BioExcel Building Blocks Source & Docs

Source and docs for BioExcel Building Blocks
Package Description Python ReadTheDocs Bioconda Docker Singularity Version Building block Wrapped tool Description Dependencies Pypi Dependencies Conda Dependencies Conda Extra Channels Keywords
biobb_analysis Biobb_analysis is the Biobb module collection to perform analysis of molecular dynamics simulations. 3.0.1 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 Creates cluster structures from a given GROMACS compatible trajectory.~Performs a Root Mean Square deviation (RMSd) analysis from a given GROMACS compatible trajectory.~Computes 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.~Extracts energy components from a given GROMACS energy file.~Corrects periodicity (image) from a given GROMACS compatible trajectory file.~Converts between GROMACS compatible structure file formats and/or extracts a selection of atoms.~Extracts an ensemble of frames containing a selection of atoms from GROMACS compatible trajectory files.~Converts between GROMACS compatible trajectory file formats and/or extracts a selection of atoms.~Calculates a structure average of a given cpptraj compatible trajectory.~Calculates the Bfactor fluctuations of a given cpptraj compatible trajectory.~Calculates the Root Mean Square deviation (RMSd) of a given cpptraj compatible trajectory.~Calculates the Root Mean Square fluctuations (RMSf) of a given cpptraj compatible trajectory.~Computes the radius of gyration (Rgyr) from a given cpptraj compatible trajectory.~Dehydrates a given cpptraj compatible trajectory stripping out solvent molecules and ions.~Strips a defined set of atoms (mask) from a given cpptraj compatible trajectory.~Extracts a particular snapshot from a given cpptraj compatible trajectory.~Extracts a particular trajectory slice from a given cpptraj compatible trajectory.~Converts between cpptraj compatible trajectory file formats and/or extracts a selection of atoms or frames.~Extracts a selection of atoms from a given cpptraj compatible trajectory.~Corrects periodicity (image) from a given cpptraj trajectory file. install_requires=['biobb_common==3.0.0']~python_requires='==3.7.*' python ==3.7.*~biobb_common ==3.0.0~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. 3.0.1 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==3.0.0']~python_requires='==3.7.*' python ==3.7.*~biobb_common ==3.0.0~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 3.0.0 in house Biobb Base structure & common elements. install_requires=['pyyaml', 'requests', 'biopython==1.76']~python_requires='==3.7.*' python ==3.7.*~pyyaml~requests~biopython ==1.76 common
biobb_io Biobb_io is the Biobb module collection to fetch data to be consumed by the rest of the Biobb building blocks. 3.0.0 Ligand~Pdb~MmbPdbVariants~MmbPdbClusterZip API Call~API Call~API Call~API Call Downloads a ligand file from the MMB REST API~Downloads a PDB file from the RCSB or MMB REST APIs.~Creates a text file containing a list of all the variants mapped to a RSCB PDB code from the corresponding UNIPROT entries.~Creates a zip file containing all the PDB files in the given sequence similarity cluster percentage of the given RSCB PDB code. install_requires=['biobb_common==3.0.0']~python_requires='==3.7.*' python ==3.7.*~biobb_common ==3.0.0 io,mmb,pdb
biobb_md Biobb_md is the Biobb module collection to perform molecular dynamics simulations. 3.0.0 Pdb2gmx~Editconf~Genion~Genrestr~Grompp~Mdrun~MakeNdx~Gmxselect~Solvate~Ndx2resttop~AppendLigand gmx pdb2gmx~gmx editconf~gmx genion~gmx genrestr~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.~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==3.0.0']~python_requires='==3.7.*' python ==3.7.*~biobb_common ==3.0.0~GROMACS ==2019.1 md,molecular,dynamics,GROMACS
biobb_model Biobb_model is the Biobb module collection to check and model 3d structures, create mutations or reconstruct missing atoms. 3.0.1 FixSideChain~Mutate 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.~Creates a new PDB file performing the mutations given in a list of amino acid mutations to the input PDB file. install_requires=['biobb_common==3.0.0', 'biobb_structure_checking==3.0.2']~python_requires='==3.7.*' python ==3.7.*~biobb_common ==3.0.0~biobb_structure_checking ==3.0.2 model,mutate,side chain
biobb_pmx Biobb_pmx is the Biobb module collection to perform PMX executions. 3.0.1 Pmxmutate~PmxGentop~Pmxanalyse pmx~pmx~pmx pmx tool to insert mutated residues in structure files for free energy simulations~pmx tool to generate hybrid GROMACS topologies: adding a B state to an .itp or .top file for a hybrid residue~pmx tool to calculate free energies from fast growth thermodynamic integration simulations. install_requires=['biobb_common==3.0.0']~python_requires='==3.7.*' python ==3.7.*~biobb_common ==3.0.0 pmx,energy
biobb_structure_utils Biobb_structure_utils is the Biobb module collection to modify or extract information from a PDB structure file. 3.0.0 CatPDB~ExtractAtoms~ExtractChain~ExtractHeteroAtoms~ExtractModel~ExtractProtein~RemoveLigand~RemovePdbWater~RenumberStructure~SortGroResidues in house~in house~in house~in house using biopython~in house~in house~in house~in house~in house~in house Class to concat two PDB structures in a single PDB file.~Class to extract atoms from a 3D structure.~Class to extract a chain from a 3D structure.~Class to extract hetero-atoms from a 3D structure.~Class to extract a model from a 3D structure.~Class to extract a protein from a 3D structure.~Class to remove the selected ligand atoms from a 3D structure.~Class 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. install_requires=['biobb_common==3.0.0', 'biobb_structure_checking==3.0.2']~python_requires='==3.7.*' python ==3.7.*~biobb_common ==3.0.0~biobb_structure_checking ==3.0.2 structure,protein,heteroatom,biopython