def createParams(self, event):
# Change to the sandbox location
goToSandbox()
# Attempt to generate the params file
try:
if (os.path.isfile("LG.params")):
os.remove("LG.params")
if (os.path.isfile("LG.fa.params")):
os.remove("LG.fa.params")
if (os.path.isfile("LG.cen.params")):
os.remove("LG.cen.params")
molfile_to_params.main([self.loadedfile, "--no-pdb", "--keep-names", "-c"])
except:
wx.MessageBox("The file " + self.loadedfile + " could not be converted to a params file!", "File Cannot Be Processed", wx.OK|wx.ICON_EXCLAMATION)
return
logInfo("Params file created successfully")
# Now read the LG.params file and grab out the atom names and their assigned types
# so the user can see them and modify them if desired
f = open("LG.fa.params", "r")
if (self.grdParamsAtoms.NumberRows > 0):
self.grdParamsAtoms.DeleteRows(0, self.grdParamsAtoms.NumberRows)
self.atomnames = []
atomtypes = []
for aline in f:
if (aline[0:4] == "ATOM"):
atomname = aline.split()[1]
atomtype = aline.split()[2]
self.atomnames.append(atomname)
atomtypes.append(atomtype)
f.close()
# Sort the atomnames to make it easier for the user to find things
for i in range(0, len(self.atomnames)-1):
lowest = i
for j in range(i+1, len(self.atomnames)):
if (self.atomnames[j] < self.atomnames[lowest]):
lowest = j
temp = self.atomnames[i]
self.atomnames[i] = self.atomnames[lowest]
self.atomnames[lowest] = temp
temp = atomtypes[i]
atomtypes[i] = atomtypes[lowest]
atomtypes[lowest] = temp
# Now add things to the grid
for i in range(0, len(self.atomnames)):
self.grdParamsAtoms.AppendRows(1)
self.grdParamsAtoms.SetRowLabelValue(i, self.atomnames[i])
self.grdParamsAtoms.SetCellValue(i, 0, atomtypes[i])
self.grdParamsAtoms.SetCellAlignment(i, 0, wx.ALIGN_CENTRE, wx.ALIGN_CENTRE)
readOnly = wx.grid.GridCellAttr()
readOnly.SetReadOnly(True)
self.grdParamsAtoms.SetRowAttr(i, readOnly)
# Update some of the atom selection menus with the list of atomnames
self.atomMenu.Clear()
self.atomMenu.AppendItems(self.atomnames)
self.NtermMenu.Clear()
self.NtermMenu.AppendItems(self.atomnames)
self.CtermMenu.Clear()
self.CtermMenu.AppendItems(self.atomnames)
self.btnAdd.Enable()
def createParams(self, event):
# Change to the sandbox location
goToSandbox()
# Attempt to generate the params file
try:
if (os.path.isfile("LG.params")):
os.remove("LG.params")
if (os.path.isfile("LG.fa.params")):
os.remove("LG.fa.params")
if (os.path.isfile("LG.cen.params")):
os.remove("LG.cen.params")
molfile_to_params.main([self.loadedfile, "--no-pdb", "--keep-names", "-c"])
except:
wx.MessageBox("The file " + self.loadedfile + " could not be converted to a params file!", "File Cannot Be Processed", wx.OK|wx.ICON_EXCLAMATION)
return
logInfo("Params file created successfully")
# Now read the LG.params file and grab out the atom names and their assigned types
# so the user can see them and modify them if desired
f = open("LG.fa.params", "r")
if (self.grdParamsAtoms.NumberRows > 0):
self.grdParamsAtoms.DeleteRows(0, self.grdParamsAtoms.NumberRows)
self.atomnames = []
atomtypes = []
for aline in f:
if (aline[0:4] == "ATOM"):
atomname = aline.split()[1]
atomtype = aline.split()[2]
self.atomnames.append(atomname)
atomtypes.append(atomtype)
f.close()
# Sort the atomnames to make it easier for the user to find things
for i in range(0, len(self.atomnames)-1):
lowest = i
for j in range(i+1, len(self.atomnames)):
if (self.atomnames[j] < self.atomnames[lowest]):
lowest = j
temp = self.atomnames[i]
self.atomnames[i] = self.atomnames[lowest]
self.atomnames[lowest] = temp
temp = atomtypes[i]
atomtypes[i] = atomtypes[lowest]
atomtypes[lowest] = temp
# Now add things to the grid
for i in range(0, len(self.atomnames)):
self.grdParamsAtoms.AppendRows(1)
self.grdParamsAtoms.SetRowLabelValue(i, self.atomnames[i])
self.grdParamsAtoms.SetCellValue(i, 0, atomtypes[i])
self.grdParamsAtoms.SetCellAlignment(i, 0, wx.ALIGN_CENTRE, wx.ALIGN_CENTRE)
readOnly = wx.grid.GridCellAttr()
readOnly.SetReadOnly(True)
self.grdParamsAtoms.SetRowAttr(i, readOnly)
# Update some of the atom selection menus with the list of atomnames
self.atomMenu.Clear()
