From 5beab314d62e1b3a8986201477c55808bc861810 Mon Sep 17 00:00:00 2001
From: yokochi47 <yokochi47@gmail.com>
Date: Tue, 27 Feb 2024 12:39:05 +0900
Subject: [PATCH] Fix ValueError and prevent numpy.RuntimeWarning: mean of
 empty slice

---
 wwpdb/utils/nmr/io/CifReader.py          |  6 ++-
 wwpdb/utils/nmr/mr/ParserListenerUtil.py | 47 ++++++++++++------------
 2 files changed, 28 insertions(+), 25 deletions(-)

diff --git a/wwpdb/utils/nmr/io/CifReader.py b/wwpdb/utils/nmr/io/CifReader.py
index 2fe13473d..afdae3377 100644
--- a/wwpdb/utils/nmr/io/CifReader.py
+++ b/wwpdb/utils/nmr/io/CifReader.py
@@ -1437,7 +1437,8 @@ def __calculateRmsd(self, chain_ids, lengths, total_models=1, eff_model_ids: lis
 
                     _rmsd.append(_rmsd_)
 
-            item['mean_rmsd'] = float(f"{np.mean(np.array(_rmsd)):.4f}")
+            if len(_rmsd) > 0:
+                item['mean_rmsd'] = float(f"{np.mean(np.array(_rmsd)):.4f}")
 
             _, v = np.linalg.eig(r)
             x = np.delete(np.abs(v), np.s_[1:], 1)
@@ -1466,7 +1467,8 @@ def __calculateRmsd(self, chain_ids, lengths, total_models=1, eff_model_ids: lis
 
                 _rmsd.append(calculate_rmsd(_bb_atom_site_p, _bb_atom_site_q))
 
-            item['medoid_rmsd'] = float(f"{np.mean(np.array(_rmsd)):.4f}")
+            if len(_rmsd) > 0:
+                item['medoid_rmsd'] = float(f"{np.mean(np.array(_rmsd)):.4f}")
 
             _item = copy.copy(item)
 
diff --git a/wwpdb/utils/nmr/mr/ParserListenerUtil.py b/wwpdb/utils/nmr/mr/ParserListenerUtil.py
index 3d3767932..15fb68cf5 100644
--- a/wwpdb/utils/nmr/mr/ParserListenerUtil.py
+++ b/wwpdb/utils/nmr/mr/ParserListenerUtil.py
@@ -5729,7 +5729,7 @@ def retrieve_label_comp_id(_seqId, _compId):
         starAtom['chain_id'], starAtom['seq_id'], starAtom['entity_id'], _ = authToStarSeq[seqKey]
         return starAtom
 
-    if chainId in offsetHolder:
+    if chainId in offsetHolder and seqId is not None:
         offset = offsetHolder[chainId]
         seqKey = (chainId, seqId + offset, compId)
         if has_aux_atom:
@@ -5739,7 +5739,7 @@ def retrieve_label_comp_id(_seqId, _compId):
             atom['seq_id'] = seqId + offset
             return starAtom
 
-    elif f'_{chainId}' in offsetHolder:
+    elif f'_{chainId}' in offsetHolder and seqId is not None:
         offset = offsetHolder[f'_{chainId}']
         seqKey = (chainId, seqId + offset, compId)
         if seqKey in authToStarSeq:
@@ -5751,27 +5751,28 @@ def retrieve_label_comp_id(_seqId, _compId):
         starAtom['chain_id'], starAtom['seq_id'], starAtom['entity_id'], _ = authToStarSeq[seqKey]
         return starAtom
 
-    for offset in range(1, 1000):
-        seqKey = (chainId, seqId + offset, compId)
-        if has_aux_atom:
-            auxSeqKey = (auxChainId, auxSeqId + offset, auxCompId)
-        if seqKey in authToStarSeq and (not has_aux_atom or (has_aux_atom and auxSeqKey in authToStarSeq)):
-            starAtom['chain_id'], starAtom['seq_id'], starAtom['entity_id'], _ = authToStarSeq[seqKey]
-            offsetHolder[chainId] = offset
-            if has_aux_atom and compId in monDict3 and auxCompId in monDict3:
-                offsetHolder[f'_{chainId}'] = offset
-            atom['seq_id'] = seqId + offset
-            return starAtom
-        seqKey = (chainId, seqId - offset, compId)
-        if has_aux_atom:
-            auxSeqKey = (auxChainId, auxSeqId + offset, auxCompId)
-        if seqKey in authToStarSeq and (not has_aux_atom or (has_aux_atom and auxSeqKey in authToStarSeq)):
-            starAtom['chain_id'], starAtom['seq_id'], starAtom['entity_id'], _ = authToStarSeq[seqKey]
-            offsetHolder[chainId] = -offset
-            if has_aux_atom and compId in monDict3 and auxCompId in monDict3:
-                offsetHolder[f'_{chainId}'] = -offset
-            atom['seq_id'] = seqId - offset
-            return starAtom
+    if seqId is not None:
+        for offset in range(1, 1000):
+            seqKey = (chainId, seqId + offset, compId)
+            if has_aux_atom:
+                auxSeqKey = (auxChainId, auxSeqId + offset, auxCompId)
+            if seqKey in authToStarSeq and (not has_aux_atom or (has_aux_atom and auxSeqKey in authToStarSeq)):
+                starAtom['chain_id'], starAtom['seq_id'], starAtom['entity_id'], _ = authToStarSeq[seqKey]
+                offsetHolder[chainId] = offset
+                if has_aux_atom and compId in monDict3 and auxCompId in monDict3:
+                    offsetHolder[f'_{chainId}'] = offset
+                atom['seq_id'] = seqId + offset
+                return starAtom
+            seqKey = (chainId, seqId - offset, compId)
+            if has_aux_atom:
+                auxSeqKey = (auxChainId, auxSeqId + offset, auxCompId)
+            if seqKey in authToStarSeq and (not has_aux_atom or (has_aux_atom and auxSeqKey in authToStarSeq)):
+                starAtom['chain_id'], starAtom['seq_id'], starAtom['entity_id'], _ = authToStarSeq[seqKey]
+                offsetHolder[chainId] = -offset
+                if has_aux_atom and compId in monDict3 and auxCompId in monDict3:
+                    offsetHolder[f'_{chainId}'] = -offset
+                atom['seq_id'] = seqId - offset
+                return starAtom
 
     _seqKey = next((_seqKey for _seqKey in authToStarSeq if chainId == _seqKey[0] and seqId == _seqKey[1]), None)
     if has_aux_atom: