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_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 |
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5.2.0 | CpptrajRandomizeIons~AmberToPDB~LeapAddIons~LeapGenTop~LeapSolvate~LeapBuildLinearStructure~ParmedCpinUtil~ParmedHMassRepartition~Pdb4amberRun~PmemdMDRun~ProcessMinOut~ProcessMDOut~SanderMDRun~CestatsRun~CphstatsRun | cpptraj~ambpdb~tLeap~tLeap~tLeap~tLeap~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~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==5.2.0']~python_requires='>=3.10' | python >=3.10~biobb_common ==5.2.0~ambertools >=22.5~numpy <=2.2.6 | Amber,AmberTools,cpptraj,parmed,leap,MD | ||
| biobb_analysis | Biobb_analysis is the Biobb module collection to perform analysis of molecular dynamics simulations |
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5.2.0 | 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==5.2.0']~python_requires='>=3.10' | python >=3.10~biobb_common ==5.2.0~gromacs >=2024.5~ambertools >=22.5 | analysis,ambertools,gromacs | ||
| biobb_chemistry | Biobb_chemistry is the Biobb module collection to perform chemistry over molecular dynamics simulations. |
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5.2.0 | AcpypeParamsAC~AcpypeParamsCNS~AcpypeParamsGMX~AcpypeParamsGMXOPLS~AcpypeConvertAMBERtoGMX~BabelConvert~BabelAddHydrogens~BabelRemoveHydrogens~BabelMinimize~ReduceAddHydrogens~ReduceRemoveHydrogens | ACPype~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.~Conversion of AMBER topologies to GROMACS.~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==5.2.0']~python_requires='>=3.10' | python >=3.10~biobb_common ==5.2.0~openbabel ==3.1.1~ambertools >=22.5~acpype >=2023.10.27 | chemistry,ambertools,acpype,babel | ||
| biobb_cmip | Biobb_cmip is the Biobb module collection to compute classical molecular interaction potentials. |
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5.2.0 | 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==5.2.0', 'mdanalysis', 'biobb_structure_checking==3.15.6']~python_requires='>=3.10' | python >=3.10~biobb_common ==5.2.0~cmip ==2.7.0~mdanalysis >=2.0.0~biobb_structure_checking==3.15.6 | classical,molecular,interaction,potentials | ||
| biobb_common | Biobb_common is the base package required to use all the biobb packages. |
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5.2.0 | FolderTest | Common FolderTest | The FolderTest module. | install_requires=['pyyaml', 'requests', 'biopython', 'jsonschema']~python_requires='>=3.10' | python >=3.10~pyyaml~requests~biopython~jsonschema | common | ||
| biobb_cp2k | Biobb_cp2k is a BioBB category for CP2K QM package, allowing setup and simulation of QM simulations using CP2K QM package |
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5.2.0 | Cp2kRun~Cp2kPrep | CP2K~in house | Run CP2K QM software~Helper bb to prepare inputs for the CP2K QM tool | install_requires=['biobb_common==5.2.0']~python_requires='>=3.10' | python >=3.10~biobb_common ==5.2.0~cp2k ==7.1.0 | CP2K,QM | ||
| biobb_dna | Biobb_dna is a package composed of different analyses for nucleic acid trajectories |
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5.2.0 | 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==5.2.0', 'pandas>=1.3.0', 'scikit-learn>=0.24.2']~python_requires='>=3.10' | python >=3.10~biobb_common ==5.2.0~curves==3.0.3~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. |
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5.2.0 | 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==5.2.0', 'scipy>=1.13.0,<1.14.0']~python_requires='>=3.10,<3.12' | python >=3.10,<3.12~sciPy >=1.13.0,<1.14.0~biobb_common ==5.2.0~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. |
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5.2.0 | 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==5.2.0']~python_requires='>=3.10' | python >=3.10~biobb_common ==5.2.0~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. |
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5.2.0 | 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==5.2.0']~python_requires='>=3.10' | python >=3.10~biobb_common ==5.2.0~godmd ==1.7~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. |
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5.2.0 | 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==5.2.0']~python_requires='>=3.10' | python >=3.10~biobb_common ==5.2.0~gromacs=2022.2=nompi_h1c20066_100 | md,molecular,dynamics,GROMACS | ||
