ambertools package

Submodules

ambertools.cpptraj_average module

Module containing the Cpptraj Average class and the command line interface.

class ambertools.cpptraj_average.CpptrajAverage(input_top_path, input_traj_path, output_cpptraj_path, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_analysis CpptrajAverage
Wrapper of the Ambertools Cpptraj module for calculating a structure average of a given cpptraj compatible trajectory.
Cpptraj (the successor to ptraj) is the main program in Ambertools for processing coordinate trajectories and data files. The parameter names and defaults are the same as the ones in the official Cpptraj manual.
Parameters:

  • input_top_path (str) – Path to the input structure or topology file. File type: input. Sample file. Accepted formats: top (edam:format_3881), pdb (edam:format_1476), prmtop (edam:format_3881), parmtop (edam:format_3881), zip (edam:format_3987).

  • input_traj_path (str) –

    Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: mdcrd (edam:format_3878), crd (edam:format_3878), cdf (edam:format_3650), netcdf (edam:format_3650), nc (edam:format_3650), restart (edam:format_3886), ncrestart (edam:format_3886), restartnc (edam:format_3886), dcd (edam:format_3878), charmm (edam:format_3887), cor (edam:format_2033), pdb (edam:format_1476), mol2 (edam:format_3816), trr (edam:format_3910), gro (edam:format_2033), binpos (edam:format_3885), xtc (edam:format_3875), cif (edam:format_1477), arc (edam:format_2333), sqm (edam:format_2033), sdf (edam:format_3814), conflib (edam:format_2033).

  • output_cpptraj_path (str) –

    Path to the output processed structure. File type: output. Sample file. Accepted formats: mdcrd (edam:format_3878), crd (edam:format_3878), netcdf (edam:format_3650), nc (edam:format_3650), rst7 (edam:format_3886), ncrst (edam:format_2033), dcd (edam:format_3878), pdb (edam:format_1476), mol2 (edam:format_3816), binpos (edam:format_3885), trr (edam:format_3910), xtc (edam:format_3875), sqm (edam:format_2033).

  • properties (dic - Python dictionary object containing the tool parameters, not input/output files) –

    • start (int) - (1) [1~100000|1] Starting frame for slicing.

    • end (int) - (-1) [-1~100000|1] Ending frame for slicing.

    • steps (int) - (1) [1~100000|1] Step for slicing.

    • mask (str) - (“all-atoms”) Mask definition. Values: c-alpha (All c-alpha atoms; protein only), backbone (Backbone atoms), all-atoms (All system atoms), heavy-atoms (System heavy atoms; not hydrogen), side-chain (All not backbone atoms), solute (All system atoms except solvent atoms), ions (All ion molecules), solvent (All solvent atoms), AnyAmberFromatMask (Amber atom selection syntax like @*).

    • format (str) - (“netcdf”) Output trajectory format. Values: crd (AMBER trajectory format), cdf (Format used by netCDF software library for writing and reading chromatography-MS data files), netcdf (Format used by netCDF software library for writing and reading chromatography-MS data files), nc (Format used by netCDF software library for writing and reading chromatography-MS data files), restart (AMBER coordinate/restart file with 6 coordinates per line), ncrestart (AMBER coordinate/restart file with 6 coordinates per line), restartnc (AMBER coordinate/restart file with 6 coordinates per line), dcd (AMBER trajectory format), charmm (Format of CHARMM Residue Topology Files (RTF)), cor (Charmm COR), pdb (Protein Data Bank format), mol2 (Complete and portable representation of a SYBYL molecule), trr (Trajectory of a simulation experiment used by GROMACS), gro (GROMACS structure), binpos (Translation of the ASCII atom coordinate format to binary code), xtc (Portable binary format for trajectories produced by GROMACS package), cif (Entry format of PDB database in mmCIF format), arc (Tinker ARC), sqm (SQM Input), sdf (One of a family of chemical-data file formats developed by MDL Information Systems), conflib (LMOD Conflib).

    • binary_path (str) - (“cpptraj”) Path to the cpptraj executable binary.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

    • container_path (str) - (None) Container path definition.

    • container_image (str) - (‘afandiadib/ambertools:serial’) Container image definition.

    • container_volume_path (str) - (‘/tmp’) Container volume path definition.

    • container_working_dir (str) - (None) Container working directory definition.

    • container_user_id (str) - (None) Container user_id definition.

    • container_shell_path (str) - (‘/bin/bash’) Path to default shell inside the container.

Examples

This is a use example of how to use the building block from Python:

from biobb_analysis.ambertools.cpptraj_average import cpptraj_average
prop = {
    'start': 1,
    'end': -1,
    'steps': 1,
    'mask': 'c-alpha',
    'format': 'pdb'
}
cpptraj_average(input_top_path='/path/to/myTopology.top',
                input_traj_path='/path/to/myTrajectory.dcd',
                output_cpptraj_path='/path/to/newStructure.pdb',
                properties=prop)
Info:
check_data_params(out_log, err_log)[source]

Checks all the input/output paths and parameters

create_instructions_file(container_io_dict, out_log, err_log)[source]

Creates an input file using the properties file settings

launch() → int[source]

Execute the CpptrajAverage ambertools.cpptraj_average.CpptrajAverage object.

ambertools.cpptraj_average.cpptraj_average(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, properties: dict | None = None, **kwargs) → int[source]

Execute the CpptrajAverage class and execute the launch() method.

ambertools.cpptraj_average.main()[source]

Command line execution of this building block. Please check the command line documentation.

ambertools.cpptraj_bfactor module

Module containing the Cpptraj Bfactor class and the command line interface.

class ambertools.cpptraj_bfactor.CpptrajBfactor(input_top_path, input_traj_path, output_cpptraj_path, input_exp_path=None, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_analysis CpptrajBfactor
Wrapper of the Ambertools Cpptraj module for calculating the Bfactor fluctuations of a given cpptraj compatible trajectory.
Cpptraj (the successor to ptraj) is the main program in Ambertools for processing coordinate trajectories and data files. The parameter names and defaults are the same as the ones in the official Cpptraj manual.
Parameters:

  • input_top_path (str) –

    Path to the input structure or topology file. File type: input. Sample file. Accepted formats: top (edam:format_3881), pdb (edam:format_1476), prmtop (edam:format_3881), parmtop (edam:format_3881), zip (edam:format_3987).

  • input_traj_path (str) –

    Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: mdcrd (edam:format_3878), crd (edam:format_3878), cdf (edam:format_3650), netcdf (edam:format_3650), nc (edam:format_3650), restart (edam:format_3886), ncrestart (edam:format_3886), restartnc (edam:format_3886), dcd (edam:format_3878), charmm (edam:format_3887), cor (edam:format_2033), pdb (edam:format_1476), mol2 (edam:format_3816), trr (edam:format_3910), gro (edam:format_2033), binpos (edam:format_3885), xtc (edam:format_3875), cif (edam:format_1477), arc (edam:format_2333), sqm (edam:format_2033), sdf (edam:format_3814), conflib (edam:format_2033).

  • input_exp_path (str) (Optional) –

    Path to the experimental reference file (required if reference = experimental). File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

  • output_cpptraj_path (str) –

    Path to the output processed analysis. File type: output. Sample file. Accepted formats: dat (edam:format_1637), agr (edam:format_2033), xmgr (edam:format_2033), gnu (edam:format_2033).

  • properties (dic - Python dictionary object containing the tool parameters, not input/output files) –

    • start (int) - (1) [1~100000|1] Starting frame for slicing

    • end (int) - (-1) [-1~100000|1] Ending frame for slicing

    • steps (int) - (1) [1~100000|1] Step for slicing

    • mask (str) - (“all-atoms”) Mask definition. Values: c-alpha (All c-alpha atoms; protein only), backbone (Backbone atoms), all-atoms (All system atoms), heavy-atoms (System heavy atoms; not hydrogen), side-chain (All not backbone atoms), solute (All system atoms except solvent atoms), ions (All ion molecules), solvent (All solvent atoms), AnyAmberFromatMask (Amber atom selection syntax like @*).

