Merge pull request #54 from Daniel-Ibarrola/main

Merged without further comments.

.gitignore

@@ -120,4 +120,7 @@ devtools/playground/*
 !devtools/playground/README.md
 !molsysmt/build/*
 !molsysmt/docs/contents/build/*
+todo.txt
 
+# pycharm
+.idea/

Untitled.ipynb

@@ -1,6 +1,17 @@
 {
- "cells": [],
+ "cells": [
+  {
+   "cell_type": "raw",
+   "source": [],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": ""
+    }
+   }
+  }
+ ],
  "metadata": {},
  "nbformat": 4,
  "nbformat_minor": 5
-}
+}

molsysmt/_private/atom_indices.py

@@ -1,25 +1,22 @@
 import numpy as np
 
+
 def complementary_atom_indices(molecular_system, atom_indices):
 
     from molsysmt.basic import get
 
     n_atoms = get(molecular_system, element='system', n_atoms=True)
 
-    mask = np.ones(n_atoms,dtype=bool)
-    mask[atom_indices]=False
+    mask = np.ones(n_atoms, dtype=bool)
+    mask[atom_indices] = False
     return list(np.where(mask)[0])
 
+
 def atom_indices_to_AmberMask(molecular_system, atom_indices):
 
     from molsysmt.basic import get
 
     n_atoms = get(molecular_system, element='system', n_atoms=True)
-    mask = np.zeros(n_atoms,dtype=int)
-    mask[atom_indices]=1
+    mask = np.zeros(n_atoms, dtype=int)
+    mask[atom_indices] = 1
     return list(mask)
-
-def atom_indices_to_csv(atom_indices):
-
-    return ",".join([str(ii) for ii in atom_indices])
-

molsysmt/_private/digestion/__init__.py

@@ -1,20 +1,18 @@
-from .atom_indices import digest_atom_indices
+from .argument import digest_argument
 from .box import digest_box
-from .box import digest_box_lengths, digest_box_lengths_value
-from .box import digest_box_angles, digest_box_angles_value
+from .box import digest_box_vectors
 from .coordinates import digest_coordinates
 from .comparison import digest_comparison
 from .element import digest_element
 from .engine import digest_engine
 from .form import digest_form, digest_to_form
-from .group_indices import digest_group_indices
-from .indices import digest_indices
+from .indices import digest_indices, digest_structure_indices, digest_multiple_structure_indices
+from .indices import digest_atom_indices, digest_group_indices
 from .item import digest_item
 from .molecular_system import digest_single_molecular_system, digest_multiple_molecular_systems
 from .output import digest_output
 from .selection import digest_selection, digest_multiple_selections
 from .step import digest_step
-from .structure_indices import digest_structure_indices, digest_multiple_structure_indices
 from .syntaxis import digest_syntaxis, digest_to_syntaxis
 from .element import digest_element
 from .time import digest_time

molsysmt/_private/digestion/argument.py

@@ -0,0 +1,16 @@
+from molsysmt.attribute.attributes import attribute_synonyms, attributes
+from ..exceptions import WrongGetArgumentError
+
+
+def digest_argument(argument, element):
+    """ Helper function to check keyword arguments passed to get function.
+    """
+    output_argument = argument.lower()
+    if output_argument in ['index', 'indices', 'name', 'names', 'id', 'ids', 'type', 'types', 'order']:
+        output_argument = '_'.join([element, output_argument])
+    if output_argument in attribute_synonyms:
+        output_argument = attribute_synonyms[output_argument]
+    if output_argument in attributes:
+        return output_argument
+    else:
+        raise WrongGetArgumentError(argument)

molsysmt/_private/digestion/box.py

@@ -1,76 +1,72 @@
 import numpy as np
 from molsysmt import puw
-from ..exceptions import *
+from ..exceptions import IncorrectShapeError
 
-def digest_box(box):
 
+def digest_box(box):
+    # TODO: Function doesn't do anything.
     return box
 
-def digest_box_lengths_value(box_lengths):
-
-    output = None
-
-    if type(box_lengths) is not np.ndarray:
-        box_lengths = np.array(box_lengths)
-
-    shape = box_lengths.shape
-
-    if len(shape)==1:
-        if shape[0]==3:
-            output = np.expand_dims(box_lengths, axis=0)
-        else:
-            raise ValueError('box_lengths array with has not the correct shape.')
-    elif len(shape)==2:
-        if shape[1]==3:
-            output = box_lengths
-        else:
-            raise ValueError('box_lengths array with has not the correct shape.')
-    else:
-        raise ValueError('box_lengths array with has not the correct shape.')
-
-    return output
-
-def digest_box_lengths(box_lengths):
-
-    output = None
-    unit = puw.get_unit(box_lengths)
-    box_lengths_value = puw.get_value(box_lengths)
-    box_lengths_value = digest_box_lengths_value(box_lengths_value)
-    output = box_lengths_value*unit
 
-    return output
+def digest_box_vectors_value(box_vectors):
+    """ Checks if box_vectors has the correct shape.
 
-def digest_box_angles_value(box_angles):
+        The array should have shape (n, 3) where n is any integer.
+        However, if a list, tuple is passed it will be converted
+        to an array with the desired shape. Also, if an array of
+        shape (3, ) is passed its dimensions will be expanded to
+        (1, 3). If an array with rank > 2 is passed and exception
+        is raised.
 
-    output = None
+        Parameters
+        ----------
+        box_vectors : np.ndarray, list or tuple
+            A quantity with the box lengths.
 
