Merge branch 'main' of github.com:BSC-CNS-EAPM/EAPM-plugins into main

EAPM/EAPM.py

@@ -91,6 +91,26 @@ def createPlugin():
 
     eapmPlugin.addBlock(ahatoolBlock)
 
+    from Blocks.EpPred import epPredBlock  # type: ignore
+
+    eapmPlugin.addBlock(epPredBlock)
+
+    # from Blocks.testBlock import testBlock  # type: ignore
+
+    # eapmPlugin.addBlock(testBlock)
+
+    from Blocks.AnalyseGlide import AnalyseGBlock  # type: ignore
+
+    eapmPlugin.addBlock(AnalyseGBlock)
+
+    # from Blocks.Rbcavity import rbCavityBlock  # type: ignore
+
+    # eapmPlugin.addBlock(rbCavityBlock)
+
+    # from Blocks.Rbdock import rbDockBlock  # type: ignore
+
+    # eapmPlugin.addBlock(rbDockBlock)
+
     # Add the configs
     from Configs.mafftConfig import mafftExecutableConfig  # type: ignore
 

EAPM/Include/Blocks/Ahatool.py

@@ -1,9 +1,7 @@
-import datetime
-import os
-import subprocess
-
 from HorusAPI import PluginBlock, PluginVariable, VariableList, VariableTypes
 
+# TODO Add to the documentation
+
 # ==========================#
 # Variable inputs
 # ==========================#
@@ -44,6 +42,13 @@
 ##############################
 #       Other variables      #
 ##############################
+removeExistingResults = PluginVariable(
+    name="Remove existing results",
+    id="remove_existing_results",
+    description="Remove existing results",
+    type=VariableTypes.BOOLEAN,
+    defaultValue=False,
+)
 prefixVar = PluginVariable(
     name="Prefix",
     id="prefix",
@@ -76,6 +81,10 @@
 
 def initialAction(block: PluginBlock):
 
+    import datetime
+    import os
+    import subprocess
+
     container_name = block.inputs.get("container_name", "bsceapm/ahatool:2.2")
     input_fasta = block.inputs.get("input_fasta", None)
     fasta = os.path.basename(input_fasta)
@@ -145,6 +154,6 @@ def initialAction(block: PluginBlock):
     action=initialAction,
     description="Iteratively search a protein sequence against a protein database",
     inputs=[inputFasta, dbPath, containerName],
-    variables=[prefixVar, startVar, evalVar, threadsVar],
+    variables=[removeExistingResults, prefixVar, startVar, evalVar, threadsVar],
     outputs=[outputAhatool],
 )

EAPM/Include/Blocks/AlignPdbEAPM.py

@@ -45,7 +45,6 @@
     type=VariableTypes.INTEGER,
     defaultValue=0,
 )
-
 chainIndexesAlign = VariableList(
     name="Chain indexes",
     id="chain_indexes",
@@ -63,15 +62,12 @@
     type=VariableTypes.INTEGER,
     defaultValue=0,
 )
-
 trajectoryChainIndexesAlign = VariableList(
     name="Trajectory chain indexes",
     id="trajectory_chain_indexes",
     description="Chain indexes of the target trajectories to use in the alignment.",
     prototypes=[trajectoryChainIndexVariable],
 )
-
-
 alignmentModeAlign = PluginVariable(
     name="Alignment mode",
     id="alignment_mode",
@@ -80,7 +76,6 @@
     defaultValue="aligned",
     allowedValues=["aligned", "exact"],
 )
-
 referenceResiduesAlign = PluginVariable(
     name="Reference residue index",
     id="reference_residues",
@@ -129,26 +124,30 @@ def initialAlign(block: PluginBlock):
     alignmentMode = block.variables.get("alignment_mode", "aligned")
     referenceResidues = block.variables.get("reference_residues", [])
 
+    import prepare_proteins
+
+    print("Loading PDB files...")
+
+    models = prepare_proteins.proteinModels(inputFolder)
+
     # Parse the chain indexes
     if chainIndexes is not None:
         chainIndexes = [x["chain_index"] for x in chainIndexes]
     else:
         chainIndexes = [0]
 