    • reference (str) - (“first”) Reference definition. Values: first (Use the first trajectory frame as reference), average (Use the average of all trajectory frames as reference), experimental (Use the experimental structure as reference).

    • binary_path (str) - (“cpptraj”) Path to the cpptraj executable binary.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

    • container_path (str) - (None) Container path definition.

    • container_image (str) - (‘afandiadib/ambertools:serial’) Container image definition.

    • container_volume_path (str) - (‘/tmp’) Container volume path definition.

    • container_working_dir (str) - (None) Container working directory definition.

    • container_user_id (str) - (None) Container user_id definition.

    • container_shell_path (str) - (‘/bin/bash’) Path to default shell inside the container.

Examples

This is a use example of how to use the building block from Python:

from biobb_analysis.ambertools.cpptraj_bfactor import cpptraj_bfactor
prop = {
    'start': 1,
    'end': -1,
    'steps': 1,
    'mask': 'c-alpha',
    'reference': 'first'
}
cpptraj_bfactor(input_top_path='/path/to/myTopology.top',
                input_traj_path='/path/to/myTrajectory.dcd',
                output_cpptraj_path='/path/to/newAnalysis.dat',
                input_exp_path= '/path/to/myExpStructure.pdb',
                properties=prop)
Info:
check_data_params(out_log, err_log)[source]

Checks all the input/output paths and parameters

create_instructions_file(container_io_dict, out_log, err_log)[source]

Creates an input file using the properties file settings

launch() → int[source]

Execute the CpptrajBfactor ambertools.cpptraj_bfactor.CpptrajBfactor object.

ambertools.cpptraj_bfactor.cpptraj_bfactor(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, input_exp_path: str | None = None, properties: dict | None = None, **kwargs) → int[source]

Execute the CpptrajBfactor class and execute the launch() method.

ambertools.cpptraj_bfactor.main()[source]

Command line execution of this building block. Please check the command line documentation.

ambertools.cpptraj_convert module

Module containing the Cpptraj Convert class and the command line interface.

class ambertools.cpptraj_convert.CpptrajConvert(input_top_path, input_traj_path, output_cpptraj_path, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_analysis CpptrajConvert
Wrapper of the Ambertools Cpptraj module for converting between cpptraj compatible trajectory file formats and/or extracting a selection of atoms or frames.
Cpptraj (the successor to ptraj) is the main program in Ambertools for processing coordinate trajectories and data files. The parameter names and defaults are the same as the ones in the official Cpptraj manual.
Parameters:

  • input_top_path (str) –

    Path to the input structure or topology file. File type: input. Sample file. Accepted formats: top (edam:format_3881), pdb (edam:format_1476), prmtop (edam:format_3881), parmtop (edam:format_3881), zip (edam:format_3987).

  • input_traj_path (str) –

    Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: mdcrd (edam:format_3878), crd (edam:format_3878), cdf (edam:format_3650), netcdf (edam:format_3650), nc (edam:format_3650), restart (edam:format_3886), ncrestart (edam:format_3886), restartnc (edam:format_3886), dcd (edam:format_3878), charmm (edam:format_3887), cor (edam:format_2033), pdb (edam:format_1476), mol2 (edam:format_3816), trr (edam:format_3910), gro (edam:format_2033), binpos (edam:format_3885), xtc (edam:format_3875), cif (edam:format_1477), arc (edam:format_2333), sqm (edam:format_2033), sdf (edam:format_3814), conflib (edam:format_2033).

  • output_cpptraj_path (str) –

    Path to the output processed trajectory. File type: output. Sample file. Accepted formats: mdcrd (edam:format_3878), crd (edam:format_3878), netcdf (edam:format_3650), nc (edam:format_3650), rst7 (edam:format_3886), ncrst (edam:format_2033), dcd (edam:format_3878), pdb (edam:format_1476), mol2 (edam:format_3816), binpos (edam:format_3885), trr (edam:format_3910), xtc (edam:format_3875), sqm (edam:format_2033).

  • properties (dic - Python dictionary object containing the tool parameters, not input/output files) –

    • start (int) - (1) [1~100000|1] Starting frame for slicing

    • end (int) - (-1) [-1~100000|1] Ending frame for slicing

    • steps (int) - (1) [1~100000|1] Step for slicing

    • mask (str) - (“all-atoms”) Mask definition. Values: c-alpha (All c-alpha atoms; protein only), backbone (Backbone atoms), all-atoms (All system atoms), heavy-atoms (System heavy atoms; not hydrogen), side-chain (All not backbone atoms), solute (All system atoms except solvent atoms), ions (All ion molecules), solvent (All solvent atoms), AnyAmberFromatMask (Amber atom selection syntax like @*).

    • format (str) - (“netcdf”) Output trajectory format. Values: crd (AMBER trajectory format), cdf (Format used by netCDF software library for writing and reading chromatography-MS data files), netcdf (Format used by netCDF software library for writing and reading chromatography-MS data files), nc (Format used by netCDF software library for writing and reading chromatography-MS data files), restart (AMBER coordinate/restart file with 6 coordinates per line), ncrestart (AMBER coordinate/restart file with 6 coordinates per line), restartnc (AMBER coordinate/restart file with 6 coordinates per line), dcd (AMBER trajectory format), charmm (Format of CHARMM Residue Topology Files (RTF)), cor (Charmm COR), pdb (Protein Data Bank format), mol2 (Complete and portable representation of a SYBYL molecule), trr (Trajectory of a simulation experiment used by GROMACS), gro (GROMACS structure), binpos (Translation of the ASCII atom coordinate format to binary code), xtc (Portable binary format for trajectories produced by GROMACS package), cif (Entry format of PDB database in mmCIF format), arc (Tinker ARC), sqm (SQM Input), sdf (One of a family of chemical-data file formats developed by MDL Information Systems), conflib (LMOD Conflib).

    • binary_path (str) - (“cpptraj”) Path to the cpptraj executable binary.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

    • container_path (str) - (None) Container path definition.

    • container_image (str) - (‘afandiadib/ambertools:serial’) Container image definition.

    • container_volume_path (str) - (‘/tmp’) Container volume path definition.

    • container_working_dir (str) - (None) Container working directory definition.

    • container_user_id (str) - (None) Container user_id definition.

    • container_shell_path (str) - (‘/bin/bash’) Path to default shell inside the container.

Examples

This is a use example of how to use the building block from Python:

from biobb_analysis.ambertools.cpptraj_convert import cpptraj_convert
prop = {
    'start': 1,
    'end': -1,
    'steps': 1,
    'mask': 'c-alpha',
    'format': 'netcdf'
}
cpptraj_convert(input_top_path='/path/to/myTopology.top',
                input_traj_path='/path/to/myTrajectory.dcd',
                output_cpptraj_path='/path/to/newTrajectory.netcdf',
                properties=prop)
Info:
check_data_params(out_log, err_log)[source]

Checks all the input/output paths and parameters

create_instructions_file(container_io_dict, out_log, err_log)[source]

Creates an input file using the properties file settings

launch() → int[source]

Execute the CpptrajConvert ambertools.cpptraj_convert.CpptrajConvert object.

ambertools.cpptraj_convert.cpptraj_convert(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, properties: dict | None = None, **kwargs) → int[source]

Execute the CpptrajConvert class and execute the launch() method.

ambertools.cpptraj_convert.main()[source]

Command line execution of this building block. Please check the command line documentation.

ambertools.cpptraj_dry module

Module containing the Cpptraj Dry class and the command line interface.

class ambertools.cpptraj_dry.CpptrajDry(input_top_path, input_traj_path, output_cpptraj_path, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_analysis CpptrajDry
Wrapper of the Ambertools Cpptraj module for dehydrating a given cpptraj compatible trajectory stripping out solvent molecules and ions.
Cpptraj (the successor to ptraj) is the main program in Ambertools for processing coordinate trajectories and data files. The parameter names and defaults are the same as the ones in the official Cpptraj manual.
Parameters:

  • input_top_path (str) –

    Path to the input structure or topology file. File type: input. Sample file. Accepted formats: top (edam:format_3881), pdb (edam:format_1476), prmtop (edam:format_3881), parmtop (edam:format_3881), zip (edam:format_3987).

