public static void AmbitTest()
{
//string smirks = "[*:1][N:2](=[O:3])=[O:4]>>[*:1][N+:2](=[O:3])[O-:4]";
//string smirks = "[N:1]1[C:2][C:3]=[C:4][C:5]1>>[N:1]1[C:2]=[C:3][C:4]=[C:5]1";
string smirks = "[#16:1]>>[#16:1](=[O])";
//string targetSmiles = "O=S(c2nc1ccc(OC)cc1n2)Cc3ncc(c(OC)c3C)C";
string targetSmiles = "CC1=CN=C(C(=C1OC)C)CS(=O)C2=NC3=C(N2)C=C(C=C3)OC"; // Omeprazole
string productSmiles = "";
IAtomContainer target = new AtomContainer();
IChemObjectBuilder icob = org.openscience.cdk.silent.SilentChemObjectBuilder.getInstance();
SMIRKSManager smrkMan = new SMIRKSManager(icob);
//SMIRKSManager smrkMan = SMIRKSManager.getDefaultSMIRKSManager();
SMIRKSReaction reaction = smrkMan.parse(smirks);
if (!smrkMan.getErrors().Equals(""))
{
throw (new Exception("Smirks Parser errors:\n" + smrkMan.getErrors()));
}
target = CdkUtil.SmilesToAtomContainer(targetSmiles);
if (smrkMan.applyTransformation(target, reaction))
{
IAtomContainer product = target;
productSmiles = CdkUtil.AtomContainerToSmiles(product);
return; // all products inside the same atomcontainer (target), could be disconnected
}
else
{
return;
}
//Generate separate products for every possible reaction(used in Toxtree)
//SMIRKSManager smrkMan = new SMIRKSManager();
//SMIRKSReaction smr = smrkMan.parse(reaction.getSMIRKS());
//IAtomContainer product = reactant; //(IAtomContainer) reactant.clone();
//IAtomContainerSet rproducts = smrkMan.applyTransformationWithSingleCopyForEachPos(product, null, smr);
//products returned in a separate atom sontainer set
}
public PipelineStack(Construct parent, string id, IPipelineStackProps props) : base(parent, id, props)
{
EcrRepository = new Repository(
this,
"EcrRepository",
new RepositoryProps
{
RepositoryName = "cdk-dotnet-example",
RemovalPolicy = RemovalPolicy.DESTROY,
});
var cdkBuild = new PipelineProject(
this,
"CdkBuild",
new PipelineProjectProps
{
BuildSpec = BuildSpec.FromSourceFilename("Infrastructure/Resources/cdk_buildspec.yml"),
Environment = new BuildEnvironment
{
BuildImage = LinuxBuildImage.AMAZON_LINUX_2,
},
});
var apiBuildTaskRole = new Role(
this,
"ApiBuildRole",
new RoleProps
{
ManagedPolicies = new[]
{
ManagedPolicy.FromAwsManagedPolicyName("AmazonEC2ContainerRegistryPowerUser"),
},
AssumedBy = new ServicePrincipal("codebuild.amazonaws.com")
});
var apiBuild = new PipelineProject(
this,
"ApiBuild",
new PipelineProjectProps
{
BuildSpec = BuildSpec.FromSourceFilename("Infrastructure/Resources/api_buildspec.yml"),
Role = apiBuildTaskRole,
Environment = new BuildEnvironment
{
BuildImage = LinuxBuildImage.AMAZON_LINUX_2,
Privileged = true,
EnvironmentVariables = new Dictionary <string, IBuildEnvironmentVariable>
{
["AWS_ACCOUNT_ID"] = CdkUtil.PlainTextBuildEnvironmentVariable(Of(this).Account),
["AWS_DEFAULT_REGION"] = CdkUtil.PlainTextBuildEnvironmentVariable(Of(this).Region),
},
},
});
var apiTest = new PipelineProject(
this,
"ApiTest",
new PipelineProjectProps
{
BuildSpec = BuildSpec.FromSourceFilename("Infrastructure/Resources/ci_buildspec.yml"),
Environment = new BuildEnvironment
{
BuildImage = LinuxBuildImage.AMAZON_LINUX_2,
Privileged = true,
},
});
var sourceOutput = new Artifact_();
var cdkBuildOutput = new Artifact_("CdkBuildOutput");
var apiBuildOutput = new Artifact_("ApiBuildOutput");
new Pipeline(
this,
"Api",
new PipelineProps
{
Stages = new IStageProps[]
{
new StageProps
{
StageName = "Source",
Actions = new IAction[]
{
new GitHubSourceAction(new GitHubSourceActionProps
{
ActionName = "GitHub",
OauthToken = SecretValue.SecretsManager(props.GitHubSecretName),
Repo = props.GitHubRepo,
Owner = props.GitHubOwner,
Output = sourceOutput,
Trigger = GitHubTrigger.WEBHOOK,
}),
},
},
new StageProps
{
StageName = "Build",
Actions = new IAction[]
{
new CodeBuildAction(new CodeBuildActionProps
{
ActionName = "ApiTest",
Project = apiTest,
Input = sourceOutput,
RunOrder = 1,
}),
new CodeBuildAction(new CodeBuildActionProps
{
ActionName = "ApiBuild",
Project = apiBuild,
Input = sourceOutput,
Outputs = new[] { apiBuildOutput },
RunOrder = 2,
}),
new CodeBuildAction(new CodeBuildActionProps
{
ActionName = "CdkBuild",
Project = cdkBuild,
Input = sourceOutput,
Outputs = new[] { cdkBuildOutput },
RunOrder = 3,
}),
},
},
new StageProps
{
StageName = "Deploy",
Actions = new IAction[]
{
new CloudFormationCreateUpdateStackAction(new CloudFormationCreateUpdateStackActionProps
{
ActionName = "ApiStack",
TemplatePath = cdkBuildOutput.AtPath($"{props.ApiStackName}.template.json"),
StackName = "Api",
AdminPermissions = true,
ParameterOverrides = new Dictionary <string, object>
{
[props.ApiImageTag] = apiBuildOutput.GetParam("metadata.json", "imageTag"),
},
ExtraInputs = new[]
{
apiBuildOutput,
},
}),
},
},
},
});
}
