BioExcel Building Blocks Source & Docs
Source and docs for BioExcel Building Blocks
| Package | Description | Python | ReadTheDocs | Bioconda | Docker | Singularity | Version | Building block | Wrapped tool | Description | Dependencies Pypi | Dependencies Conda | Dependencies Conda Extra Channels | Keywords | |
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| biobb_analysis | Biobb_analysis is the Biobb module collection to perform analysis of molecular dynamics simulations. |
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3.5.0 | GMXCluster~GMXRms~GMXRgyr~GMXEnergy~GMXImage~GMXTrjconvStr~GMXTrjconvStrEns~GMXTrjconvTrj~CpptrajAverage~CpptrajBfactor~CpptrajRms~CpptrajRmsf~CpptrajRgyr~CpptrajDry~CpptrajStrip~CpptrajSnapshot~CpptrajSlice~CpptrajConvert~CpptrajMask~CpptrajImage | gmx cluster~gmx rms~gmx gyrate~gmx energy~gmx trjconv~gmx trjconv~gmx trjconv~gmx trjconv~Ambertools cpptraj~Ambertools cpptraj~Ambertools cpptraj~Ambertools cpptraj~Ambertools cpptraj~Ambertools cpptraj~Ambertools cpptraj~Ambertools cpptraj~Ambertools cpptraj~Ambertools cpptraj~Ambertools cpptraj~Ambertools cpptraj | Wrapper of the GROMACS cluster module for clustering structures from a given GROMACS compatible trajectory.~Wrapper of the Ambertools Cpptraj module for calculating the Root Mean Square deviation (RMSd) of a given cpptraj compatible trajectory.~Wrapper of the GROMACS gyrate module for computing the radius of gyration (Rgyr) of a molecule about the x-, y- and z-axes, as a function of time, from a given GROMACS compatible trajectory.~Wrapper of the GROMACS energy module for extracting energy components from a given GROMACS energy file.~Wrapper of the GROMACS trjconv module for correcting periodicity (image) from a given GROMACS compatible trajectory file.~Wrapper of the GROMACS trjconv module for converting between GROMACS compatible structure file formats and/or extracting a selection of atoms.~Wrapper of the GROMACS trjconv module for extracting an ensemble of frames containing a selection of atoms from GROMACS compatible trajectory files.~Wrapper of the GROMACS trjconv module for converting between GROMACS compatible trajectory file formats and/or extracts a selection of atoms.~Wrapper of the Ambertools Cpptraj module for calculating a structure average of a given cpptraj compatible trajectory.~Wrapper of the Ambertools Cpptraj module for calculating the Bfactor fluctuations of a given cpptraj compatible trajectory.~Wrapper of the Ambertools Cpptraj module for calculating the Root Mean Square deviation (RMSd) of a given cpptraj compatible trajectory.~Wrapper of the Ambertools Cpptraj module for calculating the Root Mean Square fluctuations (RMSf) of a given cpptraj compatible trajectory.~Wrapper of the Ambertools Cpptraj module for computing the radius of gyration (Rgyr) from a given cpptraj compatible trajectory.~Wrapper of the Ambertools Cpptraj module for dehydrating a given cpptraj compatible trajectory stripping out solvent molecules and ions.~Wrapper of the Ambertools Cpptraj module for stripping a defined set of atoms (mask) from a given cpptraj compatible trajectory.~Wrapper of the Ambertools Cpptraj module for extracting a particular snapshot from a given cpptraj compatible trajectory.~Wrapper of the Ambertools Cpptraj module for extracting a particular trajectory slice from a given cpptraj compatible trajectory.~Wrapper of the Ambertools Cpptraj module for converting between cpptraj compatible trajectory file formats and/or extracting a selection of atoms or frames.~Wrapper of the Ambertools Cpptraj module for extracting a selection of atoms from a given cpptraj compatible trajectory.~Wrapper of the Ambertools Cpptraj module for correcting periodicity (image) from a given cpptraj trajectory file. | install_requires=['biobb_common==3.5.1']~python_requires='==3.7.*' | python ==3.7.*~biobb_common ==3.5.1~gromacs ==2019.1~ambertools ==20.0 | analysis,ambertools,gromacs | ||
| biobb_chemistry | Biobb_chemistry is the Biobb module collection to perform chemistry over molecular dynamics simulations. |