  • input_traj_path (str) –

    Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: mdcrd (edam:format_3878), crd (edam:format_3878), cdf (edam:format_3650), netcdf (edam:format_3650), nc (edam:format_3650), restart (edam:format_3886), ncrestart (edam:format_3886), restartnc (edam:format_3886), dcd (edam:format_3878), charmm (edam:format_3887), cor (edam:format_2033), pdb (edam:format_1476), mol2 (edam:format_3816), trr (edam:format_3910), gro (edam:format_2033), binpos (edam:format_3885), xtc (edam:format_3875), cif (edam:format_1477), arc (edam:format_2333), sqm (edam:format_2033), sdf (edam:format_3814), conflib (edam:format_2033).

  • output_cpptraj_path (str) –

    Path to the output processed trajectory. File type: output. Sample file. Accepted formats: mdcrd (edam:format_3878), crd (edam:format_3878), netcdf (edam:format_3650), nc (edam:format_3650), rst7 (edam:format_3886), ncrst (edam:format_2033), dcd (edam:format_3878), pdb (edam:format_1476), mol2 (edam:format_3816), binpos (edam:format_3885), trr (edam:format_3910), xtc (edam:format_3875), sqm (edam:format_2033).

  • properties (dic - Python dictionary object containing the tool parameters, not input/output files) –

    • start (int) - (1) [1~100000|1] Starting frame for slicing.

    • end (int) - (-1) [-1~100000|1] Ending frame for slicing.

    • steps (int) - (1) [1~100000|1] Step for slicing.

    • mask (str) - (“all-atoms”) Mask definition. Values: c-alpha (All c-alpha atoms; protein only), backbone (Backbone atoms), all-atoms (All system atoms), heavy-atoms (System heavy atoms; not hydrogen), side-chain (All not backbone atoms), solute (All system atoms except solvent atoms), ions (All ion molecules), solvent (All solvent atoms), AnyAmberFromatMask (Amber atom selection syntax like @*).

    • format (str) - (“netcdf”) Output trajectory format. Values: crd (AMBER trajectory format), cdf (Format used by netCDF software library for writing and reading chromatography-MS data files), netcdf (Format used by netCDF software library for writing and reading chromatography-MS data files), nc (Format used by netCDF software library for writing and reading chromatography-MS data files), restart (AMBER coordinate/restart file with 6 coordinates per line), ncrestart (AMBER coordinate/restart file with 6 coordinates per line), restartnc (AMBER coordinate/restart file with 6 coordinates per line), dcd (AMBER trajectory format), charmm (Format of CHARMM Residue Topology Files (RTF)), cor (Charmm COR), pdb (Protein Data Bank format), mol2 (Complete and portable representation of a SYBYL molecule), trr (Trajectory of a simulation experiment used by GROMACS), gro (GROMACS structure), binpos (Translation of the ASCII atom coordinate format to binary code), xtc (Portable binary format for trajectories produced by GROMACS package), cif (Entry format of PDB database in mmCIF format), arc (Tinker ARC), sqm (SQM Input), sdf (One of a family of chemical-data file formats developed by MDL Information Systems), conflib (LMOD Conflib).

    • binary_path (str) - (“cpptraj”) Path to the cpptraj executable binary.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

    • container_path (str) - (None) Container path definition.

    • container_image (str) - (‘afandiadib/ambertools:serial’) Container image definition.

    • container_volume_path (str) - (‘/tmp’) Container volume path definition.

    • container_working_dir (str) - (None) Container working directory definition.

    • container_user_id (str) - (None) Container user_id definition.

    • container_shell_path (str) - (‘/bin/bash’) Path to default shell inside the container.

Examples

This is a use example of how to use the building block from Python:

from biobb_analysis.ambertools.cpptraj_dry import cpptraj_dry
prop = {
    'start': 1,
    'end': -1,
    'steps': 1,
    'mask': 'c-alpha',
    'format': 'netcdf'
}
cpptraj_dry(input_top_path='/path/to/myTopology.top',
            input_traj_path='/path/to/myTrajectory.dcd',
            output_cpptraj_path='/path/to/newTrajectory.netcdf',
            properties=prop)
Info:
check_data_params(out_log, err_log)[source]

Checks all the input/output paths and parameters

create_instructions_file(container_io_dict, out_log, err_log)[source]

Creates an input file using the properties file settings

launch() → int[source]

Execute the CpptrajDry ambertools.cpptraj_dry.CpptrajDry object.

ambertools.cpptraj_dry.cpptraj_dry(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, properties: dict | None = None, **kwargs) → int[source]

Execute the CpptrajDry class and execute the launch() method.

ambertools.cpptraj_dry.main()[source]

Command line execution of this building block. Please check the command line documentation.

ambertools.cpptraj_image module

Module containing the Cpptraj Image class and the command line interface.

class ambertools.cpptraj_image.CpptrajImage(input_top_path, input_traj_path, output_cpptraj_path, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_analysis CpptrajImage
Wrapper of the Ambertools Cpptraj module for correcting periodicity (image) from a given cpptraj trajectory file.
Cpptraj (the successor to ptraj) is the main program in Ambertools for processing coordinate trajectories and data files. The parameter names and defaults are the same as the ones in the official Cpptraj manual.
Parameters:

  • input_top_path (str) –

    Path to the input structure or topology file. File type: input. Sample file. Accepted formats: top (edam:format_3881), pdb (edam:format_1476), prmtop (edam:format_3881), parmtop (edam:format_3881), zip (edam:format_3987).

  • input_traj_path (str) –

    Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: mdcrd (edam:format_3878), crd (edam:format_3878), cdf (edam:format_3650), netcdf (edam:format_3650), nc (edam:format_3650), restart (edam:format_3886), ncrestart (edam:format_3886), restartnc (edam:format_3886), dcd (edam:format_3878), charmm (edam:format_3887), cor (edam:format_2033), pdb (edam:format_1476), mol2 (edam:format_3816), trr (edam:format_3910), gro (edam:format_2033), binpos (edam:format_3885), xtc (edam:format_3875), cif (edam:format_1477), arc (edam:format_2333), sqm (edam:format_2033), sdf (edam:format_3814), conflib (edam:format_2033).

  • output_cpptraj_path (str) –

    Path to the output processed trajectory. File type: output. Sample file. Accepted formats: mdcrd (edam:format_3878), crd (edam:format_3878), netcdf (edam:format_3650), nc (edam:format_3650), rst7 (edam:format_3886), ncrst (edam:format_2033), dcd (edam:format_3878), pdb (edam:format_1476), mol2 (edam:format_3816), binpos (edam:format_3885), trr (edam:format_3910), xtc (edam:format_3875), sqm (edam:format_2033).

  • properties (dic - Python dictionary object containing the tool parameters, not input/output files) –

    • start (int) - (1) [1~100000|1] Starting frame for slicing.

    • end (int) - (-1) [-1~100000|1] Ending frame for slicing.

    • steps (int) - (1) [1~100000|1] Step for slicing.

    • mask (str) - (“all-atoms”) Mask definition. Values: c-alpha (All c-alpha atoms; protein only), backbone (Backbone atoms), all-atoms (All system atoms), heavy-atoms (System heavy atoms; not hydrogen), side-chain (All not backbone atoms), solute (All system atoms except solvent atoms), ions (All ion molecules), solvent (All solvent atoms), AnyAmberFromatMask (Amber atom selection syntax like @*).

