From f4b977d0729c0e7ef35fac85595d4c0d463abe2c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Rub=C3=A9n=20Chaves?= Date: Fri, 10 Jan 2025 15:13:02 +0100 Subject: [PATCH] update json/docs --- biobb_mem/docs/source/command_line.md | 244 ++++++++++-------- biobb_mem/json_schemas/fatslim_membranes.json | 6 + 2 files changed, 142 insertions(+), 108 deletions(-) diff --git a/biobb_mem/docs/source/command_line.md b/biobb_mem/docs/source/command_line.md index 3291e5d..185088f 100644 --- a/biobb_mem/docs/source/command_line.md +++ b/biobb_mem/docs/source/command_line.md @@ -6,77 +6,79 @@ biobb_command [-h] --config CONFIG --input_file(s) --output_file ----------------- -## Fatslim_membranes -Wrapper of the FATSLiM membranes module for leaflet and membrane identification. +## Cpptraj_density +Wrapper of the Ambertools Cpptraj module for calculating density profile along an axis of a given cpptraj compatible trajectory. ### Get help Command: ```python -fatslim_membranes -h +cpptraj_density -h ``` - usage: fatslim_membranes [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --output_ndx_path OUTPUT_NDX_PATH [--input_traj_path INPUT_TRAJ_PATH] + usage: cpptraj_density [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH --output_cpptraj_path OUTPUT_CPPTRAJ_PATH [--output_traj_path OUTPUT_TRAJ_PATH] Calculates the density along an axis of a given cpptraj compatible trajectory. options: -h, --help show this help message and exit --config CONFIG Configuration file - --input_traj_path INPUT_TRAJ_PATH - Path to the input trajectory to be processed. Accepted formats: gro, pdb, tng, trr, xtc. + --output_traj_path OUTPUT_TRAJ_PATH + Path to the output processed trajectory. required arguments: --input_top_path INPUT_TOP_PATH - Path to the input structure or topology file. Accepted formats: ent, gro, pdb, tpr. - --output_ndx_path OUTPUT_NDX_PATH - Path to the GROMACS index file. Accepted formats: ndx + Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip. + --input_traj_path INPUT_TRAJ_PATH + Path to the input trajectory to be processed. Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib. + --output_cpptraj_path OUTPUT_CPPTRAJ_PATH + Path to the output processed analysis. ### I / O Arguments Syntax: input_argument (datatype) : Definition Config input / output arguments for this building block: -* **input_top_path** (*string*): Path to the input topology file. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/A01JD/A01JD.pdb). Accepted formats: TPR, GRO, G96, PDB, BRK, ENT -* **input_traj_path** (*string*): Path to the GROMACS trajectory file. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/A01JD/A01JD.xtc). Accepted formats: XTC, TRR, CPT, GRO, G96, PDB, TNG -* **output_ndx_path** (*string*): Path to the output index NDX file. File type: output. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/A01JD/A01JD.ndx). Accepted formats: NDX +* **input_top_path** (*string*): Path to the input structure or topology file. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/ambertools/topology.top). Accepted formats: TOP, PDB, PRMTOP, PARMTOP, ZIP +* **input_traj_path** (*string*): Path to the input trajectory to be processed. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/ambertools/trajectory.xtc). Accepted formats: MDCRD, CRD, CDF, NETCDF, NC, RESTART, NCRESTART, RESTARTNC, DCD, CHARMM, COR, PDB, MOL2, TRR, GRO, BINPOS, XTC, CIF, ARC, SQM, SDF, CONFLIB +* **output_cpptraj_path** (*string*): Path to the output processed density analysis. File type: output. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/reference/ambertools/reference/density_default.dat). Accepted formats: DAT, AGR, XMGR, GNU +* **output_traj_path** (*string*): Path to the output processed trajectory. File type: output. