bug fixes with cached old jobs and %Vbur differences

ajs99778 · ajs99778 · commit 7b66aeb499b2 · 2022-07-04T15:19:53.000-04:00
diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-![SEQCROW](SEQCROW.png)
+![SEQCROW](SEQCROW_dev.png)
 # SEQCROW
 SEQCROW is an AaronTools-based plugin for <a href="https://www.cgl.ucsf.edu/chimerax/" target="_blank">UCSF ChimeraX</a>, a cross-platform 3D molecular graphics program.
 SEQCROW extends ChimeraX by adding tools to build and modify complex molecular structures, map new catalysts and ligands onto previously-computed structures, and manage AaronTools libraries.
diff --git a/SEQCROW_dev.png b/SEQCROW_dev.png
diff --git a/dist/SEQCROW-1.4.5a1-py3-none-any.whl b/dist/SEQCROW-1.4.5a1-py3-none-any.whl
diff --git a/src/commands/percent_Vbur.py b/src/commands/percent_Vbur.py
@@ -1036,11 +1036,14 @@ def vbur_difference_vis(
     coords1 = geom1.coordinates(atoms_within_radius1)
     coords2 = geom2.coordinates(atoms_within_radius2)
     coords2 -= center_coords2
-    basis2_inv = np.linalg.inv(basis2)
-    coords2 = np.dot(coords2, basis2_inv)
-    coords2 = np.dot(coords2, basis1)
+    h = np.dot(basis2.T, basis1)
+    u, s, v = np.linalg.svd(h)
+    R = np.matmul(v, u.T)
+    if np.sign(np.linalg.det(R)) < 0:
+        R[:, 2] *= -1
+    coords2 = np.matmul(coords2, R.T)
     coords2 += center_coords1
-    
+
     atom_dist1 = distance_matrix(coords1, coords1)
     atom_dist12 = distance_matrix(coords1, coords2)
     atom_dist2 = distance_matrix(coords2, coords2)
@@ -1195,6 +1198,8 @@ def vbur_difference_vis(
         # intersection with big sphere
         if d + r1 > radius:
             theta = np.arccos((r1 ** 2 - radius ** 2 - d ** 2) / (-2 * d * radius))
+            if np.isnan(theta):
+                continue
             h = radius * np.sin(theta)
             b = radius * np.cos(theta)
             p = b * v_n
@@ -1500,10 +1505,11 @@ def vbur_difference_vis(
         sphere = sphere[mask]
     
         sphere = np.array(sphere)
-    sphere = np.concatenate((
-        sphere,
-        np.array(center_added_points1),
-    ))
+        
+        sphere = np.concatenate((
+            sphere,
+            np.array(center_added_points1),
+        ))
     
     if len(center_added_points2) > 1:
         mask = np.ones(len(sphere), dtype=bool)
@@ -1516,10 +1522,11 @@ def vbur_difference_vis(
     
         sphere = np.array(sphere)
         n_sphere = len(sphere)
-    sphere = np.concatenate((
-        sphere,
-        np.array(center_added_points2),
-    ))
+    
+        sphere = np.concatenate((
+            sphere,
+            np.array(center_added_points2),
+        ))
 
     center_hull = ConvexHull(sphere / radius)
     sphere += center_coords1
@@ -1546,7 +1553,7 @@ def vbur_difference_vis(
             norms = -keep_sphere / radius
 
             triangles1.extend(keep_tri + len(vertices1))
-            vertices1.extend(keep_sphere + center_coords1)
+            vertices1.extend(keep_sphere)
             normals1.extend(norms)
         
     if len(add_to_mdl_2_verts) > 3:
@@ -1559,7 +1566,7 @@ def vbur_difference_vis(
             norms = -keep_sphere / radius
 
             triangles2.extend(keep_tri + len(vertices2))
-            vertices2.extend(keep_sphere + center_coords1)
+            vertices2.extend(keep_sphere)
             normals2.extend(norms)
 
