# BioBB PMX Command Line Help Generic usage: ```python biobb_command [-h] --config CONFIG --input_file(s) --output_file ``` ----------------- ## Pmxanalyse Wrapper class for the PMX analyse module. ### Get help Command: ```python 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. options: -h, --help show this help message and exit -c CONFIG, --config CONFIG This file can be a YAML file, JSON file or JSON string required arguments: --input_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](https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/data/pmx/xvg_A.zip). 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](https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/data/pmx/xvg_B.zip). Accepted formats: ZIP * **output_result_path** (*string*): Path to the TXT results file. File type: output. [Sample file](https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/reference/pmx/ref_result.txt). Accepted formats: TXT * **output_work_plot_path** (*string*): Path to the PNG plot results file. File type: output. [Sample file](https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/reference/pmx/ref_plot.png). 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](https://github.com/bioexcel/biobb_pmx/blob/master/biobb_pmx/test/data/config/config_pmxanalyse.yml) ```python properties: dpi: 600 method: CGI BAR JARZ temperature: 298.15 ``` #### [Docker config file](https://github.com/bioexcel/biobb_pmx/blob/master/biobb_pmx/test/data/config/config_pmxanalyse_docker.yml) ```python 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](https://github.com/bioexcel/biobb_pmx/blob/master/biobb_pmx/test/data/config/config_pmxanalyse_singularity.yml) ```python properties: container_image: shub://bioexcel/pmx_docker container_path: docker dpi: 600 method: CGI BAR JARZ temperature: 298.15 ``` #### Command line ```python 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](https://github.com/bioexcel/biobb_pmx/blob/master/biobb_pmx/test/data/config/config_pmxanalyse.json) ```python { "properties": { "method": "CGI BAR JARZ", "temperature": 298.15, "dpi": 600 } } ``` #### [Docker config file](https://github.com/bioexcel/biobb_pmx/blob/master/biobb_pmx/test/data/config/config_pmxanalyse_docker.json) ```python { "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](https://github.com/bioexcel/biobb_pmx/blob/master/biobb_pmx/test/data/config/config_pmxanalyse_singularity.json) ```python { "properties": { "method": "CGI BAR JARZ", "temperature": 298.15, "dpi": 600, "container_path": "docker", "container_image": "shub://bioexcel/pmx_docker" } } ``` #### Command line ```python 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 ``` ## Pmxatom_mapping Wrapper class for the PMX atom_mapping module. ### Get help Command: ```python 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 options: -h, --help show this help message and exit -c CONFIG, --config CONFIG This file can be a YAML file, JSON file or JSON string required arguments: --input_structure1_path INPUT_STRUCTURE1_PATH Path to the input ligand structure file 1. Accepted formats: pdb. --input_structure2_path INPUT_STRUCTURE2_PATH Path to the input ligand structure file 2. Accepted formats: pdb. --output_pairs1_path OUTPUT_PAIRS1_PATH Path to the output pairs for the ligand structure 1. Accepted formats: dat, txt. --output_pairs2_path OUTPUT_PAIRS2_PATH Path to the output pairs for the ligand structure 2. Accepted formats: dat, txt. --output_log_path OUTPUT_LOG_PATH Path to the log file. Accepted formats: log, txt, out. optional arguments: --output_structure1_path OUTPUT_STRUCTURE1_PATH Path to the superimposed structure for the ligand structure 1. Accepted formats: pdb. --output_structure2_path OUTPUT_STRUCTURE2_PATH Path to the superimposed structure for the ligand structure 2. Accepted formats: pdb. --output_morph1_path OUTPUT_MORPH1_PATH Path to the morphable atoms for the ligand structure 1. Accepted formats: pdb. --output_morph2_path OUTPUT_MORPH2_PATH Path to the morphable atoms for the ligand structure 2. Accepted formats: pdb. --output_scaffold1_path OUTPUT_SCAFFOLD1_PATH Path to the index of atoms to consider for the ligand structure 1. Accepted formats: ndx. --output_scaffold2_path OUTPUT_SCAFFOLD2_PATH Path to the index of atoms to consider for the ligand structure 2. Accepted formats: ndx. --output_score_path OUTPUT_SCORE_PATH Path to the morphing score. Accepted formats: dat, txt. ### 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](https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/data/pmx/lig1.pdb). Accepted formats: PDB * **input_structure2_path** (*string*): Path to the