self.atomMenu.AppendItems(self.atomnames)
self.NtermMenu.Clear()
self.NtermMenu.AppendItems(self.atomnames)
self.CtermMenu.Clear()
self.CtermMenu.AppendItems(self.atomnames)
self.btnAdd.Enable()
def createParams(self, event):
# Change to the sandbox location
goToSandbox()
self.selectedType = self.resMenu.GetStringSelection().strip()
# Before doing any of the following, we should first scan all of the params files in the Rosetta database
# to see if a file already exists for this type
# If we find a hit, we'll let the user decide based on some filename and directory information if that is the
# params file they want, because we should be using Rosetta's files if they are available
if (platform.system() == "Windows"):
root = os.environ["PYROSETTA_DATABASE"] + "\\chemical\\residue_type_sets\\fa_standard\\residue_types"
else:
root = os.environ["PYROSETTA_DATABASE"] + "/chemical/residue_type_sets/fa_standard/residue_types"
accepted = False
for dpath, dnames, fnames in os.walk(root):
for fname in fnames:
if (platform.system() == "Windows"):
fullpath = dpath + "\\" + fname
else:
fullpath = dpath + "/" + fname
if (fname.endswith(".params")):
matches = False
f = open(fullpath, "r")
for aline in f:
if (aline[0:4] == "NAME" and aline.split()[1].strip() == self.selectedType):
matches = True
break
if (matches):
# Tell the user there is a hit, what the filename was, and what the directory is
msg = "Found a parameters file that matches this unrecognized residue in Rosetta's database.\n\nFilename: " + fname.strip() + "\nDirectory: " + dpath.strip() + "\n\nDo you want to import this parameters file?"
dlg = wx.MessageDialog(self, msg, "Params File Found", wx.YES_NO | wx.ICON_EXCLAMATION | wx.CENTRE)
if (dlg.ShowModal() == wx.ID_YES):
accepted = True
dlg.Destroy()
break
dlg.Destroy()
if (accepted):
break
if (accepted):
# Copy over the file and we're done
goToSandbox("params")
f = open(fullpath, "r")
f2 = open(self.selectedType + ".fa.params", "w")
for aline in f:
f2.write(aline.strip() + "\n")
f.close()
f2.close()
wx.MessageBox("Your parameters file was imported successfully! InteractiveROSETTA will now recognize " + self.selectedType + " entries.", "Params Creation Successful", wx.OK|wx.ICON_EXCLAMATION)
self.grdParamsAtoms.ClearGrid()
self.atomMenu.Clear()
self.typeMenu.Clear()
self.btnAdd.Disable()
self.btnCreate.Disable()
self.unrecognized_types.pop(self.selectedType)
self.resMenu.Clear()
self.resMenu.AppendItems(self.unrecognized_types.keys())
self.removeMenu.Append(self.selectedType)
return
# First we have to create a temporary PDB file that contains only the ATOM/HETATM
# records for the selected unrecognized residue type
for aline in self.unrecognized_types[self.selectedType]:
if (aline[0:4] == "ATOM" or aline[0:6] == "HETATM"):
self.seqpos = int(aline[22:26])
self.chainID = aline[21].strip()
break
f = open("params.pdb", "w")
for aline in self.unrecognized_types[self.selectedType]:
f.write(aline + "\n")
f.close()
self.txtCode.SetValue(str(self.selectedType))
# Now use openbabel to convert this PDB file to a mol2 file
obConversion = openbabel.OBConversion()
obConversion.SetInAndOutFormats("pdb", "mol2")
mol = openbabel.OBMol()
obConversion.ReadFile(mol, "params.pdb")
obConversion.WriteFile(mol, 'params.mol2')
obConversion.CloseOutFile()
# Now read the mol2 file as usual
# Attempt to generate the params file
try:
if (os.path.isfile("LG.params")):
os.remove("LG.params")
if (os.path.isfile("LG.fa.params")):
os.remove("LG.fa.params")
if (os.path.isfile("LG.cen.params")):
os.remove("LG.cen.params")
#molfile_to_params.main(["params.mol2", "--no-pdb", "--keep-names"])
molfile_to_params.main(["params.mol2", "--no-pdb", "--keep-names", "-c"])
except:
if (platform.system() == "Windows"):
dlg = wx.MessageDialog(self, "OpenBabel was not able to convert this residue to a mol2 file!\n\nDid you install OpenBabel separately? If not, would you like to view the download page?", "Params File Found", wx.YES_NO | wx.ICON_EXCLAMATION | wx.CENTRE)
if (dlg.ShowModal() == wx.ID_YES):
webbrowser.open("http://sourceforge.net/projects/openbabel/files/openbabel/2.3.2/OpenBabel2.3.2a_Windows_Installer.exe/download")
