From 385a4962f87f15c1cf6bb75bcb6f86ccbc059c68 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Mon, 3 May 2021 21:19:12 +0200
Subject: [PATCH] add QMEANBrane membrane annotation in container output
---
docker/README.md | 2 ++
docker/qmeanbrane_example/out.json | 2 +-
docker/run_qmean.py | 14 +++++++++++---
3 files changed, 14 insertions(+), 4 deletions(-)
diff --git a/docker/README.md b/docker/README.md
index e19117e..51cc277 100644
--- a/docker/README.md
+++ b/docker/README.md
@@ -234,6 +234,8 @@ keys:
as the corresponding SEQRES (ATOMSEQ if SEQRES is not given as an input).
The location of a residue in SEQRES determines the location of its local score
in the score list.
+* `qmeanbrane_membrane`: Only available in case of QMEANBrane. Defines
+ transmembrane residues with the same SEQRES mapping as the local scores.
<a name="examples"></a>Examples
diff --git a/docker/qmeanbrane_example/out.json b/docker/qmeanbrane_example/out.json
index 6458759..ab7ad7c 100644
--- a/docker/qmeanbrane_example/out.json
+++ b/docker/qmeanbrane_example/out.json
@@ -1 +1 @@
-{"qmean_version": "4.2.0", "created": "2021-05-03T07:50:37", "method": "QMEANBrane", "seqres_uploaded": [{"name": "trg_seq_0", "sequence": "MNSISDERETWSGKVDFLLSVIGFAVDLANVWRFPYLCYKNGGGAFLVPYGIMLAVGGIPLFYMELALGQHNRKGAITCWGRLVPLFKGIGYAVVLIAFYVDFYYNVIIAWSLRFFFASFTNSLPWTSCNNIWNTPNCRPFESQGFQSAASEYFNRYILELNRSEGIHDLGAIKWDMALCLLIVYLICYFSLWKGISTSGKVVWFTALFPYAALLILLIRGLTLPGSFLGIQYYLTPNFSAIYKAEVWADAATQVFFSLGPGFGVLLAYASYNKYHNNVYKDALLTSFINSATSFIAGFVIFSVLGYMAHTLGVRIEDVATEGPGLVFVVYPAAIATMPASTFWALIFFMMLATLGLDSSFGGSEAIITALSDEFPKIKRNRELFVAGLFSLYFVVGLASCTQGGFYFFHLLDRYAAGYSILVAVFFEAIAVSWIYGTNRFSEDIRDMIGFPPGRYWQVCWRFVAPIFLLFITVYLLIGYEPLTYADYVYPSWANALGWCIAGSSVVMIPAVAIFKLLSTPGSLRQRFTILTTPWRDQQLVPR"}], "qmtl_version": null, "error_log": "", "info_log": "User defined workdir: my_workdir\nUse UniClust30: /uniclust30/uniclust30_2018_08\nUse compound library with creation date 2021-04-29\nUse precomputed a3m file (SEQRES md5 hash: 2044234b0bd6d322ef6c15ab03394e61)\n", "models": {"model_001": {"chains": {"A": {"atomseq": "RETWSGKVDFLLSVIGFAVDLANVWRFPYLCYKNGGGAFLVPYGIMLAVGGIPLFYMELALGQHNRKGAITCWGRLVPLFKGIGYAVVLIAFYVDFYYNVIIAWSLRFFFASFTNSLPWTSCNNIWNTPNCRPFESQGFQSAASEYFNRYILELNRSEGIHDLGAIKWDMALCLLIVYLICYFSLWKGISTSGKVVWFTALFPYAALLILLIRGLTLPGSFLGIQYYLTPNFSAIYKAEVWADAATQVFFSLGPGFGVLLAYASYNKYHNNVYKDALLTSFINSATSFIAGFVIFSVLGYMAHTLGVRIEDVATEGPGLVFVVYPAAIATMPASTFWALIFFMMLATLGLDSSFGGSEAIITALSDEFPKIKRNRELFVAGLFSLYFVVGLASCTQGGFYFFHLLDRYAAGYSILVAVFFEAIAVSWIYGTNRFSEDIRDMIGFPPGRYWQVCWRFVAPIFLLFITVYLLIGYEPLTYADYVYPSWANALGWCIAGSSVVMIPAVAIFKLLSTPGSLRQ", "seqres