BioBB FLEXSERV Command Line Help

Generic usage:

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

Pcz_animate

Extract PCA animations from a compressed PCZ file.

Get help

Command:

pcz_animate -h

usage: pcz_animate [-h] [--config CONFIG] --input_pcz_path INPUT_PCZ_PATH --output_crd_path OUTPUT_CRD_PATH

Extract PCA animations from a compressed PCZ file.

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

required arguments:
  --input_pcz_path INPUT_PCZ_PATH
                        Input compressed trajectory file. Accepted formats: pcz.
  --output_crd_path OUTPUT_CRD_PATH
                        Output animated trajectory file. Accepted formats: crd, mdcrd, inpcrd, pdb.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_pcz_path (string): Input compressed trajectory file. File type: input. Sample file. Accepted formats: PCZ
output_crd_path (string): Output PCA animated trajectory file. File type: output. Sample file. Accepted formats: CRD, MDCRD, INPCRD, PDB

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

binary_path (string): (pczdump) pczdump binary path to be used..
eigenvector (integer): (1) Eigenvector to be used for the animation.
pdb (boolean): (False) Use PDB format for output trajectory.
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file 

properties:
  eigenvector: 1
  pdb: true

Command line

pcz_animate --config config_pcz_animate.yml --input_pcz_path pcazip.pcz --output_crd_path pcazip_anim1.pdb

JSON

Common config file 

{
  "properties": {
    "eigenvector": 1,
    "pdb": true
  }
}

Command line

pcz_animate --config config_pcz_animate.json --input_pcz_path pcazip.pcz --output_crd_path pcazip_anim1.pdb

Dmd_run

Wrapper of the Discrete Molecular Dynamics tool from the FlexServ module.

Get help

Command:

dmd_run -h

usage: dmd_run [-h] [--config CONFIG] --input_pdb_path INPUT_PDB_PATH --output_log_path OUTPUT_LOG_PATH --output_crd_path OUTPUT_CRD_PATH

Generates protein conformational structures using the Discrete Molecular Dynamics method.

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

required arguments:
  --input_pdb_path INPUT_PDB_PATH
                        Input PDB file. Accepted formats: pdb.
  --output_log_path OUTPUT_LOG_PATH
                        Output log file. Accepted formats: log, out, txt.
  --output_crd_path OUTPUT_CRD_PATH
                        Output ensemble file. Accepted formats: crd, mdcrd, inpcrd.

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_log_path (string): Output log file. File type: output. Sample file. Accepted formats: LOG, OUT, TXT, O
output_crd_path (string): Output ensemble. File type: output. Sample file. Accepted formats: CRD, MDCRD, INPCRD

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

binary_path (string): (dmdgoopt) DMD binary path to be used..
dt (number): (1e-12) Integration time (s).
temperature (integer): (300) Simulation temperature (K).
frames (integer): (1000) Number of frames in the final ensemble.
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file 

properties:
  frames: 100

Command line

dmd_run --config config_dmd_run.yml --input_pdb_path structure.ca.pdb --output_log_path dmd_run_out.log --output_crd_path dmd_run_out.crd

JSON

Common config file 

{
  "properties": {
    "frames": 100
  }
}

Command line

dmd_run --config config_dmd_run.json --input_pdb_path structure.ca.pdb --output_log_path dmd_run_out.log --output_crd_path dmd_run_out.crd

Pcz_evecs

Extract PCA Eigen Vectors from a compressed PCZ file.

Get help

Command:

pcz_evecs -h

usage: pcz_evecs [-h] [--config CONFIG] --input_pcz_path INPUT_PCZ_PATH --output_json_path OUTPUT_JSON_PATH

Extract PCA Eigen Vectors from a compressed PCZ file.

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

required arguments:
  --input_pcz_path INPUT_PCZ_PATH
                        Input compressed trajectory file. Accepted formats: pcz.
  --output_json_path OUTPUT_JSON_PATH
                        Output json file with PCA evecs. Accepted formats: json.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_pcz_path (string): Input compressed trajectory file. File type: input. Sample file. Accepted formats: PCZ
output_json_path (string): Output json file with PCA Eigen Vectors. File type: output. Sample file. Accepted formats: JSON

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

binary_path (string): (pczdump) pczdump binary path to be used..
eigenvector (integer): (1) PCA mode (eigenvector) from which to extract eigen vectors..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file 

properties:
  eigenvector: 1

Command line

pcz_evecs --config config_pcz_evecs.yml --input_pcz_path pcazip.pcz --output_json_path pcz_evecs.json

JSON

Common config file 

{
  "properties": {
    "eigenvector": 1
  }
}

Command line

pcz_evecs --config config_pcz_evecs.json --input_pcz_path pcazip.pcz --output_json_path pcz_evecs.json

Pcz_similarity

Compute PCA similarity between two given compressed PCZ files.