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/reference/ambertools/trajectory_out.dcd). Accepted formats: MDCRD, CRD, CDF, NETCDF, NC, RESTART, NCRESTART, RESTARTNC, DCD, CHARMM, COR, PDB, MOL2, TRR, GRO, BINPOS, XTC, CIF, ARC, SQM, SDF, CONFLIB ### Config Syntax: input_parameter (datatype) - (default_value) Definition Config parameters for this building block: -* **selection** (*string*): (resname DPPC and element P) Molecules used in the identification using MDAnalysis selection language.. -* **cutoff** (*number*): (2.0) Cutoff distance (in nm) to be used when leaflet identification is performed.. -* **begin_frame** (*integer*): (-1) First frame index to be used for analysis.. -* **end_frame** (*integer*): (-1) Last frame index to be used for analysis.. -* **ignore_no_box** (*boolean*): (False) Ignore the absence of box information in the topology. If the topology does not contain box information, the box will be set to the minimum and maximum positions of the atoms.. -* **binary_path** (*string*): (fatslim) Path to the fatslim executable binary.. +* **start** (*integer*): (1) Starting frame for slicing. +* **end** (*integer*): (-1) Ending frame for slicing. +* **steps** (*integer*): (1) Step for slicing. +* **density_type** (*string*): (number) Number, mass, partial charge (q) or electron (Ne - q) density. Electron density will be converted to e-/Å3 by dividing the average area spanned by the other two dimensions.. +* **mask** (*string*): (*) Arbitrary number of masks for atom selection; a dataset is created and the output will contain entries for each mask.. Default: all atoms.. +* **delta** (*number*): (0.25) Resolution, i.e. determines number of slices (i.e. histogram bins).. +* **axis** (*string*): (z) Coordinate (axis) for density calculation. Vales: x, y, z.. +* **bintype** (*string*): (bincenter) Determine whether histogram bin coordinates will be based on bin center (default) or bin edges. . +* **restrict** (*string*): (None) If specified, only calculate the density within a cylinder or square shape from the specified axis as defined by a distance cutoff. . +* **cutoff** (*number*): (None) The distance cutoff for 'restrict'. Required if 'restrict' is specified.. +* **binary_path** (*string*): (cpptraj) Path to the cpptraj executable binary.. * **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.. ### YAML -#### [Common config file](https://github.com/bioexcel/biobb_mem/blob/master/biobb_mem/test/data/config/config_fatslim_membranes.yml) +#### [Common config file](https://github.com/bioexcel/biobb_mem/blob/master/biobb_mem/test/data/config/config_cpptraj_density.yml) ```python properties: - cutoff: 2.2 disable_logs: true - ignore_no_box: true - selection: (resname DPPC and name P8) ``` #### Command line ```python -fatslim_membranes --config config_fatslim_membranes.yml --input_top_path A01JD.pdb --input_traj_path A01JD.xtc --output_ndx_path A01JD.ndx +cpptraj_density --config config_cpptraj_density.yml --input_top_path topology.top --input_traj_path trajectory.xtc --output_cpptraj_path density_default.dat --output_traj_path trajectory_out.dcd ``` ### JSON -#### [Common config file](https://github.com/bioexcel/biobb_mem/blob/master/biobb_mem/test/data/config/config_fatslim_membranes.json) +#### [Common config file](https://github.com/bioexcel/biobb_mem/blob/master/biobb_mem/test/data/config/config_cpptraj_density.json) ```python { "properties": { - "disable_logs": true, - "ignore_no_box": true, - "selection": "(resname DPPC and name P8)", - "cutoff": 2.2 + "disable_logs": true } } ``` #### Command line ```python -fatslim_membranes --config config_fatslim_membranes.json --input_top_path A01JD.pdb --input_traj_path A01JD.xtc --output_ndx_path A01JD.ndx +cpptraj_density --config config_cpptraj_density.json --input_top_path topology.top --input_traj_path trajectory.xtc --output_cpptraj_path density_default.dat --output_traj_path trajectory_out.dcd ``` ## Lpp_assign_leaflets @@ -86,6 +88,15 @@ Command: ```python lpp_assign_leaflets -h ``` + /home/rchaves/miniforge3/envs/biobb_mem/lib/python3.11/site-packages/Bio/Application/__init__.py:39: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated. + + Due to the on going maintenance burden of keeping command line application + wrappers up to date, we have decided to deprecate and eventually remove these + modules. + + We instead now recommend building your command line and invoking it directly + with the subprocess module. + warnings.warn( usage: lpp_assign_leaflets [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH --output_leaflets_path OUTPUT_LEAFLETS_PATH Assign lipids to leaflets in a bilayer. @@ -152,16 +163,25 @@ lpp_assign_leaflets --config config_lpp_assign_leaflets.yml --input_top_path A01 lpp_assign_leaflets --config config_lpp_assign_leaflets.json --input_top_path A01JD.pdb --input_traj_path A01JD.xtc --output_leaflets_path leaflets_data.csv ``` -## Mda_hole -Wrapper of the MDAnalysis HOLE module for analyzing ion channel pores or transporter pathways. +## Lpp_zpositions +Wrapper of the LiPyphilic ZPositions module for calculating the z distance of lipids to the bilayer center. ### Get help Command: ```python -mda_hole -h +lpp_zpositions -h ``` - usage: mda_hole [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH --output_hole_path OUTPUT_HOLE_PATH --output_csv_path OUTPUT_CSV_PATH + /home/rchaves/miniforge3/envs/biobb_mem/lib/python3.11/site-packages/Bio/Application/__init__.py:39: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated. - Analyze ion channel pores or transporter pathways. + Due to the on going maintenance burden of keeping command line application + wrappers up to date, we have decided to deprecate and eventually remove these + modules. + + We instead now recommend building your command line and invoking it directly + with the subprocess module. + warnings.warn( + usage: lpp_zpositions [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH --output_positions_path OUTPUT_POSITIONS_PATH + + Calculate the z distance in of lipids to the bilayer center. options: -h, --help show this help message and exit @@ -172,18 +192,15 @@ mda_hole -h Path to the input structure or topology file. Accepted formats: crd, gro, mdcrd, mol2, pdb, pdbqt, prmtop, psf, top, tpr, xml, xyz. --input_traj_path INPUT_TRAJ_PATH Path to the input trajectory to be processed. Accepted formats: arc, crd, dcd, ent, gro, inpcrd, mdcrd, mol2, nc, pdb, pdbqt, restrt, tng, trr, xtc, xyz. - --output_hole_path OUTPUT_HOLE_PATH - Path to the output HOLE analysis results. Accepted formats: vmd. - --output_csv_path OUTPUT_CSV_PATH - Path to the output CSV file containing the radius and coordinates of the pore. Accepted formats: csv. + --output_positions_path OUTPUT_POSITIONS_PATH + Path to the output z positions. ### I / O Arguments Syntax: input_argument (datatype) : Definition Config input / output arguments for this building block: * **input_top_path** (*string*): Path to the input structure or topology file. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/A01JD/A01JD.pdb). Accepted formats: CRD, GRO, MDCRD, MOL2, PDB, PDBQT, PRMTOP, PSF, TOP, TPR, XML, XYZ * **input_traj_path** (*string*): Path to the input trajectory to be processed. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/A01JD/A01JD.xtc). Accepted formats: ARC, CRD, DCD, ENT, GRO, INPCRD, MDCRD, MOL2, NC, PDB, PDBQT, RESTRT, TNG, TRR, XTC, XYZ -* **output_hole_path** (*string*): Path to the output HOLE analysis results. File type: output. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/reference/mdanalysis_biobb/hole.vmd). Accepted formats: VMD -* **output_csv_path** (*string*): Path to the output CSV file containing the radius and coordinates of the pore. File type: output. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/reference/mdanalysis_biobb/hole_profile.csv). Accepted formats: CSV +* **output_positions_path** (*string*): Path to the output z positions. File type: output. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/reference/lipyphilic_biobb/zpositions.csv). Accepted formats: CSV ### Config Syntax: input_parameter (datatype) - (default_value) Definition @@ -191,55 +208,54 @@ Config parameters for this building block: * **start** (*integer*): (None) Starting frame for slicing.. * **stop** (*integer*): (None) Ending frame for slicing.. * **steps** (*integer*): (None) Step for slicing.. -* **executable** (*string*): (hole) Path to the HOLE executable.. -* **select** (*string*): (protein) The selection string to create an atom selection that the HOLE analysis is applied to.. -* **cpoint** (*array*): (None) Coordinates of a point inside the pore (Å). If None, tries to guess based on the geometry.. -* **cvect** (*array*): (None) Search direction vector. If None, tries to guess based on the geometry.. -* **sample** (*number*): (0.2) Distance of sample points in Å. This value determines how many points in the pore profile are calculated.. -* **end_radius** (*number*): (22.0) Radius in Å, which is considered to be the end of the pore.. -* **dot_density** (*integer*): (15) Density