BioBB MEM Command Line Help

Generic usage:

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

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

Lpp_assign_leaflets

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

Get help

Command:

lpp_assign_leaflets -h

/home/rchaves/miniforge3/envs/biobb_mem/lib/python3.11/site-packages/Bio/Application/__init__.py:39: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated.

Due to the on going maintenance burden of keeping command line application
wrappers up to date, we have decided to deprecate and eventually remove these
modules.

We instead now recommend building your command line and invoking it directly
with the subprocess module.
  warnings.warn(
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..
ignore_no_box (boolean): (False) Ignore the absence of box information in the trajectory. If the trajectory does not contain box information, the box will be set to the minimum and maximum positions of the atoms in the trajectory..
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
  ignore_no_box: 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_data.csv

JSON

Common config file 

{
  "properties": {
    "disable_logs": true,
    "ignore_no_box": 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_data.csv

Lpp_zpositions

Wrapper of the LiPyphilic ZPositions module for calculating the z distance of lipids to the bilayer center.

Get help

Command:

lpp_zpositions -h

/home/rchaves/miniforge3/envs/biobb_mem/lib/python3.11/site-packages/Bio/Application/__init__.py:39: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated.

Due to the on going maintenance burden of keeping command line application
wrappers up to date, we have decided to deprecate and eventually remove these
modules.

We instead now recommend building your command line and invoking it directly
with the subprocess module.
  warnings.warn(
usage: lpp_zpositions [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH --output_positions_path OUTPUT_POSITIONS_PATH

Calculate the z distance in of lipids to the bilayer center.

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_positions_path OUTPUT_POSITIONS_PATH
                         Path to the output z positions.

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_positions_path (string): Path to the output z positions. 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..
height_sel (string): (all) Atom selection for the molecules for which the z position will be calculated..
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..
ignore_no_box (boolean): (False) Ignore the absence of box information in the trajectory. If the trajectory does not contain box information, the box will be set to the minimum and maximum positions of the atoms in the trajectory..
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
  height_sel: (resname DPPC and name P8)
  ignore_no_box: true
  lipid_sel: (resname DPPC and name P8)

Command line

lpp_zpositions --config config_lpp_zpositions.yml --input_top_path A01JD.pdb --input_traj_path A01JD.xtc --output_positions_path zpositions.csv

JSON

Common config file 

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

Command line

lpp_zpositions --config config_lpp_zpositions.json --input_top_path A01JD.pdb --input_traj_path A01JD.xtc --output_positions_path zpositions.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 --output_csv_path OUTPUT_CSV_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.
  --output_csv_path OUTPUT_CSV_PATH
                        Path to the output CSV file containing the radius and coordinates of the pore. Accepted formats: csv.

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
output_csv_path (string): Path to the output CSV file containing the radius and coordinates of the pore. 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..
executable (string): (hole) Path to the HOLE executable..
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..
sample (number): (0.2) Distance of sample points in Å. This value determines how many points in the pore profile are calculated..
end_radius (number): (22.0) Radius in Å, which is considered to be the end of the pore..
dot_density (integer): (15) Density of facets for generating a 3D pore representation..
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 hole.vmd --output_csv_path hole_profile.csv

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 hole.vmd --output_csv_path hole_profile.csv

Fatslim_membranes

Wrapper of the FATSLiM membranes module for leaflet and membrane identification.

Get help

Command:

fatslim_membranes -h

/home/rchaves/miniforge3/envs/biobb_mem/lib/python3.11/site-packages/Bio/Application/__init__.py:39: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated.

Due to the on going maintenance burden of keeping command line application
wrappers up to date, we have decided to deprecate and eventually remove these
modules.

We instead now recommend building your command line and invoking it directly
with the subprocess module.
  warnings.warn(
usage: fatslim_membranes [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --output_ndx_path OUTPUT_NDX_PATH [--input_traj_path INPUT_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
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the input trajectory to be processed. Accepted formats: gro, pdb, tng, trr, xtc.

required arguments:
  --input_top_path INPUT_TOP_PATH
                        Path to the input structure or topology file. Accepted formats: ent, gro, pdb, tpr.
  --output_ndx_path OUTPUT_NDX_PATH
                        Path to the GROMACS index file. Accepted formats: ndx

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_top_path (string): Path to the input topology file. File type: input. Sample file. Accepted formats: TPR, GRO, G96, PDB, BRK, ENT
input_traj_path (string): Path to the GROMACS trajectory file. File type: input. Sample file. Accepted formats: XTC, TRR, CPT, GRO, G96, PDB, TNG
output_ndx_path (string): Path to the output index NDX file. File type: output. Sample file. Accepted formats: NDX

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

selection (string): (resname DPPC and element P) Molecules used in the identification using MDAnalysis selection language..
cutoff (number): (2.0) Cutoff distance (in nm) to be used when leaflet identification is performed..
begin_frame (integer): (-1) First frame index to be used for analysis..
end_frame (integer): (-1) Last frame index to be used for analysis..
ignore_no_box (boolean): (False) Ignore the absence of box information in the topology. If the topology does not contain box information, the box will be set to the minimum and maximum positions of the atoms..
return_hydrogen (boolean): (False) Include hydrogen atoms in the output index file..
binary_path (string): (fatslim) Path to the fatslim 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:
  cutoff: 2.2
  disable_logs: true
  ignore_no_box: true
  selection: (resname DPPC and name P8)

Command line

fatslim_membranes --config config_fatslim_membranes.yml --input_top_path A01JD.pdb --input_traj_path A01JD.xtc --output_ndx_path A01JD.ndx

JSON

Common config file 

{
  "properties": {
    "disable_logs": true,
    "ignore_no_box": true,
    "selection": "(resname DPPC and name P8)",
    "cutoff": 2.2
  }
}

Command line

fatslim_membranes --config config_fatslim_membranes.json --input_top_path A01JD.pdb --input_traj_path A01JD.xtc --output_ndx_path A01JD.ndx