BioBB PMX Command Line Help

Generic usage:

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

Pmxligand_hybrid

Wrapper class for the PMX ligand_hybrid module.

Get help

Command:

pmxligand_hybrid -h

usage: pmxligand_hybrid [-h] [-c CONFIG] --input_structure1_path INPUT_STRUCTURE1_PATH --input_structure2_path INPUT_STRUCTURE2_PATH --input_topology1_path INPUT_TOPOLOGY1_PATH --input_topology2_path INPUT_TOPOLOGY2_PATH --output_structure1_path OUTPUT_STRUCTURE1_PATH --output_structure2_path OUTPUT_STRUCTURE2_PATH --output_topology1_path OUTPUT_TOPOLOGY1_PATH --output_topology2_path OUTPUT_TOPOLOGY2_PATH --output_log_path OUTPUT_LOG_PATH [--input_scaffold1_path INPUT_SCAFFOLD1_PATH] [--input_scaffold2_path INPUT_SCAFFOLD2_PATH] [--input_pairs_path INPUT_PAIRS_PATH]

Run PMX ligand hybrid module

optional arguments:
  -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_scaffold1_path INPUT_SCAFFOLD1_PATH
                        Path to the index of atoms to consider for the ligand structure 1
  --input_scaffold2_path INPUT_SCAFFOLD2_PATH
                        Path to the index of atoms to consider for the ligand structure 2
  --input_pairs_path INPUT_PAIRS_PATH
                        Path to the input atom pair mapping.

required arguments:
  --input_structure1_path INPUT_STRUCTURE1_PATH
                        Path to the input ligand structure file 1
  --input_structure2_path INPUT_STRUCTURE2_PATH
                        Path to the input ligand structure file 2
  --input_topology1_path INPUT_TOPOLOGY1_PATH
                        Path to the input ligand topology file 1
  --input_topology2_path INPUT_TOPOLOGY2_PATH
                        Path to the input ligand topology file 2
  --output_structure1_path OUTPUT_STRUCTURE1_PATH
                        Path to the output ligand structure file 1
  --output_structure2_path OUTPUT_STRUCTURE2_PATH
                        Path to the output ligand structure file 2
  --output_topology1_path OUTPUT_TOPOLOGY1_PATH
                        Path to the output ligand topology file 1
  --output_topology2_path OUTPUT_TOPOLOGY2_PATH
                        Path to the output ligand topology file 2
  --output_log_path OUTPUT_LOG_PATH
                        Path to the log file

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_structure1_path (string): Path to the input ligand structure file 1. File type: input. Sample file. Accepted formats: PDB
input_structure2_path (string): Path to the input ligand structure file 2. File type: input. Sample file. Accepted formats: PDB
input_topology1_path (string): Path to the input ligand topology file 1. File type: input. Sample file. Accepted formats: ITP
input_topology2_path (string): Path to the input ligand topology file 2. File type: input. Sample file. Accepted formats: ITP
input_pairs_path (string): Path to the input atom pair mapping. File type: input. Sample file. Accepted formats: DAT, TXT
input_scaffold1_path (string): Path to the index of atoms to consider for the ligand structure 1. File type: input. Sample file. Accepted formats: NDX
input_scaffold2_path (string): Path to the index of atoms to consider for the ligand structure 2. File type: input. Sample file. Accepted formats: NDX
output_log_path (string): Path to the log file. File type: output. Sample file. Accepted formats: LOG, TXT, OUT
output_structure1_path (string): Path to the output hybrid structure based on the ligand 1. File type: output. Sample file. Accepted formats: PDB
output_structure2_path (string): Path to the output hybrid structure based on the ligand 2. File type: output. Sample file. Accepted formats: PDB
output_topology_path (string): Path to the output hybrid topology. File type: output. Sample file. Accepted formats: ITP
output_atomtypes_path (string): Path to the atom types for the output hybrid topology. File type: output. Sample file. Accepted formats: ITP

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

fit (boolean): (False) Fit ligand structure 1 onto ligand structure 2 (Only used if input_pairs_path is provided)..
split (boolean): (False) Split the topology into separate transitions..
scDUMm (number): (1.0) Scale dummy masses using the counterpart atoms..
scDUMa (number): (1.0) Scale bonded dummy angle parameters..
scDUMd (number): (1.0) Scale bonded dummy dihedral parameters..
deAng (boolean): (False) Decouple angles composed of 1 dummy and 2 non-dummies..
distance (number): (0.05) Distance (nm) between atoms to consider them morphable for alignment approach (Only used if input_pairs_path is not provided)..
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..
container_path (string): (None) Path to the binary executable of your container..
container_image (string): (None) Container Image identifier..
container_volume_path (string): (/inout) Path to an internal directory in the container..
container_working_dir (string): (None) Path to the internal CWD in the container..
container_user_id (string): (None) User number id to be mapped inside the container..
container_shell_path (string): (/bin/bash) Path to the binary executable of the container shell..

YAML

Common config file 

properties:
  distance: 0.05
  fit: true

Command line

pmxligand_hybrid --config config_pmxligand_hybrid.yml --input_structure1_path ligand.pdb --input_structure2_path ligand.pdb --input_topology1_path ligand.itp --input_topology2_path ligand.itp --input_pairs_path ref_mapping_pairs.dat --input_scaffold1_path atoms_to_consider.ndx --input_scaffold2_path atoms_to_consider.ndx --output_log_path atom_mapping.log --output_structure1_path superimposed_ligand.pdb --output_structure2_path superimposed_ligand.pdb --output_topology_path ligand_hybrid.itp --output_atomtypes_path ligand_hybrid_atomtypes.itp

JSON

Common config file 

{
  "properties": {
    "fit": true,
    "distance": 0.05
  }
}

Command line

pmxligand_hybrid --config config_pmxligand_hybrid.json --input_structure1_path ligand.pdb --input_structure2_path ligand.pdb --input_topology1_path ligand.itp --input_topology2_path ligand.itp --input_pairs_path ref_mapping_pairs.dat --input_scaffold1_path atoms_to_consider.ndx --input_scaffold2_path atoms_to_consider.ndx --output_log_path atom_mapping.log --output_structure1_path superimposed_ligand.pdb --output_structure2_path superimposed_ligand.pdb --output_topology_path ligand_hybrid.itp --output_atomtypes_path ligand_hybrid_atomtypes.itp

Pmxanalyse

Wrapper class for the PMX analyse module.

Get help

Command:

pmxanalyse -h

usage: pmxanalyse [-h] [-c CONFIG] --input_a_xvg_zip_path INPUT_A_XVG_ZIP_PATH --input_b_xvg_zip_path INPUT_B_XVG_ZIP_PATH --output_result_path OUTPUT_RESULT_PATH --output_work_plot_path OUTPUT_WORK_PLOT_PATH

Wrapper class for the PMX analyse module.

optional arguments:
  -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_a_xvg_zip_path INPUT_A_XVG_ZIP_PATH
                        Path the zip file containing the dgdl.xvg files of the A state. Accepted formats: zip.
  --input_b_xvg_zip_path INPUT_B_XVG_ZIP_PATH
                        Path the zip file containing the dgdl.xvg files of the B state. Accepted formats: zip.
  --output_result_path OUTPUT_RESULT_PATH
                        Path to the TXT results file. Accepted formats: txt.
  --output_work_plot_path OUTPUT_WORK_PLOT_PATH
                        Path to the PNG plot results file. Accepted formats: png.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_a_xvg_zip_path (string): Path the zip file containing the dgdl.xvg files of the A state. File type: input. Sample file. Accepted formats: ZIP
input_b_xvg_zip_path (string): Path the zip file containing the dgdl.xvg files of the B state. File type: input. Sample file. Accepted formats: ZIP
output_result_path (string): Path to the TXT results file. File type: output. Sample file. Accepted formats: TXT
output_work_plot_path (string): Path to the PNG plot results file. File type: output. Sample file. Accepted formats: PNG