| biobb_haddock | biobb_haddock is the Biobb module collection to compute information-driven flexible protein-protein docking |
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5.2.0 | CapriEval~ClustFCC~ContactMap~EMRef~FlexRef~Haddock3Extend~Haddock3Run~RigidBody~SeleTopClusts~SeleTop~Topology~Accessibility~ActpassToAmbig~PassiveFromActive~RestrainBodies | Haddock CapriEval~Haddock ClustFCC~Haddock ContactMap~Haddock EMRef~Haddock FlexRef~Haddock3 Extend~Haddock3 Run~Haddock RigidBody~Haddock SeleTopClusts~Haddock SeleTop~Haddock Topology~Haddock3 Accessibility~Haddock3 ActpassToAmbig~Haddock3 PassiveFromActive~Haddock3 RestrainBodies | 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 ContactMap module. Haddock ContactMap module generates contact maps for protein complexes.~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 Haddock3Extend module. Extends a previously run Haddock3 workflow with additional steps.~The Haddock3Run module. Runs a complete Haddock3 workflow for protein-protein docking.~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.~The Accessibility module. Calculates solvent accessibility for defining passive residues in Haddock3.~The ActpassToAmbig module. Converts active and passive residue lists to ambiguous restraints for Haddock3.~The PassiveFromActive module. Generates passive residues from active residues for Haddock3.~The RestrainBodies module. Creates restraints to maintain the relative orientation of multi-body complexes in Haddock3. | install_requires=['biobb_common==5.2.0']~python_requires='>=3.10' | python >=3.10~biobb_common ==5.2.0~haddock_biobb ==2025.5.0 | 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. |
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5.2.0 | Ligand~Pdb~AlphaFold~PdbVariants~PdbClusterZip~MemProtMDSimList~MemProtMDSimSearch~MemProtMDSim~ApiBindingSite~CanonicalFasta~Mmcif~IdealSdf~StructureInfo~MDDB | 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 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.~This class is a wrapper for downloading a trajectory / topology pair from the MDDB Database. | install_requires=['biobb_common==5.2.0']~python_requires='>=3.10' | python >=3.10~biobb_common ==5.2.0 | io,mmb,pdb,rcsb,ebi,MemProtMD,sdf,mmcif,fasta,alphafold,mddb | ||
| biobb_md | Biobb_md is the Biobb module collection to perform molecular dynamics simulations. IMPORTANT: This package has been discontinued, superseeded by biobb_gromacs. |
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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_mem | Biobb_mem is a BioBB category for membrane analysis and manipulation. It allows analysis of membrane properties and manipulation of membrane systems using tools like MDAnalysis and LiPyphilic. |
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5.2.0 | CpptrajDensity~FatslimAPL~FatslimMembranes~GorderAA~GorderCG~GorderUA~LPPAssignLeaflets~LPPFlipFlop~LPPZPositions~MDAHole | cpptraj_density~fatslim_apl~fatslim_membranes~gorder_aa~gorder_cg~gorder_ua~lpp_assign_leaflets~lpp_flip_flop~lpp_zpositions~mda_hole | Calculates the density along an axis of a given cpptraj compatible trajectory.~Calculate the area per lipid.~Identify membrane types and leaflets.~Compute atomistic lipid order parameters using gorder order tool.~Compute coarse-grained lipid order parameters using gorder order tool.~Compute united atom lipid order parameters using gorder order tool.~Assign lipids to leaflets in a bilayer.~Find flip-flop events in a lipid bilayer.~Calculate the z distance in of lipids to the bilayer center.~Wrapper of the MDAnalysis Hole module for analyzing hole geometry in protein channels and other macromolecular structures. | install_requires=['biobb_common==5.2.0']~python_requires='>=3.10' | python >=3.10~biobb_common ==5.2.0~ambertools >=22.5~lipyphilic ==0.11.0~mdahole2~fatslim_biobb ==0.2.2 | membrane,keywords | ||
| biobb_ml | Biobb_ml is the Biobb module collection to perform machine learning predictions. IMPORTANT: This package has been discontinued, superseeded by biobb_pytorch. |
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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 |
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5.2.0 | 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==5.2.0', 'biobb_structure_checking>=3.15.6', 'xmltodict']~python_requires='>=3.10' | python >=3.10~biobb_common ==5.2.0~biobb_structure_checking >=3.15.6~xmltodict | model,mutate,side chain,amide,chirality | ||
