├── LICENSE.txt ├── PLY_Files ├── 01_tetrahedron.ply ├── 02_cube.ply ├── 03_octahedron.ply ├── 04_dodecahedron.ply ├── 05_icosahedron.ply ├── 05_icosahedron_with_unused_vertex.ply ├── 06_cuboctahedron.ply ├── 07_icosidodecahedron.ply ├── 08_rhombicuboctahedron.ply ├── 09_snub_cube.ply ├── 10_truncated_cube.ply ├── 11_truncated_cuboctahedron.ply ├── 12_truncated_dodecahedron.ply ├── 13_truncated_icosahedron.ply ├── 14_truncated_octahedron.ply ├── 15_truncated_tetrahedron.ply ├── 16_gyroelongated_pentagonal_pyramid_(J11).ply ├── 17_triangular_bipyramid_(J12).ply ├── 18_pentagonal_bipyramid_(J13).ply ├── 19_gyroelongated_square_bipyramid_(J17).ply ├── 20_square_gyrobicupola_(J29).ply ├── 21_pentagonal_orthocupolarotunda_(J32).ply ├── 22_pentagonal_orthobirotunda_(J34).ply ├── 23_elongated_pentagonal_gyrobicupola_(J39).ply ├── 24_elongated_pentagonal_gyrobirotunda_(J43).ply ├── 25_gyroelongated_square_bicupola_(J45).ply ├── 26_rhombic_dodecahedron.ply ├── 27_rhombic_triacontahedron.ply ├── 28_deltoidal_icositetrahedron.ply ├── 29_pentagonal_icositetrahedron.ply ├── 30_triakis_octahedron.ply ├── 31_disdyakis_dodecahedron.ply ├── 32_triakis_icosahedron.ply ├── 33_pentakis_dodecahedron.ply ├── 34_tetrakis_hexahedron.ply ├── 35_triakis_tetrahedron.ply ├── 36_heptagonal_bipyramid.ply ├── 37_enneagonal_trapezohedron.ply ├── 38_small_stell_dodecahedron.ply ├── 39_rhombic_hexecontahedron.ply ├── 40_goldberg_dk5dgD.ply ├── 41_doublehelix.ply ├── 42_nested_cube.ply ├── 43_nested_octahedron.ply ├── 44_torus.ply ├── 45_double_torus.ply ├── 46_reinforced_cube.ply ├── 47_ball.ply ├── 48_nickedtorus.ply ├── 49_helix.ply ├── 50_rod.ply ├── 51_stickman.ply ├── 52_bottle.ply └── 53_bunny.ply ├── README.md ├── example_submission_script.py ├── pyDAEDALUS ├── 23SdomIIV_seq.txt ├── Automated_Design │ ├── ABform Replace │ │ ├── assign_staples_wChoices.py │ │ ├── dna_info.py │ │ ├── enum_scaf_bases_DX.py │ │ └── ply_to_input.py │ ├── DX_cage_design.py │ ├── PDB_loader.py │ ├── __init__.py │ ├── adj_scaf_nick_pos.py │ ├── arrange_neighbors.py │ ├── assign_scaf_to_edge.py │ ├── assign_staples_wChoices.py │ ├── constants.py │ ├── csv_staples.py │ ├── designate_edge_type.py │ ├── dna_info.py │ ├── enum_scaf_bases_DX.py │ ├── enum_scaf_bases_Hybrid.py │ ├── enum_scaf_bases_Twisted.py │ ├── gen_PDB.py │ ├── gen_schlegel.py │ ├── gen_stap_seq.py │ ├── gen_vert_to_face.py │ ├── ply_to_input.py │ ├── seq_to_text.py │ ├── set_routing_direction.py │ ├── split_edge.py │ ├── split_vert.py │ ├── util.py │ ├── xx_ConstArchive │ │ ├── constants_20190803.py │ │ ├── constants_23S5S.py │ │ ├── constants_EGFP.py │ │ ├── constants_M13.py │ │ ├── constants_old.py │ │ ├── constants_old_old.py │ │ ├── constants_old_old_old.py │ │ ├── constants_rPB66rRNA │ │ └── gen_PDB.py │ └── xx_SourceArchive │ │ └── tmpShit.bak ├── DAEDserve.py ├── EGFP_seq.txt ├── InstructionsForUse.txt ├── M13.txt ├── images │ ├── DX_Aform.png │ ├── DX_Aform_old.png │ ├── DX_Altform.png │ ├── DX_Bform.png │ ├── DX_Hform.png │ ├── DXedges.key │ └── icon.png ├── index.html ├── js │ ├── jquery-3.4.1.min.js │ ├── jquery-xmlrpc-master.zip │ ├── jquery-xmlrpc-master │ │ ├── .gitignore │ │ ├── LICENCE │ │ ├── README.md │ │ ├── bower.json │ │ ├── docs │ │ │ ├── .gitignore │ │ │ ├── Makefile │ │ │ ├── api.rst │ │ │ ├── conf.py │ │ │ ├── index.rst │ │ │ ├── make.bat │ │ │ ├── overview.rst │ │ │ ├── requirements.txt │ │ │ └── types.rst │ │ ├── jquery.xmlrpc.js │ │ ├── jquery.xmlrpc.min.js │ │ ├── tests │ │ │ ├── index.html │ │ │ ├── min.html │ │ │ ├── qunit.css │ │ │ ├── qunit.js │ │ │ ├── tests.binary.js │ │ │ ├── tests.decoding.js │ │ │ ├── tests.document.js │ │ │ ├── tests.encoding.js │ │ │ └── tests.request.js │ │ └── xmlrpc.jquery.json │ ├── jquery.xmlrpc.min.js │ └── three.min.js ├── main.js ├── oct.ply ├── package.json ├── pbip.ply ├── pyDAEDALUSX.code-workspace ├── renderFile.js ├── requirements.txt ├── testServer.py └── tet.ply ├── pyDAEDALUSX_instructions.pdf └── requirements.txt /LICENSE.txt: -------------------------------------------------------------------------------- 1 | pyDAEDALUS - software to render nearly any 3D geometry as a scaffolded DNA origami nanoparticle. 2 | Copyright (C) 2017 MIT, Bathe Lab 3 | 4 | This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. 5 | 6 | This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 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48 40 25 183 | 3 31 48 25 184 | 3 29 49 28 185 | 3 17 2 6 186 | 3 60 17 18 187 | 3 6 18 17 188 | 3 36 55 33 189 | 3 27 36 33 190 | 3 11 16 15 191 | 3 37 33 55 192 | 3 24 14 62 193 | 3 55 5 45 194 | 3 24 36 27 195 | 3 63 25 40 196 | 3 40 48 66 197 | 3 63 64 25 198 | 3 50 8 35 199 | 3 50 5 41 200 | 3 30 56 52 201 | 3 65 34 35 202 | 3 65 21 12 203 | 3 43 10 62 204 | 3 64 69 20 205 | 3 62 66 36 206 | 3 66 48 36 207 | 3 10 43 68 208 | 3 40 68 69 209 | 3 63 40 69 210 | 3 68 43 14 211 | 3 63 69 64 212 | 3 40 66 68 213 | 3 69 1 20 214 | 3 68 38 69 215 | 3 69 38 1 -------------------------------------------------------------------------------- /example_submission_script.py: -------------------------------------------------------------------------------- 1 | import xmlrpc.client 2 | import os 3 | # 4 | # connect to localhost, port 4242 running the RPC server 5 | # 6 | proxy = xmlrpc.client.ServerProxy("http://localhost:4242/") 7 | multicall = xmlrpc.client.MultiCall(proxy) 8 | # 9 | # calc: function on the RPC server to route the origami 10 | # calc(projectName, helicalForm, helicalTurns, plyFile, sequenceFile): 11 | # projectName: short descriptive name, name of the generated folder 12 | # (write "M13.txt" to use default sequence) 13 | # helicalForm: 'Bform', 'Aform', 'Hybrid', 'Twisted' 14 | # helicalTurns: multiplied by 11 (Aforms) or 10.5 (Bform) 15 | # to get minimum edge length 16 | # plyFile: Path to ply file 17 | # sequenceFile: Path to sequence file 18 | # 19 | 20 | ply_dir = "C:/pyDAEDALUSX/PLY_Files" # path to directory containing input geometries 21 | 22 | for geom in os.listdir(ply_dir): 23 | ply = os.path.join(ply_dir, geom) # path to specific geometry file 24 | name = geom # project name 25 | multicall.calc(name,"Aform",4,ply,"M13.txt"); 26 | 27 | result = multicall() 28 | -------------------------------------------------------------------------------- /pyDAEDALUS/23SdomIIV_seq.txt: -------------------------------------------------------------------------------- 1 | GCCCTGGCAGTCAGAGGCGATGAAGGACGTGCTAATCTGCGATAAGCGTCGGTAAGGTGATATGAACCGTTATAACCGGCGATTTCCGAATGGGGAAACCCAGTGTGTTTCGACACACTATCATTAACTGAATCCATAGGTTAATGAGGCGAACCGGGGGAACTGAAACATCTAAGTACCCCGAGGAAAAGAAATCAACCGAGATTCCCCCAGTAGCGGCGAGCGAACGGGGAGCAGCCCAGAGCCTGAATCAGTGTGTGTGTTAGTGGAAGCGTCTGGAAAGGCGCGCGATACAGGGTGACAGCCCCGTACACAAAAATGCACATGCTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGACCATCCTCCAAGGCTAAATACTCCTGACTGACCGATAGTGAACCAGTACCGTGAGGGAAAGGCGAAAAGAACCCCGGCGAGGGGAGTGAAAAAGAACCTGAAACCGTGTACGTACAAGCAGTGGGAGCACGCTTAGGCGTGTGACTGCGTACCTTTTGTATAATGGGTCAGCGACTTATATTCTGTAGCAAGGTTAACCGAATAGGGGAGCCGAAGGGAAACCGAGTCTTAACTGGGCGTTAAGTTGCAGGGTATAGACCCGAAACCCGGTGATCTAGCCATGGGCAGGTTGAAGGTTGGGTAACACTAACTGGAGGACCGAACCGACTAATGTTGAAAAATTAGCGGATGACTTGTGGCTGGGGGTGAAAGGCCAATCAAACCGGGAGATAGCTGGTTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGAATTCATCTCCGGGGGTAGAGCACTGTTTCGGCAAGGGGGTCATCCCGACTTACCAACCCGATGCAAACTGCGAATACCGGAGAATGTTATCACGGGAGACACACGGCGGGTGCTAACGTCCGTCGTGAAGAGGGAAACAACCCAGACCGCCAGCTAAGGTCCCAAAGTCATGGTTAAGTGGGAAACGATGTGGGAAGGCCCAGACAGCCAGGATGTTGGCTTAGAAGCAGCCATCATTTAAAGAAAGCGTAATAGCTCACTGGTCGAGTCGGCCTGCGCGGAAGATGTAACGGGGCTAAACCATGCACCGAAGCTGCGGCAGCGACGCTTATGCGTTGTTGGGTAGGGGAGCGTTCTGTAAGCCTGCGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCGGGGCAGGGTGAGTCGACCCCTAAGGCGAGGCCGAAAGGCGTAGTCGATGGGAAACAGGTTAATATTCCTGTACTTGGTGTTACTGCGAAGGGGGGACGGAGAAGGCTATGTTGGCCGGGCGACGGTTGTCCCGGTTTAAGCGTGTAGGCTGGTTTTCCAGGCAAATCCGGAAAATCAAGGCTGAGGCGTGATGACGAGGCACTACGGTGCTGAAGCAACAAATGCCCTGCTTCCAGGAAAAGCCTCTAAGCATCAGGTAACATCAAATCGTACCCCAAACCGACACAGGTGGTCAGGTAGAGAATACCAAGGCGCTTGAGAGAACTCGGGTGAAGGAACTAGGCAAAATGGTGCCGTAACTTCGGGAGAAGGCACGCTGATATGTAGGTGAAGCGACTTGCTCGTGGAGCTGAAATCAGTCGAAGATACCAGCTGGCTGCAACTGTTTATTAAAAACACAGCACTGTGCAAACACGAAAGTGGACGTATACGGTGTGACGCCTGCCCGGTGCCGGAAGGTTAATTGATGGGGTTAGCGCAAGCGAAGCTCTTGATCGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAATGATGGCCAGGCTGTCTCCACCCGAGACTCA 2 | -------------------------------------------------------------------------------- /pyDAEDALUS/Automated_Design/ABform Replace/enum_scaf_bases_DX.py: -------------------------------------------------------------------------------- 1 | import math 2 | 3 | 4 | def enum_scaf_bases_DX(route_real, route_vals, edge_length_mat_full): 5 | """ 6 | Enumerates scaffold bases for N-arm DX tile-based cages 7 | Inputs: route_real = row vector of vertices listed in visitation order 8 | (only real vertex IDs) 9 | route_vals = row vector of edge types, where the value at index 10 | j in route_vals is the edge type of the edge between the 11 | vertices route_real[j:j+1), wrapping around at end 12 | edge_length_mat_full = VxV sparse matrix of edge lengths 13 | Outputs: edge_bgn_vec = row vector of scaff nt IDs at which edge begins 14 | edge_fin_vec = row vector of scaff nt IDs at which edge finishes 15 | edge_type_vec = row vector of edge types, corresponding to 16 | edge_length_mat_full 17 | 2 is spanning tree edge: DX edge with 0 scaffold crossovers 18 | -3 is half of a non-spanning tree edge, connecting to vertex at 3' end 19 | -5 is half of a non-spanning tree edge, connecting to vertex at 5' end 20 | ########################################################################## 21 | by Sakul Ratanalert, MIT, Bathe Lab, 2016 22 | 23 | Copyright 2016. Massachusetts Institute of Technology. Rights Reserved. 24 | M.I.T. hereby makes following copyrightable material available to the 25 | public under GNU General Public License, version 2 (GPL-2.0). A copy of 26 | this license is available at https://opensource.org/licenses/GPL-2.0 27 | ########################################################################## 28 | """ 29 | # 30 | # If even: EdgeLength/2-8 31 | # EdgeLength/2-3 32 | # Elif odd: ceil(EdgeLength/2)+2 33 | # floor(EdgeLength/2)-2 34 | # 35 | # # Initialize output variables and length of route 36 | len_route = len(route_real) # length of route 37 | edge_bgn_vec = [] 38 | edge_fin_vec = [] 39 | edge_type_vec = [] 40 | 41 | for route_ID in range(len_route): # for each vertex in the route 42 | edge_bgn = route_real[route_ID] # current edge 43 | 44 | # # Find edge_fin, the other end of the edge 45 | if route_ID == len_route - 1: # if last vertex... 46 | edge_fin = route_real[0] # use first vertex in route. 47 | else: # else use next vertex 48 | edge_fin = route_real[route_ID + 1] 49 | 50 | # # Find edge_before, the vertex visited prior to edge_bgn 51 | if route_ID == 0: # if first vertex... 52 | edge_before = route_real[-1] # use last vertex in route. 53 | else: # else use previous vertex 54 | edge_before = route_real[route_ID - 1] 55 | 56 | # Get edge type: 2 (no scafold crossover) or -1 (half of an edge 57 | # with 1 scaffold crossover) 58 | route_val = route_vals[route_ID] 59 | 60 | len_edge = edge_length_mat_full[edge_bgn][edge_fin]['length'] 61 | 62 | if route_val == 2: # tree edge, edge with no scaff crossovers 63 | len_edge = int(len_edge) # len_edge should be int-able by now 64 | edge_bgn_vec = edge_bgn_vec + ([edge_bgn] * len_edge) 65 | edge_fin_vec = edge_fin_vec + ([edge_fin] * len_edge) 66 | edge_type_vec = edge_type_vec + ([route_vals[route_ID]] * len_edge) 67 | 68 | elif route_val == -1: # half non-tree edge 69 | # # Is it an even or odd multiple of 10.5? Is the length even/odd? 70 | quotient = round(len_edge / 11) 71 | quot_is_odd = quotient % 2 # 1 if odd, 0 if even multiple 72 | 73 | # # Adjust len_edge according to parity of len and quotient 74 | if quot_is_odd: # quotient is odd, scaff cross in middle +/-2 75 | len_edge_adjusted = len_edge 76 | 77 | # if returning half-strand, 3' end, 1 shorter 78 | if edge_before == edge_fin: 79 | route_val = -3 # -3 = returning half-strand 80 | len_half = math.ceil(len_edge_adjusted / 2.0)+2.0 # changed 81 | else: # outgoing half-strand, 5' end, 1 longer 82 | route_val = -5 # -5 = outgoing half-strand 83 | len_half = math.floor(len_edge_adjusted / 2.0)-2.0 # changed 84 | 85 | else: # quotient is even, scaffold 3/8 bp from middle 86 | # len is even, outgoing + returning = len_edge +/-11 87 | # if returning half-strand, 3' end, 1 shorter: 88 | if edge_before == edge_fin: 89 | route_val = -3 # -3 = returning half-strand 90 | 91 | if edge_bgn > edge_fin: # shorter half 92 | len_edge_adjusted = len_edge - 6 93 | else: # longer half 94 | len_edge_adjusted = len_edge + 16 95 | 96 | len_half = math.floor(len_edge_adjusted / 2.0) # changed 97 | 98 | else: # outgoing half-strand, 5' end, 1 longer 99 | route_val = -5 # -5 = outgoing half-strand 100 | 101 | if edge_bgn < edge_fin: # shorter half 102 | len_edge_adjusted = len_edge - 16 103 | else: # longer half 104 | len_edge_adjusted = len_edge + 6 105 | 106 | len_half = math.ceil(len_edge_adjusted / 2.0) 107 | 108 | len_half = int(len_half) # len_half should be int-able by now 109 | 110 | # # Add to edge_{bgn,fin,type}_vec 111 | edge_bgn_vec = edge_bgn_vec + ([edge_bgn] * len_half) 112 | edge_fin_vec = edge_fin_vec + ([edge_fin] * len_half) 113 | edge_type_vec = edge_type_vec + ([route_val] * len_half) 114 | 115 | return [edge_bgn_vec, edge_fin_vec, edge_type_vec] 116 | -------------------------------------------------------------------------------- /pyDAEDALUS/Automated_Design/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lcbb/pyDAEDALUS/139f47bb27144a5121d8218a8fa4a61e9ae05832/pyDAEDALUS/Automated_Design/__init__.py -------------------------------------------------------------------------------- /pyDAEDALUS/Automated_Design/adj_scaf_nick_pos.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | from copy import deepcopy 3 | from Automated_Design.util import intersect_lists 4 | 5 | 6 | def get_scaf_nick_pos(edges, route_real, edge_length_vec): 7 | first_node_in_route = route_real[0] 8 | second_node_in_route = route_real[1] 9 | min_node = min(first_node_in_route, second_node_in_route) 10 | max_node = max(first_node_in_route, second_node_in_route) 11 | 12 | edges = np.array(edges) 13 | from_nodes = np.where(edges[:, 0] == max_node)[0] 14 | to_nodes = np.where(edges[:, 1] == min_node)[0] 15 | 16 | # TODO: assured to always have 1 result? 17 | first_edge = intersect_lists(from_nodes, to_nodes)[0] 18 | 19 | first_edge_length = edge_length_vec[first_edge] 20 | if first_edge_length < 44: # == 33 21 | scaf_nick_pos = 16 22 | else: 23 | scaf_nick_pos = 19 24 | 25 | return scaf_nick_pos 26 | 27 | 28 | def adj_scaf_nick_pos(scaf_to_edge, scaf_nick_pos, num_bases): 29 | # Adjust the scaffold nick position so that there are scaf_nick_pos bases 30 | # upstream of scaffold nick. 31 | # Inputs: scaf_to_edge = Ex2 cell array, where each row corresponds to one 32 | # edge, 1st column is duplex from low ID to high ID vertex, 33 | # 2nd column is from high to low. Each element is a row vector 34 | # containing the scaffold base IDs in order on that duplex. 35 | # scaf_nick_pos = number of bases upstream of scaffold nick 36 | # num_bases = total number of scaffold bases 37 | # Outputs: scaf_to_edge_adj = scaf_to_edge with adjusted numbering 38 | ########################################################################### 39 | # by Sakul Ratanalert, MIT, Bathe Lab, 2016 40 | # 41 | # Copyright 2016. Massachusetts Institute of Technology. Rights Reserved. 