get_name()}")
-
     @property
     def structures(self) -> QuerySet:
         return CompoundStructure.objects.filter(compound=self)
@@ -872,24 +862,8 @@ class Compound(
     @staticmethod
     @transaction.atomic
     def create(
-        package: "Package",
-        smiles: str,
-        molfile: str | None = None,
-        name: str | None = None,
-        description: str | None = None,
-        *args,
-        **kwargs,
+        package: "Package", smiles: str, name: str = None, description: str = None, *args, **kwargs
     ) -> "Compound":
-        # Molfile has precendence over SMILES
-        if molfile is not None and molfile.strip() != "":
-            mol = FormatConverter.from_molfile(molfile)
-
-            if mol is None:
-                raise InvalidMolfileException("Given molfile is invalid")
-            else:
-                # Overwrite SMILES from molfile
-                smiles = FormatConverter.to_smiles(mol)
-
         if smiles is None or smiles.strip() == "":
             raise InvalidSMILESException("SMILES is required")
 
@@ -922,21 +896,19 @@ class Compound(
 
             return found_compound
 
+
         qs = CompoundStructure.objects.filter(smiles=standardized_smiles, compound__package=package)
         if subclasses:
             qs = qs.not_instance_of(*subclasses)
 
         # Check if we can find the standardized one
         if qs.exists():
+            # TODO should we add a structure?
             found_structure = qs.first()
             found_compound = found_structure.compound
 
-            # We've only found the standardized one, create the very structure
-            _ = found_compound.add_structure(
-                smiles, molfile=molfile, name=name, description=description
-            )
-
             if name:
+                found_structure.add_alias(name)
                 found_compound.add_alias(name)
 
             return found_compound
@@ -968,12 +940,7 @@ class Compound(
             )
 
         cs = CompoundStructure.create(
-            c,
-            smiles,
-            molfile=molfile,
-            name=name,
-            description=description,
-            normalized_structure=is_standardized,
+            c, smiles, name=name, description=description, normalized_structure=is_standardized
         )
 
         c.default_structure = cs
@@ -986,22 +953,11 @@ class Compound(
         self,
         smiles: str,
         name: str = None,
-        molfile: str = None,
         description: str = None,
         default_structure: bool = False,
         *args,
         **kwargs,
     ) -> "CompoundStructure":
-        # Molfile has precendence over SMILES
-        if molfile is not None and molfile.strip() != "":
-            mol = FormatConverter.from_molfile(molfile)
-
-            if mol is None:
-                raise InvalidMolfileException("Given molfile is invalid")
-            else:
-                # Overwrite SMILES from molfile
-                smiles = FormatConverter.to_smiles(mol)
-
         if smiles is None or smiles == "":
             raise ValueError("SMILES is required")
 
@@ -1021,28 +977,16 @@ class Compound(
             )
 
         if is_standardized:
-            CompoundStructure.objects.get(smiles=smiles, compound__package=self.package)
+            CompoundStructure.objects.get(smiles__in=smiles, compound__package=self.package)
 
         # Check if we find a direct match for a given SMILES and/or its standardized SMILES
-        if CompoundStructure.objects.filter(smiles=smiles, compound__package=self.package).exists():
-            found_cs = CompoundStructure.objects.get(smiles=smiles, compound__package=self.package)
-
-            if found_cs.molfile is None and (molfile is not None and molfile.strip() != ""):
-                logger.info(
-                    f"Setting molfile for found CompoundStructure(uuid={found_cs.uuid}) as it was empty"
-                )
-                found_cs.molfile = molfile
-                found_cs.save()
-
-            return found_cs
+        if CompoundStructure.objects.filter(
+            smiles__in=smiles, compound__package=self.package
+        ).exists():
+            return CompoundStructure.objects.get(smiles__in=smiles, compound__package=self.package)
 
         cs = CompoundStructure.create(
-            self,
-            smiles,
-            name=name,
-            molfile=molfile,
-            description=description,
-            normalized_structure=is_standardized,
+            self, smiles, name=name, description=description, normalized_structure=is_standardized
         )
 
         if default_structure:
@@ -1223,24 +1167,8 @@ class CompoundStructure(
     @staticmethod
     @transaction.atomic
     def create(
-        compound: Compound,
-        smiles: str,
-        molfile: str = None,
-        name: str = None,
-        description: str = None,
-        *args,
-        **kwargs,
+        compound: Compound, smiles: str, name: str = None, description: str = None, molfile: str = None, *args, **kwargs
     ):
-        # Molfile has precendence over SMILES
-        if molfile is not None and molfile.strip() != "":
-            mol = FormatConverter.from_molfile(molfile)
-
-            if mol is None:
-                raise InvalidMolfileException("Given molfile is invalid")
-            else:
-                # Overwrite SMILES from molfile
-                smiles = FormatConverter.to_smiles(mol)
-
         # Clean for potential XSS
         if name is not None:
             name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
@@ -1251,13 +1179,6 @@ class CompoundStructure(
             if name:
                 found_cs.add_alias(name)
 
-            if found_cs.molfile is None and (molfile is not None and molfile.strip() != ""):
-                logger.info(
-                    f"Setting molfile for found CompoundStructure(uuid={found_cs.uuid}) as it was empty"
-                )
-                found_cs.molfile = molfile
-                found_cs.save()
-
             return found_cs
 
         if compound.pk is None:
@@ -1268,15 +1189,14 @@ class CompoundStructure(
         if name is not None:
             cs.name = name
 
-        # We have a default here only set the value if it carries some payload
-        if description is not None and description.strip() != "":
+        if description is not None:
             cs.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
 
-        cs.compound = compound
         cs.smiles = smiles
+        cs.compound = compound
 
-        # If molfile is not None, it hase to be a valid Molfile as we've survived the parsing check
-        if molfile is not None:
+        # Check if molfile is present and valid
+        if molfile is not None and FormatConverter.from_molfile(molfile) is not None:
             cs.molfile = molfile
 
         if "normalized_structure" in kwargs:
@@ -1652,9 +1572,6 @@ class ParallelRule(Rule):
                     f"Simple rule {sr.uuid} does not belong to package {package.uuid}!"
                 )
 
-        if name is not None:
-            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
-
         # Deduplication check
         query = ParallelRule.objects.annotate(
             srs_count=Count("simple_rules", filter=Q(simple_rules__in=simple_rules), distinct=True)
@@ -1666,19 +1583,15 @@ class ParallelRule(Rule):
 
         if existing_rule_qs.exists():
             if existing_rule_qs.count() > 1:
-                logger.error(
-                    f"Found more than one ParallelRule for given input! {existing_rule_qs}"
-                )
-
-            found_rule = existing_rule_qs.first()
-            if name:
-                found_rule.add_alias(name)
-
-            return found_rule
+                logger.error(f"Found more than one reaction for given input! {existing_rule_qs}")
+            return existing_rule_qs.first()
 
         r = ParallelRule()
         r.package = package
 
+        if name is not None:
+            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+
         if name is None or name == "":
             name = f"Rule {Rule.objects.filter(package=package).count() + 1}"
 
@@ -1774,6 +1687,7 @@ class Reaction(
         rules: Union[Rule | List[Rule]] = None,
         multi_step: bool = False,
     ):
+
         # Clean for potential XSS
         if name is not None and name.strip() != "":
             name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
@@ -1843,9 +1757,7 @@ class Reaction(
         r = Reaction()
         r.package = package
 
-        if name is None or name == "":
-            name = f"Reaction {Reaction.objects.filter(package=package).count() + 1}"
-
+        if r is not None:
             r.name = name
 
         if description is not None and description.strip() != "":
@@ -2082,7 +1994,6 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
                 # add links start -> pseudo
                 new_link = {
                     "name": link["name"],
-                    "plain_name": link["plain_name"],
                     "id": link["id"],
                     "url": link["url"],
                     "image": link["image"],
@@ -2092,7 +2003,6 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
                     "source": node_url_to_idx[link["start_node_urls"][0]],
                     "target": pseudo_idx,
                     "app_domain": link.get("app_domain", None),
-                    "to_pseudo": True,
                 }
                 adjusted_links.append(new_link)
 
