Increasing pyMBE interoperability (part I)#151
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…ass when the pymbe class is instantiated
… to ParticleInstance class
…le_position,inst._particle_fix to _get_instances_df method
- create_espresso_bond_instance -_create_hydrogel_chain - create_hydrogel -_get_espresso_bond_instance - create_added_salt - create_counterions - create_bond -create_particle -create_residue -create_molecule -create_protein add methods to enable the decoupling: -set_simulation_engine -add_instances_to_engine
- algorithm to add instances to espresso system
…ows to the instance dataframe
…type in config class in order to be able to set the position as NDarrays
…presso from pymbe
_create_hydrogel_chain _delete_particles_from_engine calculate_net_charge center_object_simulation_box create_counterions create_hydrogel create_particle delete_instances_in_system Add methods: change_volume_and_rescale_particles update_instances_ids_according_to_engine_particle_ids
…t the missing particles from pymbe DB and the particles that have not been transferred yet to espresso. Add methods _add_bond, _add_particle,_check_particle_exists_in_espresso,_get_last_particle_id_in_espresso,update_instances_ids_according_to_engine_particles_ids
…ase_csv and _save_database_csv Add added_to_engine for pmb_type bond in _load_database_csv and _save_database_csv. This methods still have to pass the test due float point accuracy between save/load
…e, particle_id,position and added_to_engine. Add pymbe type bond and allowed particle_id1,particle_id2 and added_to_engine
The main modification consists on setting as the simulation engine espresso and adding to the simulation engine the instances (particles and bonds ) to the engine. Also removing espresso as an argument from pymbe methods. Adding box_l as argument to pymbe methods
-reaction_montecarlomethods -determine_reservoir_concentrations Migrate methods the following methods to the manager: -propose_unused_types -get_lj_parameters -get_radius_map -_get_label_id_map
- handy functions - reaction methods
- calculate_center_of_mass -determine_reservoir_concentrations
…ys and lists into the instances dataframe
-get_label_id_map -get_lj_parameters -get_radius_map -propose_unused_type
… reservoir concentrations
…em from setup_lj interactions
…y are migrated to espresso_engine class
…ins a numpy array that contains arrays. Thus, the approach that has worked is to loop through the array and compare them element by element
migrate create_angle_instance to simulation engine
Modify add_instances_to_engine to account for added angles.
…r the pmb_type angle
… particle_id3 and added_to_engine
…ain mpc monomer + 2 nodes Fix backbone vector so that accounts for the number of monomers in the chain
…itude instead of reduced length, because now the backbone vector in the polymeric chain between nodes is not normalized
… instead of using the magnitude
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Summary
Application of the strategy pattern to delegate the responsability of executing the simulation engine to a particular engine class (e.g
EspressoEngine).Added
EspressoEngineClassEspressoSystemProtocolClass to check that an the working engine corresponds to espresso.system instanceEspressoEngineEspressoEnginecalculate_net_charge,change_volume_and_re-scale_particles,enable_motion_of_rigid_object,etc.)add_instances_to_engineto add particles, bonds and angles to EspressoModified
create_particle,create_residue,create_molecule,etc. to avoid an explicit dependence to Espresso