42 | # M.I.T. hereby makes following copyrightable material available to the 43 | # public under GNU General Public License, version 2 (GPL-2.0). A copy of 44 | # this license is available at https://opensource.org/licenses/GPL-2.0 45 | ########################################################################### 46 | 47 | # # Initialize output vector 48 | scaf_to_edge_adj = deepcopy(scaf_to_edge) # row vec 49 | 50 | # # Adjust scaf_to_edge 51 | import numpy as np 52 | shape = np.array(scaf_to_edge_adj, dtype=np).shape # num_sides should be 2 53 | num_edges = shape[0] 54 | num_sides = shape[1] 55 | 56 | for edge_ID in range(num_edges): 57 | for sides_ID in range(num_sides): 58 | scaf_to_edge_adj[edge_ID][sides_ID] = adjust( 59 | scaf_to_edge[edge_ID][sides_ID], scaf_nick_pos, num_bases) 60 | 61 | return scaf_to_edge_adj 62 | 63 | 64 | def adjust(old_num_vec, scaf_nick_pos, num_bases): 65 | # Adjusts numbered vector by shifting by scaf_nick_pos bases, with 66 | # wraparound 67 | # Inputs: old_num_vec = numbered vector to shift 68 | # scaf_nick_pos = number of bases to shift by 69 | # num_bases = total number of bases in scaffold 70 | # Output: new_num_vec = adjusted numbered vector 71 | 72 | # Initialize 73 | new_num_vec = deepcopy(old_num_vec) 74 | 75 | for i in range(len(old_num_vec)): 76 | new_num = (int(old_num_vec[i]) - int(scaf_nick_pos)) % int(num_bases) 77 | 78 | # TODO: Doesn't this always return `new_num`? 79 | if new_num == num_bases: # if is now last base 80 | new_num_vec[i] = num_bases # set to last base 81 | else: 82 | new_num_vec[i] = new_num 83 | 84 | return new_num_vec 85 | -------------------------------------------------------------------------------- /pyDAEDALUS/Automated_Design/assign_scaf_to_edge.py: -------------------------------------------------------------------------------- 1 | from Automated_Design.util import intersect_lists, find 2 | 3 | 4 | def assign_scaf_to_edge(edges, num_edges, edge_type_mat, edge_bgn_vec, 5 | edge_fin_vec, edge_type_vec): 6 | """ 7 | # Assign enumerated scaffold bases to edges. Create vectors for each duplex 8 | # in each edge, identify to which scaffold base each edge base corresponds 9 | # Inputs: edges = Ex2 matrix where each row corresponds to one edge, 10 | # denoting the vertices being connected. 1st column > 2nd column 11 | # num_edges = number of edges, E 12 | # edge_length_mat_full = VxV sparse matrix of edge lengths 13 | # edge_bgn_vec = row vector of scaff nt IDs at which edge begins 14 | # edge_fin_vec = row vector of scaff nt IDs at which edge finishes 15 | # edge_type_vec = row vector of edge types, corresponding to 16 | # edge_length_mat_full 17 | # 2 is spanning tree edge: DX edge with 0 scaffold crossovers 18 | # -3 is half of a non-spanning tree edge, connecting to vertex at 3' end 19 | # -5 is half of a non-spanning tree edge, connecting to vertex at 5' end 20 | # Outputs: scaf_to_edge = Ex2 cell array, where each row corresponds to one 21 | # edge, 1st column is duplex from low ID to high ID vertex, 22 | # 2nd column is from high to low. Each element is a row vector 23 | # containing the scaffold base IDs in order on that duplex. 24 | ########################################################################### 25 | # by Sakul Ratanalert, MIT, Bathe Lab, 2016 26 | # 27 | # Copyright 2016. Massachusetts Institute of Technology. Rights Reserved. 28 | # M.I.T. hereby makes following copyrightable material available to the 29 | # public under GNU General Public License, version 2 (GPL-2.0). A copy of 30 | # this license is available at https://opensource.org/licenses/GPL-2.0 31 | ########################################################################### 32 | """ 33 | 34 | scaf_to_edge = [] 35 | for edge_ID in range(num_edges): # TODO: convert to `for edge in edges:` 36 | # first column low to high, second column high to low 37 | row = [None, None] 38 | for high_to_low in [1, 2]: # for each duplex direction on edge 39 | col = 2 - high_to_low 40 | 41 | if high_to_low == 1: # high to low 5' to 3' 42 | edge_bgn = edges[edge_ID][0] 43 | edge_fin = edges[edge_ID][1] 44 | else: # low_to_high 5' to 3' 45 | edge_bgn = edges[edge_ID][1] 46 | edge_fin = edges[edge_ID][0] 47 | 48 | edge_type = edge_type_mat[edge_bgn][edge_fin]['type'] 49 | if edge_type == 2: # tree edge # TODO: extract into constant 50 | bases = intersect_lists(find(edge_bgn_vec, edge_bgn), 51 | find(edge_fin_vec, edge_fin)) 52 | else: # non-tree edge 53 | bases_all = intersect_lists(find(edge_bgn_vec, edge_bgn), 54 | find(edge_fin_vec, edge_fin)) 55 | bases_5 = intersect_lists(bases_all, find(edge_type_vec, -5)) 56 | bases_3 = intersect_lists(bases_all, find(edge_type_vec, -3)) 57 | 58 | bases = bases_5 + bases_3 59 | 60 | row[col] = bases 61 | 62 | scaf_to_edge.append(row) 63 | 64 | return scaf_to_edge 65 | -------------------------------------------------------------------------------- /pyDAEDALUS/Automated_Design/csv_staples.py: -------------------------------------------------------------------------------- 1 | from os import path 2 | 3 | 4 | def csv_staples(full_file_name, named_stap_seq_list, 5 | results_foldername): # pragma: no cover 6 | """ 7 | Convert staple list to .csv file. File is saved into `results_foldername`. 8 | 9 | Parameters 10 | ---------- 11 | full_file_name : str 12 | String containing full name of file 13 | named_stap_seq_list : list 14 | List with second column identical to stap_seq_list, first column 15 | contains string of staple name. 16 | results_foldername : str 17 | Foldername to save this file into. 18 | 19 | Returns 20 | ------- 21 | None 22 | """ 23 | 24 | full_filename = path.join(results_foldername, 25 | 'staples_' + full_file_name + '.csv') 26 | fid = open(full_filename, 'w') 27 | 28 | num_stap = len(named_stap_seq_list) 29 | 30 | for stap_ID in range(num_stap): 31 | fid.write("{},{}\n".format( 32 | named_stap_seq_list[stap_ID][0], named_stap_seq_list[stap_ID][1])) 33 | 34 | fid.close() 35 | -------------------------------------------------------------------------------- /pyDAEDALUS/Automated_Design/designate_edge_type.py: -------------------------------------------------------------------------------- 1 | from networkx.algorithms.mst import prim_mst 2 | 3 | 4 | def designate_edge_type(full_graph): 5 | """ 6 | Calculate minimum spanning tree, and label the links in the full graph 7 | that are also in the min spanning tree as such: 8 | 1 is non-spanning tree edge: DX edge with 1 scaffold crossover 9 | 2 is spanning tree edge: DX edge with 0 scaffold crossovers 10 | """ 11 | tree = prim_mst(full_graph) 12 | 13 | # networkx undirected networks already implicitly can be considered a 14 | # symmetrical matrix 15 | full_tree = tree 16 | 17 | tree_edges = full_tree.edges() 18 | for edge in full_graph.edges(): 19 | if edge in tree_edges: 20 | type = 2 21 | else: 22 | type = 1 23 | i = edge[0] 24 | j = edge[1] 25 | full_graph[i][j]['type'] = type 26 | 27 | return full_graph 28 | -------------------------------------------------------------------------------- /pyDAEDALUS/Automated_Design/gen_schlegel.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | from matplotlib import pyplot as plt 3 | 4 | from Automated_Design.constants import VERMILLION, REDPURPLE, SKYBLUE, WHITE 5 | 6 | 7 | def create_2d_mapping(edges, coordinates, faces): 8 | # Choose Biggest Face: 9 | big_face = max(faces, key=len) 10 | 11 | # Initialize: 12 | num_face_vert = len(big_face) 13 | num_vert = len(coordinates) 14 | 15 | # Initialize xycoord 16 | xycoord = np.zeros(shape=(num_vert, 2)) 17 | num_repeat = 10 * num_vert # number of iterations to calculate xycoord 18 | 19 | # Set big face on unit circle 20 | angle = 2. * np.pi / num_face_vert 21 | 22 | for i in range(num_face_vert): # for each vertex in big face 23 | xycoord[big_face[i]] = [np.cos(angle * i), np.sin(angle * i)] 24 | 25 | # Calculate positions of other vertices through iterative process 26 | for repeat_ID in range(num_repeat): 27 | 28 | for vert_ID in range(num_vert): # For each vertex, 29 | if vert_ID not in big_face: # that's not in big_face, 30 | # move the xycoord of the given vertex to the centerpont 31 | # of all neighboring nodes. 32 | 33 | # # Find vert_ID 34 | find_vert_row, find_vert_col = np.where(edges == vert_ID) 35 | 36 | # # Find neighbors 37 | neighbors = [] 38 | for row, col in zip(find_vert_row, find_vert_col): 39 | find_vert_col_nbr = 1 - col 40 | neighbors.append(edges[row, find_vert_col_nbr]) 41 | neighbors = np.array(neighbors, dtype=np.int) 42 | 43 | # # Get neighbor coords 44 | nbr_coord = xycoord[neighbors, :] 45 | 46 | # # # Find midpoint 47 | num_nbr = len(find_vert_col) 48 | midpt = np.array( 49 | [sum(nbr_coord[:, 0]), sum(nbr_coord[:, 1])] 50 | ) / num_nbr 51 | 52 | # # Store as new xycoord for vert_ID 53 | xycoord[vert_ID, :] = midpt 54 | return xycoord 55 | 56 | 57 | def plot_schlegel(edges, edge_type_graph, xycoord, 58 | schlegel_filename): # pragma: no cover 59 | f = plt.figure(2, figsize=(8, 8)) 60 | f.clf() 61 | plt.xlim((-1.2, 1.2)) 62 | plt.ylim((-1.2, 1.2)) 63 | plt.axis('off') 64 | 65 | for edge in edges: 66 | # Get end vertices 67 | edge_bgn, edge_fin = edge 68 | 69 | # Get end vertex coordinates 70 | x_bgn = xycoord[edge_bgn, 0] 71 | y_bgn = xycoord[edge_bgn, 1] 72 | 73 | x_fin = xycoord[edge_fin, 0] 74 | y_fin = xycoord[edge_fin, 1] 75 | 76 | # Create vectors from beginning vertex to end 77 | x_vec = [x_bgn, x_fin] 78 | y_vec = [y_bgn, y_fin] 79 | 80 | # Only check the edge type if `edge_type_graph` is not None. If it is 81 | # None, default to coloring edges the same as if all edges weren't a 82 | # part of the spanning tree. 83 | if edge_type_graph is not None \ 84 | and (edge_type_graph.edge[edge_bgn][edge_fin]['type'] == 1): 85 | plt.plot(x_vec, y_vec, linestyle='-', color=SKYBLUE, linewidth=5) 86 | else: # if this is a non-tree edge: 87 | plt.plot(x_vec, y_vec, linestyle='-', color=REDPURPLE, linewidth=8) 88 | 89 | # Plot nodes: 90 | plt.plot(xycoord[:, 0], xycoord[:, 1], 'o', 91 | color=VERMILLION, markeredgecolor=VERMILLION, markersize=15) 92 | 93 | # Plot node labels: 94 | for i, node_xy in enumerate(xycoord): 95 | x, y = node_xy 96 | plt.text(x, y, str(i), color=WHITE, fontname='serif', 97 | horizontalalignment='center', verticalalignment='center') 98 | 99 | plt.savefig(schlegel_filename, bbox_inches='tight') 100 | 101 | 102 | def gen_schlegel(edges, coordinates, faces, schlegel_filename, 103 | edge_type_graph=None): # pragma: no cover 104 | """ 105 | Plots vertices and edges in Schlegel diagram, tracing scaffold path in 106 | colored lines. 107 | 108 | The three dimensional structure is mapped onto a 2d surface. This new 109 | surface is visualized, saved, and optionally displayed to screen. Edges 110 | that are a part of the previously calculated spanning tree (that is, the 111 | scaffold path) as marked in `edge_type_graph` are highlighted a different 112 | color. 113 | 114 | Parameters 115 | ---------- 116 | edges : numpy.ndarray 117 | Ex2 matrix where each row corresponds to one edge, denoting the 118 | vertices being connected. 1st column > 2nd column; E = number of edges 119 | coordinates : numpy.ndarray 120 | Vx3 matrix of spatial coordinates of vertices; V = number of vertices. 121 | faces : list 122 | Fx2 cell matrix, where F is the number of faces. The first column 123 | details how many vertices the face has. The second column details the 124 | vertex IDs of the face. 125 | schlegel_filename : str 126 | Filename pointing at where to save the generated plot. 127 | edge_type_graph : networkx.classes.graph.Graph 128 | A graph the links have the 'type' property. That property can have one 129 | of two values: 130 | - 1 is non-spanning tree edge: DX edge with 1 scaffold crossover 131 | - 2 is spanning tree edge: DX edge with 0 scaffold crossovers 132 | 133 | Returns 134 | ------- 135 | xycoords 136 | The 2d mapping used to plot the figure. 137 | """ 138 | 139 | xycoord = create_2d_mapping(edges, coordinates, faces) 140 | 141 | plot_schlegel(edges, edge_type_graph, xycoord, schlegel_filename) 142 | 143 | return xycoord 144 | -------------------------------------------------------------------------------- /pyDAEDALUS/Automated_Design/gen_stap_seq.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | 3 | 4 | def gen_stap_seq(staples, scaf_seq, staple_name, scaf_name, 5 | len_scaf_used): 6 | """ 7 | Generate staple sequences from scaffold sequence. 8 | 9 | Parameters 10 | ---------- 11 | staples : list 12 | List with E rows, each row contains another list. Some sub-lists may 13 | be empty as fragments are combined into full staples. Columns 0-5 14 | contain vertex staples, while 6+ contain edge staples. 15 | scaf_seq : str 16 | String of scaffold, length may be longer than 17 | required. First nucleotide will be placed at index 1 18 | short_name : str 19 | string to name staples, may be same as file_name 20 | scaf_name : str 21 | name of scaffold (string) 22 | len_scaf_used : int 23 | length of scaffold used, = 2*sum(edge_length_vec) 24 | 25 | Returns 26 | ------- 27 | stap_seq 28 | List same dimensions as staples, each cell contains string of 29 | staple's sequence 30 | stap_seq_list 31 | stap_seq arranged in a 1-column list 32 | stap_list 33 | staples arranged in the same 1-column list 34 | named_stap_seq_list 35 | List with second column identical to stap_seq_list, first column 36 | contains string of staple name 37 | """ 38 | 39 | # # Initialize outputs 40 | num_edges = len(staples) 41 | 42 | stap_seq = [] 43 | stap_seq_list = [] 44 | stap_list = [] 45 | named_stap_seq_list = [] 46 | 47 | for edge_ID in range(num_edges): 48 | staps_for_this_edge = [] 49 | for stap_ID in range(len(staples[edge_ID])): 50 | stap = staples[edge_ID][stap_ID] # obtain staple index information 51 | seq = u'' # initialize string 52 | for nt_ID in stap: 53 | # # because A binds to T, and G binds to C... 54 | if (nt_ID is None) or (scaf_seq[nt_ID] == 'A'): 55 | seq += 'T' 56 | elif scaf_seq[nt_ID] == 'T': 57 | seq += 'A' 58 | elif scaf_seq[nt_ID] == 'G': 59 | seq += 'C' 60 | elif scaf_seq[nt_ID] == 'C': 61 | seq += 'G' 62 | elif scaf_seq[nt_ID] == 'U': # in case user inputs RNA seq 63 | seq += 'A' 64 | else: 65 | # Error -- unrecognized nucleotide in scaffold sequence 66 | assert False, 'Unrecognized nucleotide in scaffold sequence' 67 | 68 | staps_for_this_edge.append(seq) 69 | 70 | if seq: # if seq exists (may have been blank) 71 | stap_seq_list.append(seq) # store seq in stap_seq_list 72 | 73 | # # Store seq in named_stap_seq_list. First number is Edge ID, 74 | # # Second is 5' end of staple. Third indicates vertex or edge 75 | # # staple. 