RNApolis 0.10.6__py3-none-any.whl → 0.10.7__py3-none-any.whl

rnapolis/common.py

@@ -1084,33 +1084,41 @@ class BaseInteractions:
         base_phosphate_interactions: List[BasePhosphate],
         other_interactions: List[OtherInteraction],
     ) -> "BaseInteractions":
-        auth2residue3d = {}
-        auth2label = {}
-        label2auth = {}
+        cni2residue = {}
+        cni2label = {}
+        cni2auth = {}
 
         for residue3d in structure3d.residues:
-            auth2residue3d[residue3d.auth] = residue3d
-            auth2label[residue3d.auth] = residue3d.label
-            label2auth[residue3d.label] = residue3d.auth
+            cni = (residue3d.chain, residue3d.number, residue3d.icode or None)
+            cni2auth[cni] = residue3d.auth
+            cni2label[cni] = residue3d.label
+            cni2residue[cni] = residue3d
 
         def unify_nt(nt: Residue) -> Residue:
             if nt.auth is not None and nt.label is not None:
                 return nt
+            cni = (nt.chain, nt.number, nt.icode or None)
             if nt.auth is not None:
-                return Residue(label=auth2label.get(nt.auth, None), auth=nt.auth)
+                return Residue(label=cni2label.get(cni, None), auth=nt.auth)
             if nt.label is not None:
-                return Residue(label=nt.label, auth=label2auth.get(nt.label, None))
+                return Residue(label=nt.label, auth=cni2auth.get(cni, None))
             return nt
 
         base_pairs_new = []
         for base_pair in base_pairs:
             nt1 = unify_nt(base_pair.nt1)
             nt2 = unify_nt(base_pair.nt2)
-            saenger = base_pair.saenger or Saenger.from_leontis_westhof(
-                auth2residue3d[nt1.auth].one_letter_name,
-                auth2residue3d[nt2.auth].one_letter_name,
-                base_pair.lw,
-            )
+
+            cni1 = (nt1.chain, nt1.number, nt1.icode or None)
+            cni2 = (nt2.chain, nt2.number, nt2.icode or None)
+            if cni1 not in cni2residue or cni2 not in cni2residue:
+                saenger = base_pair.saenger
+            else:
+                saenger = base_pair.saenger or Saenger.from_leontis_westhof(
+                    cni2residue[cni1].one_letter_name,
+                    cni2residue[cni2].one_letter_name,
+                    base_pair.lw,
+                )
             if (
                 nt1 != base_pair.nt1
                 or nt2 != base_pair.nt2

{rnapolis-0.10.6.dist-info → rnapolis-0.10.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: RNApolis
-Version: 0.10.6
+Version: 0.10.7
 Summary: A Python library containing RNA-related bioinformatics functions and classes
 Home-page: https://github.com/tzok/rnapolis-py
 Author: Tomasz Zok

{rnapolis-0.10.6.dist-info → rnapolis-0.10.7.dist-info}/RECORD

@@ -2,7 +2,7 @@ rnapolis/adapter.py,sha256=6hJTweIqUXH8CEGvi8oupFzk5etkIt8Q2bqRvgsqako,62169
 rnapolis/aligner.py,sha256=o7rQyjAZ3n4VXcnSPY3HVB8nLNRkVbl552O3NVh0mfg,3429
 rnapolis/annotator.py,sha256=HA2hfEUXdmBElObqRlASAB1FgkysjiHgwMTjEhsDiDE,30277
 rnapolis/clashfinder.py,sha256=AC9_tIx7QIk57sELq_aKfU1u3UMOXbgcccQeGHhMR6c,8517
-rnapolis/common.py,sha256=hamlW892ZF5A0dSWsl7cOCZqOpbVQMgXjVPYDFzk3pE,36347
+rnapolis/common.py,sha256=qifqTIiq43jeR1xKK3301PbRMo7vaZgjQauG-G7asSc,36686
 rnapolis/component_A.csv,sha256=koirS-AwUZwoYGItT8yn3wS6Idvmh2FANfTQcOS_xh8,2897
 rnapolis/component_C.csv,sha256=NtvsAu_YrUgTjzZm3j4poW4IZ99x3dPARB09XVIiMCc,2803
 rnapolis/component_G.csv,sha256=Z5wl8OnHRyx4XhTyBiWgRZiEvmZXhoxtVRH8bn6Vxf0,2898
@@ -22,9 +22,9 @@ rnapolis/tertiary_v2.py,sha256=SgijTv0bPqMJwsMqyQk0O8QAnS2Ozk45vk8igxt9hRs,38001
 rnapolis/transformer.py,sha256=aC0nBmHHJf5TyLvBIV57Jj3tlwpvHbPo347opfAOlQA,3844
 rnapolis/unifier.py,sha256=2ge7IB9FdRgzSAiVD39U_ciwtdDJ2fGzf8mUIudbrqY,5820
 rnapolis/util.py,sha256=IdquFO3PV1_KDqodjupzm0Rqvgy0CeSzxGHaGEHYXVU,543
-rnapolis-0.10.6.dist-info/licenses/LICENSE,sha256=ZGRu12MzCgbYA-Lt8MyBlmjvPZh7xfiD5u5wBx0enq4,1066
-rnapolis-0.10.6.dist-info/METADATA,sha256=Q2OY_Y3PZgVNaob7Xk8vruYNZ13HyFfdiRD7giJqJ_I,54611
-rnapolis-0.10.6.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-rnapolis-0.10.6.dist-info/entry_points.txt,sha256=MZMWnYBUYnis-zWDmFfuA5yXtU3W5YdQrm5HA5LrkeM,474
-rnapolis-0.10.6.dist-info/top_level.txt,sha256=LcO18koxZcWoJ21KDRRRo_tyIbmXL5z61dPitZpy8yc,9
-rnapolis-0.10.6.dist-info/RECORD,,
+rnapolis-0.10.7.dist-info/licenses/LICENSE,sha256=ZGRu12MzCgbYA-Lt8MyBlmjvPZh7xfiD5u5wBx0enq4,1066
+rnapolis-0.10.7.dist-info/METADATA,sha256=QPuGPZ96VIjvQPiLkk4bS4vstWqO6cok6e4vID33vg0,54611
+rnapolis-0.10.7.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+rnapolis-0.10.7.dist-info/entry_points.txt,sha256=MZMWnYBUYnis-zWDmFfuA5yXtU3W5YdQrm5HA5LrkeM,474
+rnapolis-0.10.7.dist-info/top_level.txt,sha256=LcO18koxZcWoJ21KDRRRo_tyIbmXL5z61dPitZpy8yc,9
+rnapolis-0.10.7.dist-info/RECORD,,