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_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 |
|
|
|
|
|
4.2.0 | 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==4.2.0']~python_requires='>=3.8' | python >=3.8~biobb_common ==4.2.0~ambertools >=22.0 | Amber,AmberTools,cpptraj,parmed,leap,nab,MD | ||
| biobb_analysis | Biobb_analysis is the Biobb module collection to perform analysis of molecular dynamics simulations |
|
|
|
|
|
4.2.0 | 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 GROMACS module for calculating the Root Mean Square deviation (RMSd) of a given GROMACS 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==4.2.0']~python_requires='>=3.8' | python >=3.8~biobb_common ==4.2.0~gromacs ==2022.2~ambertools >=22.0 | analysis,ambertools,gromacs | ||
| biobb_chemistry | Biobb_chemistry is the Biobb module collection to perform chemistry over molecular dynamics simulations. |
|
|
|
|
|
4.2.1 | 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==4.2.0']~python_requires='>=3.8' | python >=3.8~biobb_common ==4.2.0~openbabel ==3.1.1~ambertools >=22.0~acpype ==2022.7.21 | chemistry,ambertools,acpype,babel | ||
| biobb_cmip | Biobb_cmip is the Biobb module collection to compute classical molecular interaction potentials. |
|
|
|
|
|
4.2.0 | CmipRun~CmipTitration~CmipPrepareStructure~CmipPreparePDB~CmipIgnoreResidues | CMIP cmip~CMIP titration~Prepare Structure~Prepare PDB~Ignore Residues | CMIP cmip module compute classical molecular interaction potentials.~CMIP cmip module compute classical molecular interaction potentials.~Creates a CMIP suitable PDB from an standar structure file~Creates a CMIP suitable PDB from an standar PDB file~Mark residues which charges will be ignored in the CMIP potential calculations. | install_requires=['biobb_common==4.2.0', 'mdanalysis', 'biobb_structure_checking==3.13.4']~python_requires='>=3.8' | python >=3.8~biobb_common ==4.2.0~cmip ==2.7.0~mdanalysis >=2.0.0~biobb_structure_checking==3.13.4 | classical,molecular,interaction,potentials | ||
| biobb_common | Biobb_common is the base package required to use all the biobb packages. |
|
|
|
|
|
4.2.0 | in house | Biobb Base structure & common elements. | install_requires=['pyyaml', 'requests', 'biopython']~python_requires='>=3.8' | python >=3.8~pyyaml~requests~biopython | common | |||
| biobb_cp2k | Biobb_cp2k is a BioBB category for CP2K QM package, allowing setup and simulation of QM simulations using CP2K QM package |
|
|
|
|
|
4.2.0 | Cp2kRun~Cp2kPrep | CP2K~in house | Run CP2K QM software~Helper bb to prepare inputs for the CP2K QM tool | install_requires=['biobb_common==4.2.0']~python_requires='>=3.8' | python >=3.8~biobb_common ==4.2.0~cp2k ==7.1.0 | CP2K,QM | ||
| biobb_dna | Biobb_dna is a package composed of different analyses for nucleic acid trajectories |
|
|
|
|
|
4.2.4 | Curves~Canal~CanalUnzip~Canion~BIPopulations~CanonicalAG~Puckering~HelParAverages~HelParTimeSeries~DnaTimeseriesUnzip~HelParBimodality~AverageStiffness~BPStiffness~InterBasePairCorrelation~InterHelParCorrelation~InterSequenceCorrelation~IntraBasePairCorrelation~IntraHelParCorrelation~IntraSequenceCorrelation | Curves~Canal~In House~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~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.~Tool for extracting biobb_canal output files.~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.~Tool for extracting dna_timeseries output files.~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==4.2.0', 'pandas>=1.3.0', 'scikit-learn>=0.24.2']~python_requires='>=3.8' | python >=3.8~biobb_common ==4.2.0~curves==3.0.2~pandas>=1.3.0~scikit-learn>=0.24.2 | dna,curves,canal | ||