76 | if stap_ID <= 3: # Vertex staple 77 | named_stap_seq_a = staple_name + '_{}-{}-V'.format( 78 | edge_ID, stap[0]) 79 | else: # Edge staple 80 | named_stap_seq_a = staple_name + '_{}-{}-E'.format( 81 | edge_ID, stap[0]) 82 | named_stap_seq_b = seq 83 | named_stap_seq_list.append( 84 | [named_stap_seq_a, named_stap_seq_b]) 85 | 86 | stap_list.append(stap) # store stap in stap_list 87 | stap_seq.append(staps_for_this_edge) 88 | 89 | named_stap_seq_list.append([None, None]) 90 | 91 | # # Add sequence of scaffold at end 92 | block_size = 10000 93 | if len_scaf_used > block_size: # now for readabiliy, was for excel limits 94 | num_mults = int(np.floor(float(len_scaf_used) / block_size)) 95 | # leftover = len_scaf_used % 10000 96 | for i in range(num_mults): 97 | start_i = i * block_size 98 | end_i = (i + 1) * block_size 99 | named_stap_seq_a = scaf_name + '_({}-{})'.format(start_i, end_i-1) 100 | named_stap_seq_b = scaf_seq[start_i:end_i] 101 | named_stap_seq_list.append([named_stap_seq_a, named_stap_seq_b]) 102 | 103 | start_i = num_mults * block_size 104 | end_i = len_scaf_used 105 | named_stap_seq_a = scaf_name + '_({}-{})'.format(start_i, end_i-1) 106 | named_stap_seq_b = scaf_seq[start_i:end_i] 107 | named_stap_seq_list.append([named_stap_seq_a, named_stap_seq_b]) 108 | 109 | else: 110 | named_stap_seq_a = scaf_name + '_(0-{})'.format(len_scaf_used-1) 111 | named_stap_seq_b = scaf_seq[:len_scaf_used] 112 | named_stap_seq_list.append([named_stap_seq_a, named_stap_seq_b]) 113 | 114 | return [stap_seq, stap_seq_list, stap_list, named_stap_seq_list] 115 | -------------------------------------------------------------------------------- /pyDAEDALUS/Automated_Design/gen_vert_to_face.py: -------------------------------------------------------------------------------- 1 | 2 | def gen_vert_to_face(num_vert, faces): 3 | 4 | vert_to_face = [[] for i in range(num_vert)] # a list of empty lists 5 | for face_ID in range(len(faces)): 6 | face = faces[face_ID] 7 | for vert_face_ID in face: 8 | vert_to_face[vert_face_ID].append(face_ID) 9 | 10 | return vert_to_face 11 | -------------------------------------------------------------------------------- /pyDAEDALUS/Automated_Design/set_routing_direction.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | from networkx.algorithms.simple_paths import all_simple_paths 3 | 4 | 5 | def pick_longest_path(paths): 6 | return max(list(paths), key=len) 7 | 8 | 9 | def dereference_pseudonodes_in_path(path_with_pseudonodes, pseudo_vert): 10 | path_with_only_real_nodes = [] 11 | for node in path_with_pseudonodes: 12 | dereferenced = pseudo_vert[node] 13 | path_with_only_real_nodes.append(dereferenced) 14 | return path_with_only_real_nodes 15 | 16 | 17 | def check_direction(route_real, vert_to_face, faces): 18 | """ 19 | Since faces are originally given in counterclockwise order, comparing 20 | a sure-to-be-face-part-of-a-face's order to an arbitrary face will let you 21 | know if the current ordering is clockwise or counterclockwise. Return 22 | False if the former and True if the latter. 23 | """ 24 | 25 | # every face has at least three nodes and three is enough to detect 26 | # direction, so only grab first three 27 | first_face_route = np.array(route_real[0:3]) 28 | 29 | # should just have one overlapping face 30 | vtf_1 = vert_to_face[first_face_route[0]] 31 | vtf_2 = vert_to_face[first_face_route[1]] 32 | vtf_3 = vert_to_face[first_face_route[2]] 33 | first_face_ID = set(vtf_1)\ 34 | .intersection(set(vtf_2))\ 35 | .intersection(set(vtf_3)).pop() 36 | 37 | first_face = faces[first_face_ID] 38 | 39 | check_cycle = first_face + first_face 40 | correct_direction = 0 41 | for check in range(len(first_face)): # faces were given initially as 42 | excerpt_to_check = check_cycle[check:(check + 3)] 43 | distance = np.linalg.norm(first_face_route - excerpt_to_check) 44 | if distance == 0: # that is, if there is a match 45 | correct_direction = correct_direction + 1 46 | 47 | # 0->wrong direction. 1->right direction. 2 or more -> should never 48 | assert correct_direction < 2 49 | 50 | if correct_direction == 0: # routing is clockwise, wrong direction 51 | return False 52 | else: 53 | return True 54 | 55 | 56 | def set_routing_direction(edge_type_mat_allNodes, num_vert, pseudo_vert, 57 | faces, vert_to_face): 58 | """ 59 | Sets routing direction for traversing scaffold route path 60 | 61 | Parameters 62 | ---------- 63 | edge_type_mat_allNodes : networkx.classes.digraph.DiGraph 64 | Network representation including link types. Link types have the 65 | following possible values: 66 | -1 is half of a non-spanning tree edge (one side of scaffold 67 | crossover) 68 | 2 is spanning tree edge: DX edge with 0 scaffold crossovers 69 | num_vert : int 70 | number of vertices, V 71 | pseudo_vert : list 72 | row vector where value j at index i indicate that 73 | vertex i corresponds to vertex j, one of the V real vertices 74 | faces : list 75 | List of lists. The first dimension represents the face. The 76 | second dimension holds the index all nodes creating that face. 77 | vert_to_face : list 78 | List of lists. The first dimension represents the node. The 79 | second dimension holds the index of all faces that node is a part of. 80 | 81 | Returns 82 | ------- 83 | route_real 84 | row vector of vertices listed in visitation order (only real vertex 85 | IDs) 86 | route_vals 87 | row vector of edge types, where the value at index j in route_vals is 88 | the edge type of the edge between the vertices route_real(j:j+1), 89 | wrapping around at end 90 | """ 91 | 92 | # Choose a starting connected node (arbitrary start position). 93 | # Vertices #1-#V (V = number of vertices) are no longer connected in the 94 | # graph network 95 | start_node = 2*num_vert+2 # this node is a pseudo-node at Vertex 1 96 | 97 | next_nodes = edge_type_mat_allNodes.neighbors(start_node) # you'll have 2 98 | # TODO: Convert to generator, since you only need to make the second 99 | # path if the first is the wrong direction? 100 | for next_node in next_nodes: 101 | paths = all_simple_paths( 102 | edge_type_mat_allNodes, start_node, next_node) 103 | 104 | # you'll have one 1-length path because they're neighbors. You want 105 | # the other path that includes all the other nodes: 106 | path = pick_longest_path(paths) 107 | 108 | route_real = path 109 | temp_route_real = route_real + [route_real[0]] 110 | route_vals = [edge_type_mat_allNodes 111 | [temp_route_real[i]][temp_route_real[i+1]]['type'] 112 | for i in range(len(route_real))] 113 | 114 | dereferenced_path = dereference_pseudonodes_in_path(path, pseudo_vert) 115 | route_real = dereferenced_path 116 | 117 | if check_direction(route_real, vert_to_face, faces): 118 | # For consistency, start routing at a tree edge (route_vals = 2) 119 | start_route_list=[] 120 | for i in range(len(route_real)): 121 | if route_real[i] == 0 and route_vals[i] == 2: 122 | start_route_list.append(i) 123 | start_route = start_route_list[0] # in case there are multiple choices 124 | # 125 | # Shift route_real and route_vals to start at start_route 126 | route_real = route_real[start_route:] + route_real[:start_route] 127 | route_vals = route_vals[start_route:] + route_vals[:start_route] 128 | return [route_real, route_vals] 129 | 130 | raise Exception("one of the two above should have returned") 131 | -------------------------------------------------------------------------------- /pyDAEDALUS/Automated_Design/split_edge.py: -------------------------------------------------------------------------------- 1 | def split_edge(edge_type_mat): 2 | """ 3 | Add two nodes for each nontree edge to implement scaffold crossovers. 4 | Added nodes (pseudo-vertices) have a reference vertex (one of the V real 5 | vertices) to maintain relative spatial coordinates among all 6 | vertices. 7 | 8 | Parameters 9 | ---------- 10 | edge_type_mat : networkx.classes.digraph.DiGraph 11 | sparse matrix where 12 | 1 is non-spanning tree edge: DX edge with 1 scaffold crossover 13 | 2 is spanning tree edge: DX edge with 0 scaffold crossovers 14 | Returns 15 | ------- 16 | edge_type_mat_wHalfs 17 | VxV sparse matrix where 18 | -1 is half of a non-spanning tree edge (one side of scaffold 19 | crossover) 20 | 2 is spanning tree edge: DX edge with 0 scaffold crossovers 21 | pseudo_vert 22 | row vector where value j at index i indicate that vertex i corresponds 23 | to vertex j, one of the V real vertices 24 | """ 25 | # # Initialize output variables. These will be augmented from input vars 26 | edge_type_mat_wHalfs = edge_type_mat.copy() 27 | 28 | # Start with known nodes. Pseudo nodes added to graph as needed. 29 | pseudo_vert = edge_type_mat_wHalfs.nodes() 30 | 31 | non_tree_edges = [edge for edge in edge_type_mat.edges(data=True) 32 | if edge[2]['type'] == 1] 33 | 34 | # # ID non-tree edges (value 1), replace with 2 half-edges (value = -1) 35 | # edges = edge_type_mat.edges() 36 | # for i in range(num_vert): 37 | # for j in range(num_vert): 38 | # if (i, j) in edges: 39 | # properties = edge_type_mat[i][j] 40 | # if properties['type'] == 1: 41 | # !! replace the next two lines with the above 6 if you want an exact 42 | # match with the matlab code. (else, order of pseudonodes not assured) 43 | for edge in non_tree_edges: 44 | i, j, properties = edge 45 | # `i` is the node that stays. `j` is cut off and replaced by pseudo 46 | # vert. Since this digraph was built from a graph, a link from 2, 3 47 | # will also have a link from 3, 2. Meaning in the 2, 3 case, you'll 48 | # keep 2 and replace 3. And in teh 3, 2 case, you'll keep 3 and 49 | # replace 2. 50 | 51 | index_of_new_vert = len(pseudo_vert) 52 | properties['type'] = -1 53 | 54 | pseudo_vert.append(j) # vert_list[new_node_id] = original_node_id 55 | edge_type_mat_wHalfs.remove_edge(i, j) 56 | 57 | edge_type_mat_wHalfs.add_node(index_of_new_vert) 58 | edge_type_mat_wHalfs.add_edge(i, index_of_new_vert, 59 | attr_dict=properties) 60 | edge_type_mat_wHalfs.add_edge(index_of_new_vert, i, 61 | attr_dict=properties) 62 | 63 | return edge_type_mat_wHalfs, pseudo_vert 64 | -------------------------------------------------------------------------------- /pyDAEDALUS/Automated_Design/split_vert.py: -------------------------------------------------------------------------------- 1 | from Automated_Design.arrange_neighbors import arrange_neighbors 2 | 3 | 4 | def split_vert(edge_type_mat_wHalfs, pseudo_vert, num_vert, vert_to_face): 5 | """ 6 | Splits vertices into N nodes, where N is the degree of the vertex. 7 | 8 | Parameters 9 | ---------- 10 | edge_type_mat_wHalfs : networkx.classes.digraph.DiGraph 11 | VxV sparse matrix where 12 | -1 is half of a non-spanning tree edge (one side of scaffold 13 | crossover) 14 | 2 is spanning tree edge: DX edge with 0 scaffold crossovers 15 | pseudo_vert : list 16 | row vector where value j at index i indicate that 17 | vertex i corresponds to vertex j, one of the V real vertices 18 | num_vert : int 19 | number of vertices, V 20 | vert_to_face : list 21 | Vx1 cell array, each row has a row vector listing the face IDs the 22 | particular vertex belongs to 23 | 24 | Returns 25 | ------- 26 | edge_type_mat_allNodes 27 | sparse matrix where 28 | -1 is half of a non-spanning tree edge (one side of scaffold 29 | crossover) 30 | 2 is spanning tree edge: DX edge with 0 scaffold crossovers 31 | pseudo_vert 32 | updated to include new pseudo-vertices 33 | """ 34 | 35 | # # Initialize edge_type_mat_allNodes. It will be augmented from _wHalfs 36 | edge_type_mat_allNodes = edge_type_mat_wHalfs.copy() 37 | 38 | # # Initialize face_storage matrix for pseudo nodes added in this function 39 | face_assign = [None] * len(pseudo_vert) 40 | 41 | for vert_ID in range(num_vert): # for each real vertex 42 | neighbors = edge_type_mat_allNodes.in_edges(vert_ID, data=True) 43 | 44 | # # arrange_neighbors identifies which neighboring vertices share faces 45 | # # and adds nodes at the vertex to route the scaffold around the 46 | # # vertex vert_ID accordingly 47 | edge_type_mat_allNodes, pseudo_vert, face_assign = arrange_neighbors( 48 | edge_type_mat_allNodes, pseudo_vert, vert_ID, neighbors, 49 | vert_to_face, face_assign) 50 | return edge_type_mat_allNodes, pseudo_vert 51 | -------------------------------------------------------------------------------- /pyDAEDALUS/Automated_Design/util.py: -------------------------------------------------------------------------------- 1 | import networkx as nx 2 | import numpy as np 3 | 4 | 5 | def generate_graph(num_vert, edges, edge_length_vec): 6 | graph = nx.Graph() 7 | for n in range(num_vert): 8 | graph.add_node(n) 9 | for edge, length in zip(edges, edge_length_vec): 10 | graph.add_edge(edge[0], edge[1], length=float(length)) 11 | # TODO: verify the length property is not used as 'weight' in 12 | # spanning tree alg. 13 | 14 | return graph 15 | 16 | 17 | def intersect_lists(a, b): 18 | # in case `a` and `b` are np.arrays: 19 | if type(a) == np.ndarray: 20 | a = list(a.flatten()) 21 | if type(b) == np.ndarray: 22 | b = list(b.flatten()) 23 | 24 | # TODO: rewrite in a way that preverves order they're seen in? 25 | 26 | thing = set(a).intersection(set(b)) 27 | return sorted(list(thing)) 28 | 29 | 30 | def find(iterable, val): 31 | # A close-enough-to-a-match to matlab's `find` function. Ideally, usage of 32 | # this function will be refactored out. 33 | 34 | # Some times, data comes in as an array. Directly computing array equality 35 | # breaks, so they first need converted over to iterables. 36 | # If arrays, it is assumed the iterable is two dimensions and val is one. 37 | 38 | if type(iterable) == np.ndarray: 39 | iterable = [list(item) for item in iterable] 40 | if type(val) == np.ndarray: 41 | val = list(val) 42 | 43 | return [i for i in range(len(iterable)) if iterable[i] == val] 44 | -------------------------------------------------------------------------------- /pyDAEDALUS/Automated_Design/xx_ConstArchive/constants_20190803.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | 3 | 4 | SCAF_SEQ = 'GAGCGCAACGCAATTAATGTGCGCCCTGTAGCGGCGCATTAAGCGCGGCGGGTGTGGTGGTTACGCGCAGCGTGACCGCTACACTTGCCAGCGCCCTAGCGCCCGCTCCTTTCGCTTTCTTCCCTTCCTTTCTCGCCACGTTCGCCGGCTTTCCCCGTCAAGCTCTAAATCGGGGGCTCCCTTTAGGGTTCCGATTTAGTGCTTTACGGCACCTCGACCCCAAAAAACTTGATTAGGGTGATGGTTCACGTAGTGGGCCATCGCCCTGATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTTAATAGTGGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGTCTATTCTTTTGATTTATAAGGGATTTTGCCGATTTCGGCCTATTGGTTAAAAAATGAGCTGATTTAACAAAAATTTAACGCGAATTACAACCGGGGTACATATGATTGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAtAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAATACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGGTTATTGTCTCATGAGCGGATACATATTTGAATGTATTTAGAAAAATAAACAAATAGGGGTTCCGCGCACATTTCCCCGAAAAGTGCCACCTGACGTCTAAGAAACCATTATTATCATGACATTAACCTATAAAAATAGGCGTATCACGAGGCCCTTTCGTCGAATTCGTCGTCGTCCCCTCAAACTCTTGGGTGGAGAGGCTATTCGTTTAAGGTCACATCGCATGTAATTTACTTATTCTCTGTTGTTGAGCCACCCGGGCGCCAGATTTTGTTTAAAGCTTTGTCTCTTAGTTTGTATAGACAGATTCAGAGTGCAAGGTTTCGTTCGCTCGTACCTGGTTTTCCCTGGTTCTTCACAGATAGGATTTGACTTTCTACAACACTTATGCGGCTTCCTACCCGTTTGAAGGCCGATACAGGTGCTGCGCAAAATGCGGGCGAACATAGAGTATCAAAACAACGCCTTCTAATCTAGGAATATAGGGAAGATACGTATTTGCTACCATGCTTTCTTGGGTCATTAACGACCAACCTCTTTTCTTTTAAAGTAGGATTGCACAATGAATGAATACACGTGGTCCGATAACTGACCAAGTAACATGGTTATCACTaGATGTCCGCCAGACGTGTGCAAACCAACCCGGGAGTTACGTCACTAATCCTTCGCTACGTCGTGAAGATATTTACTTGTGAATATCGAGGGTAATAAGATAATAGACTGTGACTAGTATTGCCAGACTGTCGCTACCTGCAACACATAACTATCCTGAGGTTACTGCATAGTACTGATTACACCCGAGTCAAAATTTCTAACTTCTAACATGTACCTAGTAACCAGCTCAATAATTATGTCAGAATATAGCTCTGGGAACCCTCGGACAATTATGATACACGGTATTAATATCTTGCTTGCGTTAGCCACTTCTCATCTTTGGATACCGATTCTATTTTGCATAGCAGTTCCTTTTACACATATAAGAATTTCGCCATAGGTATGCTGCAG' # noqa: E501 5 | 6 | 7 | # Colors: 8 | VERMILLION = tuple(np.array([213, 94, 0], dtype=np.float) / 255) 9 | REDPURPLE = tuple(np.array([204, 121, 167], dtype=np.float) / 255) 10 | SKYBLUE = tuple(np.array([86, 180, 233], dtype=np.float) / 255) 11 | WHITE = tuple(np.array([255, 255, 255], dtype=np.float) / 255) 12 | BLU = tuple(np.array([0, 114, 178], dtype=np.float) / 255) 13 | ORANG = tuple(np.array([230, 159, 0], dtype=np.float) / 255) 14 | -------------------------------------------------------------------------------- /pyDAEDALUS/Automated_Design/xx_ConstArchive/constants_23S5S.