@@ -2100,7 +2010,6 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
                 for target in link["end_node_urls"]:
                     new_link = {
                         "name": link["name"],
-                        "plain_name": link["plain_name"],
                         "id": link["id"],
                         "url": link["url"],
                         "image": link["image"],
@@ -2111,7 +2020,6 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
                         "target": node_url_to_idx[target],
                         "app_domain": link.get("app_domain", None),
                         "multi_step": link["multi_step"],
-                        "from_pseudo": True,
                     }
                     adjusted_links.append(new_link)
 
@@ -2321,12 +2229,11 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
     def add_node(
         self,
         smiles: str,
-        molfile: str | None = None,
-        name: str | None = None,
-        description: str | None = None,
-        depth: int = -1,
+        name: Optional[str] = None,
+        description: Optional[str] = None,
+        depth: Optional[int] = -1,
     ):
-        return Node.create(self, smiles, depth, molfile=molfile, name=name, description=description)
+        return Node.create(self, smiles, depth, name=name, description=description)
 
     @transaction.atomic
     def add_edge(
@@ -2422,19 +2329,17 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
     def _url(self):
         return "{}/node/{}".format(self.pathway.url, self.uuid)
 
-    def get_name(self, include_suffix=True):
+    def get_name(self):
         non_generic_name = True
 
-        if self.name is None or self.name == "no name":
+        if self.name == "no name":
             non_generic_name = False
 
-        if non_generic_name:
-            return self.name
-        else:
-            if include_suffix:
-                return f"{self.default_node_label.name} (taken from underlying structure)"
-            else:
-                return self.default_node_label.name
+        return (
+            self.name
+            if non_generic_name
+            else f"{self.default_node_label.name} (taken from underlying structure)"
+        )
 
     def d3_json(self):
         app_domain_data = self.get_app_domain_assessment_data()
@@ -2464,9 +2369,8 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             ),
             "image_type": "svg",
             "name": self.get_name(),
-            "plain_name": self.get_name(include_suffix=False),
             "smiles": self.default_node_label.smiles,
-            "scenarios": [{"name": s.get_name(), "url": s.url} for s in self.get_scenarios()],
+            "scenarios": [{"name": s.get_name(), "url": s.url} for s in self.scenarios.all()],
             "app_domain": {
                 "inside_app_domain": app_domain_data["assessment"]["inside_app_domain"]
                 if app_domain_data
@@ -2475,7 +2379,6 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             },
             "predicted_properties": predicted_properties,
             "is_engineered_intermediate": self.kv.get("is_engineered_intermediate", False),
-            "proposed": self.get_proposed_info(),
             "timeseries": self.get_timeseries_data(),
             **structure_data,
         }
@@ -2488,43 +2391,28 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
         pathway: "Pathway",
         smiles: str,
         depth: int,
-        molfile: str | None = None,
-        name: str | None = None,
-        description: str | None = None,
+        name: Optional[str] = None,
+        description: Optional[str] = None,
     ):
-        # Molfile has precendence over SMILES
-        if molfile is not None and molfile.strip() != "":
-            mol = FormatConverter.from_molfile(molfile)
-
-            if mol is None:
-                raise InvalidMolfileException("Given molfile is invalid")
-            else:
-                # Overwrite SMILES from molfile
-                smiles = FormatConverter.to_smiles(mol)
-
         stereo_removed = False
         if pathway.predicted and FormatConverter.has_stereo(smiles):
             smiles = FormatConverter.standardize(smiles, remove_stereo=True)
             stereo_removed = True
 
-        c = Compound.create(
-            pathway.package, smiles, molfile=molfile, name=name, description=description
-        )
+        c = Compound.create(pathway.package, smiles, name=name, description=description)
 
-        structure = c.get_structure_by_smiles(smiles)
-
-        if Node.objects.filter(pathway=pathway, default_node_label=structure).exists():
-            return Node.objects.get(pathway=pathway, default_node_label=structure)
+        if Node.objects.filter(pathway=pathway, default_node_label=c.default_structure).exists():
+            return Node.objects.get(pathway=pathway, default_node_label=c.default_structure)
 
         n = Node()
         n.stereo_removed = stereo_removed
         n.pathway = pathway
         n.depth = depth
 
-        n.default_node_label = structure
+        n.default_node_label = c.default_structure
         n.save()
 
-        n.node_labels.add(structure)
+        n.node_labels.add(c.default_structure)
         n.save()
 
         return n
@@ -2572,37 +2460,6 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
 
         return res
 
-    def get_proposed_info(self):
-        collected = defaultdict(dict)
-        for ai in self.additional_information.filter(
-            type__in=["ProposedIntermediate", "TransformationProductImportance", "Confidence"],
-            scenario__isnull=False,
-        ):
-            collected[str(ai.scenario.uuid)]["scenarioId"] = ai.scenario.url
-            collected[str(ai.scenario.uuid)]["scenarioName"] = ai.scenario.name
-
-            if ai.type == "ProposedIntermediate":
-                collected[str(ai.scenario.uuid)]["proposed"] = True
-
-            if ai.type == "Confidence":
-                collected[str(ai.scenario.uuid)]["Confidence"] = ai.get().level
-
-            if ai.type == "TransformationProductImportance":
-                collected[str(ai.scenario.uuid)]["Transformation product importance"] = (
-                    ai.get().importance.value
-                )
-
-        return list(collected.values())
-
-    def get_scenarios(self):
-        qs = self.scenarios.all()
-        qs |= Scenario.objects.filter(
-            id__in=self.additional_information.filter(scenario__isnull=False)
-            .values_list("scenario", flat=True)
-            .distinct()
-        )
-        return qs.distinct()
-
 
 class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin):
     pathway = models.ForeignKey(
@@ -2624,7 +2481,6 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
     def d3_json(self):
         edge_json = {
             "name": self.get_name(),
-            "plain_name": self.get_name(include_suffix=False),
             "id": self.url,
             "url": self.url,
             "image": self.url + "?image=svg",
@@ -2739,19 +2595,17 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
 
         return res
 
-    def get_name(self, include_suffix=True):
+    def get_name(self):
         non_generic_name = True
 
         if self.name == "no name":
             non_generic_name = False
 
-        if non_generic_name:
-            return self.name
-        else:
-            if include_suffix:
-                return f"{self.edge_label.name} (taken from underlying reaction)"
-            else:
-                return self.edge_label.name
+        return (
+            self.name
+            if non_generic_name
+            else f"{self.edge_label.name} (taken from underlying reaction)"
+        )
 
 
 class EPModel(PolymorphicModel, EnviPathModel, AdditionalInformationMixin):

epdb/views.py

@@ -19,7 +19,7 @@ from sentry_sdk import capture_exception
 
 from utilities.chem import FormatConverter, IndigoUtils
 from utilities.decorators import package_permission_required
-from .exceptions import InvalidMolfileException, InvalidSMILESException
+from .exceptions import InvalidSMILESException
 
 from .logic import (
     EPDBURLParser,
@@ -1415,18 +1415,12 @@ def package_compounds(request, package_uuid):
     elif request.method == "POST":
         compound_name = request.POST.get("compound-name")
         compound_smiles = request.POST.get("compound-smiles")
-        compound_molfile = request.POST.get("compound-molfile")
         compound_description = request.POST.get("compound-description")
-
         try:
             c = Compound.create(
-                current_package,
-                compound_smiles,
-                molfile=compound_molfile,
-                name=compound_name,
-                description=compound_description,
+                current_package, compound_smiles, compound_name, compound_description
             )
-        except (InvalidSMILESException, InvalidMolfileException) as e:
+        except ValueError as e:
             raise BadRequest(str(e))
 
         return redirect(c.url)
@@ -1552,15 +1546,11 @@ def package_compound_structures(request, package_uuid, compound_uuid):
     elif request.method == "POST":
         structure_name = request.POST.get("structure-name")
         structure_smiles = request.POST.get("structure-smiles")
-        structure_molfile = request.POST.get("structure-molfile")
         structure_description = request.POST.get("structure-description")
 
         try:
             cs = current_compound.add_structure(
-                structure_smiles,
-                molfile=structure_molfile,
-                name=structure_name,
-                description=structure_description,
+                structure_smiles, structure_name, structure_description
             )
         except ValueError:
             return error(
@@ -1948,9 +1938,9 @@ def package_reactions(request, package_uuid):
     elif request.method == "POST":
         reaction_name = request.POST.get("reaction-name")
         reaction_description = request.POST.get("reaction-description")
-        reaction_smiles = request.POST.get("reaction-smiles")
-        educts = reaction_smiles.split(">>")[0].split(".")
-        products = reaction_smiles.split(">>")[1].split(".")
+        reactions_smirks = request.POST.get("reaction-smirks")
+        educts = reactions_smirks.split(">>")[0].split(".")
+        products = reactions_smirks.split(">>")[1].split(".")
 