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

method (string): (CGI BAR JARZ) Choose one or more estimators to use. .
temperature (number): (298.15) Temperature in Kelvin..
nboots (integer): (0) Number of bootstrap samples to use for the bootstrap estimate of the standard errors..
nblocks (integer): (1) Number of blocks to divide the data into for an estimate of the standard error..
integ_only (boolean): (False) Whether to do integration only..
reverseB (boolean): (False) Whether to reverse the work values for the backward (B->A) transformation..
skip (integer): (1) Skip files..
slice (string): (None) Subset of trajectories to analyze. Provide list slice, e.g. “10 50” will result in selecting dhdl_files[10:50]..
rand (integer): (None) Take a random subset of trajectories. Default is None (do not take random subset)..
index (string): (None) Zero-based index of files to analyze (e.g. “0 10 20 50 60”). It keeps the dhdl.xvg files according to their position in the list, sorted according to the filenames..
prec (integer): (2) The decimal precision of the screen/file output..
units (string): (kJ) The units of the output. .
no_ks (boolean): (False) Whether to do a Kolmogorov-Smirnov test to check whether the Gaussian assumption for CGI holds..
nbins (integer): (20) Number of histograms bins for the plot..
dpi (integer): (300) Resolution of the plot..
binary_path (string): (pmx) Path to the PMX command line interface..
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..
container_path (string): (None) Path to the binary executable of your container..
container_image (string): (gromacs/gromacs:latest) Container Image identifier..
container_volume_path (string): (/data) Path to an internal directory in the container..
container_working_dir (string): (None) Path to the internal CWD in the container..
container_user_id (string): (None) User number id to be mapped inside the container..
container_shell_path (string): (/bin/bash) Path to the binary executable of the container shell..

YAML

Common config file 

properties:
  dpi: 600
  method: CGI BAR JARZ
  temperature: 298.15

Docker config file 

properties:
  container_image: quay.io/biocontainers/pmx_biobb:4.1.3--py38ha14b6f2_0
  container_path: docker
  dpi: 600
  method: CGI BAR JARZ
  temperature: 298.15

Singularity config file 

properties:
  container_image: shub://bioexcel/pmx_docker
  container_path: docker
  dpi: 600
  method: CGI BAR JARZ
  temperature: 298.15

Command line

pmxanalyse --config config_pmxanalyse.yml --input_a_xvg_zip_path xvg_A.zip --input_b_xvg_zip_path xvg_B.zip --output_result_path ref_result.txt --output_work_plot_path ref_plot.png

JSON

Common config file 

{
  "properties": {
    "method": "CGI BAR JARZ",
    "temperature": 298.15,
    "dpi": 600
  }
}

Docker config file 

{
  "properties": {
    "method": "CGI BAR JARZ",
    "temperature": 298.15,
    "dpi": 600,
    "container_path": "docker",
    "container_image": "quay.io/biocontainers/pmx_biobb:4.1.3--py38ha14b6f2_0"
  }
}

Singularity config file 

{
  "properties": {
    "method": "CGI BAR JARZ",
    "temperature": 298.15,
    "dpi": 600,
    "container_path": "docker",
    "container_image": "shub://bioexcel/pmx_docker"
  }
}

Command line

pmxanalyse --config config_pmxanalyse.json --input_a_xvg_zip_path xvg_A.zip --input_b_xvg_zip_path xvg_B.zip --output_result_path ref_result.txt --output_work_plot_path ref_plot.png

Pmxmerge_ff

Wrapper class for the PMX merge_ff module.

Get help

Command:

pmxmerge_ff -h

usage: pmxmerge_ff [-h] [-c CONFIG] --input_topology_path INPUT_TOPOLOGY_PATH --output_topology_path OUTPUT_TOPOLOGY_PATH

Run PMX merge_ff module

optional arguments:
  -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_topology_path INPUT_TOPOLOGY_PATH
                        Path to the input ligand topologies as a zip file containing a list of itp files.
  --output_topology_path OUTPUT_TOPOLOGY_PATH
                        Path to the merged ligand topology file

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_topology_path (string): Path to the input ligand topologies as a zip file containing a list of itp files. File type: input. Sample file. Accepted formats: ZIP
output_topology_path (string): Path to the merged ligand topology file. File type: output. Sample file. Accepted formats: ITP

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

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..
container_path (string): (None) Path to the binary executable of your container..
container_image (string): (None) Container Image identifier..
container_volume_path (string): (/inout) Path to an internal directory in the container..
container_working_dir (string): (None) Path to the internal CWD in the container..
container_user_id (string): (None) User number id to be mapped inside the container..
container_shell_path (string): (/bin/bash) Path to the binary executable of the container shell..

YAML

Common config file 

properties:
  remove_tmp: true

Command line

pmxmerge_ff --config config_pmxmerge_ff.yml --input_topology_path ligand_itps.zip --output_topology_path ligand.itp

JSON

Common config file 

{
  "properties": {
    "remove_tmp": true
  }
}

Command line

pmxmerge_ff --config config_pmxmerge_ff.json --input_topology_path ligand_itps.zip --output_topology_path ligand.itp

Pmxcreate_top

Wrapper class for the PMX create_top module.

