Merge pull request #100 from dprada/main

Bug fixed in molsysmt.MolSys iterators

docs/contents/user/tools/molecular_mechanics/index.md

@@ -0,0 +1,9 @@
+# Molecular Mechanics
+
+```{eval-rst}
+.. toctree::
+   :maxdepth: 2
+
+   potential_energy_minimization.ipynb
+   get_potential_energy.ipynb
+```

docs/contents/user/tools/molecular_mechanics/potential_energy_minimization.ipynb

@@ -0,0 +1,33 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b6cc3140-dac4-4932-be1c-d335d94f726a",
+   "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": "3.9.16"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

molsysmt/_private/digestion/argument/molecular_mechanics.py

@@ -0,0 +1,10 @@
+from molsysmt._private.exceptions import ArgumentError
+
+def digest_molecular_mechanics(molecular_mechanics, caller=None):
+
+    if isinstance(molecular_mechanics, dict):
+        from molsysmt.form.molsysmt_MolecularMechanicsDict import is_molsysmt_MolecularMechanicsDict
+        if is_molsysmt_MolecularMechanicsDict(molecular_mechanics):
+            return molecular_mechanics
+
+    raise ArgumentError('molecular_mechanics', value=molecular_mechanics, caller=caller, message=None)

molsysmt/attribute/attributes.py

@@ -5,6 +5,11 @@
 _reverse_search_in_molecular_system = {}
 topological_attributes = []
 structural_attributes = []
+mechanical_attributes = []
+
+###
+### TOPOLOGICAL ATTRIBUTES
+###
 
 # atom_index
 
@@ -573,6 +578,33 @@
 
 topological_attributes.append('n_saccharides')
 
+# formal_charge
+
+attributes.append('formal_charge')
+attribute_synonyms['formal_charges'] = 'formal_charge'
+
+_required_attributes['formal_charge'] = ['formal_charge']
+_required_indices['formal_charge'] = ['indices']
+_reverse_search_in_molecular_system['formal_charge'] = False
+
+topological_attributes.append('formal_charge')
+
+# partial_charge
+
+attributes.append('partial_charge')
+attribute_synonyms['partial_charges'] = 'partial_charge'
+
+_required_attributes['partial_charge'] = ['partial_charge']
+_required_indices['partial_charge'] = ['indices']
+_reverse_search_in_molecular_system['partial_charge'] = False
+
+topological_attributes.append('partial_charge')
+
+
+###
+### STRUCTURAL ATTRIBUTES
+###
+
 # structure_id
 
 attributes.append('structure_id')
@@ -732,38 +764,230 @@
 _required_indices['b_factor'] = ['indices']
 _reverse_search_in_molecular_system['b_factor'] = False
 