    • format (str) - (“netcdf”) Output trajectory format. Values: crd (AMBER trajectory format), cdf (Format used by netCDF software library for writing and reading chromatography-MS data files), nc (Format used by netCDF software library for writing and reading chromatography-MS data files), netcdf (Format used by netCDF software library for writing and reading chromatography-MS data files), restart (AMBER coordinate/restart file with 6 coordinates per line), ncrestart (AMBER coordinate/restart file with 6 coordinates per line), restartnc (AMBER coordinate/restart file with 6 coordinates per line), dcd (AMBER trajectory format), charmm (Format of CHARMM Residue Topology Files (RTF)), cor (Charmm COR), pdb (Protein Data Bank format), mol2 (Complete and portable representation of a SYBYL molecule), trr (Trajectory of a simulation experiment used by GROMACS), gro (GROMACS structure), binpos (Translation of the ASCII atom coordinate format to binary code), xtc (Portable binary format for trajectories produced by GROMACS package), cif (Entry format of PDB database in mmCIF format), arc (Tinker ARC), sqm (SQM Input), sdf (One of a family of chemical-data file formats developed by MDL Information Systems), conflib (LMOD Conflib).

    • binary_path (str) - (“cpptraj”) Path to the cpptraj executable binary.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

    • container_path (str) - (None) Container path definition.

    • container_image (str) - (‘afandiadib/ambertools:serial’) Container image definition.

    • container_volume_path (str) - (‘/tmp’) Container volume path definition.

    • container_working_dir (str) - (None) Container working directory definition.

    • container_user_id (str) - (None) Container user_id definition.

    • container_shell_path (str) - (‘/bin/bash’) Path to default shell inside the container.

Examples

This is a use example of how to use the building block from Python:

from biobb_analysis.ambertools.cpptraj_image import cpptraj_image
prop = {
    'start': 1,
    'end': -1,
    'steps': 1,
    'mask': 'c-alpha',
    'format': 'netcdf'
}
cpptraj_image(input_top_path='/path/to/myTopology.top',
            input_traj_path='/path/to/myTrajectory.dcd',
            output_cpptraj_path='/path/to/newTrajectory.netcdf',
            properties=prop)
Info:
check_data_params(out_log, err_log)[source]

Checks all the input/output paths and parameters

create_instructions_file(container_io_dict, out_log, err_log)[source]

Creates an input file using the properties file settings

launch() → int[source]

Execute the CpptrajImage ambertools.cpptraj_image.CpptrajImage object.

ambertools.cpptraj_image.cpptraj_image(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, properties: dict | None = None, **kwargs) → int[source]

Execute the CpptrajImage class and execute the launch() method.

ambertools.cpptraj_image.main()[source]

Command line execution of this building block. Please check the command line documentation.

ambertools.cpptraj_mask module

Module containing the Cpptraj Mask class and the command line interface.

class ambertools.cpptraj_mask.CpptrajMask(input_top_path, input_traj_path, output_cpptraj_path, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_analysis CpptrajMask
Wrapper of the Ambertools Cpptraj module for extracting a selection of atoms from a given cpptraj compatible trajectory.
Cpptraj (the successor to ptraj) is the main program in Ambertools for processing coordinate trajectories and data files. The parameter names and defaults are the same as the ones in the official Cpptraj manual.
Parameters:

  • input_top_path (str) –

    Path to the input structure or topology file. File type: input. Sample file. Accepted formats: top (edam:format_3881), pdb (edam:format_1476), prmtop (edam:format_3881), parmtop (edam:format_3881), zip (edam:format_3987).

  • input_traj_path (str) –

    Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: mdcrd (edam:format_3878), crd (edam:format_3878), cdf (edam:format_3650), netcdf (edam:format_3650), nc (edam:format_3650), restart (edam:format_3886), ncrestart (edam:format_3886), restartnc (edam:format_3886), dcd (edam:format_3878), charmm (edam:format_3887), cor (edam:format_2033), pdb (edam:format_1476), mol2 (edam:format_3816), trr (edam:format_3910), gro (edam:format_2033), binpos (edam:format_3885), xtc (edam:format_3875), cif (edam:format_1477), arc (edam:format_2333), sqm (edam:format_2033), sdf (edam:format_3814), conflib (edam:format_2033).

  • output_cpptraj_path (str) –

    Path to the output processed trajectory. File type: output. Sample file. Accepted formats: mdcrd (edam:format_3878), crd (edam:format_3878), netcdf (edam:format_3650), nc (edam:format_3650), rst7 (edam:format_3886), ncrst (edam:format_2033), dcd (edam:format_3878), pdb (edam:format_1476), mol2 (edam:format_3816), binpos (edam:format_3885), trr (edam:format_3910), xtc (edam:format_3875), sqm (edam:format_2033).

  • properties (dic - Python dictionary object containing the tool parameters, not input/output files) –

    • start (int) - (1) [1~100000|1] Starting frame for slicing.

    • end (int) - (-1) [-1~100000|1] Ending frame for slicing.

    • steps (int) - (1) [1~100000|1] Step for slicing.

    • mask (str) - (“all-atoms”) Mask definition. Values: c-alpha (All c-alpha atoms; protein only), backbone (Backbone atoms), all-atoms (All system atoms), heavy-atoms (System heavy atoms; not hydrogen), side-chain (All not backbone atoms), solute (All system atoms except solvent atoms), ions (All ion molecules), solvent (All solvent atoms), AnyAmberFromatMask (Amber atom selection syntax like @*).

    • format (str) - (“netcdf”) Output trajectory format. Values: crd (AMBER trajectory format), cdf (Format used by netCDF software library for writing and reading chromatography-MS data files), netcdf (Format used by netCDF software library for writing and reading chromatography-MS data files), nc (Format used by netCDF software library for writing and reading chromatography-MS data files), restart (AMBER coordinate/restart file with 6 coordinates per line), ncrestart (AMBER coordinate/restart file with 6 coordinates per line), restartnc (AMBER coordinate/restart file with 6 coordinates per line), dcd (AMBER trajectory format), charmm (Format of CHARMM Residue Topology Files (RTF)), cor (Charmm COR), pdb (Protein Data Bank format), mol2 (Complete and portable representation of a SYBYL molecule), trr (Trajectory of a simulation experiment used by GROMACS), gro (GROMACS structure), binpos (Translation of the ASCII atom coordinate format to binary code), xtc (Portable binary format for trajectories produced by GROMACS package), cif (Entry format of PDB database in mmCIF format), arc (Tinker ARC), sqm (SQM Input), sdf (One of a family of chemical-data file formats developed by MDL Information Systems), conflib (LMOD Conflib).

    • binary_path (str) - (“cpptraj”) Path to the cpptraj executable binary.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

    • container_path (str) - (None) Container path definition.

    • container_image (str) - (‘afandiadib/ambertools:serial’) Container image definition.

    • container_volume_path (str) - (‘/tmp’) Container volume path definition.

    • container_working_dir (str) - (None) Container working directory definition.

    • container_user_id (str) - (None) Container user_id definition.

    • container_shell_path (str) - (‘/bin/bash’) Path to default shell inside the container.

Examples

This is a use example of how to use the building block from Python:

from biobb_analysis.ambertools.cpptraj_mask import cpptraj_mask
prop = {
    'start': 1,
    'end': -1,
    'steps': 1,
    'mask': 'c-alpha',
    'format': 'netcdf'
}
cpptraj_mask(input_top_path='/path/to/myTopology.top',
            input_traj_path='/path/to/myTrajectory.dcd',
            output_cpptraj_path='/path/to/newTrajectory.netcdf',
            properties=prop)
Info:
check_data_params(out_log, err_log)[source]

Checks all the input/output paths and parameters

create_instructions_file(container_io_dict, out_log, err_log)[source]

Creates an input file using the properties file settings

launch() → int[source]

Execute the CpptrajMask ambertools.cpptraj_mask.CpptrajMask object.

ambertools.cpptraj_mask.cpptraj_mask(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, properties: dict | None = None, **kwargs) → int[source]

Execute the CpptrajMask class and execute the launch() method.

ambertools.cpptraj_mask.main()[source]

Command line execution of this building block. Please check the command line documentation.

ambertools.cpptraj_rgyr module

Module containing the Cpptraj Rgyr class and the command line interface.

class ambertools.cpptraj_rgyr.CpptrajRgyr(input_top_path, input_traj_path, output_cpptraj_path, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_analysis CpptrajRgyr
Wrapper of the Ambertools Cpptraj module for computing the radius of gyration (Rgyr) from a given cpptraj compatible trajectory.
Cpptraj (the successor to ptraj) is the main program in Ambertools for processing coordinate trajectories and data files. The parameter names and defaults are the same as the ones in the official Cpptraj manual.
Parameters:

  • input_top_path (str) –

    Path to the input structure or topology file. File type: input. Sample file. Accepted formats: top (edam:format_3881), pdb (edam:format_1476), prmtop (edam:format_3881), parmtop (edam:format_3881), zip (edam:format_3987).

