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
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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..
- 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..
- 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..
- 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..
- 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..
- 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..
- 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..
- 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