Merge pull request #99 from dprada/main

Bugs fixed

dev_guide.md

@@ -5,7 +5,7 @@
 ## Get
 
 - n_atoms is always an integer even when there is no topological info.
-- n_structures is None when the form has no structural info. If the form can store structures n_structures is always an integer.
+- n_structures is None when the form has no structural info. If the form can store structures n_structures is always an integer (0, if there are no structures in the form).
 - if time, box, etc... (structural attributes) are not present in an object... the output is a list with as many Nones as structure_indices.
 
 ## Iterator

docs/contents/user/tools/basic/has_attribute.ipynb

@@ -35,12 +35,14 @@
    "cell_type": "code",
    "execution_count": 2,
    "id": "ccf509b5-a79a-41f7-b432-789945069627",
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "e8d6a25621fa4408bbe762fa10d9d03a",
+       "model_id": "d8b69a8d627f44ea9a5003b579baf6df",
        "version_major": 2,
        "version_minor": 0
       },
@@ -58,7 +60,9 @@
    "cell_type": "code",
    "execution_count": 3,
    "id": "06c8778b-b835-4bf3-9a10-448add565480",
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "molecular_system = msm.demo['pentalanine']['pentalanine.inpcrd']"
@@ -68,7 +72,9 @@
    "cell_type": "code",
    "execution_count": 4,
    "id": "86924b7a-ae89-49b9-8ef1-698fa31b9499",
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [
     {
      "data": {
@@ -89,7 +95,9 @@
    "cell_type": "code",
    "execution_count": 5,
    "id": "032488bc-9cc2-4f15-906b-717849d17885",
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [
     {
      "data": {
@@ -106,6 +114,72 @@
     "msm.has_attribute(molecular_system, attribute='group_name')"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "310b3dc5-752b-4a47-9803-cf71972e0599",
+   "metadata": {},
+   "source": [
+    "Two special strings are accepted by this method in addition to any attribute name: \"topological\" and \"structural\". These words allow us to know if a form has any topological or structural attribute. Let's illustrate this case with some few examples:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "id": "700c4658-5cac-4199-8a52-5d89128e4a73",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "psf_file = msm.demo['membrane']['membrane.psf']"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "id": "db4025f9-bac9-44f8-a470-b0eb1ab12f09",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "True"
+      ]
+     },
+     "execution_count": 7,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "msm.has_attribute(psf_file, 'topological')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "id": "41c35ded-2e7c-469f-b039-7d61bd46fe1f",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "False"
+      ]
+     },
+     "execution_count": 8,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "msm.has_attribute(psf_file, 'structural')"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "72d30572-e39a-40dc-9544-a69157b0fe5b",
@@ -127,6 +201,14 @@
     "{func}`molsysmt.basic.has_attribute`\n",
     "```"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "6a42b74a-129d-4f52-92e8-0e0f11428ded",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
@@ -145,7 +227,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13"
+   "version": "3.9.16"
   }
  },
  "nbformat": 4,

molsysmt/_private/digestion/argument/attribute.py

@@ -4,8 +4,11 @@ def digest_attribute(attribute, caller=None):
 
     from molsysmt.attribute import is_attribute
 
-    if is_attribute(attribute):
-        return attribute
+    if is_attribute(attribute.lower()):
+        return attribute.lower()
+    elif caller == 'molsysmt.basic.has_attribute.has_attribute':
+        if attribute.lower() in ['structural', 'topological']:
+            return attribute.lower()
 
     raise ArgumentError('attribute', value=attribute, caller=caller, message=None)
 

molsysmt/api_forms/api_file_dcd.py

@@ -25,4 +25,9 @@ def to_molsysmt_Structures(item, molecular_system, atom_indices='all', structure
 
     return file_dcd_to_molsysmt_Structures(item, atom_indices=atom_indices, structure_indices=structure_indices)
 
+def to_molsysmt_MolSys(item, molecular_system, atom_indices='all', structure_indices='all'):
+    from molsysmt.form.file_dcd import to_molsysmt_MolSys as file_dcd_to_molsysmt_MolSys
+
+    return file_dcd_to_molsysmt_MolSys(item, atom_indices=atom_indices, structure_indices=structure_indices)
+
 

molsysmt/api_forms/api_file_psf.py

@@ -45,17 +45,23 @@
 def to_molsysmt_MolSys(item, molecular_system, atom_indices='all', structure_indices='all'):
 
     from molsysmt.form.file_psf import to_molsysmt_MolSys as file_psf_to_molsysmt_MolSys
-    from molsysmt import convert
+    from molsysmt import convert, has_attribute
 
-    molsysmt_structures = convert(molecular_system, selection=atom_indices, structure_indices=structure_indices,
+    if has_attribute(molecular_system, 'structural'):
+
+        molsysmt_structures = convert(molecular_system, selection=atom_indices, structure_indices=structure_indices,
             to_form='molsysmt.Structures')
 
-    coordinates = molsysmt_structures.coordinates
-    time = molsysmt_structures.time
-    box = molsysmt_structures.box
-    structure_id = molsysmt_structures.structure_id
-    tmp_item = file_psf_to_molsysmt_MolSys(item, atom_indices=atom_indices, coordinates=coordinates,
+        coordinates = molsysmt_structures.coordinates
+        time = molsysmt_structures.time
+        box = molsysmt_structures.box
+        structure_id = molsysmt_structures.structure_id
+
+        tmp_item = file_psf_to_molsysmt_MolSys(item, atom_indices=atom_indices, coordinates=coordinates,
             time=time, box=box, structure_id=structure_id)
+    else:
+
+        tmp_item = file_psf_to_molsysmt_MolSys(item, atom_indices=atom_indices)
 
     return tmp_item
 

molsysmt/attribute/__init__.py

@@ -1,3 +1,4 @@
 from .is_attribute import is_attribute
 from .is_structural_attribute import is_structural_attribute
+from .is_topological_attribute import is_topological_attribute