  • input_traj_path (str) –

    Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: mdcrd (edam:format_3878), crd (edam:format_3878), cdf (edam:format_3650), netcdf (edam:format_3650), nc (edam:format_3650), restart (edam:format_3886), ncrestart (edam:format_3886), restartnc (edam:format_3886), dcd (edam:format_3878), charmm (edam:format_3887), cor (edam:format_2033), pdb (edam:format_1476), mol2 (edam:format_3816), trr (edam:format_3910), gro (edam:format_2033), binpos (edam:format_3885), xtc (edam:format_3875), cif (edam:format_1477), arc (edam:format_2333), sqm (edam:format_2033), sdf (edam:format_3814), conflib (edam:format_2033).

  • output_cpptraj_path (str) –

    Path to the output analysis. File type: output. Sample file. Accepted formats: dat (edam:format_1637), agr (edam:format_2033), xmgr (edam:format_2033), gnu (edam:format_2033).

  • properties (dic - Python dictionary object containing the tool parameters, not input/output files) –

    • start (int) - (1) [1~100000|1] Starting frame for slicing.

    • end (int) - (-1) [-1~100000|1] Ending frame for slicing.

    • steps (int) - (1) [1~100000|1] Step for slicing.

    • mask (str) - (“all-atoms”) Mask definition. Values: c-alpha (All c-alpha atoms; protein only), backbone (Backbone atoms), all-atoms (All system atoms), heavy-atoms (System heavy atoms; not hydrogen), side-chain (All not backbone atoms), solute (All system atoms except solvent atoms), ions (All ion molecules), solvent (All solvent atoms), AnyAmberFromatMask (Amber atom selection syntax like @*).

    • binary_path (str) - (“cpptraj”) Path to the cpptraj executable binary.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

    • container_path (str) - (None) Container path definition.

    • container_image (str) - (‘afandiadib/ambertools:serial’) Container image definition.

    • container_volume_path (str) - (‘/tmp’) Container volume path definition.

    • container_working_dir (str) - (None) Container working directory definition.

    • container_user_id (str) - (None) Container user_id definition.

    • container_shell_path (str) - (‘/bin/bash’) Path to default shell inside the container.

Examples

This is a use example of how to use the building block from Python:

from biobb_analysis.ambertools.cpptraj_rgyr import cpptraj_rgyr
prop = {
    'start': 1,
    'end': -1,
    'steps': 1,
    'mask': 'c-alpha'
}
cpptraj_rgyr(input_top_path='/path/to/myTopology.top',
            input_traj_path='/path/to/myTrajectory.dcd',
            output_cpptraj_path='/path/to/newAnalysis.dat',
            properties=prop)
Info:
check_data_params(out_log, err_log)[source]

Checks all the input/output paths and parameters

create_instructions_file(container_io_dict, out_log, err_log)[source]

Creates an input file using the properties file settings

launch() → int[source]

Execute the CpptrajRgyr ambertools.cpptraj_rgyr.CpptrajRgyr object.

ambertools.cpptraj_rgyr.cpptraj_rgyr(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, properties: dict | None = None, **kwargs) → int[source]

Execute the CpptrajRgyr class and execute the launch() method.

ambertools.cpptraj_rgyr.main()[source]

Command line execution of this building block. Please check the command line documentation.

ambertools.cpptraj_rms module

Module containing the Cpptraj Rms class and the command line interface.

class ambertools.cpptraj_rms.CpptrajRms(input_top_path, input_traj_path, output_cpptraj_path, input_exp_path=None, output_traj_path=None, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_analysis CpptrajRms
Wrapper of the Ambertools Cpptraj module for calculating the Root Mean Square deviation (RMSd) of a given cpptraj compatible trajectory.
Cpptraj (the successor to ptraj) is the main program in Ambertools for processing coordinate trajectories and data files. The parameter names and defaults are the same as the ones in the official Cpptraj manual.
Parameters:

  • input_top_path (str) –

    Path to the input structure or topology file. File type: input. Sample file. Accepted formats: top (edam:format_3881), pdb (edam:format_1476), prmtop (edam:format_3881), parmtop (edam:format_3881), zip (edam:format_3987).

  • input_traj_path (str) –

    Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: mdcrd (edam:format_3878), crd (edam:format_3878), cdf (edam:format_3650), netcdf (edam:format_3650), nc (edam:format_3650), restart (edam:format_3886), ncrestart (edam:format_3886), restartnc (edam:format_3886), dcd (edam:format_3878), charmm (edam:format_3887), cor (edam:format_2033), pdb (edam:format_1476), mol2 (edam:format_3816), trr (edam:format_3910), gro (edam:format_2033), binpos (edam:format_3885), xtc (edam:format_3875), cif (edam:format_1477), arc (edam:format_2333), sqm (edam:format_2033), sdf (edam:format_3814), conflib (edam:format_2033).

  • input_exp_path (str) (Optional) –

    Path to the experimental reference file (required if reference = experimental). File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

  • output_cpptraj_path (str) –

    Path to the output processed analysis. File type: output. Sample file. Accepted formats: dat (edam:format_1637), agr (edam:format_2033), xmgr (edam:format_2033), gnu (edam:format_2033).

  • output_traj_path (str) (Optional) –

    Path to the output processed trajectory. File type: output. Sample file. Accepted formats: mdcrd (edam:format_3878), crd (edam:format_3878), cdf (edam:format_3650), netcdf (edam:format_3650), nc (edam:format_3650), restart (edam:format_3886), ncrestart (edam:format_3886), restartnc (edam:format_3886), dcd (edam:format_3878), charmm (edam:format_3887), cor (edam:format_2033), pdb (edam:format_1476), mol2 (edam:format_3816), trr (edam:format_3910), gro (edam:format_2033), binpos (edam:format_3885), xtc (edam:format_3875), cif (edam:format_1477), arc (edam:format_2333), sqm (edam:format_2033), sdf (edam:format_3814), conflib (edam:format_2033).

  • properties (dic - Python dictionary object containing the tool parameters, not input/output files) –

    • start (int) - (1) [1~100000|1] Starting frame for slicing

    • end (int) - (-1) [-1~100000|1] Ending frame for slicing

    • steps (int) - (1) [1~100000|1] Step for slicing

    • mask (str) - (“all-atoms”) Mask definition. Values: c-alpha (All c-alpha atoms; protein only), backbone (Backbone atoms), all-atoms (All system atoms), heavy-atoms (System heavy atoms; not hydrogen), side-chain (All not backbone atoms), solute (All system atoms except solvent atoms), ions (All ion molecules), solvent (All solvent atoms), AnyAmberFromatMask (Amber atom selection syntax like @*).

    • reference (str) - (“first”) Reference definition. Values: first (Use the first trajectory frame as reference), average (Use the average of all trajectory frames as reference), experimental (Use the experimental structure as reference).

    • nofit (bool) - (False) Do not perform best-fit RMSD

    • norotate (bool) - (False) Translate but do not rotate coordinates

    • nomod (bool) - (False) Do not modify coordinates

    • binary_path (str) - (“cpptraj”) Path to the cpptraj executable binary.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

    • container_path (str) - (None) Container path definition.

    • container_image (str) - (‘afandiadib/ambertools:serial’) Container image definition.

    • container_volume_path (str) - (‘/tmp’) Container volume path definition.

