BioBB MEM Command Line Help

Generic usage:

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

Assign_leaflets

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

Get help

Command:

assign_leaflets -h

usage: 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.

optional arguments:
  -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

assign_leaflets --config config_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

assign_leaflets --config config_assign_leaflets.json --input_top_path A01JD.pdb --input_traj_path A01JD.xtc --output_leaflets_path leaflets.csv

Chap_run

Wrapper of the Channel Annotation Package (CHAP) for analyzing pore geometry, hydrophobicity, and hydration state in protein channels and other macromolecular structures.

Get help

Command:

chap_run -h

usage: chap_run [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH [--input_traj_path INPUT_TRAJ_PATH] [--input_index_path INPUT_INDEX_PATH] --output_obj_path OUTPUT_OBJ_PATH

Channel Annotation Package (CHAP) for analyzing pore geometry, hydrophobicity, and hydration state in protein channels and other macromolecular structures.

optional arguments:
  -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.
  --input_index_path INPUT_INDEX_PATH
                        Path to the GROMACS index file. Accepted formats: ndx.

required arguments:
  --input_top_path INPUT_TOP_PATH
                        Path to the input structure or topology file. Accepted formats: ent, gro, pdb, tpr.
  --output_obj_path OUTPUT_OBJ_PATH
                        Path to the output processed Wavefront object. Accepted formats: obj.

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
input_index_path (string): Path to the GROMACS index file. File type: input. Sample file. Accepted formats: NDX
output_obj_path (string): Path to the output Wavefront Object file containing CHAP results. File type: output. Sample file. Accepted formats: OBJ