+# temperature
+
+attributes.append('temperature')
+attribute_synonyms['temperatures'] = 'temperature'
+
+_required_attributes['temperature'] = ['temperature']
+_required_indices['temperature'] = []
+_reverse_search_in_molecular_system['temperature'] = False
+
+structural_attributes.append('temperature')
+
+###
+### MECHANICAL ATTRIBUTES
+###
+
+#  forcefield
+
+attributes.append('forcefield')
+attribute_synonyms['force field'] = 'forcefield'
+attribute_synonyms['force_field'] = 'forcefield'
+attribute_synonyms['forcefields'] = 'forcefield'
+attribute_synonyms['force fields'] = 'forcefield'
+attribute_synonyms['force_fields'] = 'forcefield'
+
+_required_attributes['forcefield'] = ['forcefield']
+_required_indices['forcefield'] = []
+_reverse_search_in_molecular_system['forcefield'] = False
+
+mechanical_attributes.append('forcefield')
+
+# non_bonded_method
+
+attributes.append('non_bonded_method')
+attribute_synonyms['non bonded method'] = 'non_bonded_method'
+
+_required_attributes['non_bonded_method'] = ['non_bonded_method']
+_required_indices['non_bonded_method'] = []
+_reverse_search_in_molecular_system['non_bonded_method'] = False
+
+mechanical_attributes.append('non_bonded_method')
+
+# non_bonded_method
+
+attributes.append('non_bonded_method')
+attribute_synonyms['non bonded method'] = 'non_bonded_method'
+
+_required_attributes['non_bonded_method'] = ['non_bonded_method']
+_required_indices['non_bonded_method'] = []
+_reverse_search_in_molecular_system['non_bonded_method'] = False
+
+mechanical_attributes.append('non_bonded_method')
+
+# cutoff_distance
+
+attributes.append('cutoff_distance')
+attribute_synonyms['cutoff distance'] = 'cutoff_distance'
+
+_required_attributes['cutoff_distance'] = ['cutoff_distance']
+_required_indices['cutoff_distance'] = []
+_reverse_search_in_molecular_system['cutoff_distance'] = False
+
+mechanical_attributes.append('cutoff_distance')
+
+# switch_distance
+
+attributes.append('switch_distance')
+attribute_synonyms['switch distance'] = 'switch_distance'
+
+_required_attributes['switch_distance'] = ['switch_distance']
+_required_indices['switch_distance'] = []
+_reverse_search_in_molecular_system['switch_distance'] = False
+
+mechanical_attributes.append('switch_distance')
+
+# dispersion_correction
+
+attributes.append('dispersion_correction')
+attribute_synonyms['dispersion correction'] = 'dispersion_correction'
+attribute_synonyms['use_dispersion_correction'] = 'dispersion_correction'
+
+_required_attributes['dispersion_correction'] = ['dispersion_correction']
+_required_indices['dispersion_correction'] = []
+_reverse_search_in_molecular_system['dispersion_correction'] = False
+
+mechanical_attributes.append('dispersion_correction')
+
+# ewald_error_tolerance
+
+attributes.append('ewald_error_tolerance')
+attribute_synonyms['ewald error tolerance'] = 'ewald_error_tolerance'
+
+_required_attributes['ewald_error_tolerance'] = ['ewald_error_tolerance']
+_required_indices['ewald_error_tolerance'] = []
+_reverse_search_in_molecular_system['ewald_error_tolerance'] = False
+
+mechanical_attributes.append('ewald_error_tolerance')
+
+# hydrogen_mass
+
+attributes.append('hydrogen_mass')
+attribute_synonyms['hydrogen mass'] = 'hydrogen_mass'
+
+_required_attributes['hydrogen_mass'] = ['hydrogen_mass']
+_required_indices['hydrogen_mass'] = []
+_reverse_search_in_molecular_system['hydrogen_mass'] = False
+
+mechanical_attributes.append('hydrogen_mass')
+
+# constraints
+
+attributes.append('constraints')
+attribute_synonyms['constraint'] = 'constraints'
+
+_required_attributes['constraints'] = ['constraints']
+_required_indices['constraints'] = []
+_reverse_search_in_molecular_system['constraints'] = False
+
+mechanical_attributes.append('constraints')
+
+# flexible_constraints
+
+attributes.append('flexible_constraints')
+attribute_synonyms['flexible constraint'] = 'flexible_constraints'
+
+_required_attributes['flexible_constraints'] = ['flexible_constraints']
+_required_indices['flexible_constraints'] = []
+_reverse_search_in_molecular_system['flexible_constraints'] = False
+
+mechanical_attributes.append('flexible_constraints')
+
+# water_model
+
+attributes.append('water_model')
+attribute_synonyms['water model'] = 'water_model'
+
+_required_attributes['water_model'] = ['water_model']
+_required_indices['water_model'] = []
+_reverse_search_in_molecular_system['water_model'] = False
+
+mechanical_attributes.append('water_model')
+
+# rigid_water
+
+attributes.append('rigid_water')
+attribute_synonyms['rigid water'] = 'rigid_water'
+
+_required_attributes['rigid_water'] = ['rigid_water']
+_required_indices['rigid_water'] = []
+_reverse_search_in_molecular_system['rigid_water'] = False
+
+mechanical_attributes.append('rigid_water')
+
+# implicit_solvent
+
+attributes.append('implicit_solvent')
+attribute_synonyms['implicit solvent'] = 'implicit_solvent'
+
+_required_attributes['implicit_solvent'] = ['implicit_solvent']
+_required_indices['implicit_solvent'] = []
+_reverse_search_in_molecular_system['implicit_solvent'] = False
+
+mechanical_attributes.append('implicit_solvent')
+
+# solute_dielectric
+
+attributes.append('solute_dielectric')
+attribute_synonyms['solute dielectric'] = 'solute_dielectric'
+
+_required_attributes['solute_dielectric'] = ['solute_dielectric']
+_required_indices['solute_dielectric'] = []
+_reverse_search_in_molecular_system['solute_dielectric'] = False
+
+mechanical_attributes.append('solute_dielectric')
+
+# solvent_dielectric
+
+attributes.append('solvent_dielectric')
+attribute_synonyms['solvent dielectric'] = 'solvent_dielectric'
+
+_required_attributes['solvent_dielectric'] = ['solvent_dielectric']
+_required_indices['solvent_dielectric'] = []
+_reverse_search_in_molecular_system['solvent_dielectric'] = False
+
+mechanical_attributes.append('solvent_dielectric')
+
+# salt_concentration
+
+attributes.append('salt_concentration')
+attribute_synonyms['salt concentration'] = 'salt_concentration'
+
+_required_attributes['salt_concentration'] = ['salt_concentration']
+_required_indices['salt_concentration'] = []
+_reverse_search_in_molecular_system['salt_concentration'] = False
+
+mechanical_attributes.append('salt_concentration')
+
+# kappa
+
+attributes.append('kappa')
+attribute_synonyms['debye_length'] = 'kappa'
+
+_required_attributes['kappa'] = ['kappa']
+_required_indices['kappa'] = []
+_reverse_search_in_molecular_system['kappa'] = False
+
+mechanical_attributes.append('kappa')
+
+
+
+
+
+
+
 
