BioBB FLEXDYN Command Line Help

Generic usage:

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

Imod_imc

Wrapper of the imc tool

Get help

Command:

imod_imc -h

usage: imod_imc [-h] [--config CONFIG] --input_pdb_path INPUT_PDB_PATH --input_dat_path INPUT_DAT_PATH --output_traj_path OUTPUT_TRAJ_PATH

Compute a Monte-Carlo IC-NMA based conformational ensemble using the imc tool from the iMODS package.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

required arguments:
  --input_pdb_path INPUT_PDB_PATH
                        Input structure file. Accepted formats: pdb
  --input_dat_path INPUT_DAT_PATH
                        Input evecs file. Accepted formats: dat
  --output_traj_path OUTPUT_TRAJ_PATH
                        Output traj file. Accepted formats: pdb.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_pdb_path (string): Input PDB file. File type: input. Sample file. Accepted formats: PDB
input_dat_path (string): Input dat with normal modes. File type: input. Sample file. Accepted formats: DAT, TXT
output_traj_path (string): Output multi-model PDB file with the generated ensemble. File type: output. Sample file. Accepted formats: PDB

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

num_structs (integer): (500) Number of structures to be generated.
num_modes (integer): (5) Number of eigenvectors to be employed.
amplitude (integer): (1) Amplitude linear factor to scale motion.
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file 

properties:
  amplitude: 6.0
  num_modes: 10
  num_structs: 10

Command line

imod_imc --config config_imod_imc.yml --input_pdb_path structure_cleaned.pdb --input_dat_path imod_imode_evecs.dat --output_traj_path imod_imc_output.pdb

JSON

Common config file 

{
  "properties": {
    "num_structs": 10,
    "num_modes": 10,
    "amplitude": 6.0
  }
}

Command line

imod_imc --config config_imod_imc.json --input_pdb_path structure_cleaned.pdb --input_dat_path imod_imode_evecs.dat --output_traj_path imod_imc_output.pdb

Imod_imode

Wrapper of the imode tool

Get help

Command:

imod_imode -h

usage: imod_imode [-h] [--config CONFIG] --input_pdb_path INPUT_PDB_PATH --output_dat_path OUTPUT_DAT_PATH

Compute the normal modes of a macromolecule using the imode tool from the iMODS package.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

required arguments:
  --input_pdb_path INPUT_PDB_PATH
                        Input structure file. Accepted formats: pdb
  --output_dat_path OUTPUT_DAT_PATH
                        Output evecs dat file. Accepted formats: dat.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_pdb_path (string): Input PDB file. File type: input. Sample file. Accepted formats: PDB
output_dat_path (string): Output dat with normal modes. File type: output. Sample file. Accepted formats: DAT, TXT

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

cg (integer): (2) Coarse-Grained model. .
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file 

properties:
  cg: 2

Command line

imod_imode --config config_imod_imode.yml --input_pdb_path structure.pdb --output_dat_path imod_imode_evecs.dat

JSON

Common config file 

{
  "properties": {
    "cg": 2
  }
}

Command line

imod_imode --config config_imod_imode.json --input_pdb_path structure.pdb --output_dat_path imod_imode_evecs.dat

Nolb_nma

Wrapper of the NOLB tool

Get help

Command:

nolb_nma -h

usage: nolb_nma [-h] [--config CONFIG] --input_pdb_path INPUT_PDB_PATH --output_pdb_path OUTPUT_PDB_PATH

Generate an ensemble of structures using the NOLB (NOn-Linear rigid Block) NMA tool.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

required arguments:
  --input_pdb_path INPUT_PDB_PATH
                        Input structure file. Accepted formats: pdb
  --output_pdb_path OUTPUT_PDB_PATH
                        Output pdb file. Accepted formats: pdb.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_pdb_path (string): Input PDB file. File type: input. Sample file. Accepted formats: PDB
output_pdb_path (string): Output multi-model PDB file with the generated ensemble. File type: output. Sample file. Accepted formats: PDB

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

num_structs (integer): (500) Number of structures to be generated.
cutoff (number): (5.0) This options specifies the interaction cutoff distance for the elastic network models (in angstroms), 5 by default. The Hessian matrix is constructed according to this interaction distance. Some artifacts should be expected for too short distances (< 5 Å)..
rmsd (number): (1.0) Maximum RMSd for decoy generation..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file 

properties:
  num_structs: 20

Command line

nolb_nma --config config_nolb_nma.yml --input_pdb_path structure.pdb --output_pdb_path nolb_output.pdb

JSON

Common config file 

{
  "properties": {
    "num_structs": 20
  }
}

Command line

nolb_nma --config config_nolb_nma.json --input_pdb_path structure.pdb --output_pdb_path nolb_output.pdb

Concoord_disco

Wrapper of the Disco tool from the Concoord package.

