From f374476678ba08b21113a96c6415cfb33260b5d8 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 13 Apr 2022 09:30:10 +0200
Subject: [PATCH] add function to extract number of contacts expected for a
certain chain
---
modules/mol/alg/pymod/lddt.py | 24 ++++++++++++++++++++++++
1 file changed, 24 insertions(+)
diff --git a/modules/mol/alg/pymod/lddt.py b/modules/mol/alg/pymod/lddt.py
index 4c7bae88b..12a4bcc73 100644
--- a/modules/mol/alg/pymod/lddt.py
+++ b/modules/mol/alg/pymod/lddt.py
@@ -496,6 +496,30 @@ class lDDTScorer:
else:
return lDDT, per_res_lDDT
+ def GetNContacts(self, target_chain, no_interchain=False):
+ """Returns number of contacts expected for a certain chain in *target*
+
+ :param target_chain: Chain in *target* for which you want the number
+ of expected contacts
+ :type target_chain: :class:`str`
+ :param no_interchain: Whether to exclude interchain contacts
+ :type no_interchain: :class:`bool`
+ :raises: :class:`RuntimeError` if specified chain doesnt exist
+ """
+ if target_chain not in self.chain_names:
+ raise RuntimeError(f"Specified chain name ({target_chain}) not in "
+ f"target")
+ ch_idx = self.chain_names.index(target_chain)
+ s = self.chain_start_indices[ch_idx]
+ e = self.n_atoms
+ if ch_idx + 1 < len(self.chain_names):
+ e = self.chain_start_indices[ch_idx+1]
+ if no_interchain:
+ return self._GetNExp(list(range(s, e)), self.ref_indices_sc)
+ else:
+ return self._GetNExp(list(range(s, e)), self.ref_indices)
+
+
def _GetExtraModelChainPenalty(self, model, chain_mapping):
"""Counts n distances in extra model chains to be added as penalty
"""
--
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