BioExcel Building Blocks Source & Docs

Source and docs for BioExcel Building Blocks
Package Description Python ReadTheDocs Bioconda Docker Version Building block Wrapped tool Description Dependencies Pypi Dependencies Conda Dependencies Conda Extra Channels Keywords
biobb_amber biobb_amber is a BioBB category for AMBER MD package, allowing setup and simulation of atomistic MD simulations using AMBER MD package and its associated AMBER tools 3.7.1 CpptrajRandomizeIons~AmberToPDB~LeapAddIons~LeapGenTop~LeapSolvate~LeapBuildLinearStructure~NabBuildDNAStructure~ParmedCpinUtil~ParmedHMassRepartition~Pdb4amberRun~PmemdMDRun~ProcessMinOut~ProcessMDOut~SanderMDRun~CestatsRun~CphstatsRun cpptraj~ambpdb~tLeap~tLeap~tLeap~tLeap~nab~parmed~parmed~pdb4amber~pmemd~process~process~sander~cestats~cphstats Swap specified ions with randomly selected solvent molecules using cpptraj tool from the AmberTools MD package~Generates a PDB structure from AMBER topology (parmtop) and coordinates (crd) files, using the ambpdb tool from the AmberTools MD package~Adds counterions to a system box for an AMBER MD system using tLeap tool from the AmberTools MD package~Generates a MD topology from a molecule structure using tLeap tool from the AmberTools MD package~Creates and solvates a system box for an AMBER MD system using tLeap tool from the AmberTools MD package~Builds a linear (unfolded) 3D structure from an AA sequence using tLeap tool from the AmberTools MD package~Builds a 3D structure from a DNA sequence using nab (Nucleic Acid Builder) tool from the AmberTools MD package~Creates a cpin file for constant pH simulations from an AMBER topology file using parmed tool from the AmberTools MD package~Performs a Hydrogen Mass Repartition from an AMBER topology file using parmed tool from the AmberTools MD package~Analyse PDB files and clean them for further usage, especially with the LEaP programs of Amber, using pdb4amber tool from the AmberTools MD package~Runs molecular dynamics using pmemd tool from the AMBER MD package~Parses the AMBER (sander) minimization output file (log) and dumps statistics that can then be plotted. Using the process_minout.pl tool from the AmberTools MD package~Parses the AMBER (sander) md output file (log) and dumps statistics that can then be plotted. Using the process_mdout.pl tool from the AmberTools MD package~Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package~Analyzing the results of constant Redox potential MD simulations using cestats tool from the AMBER MD package~Analyzing the results of constant pH MD simulations using cphstats tool from the AMBER MD package install_requires=['biobb_common==3.7.0']~python_requires='==3.7.*' python ==3.7.*~biobb_common ==3.7.0~ambertools ==20.0 Amber,AmberTools,cpptraj,parmed,leap,nab,MD
biobb_analysis Biobb_analysis is the Biobb module collection to perform analysis of molecular dynamics simulations. 3.7.0 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==3.7.0']~python_requires='==3.7.*' python ==3.7.*~biobb_common ==3.7.0~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. 3.7.0 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==3.7.0']~python_requires='==3.7.*' python ==3.7.*~biobb_common ==3.7.0~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. 3.7.0 in house Biobb Base structure & common elements. install_requires=['pyyaml', 'requests', 'biopython==1.79']~python_requires='==3.7.*' python ==3.7.*~pyyaml~requests~biopython ==1.79 common
biobb_dna Biobb_dna is a package composed of different analyses for nucleic acid trajectories 3.6.2 Curves~Canal~Canion~BIPopulations~CanonicalAG~Puckering~HelParAverages~HelParTimeSeries~HelParBimodality~AverageStiffness~BPStiffness~InterBasePairCorrelation~InterHelParCorrelation~InterSequenceCorrelation~IntraBasePairCorrelation~IntraHelParCorrelation~IntraSequenceCorrelation Curves~Canal~Canion~In House~In House~In House~In House~In House~In House~In House~In House~In House~In House~In House~In House~In House~In House Wrapper for the Cur+ program that is part of the Curves+ software suite.~Wrapper for the Canal program that is part of the Curves+ software suite.~Wrapper for the Canion executable that is part of the Curves+ software suite. ~Computation of BI/BII populations for the epsil/zeta helical parameters.~Calculate Canonical Alpha/Gamma populations from alpha and gamma parameters.~Calculate Puckering from phase parameters.~Load .ser file for a given helical parameter and read each column corresponding to a base calculating average over each one.~Created time series and histogram plots for each base pair from a helical parameter series file.