": "MNSISDERETWSGKVDFLLSVIGFAVDLANVWRFPYLCYKNGGGAFLVPYGIMLAVGGIPLFYMELALGQHNRKGAITCWGRLVPLFKGIGYAVVLIAFYVDFYYNVIIAWSLRFFFASFTNSLPWTSCNNIWNTPNCRPFESQGFQSAASEYFNRYILELNRSEGIHDLGAIKWDMALCLLIVYLICYFSLWKGISTSGKVVWFTALFPYAALLILLIRGLTLPGSFLGIQYYLTPNFSAIYKAEVWADAATQVFFSLGPGFGVLLAYASYNKYHNNVYKDALLTSFINSATSFIAGFVIFSVLGYMAHTLGVRIEDVATEGPGLVFVVYPAAIATMPASTFWALIFFMMLATLGLDSSFGGSEAIITALSDEFPKIKRNRELFVAGLFSLYFVVGLASCTQGGFYFFHLLDRYAAGYSILVAVFFEAIAVSWIYGTNRFSEDIRDMIGFPPGRYWQVCWRFVAPIFLLFITVYLLIGYEPLTYADYVYPSWANALGWCIAGSSVVMIPAVAIFKLLSTPGSLRQRFTILTTPWRDQQLVPR"}}, "original_name": "original_hhblits_alignment.pdb", "preprocessing": {"molck_log": "removing atoms with zero occupancy\n --> removed 0 atoms with zero occupancy\nremoving hydrogen atoms\n --> removed 0 hydrogen atoms\n", "atomsRemoved": 0, "residuesRemoved": 0, "chainsRemoved": 0, "chain_name_mapping": {"A": "A"}}, "scores": {"local_scores": {"A": [null, null, null, null, null, null, null, 0.534, 0.65, 0.662, 0.625, 0.62, 0.651, 0.639, 0.677, 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"ss_agreement_norm_score": 0.447, "ss_agreement_z_score": -1.735, "acc_agreement_norm_score": 0.64, "acc_agreement_z_score": -0.697, "avg_local_score": 0.613, "avg_local_score_error": null}}}, "model_002": {"chains": {"A": {"atomseq": "RETWSGKVDFLLSVIGFAVDLANVWRFPYLCYKNGGGAFLVPYGIMLAVGGIPLFYMELALGQHNRKGAITCWGRLVPLFKGIGYAVVLIAFYVDFYYNVIIAWSLRFFFASFTNSLPWTSCNNIWNTPNCRPFESQGFQSAASEYFNRYILELNRSEGIHDLGAIKWDMALCLLIVYLICYFSLWKGISTSGKVVWFTALFPYAALLILLIRGLTLPGSFLGIQYYLTPNFSAIYKAEVWADAATQVFFSLGPGFGVLLAYASYNKYHNNVYKDALLTSFINSATSFIAGFVIFSVLGYMAHTLGVRIEDVATEGPGLVFVVYPAAIATMPASTFWALIFFMMLATLGLDSSFGGSEAIITALSDEFPKIKRNRELFVAGLFSLYFVVGLASCTQGGFYFFHLLDRYAAGYSILVAVFFEAIAVSWIYGTNRFSEDIRDMIGFPPGRYWQVCWRFVAPIFLLFITVYLLIGYEPLTYADYVYPSWANALGWCIAGSSVVMIPAVAIFKLLSTPGSLRQ", "seqres": "MNSISDERETWSGKVDFLLSVIGFAVDLANVWRFPYLCYKNGGGAFLVPYGIMLAVGGIPLFYMELALGQHNRKGAITCWGRLVPLFKGIGYAVVLIAFYVDFYYNVIIAWSLRFFFASFTNSLPWTSCNNIWNTPNCRPFESQGFQSAASEYFNRYILELNRSEGIHDLGAIKWDMALCLLIVYLICYFSLWKGISTSGKVVWFTALFPYAALLILLIRGLTLPGSFLGIQYYLTPNFSAIYKAEVWADAATQVFFSLGPGFGVLLAYASYNKYHNNVYKDALLTSFINSATSFIAGFVIFSVLGYMAHTLGVRIEDVATEGPGLVFVVYPAAIATMPASTFWALIFFMMLATLGLDSSFGGSEAIITALSDEFPKIKRNRELFVAGLFSLYFVVGLASCTQGGFYFFHLLDRYAAGYSILVAVFFEAIAVSWIYGTNRFSEDIRDMIGFPPGRYWQVCWRFVAPIFLLFITVYLLIGYEPLTYADYVYPSWANALGWCIAGSSVVMIPAVAIFKLLSTPGSLRQRFTILTTPWRDQQLVPR"}}, "original_name": "shift_in_front_helix_four.pdb", "preprocessing": {"molck_log": "removing atoms with zero occupancy\n --> removed 0 atoms with zero occupancy\nremoving hydrogen atoms\n --> removed 0 hydrogen atoms\n", "atomsRemoved": 0, "residuesRemoved": 0, "chainsRemoved": 0, "chain_name_mapping": {"A": "A"}}, "scores": {"local_scores": {"A": [null, null, null, null, null, null, null, 0.516, 0.615, 0.68, 0.654, 0.651, 0.704, 0.675, 0.729, 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\ No newline at end of file
