flexdyn package

Submodules

flexdyn.concoord_dist module

Module containing the concoord_dist class and the command line interface.

class flexdyn.concoord_dist.ConcoordDist(input_structure_path: str, output_pdb_path: str, output_gro_path: str, output_dat_path: str, properties: dict | None = None, **kwargs)[source]

Bases: BiobbObject

biobb_flexdyn ConcoordDist
Wrapper of the Dist tool from the Concoord package.
Structure interpretation and bond definitions from a PDB/GRO file.
Parameters:

  • input_structure_path (str) – Input structure file. File type: input. Sample file. Accepted formats: pdb (edam:format_1476), gro (edam:format_2033).

  • output_pdb_path (str) –

    Output pdb file. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).

  • output_gro_path (str) –

    Output gro file. File type: output. Sample file. Accepted formats: gro (edam:format_2033).

  • output_dat_path (str) –

    Output dat with structure interpretation and bond definitions. File type: output. Sample file. Accepted formats: dat (edam:format_1637), txt (edam:format_2330).

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

    • binary_path (str) - (“dist”) Concoord dist binary path to be used.

    • vdw (int) - (1) Select a set of Van der Waals parameters. Values: 1 (OPLS-UA -united atoms- parameters), 2 (OPLS-AA -all atoms- parameters), 3 (PROLSQ repel parameters), 4 (Yamber2 parameters), 5 (Li et al. parameters), 6 (OPLS-X parameters -recommended for NMR structure determination-).

    • bond_angle (int) - (1) Select a set of bond/angle parameters. Values: 1 (Concoord default parameters), 2 (Engh-Huber parameters).

    • retain_hydrogens (bool) - (False) Retain hydrogen atoms

    • nb_interactions (bool) - (False) Try to find alternatives for non-bonded interactions (by default the native contacts will be preserved)

    • cutoff (float) - (4.0) cut-off radius (Angstroms) for non-bonded interacting pairs (the cut-off distances are additional to the sum of VDW radii)

    • min_distances (int) - (50) Minimum number of distances to be defined for each atom

    • damp (float) - (1.0) Multiply each distance margin by this value

    • fixed_atoms (bool) - (False) Interpret zero occupancy as atoms to keep fixed

    • 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_flexdyn.flexdyn.concoord_dist import concoord_dist
prop = {
    'vdw' : 4,
    'bond_angle' : 1
}
concoord_dist(  input_structure_path='/path/to/structure.pdb',
                output_pdb_path='/path/to/output.pdb',
                output_gro_path='/path/to/output.gro',
                output_dat_path='/path/to/output.dat',
                properties=prop)
Info:
launch()[source]

Launches the execution of the FlexDyn ConcoordDist module.

flexdyn.concoord_dist.concoord_dist(input_structure_path: str, output_pdb_path: str, output_gro_path: str, output_dat_path: str, properties: dict | None = None, **kwargs) → int[source]

Create ConcoordDist method

flexdyn.concoord_dist.main()[source]

flexdyn.concoord_disco module

Module containing the concoord_disco class and the command line interface.

class flexdyn.concoord_disco.ConcoordDisco(input_pdb_path: str, input_dat_path: str, output_traj_path: str, output_rmsd_path: str, output_bfactor_path: str, properties: dict | None = None, **kwargs)[source]

Bases: BiobbObject

biobb_flexdyn ConcoordDisco
Wrapper of the Disco tool from the Concoord package.
Structure generation based on a set of geometric constraints extracted with the Concoord Dist tool.
Parameters:

  • input_pdb_path (str) –

    Input structure file in PDB format. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

  • input_dat_path (str) –

    Input dat with structure interpretation and bond definitions. File type: input. Sample file. Accepted formats: dat (edam:format_1637), txt (edam:format_2330).

  • output_traj_path (str) –

    Output trajectory file. File type: output. Sample file. Accepted formats: pdb (edam:format_1476), xtc (edam:format_3875), gro (edam:format_2033).

  • output_rmsd_path (str) –

    Output rmsd file. File type: output. Sample file. Accepted formats: dat (edam:format_1637).

  • output_bfactor_path (str) –

    Output B-factor file. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).

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

    • binary_path (str) - (“disco”) Concoord disco binary path to be used.