~Determine binormality/bimodality from a helical parameter series dataset.~Calculate average stiffness constants for each base pair of a trajectory's series.~Calculate stiffness constants matrix between all six helical parameters for a single base pair step.~Calculate correlation between all base pairs of a single sequence and for a single helical parameter.~Calculate correlation between helical parameters for a single inter-base pair.~Calculate correlation between all base pairs of a single sequence and for a single helical parameter.~Calculate correlation between all intra-base pairs of a single sequence and for a single helical parameter.~Calculate correlation between helical parameters for a single intra-base pair.~Calculate correlation between all intra-base pairs of a single sequence and for a single helical parameter. install_requires=['biobb_common==3.6.0']~python_requires='==3.7.*'~pandas>=1.2~matplotlib>=3.3~numpy>=1.20~scikit-learn>=0.24 python ==3.7.*~biobb_common ==3.6.0~curves~pandas>=1.2~matplotlib>=3.3~numpy>=1.20~scikit-learn>=0.24 dna,curves,canal
biobb_io Biobb_io is the Biobb module collection to fetch data to be consumed by the rest of the Biobb building blocks. 3.7.0 Drugbank~Ligand~Pdb~PdbVariants~PdbClusterZip~MemProtMDSimList~MemProtMDSimSearch~MemProtMDSim~ApiBindingSite~CanonicalFasta~Mmcif~IdealSdf~StructureInfo API Call~API Call~API Call~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.~This class is a wrapper for downloading a MMCIF structure from the Protein Data Bank.~This class is a wrapper for downloading an ideal SDF ligand from the Protein Data Bank.~This class is a wrapper for getting all the available information of a structure from the Protein Data Bank. install_requires=['biobb_common==3.7.0']~python_requires='==3.7.*' python ==3.7.*~biobb_common ==3.7.0 io,mmb,pdb,rcsb,ebi,MemProtMD,sdf,mmcif,fasta
biobb_md Biobb_md is the Biobb module collection to perform molecular dynamics simulations. 3.7.0 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==3.7.0']~python_requires='==3.7.*' python ==3.7.*~biobb_common ==3.7.0~GROMACS ==2019.1 md,molecular,dynamics,GROMACS
biobb_ml Biobb_ml is the Biobb module collection to perform machine learning predictions 3.7.0 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==3.7.0', 'scikit-learn ==0.24.2', 'pandas ==1.0.5', 'seaborn ==0.10.1', 'tensorflow ==2.4.0', 'h5py ==2.10.0', 'imbalanced-learn ==0.7.0']~python_requires='==3.7.*' python ==3.7.*~biobb_common ==3.7.0~scikit-learn ==0.24.2~pandas ==1.0.5~seaborn ==0.10.1~tensorflow ==2.4.0~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 3.7.0 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==3.7.0', 'biobb_structure_checking==3.8.5']~python_requires='==3.7.*' python ==3.7.*~biobb_common ==3.7.0~biobb_structure_checking ==3.8.5 model,mutate,side chain,amide,chirality
biobb_pmx Biobb_pmx is the Biobb module collection to perform PMX executions. 3.6.0 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==3.6.0']~python_requires='==3.7.*' python ==3.7.*~biobb_common ==3.6.0~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. 3.6.1 CatPDB~ExtractAtoms~ExtractChain~ExtractHeteroAtoms~ExtractModel~ExtractMolecule~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 molecule 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==3.6.0', 'biobb_structure_checking==3.8.5']~python_requires='==3.7.*' python ==3.7.*~biobb_common ==3.6.0~biobb_structure_checking ==3.8.5 structure,protein,heteroatom,biopython
biobb_vs Biobb_vs is the Biobb module collection to perform virtual screening studies. 3.7.0 AutoDockVinaRun~BindingSite~Box~BoxResidues~ExtractModelPDBQT~FPocketRun~FPocketFilter~FPocketSelect AutoDock Vina~in house using biopython~in house~in house using biopython~in house using biopython~fpocket~in house~in house Wrapper of the AutoDock Vina software.~This class finds the binding site of the input_pdb.~This class sets the center and the size of a rectangular parallelepiped box around a set of residues or a pocket.~This class sets the center and the size of a rectangular parallelepiped box around a set of residues.~Extracts a model from a PDBQT file with several models.~Wrapper of the fpocket software for finding the binding sites of a structure.~Performs a search over the outputs of the fpocket building block.~Selects a single pocket in the outputs of the fpocket building block.. install_requires=['biobb_common==3.7.0']~python_requires='==3.7.*' python ==3.7.*~biobb_common ==3.7.0~autodock-vina ==1.1.2~fpocket ==3.1.4.2 virtual screening,autodock,vina,fpocket,binding site