+    trajectory_chain_indexes = None
     # Parse the trajectory chain indexes
     if trajectoryChainIndexes is not None:
         trajectoryChainIndexes = [x["trajectory_chain_index"] for x in trajectoryChainIndexes]
+        trajectory_chain_indexes = {}
+        for i, model in enumerate(models.models_names):
+            trajectory_chain_indexes[model] = trajectoryChainIndexes[i]
 
     # Parse the reference residues
     if referenceResidues is not None:
         referenceResidues = [x["reference_residues"] for x in referenceResidues]
 
-    import prepare_proteins
-
-    print("Loading PDB files...")
-
-    models = prepare_proteins.proteinModels(inputFolder)
-
     print("Aligning models...")
 
     import subprocess
@@ -168,7 +167,7 @@ def hookSubprocessMafft(command, **kwargs):
             pdbReference,
             outputFolder,
             chain_indexes=chainIndexes,
-            trajectory_chain_indexes=trajectoryChainIndexes,
+            trajectory_chain_indexes=trajectory_chain_indexes,
             aligment_mode=alignmentMode,
             reference_residues=referenceResidues,
             verbose=True,

EAPM/Include/Blocks/AlphaFoldEAPM.py

@@ -2,8 +2,6 @@
 Module containing the AlphaFold block for the EAPM plugin
 """
 
-import os
-
 from HorusAPI import PluginVariable, SlurmBlock, VariableTypes
 
 # ==========================#
@@ -28,7 +26,6 @@
     type=VariableTypes.STRING,
     defaultValue="alphafold",
 )
-
 removeExistingResults = PluginVariable(
     name="Remove existing results",
     id="remove_existing_results",
@@ -63,13 +60,25 @@ def initialAlphafold(block: SlurmBlock):
     folderName = block.variables.get("folder_name", "alphafold")
     removeExisting = block.variables.get("remove_existing_results", False)
 
+    cpus_per_task = block.variables.get("cpus_per_task")
+    if cpus_per_task is 1:
+        print("Alphafold requires at least 20 cpus per task. Changing to 20 cpus per task.")
+        block.variables["cpus_per_task"] = 20
+
+    partiton = block.variables.get("partition")
+    if partiton is None:
+        print("Alphafold requires an accelerated partition. Changing to acc_bscls.")
+        block.variables["partition"] = "acc_bscls"
+
+    import os
+
     # If folder already exists, raise exception
     if removeExisting and os.path.exists(folderName):
         os.system("rm -rf " + folderName)
 
     if not removeExisting and os.path.exists(folderName):
         raise Exception(
-            "The folder {} already exists. Please, choose another name or remove it.".format(
+            "The folder {} already exists. Please, choose another name or remove it with the remove existing folder option.".format(
                 folderName
             )
         )
@@ -88,7 +97,7 @@ def initialAlphafold(block: SlurmBlock):
 
     from utils import launchCalculationAction
 
-    launchCalculationAction(block, jobs, folderName)
+    launchCalculationAction(block, jobs, "alphafold", [folderName])
 
 
 def finalAlhafoldAction(block: SlurmBlock):
@@ -98,6 +107,8 @@ def finalAlhafoldAction(block: SlurmBlock):
 
     resultsFolder = block.extraData["folder_name"]
 
+    import os
+
     output_models_folder = os.path.join(downloaded_path, resultsFolder, "output_models")
 
     block.setOutput(outputModelsVariable.id, output_models_folder)
@@ -107,7 +118,7 @@ def finalAlhafoldAction(block: SlurmBlock):
 
 alphafoldBlock = SlurmBlock(
     name="Alphafold",
-    description="Run Alphafold. (For cte_power, marenostrum, nord3 and minotauro clusters or local)",
+    description="Run Alphafold. (For marenostrum, nord3 clusters or local)",
     initialAction=initialAlphafold,
     finalAction=finalAlhafoldAction,
     variables=BSC_JOB_VARIABLES + [outputAF, removeExistingResults],