| biobb_flexdyn | Biobb_flexdyn is the Biobb module collection for studies on the conformational landscape of native proteins. |
|
|
|
|
|
4.2.0 | ConcoordDisco~ConcoordDist~ImodImc~ImodImode~ImodImove~Nolb_nma~ProdyANM | Concoord~Concoord~Imods~Imods~Imods~NOLB~Prody | Wrapper of the Concoord_disco software.~Wrapper of the Concoord_dist software.~Wrapper of the imods_imc software.~Wrapper of the imods_imode software.~Wrapper of the imods_imove software.~Wrapper of the Nolb software.~Wrapper of the Prody software. | install_requires=['biobb_common==4.2.0']~python_requires='>=3.8' | python >=3.8~biobb_common ==4.2.0~imods~concoord~nolb~prody | 3D-Bioinfo,ELIXIR,FlexDyn,Bioinformatics,Workflows,BioExcel,Compatibility,Flexibility,Ensembles,Protein Structure | ||
| biobb_flexserv | Biobb_flexserv is a BioBB category for biomolecular flexibility studies on protein 3D structures. |
|
|
|
|
|
4.2.0 | BDRun~DMDRun~NMARun~PCZzip~PCZunzip~PCZanimate~PCZbfactor~PCZcollectivity~PCZevecs~PCZhinges~PCZinfo~PCZlindemann~PCZsimilarity~PCZstiffness | FlexServ BD~FlexServ DMD~FlexServ NMA~PCAsuite pczzip~PCAsuite pczunzip~PCAsuite pczanimate~PCAsuite pczbfactor~PCAsuite pczcollectivity~PCAsuite pczevecs~PCAsuite pczhinges~PCAsuite pczinfo~PCAsuite pczlindemann~PCAsuite pczsimilarity~PCAsuite pczstiffness | Run Brownian Dynamics from FlexServ~Run Discrete Molecular Dynamics from FlexServ~Run Normal Mode Analysis from FlexServ~Compress MD simulation trajectories with PCA suite~Uncompress MD simulation trajectories with PCA suite~Extract PCA animations from a compressed PCZ file~Extract residue bfactors x PCA mode from a compressed PCZ file~Extract PCA collectivity (numerical measure of how many atoms are affected by a given mode) from a compressed PCZ file~Extract PCA Eigen Vectors from a compressed PCZ file~Compute possible hinge regions (residues around which large protein movements are organized) of a molecule from a compressed PCZ file~Extract PCA info (variance, Dimensionality) from a compressed PCZ file~ComExtract Lindemann coefficient (an estimate of the solid-liquid behaviour of a protein) from a compressed PCZ file~Compute PCA similarity between two given compressed PCZ files~Extract PCA stiffness from a compressed PCZ file | install_requires=['biobb_common==4.2.0']~python_requires='>=3.8' | python >=3.8~biobb_common ==4.2.0~flexserv ==1.0.2~pcasuite ==1.0.0~perl | BD,DMD,NMA,Flexibility,Structure,3D | ||
| biobb_godmd | Biobb_godmd is the Biobb module collection to compute protein conformational transitions with the GOdMD method. |
|
|
|
|
|
4.2.0 | GoDMD_prep~GoDMD_run | GOdMD~GOdMD | Helper BioBB to prepare inputs for the GOdMD tool (protein conformational transitions).~Wrapper of the GOdMD tool to compute protein conformational transitions. | install_requires=['biobb_common==4.2.0']~python_requires='>=3.8' | python >=3.8~biobb_common ==4.2.0~godmd ==1.0.0~emboss | godmd,dmd,conformations,ensemble,transitions | ||
| biobb_gromacs | Biobb_gromacs is the Biobb module collection to perform molecular dynamics simulations using the GROMACS MD suite. |
|
|
|
|
|
4.2.0 | Pdb2gmx~Editconf~Genion~Genrestr~Grompp~Mdrun~GromppMdrun~MakeNdx~Gmxselect~Solvate~Trjcat~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~gmx trjcat~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.~Concatenates two or more GROMACS trajectory files.~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==4.2.0']~python_requires='>=3.8' | python >=3.8~biobb_common ==4.2.0~gromacs=2022.2=nompi_h1c20066_100 | md,molecular,dynamics,GROMACS | ||