Get help

Command:

pcz_similarity -h

usage: pcz_similarity [-h] [--config CONFIG] --input_pcz_path1 INPUT_PCZ_PATH1 --input_pcz_path2 INPUT_PCZ_PATH2 --output_json_path OUTPUT_JSON_PATH

Compute PCA Similarity from a given pair of compressed PCZ files.

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

required arguments:
  --input_pcz_path1 INPUT_PCZ_PATH1
                        Input compressed trajectory file 1. Accepted formats: pcz.
  --input_pcz_path2 INPUT_PCZ_PATH2
                        Input compressed trajectory file 2. Accepted formats: pcz.
  --output_json_path OUTPUT_JSON_PATH
                        Output json file with PCA similarity. Accepted formats: json.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_pcz_path1 (string): Input compressed trajectory file 1. File type: input. Sample file. Accepted formats: PCZ
input_pcz_path2 (string): Input compressed trajectory file 2. File type: input. Sample file. Accepted formats: PCZ
output_json_path (string): Output json file with PCA Similarity results. File type: output. Sample file. Accepted formats: JSON

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

amplifying_factor (number): (0.0) common displacement (dx) along the different eigenvectors. If 0, the result is the absolute similarity index (dot product)..
binary_path (string): (pczdump) pczdump binary path to be used..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..

YAML

JSON

Pcz_bfactor

Extract residue bfactors x PCA mode from a compressed PCZ file.

Get help

Command:

pcz_bfactor -h

usage: pcz_bfactor [-h] [--config CONFIG] --input_pcz_path INPUT_PCZ_PATH --output_dat_path OUTPUT_DAT_PATH [--output_pdb_path OUTPUT_PDB_PATH]

Extract residue bfactors x PCA mode from a compressed PCZ file.

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

required arguments:
  --input_pcz_path INPUT_PCZ_PATH
                        Input compressed trajectory file. Accepted formats: pcz.
  --output_dat_path OUTPUT_DAT_PATH
                        Output Bfactor x residue x PCA mode file. Accepted formats: dat, txt, csv.
  --output_pdb_path OUTPUT_PDB_PATH
                        Output PDB with Bfactor x residue x PCA mode file. Accepted formats: pdb.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_pcz_path (string): Input compressed trajectory file. File type: input. Sample file. Accepted formats: PCZ
output_dat_path (string): Output Bfactor x residue x PCA mode file. File type: output. Sample file. Accepted formats: DAT, TXT, CSV
output_pdb_path (string): Output PDB with Bfactor x residue x PCA mode 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): (pczdump) pczdump binary path to be used..
eigenvector (integer): (0) PCA mode (eigenvector) from which to extract bfactor values per residue (0 means average over all modes)..
pdb (boolean): (False) Generate a PDB file with the computed bfactors (to be easily represented with colour scale).
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file 

properties:
  eigenvector: 1
  pdb: true

Command line

pcz_bfactor --config config_pcz_bfactor.yml --input_pcz_path pcazip.pcz --output_dat_path bfactors.dat --output_pdb_path bfactors.pdb

JSON

Common config file 

{
  "properties": {
    "eigenvector": 1,
    "pdb": true
  }
}

Command line

pcz_bfactor --config config_pcz_bfactor.json --input_pcz_path pcazip.pcz --output_dat_path bfactors.dat --output_pdb_path bfactors.pdb

Nma_run

Wrapper of the Normal Mode Analysis tool from the FlexServ module.

Get help

Command:

nma_run -h

usage: nma_run [-h] [--config CONFIG] --input_pdb_path INPUT_PDB_PATH --output_log_path OUTPUT_LOG_PATH --output_crd_path OUTPUT_CRD_PATH

Generates protein conformational structures using the Normal Mode Analysis method.