         r = Reaction.create(
             current_package,
@@ -2131,14 +2121,12 @@ def package_pathways(request, package_uuid):
         else:
             prediction_setting = current_user.prediction_settings()
 
-        is_predict_mode = pw_mode in {"predict", "incremental"}
-
         pw = Pathway.create(
             current_package,
-            stand_smiles if is_predict_mode else smiles,
+            stand_smiles,
             name=name,
             description=description,
-            predicted=is_predict_mode,
+            predicted=pw_mode in {"predict", "incremental"},
         )
 
         # set mode
@@ -2379,13 +2367,10 @@ def package_pathway_nodes(request, package_uuid, pathway_uuid):
         node_name = request.POST.get("node-name")
         node_description = request.POST.get("node-description")
 
-        node_smiles = request.POST.get("node-smiles")
-        node_molfile = request.POST.get("node-molfile")
+        node_smiles = request.POST.get("node-smiles").strip()
 
         try:
-            current_pathway.add_node(
-                node_smiles, molfile=node_molfile, name=node_name, description=node_description
-            )
+            current_pathway.add_node(node_smiles, name=node_name, description=node_description)
         except InvalidSMILESException:
             return error(
                 request, "Node creation failed!", f"Given SMILES ({node_smiles}) is invalid"
@@ -2497,26 +2482,7 @@ def package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
 
             return JsonResponse({"success": current_node.url})
 
-        new_node_name = request.POST.get("node-name")
-        new_node_description = request.POST.get("node-description")
-
-        if any([new_node_name, new_node_description]):
-            if new_node_name is not None and new_node_name.strip() != "":
-                new_node_name = nh3.clean(new_node_name.strip(), tags=s.ALLOWED_HTML_TAGS).strip()
-                current_node.name = new_node_name
-
-            if new_node_description is not None and new_node_description.strip() != "":
-                new_node_description = nh3.clean(
-                    new_node_description.strip(), tags=s.ALLOWED_HTML_TAGS
-                ).strip()
-                current_node.description = new_node_description
-
-            current_node.save()
-
-            return redirect(current_node.url)
-
-        return error(request, "Node update failed!", "No changes were made to the node")
-
+        return HttpResponseBadRequest()
     else:
         return HttpResponseNotAllowed(["GET", "POST"])
 

static/css/input.css

@@ -39,7 +39,3 @@ select.select[multiple] {
   display: block;
   white-space: normal;
 }
-
-p a {
-  @apply underline;
-}

static/js/alpine/pagination.js

@@ -5,126 +5,6 @@
  */
 
 document.addEventListener('alpine:init', () => {
-
-  const basePagination = (
-    items,
-    currentPage,
-    totalPages,
-    totalItems,
-    perPage,
-    isReviewed,
-    instanceId
-  ) => ({
-    items,
-    currentPage,
-    totalPages,
-    totalItems,
-    perPage,
-    isReviewed,
-    instanceId,
-
-    get paginatedItems() {
-      return this.items;
-    },
-
-    get showingStart() {
-      if (this.totalItems === 0) return 0;
-      return (this.currentPage - 1) * this.perPage + 1;
-    },
-
-    get showingEnd() {
-      if (this.totalItems === 0) return 0;
-      return Math.min((this.currentPage - 1) * this.perPage + this.items.length, this.totalItems);
-    },
-
-    nextPage() {
-      if (this.currentPage < this.totalPages) {
-        this.fetchPage(this.currentPage + 1);
-      }
-    },
-
-    prevPage() {
-      if (this.currentPage > 1) {
-        this.fetchPage(this.currentPage - 1);
-      }
-    },
-
-    goToPage(page) {
-      if (page >= 1 && page <= this.totalPages) {
-        this.fetchPage(page);
-      }
-    },
-
-    get pageNumbers() {
-      const pages = [];
-      const total = this.totalPages;
-      const current = this.currentPage;
-
-      if (total === 0) {
-        return pages;
-      }
-
-      if (total <= 7) {
-        for (let i = 1; i <= total; i++) {
-          pages.push({ page: i, isEllipsis: false, key: `${this.instanceId}-page-${i}` });
-        }
-      } else {
-        pages.push({ page: 1, isEllipsis: false, key: `${this.instanceId}-page-1` });
-
-        let rangeStart;
-        let rangeEnd;
-
-        if (current <= 4) {
-          rangeStart = 2;
-          rangeEnd = 5;
-        } else if (current >= total - 3) {
-          rangeStart = total - 4;
-          rangeEnd = total - 1;
-        } else {
-          rangeStart = current - 1;
-          rangeEnd = current + 1;
-        }
-
-        if (rangeStart > 2) {
-          pages.push({ page: '...', isEllipsis: true, key: `${this.instanceId}-ellipsis-start` });
-        }
-
-        for (let i = rangeStart; i <= rangeEnd; i++) {
-          pages.push({ page: i, isEllipsis: false, key: `${this.instanceId}-page-${i}` });
-        }
-
-        if (rangeEnd < total - 1) {
-          pages.push({ page: '...', isEllipsis: true, key: `${this.instanceId}-ellipsis-end` });
-        }
-
-        pages.push({ page: total, isEllipsis: false, key: `${this.instanceId}-page-${total}` });
-      }
-
-      return pages;
-    }
-  });
-
-  Alpine.data('paginatedList',
-    (items, options = {}) => ({
-      ...basePagination(items,1, 0, 0, options.perPage || 50, options.isReviewed || false, options.instanceId || Math.random().toString(36).substring(2, 9),),
-
-      init() {
-        this.fetchPage(1);
-      },
-
-      async fetchPage(page) {
-        this.totalItems = this.items.length;
-        this.totalPages = Math.ceil(this.items.length / this.perPage);
-        this.currentPage = page
-
-        const start = page * this.perPage - this.perPage;
-        const end = page * this.perPage;
-        return this.items.slice(start, end);
-      }
-
-    })
-  );
-
   Alpine.data('remotePaginatedList', (options = {}) => ({
     items: [],
     currentPage: 1,

static/js/api/additional-information.js

@@ -186,40 +186,6 @@ window.AdditionalInformationApi = {
     return this._handleResponse(response, "createItem");
   },
 
-    /**
-   * Create new additional information and attach it to an object.
-
-   * @param {string} modelName - Name/type of the additional information model
-   * @param {Object} data - Data for the new item
-   * @param {string} attachObjectUrl - UUID of the object this data should be attached to
-   * @param {string} scenarioUuid - UUID of the scenario
-   * @returns {Promise<{status: string, uuid: string}>}
-   */
-  async createItemOnNonScenarioObject(modelName, data, attachObjectUrl, scenarioUuid) {
-    const sanitizedData = this.sanitizePayload(data);
-    this._log("createItemOnNonScenarioObject", { modelName, data: sanitizedData, attachObjectUrl, scenarioUuid });
-
-    sanitizedData.attach_obj_url = attachObjectUrl;
-    if (scenarioUuid) {
-      sanitizedData.scenario_uuid = scenarioUuid;
-    }
-
-
-    // Normalize model name to lowercase
-    const normalizedName = modelName.toLowerCase();
-
-    const response = await fetch(
-      `/api/v1/information/${normalizedName}/`,
-      {
-        method: "POST",
-        headers: this._buildHeaders(),
-        body: JSON.stringify(sanitizedData),
-      },
-    );
-
-    return this._handleResponse(response, "createItemOnNonScenarioObject");
-  },
-
   /**
    * Delete additional information from a scenario
    * @param {string} scenarioUuid - UUID of the scenario