     # the triangles need to be reordered so the points are 
diff --git a/src/jobs.py b/src/jobs.py
@@ -481,14 +481,12 @@ def run(self):
         else:
             self.process = subprocess.Popen(args, cwd=self.scratch_dir, stdout=log, stderr=log)
 
-        possible_fchk_name = os.path.join(
-            self.scratch_dir, self.name + ".fchk"
-        )
-        if os.path.exists(possible_fchk_name):
-            self.output_name = [
-                self.output_name,
-                possible_fchk_name
-            ]
+        for f in os.listdir(self.scratch_dir):
+            if f.lower().endswith("fchk") or f.lower().endswith("fch"):
+                self.output_name = {
+                    "out": self.output_name,
+                    "fchk": os.path.join(self.scratch_dir, f),
+                }
 
         self.process.communicate()
         self.process = None
diff --git a/src/managers/job_manager.py b/src/managers/job_manager.py
@@ -92,7 +92,10 @@ def init_queue(self):
                                     self.session,
                                     job['theory'],
                                 ]
-                                kwargs = job["job_options"]
+                                try:
+                                    kwargs = job["job_options"]
+                                except KeyError:
+                                    kwargs = {}
                                 if issubclass(job_cls, TSSJob):
                                     args.extend([
                                         job["reactant"],
diff --git a/src/residue_collection.py b/src/residue_collection.py
@@ -933,6 +933,26 @@ def get_chimera(self, session, coordsets=False, filereader=None, discard_residue
                     
                     self.update_geometry(cur_coords)
         
+        if filereader is not None and "Löwdin Charges" in filereader.other:
+            for atom, charge in zip(struc.atoms, filereader.other["Löwdin Charges"]):
+                atom.loewdinCharge = charge
+                atom.charge = charge
+            
+                if not any(attr[0] == "loewdinCharge" for attr in atom.custom_attrs):
+                    atom.register_attr(
+                        session,
+                        "loewdinCharge",
+                        "seqcrow ResidueCollection.get_chimera",
+                        attr_type=float
+                    )
+                if not any(attr[0] == "charge" for attr in atom.custom_attrs):
+                    atom.register_attr(
+                        session,
+                        "charge",
+                        "seqcrow ResidueCollection.get_chimera",
+                        attr_type=float
+                    )
+        
         if filereader is not None and "Mulliken Charges" in filereader.other:
             for atom, charge in zip(struc.atoms, filereader.other["Mulliken Charges"]):
                 atom.mullikenCharge = charge
diff --git a/src/tests/substitute_command.py b/src/tests/substitute_command.py
@@ -21,7 +21,7 @@ def test_substitute_modify(self):
         mdl = self.session.models.list()[0]
         rescol = ResidueCollection(mdl)
         
-        self.assertTrue(validate(ref, rescol))
+        self.assertTrue(validate(ref, rescol, thresh="loose"))
     
     def test_substitute_copy(self):
         ref1 = ResidueCollection(self.chlorobenzene)
@@ -35,6 +35,6 @@ def test_substitute_copy(self):
         mdl2 = self.session.models.list()[2]
         rescol2 = ResidueCollection(mdl2)
         
-        self.assertTrue(validate(ref1, rescol1))
-        self.assertTrue(validate(ref2, rescol2))
+        self.assertTrue(validate(ref1, rescol1, thresh="loose"))
+        self.assertTrue(validate(ref2, rescol2, thresh="loose"))
     
diff --git a/src/tools/cone_angle.py b/src/tools/cone_angle.py
@@ -21,6 +21,9 @@
     QTableWidgetItem,
     QHeaderView,
     QMessageBox,
+    QLabel,
+    QTabWidget,
+    QWidget,
 )
 
 from AaronTools.component import Component
@@ -59,43 +62,60 @@ def __init__(self, session, name):
         self._build_ui()
     
