# BioBB MEM Command Line Help Generic usage: ```python biobb_command [-h] --config CONFIG --input_file(s) --output_file ``` ----------------- ## Lpp_assign_leaflets Wrapper of the LiPyphilic AssignLeaflets module for assigning lipids to leaflets in a bilayer. ### Get help Command: ```python lpp_assign_leaflets -h ``` usage: lpp_assign_leaflets [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH --output_leaflets_path OUTPUT_LEAFLETS_PATH Assign lipids to leaflets in a bilayer. options: -h, --help show this help message and exit --config CONFIG Configuration file required arguments: --input_top_path INPUT_TOP_PATH Path to the input structure or topology file. Accepted formats: crd, gro, mdcrd, mol2, pdb, pdbqt, prmtop, psf, top, tpr, xml, xyz. --input_traj_path INPUT_TRAJ_PATH Path to the input trajectory to be processed. Accepted formats: arc, crd, dcd, ent, gro, inpcrd, mdcrd, mol2, nc, pdb, pdbqt, restrt, tng, trr, xtc, xyz. --output_leaflets_path OUTPUT_LEAFLETS_PATH Path to the output processed analysis. ### I / O Arguments Syntax: input_argument (datatype) : Definition Config input / output arguments for this building block: * **input_top_path** (*string*): Path to the input structure or topology file. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/data/A01JD/A01JD.pdb). Accepted formats: CRD, GRO, MDCRD, MOL2, PDB, PDBQT, PRMTOP, PSF, TOP, TPR, XML, XYZ * **input_traj_path** (*string*): Path to the input trajectory to be processed. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/data/A01JD/A01JD.xtc). Accepted formats: ARC, CRD, DCD, ENT, GRO, INPCRD, MDCRD, MOL2, NC, PDB, PDBQT, RESTRT, TNG, TRR, XTC, XYZ * **output_leaflets_path** (*string*): Path to the output leaflet assignments. File type: output. [Sample file](https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/reference/lipyphilic_biobb/leaflets.csv). Accepted formats: CSV ### Config Syntax: input_parameter (datatype) - (default_value) Definition Config parameters for this building block: * **start** (*integer*): (None) Starting frame for slicing.. * **stop** (*integer*): (None) Ending frame for slicing.. * **steps** (*integer*): (None) Step for slicing.. * **lipid_sel** (*string*): (all) Selection string for the lipids in a membrane. The selection should cover **all** residues in the membrane, including cholesterol.. * **midplane_sel** (*string*): (None) Selection string for residues that may be midplane. Any residues not in this selection will be assigned to a leaflet regardless of its proximity to the midplane. The default is `None`, in which case all lipids will be assigned to either the upper or lower leaflet.. * **midplane_cutoff** (*number*): (0.0) Minimum distance in *z* an atom must be from the midplane to be assigned to a leaflet rather than the midplane. The default is `0`, in which case all lipids will be assigned to either the upper or lower leaflet. Must be non-negative.. * **n_bins** (*integer*): (1) Number of bins in *x* and *y* to use to create a grid of membrane patches. Local membrane midpoints are computed for each patch, and lipids assigned a leaflet based on the distance to their local membrane midpoint. The default is `1`, which is equivalent to computing a single global midpoint.. * **remove_tmp** (*boolean*): (True) Remove temporal files.. * **restart** (*boolean*): (False) Do not execute if output files exist.. * **sandbox_path** (*string*): (./) Parent path to the sandbox directory.. ### YAML #### [Common config file](https://github.com/bioexcel/biobb_mem/blob/master/biobb_mem/test/data/config/config_lpp_assign_leaflets.yml) ```python properties: disable_logs: true lipid_sel: (resname DPPC and name P8) ``` #### Command line ```python lpp_assign_leaflets --config config_lpp_assign_leaflets.yml --input_top_path A01JD.pdb --input_traj_path A01JD.xtc --output_leaflets_path leaflets.csv ``` ### JSON #### [Common config file](https://github.com/bioexcel/biobb_mem/blob/master/biobb_mem/test/data/config/config_lpp_assign_leaflets.json) ```python { "properties": { "disable_logs": true, "lipid_sel": "(resname