Get help

Command:

concoord_disco -h

usage: concoord_disco [-h] [--config CONFIG] --input_pdb_path INPUT_PDB_PATH --input_dat_path INPUT_DAT_PATH --output_traj_path OUTPUT_TRAJ_PATH --output_rmsd_path OUTPUT_RMSD_PATH --output_bfactor_path OUTPUT_BFACTOR_PATH

Structure generation based on a set of geometric constraints extracted with the Concoord Dist tool.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

required arguments:
  --input_pdb_path INPUT_PDB_PATH
                        Input structure file in PDB format. Accepted formats: pdb
  --input_dat_path INPUT_DAT_PATH
                        Input dat with structure interpretation and bond definitions. Accepted formats: dat, txt
  --output_traj_path OUTPUT_TRAJ_PATH
                        Output trajectory file. Accepted formats: pdb, gro, xtc.
  --output_rmsd_path OUTPUT_RMSD_PATH
                        Output RMSd file. Accepted formats: dat.
  --output_bfactor_path OUTPUT_BFACTOR_PATH
                        Output B-factor file. Accepted formats: pdb.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_pdb_path (string): Input structure file in PDB format. File type: input. Sample file. Accepted formats: PDB
input_dat_path (string): Input dat with structure interpretation and bond definitions. File type: input. Sample file. Accepted formats: DAT, TXT
output_traj_path (string): Output trajectory file. File type: output. Sample file. Accepted formats: PDB, XTC, GRO
output_rmsd_path (string): Output rmsd file. File type: output. Sample file. Accepted formats: DAT
output_bfactor_path (string): Output B-factor file. File type: output. Sample file. Accepted formats: PDB

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

binary_path (string): (disco) Concoord disco binary path to be used..
vdw (integer): (1) Select a set of Van der Waals parameters. .
num_structs (integer): (500) Number of structures to be generated.
num_iterations (integer): (2500) Maximum number of iterations per structure.
chirality_check (integer): (2) Chirality check. .
bs (integer): (0) Number of rounds of triangular bound smoothing (default 0), (if >= 6, tetragonal BS is activated).
nofit (boolean): (False) Do not fit generated structures to reference.
seed (integer): (741265) Initial random seed.
violation (number): (1.0) Maximal acceptable sum of violations (nm).
convergence (integer): (50) Consider convergence failed after this number of non-productive iterations.
trials (integer): (25) Maximum number of trials per run.
damp (integer): (1) Damping factor for distance corrections. .
dyn (integer): (1) Number of rounds to dynamically set tolerances.
bump (boolean): (False) Do extra bump check.
pairlist_freq (integer): (10) Pairlist update frequency in steps (only valid together with bump).
cutoff (number): (0.5) Cut-off radius for pairlist (nm) (only valid together with bump).
ref (boolean): (False) Use input coordinates instead of random starting coordinates.
scale (integer): (1) Pre-scale coordinates with this factor.
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file 

properties:
  num_structs: 20
  vdw: 4

Command line

concoord_disco --config config_concoord_disco.yml --input_pdb_path structure.pdb --input_dat_path dist.dat --output_traj_path disco_trj.pdb --output_rmsd_path disco_rmsd.dat --output_bfactor_path disco_bfactor.pdb

JSON

Common config file 

{
  "properties": {
    "vdw": 4,
    "num_structs": 20
  }
}

Command line

concoord_disco --config config_concoord_disco.json --input_pdb_path structure.pdb --input_dat_path dist.dat --output_traj_path disco_trj.pdb --output_rmsd_path disco_rmsd.dat --output_bfactor_path disco_bfactor.pdb

Concoord_dist

Wrapper of the Dist tool from the Concoord package.

Get help

Command:

concoord_dist -h

usage: concoord_dist [-h] [--config CONFIG] --input_structure_path INPUT_STRUCTURE_PATH --output_pdb_path OUTPUT_PDB_PATH --output_gro_path OUTPUT_GRO_PATH --output_dat_path OUTPUT_DAT_PATH

Structure interpretation and bond definitions from a PDB/GRO file.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

required arguments:
  --input_structure_path INPUT_STRUCTURE_PATH
                        Input structure file. Accepted formats: pdb, gro.
  --output_pdb_path OUTPUT_PDB_PATH
                        Output pdb file. Accepted formats: pdb.
  --output_gro_path OUTPUT_GRO_PATH
                        Output gro file. Accepted formats: gro.
  --output_dat_path OUTPUT_DAT_PATH
                        Output dat file with structure interpretation and bond definitions. Accepted formats: dat, txt.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_structure_path (string): Input structure file. File type: input. Sample file. Accepted formats: PDB, GRO
output_pdb_path (string): Output pdb file. File type: output. Sample file. Accepted formats: PDB
output_gro_path (string): Output gro file. File type: output. Sample file. Accepted formats: GRO
output_dat_path (string): Output dat with structure interpretation and bond definitions. File type: output. Sample file. Accepted formats: DAT, TXT