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | 3 | SCAF_SEQ = 'GGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACTCTGAAGTGAAACATCTTCGGGTTGTGAGGTTAAGCGACTAAGCGTACACGGTGGATGCCCTGGCAGTCAGAGGCGATGAAGGACGTGCTAATCTGCGATAAGCGTCGGTAAGGTGATATGAACCGTTATAACCGGCGATTTCCGAATGGGGAAACCCAGTGTGTTTCGACACACTATCATTAACTGAATCCATAGGTTAATGAGGCGAACCGGGGGAACTGAAACATCTAAGTACCCCGAGGAAAAGAAATCAACCGAGATTCCCCCAGTAGCGGCGAGCGAACGGGGAGCAGCCCAGAGCCTGAATCAGTGTGTGTGTTAGTGGAAGCGTCTGGAAAGGCGCGCGATACAGGGTGACAGCCCCGTACACAAAAATGCACATGCTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGACCATCCTCCAAGGCTAAATACTCCTGACTGACCGATAGTGAACCAGTACCGTGAGGGAAAGGCGAAAAGAACCCCGGCGAGGGGAGTGAAAAAGAACCTGAAACCGTGTACGTACAAGCAGTGGGAGCACGCTTAGGCGTGTGACTGCGTACCTTTTGTATAATGGGTCAGCGACTTATATTCTGTAGCAAGGTTAACCGAATAGGGGAGCCGAAGGGAAACCGAGTCTTAACTGGGCGTTAAGTTGCAGGGTATAGACCCGAAACCCGGTGATCTAGCCATGGGCAGGTTGAAGGTTGGGTAACACTAACTGGAGGACCGAACCGACTAATGTTGAAAAATTAGCGGATGACTTGTGGCTGGGGGTGAAAGGCCAATCAAACCGGGAGATAGCTGGTTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGAATTCATCTCCGGGGGTAGAGCACTGTTTCGGCAAGGGGGTCATCCCGACTTACCAACCCGATGCAAACTGCGAATACCGGAGAATGTTATCACGGGAGACACACGGCGGGTGCTAACGTCCGTCGTGAAGAGGGAAACAACCCAGACCGCCAGCTAAGGTCCCAAAGTCATGGTTAAGTGGGAAACGATGTGGGAAGGCCCAGACAGCCAGGATGTTGGCTTAGAAGCAGCCATCATTTAAAGAAAGCGTAATAGCTCACTGGTCGAGTCGGCCTGCGCGGAAGATGTAACGGGGCTAAACCATGCACCGAAGCTGCGGCAGCGACGCTTATGCGTTGTTGGGTAGGGGAGCGTTCTGTAAGCCTGCGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCGGGGCAGGGTGAGTCGACCCCTAAGGCGAGGCCGAAAGGCGTAGTCGATGGGAAACAGGTTAATATTCCTGTACTTGGTGTTACTGCGAAGGGGGGACGGAGAAGGCTATGTTGGCCGGGCGACGGTTGTCCCGGTTTAAGCGTGTAGGCTGGTTTTCCAGGCAAATCCGGAAAATCAAGGCTGAGGCGTGATGACGAGGCACTACGGTGCTGAAGCAACAAATGCCCTGCTTCCAGGAAAAGCCTCTAAGCATCAGGTAACATCAAATCGTACCCCAAACCGACACAGGTGGTCAGGTAGAGAATACCAAGGCGCTTGAGAGAACTCGGGTGAAGGAACTAGGCAAAATGGTGCCGTAACTTCGGGAGAAGGCACGCTGATATGTAGGTGAAGCGACTTGCTCGTGGAGCTGAAATCAGTCGAAGATACCAGCTGGCTGCAACTGTTTATTAAAAACACAGCACTGTGCAAACACGAAAGTGGACGTATACGGTGTGACGCCTGCCCGGTGCCGGAAGGTTAATTGATGGGGTTAGCGCAAGCGAAGCTCTTGATCGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAATGATGGCCAGGCTGTCTCCACCCGAGACTCAGTGAAATTGAACTCGCTGTGAAGATGCAGTGCTGGAGAACTGAGGGGGGCTGCTCCTAGTACGAGAGGACCGGAGTGGACGCATCACTGGTGTTCGGGTTGTCATGCCAATGGCACTGCCCGGTAGCTAAATGCGGAAGAGATAAGTGCTGAAAGCATCTAAGCACGAAACTTGCCCCGAGATGAGTTCTCCCTGACCCTTTAAGGGTCCTGAAGGAACGTTGAAGACGACGACGTTGATAGGCCGGGTGTGTAAGCGCAGCGATGCGTTGAGCTAACCGGTACTAATGAACCGTGAGGCTTAACCTTACAACGCCGAAGCTGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATAAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCACATCTTTTATCTACATC' 4 | 5 | # Colors: 6 | VERMILLION = tuple(np.array([213, 94, 0], dtype=np.float) / 255) 7 | REDPURPLE = tuple(np.array([204, 121, 167], dtype=np.float) / 255) 8 | SKYBLUE = tuple(np.array([86, 180, 233], dtype=np.float) / 255) 9 | WHITE = tuple(np.array([255, 255, 255], dtype=np.float) / 255) 10 | BLU = tuple(np.array([0, 114, 178], dtype=np.float) / 255) 11 | ORANG = tuple(np.array([230, 159, 0], dtype=np.float) / 255) 12 | -------------------------------------------------------------------------------- /pyDAEDALUS/Automated_Design/xx_ConstArchive/constants_EGFP.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | 3 | 4 | SCAF_SEQ = 'AAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTACGGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGACAACCACTACCTGAGCACCCAGTCCGCCCTGAGCAAAGACCCCAACGAGAAGCGCGATCACATGGTCCTGCTGGAGTTCGTGACCGCCGCCGGGATCACTCTCGGCATGGACGAGCTGTACAAGTAACTGCAGGCATGCAAGCTTGGCGTAATCATGGTCATAGCTGTTTCCTGTGTGAAATTGTTATCCGCTCACAATTCCACACAA' 5 | 6 | 7 | # Colors: 8 | VERMILLION = tuple(np.array([213, 94, 0], dtype=np.float) / 255) 9 | REDPURPLE = tuple(np.array([204, 121, 167], dtype=np.float) / 255) 10 | SKYBLUE = tuple(np.array([86, 180, 233], dtype=np.float) / 255) 11 | WHITE = tuple(np.array([255, 255, 255], dtype=np.float) / 255) 12 | BLU = tuple(np.array([0, 114, 178], dtype=np.float) / 255) 13 | ORANG = tuple(np.array([230, 159, 0], dtype=np.float) / 255) 14 | -------------------------------------------------------------------------------- /pyDAEDALUS/Automated_Design/xx_ConstArchive/constants_old_old.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | 3 | 4 | SCAF_SEQ = 'AAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTACGGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGACAACCACTACCTGAGCACCCAGTCCGCCCTGAGCAAAGACCCCAACGAGAAGCGCGATCACATGGTCCTGCTGGAGTTCGTGACCGCCGCCGGGATCACTCTCGGCATGGACGAGCTGTACAAGTAACTGCAGGCATGCAAGCTTGGCGTAATCATGGTCATAGCTGTTTCCTGTGTGAAATTGTTATCCGCTCACAATTCCACACAA' 5 | 6 | 7 | # Colors: 8 | VERMILLION = tuple(np.array([213, 94, 0], dtype=np.float) / 255) 9 | REDPURPLE = tuple(np.array([204, 121, 167], dtype=np.float) / 255) 10 | SKYBLUE = tuple(np.array([86, 180, 233], dtype=np.float) / 255) 11 | WHITE = tuple(np.array([255, 255, 255], dtype=np.float) / 255) 12 | BLU = tuple(np.array([0, 114, 178], dtype=np.float) / 255) 13 | ORANG = tuple(np.array([230, 159, 0], dtype=np.float) / 255) 14 | -------------------------------------------------------------------------------- /pyDAEDALUS/Automated_Design/xx_ConstArchive/constants_old_old_old.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | 3 | SCAF_SEQ = 'GGATCAAGCTGAAAATTGAAACACTGAACAACGAAAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACTCTGAAGTGAAACATCTTCGGGTTGTGAGGTTAAGCGACTAAGCGTACACGGTGGATGCCCTGGCAGTCAGAGGCGATGAAGGACGTGCTAATCTGCGATAAGCGTCGGTAAGGTGATATGAACCGTTATAACCGGCGATTTCCGAATGGGGAAACCCAGTGTGTTTCGACACACTATCATTAACTGAATCCATAGGTTAATGAGGCGAACCGGGGGAACTGAAACATCTAAGTACCCCGAGGAAAAGAAATCAACCGAGATTCCCCCAGTAGCGGCGAGCGAACGGGGAGCAGCCCAGAGCCTGAATCAGTGTGTGTGTTAGTGGAAGCGTCTGGAAAGGCGCGCGATACAGGGTGACAGCCCCGTACACAAAAATGCACATGCTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGACCATCCTCCAAGGCTAAATACTCCTGACTGACCGATAGTGAACCAGTACCGTGAGGGAAAGGCGAAAAGAACCCCGGCGAGGGGAGTGAAAAAGAACCTGAAACCGTGTACGTACAAGCAGTGGGAGCACGCTTAGGCGTGTGACTGCGTACCTTTTGTATAATGGGTCAGCGACTTATATTCTGTAGCAAGGTTAACCGAATAGGGGAGCCGAAGGGAAACCGAGTCTTAACTGGGCGTTAAGTTGCAGGGTATAGACCCGAAACCCGGTGATCTAGCCATGGGCAGGTTGAAGGTTGGGTAACACTAACTGGAGGACCGAACCGACTAATGTTGAAAAATTAGCGGATGACTTGTGGCTGGGGGTGAAAGGCCAATCAAACCGGGAGATAGCTGGTTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGAATTCATCTCCGGGGGTAGAGCACTGTTTCGGCAAGGGGGTCATCCCGACTTACCAACCCGATGCAAACTGCGAATACCGGAGAATGTTATCACGGGAGACACACGGCGGGTGCTAACGTCCGTCGTGAAGAGGGAAACAACCCAGACCGCCAGCTAAGGTCCCAAAGTCATGGTTAAGTGGGAAACGATGTGGGAAGGCCCAGACAGCCAGGATGTTGGCTTAGAAGCAGCCATCATTTAAAGAAAGCGTAATAGCTCACTGGTCGAGTCGGCCTGCGCGGAAGATGTAACGGGGCTAAACCATGCACCGAAGCTGCGGCAGCGACGCTTATGCGTTGTTGGGTAGGGGAGCGTTCTGTAAGCCTGCGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCGGGGCAGGGTGAGTCGACCCCTAAGGCGAGGCCGAAAGGCGTAGTCGATGGGAAACAGGTTAATATTCCTGTACTTGGTGTTACTGCGAAGGGGGGACGGAGAAGGCTATGTTGGCCGGGCGACGGTTGTCCCGGTTTAAGCGTGTAGGCTGGTTTTCCAGGCAAATCCGGAAAATCAAGGCTGAGGCGTGATGACGAGGCACTACGGTGCTGAAGCAACAAATGCCCTGCTTCCAGGAAAAGCCTCTAAGCATCAGGTAACATCAAATCGTACCCCAAACCGACACAGGTGGTCAGGTAGAGAATACCAAGGCGCTTGAGAGAACTCGGGTGAAGGAACTAGGCAAAATGGTGCCGTAACTTCGGGAGAAGGCACGCTGATATGTAGGTGAAGCGACTTGCTCGTGGAGCTGAAATCAGTCGAAGATACCAGCTGGCTGCAACTGTTTATTAAAAACACAGCACTGTGCAAACACGAAAGTGGACGTATACGGTGTGACGCCTGCCCGGTGCCGGAAGGTTAATTGATGGGGTTAGCGCAAGCGAAGCTCTTGATCGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAATGATGGCCAGGCTGTCTCCACCCGAGACTCAGTGAAATTGAACTCGCTGTGAAGATGCAGTGCTGGAGAACTGAGGGGGGCTGCTCCTAGTACGAGAGGACCGGAGTGGACGCATCACTGGTGTTCGGGTTGTCATGCCAATGGCACTGCCCGGTAGCTAAATGCGGAAGAGATAAGTGCTGAAAGCATCTAAGCACGAAACTTGCCCCGAGATGAGTTCTCCCTGACCCTTTAAGGGTCCTGAAGGAACGTTGAAGACGACGACGTTGATAGGCCGGGTGTGTAAGCGCAGCGATGCGTTGAGCTAACCGGTACTAATGAACCGTGAGGCTTAACCTTACAACGCCGAAGCTGTTTTGGCGGATGAGAGAAGATTTTCAGCCTGATACAGATTAAATCAGAACGCAGAAGCGGTCTGATAAAACAGAATTTGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCACATCTTTTATCTACATC' 4 | 5 | # Colors: 6 | VERMILLION = tuple(np.array([213, 94, 0], dtype=np.float) / 255) 7 | REDPURPLE = tuple(np.array([204, 121, 167], dtype=np.float) / 255) 8 | SKYBLUE = tuple(np.array([86, 180, 233], dtype=np.float) / 255) 9 | WHITE = tuple(np.array([255, 255, 255], dtype=np.float) / 255) 10 | BLU = tuple(np.array([0, 114, 178], dtype=np.float) / 255) 11 | ORANG = tuple(np.array([230, 159, 0], dtype=np.float) / 255) 12 | -------------------------------------------------------------------------------- /pyDAEDALUS/Automated_Design/xx_ConstArchive/constants_rPB66rRNA: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | 3 | 4 | SCAF_SEQ = 'GCCCTGGCAGTCAGAGGCGATGAAGGACGTGCTAATCTGCGATAAGCGTCGGTAAGGTGATATGAACCGTTATAACCGGCGATTTCCGAATGGGGAAACCCAGTGTGTTTCGACACACTATCATTAACTGAATCCATAGGTTAATGAGGCGAACCGGGGGAACTGAAACATCTAAGTACCCCGAGGAAAAGAAATCAACCGAGATTCCCCCAGTAGCGGCGAGCGAACGGGGAGCAGCCCAGAGCCTGAATCAGTGTGTGTGTTAGTGGAAGCGTCTGGAAAGGCGCGCGATACAGGGTGACAGCCCCGTACACAAAAATGCACATGCTGTGAGCTCGATGAGTAGGGCGGGACACGTGGTATCCTGTCTGAATATGGGGGGACCATCCTCCAAGGCTAAATACTCCTGACTGACCGATAGTGAACCAGTACCGTGAGGGAAAGGCGAAAAGAACCCCGGCGAGGGGAGTGAAAAAGAACCTGAAACCGTGTACGTACAAGCAGTGGGAGCACGCTTAGGCGTGTGACTGCGTACCTTTTGTATAATGGGTCAGCGACTTATATTCTGTAGCAAGGTTAACCGAATAGGGGAGCCGAAGGGAAACCGAGTCTTAACTGGGCGTTAAGTTGCAGGGTATAGACCCGAAACCCGGTGATCTAGCCATGGGCAGGTTGAAGGTTGGGTAACACTAACTGGAGGACCGAACCGACTAATGTTGAAAAATTAGCGGATGACTTGTGGCTGGGGGTGAAAGGCCAATCAAACCGGGAGATAGCTGGTTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGAATTCATCTCCGGGGGTAGAGCACTGTTTCGGCAAGGGGGTCATCCCGACTTACCAACCCGATGCAAACTGCGAATACCGGAGAATGTTATCACGGGAGACACACGGCGGGTGCTAACGTCCGTCGTGAAGAGGGAAACAACCCAGACCGCCAGCTAAGGTCCCAAAGTCATGGTTAAGTGGGAAACGATGTGGGAAGGCCCAGACAGCCAGGATGTTGGCTTAGAAGCAGCCATCATTTAAAGAAAGCGTAATAGCTCACTGGTCGAGTCGGCCTGCGCGGAAGATGTAACGGGGCTAAACCATGCACCGAAGCTGCGGCAGCGACGCTTATGCGTTGTTGGGTAGGGGAGCGTTCTGTAAGCCTGCGAAGGTGTGCTGTGAGGCATGCTGGAGGTATCAGAAGTGCGAATGCTGACATAAGTAACGATAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCGGGGCAGGGTGAGTCGACCCCTAAGGCGAGGCCGAAAGGCGTAGTCGATGGGAAACAGGTTAATATTCCTGTACTTGGTGTTACTGCGAAGGGGGGACGGAGAAGGCTATGTTGGCCGGGCGACGGTTGTCCCGGTTTAAGCGTGTAGGCTGGTTTTCCAGGCAAATCCGGAAAATCAAGGCTGAGGCGTGATGACGAGGCACTACGGTGCTGAAGCAACAAATGCCCTGCTTCCAGGAAAAGCCTCTAAGCATCAGGTAACATCAAATCGTACCCCAAACCGACACAGGTGGTCAGGTAGAGAATACCAAGGCGCTTGAGAGAACTCGGGTGAAGGAACTAGGCAAAATGGTGCCGTAACTTCGGGAGAAGGCACGCTGATATGTAGGTGAAGCGACTTGCTCGTGGAGCTGAAATCAGTCGAAGATACCAGCTGGCTGCAACTGTTTATTAAAAACACAGCACTGTGCAAACACGAAAGTGGACGTATACGGTGTGACGCCTGCCCGGTGCCGGAAGGTTAATTGATGGGGTTAGCGCAAGCGAAGCTCTTGATCGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAATGATGGCCAGGCTGTCTCCACCCGAGACTCA' # noqa: E501 5 | 6 | 7 | # Colors: 8 | VERMILLION = tuple(np.array([213, 94, 0], dtype=np.float) / 255) 9 | REDPURPLE = tuple(np.array([204, 121, 167], dtype=np.float) / 255) 10 | SKYBLUE = tuple(np.array([86, 180, 233], dtype=np.float) / 255) 11 | WHITE = tuple(np.array([255, 255, 255], dtype=np.float) / 255) 12 | BLU = tuple(np.array([0, 114, 178], dtype=np.float) / 255) 13 | ORANG = tuple(np.array([230, 159, 0], dtype=np.float) / 255) 14 | -------------------------------------------------------------------------------- /pyDAEDALUS/DAEDserve.py: -------------------------------------------------------------------------------- 1 | from SimpleXMLRPCServer import SimpleXMLRPCServer 2 | import xmlrpclib 3 | import shutil 4 | import sys 5 | from math import floor 6 | from os import listdir, path, makedirs 7 | from Automated_Design.ply_to_input import ply_to_input 8 | from Automated_Design.DX_cage_design import DX_cage_design 9 | from Automated_Design.gen_PDB import pdbgen 10 | 11 | # class daedalusRPC(object): 12 | 13 | def calc(pName, helicalForm, helicalTurns, plyfile, seqfile): 14 | if not path.exists(pName): 15 | makedirs(pName) 16 | hMult=int(helicalTurns) 17 | hF=str(helicalForm) 18 | pFile=str(plyfile) 19 | sFile=str(seqfile) 20 | if hF=='Aform': 21 | # staple crossover asymmetry, 11 nt/helical turn 22 | minEdgeLen=hMult*11 23 | hForm=True 24 | twist=1 25 | elif hF=='Bform': 26 | # no asymmetry in staple or scaffold crossovers, 10.5 nt/helical turn 27 | minEdgeLen=floor(hMult*10.5) 28 | hForm=False 29 | twist=1 30 | elif hF=='Hybrid': 31 | # no asymmetry in staple or scaffold crossovers, 10.5 nt/helical turn 32 | minEdgeLen=hMult*11 33 | hForm=True 34 | twist=2 35 | elif hF=="Twisted": 36 | # scaffold crossover asymmetry in opposite direction, 11 nt/helical turn 37 | minEdgeLen=hMult*11 38 | hForm=True 39 | twist=3 40 | coordinates, edges, faces, edge_length_vec, file_name, \ 41 | staple_name, singleXOs = ply_to_input( 42 | str(pFile), str(pName), minEdgeLen, hForm) 43 | if (sFile=='M13.txt'): 44 | scaf_seq = [] 45 | scaf_name = [] 46 | else: 47 | scaf_name = str(pName) 48 | fSeq=open(sFile,'r') 49 | scaf_seq='' 50 | for lines in fSeq: 51 | scaf_seq=scaf_seq+lines.strip() 52 | scaf_seq = scaf_seq.upper() # Force scaffold sequence to be uppercase 53 | full_file_name = DX_cage_design( # noqa: F841 54 | coordinates, edges, faces, edge_length_vec, file_name, 55 | staple_name, singleXOs, scaf_seq, scaf_name, hForm, str(pName), 56 | twist, print_to_console=False) 57 | pdbout = pdbgen(full_file_name, hForm, str(pName)) 58 | return "Finished!" 59 | # 60 | server = SimpleXMLRPCServer(("localhost", 4242)) 61 | server.register_multicall_functions() 62 | server.register_function(calc, "calc") 63 | server.serve_forever() 64 | -------------------------------------------------------------------------------- /pyDAEDALUS/EGFP_seq.txt: -------------------------------------------------------------------------------- 1 | AAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTACGGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGACAACCACTACCTGAGCACCCAGTCCGCCCTGAGCAAAGACCCCAACGAGAAGCGCGATCACATGGTCCTGCTGGAGTTCGTGACCGCCGCCGGGATCACTCTCGGCATGGACGAGCTGTACAAGTAACTGCAGGCATGCAAGCTTGGCGTAATCATGGTCATAGCTGTTTCCTGTGTGAAATTGTTATCCGCTCACAATTCCACACAA 2 | -------------------------------------------------------------------------------- /pyDAEDALUS/InstructionsForUse.txt: -------------------------------------------------------------------------------- 1 | *** To start the backend python process *** 2 | 3 | If needed, install anaconda2 4 | (https://www.anaconda.com/distribution/#download-section) 5 | 6 | Use the anaconda2 python2 program to start a backend instance: 7 | python2 DAEDserve.py 8 | 9 | Optionally compile to a binary (note: use the pip that is part of the anaconda2 package): 10 | pip install pyinstaller 11 | Mac: pyinstaller -Fc --hiddenimport _sysconfigdata DAEDserve.py 12 | Win: pyinstaller -Fc DAEDserve.py 13 | 14 | The executable is built in the dist folder, where it could just be double-clicked to execute 15 | 16 | The server can be tested using "python2 testServer.py" in a separate command window. 17 | 18 | *** To use the GUI *** 19 | 20 | Navigate to either the pyDAEDALUSX windows or Darwin (mac) folder and double click the pyDAEDALUSX application. -------------------------------------------------------------------------------- /pyDAEDALUS/images/DX_Aform.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lcbb/pyDAEDALUS/139f47bb27144a5121d8218a8fa4a61e9ae05832/pyDAEDALUS/images/DX_Aform.png -------------------------------------------------------------------------------- /pyDAEDALUS/images/DX_Aform_old.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lcbb/pyDAEDALUS/139f47bb27144a5121d8218a8fa4a61e9ae05832/pyDAEDALUS/images/DX_Aform_old.png -------------------------------------------------------------------------------- /pyDAEDALUS/images/DX_Altform.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lcbb/pyDAEDALUS/139f47bb27144a5121d8218a8fa4a61e9ae05832/pyDAEDALUS/images/DX_Altform.png -------------------------------------------------------------------------------- /pyDAEDALUS/images/DX_Bform.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lcbb/pyDAEDALUS/139f47bb27144a5121d8218a8fa4a61e9ae05832/pyDAEDALUS/images/DX_Bform.png -------------------------------------------------------------------------------- /pyDAEDALUS/images/DX_Hform.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lcbb/pyDAEDALUS/139f47bb27144a5121d8218a8fa4a61e9ae05832/pyDAEDALUS/images/DX_Hform.png -------------------------------------------------------------------------------- /pyDAEDALUS/images/DXedges.key: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lcbb/pyDAEDALUS/139f47bb27144a5121d8218a8fa4a61e9ae05832/pyDAEDALUS/images/DXedges.key -------------------------------------------------------------------------------- /pyDAEDALUS/images/icon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lcbb/pyDAEDALUS/139f47bb27144a5121d8218a8fa4a61e9ae05832/pyDAEDALUS/images/icon.png -------------------------------------------------------------------------------- /pyDAEDALUS/index.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | pyDAEDALUS-X 6 | 7 | 8 | 9 | 10 |
