From 82f56dfe5044d7afd31dfd69bda3bdba1c84f70e Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Tue, 21 Feb 2023 14:06:21 +0100
Subject: [PATCH] lDDT: remove any requirements on residue numbers
That was 1) strictly increasing (no idea why it was there in a first place)
2) no ins codes (The residue mapper is a dict which now has actual residue
numbers as key - can handle insertion codes)
---
modules/mol/alg/pymod/lddt.py | 19 +------------------
1 file changed, 1 insertion(+), 18 deletions(-)
diff --git a/modules/mol/alg/pymod/lddt.py b/modules/mol/alg/pymod/lddt.py
index cb5d90ccf..92f41ec4c 100644
--- a/modules/mol/alg/pymod/lddt.py
+++ b/modules/mol/alg/pymod/lddt.py
@@ -738,12 +738,6 @@ class lDDTScorer:
rnums.append(None)
else:
rnums = [r.GetNumber() for r in ch.residues]
- if sum([len(rn.GetInsCode().strip("\0")) for rn in rnums]) > 0:
- raise RuntimeError(
- "Residue numbers in model must not "
- "contain insertion codes"
- )
- rnums = [rn.GetNum() for rn in rnums]
return rnums
@@ -828,20 +822,9 @@ class lDDTScorer:
f"chain {ch_name} has SEQRES "
f"ATOMSEQ mismatch"
)
- rnums.append(rnum)
+ rnums.append(mol.ResNum(rnum))
else:
rnums = [r.GetNumber() for r in ch.residues]
- if sum([len(rn.GetInsCode().strip("\0")) for rn in rnums]) > 0:
- raise RuntimeError(
- "Residue numbers in target must not "
- "contain insertion codes"
- )
- rnums = [rnum.GetNum() for rnum in rnums]
- if not all(x < y for x, y in zip(rnums, rnums[1:])):
- raise RuntimeError(
- "Residue numbers in each target chain "
- "must be monotonically increasing"
- )
assert len(rnums) == len(ch.residues)
residue_numbers[ch_name] = rnums
return residue_numbers
--
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