-# formal_charge
 
-attributes.append('formal_charge')
-attribute_synonyms['formal_charges'] = 'formal_charge'
 
-_required_attributes['formal_charge'] = ['formal_charge']
-_required_indices['formal_charge'] = ['indices']
-_reverse_search_in_molecular_system['formal_charge'] = False
 
-topological_attributes.append('formal_charge')
 
-# partial_charge
 
-attributes.append('partial_charge')
-attribute_synonyms['partial_charges'] = 'partial_charge'
 
-_required_attributes['partial_charge'] = ['partial_charge']
-_required_indices['partial_charge'] = ['indices']
-_reverse_search_in_molecular_system['partial_charge'] = False
 
-topological_attributes.append('partial_charge')
 
-# temperature
 
-attributes.append('temperature')
-attribute_synonyms['temperatures'] = 'temperature'
 
-_required_attributes['temperature'] = ['temperature']
-_required_indices['temperature'] = []
-_reverse_search_in_molecular_system['temperature'] = False
 
-structural_attributes.append('temperature')
 
 

molsysmt/attribute/is_mechanical_attribute.py

@@ -0,0 +1,6 @@
+from .attributes import mechanical_attributes
+
+def is_mechanical_attribute(attribute):
+
+    return attribute in mechanical_attributes
+

molsysmt/demo/__init__.py

@@ -112,6 +112,8 @@
 
 demo['Barnase-Barstar'] = {}
 demo['Barnase-Barstar']['barnase_barstar.pdb'] = parent.joinpath('barnase_barstar/barnase_barstar.pdb').__str__()
+demo['Barnase-Barstar']['barnase_barstar.msmpk'] = parent.joinpath('barnase_barstar/barnase_barstar.msmpk').__str__()
+demo['Barnase-Barstar']['1brs.mmtf'] = parent.joinpath('barnase_barstar/1brs.mmtf').__str__()
 
 # 1SUX
 demo['1SUX'] = {}
@@ -127,6 +129,7 @@
 demo['membrane'] = {}
 demo['membrane']['membrane.psf'] = parent.joinpath('membrane/membrane.psf').__str__()
 demo['membrane']['membrane.dcd'] = parent.joinpath('membrane/membrane.dcd').__str__()
+demo['membrane']['membrane.msmpk'] = parent.joinpath('membrane/membrane.msmpk').__str__()
 
 
 del (PurePath, parent)