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] [-c 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
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string
  --output_traj_path OUTPUT_TRAJ_PATH
                        Path to the output processed trajectory. Accepted formats: mdcrd, crd, cdf, netcdf, nc, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.

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: 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 OUTPUT_CPPTRAJ_PATH
                        Path to the output processed density analysis. Accepted formats: dat, agr, xmgr, gnu.

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

JSON

Fatslim_apl

Wrapper of the FATSLiM area per lipid module for area per lipid calculation.

Get help

Command:

fatslim_apl -h

usage: fatslim_apl [-h] [-c CONFIG] --input_top_path INPUT_TOP_PATH [--input_traj_path INPUT_TRAJ_PATH] [--input_ndx_path INPUT_NDX_PATH] -o OUTPUT_CSV_PATH

Calculate the area per lipid.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the GROMACS trajectory file. Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.
  --input_ndx_path INPUT_NDX_PATH
                        Path to the input index NDX file for lipid headgroups and the interacting group. Accepted formats: ndx.

required arguments:
  --input_top_path INPUT_TOP_PATH
                        Path to the input topology file. Accepted formats: tpr, gro, g96, pdb, brk, ent.
  -o OUTPUT_CSV_PATH, --output_csv_path OUTPUT_CSV_PATH
                        Path to the output CSV file. 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 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_ndx_path (string): Path to the input index NDX file for lipid headgroups and the interacting group. File type: input. Sample file. Accepted formats: NDX
output_csv_path (string): Path to the output CSV file. File type: output. Sample file. Accepted formats: CSV

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

lipid_selection (string): (not protein and element P) Headgroups MDAnalysis selection..
protein_selection (string): (protein and not element H) Protein selection interacting with the membrane..
cutoff (number): (3.0) This option allows user to specify the cutoff distance (in nm) to be used when performing the neighbor search needed by the APL calculation algorithm.
limit (number): (10.0) This option allows user to specify the upper limit (in nm2) for a valid area per lipid value..
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:
  ignore_no_box: true
  lipid_selection: (resname DPPC and name P8)
  remove_tmp: false

Command line

fatslim_apl --config config_fatslim_apl.yml --input_top_path A01JD.pdb --input_traj_path A01JD.xtc --input_ndx_path headgroups.ndx --output_csv_path apl.ndx

JSON

Common config file 

{
  "properties": {
    "remove_tmp": false,
    "ignore_no_box": true,
    "lipid_selection": "(resname DPPC and name P8)"
  }
}

Command line

fatslim_apl --config config_fatslim_apl.json --input_top_path A01JD.pdb --input_traj_path A01JD.xtc --input_ndx_path headgroups.ndx --output_csv_path apl.ndx

Fatslim_membranes

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

Get help

Command:

fatslim_membranes -h

usage: fatslim_membranes [-h] [-c CONFIG] --input_top_path INPUT_TOP_PATH [--input_traj_path INPUT_TRAJ_PATH] [--input_ndx_path INPUT_NDX_PATH] -o OUTPUT_NDX_PATH

Calculates the density along an axis of a given cpptraj compatible trajectory.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the GROMACS trajectory file. Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.
  --input_ndx_path INPUT_NDX_PATH
                        Path to the input lipid headgroups index NDX file. Accepted formats: ndx.

required arguments:
  --input_top_path INPUT_TOP_PATH
                        Path to the input topology file. Accepted formats: tpr, gro, g96, pdb, brk, ent.
  -o OUTPUT_NDX_PATH, --output_ndx_path OUTPUT_NDX_PATH
                        Path to the output index NDX 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
input_ndx_path (string): Path to the input lipid headgroups index NDX file. File type: input. Sample file. Accepted formats: NDX
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): (not protein and element P) Alternative ot the NDX file for choosing the Headgroups 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
  ignore_no_box: true
  remove_tmp: false
  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 --input_ndx_path A01JD.ndx --output_ndx_path leaflets.ndx

JSON

Common config file 

{
  "properties": {
    "ignore_no_box": true,
    "remove_tmp": false,
    "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 --input_ndx_path A01JD.ndx --output_ndx_path leaflets.ndx

Gorder_aa

Wrapper of the gorder atomistic module for computing lipid order parameters per atom for carbon tails.

Get help

Command:

gorder_aa -h

usage: gorder_aa [-h] [-c CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH -o OUTPUT_ORDER_PATH

Compute atomistic lipid order parameters using gorder order tool.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  --input_top_path INPUT_TOP_PATH
                        Path to the input structure or topology file. Accepted formats: tpr.
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the input trajectory to be processed. Accepted formats: xtc, trr, gro.
  -o OUTPUT_ORDER_PATH, --output_order_path OUTPUT_ORDER_PATH
                        Path to results of the order analysis. Accepted formats: yaml, xvg, 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: TPR
input_traj_path (string): Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: XTC, TRR, GRO
output_order_path (string): Path to results of the order analysis. File type: output. Sample file. Accepted formats: YAML, XVG, CSV

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

heavy_atoms (string): (@membrane and name rC3.+|C2.+) Selection query specifying the heavy atoms to be used in the analysis (typically carbon atoms in lipid tails)..
hydrogens (string): (@membrane and element name hydrogen) Selection query specifiying the hydrogen atoms to be used in the analysis (only those bonded to heavy atoms will be considered)..
handle_pbc (boolean): (True) If False, ignores periodic boundary conditions (PBC)..
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:
  handle_pbc: false
  remove_tmp: false

Command line

gorder_aa --config config_gorder_aa.yml --input_top_path A01IP.tpr --input_traj_path A01IP.xtc --output_order_path order_aa.yaml

JSON

Common config file 

{
  "properties": {
    "handle_pbc": false,
    "remove_tmp": false
  }
}

Command line

gorder_aa --config config_gorder_aa.json --input_top_path A01IP.tpr --input_traj_path A01IP.xtc --output_order_path order_aa.yaml

Gorder_cg

Wrapper of the gorder coarse-grained module for computing lipid order parameters per atom for carbon tails.