-    if type(box_angles) is not np.ndarray:
-        box_angles = np.array(box_angles)
+        Raises
+        ------
+        IncorrectShapeError
+            If box_vectors doesn't have the correct shape.
+    """
+    if not(isinstance(box_vectors, np.ndarray)):
+        box_vectors = np.array(box_vectors)
 
-    shape = box_angles.shape
+    shape = box_vectors.shape
 
-    if len(shape)==1:
-        if shape[0]==3:
-            output = np.expand_dims(box_angles, axis=0)
+    if len(shape) == 1:
+        if shape[0] == 3:
+            box_vectors = np.expand_dims(box_vectors, axis=0)
         else:
-            raise ValueError('box_angles array with has not the correct shape.')
-    elif len(shape)==2:
-        if shape[1]==3:
-            output = box_angles
-        else:
-            raise ValueError('box_angles array with has not the correct shape.')
+            raise IncorrectShapeError(expected_shape="(1, 3)", actual_shape=str(shape))
+    elif len(shape) == 2:
+        if shape[1] != 3:
+            raise IncorrectShapeError(expected_shape="(n, 3)", actual_shape=str(shape))
     else:
-        raise ValueError('box_angles array with has not the correct shape.')
-
-    return output
-
-def digest_box_angles(box_angles):
-
-    output = None
-    unit = puw.get_unit(box_angles)
-    box_angles_value = puw.get_value(box_angles)
-    box_angles_value = digest_box_angles_value(box_angles_value)
-    output = box_angles_value*unit
-
-    return output
-
+        raise IncorrectShapeError(expected_shape="(n, 3)", actual_shape=str(shape))
+
+    return box_vectors
+
+
+def digest_box_vectors(box_vectors):
+    """ Checks if box vectors have the correct shape. Can be used
+        to check box_lengths and box_angles.
+
+        Parameters
+        ----------
+        box_vectors : puw.Quantity
+            A quantity with the box vectors.
+
+        Returns
+        -------
+        puw.Quantity
+            The box vectors with the shape corrected.
+
+        Raises
+        ------
+        IncorrectShapeError
+            If box_vectors doesn't have the correct shape.
+    """
+    unit = puw.get_unit(box_vectors)
+    box_vectors = puw.get_value(box_vectors)
+    box_vectors = digest_box_vectors_value(box_vectors)
+    return box_vectors * unit

molsysmt/_private/digestion/comparison.py

@@ -2,7 +2,8 @@
 from molsysmt import puw
 from ..exceptions import *
 
-def digest_comparison(comparison):
 
+def digest_comparison(comparison):
+    # TODO: function doesn't do anything
     return comparison
 

molsysmt/_private/digestion/coordinates.py

@@ -1,6 +1,7 @@
 from ..exceptions import *
 
-def digest_coordinates(coordinates):
 
+def digest_coordinates(coordinates):
+    # TODO: function doesn't do anything
     return coordinates
 

molsysmt/_private/digestion/element.py

@@ -1,4 +1,4 @@
-from ..exceptions import *
+from ..exceptions import WrongElementError
 
 elements = [
     'atom',
@@ -11,28 +11,40 @@
     'bond',
 ]
 
-elements_from_plural={
-    'atoms' : 'atom',
-    'groups' : 'group',
-    'residue' : 'group',
-    'residues' : 'group',
-    'components' : 'component',
-    'chains' : 'chain',
-    'molecules' : 'molecule',
-    'entities' : 'entity',
-    'systems' : 'system',
-    'bonds' : 'bond',
+elements_from_plural = {
+    'atoms': 'atom',
+    'groups': 'group',
+    'residue': 'group',
+    'residues': 'group',
+    'components': 'component',
+    'chains': 'chain',
+    'molecules': 'molecule',
+    'entities': 'entity',
+    'systems': 'system',
+    'bonds': 'bond',
 }
 
+
 def digest_element(element):
+    """ Helper function to check an element type. Raises a BadCallError
+        if the element type is not supported by MolSysMT.
+
+        Parameters
+        ----------
+        element : str
+            The name of the element.
 
-    try:
-        tmp_element = element.lower()
-        if tmp_element in elements_from_plural:
-            tmp_element = elements_from_plural[tmp_element]
-        elif tmp_element not in elements:
-            raise BadCallError()
-        return tmp_element
-    except:
-        raise BadCallError()
+        Raises
+        ------
+        BadCallError
+            If the element is not a string or its name is not valid.
+    """
+    if isinstance(element, str):
+        element_name_lower = element.lower()
+        if element_name_lower in elements_from_plural:
+            return elements_from_plural[element_name_lower]
+        if element_name_lower not in elements:
+            raise WrongElementError("wrong element name")
+        return element_name_lower
 
+    raise WrongElementError("element is not a string")

molsysmt/_private/digestion/engine.py

@@ -1,4 +1,4 @@
-from ..exceptions import *
+from ..exceptions import WrongEngineError
 
 engines = [
     'Amber',
@@ -13,12 +13,26 @@
     'NGLView',
 ]
 
-engines_from_lowercase={ ii.lower() : ii for ii in engines }
+engines_from_lowercase = {ii.lower(): ii for ii in engines}
+
 
 def digest_engine(engine):
+    """ Check the name of the engine.
 
-    try:
-        return engines_from_lowercase[engine.lower()]
-    except:
-        raise BadCallError()
+        Parameters
+        ---------
+        engine : str
+            The name of the engine
 
+        Raises
+        ------
+        BadCallError
+            If the engine name is not valid.
+    """
+    if isinstance(engine, str):
+        try:
+            return engines_from_lowercase[engine.lower()]
+        except KeyError:
+            # TODO: create a wrong engine error
+            raise WrongEngineError
+    raise WrongEngineError