static/js/ketcher2/DEVNOTES.md

@@ -0,0 +1,57 @@
+## Prerequisites
+
+   Stable [Node.js](https://nodejs.org) version
+
+## Build instructions
+
+    npm install
+    npm start
+
+For production build:
+
+    npm run build
+   
+You could also build only the style with command
+
+    npm run style
+
+## Indigo Service
+
+Ketcher uses Indigo Service for server operations.
+You can use `--api-path` parameter to start with it:
+
+    npm start -- --api-path=<server-url>
+For production build:
+
+    npm run build -- --api-path=<server-url>
+
+You can find the instruction for service installation
+[here](http://lifescience.opensource.epam.com/indigo/service/index.html).
+
+## Tests instructions
+
+You can start tests for input/output `.mol`-files and render.
+
+    npm test
+
+Tests are started for all structures in `test/fixtures` directory.
+
+To start the tests separately:
+
+    npm run test-io
+    npm run test-render
+
+#### Parameters
+
+You can use following parameters to start the tests:
+ - `--fixtures` - for the choice of a specific directory with molecules
+ - `--headless` - for start of the browser in headless mode
+
+```
+npm run test-render -- --fixtures=fixtures/super --headless
+```
+
+If you have added new structures for testing to the `test/fixtures` directory 
+you have to generate `svg` from them for correct render-test with:
+
+    npm run generate-svg    

static/js/ketcher2/LICENSE

@@ -0,0 +1,184 @@
+                               Apache License
+                         Version 2.0, January 2004
+                      http://www.apache.org/licenses/
+
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+
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+
+ 5. Submission of Contributions. Unless You explicitly state otherwise,
+    any Contribution intentionally submitted for inclusion in the Work
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+    this License, without any additional terms or conditions.
+    Notwithstanding the above, nothing herein shall supersede or modify
+    the terms of any separate license agreement you may have executed
+    with Licensor regarding such Contributions.
+
+ 6. Trademarks. This License does not grant permission to use the trade
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+ 7. Disclaimer of Warranty. Unless required by applicable law or
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+    Contributor provides its Contributions) on an "AS IS" BASIS,
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+
+ 8. Limitation of Liability. In no event and under no legal theory,
+    whether in tort (including negligence), contract, or otherwise,
+    unless required by applicable law (such as deliberate and grossly
+    negligent acts) or agreed to in writing, shall any Contributor be
+    liable to You for damages, including any direct, indirect, special,
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+ 9. Accepting Warranty or Additional Liability. While redistributing
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+
+ APPENDIX: How to apply the Apache License to your work.
+    To apply the Apache License to your work, attach the following
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+ Copyright 2017 EPAM Systems
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
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+     http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
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+ See the License for the specific language governing permissions and
+ limitations under the License.

static/js/ketcher2/LICENSE-history

@@ -0,0 +1,5 @@
+ Ketcher version 1 was released under GNU Affero General Public License v3.0
+ Ketcher version 2 was re-licensed under Apache License, Version 2.
+
+ Current version is distributed by the terms of the Apache License, Version 2.
+ which is included in the file LICENSE, found at the root of the Ketcher source tree.

static/js/ketcher2/NOTICE

@@ -0,0 +1,19 @@
+ Ketcher
+ Copyright (C) 2017 EPAM Systems
+ This product includes software developed at EPAM Systems, Inc.
+
+ In addition, this product contains dependencies on files licensed under:
+
+ The FreeBSD Documentation License https://www.freebsd.org/copyright/freebsd-doc-license.html
+ The MIT License https://opensource.org/licenses/MIT
+ X11 License http://www.xfree86.org/3.3.6/COPYRIGHT2.html
+ Academic Free License https://opensource.org/licenses/AFL-3.0
+ Apache License, Version 1.0 http://www.apache.org/licenses/LICENSE-1.0
+ Apache License, Version 2.0 http://www.apache.org/licenses/LICENSE-2.0
+ The 2-Clause BSD License https://opensource.org/licenses/BSD-2-Clause
+ The 3-Clause BSD License https://opensource.org/licenses/BSD-3-Clause
+ ISC License (ISC) https://opensource.org/licenses/ISC
+ GNU Lesser General Public License version 2.1 https://opensource.org/licenses/LGPL-2.1
+ The Mozilla Public License https://opensource.org/licenses/MPL-1.0
+ Public Domain https://wiki.creativecommons.org/wiki/Public_domain
+ Unlicense http://unlicense.org/

static/js/ketcher2/README.md

@@ -0,0 +1,35 @@
+# EPAM Ketcher projects
+Copyright (c) 2017 EPAM Systems, Inc
+
+Ketcher is an open-source web-based chemical structure editor incorporating high performance, good portability, light weight, and ability to easily integrate into a custom web-application. Ketcher is designed for chemists, laboratory scientists and technicians who draw structures and reactions.
+
+## KEY FEATURES
+* Fast 2D structure representation that satisfies common chemical drawing standards
+* 3D structure visualization
+* Draw and edit structures using major tools: Atom Tool, Bond Tool, and Template Tool
+* Template library (including custom and user's templates)
+* Add atom and bond basic properties and query features, add aliases and Generic groups
+* Select, modify, and erase connected and unconnected atoms and bonds using Selection Tool, or using Shift key
+* Simple Structure Clean up Tool (checks bonds length, angles and spatial arrangement of atoms) and Advanced Structure Clean up Tool (+ stereochemistry checking and structure layout) 
+* Aromatize/De-aromatize Tool
+* Calculate CIP Descriptors Tool
+* Structure Check Tool
+* MW and Structure Parameters Calculate Tool 
+* Stereochemistry support during editing, loading, and saving chemical structures
+* Storing history of actions, with the ability to rollback to previous state
+* Ability to load and save structures and reactions in MDL Molfile or RXN file format, InChI String, ChemAxon Extended SMILES, ChemAxon Extended CML file formats
+* Easy to use R-Group and S-Group tools (Generic, Multiple group, SRU polymer, peratom, Data S-Group) 
+* Reaction Tool (reaction generating, manual and automatic atom-to-atom mapping) 
+* Flip/Rotate Tool
+* Zoom in/out, hotkeys, cut/copy/paste
+* OCR - ability to recognize structures at pictures (image files) and reproduce them
+* Copy and paste between different chemical editors
+* Settings support (Rendering, Displaying, Debugging)
+* Use of SVG to achieve best quality in-browser chemical structure rendering
+* Languages: JavaScript with third-party libraries
+
+## Build instructions
+Please read [DEVNOTES.md](DEVNOTES.md) for details.
+
+## License
+Please read [LICENSE](LICENSE) and [NOTICE](NOTICE) for details.

