26a5ab042e
- use autosummary (with custom module template) - updated module docs for all modules so that they are included with sphinx autodocs
63 lines
1.4 KiB
Python
63 lines
1.4 KiB
Python
"""
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Calculations
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============
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Mathematical helper functions.
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"""
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import math
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#: Maximum distance used to bound calculations of smallest distance
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MAX_DISTANCE = 1e6
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def squared_distance(atom1, atom2):
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"""Calculate the squared distance between two atoms.
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Args:
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atom1: first atom for distance calculation
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atom2: second atom for distance calculation
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Returns:
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distance squared
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"""
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dx = atom2.x - atom1.x
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dy = atom2.y - atom1.y
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dz = atom2.z - atom1.z
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res = dx*dx+dy*dy+dz*dz
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return res
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def distance(atom1, atom2):
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"""Calculate the distance between two atoms.
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Args:
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atom1: first atom for distance calculation
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atom2: second atom for distance calculation
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Returns:
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distance
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"""
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return math.sqrt(squared_distance(atom1, atom2))
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def get_smallest_distance(atoms1, atoms2):
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"""Calculate the smallest distance between two groups of atoms.
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Args:
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atoms1: atom group 1
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atoms2: atom group 2
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Returns:
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smallest distance between groups
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"""
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res_dist = MAX_DISTANCE
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res_atom1 = None
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res_atom2 = None
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for atom1 in atoms1:
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for atom2 in atoms2:
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dist = squared_distance(atom1, atom2)
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if dist < res_dist:
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res_dist = dist
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res_atom1 = atom1
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res_atom2 = atom2
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return [res_atom1, math.sqrt(res_dist), res_atom2]
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