Structures new

dev_guide.md

@@ -2,6 +2,8 @@
 
 ## Basic
 
+pip install --no-deps --editable .
+
 ## Get
 
 - n_atoms is always an integer even when there is no topological info.

docs/api/form/file_h5/autosummary/molsysmt.form.file_h5.get.rst

@@ -160,6 +160,7 @@
       get_inner_bond_index_from_system
       get_inner_bonded_atoms_from_atom
       get_inner_bonded_atoms_from_system
+      get_kinetic_energy_from_system
       get_molecule_id_from_atom
       get_molecule_id_from_chain
       get_molecule_id_from_component
@@ -331,8 +332,11 @@
       get_partial_charge_from_group
       get_partial_charge_from_molecule
       get_partial_charge_from_system
+      get_potential_energy_from_system
       get_structure_id_from_system
+      get_temperature_from_system
       get_time_from_system
+      get_total_energy_from_system
       get_velocities_from_system
 
 

docs/api/form/file_psf/autosummary/molsysmt.form.file_psf.get.rst

@@ -100,7 +100,6 @@
       get_component_type_from_entity
       get_component_type_from_group
       get_component_type_from_molecule
-      get_coordinates_from_atom
       get_coordinates_from_system
       get_entity_id_from_atom
       get_entity_id_from_chain

docs/api/form/mdtraj_HDF5TrajectoryFile/autosummary/molsysmt.form.mdtraj_HDF5TrajectoryFile.get.rst

@@ -160,6 +160,7 @@
       get_inner_bond_index_from_system
       get_inner_bonded_atoms_from_atom
       get_inner_bonded_atoms_from_system
+      get_kinetic_energy_from_system
       get_molecule_id_from_atom
       get_molecule_id_from_chain
       get_molecule_id_from_component
@@ -331,8 +332,11 @@
       get_partial_charge_from_group
       get_partial_charge_from_molecule
       get_partial_charge_from_system
+      get_potential_energy_from_system
       get_structure_id_from_system
+      get_temperature_from_system
       get_time_from_system
+      get_total_energy_from_system
       get_velocities_from_system
 
 

docs/api/form/molsysmt_MolSys/autosummary/molsysmt.form.molsysmt_MolSys.set.rst

@@ -14,21 +14,106 @@
    .. autosummary::
 
       set_atom_id_to_atom
+      set_atom_index_to_atom
       set_atom_name_to_atom
+      set_atom_type_to_atom
       set_b_factor_to_atom
       set_box_to_system
+      set_chain_id_to_atom
+      set_chain_id_to_chain
+      set_chain_id_to_component
+      set_chain_id_to_group
+      set_chain_id_to_molecule
+      set_chain_index_to_atom
+      set_chain_index_to_chain
+      set_chain_index_to_component
+      set_chain_index_to_group
+      set_chain_index_to_molecule
+      set_chain_name_to_atom
+      set_chain_name_to_chain
+      set_chain_name_to_component
+      set_chain_name_to_group
+      set_chain_name_to_molecule
+      set_chain_type_to_atom
+      set_chain_type_to_chain
+      set_chain_type_to_component
+      set_chain_type_to_group
+      set_chain_type_to_molecule
+      set_component_id_to_atom
+      set_component_id_to_component
+      set_component_id_to_group
+      set_component_index_to_atom
+      set_component_index_to_component
+      set_component_index_to_group
+      set_component_name_to_atom
+      set_component_name_to_component
+      set_component_name_to_group
+      set_component_type_to_atom
+      set_component_type_to_component
+      set_component_type_to_group
       set_constraints_to_system
       set_coordinates_to_atom
       set_coordinates_to_system
       set_cutoff_distance_to_system
       set_dispersion_correction_to_system
+      set_entity_id_to_atom
+      set_entity_id_to_chain
+      set_entity_id_to_component
+      set_entity_id_to_entity
+      set_entity_id_to_group
+      set_entity_id_to_molecule
+      set_entity_index_to_atom
+      set_entity_index_to_chain
+      set_entity_index_to_component
+      set_entity_index_to_entity
+      set_entity_index_to_group
+      set_entity_index_to_molecule
+      set_entity_name_to_atom
+      set_entity_name_to_chain
+      set_entity_name_to_component
+      set_entity_name_to_entity
+      set_entity_name_to_group
+      set_entity_name_to_molecule
+      set_entity_type_to_atom
+      set_entity_type_to_chain
+      set_entity_type_to_component
+      set_entity_type_to_entity
+      set_entity_type_to_group
+      set_entity_type_to_molecule
       set_ewald_error_tolerance_to_system
       set_flexible_constraints_to_system
       set_forcefield_to_system
+      set_group_id_to_atom
+      set_group_id_to_group
+      set_group_index_to_atom
+      set_group_index_to_group
+      set_group_name_to_atom
       set_group_name_to_group
+      set_group_type_to_atom
+      set_group_type_to_group
       set_hydrogen_mass_to_system
       set_implicit_solvent_to_system
       set_kappa_to_system
+      set_molecule_id_to_atom
+      set_molecule_id_to_chain
+      set_molecule_id_to_component
+      set_molecule_id_to_group
+      set_molecule_id_to_molecule
+      set_molecule_index_to_atom
+      set_molecule_index_to_chain
+      set_molecule_index_to_component
+      set_molecule_index_to_group
+      set_molecule_index_to_molecule
+      set_molecule_name_to_atom
+      set_molecule_name_to_chain
+      set_molecule_name_to_component
+      set_molecule_name_to_group
+      set_molecule_name_to_molecule
+      set_molecule_type_to_atom
+      set_molecule_type_to_chain
+      set_molecule_type_to_component
+      set_molecule_type_to_group
+      set_molecule_type_to_molecule
       set_non_bonded_method_to_system
       set_occupancy_to_atom
       set_rigid_water_to_system
@@ -38,6 +123,7 @@
       set_structure_id_to_system
       set_switch_distance_to_system
       set_time_to_system
+      set_velocities_to_atom
       set_water_model_to_system
 