| biobb_haddock | biobb_haddock is the Biobb module collection to compute classical molecular interaction potentials. |
|
|
|
|
|
4.2.1 | CapriEval~ClustFCC~EMRef~FlexRef~RigidBody~SeleTopClusts~SeleTop~Topology | Haddock CapriEval~Haddock ClustFCC~Haddock EMRef~Haddock FlexRef~Haddock RigidBody~Haddock SeleTopClusts~Haddock SeleTop~Haddock Topology | The CapriEval module. Haddock CapriEval module computes Capri evaluation for a docking.~The ClustFCC module. Haddock ClustFCC module computes clusters of structures using FCC.~The EMRef module. Haddock EMRef module computes an energy minimization refinement over selected structures.~The FlexRef module. Haddock FlexRef module computes a flexible refinement over selected structures.~The RigidBody module. Haddock RigidBody module compute rigid body docking between two molecules.~The SeleTopClusts module. Haddock SeleTop module selects the top clusters of a docking.~The SeleTop module. Haddock SeleTop module computes selects the top structures of a docking.~The Topology module. The Haddock Topology module creates a topology from a system to be used for docking. | install_requires=['biobb_common==4.2.0']~python_requires='>=3.9' | python >=3.9~biobb_common ==4.2.0~haddock_biobb ==3.0.4 | haddock,protein-protein,interaction,docking | ||
| biobb_io | Biobb_io is the Biobb module collection to fetch data to be consumed by the rest of the Biobb building blocks |
|
|
|
|
|
4.2.0 | Drugbank~Ligand~Pdb~AlphaFold~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~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 is a wrapper for downloading a PDB structure from the AlphaFold Protein Structure Database.~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==4.2.0']~python_requires='>=3.8' | python >=3.8~biobb_common ==4.2.0 | io,mmb,pdb,rcsb,ebi,MemProtMD,sdf,mmcif,fasta | ||
| biobb_md | Biobb_md is the Biobb module collection to perform molecular dynamics simulations. IMPORTANT: This package has been discontinued, superseeded by biobb_gromacs. |
|
|
|
|
|
3.7.2 | 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. |
|
|
|
|
|
4.2.0 | 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==4.2.0', 'scikit-learn ==0.24.2', 'pandas >=1.3.0', 'seaborn ==0.10.1', 'tensorflow ==2.4.0', 'h5py ==2.10.0', 'imbalanced-learn ==0.7.0']~python_requires='>=3.8' | python >=3.8~biobb_common ==4.2.0~scikit-learn ==0.24.2~pandas >=1.3.0~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 |
|
|
|
|
|
4.2.3 | FixSideChain~FixBackbone~FixPdb~Mutate~FixAmides~FixChirality~CheckingLog~FixAltLocs~FixSSBonds | in house using biobb_structure_checking~in house using biobb_structure_checking~in house using UniProt API~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.~Renumerates residues in a PDB structure according to a reference sequence from UniProt~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~Fix alternate locations from residues.~Fix SS bonds from residues. | install_requires=['biobb_common==4.2.0', 'biobb_structure_checking>=3.13.4', 'xmltodict']~python_requires='>=3.8' | python >=3.8~biobb_common ==4.2.0~biobb_structure_checking >=3.13.4~xmltodict | model,mutate,side chain,amide,chirality | ||
| biobb_pdb_tools | Biobb PDB Tools is a swiss army knife for manipulating and editing PDB files |
|
|
|
|
|
