Spaya API 1.0.0 documentation

Spaya API 1.0.0

application/json

Spaya API employs a data-driven AI approach to discover retrosynthetic routes.

An iterative exploration of all possible routes is performed until commercially available starting materials are identified.

The process of retrosynthesis consists of building possible routes from your input SMILES to commercially available starting materials and scoring them. The routes are built in the form of a graph where nodes and edges are linked together and scored by our AI models as would a chemist do. The final score you get is the one of the best route our models found, and you also get the number of steps it takes, within this route, to synthesize your molecule from the starting materials our system found.

Remember that the process is iterative and runs for a certain amount of time and/or iterations before reaching a conclusion. You can control the time it runs for with several early stopping options, but note that running for longer doesn't necessarily mean always getting better results. Our models can find an easy enough (score >= a given acceptable threshold) route in no time but then struggle for hours to find the absolute best route if it ever exists, so adjust accordingly to your own requirements and availability of starting materials. You can even ask our models to use one of your preferred intermediate products to further guide the AI through routes you know are easy for you to synthesize.

Operations

RECEIVE /retrosynthesis_api/ws/v1/batch_smiles
Start and stream result of retrosynthesis for batch of smiles

Send batch of smiles
Operation IDpublish
Accepts the following message:
Batch Retrosynthesis EntryBatchRetroSynthesisEntryMessage
A list of smiles for a retrosynthesis
application/json
Message IDBatchRetroSynthesisEntryMessage
object [BatchRetroSynthesisEntry]
required
array<string>
[ 1 .. 10000 ] items
List of SMILES

Items:
string
array<string>
must match: (building block|screening|virtual)<= 2 items
Select the type of compounds (building block or screening). A null value select them all

Items:
string
must match: (building block|screening|virtual)
array<string>
<= 1000 items
A list of smiles to add as commercial compounds

Items:
string
cc_max_delivery_days
integer
> 0
Maximum delivery time in day. A null value select them all

cc_max_price_per_g
number
> 0
Maximum price per gramme for a commercial compounds

array<string>
List of desired commercial compounds providers. An empty list select them all

Items:
string
early_stopping_score
number
[ 0 .. 1 ]decimal places <= 2
Early stopping option. Stop the process when it reaches this score for your input SMILES

Default value:0.6
filter_regio_issues
boolean
When True, disables the regioselectivity

Default value:false
array<integer>
Desired atoms indices to use as 1st disconnections (as a list of integer). This will force our models to only find routes which split exactly at the selected atoms in it's first step.

Items:
integer
array<string>
Desired forbidden substructures (as a list of SMARTS). This will force our models to exclude routes which have at least one of these structures present in one or more of the reactants.

Items:
string
array<string>
Desired imposed substructures (as a list of SMARTS). This will force our models to only find routes which have at least one of these structures present in one or more of the reactants.

Items:
string
array<string>
Desired intermediate products (as a list of SMILES). This will force our models to only find routes which have at least one of these molecules as an intermediate product. This helps guide the process through reactions or molecules you already own or have expertise with for example.

Items:
string
max_depth
integer
[ 1 .. 20 ]
Size limit of the routes produced by the model. Tells the algorithm to stop following a route when it reaches this threshold (ie. which means it's become too complex to synthesise)

Default value:15
max_nb_iterations
integer
[ 10 .. 4000 ]
Early stopping option. Stop the process when it has run for this many iterations. This is not related to the max_depth above or to the nb_steps response below. It only measures the number of times the AI model is iterated over to try to find a better route than the previous ones.

Default value:800
model
string
Model name to use, by default the latest model will be used

array<string>
<= 10000 items
List of mandatory name reactions.

Items:
string
array<string>
<= 10000 items
List of excluded name reactions.

Items:
string
array<string>
<= 10000 items
List of allowed name reactions.

Items:
string
array<string>
<= 10000 items
List of mandatory sub categories of name reactions.

Items:
string
array<string>
<= 10000 items
List of excluded sub categories of name reactions.

Items:
string
array<string>
<= 10000 items
List of allowed sub categories of name reactions.

