diff --git a/api/kinoml/datasets/pkis2/index.html b/api/kinoml/datasets/pkis2/index.html index 11d872b2..a1dffb42 100644 --- a/api/kinoml/datasets/pkis2/index.html +++ b/api/kinoml/datasets/pkis2/index.html @@ -431,7 +431,7 @@

Module Contents
-class kinoml.datasets.pkis2.PKIS2DatasetProvider
+class kinoml.datasets.pkis2.PKIS2DatasetProvider(measurements: Iterable[kinoml.core.measurements.BaseMeasurement], metadata: dict = None)

Bases: kinoml.datasets.core.DatasetProvider

Loads the PKIS2 dataset as provided in _Progress towards a public chemogenomic set for protein kinases and a call for contributions [1].

diff --git a/api/kinoml/features/protein/index.html b/api/kinoml/features/protein/index.html index 20a372f3..fbe49212 100644 --- a/api/kinoml/features/protein/index.html +++ b/api/kinoml/features/protein/index.html @@ -483,8 +483,7 @@

Module Contents
_retrieve_sequence(system: Union[kinoml.core.systems.ProteinSystem, kinoml.core.systems.ProteinLigandComplex]) → str
-

Implement in your component-specific subclass!

-
+

diff --git a/api/kinoml/ml/torch_geometric_models/index.html b/api/kinoml/ml/torch_geometric_models/index.html index 2a5da1bc..7c9319e7 100644 --- a/api/kinoml/ml/torch_geometric_models/index.html +++ b/api/kinoml/ml/torch_geometric_models/index.html @@ -449,7 +449,17 @@

Module Contents
static estimate_input_shape(input_sample)
-

+

This static method takes the same input +as .forward() would and estimates the +incoming shape so the layers can be initialized +properly.

+

Most of the time, input_sample would be a +Tensor, in which the first dimension corresponds +to systems, and the second is the input shape +we need.

+

If your .forward() method takes something else +than a Tensor, please adapt this method accordingly.

+
forward(data)
diff --git a/notebooks/getting_started.ipynb b/notebooks/getting_started.ipynb index 1fcc164b..49dea906 100644 --- a/notebooks/getting_started.ipynb +++ b/notebooks/getting_started.ipynb @@ -32,7 +32,7 @@ }, { "cell_type": "markdown", - "id": "8ede9514", + "id": "05090503", "metadata": {}, "source": [ "![KinoML object model](../../kinoml/data/fig_1_kinomltechpaper_v2.png) \n", diff --git a/searchindex.js b/searchindex.js index 6b56cdb7..9e5d4f98 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ 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ees","kinoml.modeling.MDAnalysisModeling","kinoml.modeling.OEModeling","kinoml.modeling.SCHRODINGERModeling","kinoml.modeling.alignment","kinoml.modeling","kinoml.optimize","kinoml.utils","kinoml.workflows","KinoML","OpenEye Structural Featurizer","Schrodinger Structural Featurizer","Getting started with KinoML","Kinase informed morgan 1024 experiment","Kinase informed SMILES experiment","KinoML object model","Ligand-only morgan 1024 experiment","Ligand-only SMILES experiment"],titleterms:{"1":[50,51,52,54,55],"1024":[51,54],"2":[50,51,52,54,55],"3":50,With:49,_version:0,align:42,analysi:[1,2,3],basic:50,chembl:16,common:[48,49],complex:26,compon:[4,53],condit:5,configur:[51,52,54,55],content:[0,2,3,4,5,7,8,9,10,11,13,14,15,16,17,18,20,21,22,23,24,26,27,29,30,31,33,34,35,36,37,39,40,41,42,45],core:[4,5,6,7,8,9,10,11,17,27],creat:[51,52,54,55],data:[50,51,52,54,55],databas:[12,13,14,15],dataload:[51,52,54,55],dataset:[16,17,18,19,20,21,22,51,52,54,55],datasetprovid:[50,53],defin:[51,52,54,55],disk:[51,52,54,55],dock:[23,24,25],evalu:[51,52,54,55],exampl:[7,9,10,17,20,50],experi:[51,52,54,55],featur:[26,27,28,29,30,48,49,50,51,52,53,54,55],filter:[51,52,54,55],fingerprint:[48,49],finish:[51,52,54,55],fred:48,get:50,group:[18,51,52,54,55],hybrid:48,hyper:[51,52,54,55],inform:[51,52],instal:50,introduct:50,kinas:[51,52],kinoml:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,50,53],klif:13,klifsconformationtemplatesfeatur:[48,49],ligand:[7,29,53,54,55],lightning_modul:33,load:[51,52,54,55],log:[51,52,54,55],loop:[51,52,54,55],mdanalysismodel:39,measur:[8,53],metric:2,ml:[32,33,34,35,36,37,38,50],model:[39,40,41,42,43,50,51,52,53,54,55],modul:[0,2,3,4,5,7,8,9,10,11,13,14,15,16,17,18,20,21,22,23,24,26,27,29,30,33,34,35,36,37,39,40,41,42,45],molecular:53,morgan:[51,54],most:[48,49],mostsimilarpdbligandfeatur:[48,49],note:[17,21,27,29,37],object:53,observ:[51,52,54,55],obtain:50,oecomplexfeatur:48,oedock:23,oedockingfeatur:48,oemodel:40,oeproteinstructurefeatur:48,onli:[54,55],openey:48,optim:44,p00533__pic50measur:[51,52,55],p00533__pkdmeasur:[51,52,55],p00533__pkimeasur:[51,52,55],packag:31,paramet:[51,52,54,55],pdb:14,pic50measur:54,pipelin:[48,49],pkdmeasur:54,pkimeasur:54,pkis2:20,plot:3,posit:48,prepar:[51,52,54,55],protein:[9,30,53],pytorch:[51,52,54,55],raw:[51,52,54,55],report:[51,52,54,55],reproduc:[51,52,54,55],restrain:49,run:[51,52,54,55],s:[48,49],save:[51,52,54,55],schroding:49,schrodingercomplexfeatur:49,schrodingerdock:24,schrodingerdockingfeatur:49,schrodingermodel:41,sequenc:10,setup:[51,52,54,55],shape:[48,49],smile:[52,55],split:[51,52,54,55],start:[50,51,52,54,55],structur:[48,49],submodul:[1,6,12,19,25,28,31,32,43],subpackag:31,substructur:[48,49],summari:[51,52,54,55],system:[11,53],tensor:[51,52,54,55],tensorflow_model:34,test:[50,51,52,54,55],torch_dataset:21,torch_geometric_dataset:22,torch_geometric_model:35,torch_loop:36,torch_model:37,torch_tre:38,train:[50,51,52,54,55],uniprot:15,util:45,val:[51,52,54,55],warn:47,without:49,work:[51,52,54,55],workflow:46,write:[51,52,54,55],your:50}}) 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