static/js/ketcher2/doc/help.md

@@ -0,0 +1,570 @@
+**Ketcher** is a tool to draw molecular structures and chemical
+reactions.
+
+# Ketcher Overview
+
+**Ketcher** is a tool to draw molecular structures and chemical
+reactions. Ketcher operates in two modes, the Server mode with most
+functions available and the client mode with limited functions
+available.
+
+**Ketcher** consists of the following elements:
+
+ ![](main.png "Main window")
+
+**Note** : Depending on the screen size, some tools on the _Tool
+palette_ can be displayed in expanded or collapsed forms.
+
+Using the _Tool palette_, you can
+
+  * draw and edit a molecule or reaction by clicking on and dragging
+  atoms, bonds, and other elements provided with the buttons on the
+  _Atoms_ toolbar and _Tool palette_;
+
+  * delete any element of the drawing (atom or bond) by clicking on it
+  with the Erase tool;
+
+  * delete the entire molecule or its fragment by a lasso,
+  rectangular, or fragment selection with the Erase tool;
+
+  * draw special structures (see the following sections);
+
+  * select the entire molecule or its fragment in one of the following
+  ways (click on the button to see the list of available options):
+
+    * in the expanded form
+
+      ![](expanded.png "Expanded tool")
+
+    * in the collapsed form
+
+      ![](collapsed.png "Collapsed tool")
+
+To select one atom or bond, click Lasso or Rectangle Selection tool,
+and then click the atom or bond.
+
+To select the entire structure:
+
+  * Select the Fragment Selection tool and then click the object.
+
+  * Select the Lasso or Rectangle Selection tool, and then drag the
+  mouse to select the object.
+
+  * `Ctrl-click` with the Lasso or Rectangle Selection tool.
+
+To select multiple atoms, bonds, structures, or other objects, do one
+of the following:
+
+  * `Shift-click` with the Lasso or Rectangle Selection tool selects
+  some (connected or not) atoms/bonds.
+
+  * With the Lasso or Rectangle Selection tool click and drag the
+  mouse around the atoms, bonds, or structures that you want to
+  select.
+
+**Note** : `Ctrl+Shift-click` with the Lasso or Rectangle Selection tool
+selects several structures.
+
+You can use the buttons of the _Main_ toolbar:
+
+
+ ![](toolbar.png "Tolbar")
+
+  * **Clear Canvas** (1) button to start drawing a new molecule; this
+  command clears the drawing area;
+
+  * **Open…** (2) and **Save As…** (3) buttons to import a molecule
+  from a molecular file or save it to a supported molecular file
+  format;
+
+  * **Undo** / **Redo** (4), **Cut** (5), **Copy** (6), **Paste** (7),
+  **Zoom In** / **Out** (8), and **Scaling** (9) buttons to perform
+  the corresponding actions;
+
+  * **Layout** button (10) to change the position of the structure to
+  work with it with the most convenience;
+
+  * **Clean Up** button (11) to improve the appearance of the
+  structure by assigning them uniform bond lengths and angles.
+
+  * **Aromatize** / **Dearomatize** buttons (12) to mark aromatic
+  structures (to convert a structure to the Aromatic or Kekule
+  presentation);
+
+  * **Calculate CIP** button (13) to determine R/S and E/Z
+  configurations;
+
+  * **Check Structure** button (14) to check the following properties
+  of the structure:
+
+    ![](check.png "Structure Ckeck")
+
+  * **Calculated Values** button (15) to display some properties of
+  the structure:
+
+    ![](analyse.png "Calculated Values")
+
+  * **Recognize Molecule** button (16) to recognize a structure in the
+  image file and load it to the canvas;
+
+  * **3D Viewer** button (17) to open the structure in the
+  three-dimensional Viewer;
+
+  * **Settings** button (18) to make some settings for molecular
+    files:
+    
+    ![](settings.png "Settings")
+
+  * **Help** button (19) to view Help;
+    
+  * **About** button (20) to display version and copyright information
+  of the program.
+
+**Note** : **Layout,** **Clean Up,** **Aromatize** / **Dearomatize,**
+**Calculate CIP,** **Check Structure,** **Calculated Values,**
+**Recognize Molecule** and **3D View** buttons are active only in the
+Server mode.
+
+# 3D Viewer
+
+The structure appears in a modal window after clicking on the **3D
+Viewer** button:
+
+ ![](miew.png "3D Viewer")
+
+You can perform the following actions:
+
+  * Rotate the structure holding the left mouse button;
+
+  * Zoom In/Out the structure;
+
+Ketcher Settings allow to change the appearance of the structure and background coloring.
+
+"Lines" drawing method, "Bright" atom name coloring
+method and "Light" background coloring are default.
+
+# Drawing Atoms
+
+To draw/edit atoms you can:
+
+  * select an atom in the Atoms toolbar and click inside the drawing
+  area;
+
+  * if the desired atom is absent in the toolbar, click on
+  the ![](periodic-table.png) button to invoke the Periodic Table and
+  click on the desired atom (available options: _Single_ – selection
+  of a single atom, _List_ – choose an atom from the list of selected
+  options (To allow one atom from a list of atoms of your choice at
+  that position), _Not List_ - exclude any atom on your list at that
+  position).
+
+    ![](periodic-dialog.png "Periodic Table")
+
+  * add an atom to the existing molecule by selecting an atom in the
+  _Atoms_ toolbar, clicking on an atom in the molecule, and dragging
+  the cursor; the atom will be added with a single bond; vacant
+  valences will be filled with the corresponding number of hydrogen
+  atoms;
+
+  * change an atom by selecting an atom in the _Atoms_ toolbar and
+  clicking on the atom to be changed; in the case a wrong valence thus
+  appears the atom will be underlined in red;
+
+  * change an atom by clicking on an existing atom with the
+  _Selection_ tool and waiting for a couple of seconds for the text
+  box to appear; type another atom symbol in the text box:
+
+    ![](inline-edit.png "Change Atom")
+
+  * change the charge of an atom by selecting the Charge Plus or
+  Charge Minus tool and clicking consecutively on an atom to
+  increase/decrease its charge
+
+    ![](charge.png "Ions")
+
+  * change an atom or its properties by double-clicking on the atom to
+  invoke the Atom Properties dialog (the dialog also provides atom
+  query features):
+
+    ![](atom-dialog.png "Atom Properties")
+
+  * click on the Periodic Table button, open the Extended table and
+  select a corresponding Generic group or Special Node:
+
+    ![](periodic-dialog-ext.png "Generic Groups")
+
+# Drawing Bonds
+
+To draw/edit bonds you can:
+
+  * Click an arrow on the Bond tool ![](bond.png) in the Tools palette
+  to open the drop-down list with the following bond types:
+
+    ![](bonds.png)
+
+    For the full screen format, the Bond tool from the Tools palette
+    splits into three: _Single Bond,__Single Up Bond,_ and _Any
+    Bond_,which include the corresponding bond types:
+
+    ![](bond-types.png)
+
+  * select a bond type from the drop down list and click inside the
+  drawing area; a bond of the selected type will be drawn;
+
+  * click on an atom in the molecule; a bond of the selected type will
+  be added to the atom at the angle of 120 degrees;
+
+  * add a bond to the existing molecule by clicking on an atom in the
+  molecule and dragging the cursor; in this case you can set the angle
+  manually;
+
+  * change the bond type by clicking on it;
+
+  * use the Chain Tool ![](chain.png) to draw consecutive single
+  bonds;
+
+  * change a bond or its properties by double-clicking on the bond to
+  invoke the Bond Properties dialog:
+
+    ![](bond-dialog.png "Bond Properties")
+
+  * clicking on a drawn stereo bond changes its direction.
+
+  * clicking with the Single Bond tool or Chain tool switches the bond type
+  cyclically: Single-Double-Triple-Single.
+
+# Drawing R-Groups
+
+Use the _R-Group_ toolbox ![](rgroup.png) to draw R-groups in Markush
+structures:
+
+ ![](rgroup-types.png)
+
+Selecting the _R-Group_ _Label_ Tool and clicking on an atom in the
+structure invokes the dialog to select the R-Group label for a current
+atom position in the structure:
+
+ ![](rgroup-dialog.png)
+
+Selecting the R-Group label and clicking **OK** converts the structure
+into a Markush structure with the selected R-Group label:
+
+ ![](rgroup-example1.png)
+
+**Note** : You can choose several R-Group labels simultaneously:
+
+ ![](rgroup-example2.png)
+
+Particular chemical fragments that may be substituted for a given
+R-Group form a set of R-Group members. R-Group members can be any
+structural fragment, including functional groups and single atoms or
+atom lists.
+
+To create a set of R-Group members:
+
+  1. Draw a structure to become an R-Group member.
+
+  2. Select the structure using the _R-Group Fragment Tool_ to invoke
+     the R-Group dialog; in this dialog select the label of the
+     R-Group to assign the fragment to.
+
+  3. Click on **OK** to convert the structure into an R-Group member.
+
+An R-Group attachment point is the atom in an R-Group member fragment
+that attaches the fragment to the initial Markush structure.
+
+Selecting the _Attachment Point Tool_ and clicking on an atom in the
+R-Group fragment converts this atom into an attachment point. If the
+R-Group contains more than one attachment point, you can specify one
+of them as primary and the other as secondary. You can select between
+either the primary or secondary attachment point using the dialog that
+appears after clicking on the atom:
+
+ ![](attpoints-dialog.png)
+
+If there are two attachment points on an R-Group member, there must be