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

required arguments:
  --input_pdb_path INPUT_PDB_PATH
                        Input PDB file. Accepted formats: pdb.
  --output_log_path OUTPUT_LOG_PATH
                        Output log file. Accepted formats: log, out, txt.
  --output_crd_path OUTPUT_CRD_PATH
                        Output ensemble file. Accepted formats: crd, mdcrd, inpcrd.

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_log_path (string): Output log file. File type: output. Sample file. Accepted formats: LOG, OUT, TXT, O
output_crd_path (string): Output ensemble. File type: output. Sample file. Accepted formats: CRD, MDCRD, INPCRD

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

binary_path (string): (diaghess) NMA binary path to be used..
frames (integer): (1000) Number of frames in the final ensemble.
nvecs (integer): (50) Number of vectors to take into account for the ensemble generation.
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file 

properties:
  frames: 100

Command line

nma_run --config config_nma_run.yml --input_pdb_path structure.ca.pdb --output_log_path nma_run_out.log --output_crd_path nma_run_out.crd

JSON

Common config file 

{
  "properties": {
    "frames": 100
  }
}

Command line

nma_run --config config_nma_run.json --input_pdb_path structure.ca.pdb --output_log_path nma_run_out.log --output_crd_path nma_run_out.crd

Pcz_lindemann

Extract Lindemann coefficient (an estimate of the solid-liquid behaviour of a protein) from a compressed PCZ file.

Get help

Command:

pcz_lindemann -h

usage: pcz_lindemann [-h] [--config CONFIG] --input_pcz_path INPUT_PCZ_PATH --output_json_path OUTPUT_JSON_PATH

Extract Lindemann coefficients from a compressed PCZ file.

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

required arguments:
  --input_pcz_path INPUT_PCZ_PATH
                        Input compressed trajectory file. Accepted formats: pcz.
  --output_json_path OUTPUT_JSON_PATH
                        Output json file with Lindemann coefficient report. Accepted formats: json.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_pcz_path (string): Input compressed trajectory file. File type: input. Sample file. Accepted formats: PCZ
output_json_path (string): Output json file with PCA Eigen Vectors. File type: output. Sample file. Accepted formats: JSON

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

binary_path (string): (pczdump) pczdump binary path to be used..
mask (string): (all atoms) Residue mask, in the format “:resnum1, resnum2, resnum3” (e.g. “:10,21,33”). See https://mmb.irbbarcelona.org/software/pcasuite/ for the complete format specification..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..

YAML

JSON

Pcz_stiffness

Extract PCA stiffness from a compressed PCZ file.

Get help

Command:

pcz_stiffness -h

usage: pcz_stiffness [-h] [--config CONFIG] --input_pcz_path INPUT_PCZ_PATH --output_json_path OUTPUT_JSON_PATH

Extract PCA Stiffness from a compressed PCZ file.

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

required arguments:
  --input_pcz_path INPUT_PCZ_PATH
                        Input compressed trajectory file. Accepted formats: pcz.
  --output_json_path OUTPUT_JSON_PATH
                        Output json file with PCA stiffness. Accepted formats: json.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_pcz_path (string): Input compressed trajectory file. File type: input. Sample file. Accepted formats: PCZ
output_json_path (string): Output json file with PCA Stiffness. File type: output. Sample file. Accepted formats: JSON

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

binary_path (string): (pczdump) pczdump binary path to be used..
eigenvector (integer): (0) PCA mode (eigenvector) from which to extract stiffness..
temperature (integer): (300) Temperature with which compute the apparent stiffness..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file 

properties:
  eigenvector: 0

Command line

pcz_stiffness --config config_pcz_stiffness.yml --input_pcz_path pcazip.pcz --output_json_path pcz_stiffness.json

JSON

Common config file 

{
  "properties": {
    "eigenvector": 0
  }
}

Command line

pcz_stiffness --config config_pcz_stiffness.json --input_pcz_path pcazip.pcz --output_json_path pcz_stiffness.json

Pcz_collectivity

Extract PCA collectivity (numerical measure of how many atoms are affected by a given mode) from a compressed PCZ file.

Get help

Command:

pcz_collectivity -h

usage: pcz_collectivity [-h] [--config CONFIG] --input_pcz_path INPUT_PCZ_PATH --output_json_path OUTPUT_JSON_PATH

Extract PCA collectivity (numerical measure of how many atoms are affected by a given mode) from a compressed PCZ file.