Get help

Command:

pmxcreate_top -h

usage: pmxcreate_top [-h] [-c CONFIG] --input_topology1_path INPUT_TOPOLOGY1_PATH --input_topology2_path INPUT_TOPOLOGY2_PATH --output_topology_path OUTPUT_TOPOLOGY_PATH

Run PMX create_top module

optional arguments:
  -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_topology1_path INPUT_TOPOLOGY1_PATH
                        Path to the input topology file 1
  --input_topology2_path INPUT_TOPOLOGY2_PATH
                        Path to the input topology file 2
  --output_topology_path OUTPUT_TOPOLOGY_PATH
                        Path to the complete ligand topology file

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_topology1_path (string): Path to the input topology file 1. File type: input. Sample file. Accepted formats: ITP
input_topology2_path (string): Path to the input topology file 2. File type: input. Sample file. Accepted formats: ITP
output_topology_path (string): Path to the complete ligand topology file. File type: output. Sample file. Accepted formats: ZIP

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

force_field (string): (amber99sb-star-ildn-mut.ff) Force-field to be included in the generated topology..
water (string): (tip3p) Water model to be included in the generated topology..
system_name (string): (Pmx topology) System name to be included in the generated topology..
mols (array): ([[Protein,1],[Ligand,1]]) Molecules to be included in the generated topology..
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..
container_path (string): (None) Path to the binary executable of your container..
container_image (string): (None) Container Image identifier..
container_volume_path (string): (/inout) Path to an internal directory in the container..
container_working_dir (string): (None) Path to the internal CWD in the container..
container_user_id (string): (None) User number id to be mapped inside the container..
container_shell_path (string): (/bin/bash) Path to the binary executable of the container shell..

YAML

Common config file 

properties:
  force_field: amber99sb-star-ildn-mut.ff
  mols:
  - - MOL
    - 1
  system_name: Pmx topology BioBB Tutorial
  water: spce

Command line

pmxcreate_top --config config_pmxcreate_top.yml --input_topology1_path ligand.itp --input_topology2_path ligand.itp --output_topology_path ligand_top.zip

JSON

Common config file 

{
  "properties": {
    "force_field": "amber99sb-star-ildn-mut.ff",
    "water": "spce",
    "system_name": "Pmx topology BioBB Tutorial",
    "mols": [
      [
        "MOL",
        1
      ]
    ]
  }
}

Command line

pmxcreate_top --config config_pmxcreate_top.json --input_topology1_path ligand.itp --input_topology2_path ligand.itp --output_topology_path ligand_top.zip

Pmxgentop

Wrapper class for the PMX gentop module.

Get help

Command:

pmxgentop -h

usage: pmxgentop [-h] [-c CONFIG] --input_top_zip_path INPUT_TOP_ZIP_PATH --output_top_zip_path OUTPUT_TOP_ZIP_PATH

Wrapper class for the PMX gentop module

optional arguments:
  -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_zip_path INPUT_TOP_ZIP_PATH
                        Path to the input topology zip file
  --output_top_zip_path OUTPUT_TOP_ZIP_PATH
                        Path to the output topology zip file

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_top_zip_path (string): Path the input GROMACS topology TOP and ITP files in zip format. File type: input. Sample file. Accepted formats: ZIP
output_top_zip_path (string): Path the output TOP topology in zip format. File type: output. Sample file. Accepted formats: ZIP

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

force_field (string): (amber99sb-star-ildn-mut) Force field to use. If input_top_zip_path is a top file, it’s not necessary to specify the forcefield, as it will be determined automatically. If input_top_zip_path is an itp file, then it’s needed..
split (boolean): (False) Write separate topologies for the vdW and charge transformations..
scale_mass (boolean): (False) Scale the masses of morphing atoms so that dummies have a mass of 1..
gmx_lib (string): ($CONDA_PREFIX/lib/python3.7/site-packages/pmx/data/mutff/) Path to the GMXLIB folder in your computer..
binary_path (string): (pmx) Path to the PMX command line interface..
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..
container_path (string): (None) Path to the binary executable of your container..
container_image (string): (gromacs/gromacs:latest) Container Image identifier..
container_volume_path (string): (/inout) Path to an internal directory in the container..
container_working_dir (string): (None) Path to the internal CWD in the container..
container_user_id (string): (None) User number id to be mapped inside the container..
container_shell_path (string): (/bin/bash) Path to the binary executable of the container shell..