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

b (number): (None) First frame (in picoseconds) to read from trajectory..
e (number): (None) Last frame (in picoseconds) to read from trajectory..
df (number): (None) Only use frame if t MOD dt == first time (in picoseconds)..
tu (string): (ps) Unit for time values..
sel_pathway (string): (None) Reference group that defines the permeation pathway (usually ‘Protein’)..
sel_solvent (string): (None) Group of small particles to calculate density of (usually ‘Water’)..
out_filename (string): (chap_output) Base file name for output files without file extension..
out_num_points (integer): (1000) Number of spatial sample points that are written to the JSON output file..
out_extrap_dist (number): (0.0) Extrapolation distance beyond the pathway endpoints for both JSON and OBJ output..
out_grid_dist (number): (0.15) Controls the sampling distance of vertices on the pathway surface which are subsequently interpolated to yield a smooth surface. Very small values may yield visual artifacts..
out_vis_tweak (number): (0.1) Visual tweaking factor that controls the smoothness of the pathway surface in the OBJ output. Varies between -1 and 1 (exclusively), where larger values result in a smoother surface. Negative values may result in visualisation artifacts..
out_detailed (boolean): (False) If true, CHAP will write detailed per-frame information to a newline delimited JSON file including original probe positions and spline parameters. This is mostly useful for debugging..
pf_method (string): (inplane_optim) Path finding method. The default inplane_optim implements the algorithm used in the HOLE programme, where the position of a probe sphere is optimised in subsequent parallel planes so as to maximise its radius. The alternative cylindrical simply uses a cylindrical volume as permeation pathway..
pf_vdwr_database (string): (hole_simple) Database of van-der-Waals radii to be used in pore finding..
pf_vdwr_fallback (number): (None) Fallback van-der-Waals radius for atoms that are not listed in van-der-Waals radius database. Unless this is set to a positive value, an error will be thrown if a pathway-forming atom has no associated van-der-Waals radius in the database..
pf_vdwr_json (string): (None) JSON file with user defined van-der-Waals radii. Will be ignored unless -pf-vdwr-database is set to ‘user’..
pf_align_method (string): (ipp) Method for aligning pathway coordinates across time steps..
pf_probe_step (number): (0.1) Step length for probe movement..
pf_max_free_dist (number): (1.0) Maximum radius of pore..
pf_max_probe_steps (integer): (10000) Maximum number of steps the probe is moved in either direction..
pf_sel_ipp (string): (None) Selection of atoms whose COM will be used as initial probe position. If not set, the selection specified with ‘sel-pathway’ will be used..
pf_init_probe_pos (array): (None) Initial position of probe in probe-based pore finding algorithms. If set explicitly, it will overwrite the COM-based initial position set with the ippSelflag..
pf_chan_dir_vec (array): ([0.0, 0.0, 1.0]) Channel direction vector. Will be normalised to unit vector internally..
pf_cutoff (number): (None) Cutoff for distance searches in path finding algorithm. A value of zero or less means no cutoff is applied. If unset, an appropriate cutoff is determined automatically..
sa_seed (integer): (None) Seed used in pseudo random number generation for simulated annealing. If not set explicitly, a random seed is used..
sa_max_iter (integer): (0) Number of cooling iterations in one simulated annealing run..
sa_init_temp (number): (0.1) Simulated annealing initial temperature..
sa_cooling_fac (number): (0.98) Simulated annealing cooling factor..
sa_step (number): (0.001) Step length factor used in candidate generation..
nm_max_iter (integer): (100) Number of Nelder-Mead simplex iterations in path finding algorithm..
nm_init_shift (number): (0.1) Distance of vertices in initial Nelder-Mead simplex..
pm_pl_margin (number): (0.75) Margin for determining pathway lining residues. A residue is considered to be pathway lining if it is no further than the local path radius plus this margin from the pathway’s centre line..
pm_pf_sel (string): (name CA) Distance of vertices in initial Nelder-Mead simplex..
de_method (string): (kernel) Method used for estimating the probability density of the solvent particles along the permeation pathway..
de_res (number): (0.01) Spatial resolution of the density estimator. In case of a histogram, this is the bin width, in case of a kernel density estimator, this is the spacing of the evaluation points..
de_bandwidth (number): (-1.0) Bandwidth for the kernel density estimator. Ignored for other methods. If negative or zero, bandwidth will be determined automatically to minimise the asymptotic mean integrated squared error (AMISE)..
de_bw_scale (number): (1.0) Scaling factor for the band width. Useful to set a bandwidth relative to the AMISE-optimal value..
de_eval_cutoff (number): (5.0) Evaluation range cutoff for kernel density estimator in multiples of bandwidth. Ignored for other methods. Ensures that the density falls off smoothly to zero outside the data range..
hydrophob_database (string): (wimley_white_1996) Database of hydrophobicity scale for pore forming residues..
hydrophob_fallback (number): (None) Fallback hydrophobicity for residues in the pathway defining group. If unset, residues missing in the database will cause an error.”.
hydrophob_json (string): (None) JSON file with user defined hydrophobicity scale. Will be ignored unless -hydrophobicity-database is set to ‘user’..
hydrophob_bandwidth (number): (0.35) Bandwidth for hydrophobicity kernel..
binary_path (string): (chap) Path to the CHAP 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:
  b: 1
  disable_logs: true
  e: 50
  out_num_points: 200
  pf_max_free_dist: 1.0
  pf_max_probe_steps: 500
  sel_pathway: 1

Command line

chap_run --config config_chap_run.yml --input_top_path A01JD.pdb --input_traj_path A01JD.xtc --input_index_path A01JD.ndx --output_obj_path chap_output.obj

JSON

Common config file 

{
  "properties": {
    "disable_logs": true,
    "sel_pathway": 1,
    "b": 1,
    "e": 50,
    "out_num_points": 200,
    "pf_max_probe_steps": 500,
    "pf_max_free_dist": 1.0
  }
}

Command line

chap_run --config config_chap_run.json --input_top_path A01JD.pdb --input_traj_path A01JD.xtc --input_index_path A01JD.ndx --output_obj_path chap_output.obj

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.

optional arguments:
  -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

Assign_leaflets

Get help

I / O Arguments

Config

YAML

Common config file

Command line

JSON

Common config file

Command line

Chap_run

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 