BioBB MEM Command Line Help

Generic usage:

biobb_command [-h] --config CONFIG --input_file(s) <input_file(s)> --output_file <output_file>

Lpp_assign_leaflets

Wrapper of the LiPyphilic AssignLeaflets module for assigning lipids to leaflets in a bilayer.

Get help

Command:

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. 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. 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. 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 

properties:
  disable_logs: true
  lipid_sel: (resname DPPC and name P8)

Command line

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 

{
  "properties": {
    "disable_logs": true,
    "lipid_sel": "(resname DPPC and name P8)"
  }
}

Command line

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:

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. 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. 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. 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 

properties:
  disable_logs: true
  select: protein
  steps: 5

Command line

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 

{
  "properties": {
    "disable_logs": true,
    "select": "protein",
    "steps": 5
  }
}

Command line

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:

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. Accepted formats: TOP, PDB, PRMTOP, PARMTOP, ZIP
input_traj_path (string): Path to the input trajectory to be processed. File type: input. Sample file. 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. Accepted formats: DAT, AGR, XMGR, GNU
output_traj_path (string): Path to the output processed trajectory. File type: output. Sample file. 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 

properties:
  disable_logs: true

Command line

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 

{
  "properties": {
    "disable_logs": true
  }
}

Command line

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

BioBB MEM Command Line Help

Lpp_assign_leaflets

Get help

I / O Arguments

Config

YAML

Common config file

Command line

JSON

Common config file

Command line

Mda_hole

Get help

I / O Arguments

Config

YAML

Common config file

Command line

JSON

Common config file

Command line

Cpptraj_density

Get help

I / O Arguments

Config

YAML

Common config file

Command line

JSON

Common config file

Command line

Common config file 

Common config file 

Common config file 

Common config file 

Common config file 

Common config file 