def main():
"""Calcualting an ACV from the command line
Notes
-----
Run with:
>>> fretraj -i <input pdb> -p <label parameter file (.json)> -s <label position identifier>
"""
in_filePDB, param_fileJSON, site, out_fileACV = parseCmd()
labels = cloud.labeling_params(param_fileJSON)
struct = md.load_pdb(in_filePDB)
print("Calculating accessible-contact volume...")
av = cloud.Volume(struct, site, labels)
if not out_fileACV:
out_fileACV = "ACV.pdb"
_, out_fileextACV = os.path.splitext(out_fileACV)
out_path = os.path.dirname(os.path.abspath(out_fileACV))
av.save_acv(out_fileACV, format=out_fileextACV[1:])
print(f"{out_fileACV} saved to {out_path}")
def computeACV(self):
"""
Create a cloud.Volume object at the specified label position.
If the GUI is run as a PyMOL plugin, the ACV will be rendered in the current window
"""
self.update_labelDict()
msg = "Busy..."
self.statusBar().showMessage(msg, 3000)
param_filename = "{}/{}_parameters.json".format(
self.settings["root_path"], self.fileName_pdb[:-4])
cloud.save_labels(param_filename, self.labels)
self.av[self.labelName] = cloud.Volume(self.struct, self.labelName,
self.labels)
if self.av[self.labelName].acv is None:
msg = "ACV could not be calculated!"
self.statusBar().showMessage(msg, 3000)
print(msg)
else:
av_name = self.fileName_pdb[:-4] + "-" + self.labelName.replace(
"'", "p")
av_filename = "{}/{}.pdb".format(self.settings["root_path"],
av_name)
self.av[self.labelName].save_acv(av_filename, format="pdb")
self.addLabelToList(self.av[self.labelName])
msg = "ACV successfully calculated!"
self.statusBar().showMessage(msg, 3000)
if self._pymol_running:
cmd.delete("{}*".format(av_name))
cmd.load(av_filename)
self.doubleSpinBox_contourValue.setEnabled(True)
self.spinBox_bfactor.setEnabled(True)
self.spinBox_gaussRes.setEnabled(True)
self.doubleSpinBox_gridBuffer.setEnabled(True)
self.checkBox_transparentAV.setEnabled(True)
self.pymol_update_isosurface()
cmd.zoom(self.fileName_pdb[:-4])
self.define_DA()
def test_attachID_buried(self, create_labels, load_structure):
create_labels['Position']['Cy3']['attach_id'] = 158
vol = cloud.Volume(load_structure, 'Cy3', create_labels)
assert vol.acv is None
def test_stateframe_outofrange(self, create_labels, load_structure):
create_labels['Position']['Cy3']['state'] = 2
create_labels['Position']['Cy3']['frame_mdtraj'] = 1
vol = cloud.Volume(load_structure, 'Cy3', create_labels)
assert vol.acv is None
def test_volume_pythononly(self, create_labels, load_structure):
vol = cloud.Volume(load_structure, 'Cy3', create_labels)
assert hasattr(vol.acv, 'mp')
def test_volume_LabelLib(self, create_labels, load_structure):
create_labels['Position']['Cy3']['use_LabelLib'] = True
vol = cloud.Volume(load_structure, 'Cy3', create_labels)
assert hasattr(vol.acv, 'mp')
def create_volumes(create_labels, load_structure):
vol_Cy3 = cloud.Volume(load_structure, 'Cy3', create_labels)
vol_Cy5 = cloud.Volume(load_structure, 'Cy5', create_labels)
return vol_Cy3, vol_Cy5