Get help

Command:

gorder_cg -h

usage: gorder_cg [-h] [-c CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH -o OUTPUT_ORDER_PATH

Compute coarse-grained lipid order parameters using gorder order tool.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  --input_top_path INPUT_TOP_PATH
                        Path to the input structure or topology file. Accepted formats: tpr.
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the input trajectory to be processed. Accepted formats: xtc, trr, gro.
  -o OUTPUT_ORDER_PATH, --output_order_path OUTPUT_ORDER_PATH
                        Path to results of the order analysis. Accepted formats: yaml, xvg, 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: TPR
input_traj_path (string): Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: XTC, TRR, GRO
output_order_path (string): Path to results of the order analysis. File type: output. Sample file. Accepted formats: YAML, XVG, CSV

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

beads (string): (@membrane) Selection query specifying the beads to be used in the analysis..
handle_pbc (boolean): (True) If False, ignores periodic boundary conditions (PBC)..
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:
  handle_pbc: false
  remove_tmp: false

Command line

gorder_cg --config config_gorder_cg.yml --input_top_path cg_test.tpr --input_traj_path cg_test.xtc --output_order_path order_cg.yaml

JSON

Common config file 

{
  "properties": {
    "handle_pbc": false,
    "remove_tmp": false
  }
}

Command line

gorder_cg --config config_gorder_cg.json --input_top_path cg_test.tpr --input_traj_path cg_test.xtc --output_order_path order_cg.yaml

Gorder_ua

Wrapper of the gorder united atom module for computing lipid order parameters per atom for carbon tails.

Get help

Command:

gorder_ua -h

usage: gorder_ua [-h] [-c CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH -o OUTPUT_ORDER_PATH

Compute united atom lipid order parameters using gorder order tool.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  --input_top_path INPUT_TOP_PATH
                        Path to the input structure or topology file. Accepted formats: tpr.
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the input trajectory to be processed. Accepted formats: xtc, trr, gro.
  -o OUTPUT_ORDER_PATH, --output_order_path OUTPUT_ORDER_PATH
                        Path to results of the order analysis. Accepted formats: yaml, xvg, 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: TPR
input_traj_path (string): Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: XTC, TRR, GRO
output_order_path (string): Path to results of the order analysis. File type: output. Sample file. Accepted formats: YAML, XVG, CSV

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

saturated (string): (@membrane) Selection query specifying the saturated carbons..
unsaturated (string): (None) Selection query specifying the unsaturated carbons..
handle_pbc (boolean): (True) If False, ignores periodic boundary conditions (PBC)..
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:
  remove_tmp: false

Command line

gorder_ua --config config_gorder_ua.yml --input_top_path A01JP.tpr --input_traj_path A01JP.xtc --output_order_path order_ua.yaml

JSON

Common config file 

{
  "properties": {
    "remove_tmp": false
  }
}

Command line

gorder_ua --config config_gorder_ua.json --input_top_path A01JP.tpr --input_traj_path A01JP.xtc --output_order_path order_ua.yaml

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] [-c CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH -o OUTPUT_LEAFLETS_PATH

Assign lipids to leaflets in a bilayer.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

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.
  -o OUTPUT_LEAFLETS_PATH, --output_leaflets_path OUTPUT_LEAFLETS_PATH
                        Path to the output leaflet assignments. Accepted formats: csv, npy.

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, NPY

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:
  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": {
    "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_flip_flop

Wrapper of the LiPyphilic FlipFlop module for finding flip-flop events in a lipid bilayer.

Get help

Command:

lpp_flip_flop -h

usage: lpp_flip_flop [-h] [-c CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH --input_leaflets_path INPUT_LEAFLETS_PATH -o OUTPUT_FLIP_FLOP_PATH

Find flip-flop events in a lipid bilayer.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

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.
  --input_leaflets_path INPUT_LEAFLETS_PATH
                        Path to the input leaflet assignments. Accepted formats: csv, npy.
  -o OUTPUT_FLIP_FLOP_PATH, --output_flip_flop_path OUTPUT_FLIP_FLOP_PATH
                        Path to the output flip-flop data. 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
input_leaflets_path (string): Path to the input leaflet assignments. File type: input. Sample file. Accepted formats: CSV, NPY
output_flip_flop_path (string): Path to the output flip-flop data. 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..
frame_cutoff (number): (1.0) To be counted as a successful flip-flop, a molecule must reside in its new leaflet for at least ‘frame_cutoff’ consecutive frames. The default is 1, in which case the molecule only needs to move to the opposing leaflet for a single frame for the flip-flop to be successful..
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:
  ignore_no_box: true
  lipid_sel: (resname DPPC and name P8)

Command line

lpp_flip_flop --config config_lpp_flip_flop.yml --input_top_path A01JD.pdb --input_traj_path A01JD.xtc --input_leaflets_path leaflets_data.csv --output_flip_flop_path flip_flop.csv

JSON

Common config file 

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

Command line

lpp_flip_flop --config config_lpp_flip_flop.json --input_top_path A01JD.pdb --input_traj_path A01JD.xtc --input_leaflets_path leaflets_data.csv --output_flip_flop_path flip_flop.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

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:
  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": {
    "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] [-c 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
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

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:
  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": {
    "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