    • container_working_dir (str) - (None) Container working directory definition.

    • container_user_id (str) - (None) Container user_id definition.

    • container_shell_path (str) - (‘/bin/bash’) Path to default shell inside the container.

Examples

This is a use example of how to use the building block from Python:

from biobb_analysis.ambertools.cpptraj_rms import cpptraj_rms
prop = {
    'start': 1,
    'end': -1,
    'steps': 1,
    'mask': 'c-alpha',
    'reference': 'first'
}
cpptraj_rms(input_top_path='/path/to/myTopology.top',
            input_traj_path='/path/to/myTrajectory.dcd',
            output_cpptraj_path='/path/to/newAnalysis.dat',
            input_exp_path= '/path/to/myExpStructure.pdb',
            output_traj_path='/path/to/newTrajectory.netcdf',
            properties=prop)
Info:
check_data_params(out_log, err_log)[source]

Checks all the input/output paths and parameters

create_instructions_file(container_io_dict, out_log, err_log)[source]

Creates an input file using the properties file settings

launch() → int[source]

Execute the CpptrajRms ambertools.cpptraj_rms.CpptrajRms object.

ambertools.cpptraj_rms.cpptraj_rms(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, input_exp_path: str | None = None, output_traj_path: str | None = None, properties: dict | None = None, **kwargs) → int[source]

Execute the CpptrajRms class and execute the launch() method.

ambertools.cpptraj_rms.main()[source]

Command line execution of this building block. Please check the command line documentation.

ambertools.cpptraj_rmsf module

Module containing the Cpptraj Rmsf class and the command line interface.

class ambertools.cpptraj_rmsf.CpptrajRmsf(input_top_path, input_traj_path, output_cpptraj_path, input_exp_path=None, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_analysis CpptrajRmsf
Wrapper of the Ambertools Cpptraj module for calculating the Root Mean Square fluctuations (RMSf) of a given cpptraj compatible trajectory.
Cpptraj (the successor to ptraj) is the main program in Ambertools for processing coordinate trajectories and data files. The parameter names and defaults are the same as the ones in the official Cpptraj manual.
Parameters:

  • input_top_path (str) –

    Path to the input structure or topology file. File type: input. Sample file. Accepted formats: top (edam:format_3881), pdb (edam:format_1476), prmtop (edam:format_3881), parmtop (edam:format_3881), zip (edam:format_3987).

  • input_traj_path (str) –

    Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: mdcrd (edam:format_3878), crd (edam:format_3878), cdf (edam:format_3650), netcdf (edam:format_3650), nc (edam:format_3650), restart (edam:format_3886), ncrestart (edam:format_3886), restartnc (edam:format_3886), dcd (edam:format_3878), charmm (edam:format_3887), cor (edam:format_2033), pdb (edam:format_1476), mol2 (edam:format_3816), trr (edam:format_3910), gro (edam:format_2033), binpos (edam:format_3885), xtc (edam:format_3875), cif (edam:format_1477), arc (edam:format_2333), sqm (edam:format_2033), sdf (edam:format_3814), conflib (edam:format_2033).

  • input_exp_path (str) (Optional) –

    Path to the experimental reference file (required if reference = experimental). File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

  • output_cpptraj_path (str) –

    Path to the output processed analysis. File type: output. Sample file. Accepted formats: dat (edam:format_1637), agr (edam:format_2033), xmgr (edam:format_2033), gnu (edam:format_2033).

  • properties (dic - Python dictionary object containing the tool parameters, not input/output files) –

    • start (int) - (1) [1~100000|1] Starting frame for slicing

    • end (int) - (-1) [-1~100000|1] Ending frame for slicing

    • steps (int) - (1) [1~100000|1] Step for slicing

    • mask (str) - (“all-atoms”) Mask definition. Values: c-alpha (All c-alpha atoms; protein only), backbone (Backbone atoms), all-atoms (All system atoms), heavy-atoms (System heavy atoms; not hydrogen), side-chain (All not backbone atoms), solute (All system atoms except solvent atoms), ions (All ion molecules), solvent (All solvent atoms), AnyAmberFromatMask (Amber atom selection syntax like @*).

    • reference (str) - (“first”) Reference definition. Values: first (Use the first trajectory frame as reference), average (Use the average of all trajectory frames as reference), experimental (Use the experimental structure as reference).

    • binary_path (str) - (“cpptraj”) Path to the cpptraj executable binary.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

    • container_path (str) - (None) Container path definition.

    • container_image (str) - (‘afandiadib/ambertools:serial’) Container image definition.

    • container_volume_path (str) - (‘/tmp’) Container volume path definition.

    • container_working_dir (str) - (None) Container working directory definition.

    • container_user_id (str) - (None) Container user_id definition.

    • container_shell_path (str) - (‘/bin/bash’) Path to default shell inside the container.

Examples

This is a use example of how to use the building block from Python:

from biobb_analysis.ambertools.cpptraj_rmsf import cpptraj_rmsf
prop = {
    'start': 1,
    'end': -1,
    'steps': 1,
    'mask': 'c-alpha',
    'reference': 'first'
}
cpptraj_rmsf(input_top_path='/path/to/myTopology.top',
            input_traj_path='/path/to/myTrajectory.dcd',
            output_cpptraj_path='/path/to/newAnalysis.dat',
            input_exp_path= '/path/to/myExpStructure.pdb',
            properties=prop)
Info:
check_data_params(out_log, err_log)[source]

Checks all the input/output paths and parameters

create_instructions_file(container_io_dict, out_log, err_log)[source]

Creates an input file using the properties file settings

launch() → int[source]

Execute the CpptrajRmsf ambertools.cpptraj_rmsf.CpptrajRmsf object.

ambertools.cpptraj_rmsf.cpptraj_rmsf(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, input_exp_path: str | None = None, properties: dict | None = None, **kwargs) → int[source]

Execute the CpptrajRmsf class and execute the launch() method.

ambertools.cpptraj_rmsf.main()[source]

Command line execution of this building block. Please check the command line documentation.

ambertools.cpptraj_slice module

Module containing the Cpptraj Slice class and the command line interface.

class ambertools.cpptraj_slice.CpptrajSlice(input_top_path, input_traj_path, output_cpptraj_path, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_analysis CpptrajSlice
Wrapper of the Ambertools Cpptraj module for extracting a particular trajectory slice from a given cpptraj compatible trajectory.
Cpptraj (the successor to ptraj) is the main program in Ambertools for processing coordinate trajectories and data files. The parameter names and defaults are the same as the ones in the official Cpptraj manual.
Parameters:

  • input_top_path (str) –

    Path to the input structure or topology file. File type: input. Sample file. Accepted formats: top (edam:format_3881), pdb (edam:format_1476), prmtop (edam:format_3881), parmtop (edam:format_3881), zip (edam:format_3987).

  • input_traj_path (str) –

    Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: mdcrd (edam:format_3878), crd (edam:format_3878), cdf (edam:format_3650), netcdf (edam:format_3650), nc (edam:format_3650), restart (edam:format_3886), ncrestart (edam:format_3886), restartnc (edam:format_3886), dcd (edam:format_3878), charmm (edam:format_3887), cor (edam:format_2033), pdb (edam:format_1476), mol2 (edam:format_3816), trr (edam:format_3910), gro (edam:format_2033), binpos (edam:format_3885), xtc (edam:format_3875), cif (edam:format_1477), arc (edam:format_2333), sqm (edam:format_2033), sdf (edam:format_3814), conflib (edam:format_2033).

  • output_cpptraj_path (str) –

    Path to the output processed trajectory. File type: output. Sample file. Accepted formats: mdcrd (edam:format_3878), crd (edam:format_3878), netcdf (edam:format_3650), nc (edam:format_3650), rst7 (edam:format_3886), ncrst (edam:format_2033), dcd (edam:format_3878), pdb (edam:format_1476), mol2 (edam:format_3816), binpos (edam:format_3885), trr (edam:format_3910), xtc (edam:format_3875), sqm (edam:format_2033).