input ligand structure file 2. File type: input. [Sample file](https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/data/pmx/lig2.pdb). Accepted formats: PDB * **output_pairs1_path** (*string*): Path to the output pairs for the ligand structure 1. File type: output. [Sample file](https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/reference/pmx/ref_pairs1.dat). Accepted formats: DAT, TXT * **output_pairs2_path** (*string*): Path to the output pairs for the ligand structure 2. File type: output. [Sample file](https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/reference/pmx/ref_pairs2.dat). Accepted formats: DAT, TXT * **output_log_path** (*string*): Path to the log file. File type: output. [Sample file](None). Accepted formats: LOG, TXT, OUT * **output_structure1_path** (*string*): Path to the superimposed structure for the ligand structure 1. File type: output. [Sample file](None). Accepted formats: PDB * **output_structure2_path** (*string*): Path to the superimposed structure for the ligand structure 2. File type: output. [Sample file](None). Accepted formats: PDB * **output_morph1_path** (*string*): Path to the morphable atoms for the ligand structure 1. File type: output. [Sample file](None). Accepted formats: PDB * **output_morph2_path** (*string*): Path to the morphable atoms for the ligand structure 2. File type: output. [Sample file](None). 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](None). 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](None). Accepted formats: NDX * **output_score_path** (*string*): Path to the morphing score. File type: output. [Sample file](None). 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](https://github.com/bioexcel/biobb_pmx/blob/master/biobb_pmx/test/data/config/config_pmxatom_mapping.yml) ```python properties: distance: 0.05 noalignment: false ``` #### Command line ```python pmxatom_mapping --config config_pmxatom_mapping.yml --input_structure1_path lig1.pdb --input_structure2_path lig2.pdb --output_pairs1_path ref_pairs1.dat --output_pairs2_path ref_pairs2.dat --output_log_path output.log --output_structure1_path output.pdb --output_structure2_path output.pdb --output_morph1_path output.pdb --output_morph2_path output.pdb --output_scaffold1_path output.ndx --output_scaffold2_path output.ndx --output_score_path output.dat ``` ### JSON #### [Common config file](https://github.com/bioexcel/biobb_pmx/blob/master/biobb_pmx/test/data/config/config_pmxatom_mapping.json) ```python { "properties": { "noalignment": false, "distance": 0.05 } } ``` #### Command line ```python pmxatom_mapping --config config_pmxatom_mapping.json --input_structure1_path lig1.pdb --input_structure2_path lig2.pdb --output_pairs1_path ref_pairs1.dat --output_pairs2_path ref_pairs2.dat --output_log_path output.log --output_structure1_path output.pdb --output_structure2_path output.pdb --output_morph1_path output.pdb --output_morph2_path output.pdb --output_scaffold1_path output.ndx --output_scaffold2_path output.ndx --output_score_path output.dat ``` ## Pmxcreate_top Wrapper class for the PMX create_top module. ### Get help Command: ```python pmxcreate_top -h ``` usage: pmxcreate_top [-h] [-c CONFIG] --input_topology1_path INPUT_TOPOLOGY1_PATH --input_topology2_path INPUT_TOPOLOGY2_PATH -o OUTPUT_TOPOLOGY_PATH Run PMX create_top module options: -h, --help show this help message and exit -c CONFIG, --config CONFIG This file can be a YAML file, JSON file or JSON string required arguments: --input_topology1_path INPUT_TOPOLOGY1_PATH Path to the input topology file 1. Accepted formats: itp. --input_topology2_path INPUT_TOPOLOGY2_PATH Path to the input topology file 2. Accepted formats: itp. -o OUTPUT_TOPOLOGY_PATH, --output_topology_path OUTPUT_TOPOLOGY_PATH Path to the complete ligand topology file. Accepted formats: zip. ### 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](https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/data/pmx/topo1.itp). Accepted formats: ITP * **input_topology2_path** (*string*): Path to the input topology file 2. File type: input. [Sample file](https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/data/pmx/topo2.itp). Accepted formats: ITP * **output_topology_path** (*string*): Path to the complete ligand topology file. File type: output. [Sample file](https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/reference/pmx/ref_hybridTopo.zip). 