YAML

Common config file 

properties:
  force_field: amber99sb-star-ildn-mut

Docker config file 

properties:
  container_image: quay.io/biocontainers/pmx_biobb:4.1.3--py38ha14b6f2_0
  container_path: docker
  force_field: amber99sb-star-ildn-mut

Singularity config file 

properties:
  container_image: shub://bioexcel/pmx_docker
  container_path: docker
  force_field: amber99sb-star-ildn-mut

Command line

pmxgentop --config config_pmxgentop.yml --input_top_zip_path topology.zip --output_top_zip_path ref_output_topology.zip

JSON

Common config file 

{
  "properties": {
    "force_field": "amber99sb-star-ildn-mut"
  }
}

Docker config file 

{
  "properties": {
    "force_field": "amber99sb-star-ildn-mut",
    "container_path": "docker",
    "container_image": "quay.io/biocontainers/pmx_biobb:4.1.3--py38ha14b6f2_0"
  }
}

Singularity config file 

{
  "properties": {
    "force_field": "amber99sb-star-ildn-mut",
    "container_path": "docker",
    "container_image": "shub://bioexcel/pmx_docker"
  }
}

Command line

pmxgentop --config config_pmxgentop.json --input_top_zip_path topology.zip --output_top_zip_path ref_output_topology.zip

Pmxatom_mapping

Wrapper class for the PMX atom_mapping module.

Get help

Command:

pmxatom_mapping -h

usage: pmxatom_mapping [-h] [-c CONFIG] --input_structure1_path INPUT_STRUCTURE1_PATH --input_structure2_path INPUT_STRUCTURE2_PATH --output_pairs1_path OUTPUT_PAIRS1_PATH --output_pairs2_path OUTPUT_PAIRS2_PATH --output_log_path OUTPUT_LOG_PATH [--output_structure1_path OUTPUT_STRUCTURE1_PATH] [--output_structure2_path OUTPUT_STRUCTURE2_PATH] [--output_morph1_path OUTPUT_MORPH1_PATH] [--output_morph2_path OUTPUT_MORPH2_PATH] [--output_scaffold1_path OUTPUT_SCAFFOLD1_PATH] [--output_scaffold2_path OUTPUT_SCAFFOLD2_PATH] [--output_score_path OUTPUT_SCORE_PATH]

Run PMX atom mapping module

optional arguments:
  -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_structure1_path OUTPUT_STRUCTURE1_PATH
                        Path to the superimposed structure for the ligand structure 1
  --output_structure2_path OUTPUT_STRUCTURE2_PATH
                        Path to the superimposed structure for the ligand structure 2
  --output_morph1_path OUTPUT_MORPH1_PATH
                        Path to the morphable atoms for the ligand structure 1
  --output_morph2_path OUTPUT_MORPH2_PATH
                        Path to the morphable atoms for the ligand structure 2
  --output_scaffold1_path OUTPUT_SCAFFOLD1_PATH
                        Path to the index of atoms to consider for the ligand structure 1
  --output_scaffold2_path OUTPUT_SCAFFOLD2_PATH
                        Path to the index of atoms to consider for the ligand structure 2
  --output_score_path OUTPUT_SCORE_PATH
                        Path to the morphing score. File type: output

required arguments:
  --input_structure1_path INPUT_STRUCTURE1_PATH
                        Path to the input ligand structure file 1
  --input_structure2_path INPUT_STRUCTURE2_PATH
                        Path to the input ligand structure file 2
  --output_pairs1_path OUTPUT_PAIRS1_PATH
                        Path to the output pairs for the ligand structure 1
  --output_pairs2_path OUTPUT_PAIRS2_PATH
                        Path to the output pairs for the ligand structure 2
  --output_log_path OUTPUT_LOG_PATH
                        Path to the log file