4.2.0 | Pdbchain~Pdbchainxseg~Pdbdelhetatm~Pdbfetch~Pdbmerge~Pdbmkensemble~Pdbreres~Pdbseg~Pdbsplitmodel~Pdbsplitseg~Pdbtidy~Pdbtofasta~Pdbuniqname | pdb_chain~pdb_chainxseg~pdb_delhetatm~pdb_fetch~pdb_merge~pdb_mkensemble~pdb_reres~pdb_seg~pdb_splitmodel~pdb_splitseg~pdb_tidy~pdb_tofasta~pdb_uniqname | Modifies the chain identifier column of a PDB file.~Swaps the segment identifier for the chain identifier.~Removes all HETATM records in the PDB file.~Downloads a structure in PDB format from the RCSB website.~Merges several PDB files into one.~Merges several PDB files into one multi-model (ensemble) file.~Renumbers the residues of the PDB file starting from a given number (default 1).~Modifies the segment identifier column of a PDB file.~Splits a PDB file into several, each containing one MODEL.~Splits a PDB file into several, each containing one segment.~Modifies the file to adhere (as much as possible) to the format specifications.~Extracts the residue sequence in a PDB file to FASTA format.~Renames atoms sequentially (C1, C2, O1, ...) for each HETATM residue. | install_requires=['biobb_common==4.2.0', 'pdb-tools==2.5.0']~python_requires='>=3.8' | python >=3.8~biobb_common ==4.2.0 | pdb,chain,model | ||
| biobb_pmx | Biobb_pmx is the Biobb module collection to perform PMX executions |
|
|
|
|
|
4.2.1 | Pmxmutate~PmxGentop~Pmxanalyse~Pmxatom_mapping~Pmxcreate_top~Pmxligand_hybrid~Pmxmerge_ff | pmx~pmx~pmx~pmx~pmx~pmx~pmx | Wrapper class for the PMX mutate module.~Wrapper class for the PMX gentop module.~Wrapper class for the PMX analyse module.~Wrapper class for the PMX atom mapping module.~Wrapper class for the PMX create topology module.~Wrapper class for the PMX hybrid ligand module.~Wrapper class for the PMX merge forcefield module. | install_requires=['biobb_common==4.2.0']~python_requires='>=3.8' | python >=3.8~biobb_common ==4.2.0~pmx_biobb ==4.1.3 | pmx,energy | ||
| biobb_pytorch | biobb_pytorch is the Biobb module collection to train and create ML & DL models using the popular PyTorch Python library |
|
|
|
|
|
4.2.1 | TrainMDAE~ApplyMDAE | PyTorch Autoencoder~PyTorch Autoencoder | Train a Molecular Dynamics AutoEncoder (MDAE) PyTorch model.~Apply a Molecular Dynamics AutoEncoder (MDAE) PyTorch model. | install_requires=['biobb_common==4.2.0', 'torch']~python_requires='>=3.8' | python >=3.8~biobb_common ==4.2.0~pytorch | md,molecular,dynamics,pytorch | ||
| biobb_structure_utils | Biobb_structure_utils is the Biobb module collection to modify or extract information from a PDB structure file. |
|
|
|
|
|
4.2.0 | CatPDB~ExtractAtoms~ExtractChain~ExtractHeteroAtoms~ExtractResidues~ClosestResidues~RemoveMolecules~ExtractModel~ExtractMolecule~RemoveLigand~RemovePdbWater~RenumberStructure~SortGroResidues~StrCheckAddHydrogens~StructureCheck | in house~in house~Structure Checking from MDWeb~in house using biopython~in house using biopython~in house using biopython~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.~Class to extract residues from a 3D structure.~Class to search closest residues from a 3D structure using Biopython.~Class to remove molecules from a 3D structure using Biopython.~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==4.2.0', 'biobb_structure_checking==3.13.4']~python_requires='>=3.8' | python >=3.8~biobb_common ==4.2.0~biobb_structure_checking ==3.13.4 | structure,protein,heteroatom,biopython | ||
| biobb_vs | Biobb_vs is the Biobb module collection to perform virtual screening studies. |
|
|
|
|
|
4.2.0 | 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==4.2.0']~python_requires='>=3.8' | python >=3.8~biobb_common ==4.2.0~vina ==1.2.3~fpocket ==4.1 | virtual screening,autodock,vina,fpocket,binding site |