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49 | 50 | 51 | 52 | 53 | 54 | 55 | -------------------------------------------------------------------------------- /pyDAEDALUS/js/jquery-xmlrpc-master.zip: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lcbb/pyDAEDALUS/139f47bb27144a5121d8218a8fa4a61e9ae05832/pyDAEDALUS/js/jquery-xmlrpc-master.zip -------------------------------------------------------------------------------- /pyDAEDALUS/js/jquery-xmlrpc-master/.gitignore: -------------------------------------------------------------------------------- 1 | bower_components/ 2 | -------------------------------------------------------------------------------- /pyDAEDALUS/js/jquery-xmlrpc-master/LICENCE: -------------------------------------------------------------------------------- 1 | This is free and unencumbered software released into the public domain. 2 | 3 | Anyone is free to copy, modify, publish, use, compile, sell, or 4 | distribute this software, either in source code form or as a compiled 5 | binary, for any purpose, commercial or non-commercial, and by any 6 | means. 7 | 8 | In jurisdictions that recognize copyright laws, the author or authors 9 | of this software dedicate any and all copyright interest in the 10 | software to the public domain. We make this dedication for the benefit 11 | of the public at large and to the detriment of our heirs and 12 | successors. We intend this dedication to be an overt act of 13 | relinquishment in perpetuity of all present and future rights to this 14 | software under copyright law. 15 | 16 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, 17 | EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF 18 | MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. 19 | IN NO EVENT SHALL THE AUTHORS BE LIABLE FOR ANY CLAIM, DAMAGES OR 20 | OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, 21 | ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR 22 | OTHER DEALINGS IN THE SOFTWARE. 23 | 24 | For more information, please refer to 25 | -------------------------------------------------------------------------------- /pyDAEDALUS/js/jquery-xmlrpc-master/README.md: -------------------------------------------------------------------------------- 1 | jQuery XML-RPC library 2 | ====================== 3 | 4 | This is a small library that sits on top of jQuery for communicating with 5 | XML-RPC services - without worrying about the horrible bloat of XML-RPC. Using 6 | this library, you can pass JSON parameters to the library, and receive 7 | responses in JSON. Encoding the JSON document is handled for you, intelligently 8 | mapping types between the two languages. 9 | 10 | Installing 11 | ---------- 12 | 13 | Simply include the jQuery library, and this library in your page: 14 | 15 | ```html 16 | 17 | 18 | ``` 19 | 20 | This was built upon jQuery 1.8.1. It will probably work with old versions, and 21 | will probably continue to work with new versions. 22 | 23 | Using 24 | ----- 25 | 26 | The `jQuery.xmlrpc` function is the main work-horse of this library. Call it 27 | like so: 28 | 29 | ```javascript 30 | $.xmlrpc({ 31 | url: '/RPC2', 32 | methodName: 'foo', 33 | params: ['bar', 1, 4.6, true, [1, 2, 3], {name: 'value'}], 34 | success: function(response, status, jqXHR) { /* ... */ }, 35 | error: function(jqXHR, status, error) { /* ... */ } 36 | }); 37 | ``` 38 | 39 | It takes all of the same arguments as `jQuery.ajax`, so refer there for more 40 | documentation. The two new keys added are: 41 | 42 | ### `methodName` 43 | 44 | This is method put in the `` element from XML-RPC. It should be a 45 | string. The XML-RPC service you are communicating with will determine valid 46 | method names you can call. 47 | 48 | ### `params` 49 | 50 | An array of parameters to send. Specify an empty array, or do not supply this 51 | key at all if you do not want to send any parameters. 52 | 53 | See the docs section on [Encoding and Decoding XML-RPC Documents][encoding] for 54 | more information. 55 | 56 | ### Getting data back 57 | 58 | When the XML-RPC call returns, the contents of the `` element are 59 | parsed into JSON and supplied to the `success` callback of the AJAX call as the 60 | first parameter, much like a JSON request. 61 | 62 | ### Handling errors 63 | 64 | If any HTTP errors occur during transport, the normal jQuery AJAX error 65 | handling will be used. If the XML-RPC service successfully replies, but replies 66 | with a `` response, an `$.xmlrpc.XmlRpcFault` is thrown. This error will 67 | be sent as the third parameter to the `error` callback of the AJAX call, as 68 | with other errors. 69 | 70 | Documentation 71 | ------------- 72 | 73 | [The full documentation can be found on Read The Docs][docs]. 74 | 75 | [docs]: http://jquery-xml-rpc.readthedocs.org/ "Documentation" 76 | [encoding]: http://jquery-xml-rpc.readthedocs.org/en/latest/types.html#encoding-and-decoding-xml-rpc-documents 77 | "Encoding and Decoding XML-RPC Documents" 78 | -------------------------------------------------------------------------------- /pyDAEDALUS/js/jquery-xmlrpc-master/bower.json: -------------------------------------------------------------------------------- 1 | { 2 | "name": "jquery-xmlrpc", 3 | "version": "0.4.4", 4 | "main": ["jquery.xmlrpc.js", "jquery.xmlrpc.min.js"], 5 | "dependencies": { 6 | "jquery": ">1.10.2" 7 | }, 8 | "devDependencies": { 9 | "jquery-mockjax": "~1.5.3" 10 | } 11 | } 12 | -------------------------------------------------------------------------------- /pyDAEDALUS/js/jquery-xmlrpc-master/docs/.gitignore: -------------------------------------------------------------------------------- 1 | _build/ 2 | -------------------------------------------------------------------------------- /pyDAEDALUS/js/jquery-xmlrpc-master/docs/index.rst: -------------------------------------------------------------------------------- 1 | Welcome to jQuery XML-RPC's documentation! 2 | ========================================== 3 | 4 | This is a small library that sits on top of jQuery for communicating with 5 | XML-RPC services - without worrying about the horrible bloat of XML-RPC. Using 6 | this library, you can pass JSON parameters to the library, and receive 7 | responses in JSON. Encoding the JSON document is handled for you, intelligently 8 | mapping types between the two languages. 9 | 10 | Contents: 11 | 12 | .. toctree:: 13 | :maxdepth: 2 14 | 15 | overview 16 | types 17 | api 18 | -------------------------------------------------------------------------------- /pyDAEDALUS/js/jquery-xmlrpc-master/docs/make.bat: -------------------------------------------------------------------------------- 1 | @ECHO OFF 2 | 3 | REM Command file for Sphinx documentation 4 | 5 | if "%SPHINXBUILD%" == "" ( 6 | set SPHINXBUILD=sphinx-build 7 | ) 8 | set BUILDDIR=_build 9 | set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% . 10 | set I18NSPHINXOPTS=%SPHINXOPTS% . 11 | if NOT "%PAPER%" == "" ( 12 | set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS% 13 | set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS% 14 | ) 15 | 16 | if "%1" == "" goto help 17 | 18 | if "%1" == "help" ( 19 | :help 20 | echo.Please use `make ^` where ^ is one of 21 | echo. html to make standalone HTML files 22 | echo. dirhtml to make HTML files named index.html in directories 23 | echo. singlehtml to make a single large HTML file 24 | echo. pickle to make pickle files 25 | echo. json to make JSON files 26 | echo. htmlhelp to make HTML files and a HTML help project 27 | echo. qthelp to make HTML files and a qthelp project 28 | echo. devhelp to make HTML files and a Devhelp project 29 | echo. epub to make an epub 30 | echo. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter 31 | echo. text to make text files 32 | echo. man to make manual pages 33 | echo. texinfo to make Texinfo files 34 | echo. gettext to make PO message catalogs 35 | echo. changes to make an overview over all changed/added/deprecated items 36 | echo. linkcheck to check all external links for integrity 37 | echo. doctest to run all doctests embedded in the documentation if enabled 38 | goto end 39 | ) 40 | 41 | if "%1" == "clean" ( 42 | for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i 43 | del /q /s %BUILDDIR%\* 44 | goto end 45 | ) 46 | 47 | if "%1" == "html" ( 48 | %SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html 49 | if errorlevel 1 exit /b 1 50 | echo. 51 | echo.Build finished. The HTML pages are in %BUILDDIR%/html. 52 | goto end 53 | ) 54 | 55 | if "%1" == "dirhtml" ( 56 | %SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml 57 | if errorlevel 1 exit /b 1 58 | echo. 59 | echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml. 60 | goto end 61 | ) 62 | 63 | if "%1" == "singlehtml" ( 64 | %SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml 65 | if errorlevel 1 exit /b 1 66 | echo. 67 | echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml. 68 | goto end 69 | ) 70 | 71 | if "%1" == "pickle" ( 72 | %SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle 73 | if errorlevel 1 exit /b 1 74 | echo. 75 | echo.Build finished; now you can process the pickle files. 76 | goto end 77 | ) 78 | 79 | if "%1" == "json" ( 80 | %SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json 81 | if errorlevel 1 exit /b 1 82 | echo. 83 | echo.Build finished; now you can process the JSON files. 84 | goto end 85 | ) 86 | 87 | if "%1" == "htmlhelp" ( 88 | %SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp 89 | if errorlevel 1 exit /b 1 90 | echo. 91 | echo.Build finished; now you can run HTML Help Workshop with the ^ 92 | .hhp project file in %BUILDDIR%/htmlhelp. 93 | goto end 94 | ) 95 | 96 | if "%1" == "qthelp" ( 97 | %SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp 98 | if errorlevel 1 exit /b 1 99 | echo. 100 | echo.Build finished; now you can run "qcollectiongenerator" with the ^ 101 | .qhcp project file in %BUILDDIR%/qthelp, like this: 102 | echo.^> qcollectiongenerator %BUILDDIR%\qthelp\jQueryXML-RPC.qhcp 103 | echo.To view the help file: 104 | echo.^> assistant -collectionFile %BUILDDIR%\qthelp\jQueryXML-RPC.ghc 105 | goto end 106 | ) 107 | 108 | if "%1" == "devhelp" ( 109 | %SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp 110 | if errorlevel 1 exit /b 1 111 | echo. 112 | echo.Build finished. 113 | goto end 114 | ) 115 | 116 | if "%1" == "epub" ( 117 | %SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub 118 | if errorlevel 1 exit /b 1 119 | echo. 120 | echo.Build finished. The epub file is in %BUILDDIR%/epub. 121 | goto end 122 | ) 123 | 124 | if "%1" == "latex" ( 125 | %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex 126 | if errorlevel 1 exit /b 1 127 | echo. 128 | echo.Build finished; the LaTeX files are in %BUILDDIR%/latex. 129 | goto end 130 | ) 131 | 132 | if "%1" == "text" ( 133 | %SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text 134 | if errorlevel 1 exit /b 1 135 | echo. 136 | echo.Build finished. The text files are in %BUILDDIR%/text. 137 | goto end 138 | ) 139 | 140 | if "%1" == "man" ( 141 | %SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man 142 | if errorlevel 1 exit /b 1 143 | echo. 144 | echo.Build finished. The manual pages are in %BUILDDIR%/man. 145 | goto end 146 | ) 147 | 148 | if "%1" == "texinfo" ( 149 | %SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo 150 | if errorlevel 1 exit /b 1 151 | echo. 152 | echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo. 153 | goto end 154 | ) 155 | 156 | if "%1" == "gettext" ( 157 | %SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale 158 | if errorlevel 1 exit /b 1 159 | echo. 160 | echo.Build finished. The message catalogs are in %BUILDDIR%/locale. 161 | goto end 162 | ) 163 | 164 | if "%1" == "changes" ( 165 | %SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes 166 | if errorlevel 1 exit /b 1 167 | echo. 168 | echo.The overview file is in %BUILDDIR%/changes. 169 | goto end 170 | ) 171 | 172 | if "%1" == "linkcheck" ( 173 | %SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck 174 | if errorlevel 1 exit /b 1 175 | echo. 176 | echo.Link check complete; look for any errors in the above output ^ 177 | or in %BUILDDIR%/linkcheck/output.txt. 178 | goto end 179 | ) 180 | 181 | if "%1" == "doctest" ( 182 | %SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest 183 | if errorlevel 1 exit /b 1 184 | echo. 185 | echo.Testing of doctests in the sources finished, look at the ^ 186 | results in %BUILDDIR%/doctest/output.txt. 187 | goto end 188 | ) 189 | 190 | :end 191 | -------------------------------------------------------------------------------- /pyDAEDALUS/js/jquery-xmlrpc-master/docs/overview.rst: -------------------------------------------------------------------------------- 1 | .. _installing: 2 | 3 | ========== 4 | Installing 5 | ========== 6 | 7 | Simply include the jQuery library, and this library in your page: 8 | 9 | .. code-block:: html 10 | 11 | 12 | 13 | 14 | This was built upon jQuery 1.8.1. It will probably work with old versions, and 15 | will probably continue to work with new versions. 16 | 17 | .. _using: 18 | 19 | ===== 20 | Using 21 | ===== 22 | 23 | The ``jQuery.xmlrpc`` function is the main work-horse of this library. 24 | Call it like so: 25 | 26 | .. code-block:: javascript 27 | 28 | $.xmlrpc({ 29 | url: '/RPC2', 30 | methodName: 'foo', 31 | params: ['bar', 1, 4.6, true, [1, 2, 3], {name: 'value'}], 32 | success: function(response, status, jqXHR) { }, 33 | error: function(jqXHR, status, error) { } 34 | }); 35 | 36 | It takes all of the same arguments as ``jQuery.ajax``, 37 | so refer there for more documentation. 38 | The two new keys added are: 39 | 40 | ``methodName`` 41 | This is method put in the ```` element from XML-RPC. It should be a 42 | string. The XML-RPC service you are communicating with will determine valid 43 | method names you can call. 44 | 45 | ``params`` 46 | An array of parameters to send. Specify an empty array, or do not supply this 47 | key at all if you do not want to send any parameters. 48 | 49 | See the docs section on [Encoding and Decoding XML-RPC Documents][encoding] for 50 | more information. 51 | 52 | Getting data back 53 | ----------------- 54 | 55 | When the XML-RPC call returns, 56 | the contents of the ```` element are parsed into JSON and 57 | supplied to the ``success`` callback of the AJAX call as the first parameter, 58 | much like a JSON request. 59 | 60 | Handling errors 61 | --------------- 62 | 63 | If any HTTP errors occur during transport, 64 | the normal jQuery AJAX error handling will be used. 65 | If the XML-RPC service successfully replies, 66 | but replies with a ```` response, 67 | an ``$.xmlrpc.XmlRpcFault`` is thrown. 68 | This error will be sent as the third parameter to the ``error`` callback 69 | of the AJAX call, as with other errors. 