gorder package

Submodules

gorder.gorder_aa module

Module containing the gorder all atom class and the command line interface.

class gorder.gorder_aa.GorderAA(input_top_path, input_traj_path, output_order_path=None, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_mem GorderAA
Wrapper of the gorder atomistic module for computing lipid order parameters per atom for carbon tails.
gorder uses GSL for all its selections.
Parameters:

  • input_top_path (str) – Path to the input structure or topology file. File type: input. Sample file. Accepted formats: tpr (edam:format_2333).

  • input_traj_path (str) –

    Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: xtc (edam:format_3875), trr (edam:format_3910), gro (edam:format_2033).

  • output_order_path (str) –

    Path to results of the order analysis. File type: output. Sample file. Accepted formats: yaml (edam:format_3570), xvg (edam:format_2330), csv (edam:format_3752).

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

    • heavy_atoms (str) - (“@membrane and name r’C3.+|C2.+’”) Selection query specifying the heavy atoms to be used in the analysis (typically carbon atoms in lipid tails).

    • hydrogens (str) - (“@membrane and element name hydrogen”) Selection query specifiying the hydrogen atoms to be used in the analysis (only those bonded to heavy atoms will be considered).

    • handle_pbc (bool) - (True) If False, ignores periodic boundary conditions (PBC).

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

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

    • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

Examples

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

from biobb_mem.gorder.gorder_aa import gorder_aa
prop = {
    'handle_pbc': False
}
gorder_aa(input_top_path='/path/to/myTopology.tpr',
          input_traj_path='/path/to/myTrajectory.xtc',
          output_order_path='/path/to/orderAnalysis.yaml',
          properties=prop)
Info:
launch() → int[source]

Execute the GorderAA object.

gorder.gorder_aa.gorder_aa(input_top_path: str, input_traj_path: str, output_order_path: str = None, properties: dict = None, **kwargs) → int[source]
biobb_mem GorderAA
Wrapper of the gorder atomistic module for computing lipid order parameters per atom for carbon tails.
gorder uses GSL for all its selections.
Parameters:

  • input_top_path (str) –

    Path to the input structure or topology file. File type: input. Sample file. Accepted formats: tpr (edam:format_2333).

  • input_traj_path (str) –

    Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: xtc (edam:format_3875), trr (edam:format_3910), gro (edam:format_2033).

  • output_order_path (str) –

    Path to results of the order analysis. File type: output. Sample file. Accepted formats: yaml (edam:format_3570), xvg (edam:format_2330), csv (edam:format_3752).

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

    • heavy_atoms (str) - (“@membrane and name r’C3.+|C2.+’”) Selection query specifying the heavy atoms to be used in the analysis (typically carbon atoms in lipid tails).

    • hydrogens (str) - (“@membrane and element name hydrogen”) Selection query specifiying the hydrogen atoms to be used in the analysis (only those bonded to heavy atoms will be considered).

    • handle_pbc (bool) - (True) If False, ignores periodic boundary conditions (PBC).

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

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

    • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

Examples

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

from biobb_mem.gorder.gorder_aa import gorder_aa
prop = {
    'handle_pbc': False
}
gorder_aa(input_top_path='/path/to/myTopology.tpr',
          input_traj_path='/path/to/myTrajectory.xtc',
          output_order_path='/path/to/orderAnalysis.yaml',
          properties=prop)
Info:

gorder.gorder_cg module

Module containing the gorder coarse-grained class and the command line interface.

class gorder.gorder_cg.GorderCG(input_top_path, input_traj_path, output_order_path=None, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_mem GorderCG
Wrapper of the gorder coarse-grained module for computing lipid order parameters per atom for carbon tails.
gorder uses GSL for all its selections.
Parameters:

  • input_top_path (str) –

    Path to the input structure or topology file. File type: input. Sample file. Accepted formats: tpr (edam:format_2333).

  • input_traj_path (str) –

    Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: xtc (edam:format_3875), trr (edam:format_3910), gro (edam:format_2033).

  • output_order_path (str) –

    Path to results of the order analysis. File type: output. Sample file. Accepted formats: yaml (edam:format_3570), xvg (edam:format_2330), csv (edam:format_3752).

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

    • beads (str) - (“@membrane”) Selection query specifying the beads to be used in the analysis.

    • handle_pbc (bool) - (True) If False, ignores periodic boundary conditions (PBC).