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

binary_path (string): (dist) Concoord dist binary path to be used..
vdw (integer): (1) Select a set of Van der Waals parameters. .
bond_angle (integer): (1) Select a set of bond/angle parameters. .
retain_hydrogens (boolean): (False) Retain hydrogen atoms.
nb_interactions (boolean): (False) Try to find alternatives for non-bonded interactions (by default the native contacts will be preserved).
cutoff (number): (4.0) cut-off radius (Angstroms) for non-bonded interacting pairs (the cut-off distances are additional to the sum of VDW radii).
min_distances (integer): (50) Minimum number of distances to be defined for each atom.
damp (number): (1.0) Multiply each distance margin by this value.
fixed_atoms (boolean): (False) Interpret zero occupancy as atoms to keep fixed.
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file 

properties:
  bond_angle: 1
  vdw: 1

Command line

concoord_dist --config config_concoord_dist.yml --input_structure_path structure.pdb --output_pdb_path dist.pdb --output_gro_path dist.gro --output_dat_path dist.dat

JSON

Common config file 

{
  "properties": {
    "vdw": 1,
    "bond_angle": 1
  }
}

Command line

concoord_dist --config config_concoord_dist.json --input_structure_path structure.pdb --output_pdb_path dist.pdb --output_gro_path dist.gro --output_dat_path dist.dat

Imod_imove

Wrapper of the imove tool

Get help

Command:

imod_imove -h

usage: imod_imove [-h] [--config CONFIG] --input_pdb_path INPUT_PDB_PATH --input_dat_path INPUT_DAT_PATH --output_pdb_path OUTPUT_PDB_PATH

Animate the normal modes of a macromolecule using the imove tool from the iMODS package.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

required arguments:
  --input_pdb_path INPUT_PDB_PATH
                        Input structure file. Accepted formats: pdb
  --input_dat_path INPUT_DAT_PATH
                        Input evecs file. Accepted formats: dat
  --output_pdb_path OUTPUT_PDB_PATH
                        Output pdb file. Accepted formats: pdb.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_pdb_path (string): Input PDB file. File type: input. Sample file. Accepted formats: PDB
input_dat_path (string): Input dat with normal modes. File type: input. Sample file. Accepted formats: DAT, TXT
output_pdb_path (string): Output multi-model PDB file with the generated animation by Principal Component. File type: output. Sample file. Accepted formats: PDB

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

pc (integer): (1) Principal Component..
num_frames (integer): (11) Number of frames to be generated.
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file 

properties:
  pc: 1

Command line

imod_imove --config config_imod_imove.yml --input_pdb_path structure_cleaned.pdb --input_dat_path imod_imode_evecs.dat --output_pdb_path imod_imove_output.pdb

JSON

Common config file 

{
  "properties": {
    "pc": 1
  }
}

Command line

imod_imove --config config_imod_imove.json --input_pdb_path structure_cleaned.pdb --input_dat_path imod_imode_evecs.dat --output_pdb_path imod_imove_output.pdb

Prody_anm

Wrapper of the ANM tool from the Prody package.

Get help

Command:

prody_anm -h

usage: prody_anm [-h] [--config CONFIG] --input_pdb_path INPUT_PDB_PATH --output_pdb_path OUTPUT_PDB_PATH

Generate an ensemble of structures using the Prody Anisotropic Network Model (ANM), for coarse-grained NMA.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

required arguments:
  --input_pdb_path INPUT_PDB_PATH
                        Input structure file. Accepted formats: pdb
  --output_pdb_path OUTPUT_PDB_PATH
                        Output pdb file. Accepted formats: pdb.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_pdb_path (string): Input PDB file. File type: input. Sample file. Accepted formats: PDB
output_pdb_path (string): Output multi-model PDB file with the generated ensemble. File type: output. Sample file. Accepted formats: PDB

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

num_structs (integer): (500) Number of structures to be generated.
selection (string): (calpha) Atoms selection (Prody syntax: http://prody.csb.pitt.edu/manual/reference/atomic/select.html).
cutoff (number): (15.0) Cutoff distance (Å) for pairwise interactions, minimum is 4.0 Å.
gamma (number): (1.0) Spring constant.
rmsd (number): (1.0) Average RMSD that the conformations will have with respect to the initial conformation.
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file 

properties:
  num_structs: 20
  rmsd: 4.0

Command line

prody_anm --config config_prody_anm.yml --input_pdb_path structure.pdb --output_pdb_path prody_output.pdb

JSON

Common config file 

{
  "properties": {
    "num_structs": 20,
    "rmsd": 4.0
  }
}

Command line

prody_anm --config config_prody_anm.json --input_pdb_path structure.pdb --output_pdb_path prody_output.pdb