  • properties (dic - Python dictionary object containing the tool parameters, not input/output files) –

    • start (int) - (1) [1~100000|1] Starting frame for slicing.

    • end (int) - (-1) [-1~100000|1] Ending frame for slicing.

    • steps (int) - (1) [1~100000|1] Step for slicing.

    • mask (str) - (“all-atoms”) Mask definition. Values: c-alpha (All c-alpha atoms; protein only), backbone (Backbone atoms), all-atoms (All system atoms), heavy-atoms (System heavy atoms; not hydrogen), side-chain (All not backbone atoms), solute (All system atoms except solvent atoms), ions (All ion molecules), solvent (All solvent atoms), AnyAmberFromatMask (Amber atom selection syntax like @*).

    • format (str) - (“netcdf”) Output trajectory format. Values: crd (AMBER trajectory format), cdf (Format used by netCDF software library for writing and reading chromatography-MS data files), netcdf (Format used by netCDF software library for writing and reading chromatography-MS data files), nc (Format used by netCDF software library for writing and reading chromatography-MS data files), restart (AMBER coordinate/restart file with 6 coordinates per line), ncrestart (AMBER coordinate/restart file with 6 coordinates per line), restartnc (AMBER coordinate/restart file with 6 coordinates per line), dcd (AMBER trajectory format), charmm (Format of CHARMM Residue Topology Files (RTF)), cor (Charmm COR), pdb (Protein Data Bank format), mol2 (Complete and portable representation of a SYBYL molecule), trr (Trajectory of a simulation experiment used by GROMACS), gro (GROMACS structure), binpos (Translation of the ASCII atom coordinate format to binary code), xtc (Portable binary format for trajectories produced by GROMACS package), cif (Entry format of PDB database in mmCIF format), arc (Tinker ARC), sqm (SQM Input), sdf (One of a family of chemical-data file formats developed by MDL Information Systems), conflib (LMOD Conflib).

    • binary_path (str) - (“cpptraj”) Path to the cpptraj executable binary.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

    • container_path (str) - (None) Container path definition.

    • container_image (str) - (‘afandiadib/ambertools:serial’) Container image definition.

    • container_volume_path (str) - (‘/tmp’) Container volume path definition.

    • container_working_dir (str) - (None) Container working directory definition.

    • container_user_id (str) - (None) Container user_id definition.

    • container_shell_path (str) - (‘/bin/bash’) Path to default shell inside the container.

Examples

This is a use example of how to use the building block from Python:

from biobb_analysis.ambertools.cpptraj_slice import cpptraj_slice
prop = {
    'start': 1,
    'end': -1,
    'steps': 1,
    'mask': 'c-alpha',
    'format': 'netcdf'
}
cpptraj_slice(input_top_path='/path/to/myTopology.top',
            input_traj_path='/path/to/myTrajectory.dcd',
            output_cpptraj_path='/path/to/newTrajectory.netcdf',
            properties=prop)
Info:
check_data_params(out_log, err_log)[source]

Checks all the input/output paths and parameters

create_instructions_file(container_io_dict, out_log, err_log)[source]

Creates an input file using the properties file settings

launch() → int[source]

Execute the CpptrajSlice ambertools.cpptraj_slice.CpptrajSlice object.

ambertools.cpptraj_slice.cpptraj_slice(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, properties: dict | None = None, **kwargs) → int[source]

Execute the CpptrajSlice class and execute the launch() method.

ambertools.cpptraj_slice.main()[source]

Command line execution of this building block. Please check the command line documentation.

ambertools.cpptraj_snapshot module

Module containing the Cpptraj Snapshot class and the command line interface.

class ambertools.cpptraj_snapshot.CpptrajSnapshot(input_top_path, input_traj_path, output_cpptraj_path, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_analysis CpptrajSnapshot
Wrapper of the Ambertools Cpptraj module for extracting a particular snapshot from a given cpptraj compatible trajectory.
Cpptraj (the successor to ptraj) is the main program in Ambertools for processing coordinate trajectories and data files. The parameter names and defaults are the same as the ones in the official Cpptraj manual.
Parameters:

  • input_top_path (str) –

    Path to the input structure or topology file. File type: input. Sample file. Accepted formats: top (edam:format_3881), pdb (edam:format_1476), prmtop (edam:format_3881), parmtop (edam:format_3881), zip (edam:format_3987).

  • input_traj_path (str) –

    Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: mdcrd (edam:format_3878), crd (edam:format_3878), cdf (edam:format_3650), netcdf (edam:format_3650), nc (edam:format_3650), restart (edam:format_3886), ncrestart (edam:format_3886), restartnc (edam:format_3886), dcd (edam:format_3878), charmm (edam:format_3887), cor (edam:format_2033), pdb (edam:format_1476), mol2 (edam:format_3816), trr (edam:format_3910), gro (edam:format_2033), binpos (edam:format_3885), xtc (edam:format_3875), cif (edam:format_1477), arc (edam:format_2333), sqm (edam:format_2033), sdf (edam:format_3814), conflib (edam:format_2033).

  • output_cpptraj_path (str) –

    Path to the output processed structure. File type: output. Sample file. Accepted formats: mdcrd (edam:format_3878), crd (edam:format_3878), netcdf (edam:format_3650), nc (edam:format_3650), rst7 (edam:format_3886), ncrst (edam:format_2033), dcd (edam:format_3878), pdb (edam:format_1476), mol2 (edam:format_3816), binpos (edam:format_3885), trr (edam:format_3910), xtc (edam:format_3875), sqm (edam:format_2033).

  • properties (dic - Python dictionary object containing the tool parameters, not input/output files) –

    • snapshot (int) - (1) [1~100000|1] Frame to be captured for snapshot

    • mask (str) - (“all-atoms”) Mask definition. Values: c-alpha (All c-alpha atoms; protein only), backbone (Backbone atoms), all-atoms (All system atoms), heavy-atoms (System heavy atoms; not hydrogen), side-chain (All not backbone atoms), solute (All system atoms except solvent atoms), ions (All ion molecules), solvent (All solvent atoms), AnyAmberFromatMask (Amber atom selection syntax like @*).

    • format (str) - (“netcdf”) Output trajectory format. Values: crd (AMBER trajectory format), cdf (Format used by netCDF software library for writing and reading chromatography-MS data files), netcdf (Format used by netCDF software library for writing and reading chromatography-MS data files), nc (Format used by netCDF software library for writing and reading chromatography-MS data files), restart (AMBER coordinate/restart file with 6 coordinates per line), ncrestart (AMBER coordinate/restart file with 6 coordinates per line), restartnc (AMBER coordinate/restart file with 6 coordinates per line), dcd (AMBER trajectory format), charmm (Format of CHARMM Residue Topology Files (RTF)), cor (Charmm COR), pdb (Protein Data Bank format), mol2 (Complete and portable representation of a SYBYL molecule), trr (Trajectory of a simulation experiment used by GROMACS), gro (GROMACS structure), binpos (Translation of the ASCII atom coordinate format to binary code), xtc (Portable binary format for trajectories produced by GROMACS package), cif (Entry format of PDB database in mmCIF format), arc (Tinker ARC), sqm (SQM Input), sdf (One of a family of chemical-data file formats developed by MDL Information Systems), conflib (LMOD Conflib).

    • binary_path (str) - (“cpptraj”) Path to the cpptraj executable binary.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

    • container_path (str) - (None) Container path definition.

    • container_image (str) - (‘afandiadib/ambertools:serial’) Container image definition.

    • container_volume_path (str) - (‘/tmp’) Container volume path definition.

    • container_working_dir (str) - (None) Container working directory definition.

    • container_user_id (str) - (None) Container user_id definition.

    • container_shell_path (str) - (‘/bin/bash’) Path to default shell inside the container.