Items:
string
array<integer>
Desired atoms indices to protected bonds (as a list of integer). This constrains our model to not break the bond

Items:
integer
remove_chirality
boolean
When True, remove the chirality from all inputs

Default value:false
Additional properties are allowed.
object
Authorization
required
string
must match: ^Bearer .*$
Bearer token as 'Authorization' or as custom header name (ex: X-Iktos-Authorization) 'Bearer '

Additional properties are allowed.
Examples
{ "batch_smiles": [ "string" ], "cc_catalog": [ "string" ], "cc_extra_compounds_smiles": [ "string" ], "cc_max_delivery_days": 0, "cc_max_price_per_g": 0, "cc_providers": [ "string" ], "early_stopping_score": 0.6, "filter_regio_issues": false, "first_disconnections": [ 0 ], "forbidden_structures": [ "string" ], "imposed_structures": [ "string" ], "intermediate_smiles": [ "string" ], "max_depth": 15, "max_nb_iterations": 800, "model": "string", "name_reactions_at_least": [ "string" ], "name_reactions_categories_at_least": [ "string" ], "name_reactions_categories_exclude": [ "string" ], "name_reactions_categories_only": [ "string" ], "name_reactions_exclude": [ "string" ], "name_reactions_only": [ "string" ], "name_reactions_sub_categories_at_least": [ "string" ], "name_reactions_sub_categories_exclude": [ "string" ], "name_reactions_sub_categories_only": [ "string" ], "protected_bonds": [ 0 ], "remove_chirality": false }

This example has been generated automatically.
{ "Authorization": "string" }

This example has been generated automatically.
SEND /retrosynthesis_api/ws/v1/batch_smiles
Start and stream result of retrosynthesis for batch of smiles

Get result of retrosynthesis
Operation IDsubscribe
Accepts the following message:
Retrosynthesis ResultRetroSynthesisResultMessage
Result of a retrosynthesis
application/json
Message IDRetroSynthesisResultMessage
object [RetroSynthesisResult]
nb_steps
integer
>= 1
When done, it gives you the depth (as in an acyclic directed graph or tree depth) of the longest linear sequence of the best route.

progress
integer
[ 0 .. 100 ]
Retrosynthesis progression

Default value:0
rscore
number
[ 0 .. 1 ]
When done, gives you the synthetic access AI-Score of your input molecule. The AI-score is a metric provided by the Spaya algorithms, related to the probability of a disconnection to happen and consequently to the confidence the algorithm has on this disconnection/route.

smiles
required
string
Your input SMILES

allOf
Default value:"SUBMITTED"
Consists of EntryStatusCode:
string
Smiles status:

SUBMITTED: The SMILES is in queue and should be processed soon

RUNNING: The SMILES is being processed

DONE: The process has finished running

(found all the possible routes or stopped early because of your options above)

INVALID_SMILES: The SMILES is not valid

ERROR*: Something went wrong

KILLED*: Stopped manually

*Please reach out to our support team for more detailed diagnostics of these statuses.

Allowed values:
"SUBMITTED"
"RUNNING"
"DONE"
"INVALID SMILES"
"ERROR"
"KILLED"
"NEW"
"QUOTA_EXCEEDED"
"PENDING"
Additional properties are allowed.
Examples
{ "nb_steps": 1, "progress": 0, "rscore": 1, "smiles": "string", "status": "SUBMITTED" }

This example has been generated automatically.

Messages

#1Batch Retrosynthesis EntryBatchRetroSynthesisEntryMessage
A list of smiles for a retrosynthesis
- application/json
Message IDBatchRetroSynthesisEntryMessage
object [BatchRetroSynthesisEntry]
required
array<string>
[ 1 .. 10000 ] items
List of SMILES

Items:
string
array<string>
must match: (building block|screening|virtual)<= 2 items
Select the type of compounds (building block or screening). A null value select them all

Items:
string
must match: (building block|screening|virtual)
array<string>
<= 1000 items
A list of smiles to add as commercial compounds

Items:
string
cc_max_delivery_days
integer
> 0
Maximum delivery time in day. A null value select them all

cc_max_price_per_g
number
> 0
Maximum price per gramme for a commercial compounds

array<string>
List of desired commercial compounds providers. An empty list select them all

Items:
string
early_stopping_score
number
[ 0 .. 1 ]decimal places <= 2
Early stopping option. Stop the process when it reaches this score for your input SMILES

Default value:0.6
filter_regio_issues
boolean
When True, disables the regioselectivity

Default value:false
array<integer>
Desired atoms indices to use as 1st disconnections (as a list of integer). This will force our models to only find routes which split exactly at the selected atoms in it's first step.