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

required arguments:
  --input_pcz_path INPUT_PCZ_PATH
                        Input compressed trajectory file. Accepted formats: pcz.
  --output_json_path OUTPUT_JSON_PATH
                        Output json file with PCA collectivity. Accepted formats: json.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_pcz_path (string): Input compressed trajectory file. File type: input. Sample file. Accepted formats: PCZ
output_json_path (string): Output json file with PCA Collectivity indexes per mode. File type: output. Sample file. Accepted formats: JSON

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

eigenvector (integer): (0) PCA mode (eigenvector) from which to extract stiffness..
binary_path (string): (pczdump) pczdump binary path to be used..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file 

properties:
  eigenvector: 0

Command line

pcz_collectivity --config config_pcz_collectivity.yml --input_pcz_path pcazip.pcz --output_json_path pcz_collectivity.json

JSON

Common config file 

{
  "properties": {
    "eigenvector": 0
  }
}

Command line

pcz_collectivity --config config_pcz_collectivity.json --input_pcz_path pcazip.pcz --output_json_path pcz_collectivity.json

Pcz_zip

Wrapper of the pcazip tool from the PCAsuite FlexServ module.

Get help

Command:

pcz_zip -h

usage: pcz_zip [-h] [--config CONFIG] --input_pdb_path INPUT_PDB_PATH --input_crd_path INPUT_CRD_PATH --output_pcz_path OUTPUT_PCZ_PATH

Compress Molecular Dynamics (MD) trajectories using Principal Component Analysis (PCA) algorithms.

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

required arguments:
  --input_pdb_path INPUT_PDB_PATH
                        Input PDB file. Accepted formats: pdb.
  --input_crd_path INPUT_CRD_PATH
                        Input trajectory file. Accepted formats: crd, mdcrd, inpcrd.
  --output_pcz_path OUTPUT_PCZ_PATH
                        Output compressed trajectory file. Accepted formats: pcz.

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_crd_path (string): Input Trajectory file. File type: input. Sample file. Accepted formats: CRD, MDCRD, INPCRD
output_pcz_path (string): Output compressed trajectory. File type: output. Sample file. Accepted formats: PCZ

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

binary_path (string): (pcazip) pcazip binary path to be used..
neigenv (integer): (0) Number of generated eigenvectors.
variance (integer): (90) Percentage of variance captured by the final set of eigenvectors.
verbose (boolean): (False) Make output verbose.
gauss_rmsd (boolean): (False) Use a gaussian RMSd for fitting.
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file 

properties:
  variance: 90

Command line

pcz_zip --config config_pcz_zip.yml --input_pdb_path structure.ca.pdb --input_crd_path traj.crd --output_pcz_path pcazip.pcz

JSON

Common config file 

{
  "properties": {
    "variance": 90
  }
}

Command line

pcz_zip --config config_pcz_zip.json --input_pdb_path structure.ca.pdb --input_crd_path traj.crd --output_pcz_path pcazip.pcz

Pcz_hinges

Compute possible hinge regions (residues around which large protein movements are organized) of a molecule from a compressed PCZ file.

Get help

Command:

pcz_hinges -h

usage: pcz_hinges [-h] [--config CONFIG] --input_pcz_path INPUT_PCZ_PATH --output_json_path OUTPUT_JSON_PATH

Compute possible hinge regions (residues around which large protein movements are organized) of a molecule from a compressed PCZ file.

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

required arguments:
  --input_pcz_path INPUT_PCZ_PATH
                        Input compressed trajectory file. Accepted formats: pcz.
  --output_json_path OUTPUT_JSON_PATH
                        Output hinge regions x PCA mode file. Accepted formats: json.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_pcz_path (string): Input compressed trajectory file. File type: input. Sample file. Accepted formats: PCZ
output_json_path (string): Output hinge regions x PCA mode file. File type: output. Sample file. Accepted formats: JSON

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

binary_path (string): (pczdump) pczdump binary path to be used..
eigenvector (integer): (0) PCA mode (eigenvector) from which to extract bfactor values per residue (0 means average over all modes)..
method (string): (Dynamic_domain) Method to compute the hinge regions (Options: Bfactor_slope, Force_constant, Dynamic_domain).
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file 

properties:
  eigenvector: 0
  method: Bfactor_slope

Command line

pcz_hinges --config config_pcz_hinges.yml --input_pcz_path pcazip.pcz --output_json_path hinges.json

JSON

Common config file 

{
  "properties": {
    "eigenvector": 0,
    "method": "Bfactor_slope"
  }
}

Command line

pcz_hinges --config config_pcz_hinges.json --input_pcz_path pcazip.pcz --output_json_path hinges.json

Pcz_info

Extract PCA info (variance, Dimensionality) from a compressed PCZ file.

