Created
September 7, 2018 17:43
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Python functions to detect whether a spring network realization is feasible in 2D
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| def isFlipped(sites1, sites2, bonds): | |
| """ | |
| Check if neighbors of a vertex | |
| have changed the cyclic order. | |
| """ | |
| def sortClockwiseAroundVertex(coordinates, root, neighbors): | |
| ''' | |
| Sort the neighbors of a vertex, | |
| such that the one with lowest index | |
| appears first. | |
| ''' | |
| dr = coordinates[neighbors] - coordinates[root] | |
| angles = np.arctan2(dr[:,1], dr[:,0])*180/(np.pi) | |
| negAngles = angles<0 | |
| angles[negAngles] += 360 | |
| sortedarg = np.argsort(angles) | |
| rollCounter = np.argmin(sortedarg) | |
| idx = np.roll(sortedarg,shift=len(sortedarg)-rollCounter) | |
| return np.array(neighbors)[idx] | |
| n1,n2 = len(sites1), len(sites2) | |
| if n1 != n2: | |
| return 'Two conformations should have the same number of vertices.' | |
| N = n1 | |
| # build the graph for neighbor lookup | |
| G = nx.Graph([b for b in bonds]) | |
| for root in range(N): | |
| neighbors = list(G.neighbors(root)) | |
| sortIn1 = sortClockwiseAroundVertex(sites1, root, neighbors) | |
| sortIn2 = sortClockwiseAroundVertex(sites2, root, neighbors) | |
| if np.any(sortIn1 != sortIn2): | |
| return False | |
| return True | |
| def isPhysical1(state1, state2, bonds): | |
| """ | |
| Check if vertices forming a triangle have | |
| changed their cyclic order, | |
| """ | |
| def sortClockwisePolygon(coordinates, indices): | |
| '''A set of coordinates''' | |
| coordinates = coordinates[indices] | |
| center = np.mean(coordinates,0) | |
| arr = coordinates - center | |
| angles = np.arctan2(arr[:,1], arr[:,0])*180/(np.pi) | |
| negAngles = angles<0 | |
| angles[negAngles] += 360 | |
| sortedarg = np.argsort(angles) | |
| rollCounter = np.argmin(sortedarg) | |
| idx = np.roll(sortedarg,shift=len(sortedarg)-rollCounter) | |
| return np.array(indices)[idx] | |
| n1,n2 = len(state1), len(state2) | |
| if n1 != n2: | |
| return 'Two conformations should have the same number of vertices.' | |
| n = n1 | |
| #tris = combinations(np.arange(n), r=3) | |
| G=nx.Graph([b for b in bonds]) | |
| tris = [item for item in nx.find_cliques(G) if len(item)==3] | |
| for i,tri in enumerate(tris): | |
| s1 = sortClockwisePolygon(state1, list(tri)) | |
| s2 = sortClockwisePolygon(state2, list(tri)) | |
| if np.any(s1!=s2): | |
| return False | |
| return True |
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