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\ No newline at end of file
diff --git a/docker/run_qmean.py b/docker/run_qmean.py
index b3984eb..1f7d2fa 100755
--- a/docker/run_qmean.py
+++ b/docker/run_qmean.py
@@ -322,6 +322,7 @@ class ModelScorer:
# the following members remain empty until you call score()
self.local_scores = None
self.global_scores = None
+ self.qmeanbrane_membrane = None # only set in case of QMEANBrane
def to_json(self):
out_dict = dict()
@@ -339,6 +340,8 @@ class ModelScorer:
"local_scores": self.local_scores,
"global_scores": self.global_scores,
}
+ if self.qmeanbrane_membrane:
+ out_dict["qmeanbrane_membrane"] = self.qmeanbrane_membrane
return out_dict
def score(
@@ -420,6 +423,7 @@ class ModelScorer:
)
local_scores = dict()
+ qmeanbrane_membrane = None
if scoring_function in ["QMEANDisCo", "QMEAN"]:
for chn, seq in zip(scorer.model.chains, self.seqres_list):
@@ -434,6 +438,7 @@ class ModelScorer:
local_scores[chn.GetName()] = score_list
elif scoring_function == "QMEANBrane":
# the global scores are the same as QMEAN but the local ones change
+ qmeanbrane_membrane = dict()
settings = qmean_config.MembraneSettings()
peptide_sel = self.processed_model.Select("peptide=True")
res = mqa_result_membrane.LocalMembraneResult.Create(
@@ -445,23 +450,26 @@ class ModelScorer:
)
for ch, s in zip(peptide_sel.chains, self.seqres_list):
- score_list = list([None] * len(s))
- local_scores[ch.GetName()] = score_list
-
+ local_scores[ch.GetName()] = list([None] * len(s))
+ qmeanbrane_membrane[ch.GetName()] = list([None] * len(s))
chain_name_idx = res.score_table.GetColIndex("chain")
rnum_idx = res.score_table.GetColIndex("rnum")
+ membrane_idx = res.score_table.GetColIndex("membrane")
score_idx = res.score_table.GetColIndex("QMEAN")
for r in res.score_table.rows:
chain_name = r[chain_name_idx]
rnum = r[rnum_idx]
score = r[score_idx]
+ mem = r[membrane_idx]
local_scores[chain_name][rnum - 1] = format_float(score)
+ qmeanbrane_membrane[chain_name][rnum - 1] = mem
else:
raise RuntimeError(f"Unknown scoring function {scoring_function}")
self.local_scores = local_scores
self.global_scores = global_scores
+ self.qmeanbrane_membrane = qmeanbrane_membrane
def _load_model(self):
"""Read OST entity either from mmCIF or PDB."""
--
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