of facets for generating a 3D pore representation.. +* **lipid_sel** (*string*): (all) Selection string for the lipids in a membrane. The selection should cover **all** residues in the membrane, including cholesterol.. +* **height_sel** (*string*): (all) Atom selection for the molecules for which the z position will be calculated.. +* **n_bins** (*integer*): (1) Number of bins in *x* and *y* to use to create a grid of membrane patches. Local membrane midpoints are computed for each patch, and lipids assigned a leaflet based on the distance to their local membrane midpoint. The default is `1`, which is equivalent to computing a single global midpoint.. +* **ignore_no_box** (*boolean*): (False) Ignore the absence of box information in the trajectory. If the trajectory does not contain box information, the box will be set to the minimum and maximum positions of the atoms in the trajectory.. * **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.. ### YAML -#### [Common config file](https://github.com/bioexcel/biobb_mem/blob/master/biobb_mem/test/data/config/config_mda_hole.yml) +#### [Common config file](https://github.com/bioexcel/biobb_mem/blob/master/biobb_mem/test/data/config/config_lpp_zpositions.yml) ```python properties: disable_logs: true - select: protein - steps: 5 + height_sel: (resname DPPC and name P8) + ignore_no_box: true + lipid_sel: (resname DPPC and name P8) ``` #### Command line ```python -mda_hole --config config_mda_hole.yml --input_top_path A01JD.pdb --input_traj_path A01JD.xtc --output_hole_path hole.vmd --output_csv_path hole_profile.csv +lpp_zpositions --config config_lpp_zpositions.yml --input_top_path A01JD.pdb --input_traj_path A01JD.xtc --output_positions_path zpositions.csv ``` ### JSON -#### [Common config file](https://github.com/bioexcel/biobb_mem/blob/master/biobb_mem/test/data/config/config_mda_hole.json) +#### [Common config file](https://github.com/bioexcel/biobb_mem/blob/master/biobb_mem/test/data/config/config_lpp_zpositions.json) ```python { "properties": { "disable_logs": true, - "select": "protein", - "steps": 5 + "ignore_no_box": true, + "lipid_sel": "(resname DPPC and name P8)", + "height_sel": "(resname DPPC and name P8)" } } ``` #### Command line ```python -mda_hole --config config_mda_hole.json --input_top_path A01JD.pdb --input_traj_path A01JD.xtc --output_hole_path hole.vmd --output_csv_path hole_profile.csv +lpp_zpositions --config config_lpp_zpositions.json --input_top_path A01JD.pdb --input_traj_path A01JD.xtc --output_positions_path zpositions.csv ``` -## Lpp_zpositions -Wrapper of the LiPyphilic ZPositions module for calculating the z distance of lipids to the bilayer center. +## Mda_hole +Wrapper of the MDAnalysis HOLE module for analyzing ion channel pores or transporter pathways. ### Get help Command: ```python -lpp_zpositions -h +mda_hole -h ``` - usage: lpp_zpositions [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH --output_positions_path OUTPUT_POSITIONS_PATH + usage: mda_hole [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH --output_hole_path OUTPUT_HOLE_PATH --output_csv_path OUTPUT_CSV_PATH - Calculate the z distance in of lipids to the bilayer center. + Analyze ion channel pores or transporter pathways. options: -h, --help show this help message and exit @@ -250,15 +266,18 @@ lpp_zpositions -h Path to the input structure or topology file. Accepted formats: crd, gro, mdcrd, mol2, pdb, pdbqt, prmtop, psf, top, tpr, xml, xyz. --input_traj_path INPUT_TRAJ_PATH Path to the input trajectory to be processed. Accepted formats: arc, crd, dcd, ent, gro, inpcrd, mdcrd, mol2, nc, pdb, pdbqt, restrt, tng, trr, xtc, xyz. - --output_positions_path OUTPUT_POSITIONS_PATH - Path to the output z positions. + --output_hole_path OUTPUT_HOLE_PATH + Path to the output HOLE analysis results. Accepted formats: vmd. + --output_csv_path OUTPUT_CSV_PATH + Path to the output CSV file containing the radius and coordinates of the pore. Accepted formats: csv. ### I / O Arguments Syntax: input_argument (datatype) : Definition Config input / output arguments for this building block: * **input_top_path** (*string*): Path to the input structure or topology file. