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nipah_config.yaml
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#These are parameters for different site subsets of the RBP
contact_sites: [239, 240, 241, 242, 305, 388, 389, 401, 402, 458, 488, 489, 490, 491, 492, 501, 504, 505, 506, 507, 530, 531, 532, 533, 555, 557, 558, 559, 579, 580, 581, 583, 588]
efnb2_contact_sites: [216, 238, 239, 240, 241, 242, 305, 388, 389, 401, 402, 404, 458, 488, 489, 490, 491, 492, 501, 503, 504, 505, 506, 507, 528, 530, 531, 532, 533, 555, 557, 558, 559, 579, 580, 581, 583, 584, 588]
efnb3_contact_sites: [217, 218, 238, 239, 240, 241, 242, 305, 388, 389, 401, 402, 458, 488, 489, 490, 491, 492, 501, 504, 505, 506, 507, 529, 530, 531, 532, 533, 554, 555, 557, 558, 559, 579, 580, 581, 583, 584, 588, 589, 590]
glycans: [159, 306, 378, 417, 481, 529]
dimerization: [160, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 202, 203, 204, 205, 206, 208, 210, 212, 237, 238, 239, 240, 242, 247, 249, 256, 258, 259, 260, 261, 266, 267, 268, 270, 323, 324, 325, 331, 584, 589, 591]
dimer_A: [160, 162, 163, 164, 165, 166, 169, 171, 205, 206, 208, 247, 249, 256, 258, 259, 260, 261, 266, 267, 268, 270, 323, 324, 325, 331]
dimer_B: [167, 168, 170, 171, 172, 202, 203, 204, 205, 208, 210, 212, 237, 238, 239, 240, 242, 258, 584, 589, 591]
nipah_poly: [82, 89, 135, 172, 228, 236, 274, 288, 299, 325, 328, 329, 335, 339, 344, 376, 381, 384, 385, 386, 404, 421, 423, 424, 426, 427, 470, 478, 481, 498, 502, 545]
hendra_poly: [76, 82, 85, 86, 89, 90, 96, 98, 136, 144, 174, 175, 176, 180, 187, 194, 195, 196, 201, 209, 210, 211, 212, 213, 215, 224, 226, 228, 236, 241, 244, 245, 261, 265, 277, 279, 280, 284, 285, 287, 288, 289, 293, 299, 309, 311, 312, 315, 316, 317, 322, 326, 327, 329, 333, 334, 335, 337, 338, 339, 340, 342, 344, 371, 376, 385, 386, 388, 392, 401, 402, 403, 404, 420, 422, 423, 424, 425, 426, 427, 432, 434, 437, 446, 458, 466, 470, 473, 476, 478, 483, 498, 502, 507, 517, 520, 525, 527, 538, 548, 549, 550, 553, 554, 564, 569, 571, 586, 599, 602]
beta_sheet: [201, 202, 203, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 263, 264, 265, 266, 267, 268, 269, 270, 271, 279, 280, 281, 282, 283, 284, 285, 286, 287, 290, 291, 292, 293, 294, 295, 296, 297, 314, 315, 316, 317, 318, 319, 320, 332, 333, 334, 335, 336, 340, 341, 347, 348, 349, 350, 356, 357, 358, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 426, 427, 428, 429, 430, 442, 443, 444, 445, 446, 447, 450, 451, 452, 453, 454, 455, 465, 466, 467, 468, 469, 470, 471, 476, 477, 478, 479, 511, 512, 513, 514, 515, 520, 521, 522, 523, 524, 525, 526, 535, 536, 537, 538, 539, 540, 541, 544, 545, 546, 547, 548, 549, 550, 557, 558, 559, 560, 561, 562, 563, 564, 565, 566, 567, 568, 571, 572, 573, 574, 575, 576, 577, 578, 579, 580, 581, 587, 588, 591, 592, 593, 594, 595, 596]
### Functional selection filtering parameters
func_times_seen_cutoff: 2
func_std_cutoff: 1
percent_selections: 0.5 #mutants must be present in at least 50% of selections
### Binding filtering parameters
min_times_seen_binding: 2.5 #2
max_binding_std: 2 #3
min_func_effect_for_binding: -1.5
### Antibody escape filtering parameters
min_times_seen_ab: 2
max_ab_std: 3
frac_models: 0.5
min_func_effect_for_ab: -2
### Heatmap parameters
effect_color: 'redblue'
entropy_color: 'browns'
strokewidth_size: 0.5 #strokesize around boxes
background_color: "#d1d3d4" #color for cells without observations
### General Figure properties
width: 200
height: 200
neut_curve_width: 300
neut_curve_height: 200
bubble_width: 300
bubble_height: 250
large_line_width: 800
large_line_height: 100