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](https://github.com/bioexcel/biobb_pmx/blob/master/biobb_pmx/test/data/config/config_pmxcreate_top.yml) ```python properties: force_field: amber99sb-star-ildn-mut.ff mols: - - MOL - 1 system_name: Pmx topology BioBB Tutorial water: spce ``` #### Command line ```python pmxcreate_top --config config_pmxcreate_top.yml --input_topology1_path topo1.itp --input_topology2_path topo2.itp --output_topology_path ref_hybridTopo.zip ``` ### JSON #### [Common config file](https://github.com/bioexcel/biobb_pmx/blob/master/biobb_pmx/test/data/config/config_pmxcreate_top.json) ```python { "properties": { "force_field": "amber99sb-star-ildn-mut.ff", "water": "spce", "system_name": "Pmx topology BioBB Tutorial", "mols": [ [ "MOL", 1 ] ] } } ``` #### Command line ```python pmxcreate_top --config config_pmxcreate_top.json --input_topology1_path topo1.itp --input_topology2_path topo2.itp --output_topology_path ref_hybridTopo.zip ``` ## Pmxgentop Wrapper class for the PMX gentop module. ### Get help Command: ```python pmxgentop -h ``` usage: pmxgentop [-h] [-c CONFIG] -i INPUT_TOP_ZIP_PATH -o OUTPUT_TOP_ZIP_PATH Wrapper class for the PMX gentop module options: -h, --help show this help message and exit -c CONFIG, --config CONFIG This file can be a YAML file, JSON file or JSON string required arguments: -i INPUT_TOP_ZIP_PATH, --input_top_zip_path INPUT_TOP_ZIP_PATH Path the input GROMACS topology TOP and ITP files in zip format. Accepted formats: zip. -o OUTPUT_TOP_ZIP_PATH, --output_top_zip_path OUTPUT_TOP_ZIP_PATH Path the output TOP topology in zip format. Accepted formats: zip. ### 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](https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/data/pmx/topology.zip). Accepted formats: ZIP * **output_top_zip_path** (*string*): Path the output TOP topology in zip format. File type: output. [Sample file](https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/reference/pmx/ref_output_topology.zip). 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](https://github.com/bioexcel/biobb_pmx/blob/master/biobb_pmx/test/data/config/config_pmxgentop.yml) ```python properties: force_field: amber99sb-star-ildn-mut ``` #### [Docker config file](https://github.com/bioexcel/biobb_pmx/blob/master/biobb_pmx/test/data/config/config_pmxgentop_docker.yml) ```python 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](https://github.com/bioexcel/biobb_pmx/blob/master/biobb_pmx/test/data/config/config_pmxgentop_singularity.yml) ```python properties: container_image: shub://bioexcel/pmx_docker container_path: docker force_field: amber99sb-star-ildn-mut ``` #### Command line ```python pmxgentop --config config_pmxgentop.yml --input_top_zip_path topology.zip --output_top_zip_path ref_output_topology.zip ``` ### JSON #### [Common config file](https://github.com/bioexcel/biobb_pmx/blob/master/biobb_pmx/test/data/config/config_pmxgentop.json) ```python { "properties": { "force_field": "amber99sb-star-ildn-mut" } } ``` #### [Docker config file](https://github.com/bioexcel/biobb_pmx/blob/master/biobb_pmx/test/data/config/config_pmxgentop_docker.json) ```python { "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](https://github.com/bioexcel/biobb_pmx/blob/master/biobb_pmx/test/data/config/config_pmxgentop_singularity.json) ```python { "properties": { "force_field": "amber99sb-star-ildn-mut", "container_path": "docker", "container_image": "shub://bioexcel/pmx_docker" } } ``` #### Command line ```python pmxgentop --config config_pmxgentop.json --input_top_zip_path topology.zip --output_top_zip_path ref_output_topology.zip ``` ## Pmxligand_hybrid Wrapper class for the PMX ligand_hybrid module. ### Get help Command: ```python 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 [--input_pairs_path INPUT_PAIRS_PATH] [--input_scaffold1_path INPUT_SCAFFOLD1_PATH] [--input_scaffold2_path INPUT_SCAFFOLD2_PATH] --output_log_path OUTPUT_LOG_PATH --output_structure1_path OUTPUT_STRUCTURE1_PATH --output_structure2_path OUTPUT_STRUCTURE2_PATH --output_topology_path OUTPUT_TOPOLOGY_PATH --output_atomtypes_path OUTPUT_ATOMTYPES_PATH Run PMX ligand hybrid module options: -h, --help show this help message and exit -c CONFIG, --config CONFIG This file can be a YAML file, JSON file or JSON string required arguments: --input_structure1_path INPUT_STRUCTURE1_PATH Path to the input ligand structure file 1. Accepted formats: pdb. --input_structure2_path INPUT_STRUCTURE2_PATH Path to the input ligand structure file 2. Accepted formats: pdb. --input_topology1_path INPUT_TOPOLOGY1_PATH Path to the input ligand topology file 1. Accepted formats: itp. --input_topology2_path INPUT_TOPOLOGY2_PATH Path to the input ligand topology file 2. Accepted formats: itp. --output_log_path OUTPUT_LOG_PATH Path to the log file. Accepted formats: log, txt, out. --output_structure1_path