    • vdw (int) - (1) Select a set of Van der Waals parameters. Values: 1 (OPLS-UA -united atoms- parameters), 2 (OPLS-AA -all atoms- parameters), 3 (PROLSQ repel parameters), 4 (Yamber2 parameters), 5 (Li et al. parameters), 6 (OPLS-X parameters -recommended for NMR structure determination-)

    • num_structs (int) - (500) Number of structures to be generated

    • num_iterations (int) - (2500) Maximum number of iterations per structure

    • chirality_check (int) - (2) Chirality check. Values: 0 (no chirality checks), 1 (only check afterwards), 2 (check on the fly)

    • bs (int) - (0) Number of rounds of triangular bound smoothing (default 0), (if >= 6, tetragonal BS is activated)

    • nofit (bool) - (False) Do not fit generated structures to reference

    • seed (int) - (741265) Initial random seed

    • violation (float) - (1.0) Maximal acceptable sum of violations (nm)

    • nofit (bool) - (False) Do not fit generated structures to reference

    • convergence (int) - (50) Consider convergence failed after this number of non-productive iterations

    • trials (int) - (25) Maximum number of trials per run

    • damp (int) - (1) Damping factor for distance corrections. Values: 1 (default), 2 (for cases with convergence problems)

    • dyn (int) - (1) Number of rounds to dynamically set tolerances

    • bump (bool) - (False) Do extra bump check

    • pairlist_freq (int) - (10) Pairlist update frequency in steps (only valid together with bump)

    • cutoff (float) - (0.5) Cut-off radius for pairlist (nm) (only valid together with bump)

    • ref (bool) - (False) Use input coordinates instead of random starting coordinates

    • scale (int) - (1) Pre-scale coordinates with this factor

    • 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_flexdyn.flexdyn.concoord_disco import concoord_disco
prop = {
    'vdw' : 4,
    'num_structs' : 20
}
concoord_disco(     input_pdb_path='/path/to/dist_input.pdb',
                    input_dat_path='/path/to/dist_input.dat',
                    output_traj_path='/path/to/disco_out_traj.pdb',
                    output_rmsd_path='/path/to/disco_out_rmsd.dat',
                    output_bfactor_path='/path/to/disco_out_bfactor.pdb',
                    properties=prop)
Info:
launch()[source]

Launches the execution of the FlexDyn ConcoordDisco module.

flexdyn.concoord_disco.concoord_disco(input_pdb_path: str, input_dat_path: str, output_traj_path: str, output_rmsd_path: str, output_bfactor_path: str, properties: dict | None = None, **kwargs) → int[source]

Create ConcoordDisco method

flexdyn.concoord_disco.main()[source]

flexdyn.imod_imode module

Module containing the imode class and the command line interface.

class flexdyn.imod_imode.ImodImode(input_pdb_path: str, output_dat_path: str, properties: dict | None = None, **kwargs)[source]

Bases: BiobbObject

biobb_flexdyn imod_imode
Wrapper of the imode tool
Compute the normal modes of a macromolecule using the imode tool from the iMODS package.
Parameters:

  • input_pdb_path (str) –

    Input PDB file. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

  • output_dat_path (str) –

    Output dat with normal modes. File type: output. Sample file. Accepted formats: dat (edam:format_1637), txt (edam:format_2330).

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

    • cg (int) - (2) Coarse-Grained model. Values: 0 (CA), 1 (C5), 2 (Heavy atoms).

    • 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_flexdyn.flexdyn.imod_imode import imod_imode
prop = {
    'cg' : 2
}
imod_imode(   input_pdb_path='/path/to/structure.pdb',
        output_dat_path='/path/to/output_evecs.dat',
        properties=prop)
Info:
launch()[source]

Launches the execution of the FlexDyn iMOD imode module.

flexdyn.imod_imode.imod_imode(input_pdb_path: str, output_dat_path: str, properties: dict | None = None, **kwargs) → int[source]

Create ImodImode method

flexdyn.imod_imode.main()[source]

flexdyn.imod_imove module

Module containing the imode class and the command line interface.

class flexdyn.imod_imove.ImodImove(input_pdb_path: str, input_dat_path: str, output_pdb_path: str, properties: dict | None = None, **kwargs)[source]

Bases: BiobbObject

biobb_flexdyn imod_imove
Wrapper of the imove tool
Compute the normal modes of a macromolecule using the imove tool from the iMODS package.
Parameters:

  • input_pdb_path (str) –

    Input PDB file. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

  • input_dat_path (str) –

    Input dat with normal modes. File type: input. Sample file. Accepted formats: dat (edam:format_1637), txt (edam:format_2330).

  • output_pdb_path (str) –

    Output multi-model PDB file with the generated animation by Principal Component. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).

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

    • pc (int) - (1) Principal Component.

    • num_frames (int) - (11) Number of frames to be generated

    • 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_flexdyn.flexdyn.imod_imove import imod_imove
prop = {
    'pc' : 1
}
imod_imove(   input_pdb_path='/path/to/structure.pdb',
              input_dat_path='/path/to/input_evecs.dat',
              output_pdb_path='/path/to/output_anim.pdb',
              properties=prop)
Info:
launch()[source]

Launches the execution of the FlexDyn iMOD imove module.

flexdyn.imod_imove.imod_imove(input_pdb_path: str, input_dat_path: str, output_pdb_path: str, properties: dict | None = None, **kwargs) → int[source]

Create ImodImove method

flexdyn.imod_imove.main()[source]

flexdyn.imod_imc module

Module containing the imode class and the command line interface.

class flexdyn.imod_imc.ImodImc(input_pdb_path: str, input_dat_path: str, output_traj_path: str, properties: dict | None = None, **kwargs)[source]

Bases: BiobbObject

biobb_flexdyn imod_imc
Wrapper of the imc tool
Compute a Monte-Carlo IC-NMA based conformational ensemble using the imc tool from the iMODS package.
Parameters:

  • input_pdb_path (str) –

    Input PDB file. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

  • input_dat_path (str) –

    Input dat with normal modes. File type: input. Sample file. Accepted formats: dat (edam:format_1637), txt (edam:format_2330).