Get help

Command:

pcz_info -h

usage: pcz_info [-h] [--config CONFIG] --input_pcz_path INPUT_PCZ_PATH --output_json_path OUTPUT_JSON_PATH

Extract PCA info from a compressed PCZ file.

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

required arguments:
  --input_pcz_path INPUT_PCZ_PATH
                        Input compressed trajectory file. Accepted formats: pcz.
  --output_json_path OUTPUT_JSON_PATH
                        Output json file with PCA info such as number of components, variance and dimensionality. Accepted formats: json.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_pcz_path (string): Input compressed trajectory file. File type: input. Sample file. Accepted formats: PCZ
output_json_path (string): Output json file with PCA info such as number of components, variance and dimensionality. File type: output. Sample file. Accepted formats: JSON

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

binary_path (string): (pczdump) pczdump binary path to be used..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..

YAML

JSON

Bd_run

Wrapper of the Browian Dynamics tool from the FlexServ module.

Get help

Command:

bd_run -h

usage: bd_run [-h] [--config CONFIG] --input_pdb_path INPUT_PDB_PATH --output_log_path OUTPUT_LOG_PATH --output_crd_path OUTPUT_CRD_PATH

Generates protein conformational structures using the Brownian Dynamics method.

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

required arguments:
  --input_pdb_path INPUT_PDB_PATH
                        Input PDB file. Accepted formats: pdb.
  --output_log_path OUTPUT_LOG_PATH
                        Output log file. Accepted formats: log, out, txt.
  --output_crd_path OUTPUT_CRD_PATH
                        Output ensemble file. Accepted formats: crd, mdcrd, inpcrd.

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_log_path (string): Output log file. File type: output. Sample file. Accepted formats: LOG, OUT, TXT, O
output_crd_path (string): Output ensemble. File type: output. Sample file. Accepted formats: CRD, MDCRD, INPCRD

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

binary_path (string): (bd) BD binary path to be used..
time (integer): (1000000) Total simulation time (ps).
dt (number): (1e-15) Integration time (ps).
wfreq (integer): (1000) Writing frequency (ps).
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file 

properties:
  time: 10000
  wfreq: 100

Command line

bd_run --config config_bd_run.yml --input_pdb_path structure.ca.pdb --output_log_path bd_run_out.log --output_crd_path bd_run_out.crd

JSON

Common config file 

{
  "properties": {
    "time": 10000,
    "wfreq": 100
  }
}

Command line

bd_run --config config_bd_run.json --input_pdb_path structure.ca.pdb --output_log_path bd_run_out.log --output_crd_path bd_run_out.crd

Pcz_unzip

Wrapper of the pcaunzip tool from the PCAsuite FlexServ module.

Get help

Command:

pcz_unzip -h

usage: pcz_unzip [-h] [--config CONFIG] --input_pcz_path INPUT_PCZ_PATH --output_crd_path OUTPUT_CRD_PATH

Uncompress Molecular Dynamics (MD) compressed trajectories using Principal Component Analysis (PCA) algorithms.

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

required arguments:
  --input_pcz_path INPUT_PCZ_PATH
                        Input compressed trajectory file. Accepted formats: pcz.
  --output_crd_path OUTPUT_CRD_PATH
                        Output trajectory file. Accepted formats: crd, mdcrd, inpcrd, pdb.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_pcz_path (string): Input compressed trajectory. File type: input. Sample file. Accepted formats: PCZ
output_crd_path (string): Output uncompressed trajectory. File type: output. Sample file. Accepted formats: CRD, MDCRD, INPCRD, PDB

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

binary_path (string): (pcaunzip) pcaunzip binary path to be used..
verbose (boolean): (False) Make output verbose.
pdb (boolean): (False) Use PDB format for output trajectory.
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file 

properties:
  pdb: false

Command line

pcz_unzip --config config_pcz_unzip.yml --input_pcz_path pcazip.pcz --output_crd_path traj.crd

JSON

Common config file 

{
  "properties": {
    "pdb": false
  }
}

Command line

pcz_unzip --config config_pcz_unzip.json --input_pcz_path pcazip.pcz --output_crd_path traj.crd