OUTPUT_STRUCTURE1_PATH Path to the output hybrid structure based on the ligand 1. Accepted formats: pdb. --output_structure2_path OUTPUT_STRUCTURE2_PATH Path to the output hybrid structure based on the ligand 2. Accepted formats: pdb. --output_topology_path OUTPUT_TOPOLOGY_PATH Path to the output hybrid topology. Accepted formats: itp. --output_atomtypes_path OUTPUT_ATOMTYPES_PATH Path to the atom types for the output hybrid topology. Accepted formats: itp. optional arguments: --input_pairs_path INPUT_PAIRS_PATH Path to the input atom pair mapping. Accepted formats: dat, txt. --input_scaffold1_path INPUT_SCAFFOLD1_PATH Path to the index of atoms to consider for the ligand structure 1. Accepted formats: ndx. --input_scaffold2_path INPUT_SCAFFOLD2_PATH Path to the index of atoms to consider for the ligand structure 2. Accepted formats: ndx. ### 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](https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/data/pmx/lig1.pdb). Accepted formats: PDB * **input_structure2_path** (*string*): Path to the input ligand structure file 2. File type: input. [Sample file](https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/data/pmx/lig2.pdb). Accepted formats: PDB * **input_topology1_path** (*string*): Path to the input ligand topology file 1. File type: input. [Sample file](https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/data/pmx/topoLig1.itp). Accepted formats: ITP * **input_topology2_path** (*string*): Path to the input ligand topology file 2. File type: input. [Sample file](https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/data/pmx/topoLig2.itp). Accepted formats: ITP * **input_pairs_path** (*string*): Path to the input atom pair mapping. File type: input. [Sample file](https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/data/pmx/myPairs1.dat). 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](None). 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](None). Accepted formats: NDX * **output_log_path** (*string*): Path to the log file. File type: output. [Sample file](None). 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](https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/reference/pmx/ref_hybridStructure1.pdb). Accepted formats: PDB * **output_structure2_path** (*string*): Path to the output hybrid structure based on the ligand 2. File type: output. [Sample file](https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/reference/pmx/ref_hybridStructure2.pdb). Accepted formats: PDB * **output_topology_path** (*string*): Path to the output hybrid topology. File type: output. [Sample file](https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/reference/pmx/ref_hybridTopology.itp). Accepted formats: ITP * **output_atomtypes_path** (*string*): Path to the atom types for the output hybrid topology. File type: output. [Sample file](https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/reference/pmx/ref_hybridAtomTypes.itp). 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](https://github.com/bioexcel/biobb_pmx/blob/master/biobb_pmx/test/data/config/config_pmxligand_hybrid.yml) ```python properties: distance: 0.05 fit: true ``` #### Command line ```python pmxligand_hybrid --config config_pmxligand_hybrid.yml --input_structure1_path lig1.pdb --input_structure2_path lig2.pdb --input_topology1_path topoLig1.itp --input_topology2_path topoLig2.itp --input_pairs_path myPairs1.dat --input_scaffold1_path input.ndx --input_scaffold2_path input.ndx --output_log_path output.log --output_structure1_path ref_hybridStructure1.pdb --output_structure2_path ref_hybridStructure2.pdb --output_topology_path ref_hybridTopology.itp --output_atomtypes_path ref_hybridAtomTypes.itp ``` ### JSON #### [Common config file](https://github.com/bioexcel/biobb_pmx/blob/master/biobb_pmx/test/data/config/config_pmxligand_hybrid.json) ```python { "properties": { "fit": true, "distance": 0.05 } } ``` #### Command line ```python pmxligand_hybrid --config config_pmxligand_hybrid.json --input_structure1_path lig1.pdb --input_structure2_path lig2.pdb --input_topology1_path topoLig1.itp --input_topology2_path topoLig2.itp --input_pairs_path myPairs1.dat --input_scaffold1_path input.ndx --input_scaffold2_path input.ndx --output_log_path output.log --output_structure1_path ref_hybridStructure1.pdb --output_structure2_path ref_hybridStructure2.pdb --output_topology_path ref_hybridTopology.itp --output_atomtypes_path ref_hybridAtomTypes.itp ``` ## Pmxmerge_ff Wrapper class for the PMX merge_ff module. ### Get help Command: ```python pmxmerge_ff -h ``` usage: pmxmerge_ff [-h] [-c CONFIG] -i