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3.5.0 | AcpypeParamsAC~AcpypeParamsCNS~AcpypeParamsGMX~AcpypeParamsGMXOPLS~BabelConvert~BabelAddHydrogens~BabelRemoveHydrogens~BabelMinimize~ReduceAddHydrogens~ReduceRemoveHydrogens | ACPype~ACPype~ACPype~ACPype~OpenBabel~OpenBabel~OpenBabel~OpenBabel~AmberTools Reduce~AmberTools Reduce | Small molecule parameterization for AMBER MD package.~Small molecule parameterization for CNS/XPLOR MD package.~Small molecule parameterization for GROMACS MD package.~Small molecule parameterization for OPLS/AA MD package.~Small molecule format conversion.~Adds hydrogen atoms to small molecules.~Removes hydrogen atoms to small molecules.~Energetically minimize small molecules.~Adds hydrogen atoms to small molecules.~Removes hydrogen atoms to small molecules. | install_requires=['biobb_common==3.5.1']~python_requires='==3.7.*' | python ==3.7.*~biobb_common ==3.5.1~openbabel ==2.4.1~ambertools ==20.0~acpype ==2019.10.05.12.26 | chemistry,ambertools,acpype,babel | ||
| biobb_common | Biobb_common is the base package required to use the biobb packages. |
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3.5.1 | in house | Biobb Base structure & common elements. | install_requires=['pyyaml', 'requests', 'biopython==1.78']~python_requires='==3.7.*' | python ==3.7.*~pyyaml~requests~biopython ==1.78 | common | |||
| biobb_io | Biobb_io is the Biobb module collection to fetch data to be consumed by the rest of the Biobb building blocks. |
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3.5.0 | Drugbank~Ligand~Pdb~PdbVariants~PdbClusterZip~MemProtMDSimList~MemProtMDSimSearch~MemProtMDSim~BindingSite~CanonicalFasta | API Call~API Call~API Call~API Call~API Call~API Call~API Call~API Call~API Call~API Call | This class is a wrapper for the Drugbank REST API.~This class is a wrapper for downloading a PDB ligand from the Protein Data Bank.~This class is a wrapper for downloading a PDB structure from the Protein Data Bank.~This class creates a text file containing a list of all the variants mapped to a PDB code from the corresponding UNIPROT entries.~This class is a wrapper for downloading a PDB cluster from the Protein Data Bank.~This class is a wrapper of the MemProtMD to get all available membrane-protein systems from its REST API.~This class is a wrapper of the MemProtMD to perform advanced searches in the MemProtMD DB using its REST API.~This class is a wrapper of the MemProtMD to download a simulation using its REST API.~This class is a wrapper for the PDBe REST API Binding Sites endpoint.~This class is a wrapper for downloading a FASTA structure from the Protein Data Bank. | install_requires=['biobb_common==3.5.1']~python_requires='==3.7.*' | python ==3.7.*~biobb_common ==3.5.1 | io,mmb,pdb,rcsb,ebi,MemProtMD | ||
| biobb_md | Biobb_md is the Biobb module collection to perform molecular dynamics simulations. |
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3.5.1 | Pdb2gmx~Editconf~Genion~Genrestr~Grompp~Mdrun~GromppMdrun~MakeNdx~Gmxselect~Solvate~Ndx2resttop~AppendLigand | gmx pdb2gmx~gmx editconf~gmx genion~gmx genrestr~gmx grompp~gmx mdrun~gmx grompp & gmx mdrun~gmx make_ndx~gmx select~gmx solvate~in house~in house | Creates a compressed (ZIP) GROMACS topology (TOP and ITP files) from a given PDB file.~Creates a GROMACS structure file (GRO) adding the information of the solvent box to the input structure file.~Creates a new compressed GROMACS topology adding ions until reaching the desired concentration to the input compressed GROMACS topology. ~Creates a new GROMACS compressed topology applying the indicated force restrains to the given input compressed topology.~Creates a GROMACS portable binary run input file (TPR) applying the desired properties from the input compressed GROMACS topology.~Performs molecular dynamics simulations from an input GROMACS TPR file.~Combination of Grompp & Mdrun blocks. Grompp, creates a GROMACS portable binary run input file (TPR) applying the desired properties from the input compressed GROMACS topology. Mdrun, performs molecular dynamics simulations from an input GROMACS TPR file.~Creates a GROMACS index file (NDX) from an input selection and an input GROMACS structure file.~Creates a GROMACS index file (NDX) from an input selection and an input GROMACS structure file.~Creates a new compressed GROMACS topology file adding solvent molecules to a given input compressed GROMACS topology file.~Creates a new GROMACS compressed topology applying the force restrains to the input groups in the input index file to the given input compressed topology.~Takes a ligand ITP file and inserts it in a topology. | install_requires=['biobb_common==3.5.1']~python_requires='==3.7.*' | python ==3.7.*~biobb_common ==3.5.1~GROMACS ==2019.1 | md,molecular,dynamics,GROMACS | ||