DPPC and name P8)" } } ``` #### Command line ```python lpp_assign_leaflets --config config_lpp_assign_leaflets.json --input_top_path A01JD.pdb --input_traj_path A01JD.xtc --output_leaflets_path leaflets.csv ``` ## Mda_hole Wrapper of the MDAnalysis HOLE module for analyzing ion channel pores or transporter pathways. ### Get help Command: ```python mda_hole -h ``` usage: mda_hole [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH --output_hole_path OUTPUT_HOLE_PATH Analyze ion channel pores or transporter pathways. options: -h, --help show this help message and exit --config CONFIG Configuration file required arguments: --input_top_path INPUT_TOP_PATH Path to the input structure or topology file. Accepted formats: crd, gro, mdcrd, mol2, pdb, pdbqt, prmtop, psf, top, tpr, xml, xyz. --input_traj_path INPUT_TRAJ_PATH Path to the input trajectory to be processed. Accepted formats: arc, crd, dcd, ent, gro, inpcrd, mdcrd, mol2, nc, pdb, pdbqt, restrt, tng, trr, xtc, xyz. --output_hole_path OUTPUT_HOLE_PATH Path to the output HOLE analysis results. Accepted formats: vmd. ### I / O Arguments Syntax: input_argument (datatype) : Definition Config input / output arguments for this building block: * **input_top_path** (*string*): Path to the input structure or topology file. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/data/A01JD/A01JD.pdb). Accepted formats: CRD, GRO, MDCRD, MOL2, PDB, PDBQT, PRMTOP, PSF, TOP, TPR, XML, XYZ * **input_traj_path** (*string*): Path to the input trajectory to be processed. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/data/A01JD/A01JD.xtc). Accepted formats: ARC, CRD, DCD, ENT, GRO, INPCRD, MDCRD, MOL2, NC, PDB, PDBQT, RESTRT, TNG, TRR, XTC, XYZ * **output_hole_path** (*string*): Path to the output HOLE analysis results. File type: output. [Sample file](None). Accepted formats: VMD ### Config Syntax: input_parameter (datatype) - (default_value) Definition Config parameters for this building block: * **start** (*integer*): (None) Starting frame for slicing.. * **stop** (*integer*): (None) Ending frame for slicing.. * **steps** (*integer*): (None) Step for slicing.. * **select** (*string*): (protein) The selection string to create an atom selection that the HOLE analysis is applied to.. * **cpoint** (*array*): (None) Coordinates of a point inside the pore (Å). If None, tries to guess based on the geometry.. * **cvect** (*array*): (None) Search direction vector. If None, tries to guess based on the geometry.. * **executable** (*string*): (hole) Path to the HOLE executable.. * **remove_tmp** (*boolean*): (True) Remove temporal files.. * **restart** (*boolean*): (False) Do not execute if output files exist.. * **sandbox_path** (*string*): (./) Parent path to the sandbox directory.. ### YAML #### [Common config file](https://github.com/bioexcel/biobb_mem/blob/master/biobb_mem/test/data/config/config_mda_hole.yml) ```python properties: disable_logs: true select: protein steps: 5 ``` #### Command line ```python mda_hole --config config_mda_hole.yml --input_top_path A01JD.pdb --input_traj_path A01JD.xtc --output_hole_path output.vmd ``` ### JSON #### [Common config file](https://github.com/bioexcel/biobb_mem/blob/master/biobb_mem/test/data/config/config_mda_hole.json) ```python { "properties": { "disable_logs": true, "select": "protein", "steps": 5 } } ``` #### Command line ```python mda_hole --config config_mda_hole.json --input_top_path A01JD.pdb --input_traj_path A01JD.xtc --output_hole_path output.vmd ``` ## Cpptraj_density Wrapper of the Ambertools Cpptraj module for calculating density profile along an axis of a given cpptraj compatible trajectory. ### Get help Command: ```python cpptraj_density -h ``` usage: cpptraj_density [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH --output_cpptraj_path OUTPUT_CPPTRAJ_PATH [--output_traj_path OUTPUT_TRAJ_PATH] Calculates the density along an axis of a given cpptraj compatible trajectory. options: -h, --help show this help message and exit --config CONFIG Configuration file --output_traj_path OUTPUT_TRAJ_PATH Path to the output processed trajectory. required arguments: --input_top_path INPUT_TOP_PATH Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip. --input_traj_path INPUT_TRAJ_PATH Path to the input trajectory to be processed. Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib. --output_cpptraj_path OUTPUT_CPPTRAJ_PATH Path to the output processed analysis. ### I / O Arguments Syntax: input_argument (datatype) : Definition Config input / output arguments for this building block: * **input_top_path** (*string*): Path to the input structure or topology file. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/data/ambertools/topology.top). Accepted formats: TOP, PDB, PRMTOP, PARMTOP, ZIP * **input_traj_path** (*string*): Path to the input trajectory to be processed. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/data/ambertools/trajectory.xtc). Accepted formats: MDCRD, CRD, CDF, NETCDF, NC, RESTART, NCRESTART, RESTARTNC, DCD, CHARMM, COR, PDB, MOL2, TRR, GRO, BINPOS, XTC, CIF, ARC, SQM, SDF, CONFLIB * **output_cpptraj_path** (*string*): Path to the output processed density analysis. File type: output. [Sample file](https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/reference/ambertools/reference/density_default.dat). Accepted formats: DAT, AGR, XMGR, GNU * **output_traj_path** (*string*): Path to the output processed trajectory. File type: output. [Sample file](https://github.com/bioexcel/biobb_mem/raw/master/biobb_mem/test/reference/ambertools/trajectory_out.dcd). Accepted formats: MDCRD, CRD, CDF, NETCDF, NC, RESTART, NCRESTART, RESTARTNC, DCD, CHARMM, COR, PDB, MOL2, TRR, GRO, BINPOS, XTC, CIF, ARC, SQM, SDF, CONFLIB ### Config Syntax: input_parameter (datatype) - (default_value) Definition Config parameters for this building block: * **start** (*integer*): (1) Starting frame for slicing. * **end** (*integer*): (-1) Ending frame for slicing. * **steps** (*integer*): (1) Step for slicing. * **density_type** (*string*): (number) Number, mass, partial charge (q) or electron (Ne - q) density. Electron density will be converted to e-/Å3 by dividing the average area spanned by the other two dimensions.. * **mask** (*string*): (*) Arbitrary number of masks for atom selection; a dataset is created and the output will contain entries for each mask.. Default: all atoms.. * **delta** (*number*): (0.25) Resolution, i.e. determines number of slices (i.e. histogram bins).. * **axis** (*string*): (z) Coordinate (axis) for density calculation. Vales: x, y, z.. * **bintype** (*string*): (bincenter) Determine whether histogram bin coordinates will be based on bin center (default) or bin edges. . * **restrict** (*string*): (None) If specified, only calculate the density within a cylinder or square shape from the specified axis as defined by a distance cutoff. . * **cutoff** (*number*): (None) The distance cutoff for 'restrict'. Required if 'restrict' is specified.. * **binary_path** (*string*): (cpptraj) Path to the cpptraj executable binary.. * **remove_tmp** (*boolean*): (True) Remove temporal files.. * **restart** (*boolean*): (False) Do not execute if output files exist.. * **sandbox_path** (*string*): (./) Parent path to the sandbox directory.. ### YAML #### [Common config file](https://github.com/bioexcel/biobb_mem/blob/master/biobb_mem/test/data/config/config_cpptraj_density.yml) ```python properties: disable_logs: true ``` #### Command line ```python cpptraj_density --config config_cpptraj_density.yml --input_top_path topology.top --input_traj_path trajectory.xtc --output_cpptraj_path density_default.dat --output_traj_path trajectory_out.dcd ``` ### JSON #### [Common config file](https://github.com/bioexcel/biobb_mem/blob/master/biobb_mem/test/data/config/config_cpptraj_density.json) ```python { "properties": { "disable_logs": true } } ``` #### Command line ```python cpptraj_density --config config_cpptraj_density.json --input_top_path topology.top --input_traj_path trajectory.xtc --output_cpptraj_path density_default.dat --output_traj_path trajectory_out.dcd ```