| biobb_pdb_tools | Biobb PDB Tools is a swiss army knife for manipulating and editing PDB files |
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5.2.0 | Pdbchain~Pdbchainxseg~Pdbdelhetatm~Pdbfetch~Pdbfixinsert~Pdbkeepcoord~Pdbmerge~Pdbmkensemble~Pdbreres~Pdbseg~Pdbselaltloc~Pdbselchain~Pdbselres~Pdbsplitmodel~Pdbsplitseg~Pdbtidy~Pdbtofasta~Pdbuniqname | pdb_chain~pdb_chainxseg~pdb_delhetatm~pdb_fetch~pdb_fixinsert~pdb_keepcoord~pdb_merge~pdb_mkensemble~pdb_reres~pdb_seg~pdb_selaltloc~pdb_selchain~pdb_selres~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.~Deletes insertion codes and shifts the residue numbering of downstream residues.~Removes all non-coordinate records from the file.~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.~Selects alternative locations from a PDB file.~Extracts one or more chains from a PDB file.~Selects residues by their index, piecewise or in a range.~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==5.2.0', 'pdb-tools==2.5.0']~python_requires='>=3.10' | python >=3.10~biobb_common ==5.2.0 | pdb,chain,model | ||
| biobb_pmx | Biobb_pmx is the Biobb module collection to perform PMX executions |
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5.2.1 | 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==5.2.0']~python_requires='>=3.10' | python >=3.10~biobb_common ==5.2.0~pmx_biobb >=5.2.2 | pmx,energy | ||
| biobb_pytorch | Biobb_pytorch is a BioBB category for creating and training Machine Learning and Deep Learning models using PyTorch. It allows building, training, and evaluating Molecular Dynamics AutoEncoders (MDAE) and other PyTorch-based models for analyzing molecular dynamics trajectories. |
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5.1.1 | BuildMDAE~MDFeaturePipeline~TrainMDAE~EvaluateMDAE~EncodeMDAE~DecodeMDAE~GeneratePlumedMDAE~Feat2TrajMDAE~LRPMDAE~ApplyMDAE | build_mdae~md_feature_pipeline~train_mdae~evaluate_mdae~encode_mdae~decode_mdae~generate_plumed_mdae~feat2traj_mdae~lrp_mdae~apply_mdae | Build a PyTorch autoencoder model (MDAE) from input statistics and hyperparameters.~Obtain Molecular Dynamics features for PyTorch MDAE model training (dataset and statistics).~Train a PyTorch autoencoder model (MDAE) from an input dataset and initial model, optionally saving the trained model and training metrics.~Evaluate a trained PyTorch autoencoder model (MDAE) on a dataset, computing loss and collecting model evaluation variables.~Apply the encoder part of a trained MDAE model to a dataset, producing latent variables (collective variables).~Apply the decoder part of a trained MDAE model to latent variables, reconstructing molecular dynamics features.~Generate a PLUMED input file, a features.dat file and a TorchScript (.ptc) model from a trained MDAE model and feature statistics, suitable for biased molecular dynamics simulations.~Convert reconstructed molecular dynamics features (e.g. decoded coordinates) into an MD trajectory file using topology information from the stats file and/or a topology file.~Perform Layer-wise Relevance Propagation on the encoder of a trained MDAE model to obtain global feature importance scores.~Apply a Molecular Dynamics AutoEncoder (MDAE) PyTorch model, the resulting denoised molecular dynamics or the reduced the dimensionality of molecular dynamics data can be used to analyze the dynamic properties of the system. | install_requires=['biobb_common==5.1.1', 'torch', 'lightning', 'mlcolvar', 'mdtraj']~python_requires='>=3.9' | python >=3.9~biobb_common ==5.1.1~pytorch~pytorch-lightning~mlcolvar~mdtraj | pytorch,machine learning,deep learning,autoencoder,molecular dynamics,neural networks,MDAE | ||
| 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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5.2.0 | 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==5.2.0', 'biobb_structure_checking>=3.15.6']~python_requires='>=3.10' | python >=3.10~biobb_common ==5.2.0~biobb_structure_checking >=3.15.6 | structure,protein,heteroatom,biopython | ||
| biobb_vs | Biobb_vs is the Biobb module collection to perform virtual screening studies. |
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5.2.0 | 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==5.2.0']~python_requires='>=3.10' | python >=3.10~biobb_common ==5.2.0~vina ==1.2.3~fpocket ==4.1 | virtual screening,autodock,vina,fpocket,binding site |