70 | -------------------------------------------------------------------------------- /pyDAEDALUS/js/jquery-xmlrpc-master/docs/requirements.txt: -------------------------------------------------------------------------------- 1 | Sphinx==1.1.3 2 | -------------------------------------------------------------------------------- /pyDAEDALUS/js/jquery-xmlrpc-master/docs/types.rst: -------------------------------------------------------------------------------- 1 | .. _types: 2 | 3 | ===== 4 | Types 5 | ===== 6 | 7 | JSON and XML-RPC are two unrelated markup languages, so converting between the 8 | types requires a small understanding of both languages. Luckily, most of the 9 | types have a direct mapping between the two languages. 10 | 11 | Encoding and Decoding XML-RPC Documents 12 | --------------------------------------- 13 | 14 | Use the following table to see how XML-RPC types are mapped to JavaScript 15 | types: 16 | 17 | +-------------------------+-----------------+ 18 | | XML-RPC | JavaScript | 19 | +=========================+=================+ 20 | | ```` | ``null`` | 21 | +-------------------------+-----------------+ 22 | | ```` | ``Array`` | 23 | +-------------------------+-----------------+ 24 | | ```` | ``Object`` | 25 | +-------------------------+-----------------+ 26 | | ```` | ``String`` | 27 | +-------------------------+-----------------+ 28 | | ```` | ``Boolean`` | 29 | +-------------------------+-----------------+ 30 | | ```` | ``Number`` | 31 | +-------------------------+ | 32 | | ```` | | 33 | +-------------------------+ | 34 | | ```` | | 35 | +-------------------------+ | 36 | | ```` | | 37 | +-------------------------+-----------------+ 38 | | ```` | ``Number`` | 39 | +-------------------------+-----------------+ 40 | | ```` | ``Date`` | 41 | +-------------------------+-----------------+ 42 | | ```` | ``ArrayBuffer`` | 43 | +-------------------------+-----------------+ 44 | 45 | .. note:: JavaScript does not have separate types for integers and floats, it simply 46 | has ``Number``. As such, it is impossible to tell if ``4`` really means 47 | ``4`` or ``4``. If this is an issue for you, read on. 48 | 49 | Forcing types 50 | ~~~~~~~~~~~~~ 51 | 52 | Some times, the automatic type guessing going from JSON to XML-RPC may not work 53 | for you. The most common source of this problem is in encoding numbers. The 54 | library may sometimes encode a ``Number`` as a ```` instead of a ````, as 55 | there is no reliable way of determining what was actually desired. 56 | 57 | To force a type, wrap the value in a call to ``$.xmlrpc.force``. The types are 58 | named after their XML-RPC equivalents, as mentioned in the above table. 59 | 60 | 61 | To force a floating point JavaScript ``Number`` 62 | to be encoded as an ```` 63 | and sent as a parameter, use the following: 64 | 65 | .. code-block:: javascript 66 | 67 | var forcedValue = $.xmlrpc.force('i8', 4.5) 68 | 69 | $.xmlrpc({ 70 | url: '/RPC2', 71 | methodName: 'foo', 72 | params: [forcedValue] 73 | }); 74 | 75 | Adding and Extending Types 76 | -------------------------- 77 | 78 | You can add your own types to XML-RPC by adding a member to ``$.xmlrpc.types``, 79 | combined with the ``$.xmlrpc.makeType`` function. See 80 | :ref:`xmlrpc-makeType` for more information 81 | -------------------------------------------------------------------------------- /pyDAEDALUS/js/jquery-xmlrpc-master/jquery.xmlrpc.min.js: -------------------------------------------------------------------------------- 1 | !function(e){"use strict";var t=function(){Error.apply(this,arguments)};t.prototype=new Error,t.prototype.type="XML-RPC fault";var n=e.xmlrpc=function(t,i){2===arguments.length?i.url=t:(i=t,t=i.url),i.dataType="xml json",i.type="POST",i.contentType="text/xml",i.converters={"xml json":n.parseDocument};var r=n.document(i.methodName,i.params||[]);return i.data="XMLSerializer"in window?(new window.XMLSerializer).serializeToString(r):r.xml,e.ajax(i)};n.createXMLDocument=function(){if(document.implementation&&"createDocument"in document.implementation)return document.implementation.createDocument(null,null,null);var e,t,n=["MSXML6.DomDocument","MSXML3.DomDocument","MSXML2.DomDocument","MSXML.DomDocument","Microsoft.XmlDom"];for(e=0,t=n.length;t>e;e++)try{return new ActiveXObject(n[e])}catch(i){}},n.document=function(t,i){var r=n.createXMLDocument(),a=function(t){return e(r.createElement(t))},o=a("methodName").text(t),s=a("params").append(e.map(i,function(e){var t=a("value").append(n.toXmlRpc(e,a));return a("param").append(t)})),u=a("methodCall").append(o,s);return r.appendChild(u.get(0)),r};var i=function(e){return e===parseInt(e,10)&&!isNaN(e)};n.toXmlRpc=function(t,n){if(t instanceof r)return t.toXmlRpc(n);var a=e.xmlrpc.types,o=e.type(t);switch(o){case"undefined":case"null":return a.nil.encode(t,n);case"date":return a["datetime.iso8601"].encode(t,n);case"object":return t instanceof ArrayBuffer?a.base64.encode(t,n):a.struct.encode(t,n);case"number":return i(t)?a["int"].encode(t,n):a["double"].encode(t,n);case"array":case"boolean":case"string":return a[o].encode(t,n);default:throw new Error("Unknown type",t)}},n.parseDocument=function(i){var r=e(i),a=r.children("methodresponse"),o=a.find("> fault");if(0===o.length){var s=a.find("> params > param > value > *"),u=s.toArray().map(n.parseNode);return u}var l=n.parseNode(o.find("> value > *").get(0)),c=new t(l.faultString);throw c.msg=c.message=l.faultString,c.type=c.code=l.faultCode,c},n.parseNode=function(e){if(void 0===e)return null;var t=e.nodeName.toLowerCase();if(t in n.types)return n.types[t].decode(e);throw new Error("Unknown type "+t)},n.parseValue=function(t){var i=e(t).children()[0];return i?n.parseNode(i):e(t).text()};var r=function(){};e.xmlrpc.types={},n.makeType=function(t,i,a,o){var s;if(s=function(e){this.value=e},s.prototype=new r,s.prototype.tagName=t,i){var u=a,l=o;a=function(e,t){var n=u(e);return t(s.tagName).text(n)},o=function(t){return l(e(t).text(),t)}}s.prototype.toXmlRpc=function(e){return s.encode(this.value,e)},s.tagName=t,s.encode=a,s.decode=o,n.types[t.toLowerCase()]=s};var a=function(e){return""+Math.floor(e)},o=function(e){return parseInt(e,10)};n.makeType("int",!0,a,o),n.makeType("i4",!0,a,o),n.makeType("i8",!0,a,o),n.makeType("i16",!0,a,o),n.makeType("i32",!0,a,o),n.makeType("double",!0,String,function(e){return parseFloat(e,10)}),n.makeType("string",!0,String,String),n.makeType("boolean",!0,function(e){return e?"1":"0"},function(e){return"1"===e});var s=function(e){return 10>e?"0"+e:e};n.makeType("dateTime.iso8601",!0,function(e){return[e.getUTCFullYear(),"-",s(e.getUTCMonth()+1),"-",s(e.getUTCDate()),"T",s(e.getUTCHours()),":",s(e.getUTCMinutes()),":",s(e.getUTCSeconds()),"Z"].join("")},function(e){return new Date(e)}),n.binary=function(){var e="=",t="ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/".split(""),n=t.reduce(function(e,t,n){return e[t]=n,e},{});return{toBase64:function(n){for(var i,r=[],a=new Uint8Array(n),o=0;o>18)%64]),r.push(t[(i>>12)%64]),r.push(t[(i>>6)%64]),r.push(t[(i>>0)%64]);for(var s=3-(n.byteLength%3||3);s--;)r[r.length-s-1]=e;return r.join("")},fromBase64:function(t){t=t.replace(/\s/g, '');var i=t.length,r=3*(i/4);t.charAt(i-1)===e&&r--,t.charAt(i-2)===e&&r--;for(var a,o=new ArrayBuffer(r),s=new Uint8Array(o),u=0,l=0;i>u;u+=4,l+=3)a=(n[t[u+0]]<<18)+(n[t[u+1]]<<12)+(n[t[u+2]]<<6)+(n[t[u+3]]<<0),s[l+0]=(a>>16)%256,s[l+1]=(a>>8)%256,s[l+2]=(a>>0)%256;return o}}}(),n.makeType("base64",!0,function(e){return n.binary.toBase64(e)},function(e){return n.binary.fromBase64(e)}),n.makeType("nil",!1,function(e,t){return t("nil")},function(){return null}),n.makeType("struct",!1,function(t,i){var r=i("struct");return e.each(t,function(e,t){var a=i("name").text(e),o=i("value").append(n.toXmlRpc(t,i));r.append(i("member").append(a,o))}),r},function(t){return e(t).find("> member").toArray().reduce(function(t,i){var r=e(i),a=r.find("> name").text(),o=n.parseValue(r.find("> value"));return t[a]=o,t},{})}),n.makeType("array",!1,function(t,i){var r=i("array"),a=i("data");return e.each(t,function(e,t){a.append(i("value").append(n.toXmlRpc(t,i)))}),r.append(a),r},function(t){return e(t).find("> data > value").toArray().map(n.parseValue)}),n.force=function(e,t){return new n.types[e](t)}}(jQuery); 2 | -------------------------------------------------------------------------------- /pyDAEDALUS/js/jquery-xmlrpc-master/tests/index.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | jQuery XML-RPC tests 6 | 7 | 8 | 9 |
10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | -------------------------------------------------------------------------------- /pyDAEDALUS/js/jquery-xmlrpc-master/tests/min.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | jQuery XML-RPC minified tests 6 | 7 | 8 | 9 |
10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | -------------------------------------------------------------------------------- /pyDAEDALUS/js/jquery-xmlrpc-master/tests/qunit.css: -------------------------------------------------------------------------------- 1 | /** 2 | * QUnit v1.10.0 - A JavaScript Unit Testing Framework 3 | * 4 | * http://qunitjs.com 5 | * 6 | * Copyright 2012 jQuery Foundation and other contributors 7 | * Released under the MIT license. 8 | * http://jquery.org/license 9 | */ 10 | 11 | /** Font Family and Sizes */ 12 | 13 | #qunit-tests, #qunit-header, #qunit-banner, #qunit-testrunner-toolbar, #qunit-userAgent, #qunit-testresult { 14 | font-family: "Helvetica Neue Light", "HelveticaNeue-Light", "Helvetica Neue", Calibri, Helvetica, Arial, sans-serif; 15 | } 16 | 17 | #qunit-testrunner-toolbar, #qunit-userAgent, #qunit-testresult, #qunit-tests li { font-size: small; } 18 | #qunit-tests { font-size: smaller; } 19 | 20 | 21 | /** Resets */ 22 | 23 | #qunit-tests, #qunit-tests ol, #qunit-header, #qunit-banner, #qunit-userAgent, #qunit-testresult, #qunit-modulefilter { 24 | margin: 0; 25 | padding: 0; 26 | } 27 | 28 | 29 | /** Header */ 30 | 31 | #qunit-header { 32 | padding: 0.5em 0 0.5em 1em; 33 | 34 | color: #8699a4; 35 | background-color: #0d3349; 36 | 37 | font-size: 1.5em; 38 | line-height: 1em; 39 | font-weight: normal; 40 | 41 | border-radius: 5px 5px 0 0; 42 | -moz-border-radius: 5px 5px 0 0; 43 | -webkit-border-top-right-radius: 5px; 44 | -webkit-border-top-left-radius: 5px; 45 | } 46 | 47 | #qunit-header a { 48 | text-decoration: none; 49 | color: #c2ccd1; 50 | } 51 | 52 | #qunit-header a:hover, 53 | #qunit-header a:focus { 54 | color: #fff; 55 | } 56 | 57 | #qunit-testrunner-toolbar label { 58 | display: inline-block; 59 | padding: 0 .5em 0 .1em; 60 | } 61 | 62 | #qunit-banner { 63 | height: 5px; 64 | } 65 | 66 | #qunit-testrunner-toolbar { 67 | padding: 0.5em 0 0.5em 2em; 68 | color: #5E740B; 69 | background-color: #eee; 70 | overflow: hidden; 71 | } 72 | 73 | #qunit-userAgent { 74 | padding: 0.5em 0 0.5em 2.5em; 75 | background-color: #2b81af; 76 | color: #fff; 77 | text-shadow: rgba(0, 0, 0, 0.5) 2px 2px 1px; 78 | } 79 | 80 | #qunit-modulefilter-container { 81 | float: right; 82 | } 83 | 84 | /** Tests: Pass/Fail */ 85 | 86 | #qunit-tests { 87 | list-style-position: inside; 88 | } 89 | 90 | #qunit-tests li { 91 | padding: 0.4em 0.5em 0.4em 2.5em; 92 | border-bottom: 1px solid #fff; 93 | list-style-position: inside; 94 | } 95 | 96 | #qunit-tests.hidepass li.pass, #qunit-tests.hidepass li.running { 97 | display: none; 98 | } 99 | 100 | #qunit-tests li strong { 101 | cursor: pointer; 102 | } 103 | 104 | #qunit-tests li a { 105 | padding: 0.5em; 106 | color: #c2ccd1; 107 | text-decoration: none; 108 | } 109 | #qunit-tests li a:hover, 110 | #qunit-tests li a:focus { 111 | color: #000; 112 | } 113 | 114 | #qunit-tests ol { 115 | margin-top: 0.5em; 116 | padding: 0.5em; 117 | 118 | background-color: #fff; 119 | 120 | border-radius: 5px; 121 | -moz-border-radius: 5px; 122 | -webkit-border-radius: 5px; 123 | } 124 | 125 | #qunit-tests table { 126 | border-collapse: collapse; 127 | margin-top: .2em; 128 | } 129 | 130 | #qunit-tests th { 131 | text-align: right; 132 | vertical-align: top; 133 | padding: 0 .5em 0 0; 134 | } 135 | 136 | #qunit-tests td { 137 | vertical-align: top; 138 | } 139 | 140 | #qunit-tests pre { 141 | margin: 0; 142 | white-space: pre-wrap; 143 | word-wrap: break-word; 144 | } 145 | 146 | #qunit-tests del { 147 | background-color: #e0f2be; 148 | color: #374e0c; 149 | text-decoration: none; 150 | } 151 | 152 | #qunit-tests ins { 153 | background-color: #ffcaca; 154 | color: #500; 155 | text-decoration: none; 156 | } 157 | 158 | /*** Test Counts */ 159 | 160 | #qunit-tests b.counts { color: black; } 161 | #qunit-tests b.passed { color: #5E740B; } 162 | #qunit-tests b.failed { color: #710909; } 163 | 164 | #qunit-tests li li { 165 | padding: 5px; 166 | background-color: #fff; 167 | border-bottom: none; 168 | list-style-position: inside; 169 | } 170 | 171 | /*** Passing Styles */ 172 | 173 | #qunit-tests li li.pass { 174 | color: #3c510c; 175 | background-color: #fff; 176 | border-left: 10px solid #C6E746; 177 | } 178 | 179 | #qunit-tests .pass { color: #528CE0; background-color: #D2E0E6; } 180 | #qunit-tests .pass .test-name { color: #366097; } 181 | 182 | #qunit-tests .pass .test-actual, 183 | #qunit-tests .pass .test-expected { color: #999999; } 184 | 185 | #qunit-banner.qunit-pass { background-color: #C6E746; } 186 | 187 | /*** Failing Styles */ 188 | 189 | #qunit-tests li li.fail { 190 | color: #710909; 191 | background-color: #fff; 192 | border-left: 10px solid #EE5757; 193 | white-space: pre; 194 | } 195 | 196 | #qunit-tests > li:last-child { 197 | border-radius: 0 0 5px 5px; 198 | -moz-border-radius: 0 0 5px 5px; 199 | -webkit-border-bottom-right-radius: 5px; 200 | -webkit-border-bottom-left-radius: 5px; 201 | } 202 | 203 | #qunit-tests .fail { color: #000000; background-color: #EE5757; } 204 | #qunit-tests .fail .test-name, 205 | #qunit-tests .fail .module-name { color: #000000; } 206 | 207 | #qunit-tests .fail .test-actual { color: #EE5757; } 208 | #qunit-tests .fail .test-expected { color: green; } 209 | 210 | #qunit-banner.qunit-fail { background-color: #EE5757; } 211 | 212 | 213 | /** Result */ 214 | 215 | #qunit-testresult { 216 | padding: 0.5em 0.5em 0.5em 2.5em; 217 | 218 | color: #2b81af; 219 | background-color: #D2E0E6; 220 | 221 | border-bottom: 1px solid white; 222 | } 223 | #qunit-testresult .module-name { 224 | font-weight: bold; 225 | } 226 | 227 | /** Fixture */ 228 | 229 | #qunit-fixture { 230 | position: absolute; 231 | top: -10000px; 232 | left: -10000px; 233 | width: 1000px; 234 | height: 1000px; 235 | } 236 | -------------------------------------------------------------------------------- /pyDAEDALUS/js/jquery-xmlrpc-master/tests/tests.binary.js: -------------------------------------------------------------------------------- 1 | /*jshint browser:true jquery:true */ 2 | /*globals deepEqual equal ok assert test module */ 3 | (function() { 4 | "use strict"; 5 | module("Binary"); 6 | 7 | /** 8 | * Make an array buffer out of an array of ints 9 | */ 10 | var makeArrayBuffer = function(uint8s) { 11 | var ab = new ArrayBuffer(uint8s.length); 12 | var uint8 = new Uint8Array(ab); 13 | 14 | uint8s.forEach(function(val, i) { 15 | uint8[i] = val; 16 | }); 17 | 18 | return ab; 19 | }; 20 | 21 | /** 22 | * A wrapper around `ok` that acts like `equal`, but works on ArrayBuffers 23 | * Call like: 24 | * 25 | * abEqual(testArrayBuffer, expectedArrayBuffer, message); 26 | */ 27 | var abEqual = function(ab1, ab2) { 28 | var args = [].slice.call(arguments, 2); 29 | 30 | var allGood = (function() { 31 | 32 | var uint81 = new Uint8Array(ab1); 33 | var uint82 = new Uint8Array(ab2); 34 | 35 | if (uint81.length != uint82.length) return false; 36 | 37 | for (var i = 0; i < uint81.length; i++) { 38 | if (uint81[i] !