INPUT_TOPOLOGY_PATH -o OUTPUT_TOPOLOGY_PATH Run PMX merge_ff module options: -h, --help show this help message and exit -c CONFIG, --config CONFIG This file can be a YAML file, JSON file or JSON string required arguments: -i INPUT_TOPOLOGY_PATH, --input_topology_path INPUT_TOPOLOGY_PATH Path to the input ligand topologies as a zip file containing a list of itp files. Accepted formats: zip. -o OUTPUT_TOPOLOGY_PATH, --output_topology_path OUTPUT_TOPOLOGY_PATH Path to the merged ligand topology file. Accepted formats: itp. ### 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](https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/data/pmx/itps_to_merge.zip). Accepted formats: ZIP * **output_topology_path** (*string*): Path to the merged ligand topology file. File type: output. [Sample file](https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/reference/pmx/ref_mergedTopology.itp). 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](https://github.com/bioexcel/biobb_pmx/blob/master/biobb_pmx/test/data/config/config_pmxmerge_ff.yml) ```python properties: remove_tmp: true ``` #### Command line ```python pmxmerge_ff --config config_pmxmerge_ff.yml --input_topology_path itps_to_merge.zip --output_topology_path ref_mergedTopology.itp ``` ### JSON #### [Common config file](https://github.com/bioexcel/biobb_pmx/blob/master/biobb_pmx/test/data/config/config_pmxmerge_ff.json) ```python { "properties": { "remove_tmp": true } } ``` #### Command line ```python pmxmerge_ff --config config_pmxmerge_ff.json --input_topology_path itps_to_merge.zip --output_topology_path ref_mergedTopology.itp ``` ## Pmxmutate Wrapper class for the PMX mutate module. ### Get help Command: ```python pmxmutate -h ``` usage: pmxmutate [-h] [-c CONFIG] --input_structure_path INPUT_STRUCTURE_PATH -o OUTPUT_STRUCTURE_PATH [--input_b_structure_path INPUT_B_STRUCTURE_PATH] Run PMX mutate module options: -h, --help show this help message and exit -c CONFIG, --config CONFIG This file can be a YAML file, JSON file or JSON string required arguments: --input_structure_path INPUT_STRUCTURE_PATH Path to the input structure file. Accepted formats: pdb, gro. -o OUTPUT_STRUCTURE_PATH, --output_structure_path OUTPUT_STRUCTURE_PATH Path to the output structure file. Accepted formats: pdb, gro. optional arguments: --input_b_structure_path INPUT_B_STRUCTURE_PATH Path to the mutated input structure file. Accepted formats: pdb, gro. ### 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](https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/data/pmx/frame99.pdb). Accepted formats: PDB, GRO * **output_structure_path** (*string*): Path to the output structure file. File type: output. [Sample file](https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/reference/pmx/ref_output_structure.pdb). Accepted formats: PDB, GRO * **input_b_structure_path** (*string*): Path to the mutated input structure file. File type: input. [Sample file](None). 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](https://github.com/bioexcel/biobb_pmx/blob/master/biobb_pmx/test/data/config/config_pmxmutate.yml) ```python properties: force_field: amber99sb-star-ildn-mut mutation_list: 10Ala ``` #### [Docker config file](https://github.com/bioexcel/biobb_pmx/blob/master/biobb_pmx/test/data/config/config_pmxmutate_docker.yml) ```python 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](https://github.com/bioexcel/biobb_pmx/blob/master/biobb_pmx/test/data/config/config_pmxmutate_singularity.yml) ```python properties: container_image: shub://bioexcel/pmx_docker container_path: singularity force_field: amber99sb-star-ildn-mut mutation_list: 2Ala, 3Val ``` #### Command line ```python 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](https://github.com/bioexcel/biobb_pmx/blob/master/biobb_pmx/test/data/config/config_pmxmutate.json) ```python { "properties": { "mutation_list": "10Ala", "force_field": "amber99sb-star-ildn-mut" } } ``` #### [Docker config file](https://github.com/bioexcel/biobb_pmx/blob/master/biobb_pmx/test/data/config/config_pmxmutate_docker.json) ```python { "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](https://github.com/bioexcel/biobb_pmx/blob/master/biobb_pmx/test/data/config/config_pmxmutate_singularity.json) ```python { "properties": { "mutation_list": "2Ala, 3Val", "force_field": "amber99sb-star-ildn-mut", "container_path": "singularity", "container_image": "shub://bioexcel/pmx_docker" } } ``` #### Command line ```python pmxmutate --config config_pmxmutate.json --input_structure_path frame99.pdb --output_structure_path ref_output_structure.pdb --input_b_structure_path input.pdb ```