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/A01JD/A01JD.pdb). Accepted formats: CRD, GRO, MDCRD, MOL2, PDB, PDBQT, PRMTOP, PSF, TOP, TPR, XML, XYZ * **input_traj_path** (*string*): Path to the input trajectory to be processed. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/A01JD/A01JD.xtc). Accepted formats: ARC, CRD, DCD, ENT, GRO, INPCRD, MDCRD, MOL2, NC, PDB, PDBQT, RESTRT, TNG, TRR, XTC, XYZ -* **output_positions_path** (*string*): Path to the output z positions. File type: output. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/reference/lipyphilic_biobb/zpositions.csv). Accepted formats: CSV +* **output_hole_path** (*string*): Path to the output HOLE analysis results. File type: output. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/reference/mdanalysis_biobb/hole.vmd). Accepted formats: VMD +* **output_csv_path** (*string*): Path to the output CSV file containing the radius and coordinates of the pore. File type: output. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/reference/mdanalysis_biobb/hole_profile.csv). Accepted formats: CSV ### Config Syntax: input_parameter (datatype) - (default_value) Definition @@ -266,115 +285,124 @@ Config parameters for this building block: * **start** (*integer*): (None) Starting frame for slicing.. * **stop** (*integer*): (None) Ending frame for slicing.. * **steps** (*integer*): (None) Step for slicing.. -* **lipid_sel** (*string*): (all) Selection string for the lipids in a membrane. The selection should cover **all** residues in the membrane, including cholesterol.. -* **height_sel** (*string*): (all) Atom selection for the molecules for which the z position will be calculated.. -* **n_bins** (*integer*): (1) Number of bins in *x* and *y* to use to create a grid of membrane patches. Local membrane midpoints are computed for each patch, and lipids assigned a leaflet based on the distance to their local membrane midpoint. The default is `1`, which is equivalent to computing a single global midpoint.. -* **ignore_no_box** (*boolean*): (False) Ignore the absence of box information in the trajectory. If the trajectory does not contain box information, the box will be set to the minimum and maximum positions of the atoms in the trajectory.. +* **executable** (*string*): (hole) Path to the HOLE executable.. +* **select** (*string*): (protein) The selection string to create an atom selection that the HOLE analysis is applied to.. +* **cpoint** (*array*): (None) Coordinates of a point inside the pore (Å). If None, tries to guess based on the geometry.. +* **cvect** (*array*): (None) Search direction vector. If None, tries to guess based on the geometry.. +* **sample** (*number*): (0.2) Distance of sample points in Å. This value determines how many points in the pore profile are calculated.. +* **end_radius** (*number*): (22.0) Radius in Å, which is considered to be the end of the pore.. +* **dot_density** (*integer*): (15) Density of facets for generating a 3D pore representation.. * **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.. ### YAML -#### [Common config file](https://github.com/bioexcel/biobb_mem/blob/master/biobb_mem/test/data/config/config_lpp_zpositions.yml) +#### [Common config file](https://github.com/bioexcel/biobb_mem/blob/master/biobb_mem/test/data/config/config_mda_hole.yml) ```python properties: disable_logs: true - height_sel: (resname DPPC and name P8) - ignore_no_box: true - lipid_sel: (resname DPPC and name P8) + select: protein + steps: 5 ``` #### Command line ```python -lpp_zpositions --config config_lpp_zpositions.yml --input_top_path A01JD.pdb --input_traj_path A01JD.xtc --output_positions_path zpositions.csv +mda_hole --config config_mda_hole.yml --input_top_path A01JD.pdb --input_traj_path A01JD.xtc --output_hole_path hole.vmd --output_csv_path hole_profile.csv ``` ### JSON -#### [Common config file](https://github.com/bioexcel/biobb_mem/blob/master/biobb_mem/test/data/config/config_lpp_zpositions.json) +#### [Common config file](https://github.com/bioexcel/biobb_mem/blob/master/biobb_mem/test/data/config/config_mda_hole.json) ```python { "properties": { "disable_logs": true, - "ignore_no_box": true, - "lipid_sel": "(resname DPPC and name P8)", - "height_sel": "(resname DPPC and name P8)" + "select": "protein", + "steps": 5 } } ``` #### Command line ```python -lpp_zpositions --config config_lpp_zpositions.json --input_top_path A01JD.pdb --input_traj_path A01JD.xtc --output_positions_path zpositions.csv +mda_hole --config config_mda_hole.json --input_top_path A01JD.pdb --input_traj_path A01JD.xtc --output_hole_path hole.vmd --output_csv_path hole_profile.csv ``` -## Cpptraj_density -Wrapper of the Ambertools Cpptraj module for calculating density profile along an axis of a given cpptraj compatible trajectory. +## Fatslim_membranes +Wrapper of the FATSLiM membranes module for leaflet and membrane identification. ### Get help Command: ```python -cpptraj_density -h +fatslim_membranes -h ``` - usage: cpptraj_density [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH --output_cpptraj_path OUTPUT_CPPTRAJ_PATH [--output_traj_path OUTPUT_TRAJ_PATH] + /home/rchaves/miniforge3/envs/biobb_mem/lib/python3.11/site-packages/Bio/Application/__init__.py:39: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated. + + Due to the on going maintenance burden of keeping command line application + wrappers up to date, we have decided to deprecate and eventually remove these + modules. + + We instead now recommend building your command line and invoking it directly + with the subprocess module. + warnings.warn( + usage: fatslim_membranes [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --output_ndx_path OUTPUT_NDX_PATH [--input_traj_path INPUT_TRAJ_PATH] Calculates the density along an axis of a given cpptraj compatible trajectory. options: -h, --help show this help message and exit --config CONFIG Configuration file - --output_traj_path OUTPUT_TRAJ_PATH - Path to the output processed trajectory. + --input_traj_path INPUT_TRAJ_PATH + Path to the input trajectory to be processed. Accepted formats: gro, pdb, tng, trr, xtc. required arguments: --input_top_path INPUT_TOP_PATH - Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip. - --input_traj_path INPUT_TRAJ_PATH - Path to the input trajectory to be processed. Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib. - --output_cpptraj_path OUTPUT_CPPTRAJ_PATH - Path to the output processed analysis. + Path to the input structure or topology file. Accepted formats: ent, gro, pdb, tpr. + --output_ndx_path OUTPUT_NDX_PATH + Path to the GROMACS index file. Accepted formats: ndx ### I / O Arguments Syntax: input_argument (datatype) : Definition Config input / output arguments for this building block: -* **input_top_path** (*string*): Path to the input structure or topology file. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/ambertools/topology.top). Accepted formats: TOP, PDB, PRMTOP, PARMTOP, ZIP -* **input_traj_path** (*string*): Path to the input trajectory to be processed. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/ambertools/trajectory.xtc). Accepted formats: MDCRD, CRD, CDF, NETCDF, NC, RESTART, NCRESTART, RESTARTNC, DCD, CHARMM, COR, PDB, MOL2, TRR, GRO, BINPOS, XTC, CIF, ARC, SQM, SDF, CONFLIB -* **output_cpptraj_path** (*string*): Path to the output processed density analysis. File type: output. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/reference/ambertools/reference/density_default.dat). Accepted formats: DAT, AGR, XMGR, GNU -* **output_traj_path** (*string*): Path to the output processed trajectory. File type: output. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/reference/ambertools/trajectory_out.dcd). Accepted formats: MDCRD, CRD, CDF, NETCDF, NC, RESTART, NCRESTART, RESTARTNC, DCD, CHARMM, COR, PDB, MOL2, TRR, GRO, BINPOS, XTC, CIF, ARC, SQM, SDF, CONFLIB +* **input_top_path** (*string*): Path to the input topology file. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/A01JD/A01JD.pdb). Accepted formats: TPR, GRO, G96, PDB, BRK, ENT +* **input_traj_path** (*string*): Path to the GROMACS trajectory file. File type: input. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/A01JD/A01JD.xtc). Accepted formats: XTC, TRR, CPT, GRO, G96, PDB, TNG +* **output_ndx_path** (*string*): Path to the output index NDX file. File type: output. [Sample file](https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/A01JD/A01JD.ndx). Accepted formats: NDX ### Config Syntax: input_parameter (datatype) - (default_value) Definition Config parameters for this building block: -* **start** (*integer*): (1) Starting frame for slicing. -* **end** (*integer*): (-1) Ending frame for slicing. -* **steps** (*integer*): (1) Step for slicing. -* **density_type** (*string*): (number) Number, mass, partial charge (q) or electron (Ne - q) density. Electron density will be converted to e-/Å3 by dividing the average area spanned by the other two dimensions.. -* **mask** (*string*): (*) Arbitrary number of masks for atom selection; a dataset is created and the output will contain entries for each mask.. Default: all atoms.. -* **delta** (*number*): (0.25) Resolution, i.e. determines number of slices (i.e. histogram bins).. -* **axis** (*string*): (z) Coordinate (axis) for density calculation. Vales: x, y, z.. -* **bintype** (*string*): (bincenter) Determine whether histogram bin coordinates will be based on bin center (default) or bin edges. . -* **restrict** (*string*): (None) If specified, only calculate the density within a cylinder or square shape from the specified axis as defined by a distance cutoff. . -* **cutoff** (*number*): (None) The distance cutoff for 'restrict'. Required if 'restrict' is specified.. -* **binary_path** (*string*): (cpptraj) Path to the cpptraj executable binary.. +* **selection** (*string*): (resname DPPC and element P) Molecules used in the identification using MDAnalysis selection language.. +* **cutoff** (*number*): (2.0) Cutoff distance (in nm) to be used when leaflet identification is performed.. +* **begin_frame** (*integer*): (-1) First frame index to be used for analysis.. +* **end_frame** (*integer*): (-1) Last frame index to be used for analysis.. +* **ignore_no_box** (*boolean*): (False) Ignore the absence of box information in the topology. If the topology does not contain box information, the box will be set to the minimum and maximum positions of the atoms.. +* **return_hydrogen** (*boolean*): (False) Include hydrogen atoms in the output index file.. +* **binary_path** (*string*): (fatslim) Path to the fatslim executable binary.. * **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.. ### YAML -#### [Common config file](https://github.com/bioexcel/biobb_mem/blob/master/biobb_mem/test/data/config/config_cpptraj_density.yml) +#### [Common config file](https://github.com/bioexcel/biobb_mem/blob/master/biobb_mem/test/data/config/config_fatslim_membranes.yml) ```python properties: + cutoff: 2.2 disable_logs: true + ignore_no_box: true + selection: (resname DPPC and name P8) ``` #### Command line ```python -cpptraj_density --config config_cpptraj_density.yml --input_top_path topology.top --input_traj_path trajectory.xtc --output_cpptraj_path density_default.dat --output_traj_path trajectory_out.dcd +fatslim_membranes --config config_fatslim_membranes.yml --input_top_path A01JD.pdb --input_traj_path A01JD.xtc --output_ndx_path A01JD.ndx ``` ### JSON -#### [Common config file](https://github.com/bioexcel/biobb_mem/blob/master/biobb_mem/test/data/config/config_cpptraj_density.json) +#### [Common config file](https://github.com/bioexcel/biobb_mem/blob/master/biobb_mem/test/data/config/config_fatslim_membranes.json) ```python { "properties": { - "disable_logs": true + "disable_logs": true, + "ignore_no_box": true, + "selection": "(resname DPPC and name P8)", + "cutoff": 2.2 } } ``` #### Command line ```python -cpptraj_density --config config_cpptraj_density.json --input_top_path topology.top --input_traj_path trajectory.xtc --output_cpptraj_path density_default.dat --output_traj_path trajectory_out.dcd +fatslim_membranes --config config_fatslim_membranes.json --input_top_path A01JD.pdb --input_traj_path A01JD.xtc --output_ndx_path A01JD.ndx ``` diff --git a/biobb_mem/json_schemas/fatslim_membranes.json b/biobb_mem/json_schemas/fatslim_membranes.json index 4cf07a3..9c5125d 100644 --- a/biobb_mem/json_schemas/fatslim_membranes.json +++ b/biobb_mem/json_schemas/fatslim_membranes.json @@ -168,6 +168,12 @@ "wf_prop": false, "description": "Ignore the absence of box information in the topology. If the topology does not contain box information, the box will be set to the minimum and maximum positions of the atoms." }, + "return_hydrogen": { + "type": "boolean", + "default": false, + "wf_prop": false, + "description": "Include hydrogen atoms in the output index file." + }, "binary_path": { "type": "string", "default": "fatslim",