== uint82[i]) return false; 39 | } 40 | 41 | return true; 42 | })(); 43 | 44 | args.unshift(allGood); 45 | 46 | ok.apply(null, args); 47 | }; 48 | 49 | /** 50 | * Naive range() function. Only supports forward steps 51 | */ 52 | var range = function(start, stop) { 53 | var acc = []; 54 | for (var i = start; i < stop; i++) { 55 | acc.push(i); 56 | } 57 | return acc; 58 | }; 59 | 60 | test("base64 encoding", function() { 61 | equal($.xmlrpc.binary.toBase64(makeArrayBuffer([1, 2, 3, 4, 5])), "AQIDBAU=", 62 | "ArrayBuffer encoded to base64 string"); 63 | }); 64 | 65 | test("base64 decoding", function() { 66 | abEqual($.xmlrpc.binary.fromBase64("AQIDBAU="), makeArrayBuffer([1, 2, 3, 4, 5]), 67 | "Base64 string decoded into ArrayBuffer"); 68 | }); 69 | 70 | test("base64 round trip", function() { 71 | var max = 20, low, high; 72 | for (low = 0; low < max; low++) { 73 | for (high = low + 1; high < max; high++) { 74 | var ab = makeArrayBuffer(range(low, high)); 75 | abEqual(ab, $.xmlrpc.binary.fromBase64($.xmlrpc.binary.toBase64(ab)), 76 | "Range from " + low + " to " + high + " encodes and decodes"); 77 | } 78 | } 79 | }); 80 | })(); 81 | -------------------------------------------------------------------------------- /pyDAEDALUS/js/jquery-xmlrpc-master/tests/tests.decoding.js: -------------------------------------------------------------------------------- 1 | /*jshint browser:true jquery:true */ 2 | /*globals deepEqual equal ok assert test module */ 3 | (function() { 4 | "use strict"; 5 | module("Decoding"); 6 | 7 | /** 8 | * Generate an element from a string, and return just that element 9 | */ 10 | function el(xml) { 11 | return $(xml)[0]; 12 | } 13 | 14 | test("JavaScript primitive value decoding", function($xml) { 15 | 16 | equal($.xmlrpc.parseNode(el('1')), true, 17 | ' true node decodes'); 18 | 19 | equal($.xmlrpc.parseNode(el('0')), false, 20 | ' false node decodes'); 21 | 22 | 23 | equal($.xmlrpc.parseNode(el('4')), 4, 24 | ' node decodes'); 25 | equal($.xmlrpc.parseNode(el('5')), 5, 26 | ' node decodes'); 27 | equal($.xmlrpc.parseNode(el('6')), 6, 28 | ' node decodes'); 29 | equal($.xmlrpc.parseNode(el('7')), 7, 30 | ' node decodes'); 31 | equal($.xmlrpc.parseNode(el('8.9')), 8.9, 32 | ' node decodes'); 33 | 34 | equal($.xmlrpc.parseNode(el('')), null, 35 | ' node decodes'); 36 | equal($.xmlrpc.parseNode(el('Hello')), null, 37 | ' node decodes, even when not empty'); 38 | 39 | equal($.xmlrpc.parseNode(el('Hello')), "Hello", 40 | ' node decodes'); 41 | 42 | equal($.xmlrpc.parseNode(el('')), "", 43 | 'Empty node decodes'); 44 | 45 | var timestamp = 1350943077000; 46 | var datestring = "2012-10-22T21:57:57Z"; 47 | var dateNode = el('' + datestring + ''); 48 | equal($.xmlrpc.parseNode(dateNode).getTime(), timestamp, 49 | " node decodes"); 50 | }); 51 | 52 | test("Array decoding", function($xml) { 53 | deepEqual($.xmlrpc.parseNode(el('4Hello')), 54 | [4, "Hello"], 55 | "Simple array decodes"); 56 | 57 | deepEqual($.xmlrpc.parseNode(el('')), 58 | [], 59 | "Empty array decodes"); 60 | 61 | deepEqual( 62 | $.xmlrpc.parseNode(el( 63 | '' + 64 | '1' + 65 | '' + 66 | '2' + 67 | '' + 68 | '' 69 | )), 70 | [1, [2]], 71 | "Array containing array encodes"); 72 | 73 | // Childless value nodes should be treated like string nodes 74 | deepEqual( 75 | $.xmlrpc.parseNode(el( 76 | '' + 77 | 'String node' + 78 | '' + 79 | 'Raw value string' + 80 | '' 81 | )), 82 | ["String node", "", "Raw value string"], 83 | "Array containing childless nodes parses correctly"); 84 | }); 85 | 86 | test("Struct decoding", function($xml) { 87 | deepEqual( 88 | $.xmlrpc.parseNode(el( 89 | '' + 90 | '' + 91 | 'foo' + 92 | '4' + 93 | '' + 94 | '' + 95 | 'bar' + 96 | 'Hello' + 97 | '' + 98 | '')), 99 | {foo: 4, bar: "Hello"}, 100 | "Simple decodes"); 101 | 102 | deepEqual($.xmlrpc.parseNode(el('')), {}, 103 | "Empty decodes"); 104 | 105 | deepEqual( 106 | $.xmlrpc.parseNode(el( 107 | '' + 108 | '' + 109 | 'foo' + 110 | '4' + 111 | '' + 112 | '' + 113 | 'bar' + 114 | '' + 115 | '' + 116 | 'baz' + 117 | '5' + 118 | '' + 119 | '' + 120 | '' + 121 | '')), 122 | {foo: 4, bar: {baz: 5}}, 123 | "struct containing struct decodes"); 124 | 125 | deepEqual( 126 | $.xmlrpc.parseNode(el( 127 | '' + 128 | '' + 129 | 'stringNode' + 130 | 'String node' + 131 | '' + 132 | '' + 133 | 'emptyValue' + 134 | '' + 135 | '' + 136 | '' + 137 | 'rawStringValue' + 138 | 'Raw string value' + 139 | '' + 140 | '')), 141 | { 142 | stringNode: "String node", 143 | emptyValue: "", 144 | rawStringValue: "Raw string value" 145 | }, 146 | "Struct with childless nodes parses correctly"); 147 | }); 148 | 149 | })(); 150 | -------------------------------------------------------------------------------- /pyDAEDALUS/js/jquery-xmlrpc-master/tests/tests.document.js: -------------------------------------------------------------------------------- 1 | /*jshint browser:true jquery:true */ 2 | /*globals deepEqual equal ok assert test module throws */ 3 | (function() { 4 | "use strict"; 5 | module("Document"); 6 | 7 | /** 8 | * Serialize a Document to a string easily 9 | */ 10 | var s = (function() { 11 | var serializer = new XMLSerializer(); 12 | return function($node) { 13 | return serializer.serializeToString($node); 14 | }; 15 | })(); 16 | 17 | var d = (function() { 18 | var parser = new DOMParser(); 19 | return function(xml) { 20 | return parser.parseFromString(xml, "text/xml"); 21 | }; 22 | })(); 23 | 24 | test("Creating a document", function() { 25 | equal(s($.xmlrpc.document('method', [4, 'foo'])), 26 | '' + 27 | 'method' + 28 | '' + 29 | '4' + 30 | 'foo' + 31 | '' + 32 | '', 33 | 'Can create a simple document'); 34 | 35 | equal(s($.xmlrpc.document('empty', [])), 36 | '' + 37 | 'empty' + 38 | '' + 39 | '', 40 | 'Can create an empty document'); 41 | }); 42 | 43 | test("Decoding a document", function() { 44 | 45 | deepEqual( 46 | $.xmlrpc.parseDocument(d( 47 | '' + 48 | '' + 49 | '' + 50 | '4' + 51 | 'Hello' + 52 | '' + 53 | '')), 54 | [4, "Hello"], 55 | "Can parse a simple response"); 56 | 57 | deepEqual( 58 | $.xmlrpc.parseDocument(d( 59 | '' + 60 | '' + 61 | '' + 62 | '')), 63 | [], 64 | "Can parse an empty response"); 65 | 66 | deepEqual( 67 | $.xmlrpc.parseDocument(d( 68 | '' + 69 | '' + 70 | '' + 71 | '4' + 72 | '' + 73 | '1' + 74 | '' + 75 | '2' + 76 | '' + 77 | '' + 78 | '' + 79 | '')), 80 | [4, [1, [2]]], 81 | "Can parse a complex response"); 82 | 83 | }); 84 | 85 | test("Handling errors", 5, function() { 86 | throws( 87 | function() { 88 | $.xmlrpc.parseDocument(d( 89 | '' + 90 | '' + 91 | '' + 92 | '' + 93 | '' + 94 | 'faultCode' + 95 | '4' + 96 | '' + 97 | '' + 98 | 'faultString' + 99 | 'Too many parameters.' + 100 | '' + 101 | '' + 102 | '' + 103 | '' 104 | )); 105 | }, 106 | $.xmlrpc.XmlRpcFault, 107 | "Parsing a fault response throws an error"); 108 | 109 | try { 110 | $.xmlrpc.parseDocument(d( 111 | '' + 112 | '' + 113 | '' + 114 | '' + 115 | '' + 116 | '' + 117 | 'faultCode' + 118 | '4' + 119 | '' + 120 | '' + 121 | 'faultString' + 122 | 'Error message' + 123 | '' + 124 | '' + 125 | '' + 126 | '' + 127 | '' 128 | )); 129 | ok(false, "Should have thrown an error"); 130 | } catch (e) { 131 | equal(e.code, 4, "Error code is present"); 132 | equal(e.type, 4, "Error type is present"); 133 | 134 | equal(e.msg, "Error message", "Error message is present"); 135 | equal(e.message, "Error message", "Error message is present"); 136 | } 137 | 138 | }); 139 | 140 | })(); 141 | -------------------------------------------------------------------------------- /pyDAEDALUS/js/jquery-xmlrpc-master/tests/tests.encoding.js: -------------------------------------------------------------------------------- 1 | /*jshint browser:true jquery:true */ 2 | /*globals deepEqual equal ok assert test module */ 3 | (function() { 4 | "use strict"; 5 | module("Encoding"); 6 | 7 | /** 8 | * Serialize an Element to a string easily 9 | */ 10 | var s = (function() { 11 | var serializer = new XMLSerializer(); 12 | return function($node) { 13 | return serializer.serializeToString($node[0]); 14 | }; 15 | })(); 16 | 17 | /** 18 | * A wrapper around test functions that makes an $xml function for testing 19 | * with. Kinda like a Python decorator 20 | */ 21 | var need$xml = function(fn) { 22 | return function() { 23 | var doc = document.implementation.createDocument(null, null, null); 24 | var $xml = function(name) { 25 | return $(doc.createElement(name)); 26 | }; 27 | 28 | var args = [].slice.call(arguments); 29 | args.unshift($xml); 30 | 31 | return fn.apply(this, args); 32 | }; 33 | }; 34 | 35 | test("JavaScript primitive value encoding", need$xml(function($xml) { 36 | var types = $.xmlrpc.types; 37 | 38 | deepEqual(types.boolean.encode(true, $xml), $xml('boolean').text('1'), 39 | "Boolean true encodes to 1"); 40 | 41 | deepEqual(types.boolean.encode(false, $xml), $xml('boolean').text('0'), 42 | "Boolean true encodes to 0"); 43 | 44 | 45 | deepEqual(types.int.encode(3, $xml), $xml('int').text('3'), 46 | "Integer 3 encodes to 3"); 47 | deepEqual(types.i8.encode(4, $xml), $xml('i8').text('4'), 48 | "Integer 3 encodes to 4"); 49 | deepEqual(types.double.encode(5.5, $xml), $xml('double').text('5.5'), 50 | "Double 5.5 encodes to 5.5"); 51 | 52 | deepEqual(types.nil.encode(null, $xml), $xml('nil'), 53 | "Null encodes to "); 54 | deepEqual(types.nil.encode("hello", $xml), $xml('nil'), 55 | "Null encodes to when supplied a non-null value"); 56 | 57 | deepEqual(types.string.encode("Hello, World!", $xml), $xml('string').text("Hello, World!"), 58 | "String encodes to ..."); 59 | deepEqual(types.string.encode("", $xml), $xml('string').text(""), 60 | "Empty String encodes to "); 61 | 62 | var timestamp = 1350943077107; 63 | var datestring = "2012-10-22T21:57:57Z"; 64 | var date = new Date(); 65 | date.setTime(timestamp); 66 | deepEqual(types['datetime.iso8601'].encode(date, $xml), $xml('dateTime.iso8601').text(datestring), 67 | "Date encodes to ..."); 68 | 69 | })); 70 | 71 | test("Array encoding", need$xml(function($xml) { 72 | var types = $.xmlrpc.types; 73 | 74 | equal(s(types.array.encode([4, "Hello"], $xml)), 75 | '4Hello', 76 | "Simple array encodes"); 77 | 78 | // If not all browsers encode this to , this will fail. 79 | equal(s(types.array.encode([], $xml)), 80 | '', 81 | "Empty array encodes"); 82 | 83 | equal(s(types.array.encode([1, [2]], $xml)), 84 | '' + 85 | '1' + 86 | '' + 87 | '2' + 88 | '' + 89 | '', 90 | "Array containing array encodes"); 91 | })); 92 | 93 | test("Guessing types", need$xml(function($xml) { 94 | ok($.xmlrpc.toXmlRpc(4, $xml).is('int'), 95 | "Number 4 guessed to be "); 96 | 97 | ok($.xmlrpc.toXmlRpc(4.5, $xml).is('double'), 98 | "Number 4.5 guessed to be "); 99 | 100 | ok($.xmlrpc.toXmlRpc(true, $xml).is('boolean'), 101 | "Boolean guessed to be "); 102 | 103 | ok($.xmlrpc.toXmlRpc(null, $xml).is('nil'), 104 | "null guessed to be "); 105 | 106 | ok($.xmlrpc.toXmlRpc(undefined, $xml).is('nil'), 107 | "undefined guessed to be "); 108 | 109 | ok($.xmlrpc.toXmlRpc("Hello", $xml).is('string'), 110 | "String guessed to be "); 111 | 112 | ok($.xmlrpc.toXmlRpc(new Date(), $xml).is('dateTime\\.iso8601'), 113 | "Date guessed to be "); 114 | 115 | ok($.xmlrpc.toXmlRpc({foo: 'bar'}, $xml).is('struct'), 116 | "Object guessed to be "); 117 | 118 | ok($.xmlrpc.toXmlRpc([], $xml).is('array'), 119 | "Array guessed to be "); 120 | 121 | ok($.xmlrpc.toXmlRpc(new ArrayBuffer(), $xml).is('base64'), 122 | "ArrayBuffer guessed to be "); 123 | })); 124 | 125 | })(); 126 | -------------------------------------------------------------------------------- /pyDAEDALUS/js/jquery-xmlrpc-master/tests/tests.request.js: -------------------------------------------------------------------------------- 1 | /*jshint browser:true */ 2 | /*globals $ deepEqual equal ok assert test module throws */ 3 | (function() { 4 | "use strict"; 5 | module("Request"); 6 | 7 | /** 8 | * Serialize a Document to a string easily 9 | */ 10 | var s = (function() { 11 | var serializer = new XMLSerializer(); 12 | return function($node) { 13 | return serializer.serializeToString($node); 14 | }; 15 | })(); 16 | 17 | var d = (function() { 18 | var parser = new DOMParser(); 19 | return function(xml) { 20 | return parser.parseFromString(xml, "text/xml"); 21 | }; 22 | })(); 23 | 24 | $.mockjax({ 25 | url: '/mock/xmlrpc/hello', 26 | contentType: 'text/xml', 27 | responseTime: 1, 28 | responseText: ( 29 | '' + 30 | '' + 31 | '' + 32 | '4' + 33 | 'World!' + 34 | '' + 35 | '' 36 | ) 37 | }); 38 | 39 | $.mockjax({ 40 | url: '/mock/xmlrpc/empty', 41 | contentType: 'text/xml', 42 | responseTime: 1, 43 | responseText: ( 44 | '' + 45 | '' + 46 | '' + 47 | '' + 48 | '' 49 | ) 50 | }); 51 | 52 | asyncTest("Make a simple request", function() { 53 | expect(2); 54 | $.xmlrpc("/mock/xmlrpc/hello", { 55 | 'methodName': 'test-method', 56 | 'params': [1, "Hello"], 57 | 'success': function(data, status) { 58 | deepEqual(this.data, 59 | "test-method" + 60 | "1" + 61 | "Hello" + 62 | "", 63 | "Request body was encoded correctly!"); 64 | deepEqual(data, [4, 'World!'], 65 | "Response body was decoded correctly!"); 66 | start(); 67 | }, 68 | 'error': function() { 69 | ok(false, arguments); 70 | } 71 | }); 72 | }); 73 | 74 | asyncTest("Make a request with no params", function() { 75 | expect(2); 76 | $.xmlrpc("/mock/xmlrpc/empty", { 77 | 'methodName': 'test-method', 78 | 'success': function(data, request) { 79 | deepEqual(this.data, 80 | "test-method" + 81 | "", 82 | "Request body was encoded correctly!"); 83 | deepEqual(data, [], 84 | "Response body was decoded correctly!"); 85 | start(); 86 | }, 87 | 'error': function() { 88 | ok(false, arguments); 89 | } 90 | }); 91 | }); 92 | 93 | })(); 94 | -------------------------------------------------------------------------------- /pyDAEDALUS/js/jquery-xmlrpc-master/xmlrpc.jquery.json: -------------------------------------------------------------------------------- 1 | { 2 | "name": "xmlrpc", 3 | "version": "0.4.4", 4 | "title": "XML-RPC over AJAX", 5 | "description": "Interact with remote XML-RPC services using AJAX", 6 | "author": { 7 | "name": "Tim Heap", 8 | "email": "heap.tim@gmail.com", 9 | "url": "http://timheap.me" 10 | }, 11 | "licenses": [ 12 | {"url": "http://unlicense.org/"} 13 | ], 14 | "dependencies": { 15 | "jquery": ">1.8.0" 16 | }, 17 | "keywords": [ 18 | "xmlrpc", "xml-rpc", 19 | "ajax", 20 | "xml", 21 | "remote-service" 22 | ], 23 | "homepage": "https://github.com/timheap/jquery-xmlrpc", 24 | "docs": "http://jquery-xml-rpc.readthedocs.org/" 25 | } 26 | -------------------------------------------------------------------------------- /pyDAEDALUS/js/jquery.xmlrpc.min.js: -------------------------------------------------------------------------------- 1 | !function(e){"use strict";var t=function(){Error.apply(this,arguments)};t.prototype=new Error,t.prototype.type="XML-RPC fault";var n=e.xmlrpc=function(t,i){2===arguments.length?i.url=t:(i=t,t=i.url),i.dataType="xml json",i.type="POST",i.contentType="text/xml",i.converters={"xml json":n.parseDocument};var r=n.document(i.methodName,i.params||[]);return i.data="XMLSerializer"in window?