     def _build_ui(self):
+        tabs = QTabWidget()
+        
         layout = QFormLayout()
+        layout.addRow(tabs)
+        
+        cone_widget = QWidget()
+        cone_layout = QFormLayout(cone_widget)
+
+        cone_layout.addRow("1.", QLabel("select ligand"))
+
+        set_ligand_button = QPushButton("set ligand to current selection")
+        set_ligand_button.clicked.connect(self.set_ligand)
+        cone_layout.addRow("2.", set_ligand_button)
+        self.set_ligand_button = set_ligand_button
+
+        cone_layout.addRow("3.", QLabel("change selection to metal center"))
+
+        calc_cone_button = QPushButton("calculate cone angle")
+        calc_cone_button.clicked.connect(self.calc_cone)
+        cone_layout.addRow("4.", calc_cone_button)
+        self.calc_cone_button = calc_cone_button
+
+        tabs.addTab(cone_widget, "cone angle")
+
+        settings = QWidget()
+        settings_layout = QFormLayout(settings)
 
         self.cone_option = QComboBox()
         self.cone_option.addItems(["Tolman (Unsymmetrical)", "Exact"])
         ndx = self.cone_option.findText(self.settings.cone_option, Qt.MatchExactly)
         self.cone_option.setCurrentIndex(ndx)
-        layout.addRow("method:", self.cone_option)
+        settings_layout.addRow("method:", self.cone_option)
 
         self.radii_option = QComboBox()
         self.radii_option.addItems(["Bondi", "UMN"])
         ndx = self.radii_option.findText(self.settings.radii, Qt.MatchExactly)
         self.radii_option.setCurrentIndex(ndx)
-        layout.addRow("radii:", self.radii_option)
+        settings_layout.addRow("radii:", self.radii_option)
 
         self.display_cone = QCheckBox()
         self.display_cone.setChecked(self.settings.display_cone)
-        layout.addRow("show cone:", self.display_cone)
-        
+        settings_layout.addRow("show cone:", self.display_cone)
+
         self.display_radii = QCheckBox()
         self.display_radii.setChecked(self.settings.display_radii)
-        layout.addRow("show radii:", self.display_radii)
+        settings_layout.addRow("show radii:", self.display_radii)
 
-        set_ligand_button = QPushButton("set ligand to current selection")
-        set_ligand_button.clicked.connect(self.set_ligand)
-        layout.addRow(set_ligand_button)
-        self.set_ligand_button = set_ligand_button
-
-        calc_cone_button = QPushButton("calculate cone angle for ligand on selected center")
-        calc_cone_button.clicked.connect(self.calc_cone)
-        layout.addRow(calc_cone_button)
-        self.calc_cone_button = calc_cone_button
-        
         remove_cone_button = QPushButton("remove cone visualizations")
         remove_cone_button.clicked.connect(self.del_cone)
-        layout.addRow(remove_cone_button)
+        settings_layout.addRow(remove_cone_button)
         self.remove_cone_button = remove_cone_button
         
+        tabs.addTab(settings, "options")
+
         self.table = QTableWidget()
         self.table.setColumnCount(3)
         self.table.setHorizontalHeaderLabels(
@@ -291,8 +311,6 @@ def calc_cone(self, *args):
             at_center = rescol.find_exact(AtomSpec(center_atom.atomspec))[0]
             if center_atom.structure in self.ligands:
                 lig_atoms = [AtomSpec(atom.atomspec) for atom in self.ligands[center_atom.structure]]
-                print("structure in ligand list")
-                print(rescol.find(BondedTo(at_center), lig_atoms))
                 comp = Component(
                     rescol.find(
                         lig_atoms,
diff --git a/src/tools/percent_Vbur.py b/src/tools/percent_Vbur.py
@@ -8,10 +8,26 @@
 