| biobb_ml | Biobb_ml is the Biobb module collection to perform machine learning predictions. |
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3.5.0 | LinearRegression~PolynomialRegression~RandomForestRegressor~RegressionPredict~DecisionTree~KNeighborsCoefficient~KNeighborsTrain~LogisticRegression~RandomForestClassifier~SupportVectorMachine~ClassificationPredict~AgglomerativeCoefficient~AgglClustering~DBSCANClustering~KMeansCoefficient~KMeansClustering~SpectralCoefficient~SpecClustering~ClusteringPredict~CorrelationMatrix~Dendrogram~DropColumns~DummyVariables~MapVariables~PairwiseComparison~ScaleColumns~AutoencoderNeuralNetwork~ClassificationNeuralNetwork~RecurrentNeuralNetwork~RegressionNeuralNetwork~DecodingNeuralNetwork~PredictNeuralNetwork~PLSComponents~PLS_Regression~PrincipalComponentAnalysis~Oversampling~Resampling~Undersampling | sklearn.linear_model.LinearRegression~sklearn.linear_model.LinearRegression~sklearn.ensemble.RandomForestRegressor~In house using sklearn~sklearn.model.DecisionTreeClassifier~sklearn.neighbors.KNeighborsClassifier~sklearn.neighbors.KNeighborsClassifier~sklearn.linear_model.LogisticRegression~sklearn.ensemble.RandomForestClassifier~sklearn.svm.SVC~In house using sklearn~sklearn.cluster.AgglomerativeClustering~sklearn.cluster.AgglomerativeClustering~sklearn.cluster.DBSCAN~sklearn.cluster.KMeans~sklearn.cluster.KMeans~klearn.cluster.SpectralClustering~sklearn.cluster.SpectralClustering~In house using sklearn~In house~In house~In house~In house~In house~In house~In house~tf.keras.layers.LSTM~tf.keras.Sequential~tf.keras.layers.LSTM~tf.keras.Sequential~In house using TensorFlow~In house using TensorFlow~sklearn.cross_decomposition.PLSRegression~sklearn.cross_decomposition.PLSRegression~sklearn.decomposition.PCA~imblearn.over_sampling~imblearn.combine~imblearn.under_sampling | Wrapper of the scikit-learn LinearRegression method.~Wrapper of the scikit-learn LinearRegression method with PolynomialFeatures.~Wrapper of the scikit-learn RandomForestRegressor method.~Makes predictions from an input dataset and a given regression model.~Wrapper of the scikit-learn DecisionTreeClassifier method.~Wrapper of the scikit-learn KNeighborsClassifier method.~Wrapper of the scikit-learn KNeighborsClassifier method.~Wrapper of the scikit-learn LogisticRegression method.~Wrapper of the scikit-learn RandomForestClassifier method.~Wrapper of the scikit-learn SupportVectorMachine method.~Makes predictions from an input dataset and a given classification model.~Wrapper of the scikit-learn AgglomerativeCoefficient method.~Wrapper of the scikit-learn AgglomerativeClustering method.~Wrapper of the scikit-learn DBSCAN method.~Wrapper of the scikit-learn KMeans method.~Wrapper of the scikit-learn KMeans method.~Wrapper of the scikit-learn SpectralClustering method.~Wrapper of the scikit-learn SpectralClustering method.~Makes predictions from an input dataset and a given clustering model.~Generates a correlation matrix from a given dataset.~Generates a dendrogram from a given dataset.~Drops columns from a given dataset.~Converts categorical variables into dummy/indicator variables (binaries).~Maps the values of a given dataset.~Generates a pairwise comparison from a given dataset.~Scales columns from a given dataset.~Wrapper of the TensorFlow Keras LSTM method for encoding.~Wrapper of the TensorFlow Keras Sequential method for classification.~Wrapper of the TensorFlow Keras LSTM method using Recurrent Neural Networks.~Wrapper of the TensorFlow Keras Sequential method for regression.~Wrapper of the TensorFlow Keras LSTM method for decoding.~Makes predictions from an input dataset and a given model.~Wrapper of the scikit-learn PLSRegression method.