Items:
integer
array<string>
Desired forbidden substructures (as a list of SMARTS). This will force our models to exclude routes which have at least one of these structures present in one or more of the reactants.

Items:
string
array<string>
Desired imposed substructures (as a list of SMARTS). This will force our models to only find routes which have at least one of these structures present in one or more of the reactants.

Items:
string
array<string>
Desired intermediate products (as a list of SMILES). This will force our models to only find routes which have at least one of these molecules as an intermediate product. This helps guide the process through reactions or molecules you already own or have expertise with for example.

Items:
string
max_depth
integer
[ 1 .. 20 ]
Size limit of the routes produced by the model. Tells the algorithm to stop following a route when it reaches this threshold (ie. which means it's become too complex to synthesise)

Default value:15
max_nb_iterations
integer
[ 10 .. 4000 ]
Early stopping option. Stop the process when it has run for this many iterations. This is not related to the max_depth above or to the nb_steps response below. It only measures the number of times the AI model is iterated over to try to find a better route than the previous ones.

Default value:800
model
string
Model name to use, by default the latest model will be used

array<string>
<= 10000 items
List of mandatory name reactions.

Items:
string
array<string>
<= 10000 items
List of excluded name reactions.

Items:
string
array<string>
<= 10000 items
List of allowed name reactions.

Items:
string
array<string>
<= 10000 items
List of mandatory sub categories of name reactions.

Items:
string
array<string>
<= 10000 items
List of excluded sub categories of name reactions.

Items:
string
array<string>
<= 10000 items
List of allowed sub categories of name reactions.

Items:
string
array<integer>
Desired atoms indices to protected bonds (as a list of integer). This constrains our model to not break the bond

Items:
integer
remove_chirality
boolean
When True, remove the chirality from all inputs

Default value:false
Additional properties are allowed.
object
Authorization
required
string
must match: ^Bearer .*$
Bearer token as 'Authorization' or as custom header name (ex: X-Iktos-Authorization) 'Bearer '

Additional properties are allowed.
#2Retrosynthesis ResultRetroSynthesisResultMessage
Result of a retrosynthesis
- application/json
Message IDRetroSynthesisResultMessage
object [RetroSynthesisResult]
nb_steps
integer
>= 1
When done, it gives you the depth (as in an acyclic directed graph or tree depth) of the longest linear sequence of the best route.

progress
integer
[ 0 .. 100 ]
Retrosynthesis progression

Default value:0
rscore
number
[ 0 .. 1 ]
When done, gives you the synthetic access AI-Score of your input molecule. The AI-score is a metric provided by the Spaya algorithms, related to the probability of a disconnection to happen and consequently to the confidence the algorithm has on this disconnection/route.

smiles
required
string
Your input SMILES

allOf
Default value:"SUBMITTED"
Consists of EntryStatusCode:
string
Smiles status:

SUBMITTED: The SMILES is in queue and should be processed soon

RUNNING: The SMILES is being processed

DONE: The process has finished running

(found all the possible routes or stopped early because of your options above)

INVALID_SMILES: The SMILES is not valid

ERROR*: Something went wrong

KILLED*: Stopped manually

*Please reach out to our support team for more detailed diagnostics of these statuses.

Allowed values:
"SUBMITTED"
"RUNNING"
"DONE"
"INVALID SMILES"
"ERROR"
"KILLED"
"NEW"
"QUOTA_EXCEEDED"
"PENDING"
Additional properties are allowed.

Schemas

object
Authorization
required
string
must match: ^Bearer .*$
Bearer token as 'Authorization' or as custom header name (ex: X-Iktos-Authorization) 'Bearer '

Additional properties are allowed.
object [BatchRetroSynthesisEntry]
required
array<string>
[ 1 .. 10000 ] items
List of SMILES

Items:
string
array<string>
must match: (building block|screening|virtual)<= 2 items
Select the type of compounds (building block or screening). A null value select them all

Items:
string
must match: (building block|screening|virtual)
array<string>
<= 1000 items
A list of smiles to add as commercial compounds

Items:
string
cc_max_delivery_days
integer
> 0
Maximum delivery time in day. A null value select them all

cc_max_price_per_g
number
> 0
Maximum price per gramme for a commercial compounds

array<string>
List of desired commercial compounds providers. An empty list select them all

Items:
string
early_stopping_score
number
[ 0 .. 1 ]decimal places <= 2
Early stopping option. Stop the process when it reaches this score for your input SMILES

Default value:0.6
filter_regio_issues
boolean
When True, disables the regioselectivity

Default value:false
array<integer>
Desired atoms indices to use as 1st disconnections (as a list of integer). This will force our models to only find routes which split exactly at the selected atoms in it's first step.