(new window.XMLSerializer).serializeToString(r):r.xml,e.ajax(i)};n.createXMLDocument=function(){if(document.implementation&&"createDocument"in document.implementation)return document.implementation.createDocument(null,null,null);var e,t,n=["MSXML6.DomDocument","MSXML3.DomDocument","MSXML2.DomDocument","MSXML.DomDocument","Microsoft.XmlDom"];for(e=0,t=n.length;t>e;e++)try{return new ActiveXObject(n[e])}catch(i){}},n.document=function(t,i){var r=n.createXMLDocument(),a=function(t){return e(r.createElement(t))},o=a("methodName").text(t),s=a("params").append(e.map(i,function(e){var t=a("value").append(n.toXmlRpc(e,a));return a("param").append(t)})),u=a("methodCall").append(o,s);return r.appendChild(u.get(0)),r};var i=function(e){return e===parseInt(e,10)&&!isNaN(e)};n.toXmlRpc=function(t,n){if(t instanceof r)return t.toXmlRpc(n);var a=e.xmlrpc.types,o=e.type(t);switch(o){case"undefined":case"null":return a.nil.encode(t,n);case"date":return a["datetime.iso8601"].encode(t,n);case"object":return t instanceof ArrayBuffer?a.base64.encode(t,n):a.struct.encode(t,n);case"number":return i(t)?a["int"].encode(t,n):a["double"].encode(t,n);case"array":case"boolean":case"string":return a[o].encode(t,n);default:throw new Error("Unknown type",t)}},n.parseDocument=function(i){var r=e(i),a=r.children("methodresponse"),o=a.find("> fault");if(0===o.length){var s=a.find("> params > param > value > *"),u=s.toArray().map(n.parseNode);return u}var l=n.parseNode(o.find("> value > *").get(0)),c=new t(l.faultString);throw c.msg=c.message=l.faultString,c.type=c.code=l.faultCode,c},n.parseNode=function(e){if(void 0===e)return null;var t=e.nodeName.toLowerCase();if(t in n.types)return n.types[t].decode(e);throw new Error("Unknown type "+t)},n.parseValue=function(t){var i=e(t).children()[0];return i?n.parseNode(i):e(t).text()};var r=function(){};e.xmlrpc.types={},n.makeType=function(t,i,a,o){var s;if(s=function(e){this.value=e},s.prototype=new r,s.prototype.tagName=t,i){var u=a,l=o;a=function(e,t){var n=u(e);return t(s.tagName).text(n)},o=function(t){return l(e(t).text(),t)}}s.prototype.toXmlRpc=function(e){return s.encode(this.value,e)},s.tagName=t,s.encode=a,s.decode=o,n.types[t.toLowerCase()]=s};var a=function(e){return""+Math.floor(e)},o=function(e){return parseInt(e,10)};n.makeType("int",!0,a,o),n.makeType("i4",!0,a,o),n.makeType("i8",!0,a,o),n.makeType("i16",!0,a,o),n.makeType("i32",!0,a,o),n.makeType("double",!0,String,function(e){return parseFloat(e,10)}),n.makeType("string",!0,String,String),n.makeType("boolean",!0,function(e){return e?"1":"0"},function(e){return"1"===e});var s=function(e){return 10>e?"0"+e:e};n.makeType("dateTime.iso8601",!0,function(e){return[e.getUTCFullYear(),"-",s(e.getUTCMonth()+1),"-",s(e.getUTCDate()),"T",s(e.getUTCHours()),":",s(e.getUTCMinutes()),":",s(e.getUTCSeconds()),"Z"].join("")},function(e){return new Date(e)}),n.binary=function(){var e="=",t="ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/".split(""),n=t.reduce(function(e,t,n){return e[t]=n,e},{});return{toBase64:function(n){for(var i,r=[],a=new Uint8Array(n),o=0;o>18)%64]),r.push(t[(i>>12)%64]),r.push(t[(i>>6)%64]),r.push(t[(i>>0)%64]);for(var s=3-(n.byteLength%3||3);s--;)r[r.length-s-1]=e;return r.join("")},fromBase64:function(t){t=t.replace(/\s/g, '');var i=t.length,r=3*(i/4);t.charAt(i-1)===e&&r--,t.charAt(i-2)===e&&r--;for(var a,o=new ArrayBuffer(r),s=new Uint8Array(o),u=0,l=0;i>u;u+=4,l+=3)a=(n[t[u+0]]<<18)+(n[t[u+1]]<<12)+(n[t[u+2]]<<6)+(n[t[u+3]]<<0),s[l+0]=(a>>16)%256,s[l+1]=(a>>8)%256,s[l+2]=(a>>0)%256;return o}}}(),n.makeType("base64",!0,function(e){return n.binary.toBase64(e)},function(e){return n.binary.fromBase64(e)}),n.makeType("nil",!1,function(e,t){return t("nil")},function(){return null}),n.makeType("struct",!1,function(t,i){var r=i("struct");return e.each(t,function(e,t){var a=i("name").text(e),o=i("value").append(n.toXmlRpc(t,i));r.append(i("member").append(a,o))}),r},function(t){return e(t).find("> member").toArray().reduce(function(t,i){var r=e(i),a=r.find("> name").text(),o=n.parseValue(r.find("> value"));return t[a]=o,t},{})}),n.makeType("array",!1,function(t,i){var r=i("array"),a=i("data");return e.each(t,function(e,t){a.append(i("value").append(n.toXmlRpc(t,i)))}),r.append(a),r},function(t){return e(t).find("> data > value").toArray().map(n.parseValue)}),n.force=function(e,t){return new n.types[e](t)}}(jQuery); 2 | -------------------------------------------------------------------------------- /pyDAEDALUS/main.js: -------------------------------------------------------------------------------- 1 | const { app, BrowserWindow } = require('electron'); 2 | const {ipcMain, dialog} = require('electron') 3 | const path = require ('path'); 4 | const fs = require('fs'); 5 | const os = require('os'); 6 | // var zerorpc = require("zerorpc"); 7 | 8 | // Keep a global reference of the window object, if you don't, the window will 9 | // be closed automatically when the JavaScript object is garbage collected. 10 | let win 11 | 12 | function createWindow () { 13 | // call python DAEDALUS Server 14 | // var subpy = require('child_process').spawn('./dist/DAEDserve'); 15 | // Create the window. 16 | win = new BrowserWindow({ 17 | width: 500, 18 | height: 440, 19 | webPreferences: { 20 | nodeIntegration: true 21 | } 22 | }) 23 | 24 | // and load the index.html of the app. 25 | win.loadFile('index.html') 26 | 27 | // Open the DevTools. 28 | // win.webContents.openDevTools() 29 | 30 | // Emitted when the window is closed. 31 | win.on('closed', () => { 32 | // Dereference the window object, usually you would store windows 33 | // in an array if your app supports multi windows, this is the time 34 | // when you should delete the corresponding element. 35 | // subpy.kill('SIGINT'); 36 | win = null 37 | }) 38 | } 39 | var plyfile='tet.ply' 40 | var seqfile='M13.txt' 41 | // This method will be called when Electron has finished 42 | // initialization and is ready to create browser windows. 43 | // Some APIs can only be used after this event occurs. 44 | app.on('ready', createWindow) 45 | 46 | // Quit when all windows are closed. 47 | app.on('window-all-closed', () => { 48 | // On macOS it is common for applications and their menu bar 49 | // to stay active until the user quits explicitly with Cmd + Q 50 | if (process.platform !== 'darwin') { 51 | app.quit() 52 | } 53 | }) 54 | 55 | app.on('activate', () => { 56 | // On macOS it's common to re-create a window in the app when the 57 | // dock icon is clicked and there are no other windows open. 58 | if (win === null) { 59 | createWindow() 60 | } 61 | }) 62 | 63 | // In this file you can include the rest of your app's specific main process 64 | // code. You can also put them in separate files and require them here. 65 | 66 | ipcMain.on('open-plyfile-dialog', (event) => { 67 | let plyfiles = dialog.showOpenDialogSync({ properties: ['openFile'] }) 68 | plyfile = plyfiles[0] 69 | win.webContents.send('plyTableUpdate',plyfile); 70 | }) 71 | ipcMain.on('open-seqfile-dialog', (event) => { 72 | let seqfiles = dialog.showOpenDialogSync({ properties: ['openFile'] }) 73 | seqfile = seqfiles[0] 74 | win.webContents.send('seqTableUpdate',seqfile); 75 | }) 76 | ipcMain.on('changeDX', (event, args) => { 77 | dxType = args 78 | win.webContents.send('dxUpdate',dxType); 79 | }) 80 | 81 | exports.handleForm = function handleForm(targetWindow, projName, helicalForm, helicalTurns) { 82 | // var client = new zerorpc.Client(); 83 | // client.connect("tcp://127.0.0.1:4242"); 84 | 85 | win.webContents.send('finishedUpdate',"Processing...", projName, helicalForm, helicalTurns, plyfile, seqfile); 86 | // client.invoke("calc", projName, helicalForm, helicalTurns, plyfile, seqfile, function(error, results) { 87 | // console.log(error); 88 | // let tmpSt=results.toString() 89 | // console.log(tmpSt); 90 | // if (tmpSt==="Finished!") { 91 | // win.webContents.send('finishedUpdate',"Success!"); 92 | // } 93 | // }); 94 | }; 95 | -------------------------------------------------------------------------------- /pyDAEDALUS/oct.ply: -------------------------------------------------------------------------------- 1 | ply 2 | format ascii 1.0 3 | element vertex 6 4 | property float32 x 5 | property float32 y 6 | property float32 z 7 | element face 8 8 | property list uint8 int32 vertex_indices 9 | end_header 10 | 0.000000 0.000000 1.000000 11 | 0.000000 0.000000 -1.000000 12 | 0.000000 1.000000 0.000000 13 | 0.000000 -1.000000 0.000000 14 | 1.000000 0.000000 0.000000 15 | -1.000000 0.000000 0.000000 16 | 3 0 4 2 17 | 3 0 3 4 18 | 3 0 5 3 19 | 3 0 2 5 20 | 3 1 2 4 21 | 3 1 4 3 22 | 3 1 3 5 23 | 3 1 5 2 24 | -------------------------------------------------------------------------------- /pyDAEDALUS/package.json: -------------------------------------------------------------------------------- 1 | { 2 | "name": "pyDAEDALUSX", 3 | "productName": "pyDAEDALUSX", 4 | "version": "0.1.0", 5 | "description": "Python DAEDALUS for RNA or DNA routing with a GUI", 6 | "main": "main.js", 7 | "scripts": { 8 | "start": "electron ." 9 | }, 10 | "author": "Sakul Ratanalert, Tyson Shepherd", 11 | "license": "MIT", 12 | "devDependencies": { 13 | "electron": "^7.1.1", 14 | "electron-packager": "^14.1.0", 15 | "electron-rebuild": "^1.8.6" 16 | } 17 | } 18 | -------------------------------------------------------------------------------- /pyDAEDALUS/pbip.ply: -------------------------------------------------------------------------------- 1 | ply 2 | format ascii 1.0 3 | element vertex 7 4 | property float32 x 5 | property float32 y 6 | property float32 z 7 | element face 10 8 | property list uint8 int32 vertex_indices 9 | end_header 10 | -0.794100 0.302600 -0.037700 11 | -0.494400 -0.498800 0.480000 12 | -0.096600 -0.305400 -0.416900 13 | 0.003600 0.685800 -0.503300 14 | 0.096600 0.305400 0.416900 15 | 0.488600 -0.610900 0.334300 16 | 0.796300 0.121200 -0.273400 17 | 3 3 2 0 18 | 3 2 1 0 19 | 3 2 5 1 20 | 3 0 4 3 21 | 3 0 1 4 22 | 3 4 1 5 23 | 3 2 3 6 24 | 3 3 4 6 25 | 3 5 2 6 26 | 3 4 5 6 27 | -------------------------------------------------------------------------------- /pyDAEDALUS/pyDAEDALUSX.code-workspace: -------------------------------------------------------------------------------- 1 | { 2 | "folders": [ 3 | { 4 | "path": "." 5 | } 6 | ] 7 | } -------------------------------------------------------------------------------- /pyDAEDALUS/renderFile.js: -------------------------------------------------------------------------------- 1 | const { remote, ipcRenderer } = require('electron'); 2 | const { handleForm} = remote.require('./main'); 3 | const currentWindow = remote.getCurrentWindow(); 4 | 5 | const submitFormButton = document.querySelector("#ipcForm2"); 6 | const responseParagraph = document.getElementById('response'); 7 | const dximgParagraph = document.getElementById('DXimg'); 8 | const plyTableCell = document.getElementById('plyTable'); 9 | const seqTableCell = document.getElementById('seqTable'); 10 | const helF = document.getElementById("helicalForm"); 11 | const selectPlyBtn = document.getElementById('select-ply'); 12 | const selectSeqBtn = document.getElementById('select-seq'); 13 | 14 | submitFormButton.addEventListener("submit", function(event){ 15 | event.preventDefault(); // stop the form from submitting 16 | let projName = document.getElementById("projName").value; 17 | let helicalForm = document.getElementById("helicalForm").value; 18 | let helicalTurns = document.getElementById("helicalTurns").value; 19 | handleForm(currentWindow, projName, helicalForm, helicalTurns) 20 | }); 21 | 22 | ipcRenderer.on('form-received', function(event, args){ 23 | responseParagraph.innerHTML = args 24 | /* 25 | you could choose to submit the form here after the main process completes 26 | and use this as a processing step 27 | */ 28 | }); 29 | 30 | ipcRenderer.on('plyTableUpdate', function(event, args){ 31 | plyTableCell.innerHTML = args 32 | }); 33 | 34 | ipcRenderer.on('seqTableUpdate', function(event, args){ 35 | seqTableCell.innerHTML = args 36 | }); 37 | 38 | ipcRenderer.on('finishedUpdate', function(event, args, projNameA, helicalFormA, helicalTurnsA, plyfileA, seqfileA){ 39 | responseParagraph.innerHTML = args 40 | $.xmlrpc({ 41 | url: 'http://localhost:4242', 42 | methodName: 'calc', 43 | params: [projNameA, helicalFormA, helicalTurnsA, plyfileA, seqfileA], 44 | success: function(response, status, jqXHR) { responseParagraph.innerHTML = "Success!" }, 45 | error: function(jqXHR, status, error) { responseParagraph.innerHTML = "Fail!" } 46 | }); 47 | }); 48 | 49 | ipcRenderer.on('dxUpdate', function(event, args){ 50 | if (args==="Bform") { 51 | dximgParagraph.innerHTML = '

' 52 | } 53 | if (args==="Aform") { 54 | dximgParagraph.innerHTML = '

' 55 | } 56 | if (args==="Hybrid") { 57 | dximgParagraph.innerHTML = '

' 58 | } 59 | if (args==="Twisted") { 60 | dximgParagraph.innerHTML = '

' 61 | } 62 | }); 63 | 64 | selectPlyBtn.addEventListener('click', (event) => { 65 | ipcRenderer.send('open-plyfile-dialog') 66 | }) 67 | 68 | selectSeqBtn.addEventListener('click', (event) => { 69 | ipcRenderer.send('open-seqfile-dialog') 70 | }) 71 | 72 | helF.addEventListener('change', (event) => { 73 | let dxChoice = document.getElementById("helicalForm").value; 74 | console.log(dxChoice) 75 | ipcRenderer.send('changeDX', dxChoice) 76 | }); 77 | -------------------------------------------------------------------------------- /pyDAEDALUS/requirements.txt: -------------------------------------------------------------------------------- 1 | numpy>=1.11.1 2 | matplotlib>=1.5.1 3 | networkx==1.11 4 | scipy>=0.18.0 5 | click>=6.6 6 | mpmath>=0.19 7 | mock>=2.0.0 8 | tqdm>=4.9.0 9 | flake8>=3.2.0 10 | -------------------------------------------------------------------------------- /pyDAEDALUS/testServer.py: -------------------------------------------------------------------------------- 1 | import xmlrpc.client 2 | # 3 | # connect to localhost, port 4242 running the RPC server 4 | # 5 | proxy = xmlrpc.client.ServerProxy("http://localhost:4242/") 6 | multicall = xmlrpc.client.MultiCall(proxy) 7 | # 8 | # calc: function on the RPC server to route the origami 9 | # calc(projectName, helicalForm, helicalTurns, plyFile, sequenceFile): 10 | # projectName: short descriptive name, name of the generated folder 11 | # helicalForm: 'Bform', 'Aform', 'Hybrid', 'Twisted' 12 | # helicalTurns: multiplied by 11 (Aforms) or 10.5 (Bform) 13 | # plyFile: Path to ply file 14 | # sequenceFile: Path to sequence file 15 | # 16 | multicall.calc("TestTet66","Aform",6,"./tet.ply","./M13.txt"); 17 | result = multicall() 18 | multicall.calc("TestOct66","Aform",6,"./oct.ply","./M13.txt"); 19 | result = multicall() 20 | multicall.calc("TestOct44","Aform",4,"./oct.ply","./M13.txt"); 21 | result = multicall() 22 | multicall.calc("TestPBip66","Aform",6,"./pbip.ply","./M13.txt"); 23 | result = multicall() 24 | -------------------------------------------------------------------------------- /pyDAEDALUS/tet.ply: -------------------------------------------------------------------------------- 1 | ply 2 | format ascii 1.0 3 | element vertex 4 4 | property float32 x 5 | property float32 y 6 | property float32 z 7 | element face 4 8 | property list uint8 int32 vertex_indices 9 | end_header 10 | 0.000000 0.000000 0.612372 11 | -0.288675 -0.500000 -0.204124 12 | -0.288675 0.500000 -0.204124 13 | 0.577350 0.000000 -0.204124 14 | 3 0 2 1 15 | 3 0 1 3 16 | 3 0 3 2 17 | 3 1 2 3 18 | -------------------------------------------------------------------------------- /pyDAEDALUSX_instructions.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lcbb/pyDAEDALUS/139f47bb27144a5121d8218a8fa4a61e9ae05832/pyDAEDALUSX_instructions.pdf -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- 1 | numpy>=1.11.1 2 | matplotlib>=1.5.1 3 | networkx==1.11 4 | scipy>=0.18.0 5 | click>=6.6 6 | mpmath>=0.19 7 | mock>=2.0.0 8 | tqdm>=4.9.0 9 | flake8>=3.2.0 10 | --------------------------------------------------------------------------------