~Wrapper of the scikit-learn PLSRegression method.~Wrapper of the scikit-learn PCA method.~Wrapper of most of the imblearn.over_sampling methods.~Wrapper of the imblearn.combine methods.~Wrapper of most of the imblearn.under_sampling methods. | install_requires=['biobb_common==3.5.1', 'scikit-learn ==0.23.1', 'pandas ==1.0.5', 'seaborn ==0.10.1', 'tensorflow ==2.1.0', 'h5py ==2.10.0', 'imbalanced-learn ==0.7.0']~python_requires='==3.7.*' | python ==3.7.*~biobb_common ==3.5.1~scikit-learn ==0.23.1~pandas ==1.0.5~seaborn ==0.10.1~tensorflow ==2.1.0~h5py ==2.10.0~imbalanced-learn ==0.7.0 | machine learning,deep learning,neural networks,regression,classification,clustering,dimensionality reduction,resampling,scikit-learn,tensorflow,imblearn | ||
| biobb_model | Biobb_model is the Biobb module collection to check and model 3d structures, create mutations or reconstruct missing atoms. |
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3.5.1 | FixSideChain~FixBackbone~Mutate~FixAmides~FixChirality~CheckingLog | in house using biobb_structure_checking~in house using biobb_structure_checking~in house using biobb_structure_checking~in house using biobb_structure_checking~in house using biobb_structure_checking~in house using biobb_structure_checking | Reconstructs the missing side chains and heavy atoms of the given PDB file.~Reconstructs the missing backbone atoms of the given PDB file.~Creates a new PDB file performing the mutations given in a list of amino acid mutations to the input PDB file.~Creates a new PDB file flipping the clashing amide groups.~Creates a new PDB file fixing stereochemical errors in residue side-chains changing It's chirality.~Creates a log report o stereochemical errors in the input structure | install_requires=['biobb_common==3.5.1', 'biobb_structure_checking==3.7.3']~python_requires='==3.7.*' | python ==3.7.*~biobb_common ==3.5.1~biobb_structure_checking ==3.7.3 | model,mutate,side chain,amide,chirality | ||
| biobb_pmx | Biobb_pmx is the Biobb module collection to perform PMX executions. |
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3.5.0 | Pmxmutate~PmxGentop~Pmxanalyse | pmx~pmx~pmx | Wrapper class for the PMX mutate module.~Wrapper class for the PMX gentop module.~Wrapper class for the PMX analyse module. | install_requires=['biobb_common==3.5.1']~python_requires='==3.7.*' | python ==3.7.*~biobb_common ==3.5.1~pmx_biobb ==1.0.0 | pmx,energy | ||
| biobb_structure_utils | Biobb_structure_utils is the Biobb module collection to modify or extract information from a PDB structure file. |
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3.5.2 | CatPDB~ExtractAtoms~ExtractChain~ExtractHeteroAtoms~ExtractModel~ExtractProtein~RemoveLigand~RemovePdbWater~RenumberStructure~SortGroResidues~StrCheckAddHydrogens~StructureCheck | in house~in house~Structure Checking from MDWeb~in house using biopython~Structure Checking from MDWeb~Structure Checking from MDWeb~in house~Structure Checking from MDWeb~in house~in house~Structure Checking from MDWeb~Structure Checking from MDWeb | Class to concat two PDB structures in a single PDB file.~Class to extract atoms from a 3D structure.~This class is a wrapper of the Structure Checking tool to extract a chain from a 3D structure.~Class to extract hetero-atoms from a 3D structure.~This class is a wrapper of the Structure Checking tool to extract a model from a 3D structure.~This class is a wrapper of the Structure Checking tool to extract a protein from a 3D structure.~Class to remove the selected ligand atoms from a 3D structure.~This class is a wrapper of the Structure Checking tool to remove water molecules from PDB 3D structures.~Class to renumber atomic indexes from a 3D structure.~Class to sort the selected residues from a GRO 3D structure.~This class is a wrapper of the Structure Checking tool to add hydrogens to a 3D structure.~This class is a wrapper of the Structure Checking tool to generate summary checking results on a json file. | install_requires=['biobb_common==3.5.1', 'biobb_structure_checking==3.7.3']~python_requires='==3.7.*' | python ==3.7.*~biobb_common ==3.5.1~biobb_structure_checking ==3.7.3 | structure,protein,heteroatom,biopython |