Examples

This is a use example of how to use the building block from Python:

from biobb_analysis.ambertools.cpptraj_snapshot import cpptraj_snapshot
prop = {
    'snapshot': 12,
    'mask': 'c-alpha',
    'format': 'pdb'
}
cpptraj_snapshot(input_top_path='/path/to/myTopology.top',
                input_traj_path='/path/to/myTrajectory.dcd',
                output_cpptraj_path='/path/to/newStructure.pdb',
                properties=prop)
Info:
check_data_params(out_log, err_log)[source]

Checks all the input/output paths and parameters

create_instructions_file(container_io_dict, out_log, err_log)[source]

Creates an input file using the properties file settings

launch() → int[source]

Execute the CpptrajSnapshot ambertools.cpptraj_snapshot.CpptrajSnapshot object.

ambertools.cpptraj_snapshot.cpptraj_snapshot(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, properties: dict | None = None, **kwargs) → int[source]

Execute the CpptrajSnapshot class and execute the launch() method.

ambertools.cpptraj_snapshot.main()[source]

Command line execution of this building block. Please check the command line documentation.

ambertools.cpptraj_strip module

Module containing the Cpptraj Strip class and the command line interface.

class ambertools.cpptraj_strip.CpptrajStrip(input_top_path, input_traj_path, output_cpptraj_path, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_analysis CpptrajStrip
Wrapper of the Ambertools Cpptraj module for stripping a defined set of atoms (mask) from a given cpptraj compatible trajectory.
Cpptraj (the successor to ptraj) is the main program in Ambertools for processing coordinate trajectories and data files. The parameter names and defaults are the same as the ones in the official Cpptraj manual.
Parameters:

  • input_top_path (str) –

    Path to the input structure or topology file. File type: input. Sample file. Accepted formats: top (edam:format_3881), pdb (edam:format_1476), prmtop (edam:format_3881), parmtop (edam:format_3881), zip (edam:format_3987).

  • input_traj_path (str) –

    Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: mdcrd (edam:format_3878), crd (edam:format_3878), cdf (edam:format_3650), netcdf (edam:format_3650), nc (edam:format_3650), restart (edam:format_3886), ncrestart (edam:format_3886), restartnc (edam:format_3886), dcd (edam:format_3878), charmm (edam:format_3887), cor (edam:format_2033), pdb (edam:format_1476), mol2 (edam:format_3816), trr (edam:format_3910), gro (edam:format_2033), binpos (edam:format_3885), xtc (edam:format_3875), cif (edam:format_1477), arc (edam:format_2333), sqm (edam:format_2033), sdf (edam:format_3814), conflib (edam:format_2033).

  • output_cpptraj_path (str) –

    Path to the output processed trajectory. File type: output. Sample file. Accepted formats: mdcrd (edam:format_3878), crd (edam:format_3878), netcdf (edam:format_3650), nc (edam:format_3650), rst7 (edam:format_3886), ncrst (edam:format_2033), dcd (edam:format_3878), pdb (edam:format_1476), mol2 (edam:format_3816), binpos (edam:format_3885), trr (edam:format_3910), xtc (edam:format_3875), sqm (edam:format_2033).

  • properties (dic - Python dictionary object containing the tool parameters, not input/output files) –

    • start (int) - (1) [1~100000|1] Starting frame for slicing.

    • end (int) - (-1) [-1~100000|1] Ending frame for slicing.

    • steps (int) - (1) [1~100000|1] Step for slicing.

    • mask (str) - (“all-atoms”) Mask definition. Values: c-alpha (All c-alpha atoms; protein only), backbone (Backbone atoms), all-atoms (All system atoms), heavy-atoms (System heavy atoms; not hydrogen), side-chain (All not backbone atoms), solute (All system atoms except solvent atoms), ions (All ion molecules), solvent (All solvent atoms), AnyAmberFromatMask (Amber atom selection syntax like @*).

    • format (str) - (“netcdf”) Output trajectory format. Values: crd (AMBER trajectory format), cdf (Format used by netCDF software library for writing and reading chromatography-MS data files), netcdf (Format used by netCDF software library for writing and reading chromatography-MS data files), nc (Format used by netCDF software library for writing and reading chromatography-MS data files), restart (AMBER coordinate/restart file with 6 coordinates per line), ncrestart (AMBER coordinate/restart file with 6 coordinates per line), restartnc (AMBER coordinate/restart file with 6 coordinates per line), dcd (AMBER trajectory format), charmm (Format of CHARMM Residue Topology Files (RTF)), cor (Charmm COR), pdb (Protein Data Bank format), mol2 (Complete and portable representation of a SYBYL molecule), trr (Trajectory of a simulation experiment used by GROMACS), gro (GROMACS structure), binpos (Translation of the ASCII atom coordinate format to binary code), xtc (Portable binary format for trajectories produced by GROMACS package), cif (Entry format of PDB database in mmCIF format), arc (Tinker ARC), sqm (SQM Input), sdf (One of a family of chemical-data file formats developed by MDL Information Systems), conflib (LMOD Conflib).

    • binary_path (str) - (“cpptraj”) Path to the cpptraj executable binary.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

    • container_path (str) - (None) Container path definition.

    • container_image (str) - (‘afandiadib/ambertools:serial’) Container image definition.

    • container_volume_path (str) - (‘/tmp’) Container volume path definition.

    • container_working_dir (str) - (None) Container working directory definition.

    • container_user_id (str) - (None) Container user_id definition.

    • container_shell_path (str) - (‘/bin/bash’) Path to default shell inside the container.

Examples

This is a use example of how to use the building block from Python:

from biobb_analysis.ambertools.cpptraj_strip import cpptraj_strip
prop = {
    'start': 1,
    'end': -1,
    'steps': 1,
    'mask': 'c-alpha',
    'format': 'netcdf'
}
cpptraj_strip(input_top_path='/path/to/myTopology.top',
            input_traj_path='/path/to/myTrajectory.dcd',
            output_cpptraj_path='/path/to/newTrajectory.netcdf',
            properties=prop)
Info:
check_data_params(out_log, err_log)[source]

Checks all the input/output paths and parameters

create_instructions_file(container_io_dict, out_log, err_log)[source]

Creates an input file using the properties file settings

launch() → int[source]

Execute the CpptrajStrip ambertools.cpptraj_strip.CpptrajStrip object.

ambertools.cpptraj_strip.cpptraj_strip(input_top_path: str, input_traj_path: str, output_cpptraj_path: str, properties: dict | None = None, **kwargs) → int[source]

Execute the CpptrajStrip class and execute the launch() method.

ambertools.cpptraj_strip.main()[source]

Command line execution of this building block. Please check the command line documentation.

ambertools.cpptraj_input module

Module containing the Cpptraj Input class and the command line interface.

class ambertools.cpptraj_input.CpptrajInput(input_instructions_path=None, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_analysis CpptrajInput
Wrapper of the Ambertools Cpptraj module for performing multiple analysis and trajectory operations of a given trajectory.
Cpptraj (the successor to ptraj) is the main program in Ambertools for processing coordinate trajectories and data files. The parameter names and defaults are the same as the ones in the official Cpptraj manual.
Parameters:

  • input_instructions_path (str) –

    Path of the instructions file. File type: input. Sample file. Accepted formats: in (edam:format_2033).

  • properties (dic - Python dictionary object containing the tool parameters, not input/output files) –

    • binary_path (str) - (“cpptraj”) Path to the cpptraj executable binary.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

Examples

This is a use example of how to use the building block from Python:

from biobb_analysis.ambertools.cpptraj_input import cpptraj_input
prop = { }
cpptraj_input(input_instructions_path='/path/to/myInstructions.in',
                properties=prop)
Info:
create_instrucions_file()[source]

Creates an input file using paths provideed in the configuration file (only used for test purposes)

launch() → int[source]

Execute the CpptrajInput ambertools.cpptraj_input.CpptrajInput object.

ambertools.cpptraj_input.cpptraj_input(input_instructions_path: str, properties: dict | None = None, **kwargs) → int[source]

Execute the CpptrajInput class and execute the launch() method.

ambertools.cpptraj_input.main()[source]

Command line execution of this building block. Please check the command line documentation.