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_structure1_path (string): Path to the input ligand structure file 1. File type: input. Sample file. Accepted formats: PDB
input_structure2_path (string): Path to the input ligand structure file 2. File type: input. Sample file. Accepted formats: PDB
output_pairs1_path (string): Path to the output pairs for the ligand structure 1. File type: output. Sample file. Accepted formats: DAT, TXT
output_pairs2_path (string): Path to the output pairs for the ligand structure 2. File type: output. Sample file. Accepted formats: DAT, TXT
output_log_path (string): Path to the log file. File type: output. Sample file. Accepted formats: LOG, TXT, OUT
output_structure1_path (string): Path to the superimposed structure for the ligand structure 1. File type: output. Sample file. Accepted formats: PDB
output_structure2_path (string): Path to the superimposed structure for the ligand structure 2. File type: output. Sample file. Accepted formats: PDB
output_morph1_path (string): Path to the morphable atoms for the ligand structure 1. File type: output. Sample file. Accepted formats: PDB
output_morph2_path (string): Path to the morphable atoms for the ligand structure 2. File type: output. Sample file. Accepted formats: PDB
output_scaffold1_path (string): Path to the index of atoms to consider for the ligand structure 1. File type: output. Sample file. Accepted formats: NDX
output_scaffold2_path (string): Path to the index of atoms to consider for the ligand structure 2. File type: output. Sample file. Accepted formats: NDX
output_score_path (string): Path to the morphing score. File type: output. Sample file. Accepted formats: DAT, TXT

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

noalignment (boolean): (False) Should the alignment method be disabled..
nomcs (boolean): (False) Should the MCS method be disabled..
noH2H (boolean): (True) Should non-polar hydrogens be discarded from morphing into any other hydrogen..
H2Hpolar (boolean): (False) Should polar hydrogens be morphed into polar hydrogens..
H2Heavy (boolean): (False) Should hydrogen be morphed into a heavy atom..
RingsOnly (boolean): (False) Should rings only be used in the MCS search and alignemnt..
dMCS (boolean): (False) Should the distance criterium be also applied in the MCS based search..
swap (boolean): (False) Try swapping the molecule order which would be a cross-check and require double execution time..
nochirality (boolean): (True) Perform chirality check for MCS mapping..
distance (number): (0.05) Distance (nm) between atoms to consider them morphable for alignment approach..
timeout (integer): (10) Maximum time (s) for an MCS search..
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..
container_path (string): (None) Path to the binary executable of your container..
container_image (string): (None) Container Image identifier..
container_volume_path (string): (/inout) Path to an internal directory in the container..
container_working_dir (string): (None) Path to the internal CWD in the container..
container_user_id (string): (None) User number id to be mapped inside the container..
container_shell_path (string): (/bin/bash) Path to the binary executable of the container shell..

YAML

Common config file 

properties:
  distance: 0.05
  noalignment: false

Command line

pmxatom_mapping --config config_pmxatom_mapping.yml --input_structure1_path ligand.pdb --input_structure2_path ligand.pdb --output_pairs1_path ref_mapping_pairs.dat --output_pairs2_path ref_mapping_pairs.dat --output_log_path atom_mapping.log --output_structure1_path superimposed_ligand.pdb --output_structure2_path superimposed_ligand.pdb --output_morph1_path superimposed_ligand.pdb --output_morph2_path superimposed_ligand.pdb --output_scaffold1_path atoms_to_consider.ndx --output_scaffold2_path atoms_to_consider.ndx --output_score_path morph_score.dat

JSON

Common config file 

{
  "properties": {
    "noalignment": false,
    "distance": 0.05
  }
}

Command line

pmxatom_mapping --config config_pmxatom_mapping.json --input_structure1_path ligand.pdb --input_structure2_path ligand.pdb --output_pairs1_path ref_mapping_pairs.dat --output_pairs2_path ref_mapping_pairs.dat --output_log_path atom_mapping.log --output_structure1_path superimposed_ligand.pdb --output_structure2_path superimposed_ligand.pdb --output_morph1_path superimposed_ligand.pdb --output_morph2_path superimposed_ligand.pdb --output_scaffold1_path atoms_to_consider.ndx --output_scaffold2_path atoms_to_consider.ndx --output_score_path morph_score.dat

Pmxmutate

Wrapper class for the PMX mutate module.