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

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

    • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

Examples

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

from biobb_mem.gorder.gorder_cg import gorder_cg
prop = {
    'handle_pbc': False
}
gorder_cg(input_top_path='/path/to/myTopology.tpr',
          input_traj_path='/path/to/myTrajectory.xtc',
          output_order_path='/path/to/orderAnalysis.yaml',
          properties=prop)
Info:
launch() → int[source]

Execute the GorderCG object.

gorder.gorder_cg.gorder_cg(input_top_path: str, input_traj_path: str, output_order_path: str = None, properties: dict = None, **kwargs) → int[source]
biobb_mem GorderCG
Wrapper of the gorder coarse-grained module for computing lipid order parameters per atom for carbon tails.
gorder uses GSL for all its selections.
Parameters:

  • input_top_path (str) –

    Path to the input structure or topology file. File type: input. Sample file. Accepted formats: tpr (edam:format_2333).

  • input_traj_path (str) –

    Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: xtc (edam:format_3875), trr (edam:format_3910), gro (edam:format_2033).

  • output_order_path (str) –

    Path to results of the order analysis. File type: output. Sample file. Accepted formats: yaml (edam:format_3570), xvg (edam:format_2330), csv (edam:format_3752).

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

    • beads (str) - (“@membrane”) Selection query specifying the beads to be used in the analysis.

    • handle_pbc (bool) - (True) If False, ignores periodic boundary conditions (PBC).

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

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

    • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

Examples

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

from biobb_mem.gorder.gorder_cg import gorder_cg
prop = {
    'handle_pbc': False
}
gorder_cg(input_top_path='/path/to/myTopology.tpr',
          input_traj_path='/path/to/myTrajectory.xtc',
          output_order_path='/path/to/orderAnalysis.yaml',
          properties=prop)
Info:

gorder.gorder_ua module

Module containing the gorder united atom class and the command line interface.

class gorder.gorder_ua.GorderUA(input_top_path, input_traj_path, output_order_path=None, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_mem GorderUA
Wrapper of the gorder united atom module for computing lipid order parameters per atom for carbon tails.
gorder uses GSL for all its selections.
Parameters:

  • input_top_path (str) –

    Path to the input structure or topology file. File type: input. Sample file. Accepted formats: tpr (edam:format_2333).

  • input_traj_path (str) –

    Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: xtc (edam:format_3875), trr (edam:format_3910), gro (edam:format_2033).

  • output_order_path (str) –

    Path to results of the order analysis. File type: output. Sample file. Accepted formats: yaml (edam:format_3570), xvg (edam:format_2330), csv (edam:format_3752).

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

    • saturated (str) - (“@membrane”) Selection query specifying the saturated carbons.

    • unsaturated (str) - (None) Selection query specifying the unsaturated carbons.

    • handle_pbc (bool) - (True) If False, ignores periodic boundary conditions (PBC).

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

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

    • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

Examples

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

from biobb_mem.gorder.gorder_ua import gorder_ua
prop = {
    'handle_pbc': False
}
gorder_ua(input_top_path='/path/to/myTopology.tpr',
          input_traj_path='/path/to/myTrajectory.xtc',
          output_order_path='/path/to/orderAnalysis.yaml',
          properties=prop)
Info:
launch() → int[source]

Execute the GorderUA object.

gorder.gorder_ua.gorder_ua(input_top_path: str, input_traj_path: str, output_order_path: str = None, properties: dict = None, **kwargs) → int[source]
biobb_mem GorderUA
Wrapper of the gorder united atom module for computing lipid order parameters per atom for carbon tails.
gorder uses GSL for all its selections.
Parameters:

  • input_top_path (str) –

    Path to the input structure or topology file. File type: input. Sample file. Accepted formats: tpr (edam:format_2333).

  • input_traj_path (str) –

    Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: xtc (edam:format_3875), trr (edam:format_3910), gro (edam:format_2033).

  • output_order_path (str) –

    Path to results of the order analysis. File type: output. Sample file. Accepted formats: yaml (edam:format_3570), xvg (edam:format_2330), csv (edam:format_3752).

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

    • saturated (str) - (“@membrane”) Selection query specifying the saturated carbons.

    • unsaturated (str) - (None) Selection query specifying the unsaturated carbons.

    • handle_pbc (bool) - (True) If False, ignores periodic boundary conditions (PBC).

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

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

    • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

Examples

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

from biobb_mem.gorder.gorder_ua import gorder_ua
prop = {
    'handle_pbc': False
}
gorder_ua(input_top_path='/path/to/myTopology.tpr',
          input_traj_path='/path/to/myTrajectory.xtc',
          output_order_path='/path/to/orderAnalysis.yaml',
          properties=prop)
Info: