diff --git a/modules/gui/src/data_viewer/data_viewer_panel_base.cc b/modules/gui/src/data_viewer/data_viewer_panel_base.cc
index c89f27655663dfb8c6b6becb455d5ef39756b8ac..205012c1321d161599fdada91b6d16d3b8caf974 100644
--- a/modules/gui/src/data_viewer/data_viewer_panel_base.cc
+++ b/modules/gui/src/data_viewer/data_viewer_panel_base.cc
@@ -1071,7 +1071,11 @@ void DataViewerPanelBase::draw_pixel_values(QPainter& painter)
unsigned char rgb = (rv>130.0) ? 0 : 255;
painter.setPen(QColor(rgb,rgb,rgb));
int string_h=painter.fontMetrics().height();
+#if (QT_VERSION < QT_VERSION_CHECK(5,11,0))
+ int string_w=painter.fontMetrics().width(value_string);
+#else
int string_w=painter.fontMetrics().horizontalAdvance(value_string);
+#endif
painter.drawText(p.x() - string_w/2, p.y() + string_h/2, value_string);
}
}
@@ -1087,7 +1091,11 @@ void DataViewerPanelBase::draw_pixel_values(QPainter& painter)
unsigned char rgb = (rv>130.0) ? 0 : 255;
painter.setPen(QColor(rgb,rgb,rgb));
int string_h=painter.fontMetrics().height();
+#if (QT_VERSION < QT_VERSION_CHECK(5,11,0))
+ int string_w=painter.fontMetrics().width(value_string);
+#else
int string_w=painter.fontMetrics().horizontalAdvance(value_string);
+#endif
painter.drawText(p.x() - string_w/2, p.y() + string_h/2, value_string);
}
}
diff --git a/modules/gui/src/python_shell/python_shell_widget.cc b/modules/gui/src/python_shell/python_shell_widget.cc
index 040ee6b1f91772de9003ceabc15d76c9dbc7e2b0..a7d4ae61a85787962391a82aeb6f63185c1084e1 100644
--- a/modules/gui/src/python_shell/python_shell_widget.cc
+++ b/modules/gui/src/python_shell/python_shell_widget.cc
@@ -76,7 +76,11 @@ PythonShellWidget::PythonShellWidget(QWidget* parent):
setUndoRedoEnabled(false);
setFont(QFont("Courier",font().pointSize()+2));
QFontMetrics metrics(font());
+#if (QT_VERSION < QT_VERSION_CHECK(5,11,0))
+ setTabStopWidth(2*metrics.width(" "));
+#else
setTabStopDistance(2*metrics.horizontalAdvance(" "));
+#endif
setMaximumBlockCount(1000000);
textCursor().block().setUserState(BLOCKTYPE_ACTIVE);
@@ -534,7 +538,11 @@ void PythonShellWidget::OnExecuteStateEntered()
void PythonShellWidget::SetTabWidth(int width) {
tab_width_=width;
QFontMetrics metrics(font());
+#if (QT_VERSION < QT_VERSION_CHECK(5,11,0))
+ setTabStopWidth(tab_width_*metrics.width(" "));
+#else
setTabStopDistance(tab_width_*metrics.horizontalAdvance(" "));
+#endif
}
diff --git a/modules/gui/src/sequence_viewer/sequence_table_view.cc b/modules/gui/src/sequence_viewer/sequence_table_view.cc
index c72842704ecc71c4bc161bc27681ffb71c4058d2..95aa637cd4fc8995736fb2646f641721dacbb4f9 100644
--- a/modules/gui/src/sequence_viewer/sequence_table_view.cc
+++ b/modules/gui/src/sequence_viewer/sequence_table_view.cc
@@ -477,7 +477,11 @@ void SequenceTableView::keyPressEvent(QKeyEvent* event)
}
int SequenceTableView::sizeHintForColumn(int column) const {
- return this->fontMetrics().horizontalAdvance('W');
+#if (QT_VERSION < QT_VERSION_CHECK(5,11,0))
+ return this->fontMetrics().width('W');
+#else
+ return this->fontMetrics().horizontalAdvance('W');
+#endif
}
int SequenceTableView::sizeHintForRow(int row) const {
diff --git a/modules/mol/alg/pymod/dockq.py b/modules/mol/alg/pymod/dockq.py
index c22ca78d21746de90900b2a1f539d931c8cc65a8..126c8f57519472b8cb74ccaa45e5b0719c9043f8 100644
--- a/modules/mol/alg/pymod/dockq.py
+++ b/modules/mol/alg/pymod/dockq.py
@@ -1,5 +1,6 @@
from ost import geom
from ost import mol
+from ost import seq
def _PreprocessStructures(mdl, ref, mdl_ch1, mdl_ch2, ref_ch1, ref_ch2,
ch1_aln = None, ch2_aln = None):
@@ -15,7 +16,56 @@ def _PreprocessStructures(mdl, ref, mdl_ch1, mdl_ch2, ref_ch1, ref_ch2,
ref_residues_1 = list()
ref_residues_2 = list()
- if ch1_aln is None and ch2_aln is None:
+ if ch1_aln is not None and ch2_aln is not None:
+ # there are potentially already views attached to the alns but
+ # we go for *mdl* and *ref* here
+ if ch1_aln.GetCount() != 2 or ch2_aln.GetCount() != 2:
+ raise RuntimeError("Expect exactly two sequences in provided alns!")