+two corresponding attachments (bonds) to the R-Group atom that has the
+same R-Group label. Clicking on **OK** in the above dialog creates the
+attachment point.
+
+Schematically, the entire process of the R-Group member creation can
+be presented as:
+
+ ![](rgroup-example3.png)
+
+ ![](rgroup-example4.png)
+
+# R-Group Logic
+
+**Ketcher** enables one to add logic when using R-Groups. To access
+the R-Group logic:
+
+  1. Create an R-Group member fragment as described above.
+
+  2. Move the cursor over the entire fragment for the green frame to
+     appear, then click inside the fragment. The following dialog
+     appears:
+
+     ![](rlogic-dialog.png)
+
+  3. Specify **Occurrence** to define how many of an R-Group
+     occurs. If an R-Group atom appears several times in the initial
+     structure, you will specify **Occurrence**">n", n
+     being the number of occurrences; if it appears once, you see
+     "R1 > 0".
+
+  4. Specify H at **unoccupied** R-Group sites ( **RestH** ): check or
+     clear the checkbox.
+
+  5. Specify the logical **Condition**. Use the R-Group condition **If
+     R(i) Then** to specify whether the presence of an R-Group is
+     dependent on the presence of another R-Group.
+
+
+# Marking S-Groups
+
+To mark S-Groups, use the _S-Group tool_ ![](sgroup.png) and the
+following dialog that appears after selecting a fragment with this
+tool:
+
+ ![](sgroup-dialog.png "S-Group Dialog")
+
+Available S-Group types:
+
+_Generic_
+
+Generic is a pair of brackets without any labels.
+
+_Multiple group_
+
+A Multiple group indicates a number of replications of a fragment or a part of a
+structure in contracted form.
+
+_SRU Polymer_
+
+The Structural Repeating Unit (SRU) brackets enclose the structural
+repeating of a polymer. You have three available patterns:
+head-to-tail (the default), head-to-head, and either/unknown.
+
+_Superatom_
+
+An abbreviated structure (abbreviation) is all or part of a structure
+(molecule or reaction component) that has been abbreviated to a text
+label. Structures that you abbreviate keep their chemical
+significance, but their underlying structure is hidden. The current
+version can't display contracted structures but correctly
+saves/reads them into/from files.
+
+# Data S-Groups
+
+The _Data S-Groups Tool_ ![](sdata.png) is a separate tool for
+comfortable use with the accustomed set of descriptors (like Attached
+Data in **Marvin** Editor).
+
+You can attach data to an atom, a fragment, a single bond, or a
+group. The defined set of _Names_ and _Values_ is introduced for each
+type of selected elements:
+
+ ![](sdata-dialog.png)
+
+  * Select the appropriate S-Group Field Name.
+
+  * Select or type the appropriate Field Value.
+
+  * Labels can be specified as Absolute, Relative or Attached.
+
+# Changing Structure Display
+
+Use the _Flip/Rotate_ tool ![](transform.png) to change the structure
+display:
+
+ ![](transform-types.png)
+
+For the full screen format, the _Flip/Rotate_ tool is split into
+separate buttons:
+
+ ![](rotate.png)
+
+_Rotate Tool_
+
+This tool allows rotating objects.
+  * If some objects are selected, the tool rotates the selected objects.
+  * If no objects are selected, or all objects are selected, the tool rotates the whole canvas
+  * The default rotation step is 15 degrees. 
+  * Press and hold the Ctrl key for more gradual continuous rotation with 1 degree rotation step
+
+Select any bond on the structure and click Alt+H to rotate the structure so that the selected bond is placed horizontally.
+Select any bond on the structure and click Alt+V to rotate the structure so that the selected bond is placed vertically.
+
+_Flip Tool_
+
+This tool flips the objects horizontally or vertically.
+  * If some objects are selected, the Horizontal Flip tool (or Alt+H) flips the selected objects horizontally
+  * If no objects are selected, or all objects are selected, the Horizontal Flip tool (or Alt+H) flips each structure horizontally
+  * If some objects are selected, the Vertical Flip tool (or Alt+V) flips the selected objects vertically
+  * If no objects are selected, or all objects are selected, the Vertical Flip tool (or Alt+V) flips each structure vertically
+
+# Drawing Reactions
+
+To draw/edit reactions you can
+
+  * draw reagents and products as described above;
+  * use options of the _Reaction Arrow Tool_ ![](reaction.png) to draw an
+  arrow and pluses in the reaction equation and map same atoms in
+  reagents and products.
+
+    ![](reaction-types.png)
+
+**Note** : Reaction Auto-Mapping Tool is available only in the Server
+mode.
+
+# Templates toolbar
+
+You can add templates (rings or other predefined structures) to the
+structure using the _Templates_ toolbar together with the _Custom
+Templates_ button located at the bottom:
+
+ ![](template.png)
+
+To add a ring to the molecule, select a ring from the toolbar and
+click inside the drawing area, or click on an atom or a bond in the
+molecule.
+
+Rules of using templates:
+
+  * Selecting a template and clicking on an atom in the existing
+  structure adds the template to the structure connected with a single
+  bond:
+
+    ![](template-example1.png)
+
+  * Selecting a template and dragging the cursor from an atom in the
+  existing structure adds the template directly to this atom resulting
+  in the fused structure:
+
+    ![](template-example2.png)
+
+  * Dragging the cursor from an atom in the existing structure results
+  in the single bond attachment if the cursor is dragged to more than
+  the bond length; otherwise the fused structure is drawn.
+  * Selecting a template and clicking on a bond in the existing
+  structure created a bond-to-bond fused structure:
+
+    ![](template-example3.png)
+
+  * The bond in the initial structure is replaced with the bond in the
+  template.
+
+  * This procedure doesn't change the length of the bond in the
+  initial structure.
+
+  * Dragging the cursor relative to the initial bond applies the
+  template at the corresponding side of the bond.
+
+**Note** : The added template will be fused by the default attachment
+atom or bond preset in the program.
+
+**Note** : User is able to define the attachment atom and bond by clicking
+the Edit button for template structure.
+
+
+The _Custom Templates_ button ![](template-lib.png)invokes the scrolling
+list of templates available in the program; both built-in and created
+by user:
+
+ ![](template-dialog.png)
+
+
+To create a user template:
+* draw a structure.
+* click the Save as button.
+* click the Save to Templates button.
+* enter a name and define the attachment atom and bond.
+
+# Working with Files
+
+Ketcher supports the following molecular formats that can be entered
+either manually or from files:
+
+  * MDL Molfile or RXN file;
+
+  * Daylight SMILES (Server mode only);
+
+  * Daylight SMARTS (Server mode only);
+
+  * InChi string (Server mode only);
+
+  * CML file (Server mode only).
+
+You can use the **Open…** and **Save As…** buttons of the _Main_
+toolbar to import a molecule from a molecular file or save it to a
+supported molecular file format. The _Open Structure_ dialog enables
+one to either browse for a file (Server mode) or manually input, e.g.,
+the Molfile ctable for the molecule to be imported:
+
+ ![](open.png)
+
+The _Save Structure_ dialog enables one to save the molecular file:
+
+ ![](save.png)
+
+**Note** : In the standalone version only mol/rxn are supported for
+Open and mol/rxn/SMILES for Save.
+
+
+# Hotkeys
+
+You can use keyboard hotkeys (including Numeric keypad) for some
+features/commands of the Editor. To display the hotkeys just place the
+cursor over a toolbar button. If a hotkey is available for the button,
+it will appear in brackets after the description of the button.
+
+| Key | Action |
+| --- | --- |
+| `Esc` | Switching between the Lasso/Rectangle/Fragment Selection tools |
+| `Del` | Delete the selected objects |
+| `0` | Draw Any bond. |
+| `1` | Single / Single Up / Single Down / Single Up/Down bond. Consecutive pressing switches between these types. |
+| `2` | Double / Double Cis/Trans bond |
+| `3` | Draw a triple bond. |
+| `4` | Draw an aromatic bond. |
+| `5` | Charge Plus/Charge Minus |
+| `A` | Draw any atom |
+| `H` | Draw a hydrogen |
+| `C` | Draw a carbon |
+| `N` | Draw a nitrogen |
+| `O` | Draw an oxygen |
+| `S` | Draw a sulfur |
+| `F` | Draw a fluorine |
+| `P` | Draw a phosphorus |
+| `I` | Draw an iodine |
+| `T` | Basic templates. Consecutive pressing switches between different templates |
+| `Shift+t` | Open template library |
+| `Alt+r` | Rotate tool |
+| `Alt+v` | Flip vertically |
+| `Alt+h` | Flip horizontally |
+| `Ctrl+g` | S-Group tool / Data S-Group tool |
+| `Ctrl+d` | Align and select all S-Group data
+| `Ctrl+r` | Switching between the R-Group Label Tool/R-Group Fragment Tool/Attachment Point Tool |
+| `Ctrl+Shift+r`  | R-Group Fragment Tool |
+| `Ctrl+Del` | Clear canvas |
+| `Ctrl+o` | Open |
+| `Ctrl+s` | Save As |
+| `Ctrl+z` | Undo |
+| `Ctrl+Shift+z` | Redo |
+| `Ctrl+x` | Cut selected objects |
+| `Ctrl+c` | Copy selected objects |
+| `Ctrl+v` | Paste selected objects |
+| `+` | Zoom In |
+| `-` | Zoom Out |
+| `Ctrl+l` | Layout |
+| `Ctrl+Shift+l` | Clean Up |
+| `Ctrl+p` | Calculate CIP |
+| `?` | Help |
+
+**Note** : Please, use `Ctrl+V` to paste the selected object in
+Google Chrome and Mozilla Firefox browsers.
+
+**Note 2** : Probably, you have forbidden access to the local storage.
+If you are using IE10 or IE11 and didn't forbid access to local storage 
+intentionally, you can pay attention here: https://stackoverflow.com/a/20848924