Items:
integer
array<string>
Desired forbidden substructures (as a list of SMARTS). This will force our models to exclude routes which have at least one of these structures present in one or more of the reactants.

Items:
string
array<string>
Desired imposed substructures (as a list of SMARTS). This will force our models to only find routes which have at least one of these structures present in one or more of the reactants.

Items:
string
array<string>
Desired intermediate products (as a list of SMILES). This will force our models to only find routes which have at least one of these molecules as an intermediate product. This helps guide the process through reactions or molecules you already own or have expertise with for example.

Items:
string
max_depth
integer
[ 1 .. 20 ]
Size limit of the routes produced by the model. Tells the algorithm to stop following a route when it reaches this threshold (ie. which means it's become too complex to synthesise)

Default value:15
max_nb_iterations
integer
[ 10 .. 4000 ]
Early stopping option. Stop the process when it has run for this many iterations. This is not related to the max_depth above or to the nb_steps response below. It only measures the number of times the AI model is iterated over to try to find a better route than the previous ones.

Default value:800
model
string
Model name to use, by default the latest model will be used

array<string>
<= 10000 items
List of mandatory name reactions.

Items:
string
array<string>
<= 10000 items
List of excluded name reactions.

Items:
string
array<string>
<= 10000 items
List of allowed name reactions.

Items:
string
array<string>
<= 10000 items
List of mandatory sub categories of name reactions.

Items:
string
array<string>
<= 10000 items
List of excluded sub categories of name reactions.

Items:
string
array<string>
<= 10000 items
List of allowed sub categories of name reactions.

Items:
string
array<integer>
Desired atoms indices to protected bonds (as a list of integer). This constrains our model to not break the bond

Items:
integer
remove_chirality
boolean
When True, remove the chirality from all inputs

Default value:false
Additional properties are allowed.
EntryStatusCode
string
Smiles status:

SUBMITTED: The SMILES is in queue and should be processed soon

RUNNING: The SMILES is being processed

DONE: The process has finished running

(found all the possible routes or stopped early because of your options above)

INVALID_SMILES: The SMILES is not valid

ERROR*: Something went wrong

KILLED*: Stopped manually

*Please reach out to our support team for more detailed diagnostics of these statuses.

Allowed values:
"SUBMITTED"
"RUNNING"
"DONE"
"INVALID SMILES"
"ERROR"
"KILLED"
"NEW"
"QUOTA_EXCEEDED"
"PENDING"
object [RetroSynthesisResult]
nb_steps
integer
>= 1
When done, it gives you the depth (as in an acyclic directed graph or tree depth) of the longest linear sequence of the best route.

progress
integer
[ 0 .. 100 ]
Retrosynthesis progression

Default value:0
rscore
number
[ 0 .. 1 ]
When done, gives you the synthetic access AI-Score of your input molecule. The AI-score is a metric provided by the Spaya algorithms, related to the probability of a disconnection to happen and consequently to the confidence the algorithm has on this disconnection/route.

smiles
required
string
Your input SMILES

allOf
Default value:"SUBMITTED"
Consists of EntryStatusCode:
string
Smiles status:

SUBMITTED: The SMILES is in queue and should be processed soon

RUNNING: The SMILES is being processed

DONE: The process has finished running

(found all the possible routes or stopped early because of your options above)

INVALID_SMILES: The SMILES is not valid

ERROR*: Something went wrong

KILLED*: Stopped manually

*Please reach out to our support team for more detailed diagnostics of these statuses.

Allowed values:
"SUBMITTED"
"RUNNING"
"DONE"
"INVALID SMILES"
"ERROR"
"KILLED"
"NEW"
"QUOTA_EXCEEDED"
"PENDING"
Additional properties are allowed.

Spaya API 1.0.0

Operations

RECEIVE /retrosynthesis_api/ws/v1/batch_smiles

Examples

This example has been generated automatically.

This example has been generated automatically.

SEND /retrosynthesis_api/ws/v1/batch_smiles

Examples

This example has been generated automatically.

Messages

Schemas