[4] Implement frame based backmapping

bin/polyply

@@ -162,7 +162,11 @@ def main(): # pylint: disable=too-many-locals,too-many-statements
                                          ' when RW fails in first attempt'))
 
     backmap_group = parser_gen_coords.add_argument_group('Options for backmapping')
-    backmap_group.add_argument('-back_fudge', dest='bfudge', type=float, default=0.4,
+    backmap_group.add_argument('-bm_mode', dest='bmode', type=str, default='automatic',
+                               choices=['automatic', 'by-bonds'],
+                               help='choose which backmapping mode to use.')
+
+    backmap_group.add_argument('-bm_fudge', dest='bfudge', type=float, default=0.4,
                                help='factor by which to scale the coordinates when backmapping.')
 
     parser_gen_coords.set_defaults(func=gen_coords)

polyply/data/martini2/nucleobase_templates.bld

@@ -0,0 +1,214 @@
+[ template ]
+resname DC
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+BB2 SN0 20.58 14.06 7.39
+BB3 SC2 21.88 15.28 6.42
+SC1 TN0 20.0 16.59 5.02
+SC2 TY2 19.75 15.72 3.18
+SC3 TY3 18.78 18.5 3.87
+[ bonds ]
+BB1 BB2
+BB2 BB3
+BB3 SC1
+SC1 SC2
+SC1 SC3
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+
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+SC2 TG2 13.75 21.28 18.44
+SC3 TG3 14.47 19.57 20.76
+SC4 TNa 12.7 17.71 19.53
+[ bonds ]
+BB1 BB2
+BB2 BB3
+BB3 SC1
+SC1 SC2
+SC1 SC4
+SC2 SC3
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+
+[ template ]
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+SC2 TT2 6.09 14.98 14.1
+SC3 TT3 4.73 14.22 11.26
+[ bonds ]
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+SC2 TA2 -1.94 15.49 6.74
+SC3 TA3 -2.86 17.29 5.16
+SC4 TNa -0.74 18.49 6.55
+[ bonds ]
+BB1 BB2
+BB2 BB3
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+
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+SC3 TA3 5.34 10.85 16.11
+SC4 TNa 4.45 13.43 15.58
+[ bonds ]
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+SC2 SC3
+SC2 SC4
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+[ template ]
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+SC3 TY3 12.24 1.45 9.49
+[ bonds ]
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+
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+SC3 TG3 1.09 18.29 20.18
+SC4 TNa 2.45 18.28 22.67
+[ bonds ]
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+SC2 SC4
+SC3 SC4
+
+[ template ]
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+SC3 TA3 9.15 3.41 7.83
+SC4 TNa 9.45 4.45 10.32
+[ bonds ]
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+[ template ]
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+SC3 TT3 9.48 7.46 4.18
+[ bonds ]
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+SC1 SC2
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+BB3 SC2 8.88 23.93 27.96
+SC1 TN0 7.91 21.68 27.02
+SC2 TT2 9.18 20.96 25.44
+SC3 TT3 6.18 19.92 26.09
+[ bonds ]
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+BB2 BB3
+BB3 SC1
+SC1 SC2
+SC1 SC3
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+
+[ template ]
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+BB3 SC2 1.04 28.71 15.7
+SC1 TN0 -0.63 28.54 18.26
+SC2 TG2 -3.46 29.44 18.57
+SC3 TG3 -2.29 28.72 21.19
+SC4 TNa 0.12 28.43 19.67
+[ bonds ]
+BB1 BB2
+BB2 BB3
+BB3 SC1
+SC1 SC2
+SC1 SC4
+SC2 SC3
+SC2 SC4
+SC3 SC4
+
+[ template ]
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+[ atoms ]
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+BB3 SC2 13.82 23.52 3.27
+SC1 TN0 11.87 24.43 1.57
+SC2 TY2 10.93 22.83 0.64
+SC3 TY3 10.69 25.71 -0.3
+[ bonds ]
+BB2 BB3
+BB3 SC1
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+SC1 SC3
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+