+
+ tmp = ch1_aln.GetSequence(0)
+ ref_s1 = seq.CreateSequence(tmp.GetName(), str(tmp))
+ ref_s1.SetOffset(tmp.GetOffset())
+ ref_s1.AttachView(ref.Select(f"cname={ref_ch1}"))
+ tmp = ch1_aln.GetSequence(1)
+ mdl_s1 = seq.CreateSequence(tmp.GetName(), str(tmp))
+ mdl_s1.SetOffset(tmp.GetOffset())
+ mdl_s1.AttachView(mdl.Select(f"cname={mdl_ch1}"))
+ new_ch1_aln = seq.CreateAlignment(ref_s1, mdl_s1)
+ for col in new_ch1_aln:
+ if col[0] != '-' and col[1] != '-':
+ ref_r = col.GetResidue(0)
+ mdl_r = col.GetResidue(1)
+ if not (ref_r.IsValid() and ref_r.one_letter_code == col[0]):
+ raise RuntimeError("DockQ: mismatch between provided "
+ "alignments and ATOMSEQ in structures")
+ if not (mdl_r.IsValid() and mdl_r.one_letter_code == col[1]):
+ raise RuntimeError("DockQ: mismatch between provided "
+ "alignments and ATOMSEQ in structures")
+ ref_residues_1.append(ref_r)
+ mdl_residues_1.append(mdl_r)
+
+ tmp = ch2_aln.GetSequence(0)
+ ref_s2 = seq.CreateSequence(tmp.GetName(), str(tmp))
+ ref_s2.SetOffset(tmp.GetOffset())
+ ref_s2.AttachView(ref.Select(f"cname={ref_ch2}"))
+ tmp = ch2_aln.GetSequence(1)
+ mdl_s2 = seq.CreateSequence(tmp.GetName(), str(tmp))
+ mdl_s2.SetOffset(tmp.GetOffset())
+ mdl_s2.AttachView(mdl.Select(f"cname={mdl_ch2}"))
+ new_ch2_aln = seq.CreateAlignment(ref_s2, mdl_s2)
+ for col in new_ch2_aln:
+ if col[0] != '-' and col[1] != '-':
+ ref_r = col.GetResidue(0)
+ mdl_r = col.GetResidue(1)
+ if not (ref_r.IsValid() and ref_r.one_letter_code == col[0]):
+ raise RuntimeError("DockQ: mismatch between provided "
+ "alignments and ATOMSEQ in structures")
+ if not (mdl_r.IsValid() and mdl_r.one_letter_code == col[1]):
+ raise RuntimeError("DockQ: mismatch between provided "
+ "alignments and ATOMSEQ in structures")
+ ref_residues_2.append(ref_r)
+ mdl_residues_2.append(mdl_r)
+ else:
# go by residue numbers
for mdl_r in mdl.Select(f"cname={mdl_ch1}").residues:
ref_r = ref.FindResidue(ref_ch1, mdl_r.GetNumber())
@@ -27,8 +77,6 @@ def _PreprocessStructures(mdl, ref, mdl_ch1, mdl_ch2, ref_ch1, ref_ch2,
if ref_r.IsValid():
mdl_residues_2.append(mdl_r)
ref_residues_2.append(ref_r)
- else:
- raise NotImplementedError("No aln mapping implemented yet")
new_mdl = mdl.handle.CreateEmptyView()
new_ref = ref.handle.CreateEmptyView()
diff --git a/modules/mol/alg/pymod/scoring.py b/modules/mol/alg/pymod/scoring.py
index 1cb97530eadd1f90f30a31b25df4405c798cf7b2..a2fd44555d11563032e9152e0ad61b42245f445a 100644
--- a/modules/mol/alg/pymod/scoring.py
