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
biobb_analysis Biobb_analysis is the Biobb module collection to perform analysis of molecular dynamics simulations. 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. 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. 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. 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. 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. 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. 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. 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. 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