static/js/ketcher2/gulpfile.js

@@ -0,0 +1,310 @@
+/****************************************************************************
+ * Copyright 2017 EPAM Systems
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ ***************************************************************************/
+
+var gulp = require('gulp');
+var gutil = require('gulp-util');
+var plugins = require('gulp-load-plugins')();
+
+var browserify = require('browserify');
+var source = require('vinyl-source-stream');
+var buffer = require('vinyl-buffer');
+var budo = require('budo');
+var istanbul = require('browserify-babel-istanbul');
+
+var fs = require('fs');
+var cp = require('child_process');
+var del = require('del');
+var minimist = require('minimist');
+var MarkdownIt = require('markdown-it');
+
+var pkg = require('./package.json');
+var options = minimist(process.argv.slice(2), {
+	string: ['dist', 'api-path', 'build-number', 'build-date',
+	         'miew-path'],
+	boolean: ['sgroup-data-special', 'no-generics', 'no-reactions',
+	          'no-sgroup', 'no-rgroup', 'rgroup-label-only'],
+	default: {
+		'dist': 'dist',
+		'api-path': '',
+		'miew-path': '',
+		'build-number': '',
+		'build-date': new Date() // TODO: format me
+	}
+});
+
+var distrib = ['LICENSE', 'demo.html', 'library.sdf', 'library.svg'];
+
+var bundleConfig = {
+	entries: 'script',
+	extensions: ['.js', '.jsx', '.es'],
+	debug: true,
+	standalone: pkg.name,
+	transform: [
+		['exposify', {
+			expose: {'raphael': 'Raphael' }
+		}],
+		['browserify-replace', {
+			replace: [
+				{ from: '__VERSION__', to: pkg.version },
+				{ from: '__API_PATH__', to: options['api-path'] },
+				{ from: '__BUILD_NUMBER__', to: options['build-number'] },
+				{ from: '__BUILD_DATE__', to: options['build-date'] },
+				{ from: '__MIEW_PATH__', to: options['miew-path'] },
+			]
+		}],
+		['babelify', {
+			presets: [
+				["env", {
+					"targets": {
+						"browsers": ["last 2 versions", "safari > 8", "chrome > 52"]
+					},
+					"useBuiltIns": true
+				}],
+				"react"],
+			plugins: ['lodash', 'transform-class-properties', 'transform-object-rest-spread']
+		}]
+	]
+};
+
+var iconfont = null;
+
+gulp.task('script', ['patch-version'], function() {
+	bundleConfig.transform.push(
+		['loose-envify', {
+			NODE_ENV: 'production',
+			global: true
+		}]
+	);
+	return browserify(bundleConfig).bundle()
+		// Don't transform, see: http://git.io/vcJlV
+		.pipe(source(`${pkg.name}.js`)).pipe(buffer())
+		.pipe(plugins.sourcemaps.init({ loadMaps: true }))
+		.pipe(plugins.uglify({
+			compress: {
+				global_defs: {
+					DEBUG: false
+				},
+				dead_code: true
+		}}))
+		.pipe(plugins.header(fs.readFileSync('script/banner.js', 'utf8')))
+		.pipe(plugins.sourcemaps.write('./'))
+		.pipe(gulp.dest(options.dist));
+});
+
+gulp.task('test-render', function() {
+	return browserify({
+		entries: 'test/render/render-test.js',
+		debug: true,
+		transform: [
+			istanbul,
+			['exposify', {
+				expose: {
+					raphael: 'Raphael',
+					resemblejs: 'resemble'
+				}
+			}]
+		]
+	}).bundle()
+		.pipe(source('render-test.js'))
+		.pipe(plugins.header(fs.readFileSync('script/banner.js', 'utf8')))
+		.pipe(gulp.dest('./test/dist'));
+});
+
+gulp.task('style', ['font'], function () {
+	return gulp.src('style/index.less')
+		.pipe(plugins.sourcemaps.init())
+		.pipe(plugins.rename(pkg.name))
+		.pipe(plugins.less({
+			paths: ['node_modules/normalize.css'],
+			modifyVars: iconfont
+		}))
+	    // don't use less plugins due http://git.io/vqVDy bug
+		.pipe(plugins.autoprefixer({ browsers: ['> 0.5%'] }))
+		.pipe(plugins.cleanCss({compatibility: 'ie8'}))
+		.pipe(plugins.sourcemaps.write('./'))
+		.pipe(gulp.dest(options.dist));
+});
+
+gulp.task('html', ['patch-version'], function () {
+	var hbs = plugins.hb()
+	    .partials('template/menu/*.hbs')
+	    .partials('template/dialog/*.hbs')
+	    .data(Object.assign({ pkg: pkg }, options));
+	return gulp.src('template/index.hbs')
+		.pipe(hbs)
+		.pipe(plugins.rename('ketcher.html'))
+		.pipe(gulp.dest(options.dist));
+});
+
+gulp.task('doc', function () {
+	return gulp.src('doc/*.{png, jpg, gif}')
+		.pipe(gulp.dest(options.dist + '/doc'));
+});
+
+gulp.task('help', ['doc'], function () {
+	return gulp.src('doc/help.md')
+		.pipe(plugins.tap(markdownify()))
+		.pipe(gulp.dest(options.dist + '/doc'));
+});
+
+gulp.task('font', function (cb) {
+	return iconfont ? cb() : gulp.src(['icons/*.svg'])
+		.pipe(plugins.iconfont({
+			fontName: pkg.name,
+			formats: ['ttf', 'svg', 'eot', 'woff'],
+			timestamp: options['build-date'],
+			normalize: true
+		}))
+		.on('glyphs', function(glyphs) {
+			iconfont = glyphReduce(glyphs);
+		})
+		.pipe(gulp.dest(options.dist));
+});
+
+gulp.task('images', function () {
+	return gulp.src('images/*')
+		.pipe(gulp.dest(options.dist + '/images'));
+});
+
+gulp.task('copy', ['images'], function () {
+	return gulp.src(['raphael'].map(require.resolve)
+	                .concat(distrib))
+		.pipe(gulp.dest(options.dist));
+});
+
+gulp.task('patch-version', function (cb) {
+	if (pkg.rev)
+		return cb();
+	cp.exec('git rev-list ' + pkg.version + '..HEAD --count', function (err, stdout, stderr) {
+		if (err && stderr.toString().search('path not in') > 0) {
+			cb(new Error('Could not fetch revision. ' +
+			             'Please git tag the package version.'));
+		}
+		else if (!err && stdout > 0) {
+			pkg.rev =  stdout.toString().trim();
+			pkg.version += ('+r' + pkg.rev);
+		}
+		cb();
+	});
+});
+
+gulp.task('lint', function () {
+	return gulp.src('script/**')
+		.pipe(plugins.eslint())
+		.pipe(plugins.eslint.format())
+		.pipe(plugins.eslint.failAfterError());
+});
+
+gulp.task('check-epam-email', function(cb) {
+	// TODO: should be pre-push and check remote origin
+	try {
+		var email = cp.execSync('git config user.email').toString().trim();
+		if (/@epam.com$/.test(email))
+			cb();
+		else {
+			cb(new Error('Email ' + email + ' is not from EPAM domain.'));
+			gutil.log('To check git project\'s settings run `git config --list`');
+			gutil.log('Could not continue. Bye!');
+		}
+	} catch(e) {};
+});
+
+gulp.task('check-deps-exact', function (cb) {
+	var semver = require('semver'); // TODO: output corrupted packages
+	var allValid = ['dependencies', 'devDependencies'].every(d => {
+		var dep = pkg[d];
+		return Object.keys(dep).every(name => {
+			var ver = dep[name];
+			return (semver.valid(ver) && semver.clean(ver));
+		});
+	});
+	if (!allValid) {
+		cb(new gutil.PluginError('check-deps-exact',
+		                         'All top level dependencies should be installed' +
+		                         'using `npm install --save-exact` command'));
+	} else
+		cb();
+});
+
+gulp.task('clean', function () {
+	return del.sync([options.dist + '/**', pkg.name + '-*.zip']);
+});
+
+gulp.task('archive', ['clean', 'assets', 'code'], function () {
+	var an = pkg.name + '-' + pkg.version;
+	return gulp.src(['**', '!*.map'], { cwd: options.dist })
+		.pipe(plugins.rename(function (path) {
+			path.dirname = an + '/' + path.dirname;
+			return path;
+		}))
+		.pipe(plugins.zip(an + '.zip'))
+		.pipe(gulp.dest('.'));
+});
+
+gulp.task('serve', ['clean', 'style', 'html', 'assets'], function(cb) {
+	var server = budo(`${bundleConfig.entries}:${pkg.name}.js`, {
+		dir: options.dist,
+		browserify: bundleConfig,
+		stream: process.stdout,
+		host: '0.0.0.0',
+		live: true,
+		watchGlob: `${options.dist}/*.{html,css}`,
+		staticOptions: {
+			index: `ketcher.html`
+		}
+	}).on('exit', cb);
+
+	gulp.watch('style/**.less', ['style']);
+	gulp.watch('template/**', ['html']);
+	gulp.watch('doc/**', ['help']);
+	gulp.watch(['gulpfile.js', 'package.json'], function() {
+	server.close();
+		cp.spawn('gulp', process.argv.slice(2), {
+			stdio: 'inherit'
+		});
+		process.exit(0);
+	});
+
+	return server;
+});
+
+function markdownify (options) {
+	var header = '<!DOCTYPE html>';
+	var footer = '';
+	var md = MarkdownIt(Object.assign({
+		html: true,
+		linkify: true,
+		typographer: true
+	}, options));
+	return function process (file) {
+		var data = md.render(file.contents.toString());
+		file.contents = new Buffer(header + data + footer);
+		file.path = gutil.replaceExtension(file.path, '.html');
+	};
+}
+
+function glyphReduce(glyphs) {
+	return glyphs.reduce(function (res, glyph) {
+		res['icon-' + glyph.name] = "'" + glyph.unicode[0] + "'";
+		return res;
+	}, {});
+}
+
+gulp.task('pre-commit', ['lint', 'check-epam-email',
+                         'check-deps-exact']);
+gulp.task('assets', ['copy', 'help']);
+gulp.task('code', ['style', 'script', 'html']);
+gulp.task('build', ['clean', 'code', 'assets']);