+++ b/modules/mol/alg/pymod/scoring.py
@@ -878,28 +878,43 @@ class Scorer:
nonmapped_interface_counts = list()
flat_mapping = self.mapping.GetFlatMapping()
+ pep_seqs = set([s.GetName() for s in self.chain_mapper.polypep_seqs])
for trg_int in self.qs_scorer.qsent1.interacting_chains:
trg_ch1 = trg_int[0]
trg_ch2 = trg_int[1]
- if trg_ch1 in flat_mapping and trg_ch2 in flat_mapping:
- mdl_ch1 = flat_mapping[trg_ch1]
- mdl_ch2 = flat_mapping[trg_ch2]
- res = dockq.DockQ(self.model, self.target, mdl_ch1, mdl_ch2,
- trg_ch1, trg_ch2)
- if res["nnat"] > 0:
- self._dockq_interfaces.append((trg_ch1, trg_ch2,
- mdl_ch1, mdl_ch2))
- self._dockq_native_contacts.append(res["nnat"])
- self._dockq_scores.append(res["DockQ"])
- else:
- # interface which is not covered by mdl... let's run DockQ with
- # trg as trg/mdl in order to get the native contacts out
- res = dockq.DockQ(self.target, self.target,
- trg_ch1, trg_ch2, trg_ch1, trg_ch2)
- if res["nnat"] > 0:
- self._dockq_nonmapped_interfaces.append((trg_ch1,
- trg_ch2))
- self._dockq_nonmapped_interfaces_counts.append(res["nnat"])
+ if trg_ch1 in pep_seqs and trg_ch2 in pep_seqs:
+ if trg_ch1 in flat_mapping and trg_ch2 in flat_mapping:
+ mdl_ch1 = flat_mapping[trg_ch1]
+ mdl_ch2 = flat_mapping[trg_ch2]
+ aln1 = self.mapping.alns[(trg_ch1, mdl_ch1)]
+ aln2 = self.mapping.alns[(trg_ch2, mdl_ch2)]
+ # we're operating on the model/target from the MappingResult
+ # as their ATOMSEQ corresponds to the alignments above.
+ # Residues that do not contain all atoms required for
+ # ChainMapper (e.g. N, CA, C, CB) are removed which triggers
+ # a mismatch error in DockQ
+ model = self.mapping.model
+ target = self.mapping.target
+ res = dockq.DockQ(model, target, mdl_ch1, mdl_ch2,
+ trg_ch1, trg_ch2, ch1_aln=aln1,
+ ch2_aln=aln2)
+ if res["nnat"] > 0:
+ self._dockq_interfaces.append((trg_ch1, trg_ch2,
+ mdl_ch1, mdl_ch2))
+ self._dockq_native_contacts.append(res["nnat"])
+ self._dockq_scores.append(res["DockQ"])
+ else:
+ # interface which is not covered by mdl... let's run DockQ
+ # with trg as trg/mdl in order to get the native contacts
+ # out
+ # no need to pass alns as the residue numbers match for sure
+ res = dockq.DockQ(self.target, self.target,
+ trg_ch1, trg_ch2, trg_ch1, trg_ch2)
+ nnat = res["nnat"]
+ if nnat > 0:
+ self._dockq_nonmapped_interfaces.append((trg_ch1,
+ trg_ch2))
+ self._dockq_nonmapped_interfaces_counts.append(nnat)
# there are 4 types of combined scores
# - simple average