From d96fc204e217b81da7ba67d7ebee24f2adf0d213 Mon Sep 17 00:00:00 2001
From: B13nch3n <b13nch3n_01@theb-si.de>
Date: Thu, 10 Nov 2022 17:10:00 +0100
Subject: [PATCH] Allow homo-di-mers
---
Dockerfile | 2 +-
translate2modelcif.py | 14 ++++++++++++++
2 files changed, 15 insertions(+), 1 deletion(-)
diff --git a/Dockerfile b/Dockerfile
index 9eb82c8..3d95b53 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -44,7 +44,7 @@ RUN set -e pipefail; \
ARG ADD_DEV
RUN set -e pipefail; \
if test xYES = x`echo ${ADD_DEV} | tr '[:lower:]' '[:upper:]'`; then \
- apt-get install -y pip emacs; \
+ apt-get install -y pip emacs less; \
pip install black pylint; \
apt-get remove -y pip; \
apt-get -y autoremove; \
diff --git a/translate2modelcif.py b/translate2modelcif.py
index b0ff7fe..82beb3b 100644
--- a/translate2modelcif.py
+++ b/translate2modelcif.py
@@ -663,9 +663,23 @@ def _get_entities(pdb_file, up_acs):
"""Gather data for the mmCIF (target) entities."""
entities = []
ost_ent = io.LoadPDB(pdb_file)
+ already_seen = []
for i, chn in enumerate(ost_ent.chains):
cif_ent = {}
sqe = _get_sequence(chn)
+ try:
+ e_idx = already_seen.index(up_acs[i])
+ except ValueError:
+ pass
+ else:
+ if sqe != entities[e_idx]["pdb_sequence"]:
+ _abort_msg(
+ "Sequences are different for two chains of the same "
+ "UniProtKB AC. This case is not implemented, yet."
+ )
+ entities[e_idx]["pdb_chain_id"].append(chn.name)
+ continue
+ already_seen.append(up_acs[i])
upkb = _get_upkb_for_sequence(sqe, up_acs[i])
cif_ent["pdb_sequence"] = sqe
cif_ent["pdb_chain_id"] = [chn.name]
--
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