  • output_traj_path (str) –

    Output multi-model PDB file with the generated ensemble. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).

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

    • num_structs (int) - (500) Number of structures to be generated

    • num_modes (int) - (5) Number of eigenvectors to be employed

    • amplitude (int) - (1) Amplitude linear factor to scale motion

    • 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_flexdyn.flexdyn.imod_imc import imod_imc
prop = {
    'num_structs' : 500
}
imod_imc(   input_pdb_path='/path/to/structure.pdb',
              input_dat_path='/path/to/input_evecs.dat',
              output_traj_path='/path/to/output_ensemble.pdb',
              properties=prop)
Info:
launch()[source]

Launches the execution of the FlexDyn iMOD imc module.

flexdyn.imod_imc.imod_imc(input_pdb_path: str, input_dat_path: str, output_traj_path: str, properties: dict | None = None, **kwargs) → int[source]

Create ImodImc method

flexdyn.imod_imc.main()[source]

flexdyn.prody_anm module

Module containing the prody_anm class and the command line interface.

class flexdyn.prody_anm.ProdyANM(input_pdb_path: str, output_pdb_path: str, properties: dict | None = None, **kwargs)[source]

Bases: BiobbObject

biobb_flexdyn ProdyANM
Wrapper of the ANM tool from the Prody package.
Generate an ensemble of structures using the Prody Anisotropic Network Model (ANM), for coarse-grained NMA.
Parameters:

  • input_pdb_path (str) –

    Input PDB file. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

  • output_pdb_path (str) –

    Output multi-model PDB file with the generated ensemble. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).

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

    • num_structs (int) - (500) Number of structures to be generated

    • selection (str) - (calpha) Atoms selection (Prody syntax: http://prody.csb.pitt.edu/manual/reference/atomic/select.html)

    • cutoff (float) - (15.0) Cutoff distance (Å) for pairwise interactions, minimum is 4.0 Å

    • gamma (float) - (1.0) Spring constant

    • rmsd (float) - (1.0) Average RMSD that the conformations will have with respect to the initial conformation

    • 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_flexdyn.flexdyn.prody_anm import prody_anm
prop = {
    'num_structs' : 20,
    'rmsd' : 4.0
}
prody_anm(  input_pdb_path='/path/to/structure.pdb',
            output_pdb_path='/path/to/output.pdb',
            properties=prop)
Info:
launch()[source]

Launches the execution of the FlexDyn ConcoordDist module.

flexdyn.prody_anm.main()[source]
flexdyn.prody_anm.prody_anm(input_pdb_path: str, output_pdb_path: str, properties: dict | None = None, **kwargs) → int[source]

Create ProdyANM method

flexdyn.nolb_nma module

Module containing the nolb class and the command line interface.

class flexdyn.nolb_nma.Nolb_nma(input_pdb_path: str, output_pdb_path: str, properties: dict | None = None, **kwargs)[source]

Bases: BiobbObject

biobb_flexdyn Nolb_nma
Wrapper of the NOLB tool
Generate an ensemble of structures using the NOLB (NOn-Linear rigid Block) NMA tool.
Parameters:

  • input_pdb_path (str) –

    Input PDB file. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

  • output_pdb_path (str) –

    Output multi-model PDB file with the generated ensemble. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).

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

    • num_structs (int) - (500) Number of structures to be generated

    • cutoff (float) - (5.0) This options specifies the interaction cutoff distance for the elastic network models (in angstroms), 5 by default. The Hessian matrix is constructed according to this interaction distance. Some artifacts should be expected for too short distances (< 5 Å).

    • rmsd (float) - (1.0) Maximum RMSd for decoy generation.

    • 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_flexdyn.flexdyn.nolb_nma import nolb_nma
prop = {
    'num_structs' : 20
}
nolb_nma(   input_pdb_path='/path/to/structure.pdb',
        output_pdb_path='/path/to/output.pdb',
        properties=prop)
Info:
launch()[source]

Launches the execution of the FlexDyn NOLB module.

flexdyn.nolb_nma.main()[source]
flexdyn.nolb_nma.nolb_nma(input_pdb_path: str, output_pdb_path: str, properties: dict | None = None, **kwargs) → int[source]

Create Nolb_nma method