 from Qt.QtCore import Qt
 from Qt.QtGui import QKeySequence
-from Qt.QtWidgets import QPushButton, QFormLayout, QComboBox, QCheckBox, QMenuBar, QAction, \
-    QFileDialog, QApplication, QTableWidget, QTableWidgetItem, \
-    QHeaderView, QSpinBox, QWidget, QGridLayout, \
-    QTabWidget, QDoubleSpinBox, QMessageBox
+from Qt.QtWidgets import (
+    QPushButton,
+    QFormLayout,
+    QComboBox,
+    QCheckBox,
+    QMenuBar,
+    QAction,
+    QFileDialog,
+    QApplication,
+    QTableWidget,
+    QTableWidgetItem,
+    QHeaderView,
+    QSpinBox,
+    QWidget,
+    QGridLayout,
+    QTabWidget,
+    QDoubleSpinBox,
+    QMessageBox,
+    QLabel,
+)
 
 from SEQCROW.commands.percent_Vbur import percent_vbur as percent_vbur_cmd
 from SEQCROW.tools.per_frame_plot import NavigationToolbar
@@ -101,14 +117,15 @@ def _build_ui(self):
         self.scale.setRange(1., 1.5)
         settings_layout.addRow("VDW scale:", self.scale)
         
+        calc_layout.addRow("1.", QLabel("select ligand"))
         set_ligand_atoms = QPushButton("set ligands to current selection")
         set_ligand_atoms.clicked.connect(self.set_ligand_atoms)
         set_ligand_atoms.setToolTip(
             "specify atoms to use in calculation\n" +
             "by default, all atoms will be used unless a single center is specified\n" +
             "in the case of a single center, all atoms except the center is used"
         )
-        calc_layout.addRow(set_ligand_atoms)
+        calc_layout.addRow("2.", set_ligand_atoms)
         self.set_ligand_atoms = set_ligand_atoms
         
         self.radius = QDoubleSpinBox()
@@ -197,13 +214,13 @@ def _build_ui(self):
             lambda text, widget=mc_widget: widget.setVisible(text == "Monte-Carlo")
         )
 
-        self.use_centroid = QCheckBox()
+        calc_layout.addRow("3.", QLabel("change selection to reaction center"))
+        self.use_centroid = QCheckBox("use centroid of centers")
         self.use_centroid.setChecked(self.settings.use_centroid)
         self.use_centroid.setToolTip(
-            "place the center between selected atoms\n" +
-            "might be useful for polydentate ligands"
+            "place the center between selected atoms"
         )
-        calc_layout.addRow("use centroid of centers:", self.use_centroid)
+        calc_layout.addRow(self.use_centroid)
 
 
         self.steric_map = QCheckBox()
@@ -342,7 +359,7 @@ def _build_ui(self):
 
         calc_vbur_button = QPushButton("calculate % buried volume for selected centers")
         calc_vbur_button.clicked.connect(self.calc_vbur)
-        calc_layout.addRow(calc_vbur_button)
+        calc_layout.addRow("4.", calc_vbur_button)
         self.calc_vbur_button = calc_vbur_button
         
         remove_vbur_button = QPushButton("remove % buried volume visualizations")
@@ -720,7 +737,6 @@ def calc_vbur(self):
         self.table.resizeColumnToContents(1)
         self.table.resizeColumnToContents(2)
 
-    
     def header_check(self, state):
         """user has [un]checked the 'include header' option on the menu"""
         if state:

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-![SEQCROW](SEQCROW.png)`
	`1`	`+![SEQCROW](SEQCROW_dev.png)`
`2`	`2`	`# SEQCROW`
`3`	`3`	`SEQCROW is an AaronTools-based plugin for <a href="https://www.cgl.ucsf.edu/chimerax/" target="_blank">UCSF ChimeraX</a>, a cross-platform 3D molecular graphics program.`
`4`	`4`	`SEQCROW extends ChimeraX by adding tools to build and modify complex molecular structures, map new catalysts and ligands onto previously-computed structures, and manage AaronTools libraries.`