 

docs/api/form/molsysmt_Structures/autosummary/molsysmt.form.molsysmt_Structures.set.rst

@@ -20,6 +20,8 @@
       set_occupancy_to_atom
       set_structure_id_to_system
       set_time_to_system
+      set_velocities_to_atom
+      set_velocities_to_system
 
 
 

docs/api/form/molsysmt_Topology/autosummary/molsysmt.form.molsysmt_Topology.set.rst

@@ -9,14 +9,6 @@
 
 
 
-   .. rubric:: Functions
-
-   .. autosummary::
-
-      set_atom_id_to_atom
-      set_atom_name_to_atom
-      set_group_name_to_group
-
 
 
 

docs/api/form/openmm_Context/autosummary/molsysmt.form.openmm_Context.get.rst

@@ -333,6 +333,7 @@
       get_partial_charge_from_system
       get_structure_id_from_system
       get_time_from_system
+      get_velocities_from_atom
       get_velocities_from_system
 
 

docs/api/form/openmm_Context/autosummary/molsysmt.form.openmm_Context.set.rst

@@ -9,6 +9,13 @@
 
 
 
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      set_coordinates_to_atom
+      set_coordinates_to_system
+
 
 
 

docs/contents/user/intro/native_forms/file_h5msm.ipynb

@@ -0,0 +1,43 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "efce3e3e-6878-4ba2-9186-3ac5b1b24764",
+   "metadata": {},
+   "source": [
+    "# file:h5msm\n",
+    "\n",
+    "To be written"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "06dd6d43-dfeb-4b0c-a649-cbf5caa19485",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

docs/contents/user/intro/native_forms/index.md

@@ -5,4 +5,5 @@
    :maxdepth: 1
 
    MolSys.ipynb
+   file_h5msm.ipynb
 ```

docs/contents/user/intro/native_forms/MolSys.ipynb → docs/contents/user/intro/native_forms/molsysmt_MolSys.ipynb

@@ -35,7 +35,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.12"
+   "version": "3.10.13"
   }
  },
  "nbformat": 4,

docs/contents/user/intro/native_forms/molsysmt_Topology.ipynb

@@ -0,0 +1,65 @@
+{
+ "cells": [
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "id": "bdc76b08-dda7-4000-a71f-2cb0611f9ac5",
+   "metadata": {},
+   "source": [
+    "# MolSysMT.Topology\n",
+    "\n",
+    "To be written\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "4e0be295-7699-46ee-97cf-83d4118ecb82",
+   "metadata": {},
+   "source": [
+    "## chain dataframe"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "f0edbf0a-676f-4b70-a924-d5a0d0dd2651",
+   "metadata": {},
+   "source": [
+    "### chain type\n",
+    "\n",
+    "chain type takes the value:\n",
+    "\n",
+    "- 'system': when the chain contains every atom in the molecular system\n",
+    "- 'molecule_type/s + molecule_type/s + ...' where the list of molecule types apparences is ['protein', 'peptide', 'dna', 'rna', 'oligosaccharide', 'small molecule', 'lipid', 'ion', 'water']. The singular or plural form of the molecule type is used if a single or multiple molecules are of the same type are contained in the chain. For example 'dna + ions + waters' or 'protein + small molecule + lipids + ions + waters'."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "f84bf92d-2d55-48d6-a593-4f56e8352ed0",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

molsysmt/__init__.py

@@ -34,7 +34,7 @@
 from . import hbonds
 from . import thirds
 
-from . import systems
+from .systems import systems
 
 # Adding molsysmt to nglview
 

molsysmt/_private/__init__.py

@@ -1,2 +1,3 @@
 from . import digestion
+from . import variables
 from .conversion_shortcuts import _multiple_conversion_shortcuts

molsysmt/_private/digestion/argument/check_if_None.py

@@ -0,0 +1,9 @@
+from ...exceptions import ArgumentError
+
+def digest_check_if_None(check_if_None, caller=None):
+
+    if isinstance(check_if_None, bool):
+        return check_if_None
+
+    raise ArgumentError('check_if_None', value=check_if_None, caller=caller, message=None)
+

molsysmt/_private/digestion/argument/constant_box.py

@@ -0,0 +1,9 @@
+from ...exceptions import ArgumentError
+
+def digest_constant_box(constant_box, caller=None):
+
+    if isinstance(constant_box, bool):
+        return constant_box
+
+    raise ArgumentError('constant_box', value=constant_box, caller=caller, message=None)
+

molsysmt/_private/digestion/argument/constant_id_step.py

@@ -0,0 +1,9 @@
+from ...exceptions import ArgumentError
+
+def digest_constant_id_step(constant_id_step, caller=None):
+
+    if isinstance(constant_id_step, bool):
+        return constant_id_step
+
+    raise ArgumentError('constant_id_step', value=constant_id_step, caller=caller, message=None)
+

molsysmt/_private/digestion/argument/constant_time_step.py

@@ -0,0 +1,9 @@
+from ...exceptions import ArgumentError
+
+def digest_constant_time_step(constant_time_step, caller=None):
+
+    if isinstance(constant_time_step, bool):
+        return constant_time_step
+
+    raise ArgumentError('constant_time_step', value=constant_time_step, caller=caller, message=None)
+