Get help

Command:

pmxmutate -h

usage: pmxmutate [-h] [-c CONFIG] --input_structure_path INPUT_STRUCTURE_PATH --output_structure_path OUTPUT_STRUCTURE_PATH [--input_b_structure_path INPUT_B_STRUCTURE_PATH]

Run PMX mutate module

optional arguments:
  -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_b_structure_path INPUT_B_STRUCTURE_PATH
                        Path to the mutated input structure file

required arguments:
  --input_structure_path INPUT_STRUCTURE_PATH
                        Path to the input structure file
  --output_structure_path OUTPUT_STRUCTURE_PATH
                        Path to the output structure file

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_structure_path (string): Path to the input structure file. File type: input. Sample file. Accepted formats: PDB, GRO
output_structure_path (string): Path to the output structure file. File type: output. Sample file. Accepted formats: PDB, GRO
input_b_structure_path (string): Path to the mutated input structure file. File type: input. Sample file. Accepted formats: PDB, GRO

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

mutation_list (string): (2Ala) Mutation list in the format “Chain:Resnum MUT_AA_Code” or “Chain:Resnum MUT_NA_Code” (no spaces between the elements) separated by commas. If no chain is provided as chain code all the chains in the pdb file will be mutated. ie: “A:15CYS”. Possible MUT_AA_Code: ‘ALA’, ‘ARG’, ‘ASN’, ‘ASP’, ‘ASPH’, ‘ASPP’, ‘ASH’, ‘CYS’, ‘CYS2’, ‘CYN’, ‘CYX’, ‘CYM’, ‘CYSH’, ‘GLU’, ‘GLUH’, ‘GLUP’, ‘GLH’, ‘GLN’, ‘GLY’, ‘HIS’, ‘HIE’, ‘HISE’, ‘HSE’, ‘HIP’, ‘HSP’, ‘HISH’, ‘HID’, ‘HSD’, ‘ILE’, ‘LEU’, ‘LYS’, ‘LYSH’, ‘LYP’, ‘LYN’, ‘LSN’, ‘MET’, ‘PHE’, ‘PRO’, ‘SER’, ‘SP1’, ‘SP2’, ‘THR’, ‘TRP’, ‘TYR’, ‘VAL’. Possible MUT_NA_Codes: ‘A’, ‘T’, ‘C’, ‘G’, ‘U’..
force_field (string): (amber99sb-star-ildn-mut) Forcefield to use..
resinfo (boolean): (False) Show the list of 3-letter -> 1-letter residues..
gmx_lib (string): ($CONDA_PREFIX/lib/python3.7/site-packages/pmx/data/mutff/) Path to the GMXLIB folder in your computer..
binary_path (string): (pmx) Path to the PMX command line interface..
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..
container_path (string): (None) Path to the binary executable of your container..
container_image (string): (None) Container Image identifier..
container_volume_path (string): (/inout) Path to an internal directory in the container..
container_working_dir (string): (None) Path to the internal CWD in the container..
container_user_id (string): (None) User number id to be mapped inside the container..
container_shell_path (string): (/bin/bash) Path to the binary executable of the container shell..

YAML

Common config file 

properties:
  force_field: amber99sb-star-ildn-mut
  mutation_list: 10Ala

Docker config file 

properties:
  container_image: quay.io/biocontainers/pmx_biobb:4.1.3--py38ha14b6f2_0
  container_path: docker
  force_field: amber99sb-star-ildn-mut
  mutation_list: 2Ala, 3Val

Singularity config file 

properties:
  container_image: shub://bioexcel/pmx_docker
  container_path: singularity
  force_field: amber99sb-star-ildn-mut
  mutation_list: 2Ala, 3Val

Command line

pmxmutate --config config_pmxmutate.yml --input_structure_path frame99.pdb --output_structure_path ref_output_structure.pdb --input_b_structure_path input.pdb

JSON

Common config file 

{
  "properties": {
    "mutation_list": "10Ala",
    "force_field": "amber99sb-star-ildn-mut"
  }
}

Docker config file 

{
  "properties": {
    "mutation_list": "2Ala, 3Val",
    "force_field": "amber99sb-star-ildn-mut",
    "container_path": "docker",
    "container_image": "quay.io/biocontainers/pmx_biobb:4.1.3--py38ha14b6f2_0"
  }
}

Singularity config file 

{
  "properties": {
    "mutation_list": "2Ala, 3Val",
    "force_field": "amber99sb-star-ildn-mut",
    "container_path": "singularity",
    "container_image": "shub://bioexcel/pmx_docker"
  }
}

Command line

pmxmutate --config config_pmxmutate.json --input_structure_path frame99.pdb --output_structure_path ref_output_structure.pdb --input_b_structure_path input.pdb