static/js/ketcher2/icons/about.svg

@@ -0,0 +1,60 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!-- Generated by IcoMoon.io -->
+
+<svg
+   xmlns:dc="http://purl.org/dc/elements/1.1/"
+   xmlns:cc="http://creativecommons.org/ns#"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+   xmlns:svg="http://www.w3.org/2000/svg"
+   xmlns="http://www.w3.org/2000/svg"
+   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+   version="1.1"
+   width="1000"
+   height="1000"
+   viewBox="0 0 1000 1000"
+   id="svg2"
+   inkscape:version="0.91 r13725"
+   sodipodi:docname="about.svg">
+  <metadata
+     id="metadata11">
+    <rdf:RDF>
+      <cc:Work
+         rdf:about="">
+        <dc:format>image/svg+xml</dc:format>
+        <dc:type
+           rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
+        <dc:title></dc:title>
+      </cc:Work>
+    </rdf:RDF>
+  </metadata>
+  <defs
+     id="defs9" />
+  <sodipodi:namedview
+     pagecolor="#ffffff"
+     bordercolor="#666666"
+     borderopacity="1"
+     objecttolerance="10"
+     gridtolerance="10"
+     guidetolerance="10"
+     inkscape:pageopacity="0"
+     inkscape:pageshadow="2"
+     inkscape:window-width="1280"
+     inkscape:window-height="974"
+     id="namedview7"
+     showgrid="false"
+     inkscape:zoom="0.52678571"
+     inkscape:cx="708.89624"
+     inkscape:cy="375.86441"
+     inkscape:window-x="0"
+     inkscape:window-y="23"
+     inkscape:window-maximized="1"
+     inkscape:current-layer="svg2" />
+  <g
+     id="icomoon-ignore"
+     transform="translate(0,552)" />
+  <path
+     d="m 666.66667,812.5 0,-104.16667 c 0,-11.71875 -9.11459,-20.83333 -20.83334,-20.83333 l -62.5,0 0,-333.33333 c 0,-11.71875 -9.11458,-20.83334 -20.83333,-20.83334 l -208.33333,0 c -11.71875,0 -20.83334,9.11459 -20.83334,20.83334 l 0,104.16666 c 0,11.71875 9.11459,20.83334 20.83334,20.83334 l 62.5,0 0,208.33333 -62.5,0 c -11.71875,0 -20.83334,9.11458 -20.83334,20.83333 l 0,104.16667 c 0,11.71875 9.11459,20.83333 20.83334,20.83333 l 291.66666,0 c 11.71875,0 20.83334,-9.11458 20.83334,-20.83333 z m -83.33334,-583.33333 0,-104.16667 c 0,-11.71875 -9.11458,-20.83333 -20.83333,-20.83333 l -125,0 c -11.71875,0 -20.83333,9.11458 -20.83333,20.83333 l 0,104.16667 C 416.66667,240.88542 425.78125,250 437.5,250 l 125,0 c 11.71875,0 20.83333,-9.11458 20.83333,-20.83333 z M 1000,500 c 0,276.04167 -223.95833,500 -500,500 C 223.95833,1000 0,776.04167 0,500 0,223.95833 223.95833,0 500,0 c 276.04167,0 500,223.95833 500,500 z"
+     id="path5"
+     inkscape:connector-curvature="0" />
+</svg>

static/js/ketcher2/icons/analyse.svg

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static/js/ketcher2/icons/arom.svg

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static/js/ketcher2/icons/bond-any.svg

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static/js/ketcher2/icons/bond-aromatic.svg

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static/js/ketcher2/icons/bond-crossed.svg

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static/js/ketcher2/icons/bond-double.svg

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static/js/ketcher2/icons/bond-doublearomatic.svg

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static/js/ketcher2/icons/bond-down.svg

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static/js/ketcher2/icons/bond-single.svg

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static/js/ketcher2/icons/bond-singlearomatic.svg

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static/js/ketcher2/icons/bond-singledouble.svg

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static/js/ketcher2/icons/bond-triple.svg

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static/js/ketcher2/icons/bond-up.svg

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static/js/ketcher2/icons/bond-updown.svg

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static/js/ketcher2/icons/chain.svg

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static/js/ketcher2/icons/charge-minus.svg

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static/js/ketcher2/icons/charge-plus.svg

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static/js/ketcher2/icons/check.svg

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static/js/ketcher2/icons/chiral-flag.svg

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static/js/ketcher2/icons/cip.svg

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static/js/ketcher2/icons/clean.svg

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static/js/ketcher2/icons/copy.svg

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static/js/ketcher2/icons/cut.svg

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