dlg.Destroy()
else:
wx.MessageBox("OpenBabel was not able to convert this residue to a mol2 file!", "File Cannot Be Processed", wx.OK|wx.ICON_EXCLAMATION)
return
logInfo("Params file created successfully")
# Now read the LG.params file and grab out the atom names and their assigned types
# so the user can see them and modify them if desired
f = open("LG.fa.params", "r")
if (self.grdParamsAtoms.NumberRows > 0):
self.grdParamsAtoms.DeleteRows(0, self.grdParamsAtoms.NumberRows)
self.atomnames = []
atomtypes = []
for aline in f:
if (aline[0:4] == "ATOM"):
atomname = aline.split()[1]
atomtype = aline.split()[2]
self.atomnames.append(atomname)
atomtypes.append(atomtype)
f.close()
# Sort the atomnames to make it easier for the user to find things
for i in range(0, len(self.atomnames)-1):
lowest = i
for j in range(i+1, len(self.atomnames)):
if (self.atomnames[j] < self.atomnames[lowest]):
lowest = j
temp = self.atomnames[i]
self.atomnames[i] = self.atomnames[lowest]
self.atomnames[lowest] = temp
temp = atomtypes[i]
atomtypes[i] = atomtypes[lowest]
atomtypes[lowest] = temp
# Now add things to the grid
for i in range(0, len(self.atomnames)):
self.grdParamsAtoms.AppendRows(1)
self.grdParamsAtoms.SetRowLabelValue(i, self.atomnames[i])
self.grdParamsAtoms.SetCellValue(i, 0, atomtypes[i])
self.grdParamsAtoms.SetCellAlignment(i, 0, wx.ALIGN_CENTRE, wx.ALIGN_CENTRE)
readOnly = wx.grid.GridCellAttr()
readOnly.SetReadOnly(True)
self.grdParamsAtoms.SetRowAttr(i, readOnly)
# Update some of the atom selection menus with the list of atomnames
self.atomMenu.Clear()
self.atomMenu.AppendItems(self.atomnames)
self.NtermMenu.Clear()
self.NtermMenu.AppendItems(self.atomnames)
self.CtermMenu.Clear()
self.CtermMenu.AppendItems(self.atomnames)
self.btnAdd.Enable()
def molfile2params_quick(mdlfile, name):
molfile_to_params.main([mdlfile, "-n" + name])
def createParams(self, event):
# Change to the sandbox location
goToSandbox()
self.selectedType = self.resMenu.GetStringSelection().strip()
# Before doing any of the following, we should first scan all of the params files in the Rosetta database
# to see if a file already exists for this type
# If we find a hit, we'll let the user decide based on some filename and directory information if that is the
# params file they want, because we should be using Rosetta's files if they are available
if (platform.system() == "Windows"):
root = os.environ[
"PYROSETTA_DATABASE"] + "\\chemical\\residue_type_sets\\fa_standard\\residue_types"
else:
root = os.environ[
"PYROSETTA_DATABASE"] + "/chemical/residue_type_sets/fa_standard/residue_types"
accepted = False
for dpath, dnames, fnames in os.walk(root):
for fname in fnames:
if (platform.system() == "Windows"):
fullpath = dpath + "\\" + fname
else:
fullpath = dpath + "/" + fname
if (fname.endswith(".params")):
matches = False
f = open(fullpath, "r")
for aline in f:
if (aline[0:4] == "NAME" and aline.split()[1].strip()
== self.selectedType):
matches = True
break
if (matches):
# Tell the user there is a hit, what the filename was, and what the directory is
msg = "Found a parameters file that matches this unrecognized residue in Rosetta's database.\n\nFilename: " + fname.strip(
) + "\nDirectory: " + dpath.strip(
) + "\n\nDo you want to import this parameters file?"
dlg = wx.MessageDialog(
self, msg, "Params File Found",
wx.YES_NO | wx.ICON_EXCLAMATION | wx.CENTRE)
if (dlg.ShowModal() == wx.ID_YES):
accepted = True
dlg.Destroy()
break
dlg.Destroy()
if (accepted):
break
if (accepted):
# Copy over the file and we're done
goToSandbox("params")
f = open(fullpath, "r")
f2 = open(self.selectedType + ".fa.params", "w")
for aline in f:
f2.write(aline.strip() + "\n")
f.close()
f2.close()
wx.MessageBox(
"Your parameters file was imported successfully! InteractiveROSETTA will now recognize "
+ self.selectedType + " entries.",
"Params Creation Successful", wx.OK | wx.ICON_EXCLAMATION)
self.grdParamsAtoms.ClearGrid()
self.atomMenu.Clear()
self.typeMenu.Clear()
self.btnAdd.Disable()
self.btnCreate.Disable()
self.unrecognized_types.pop(self.selectedType)
self.resMenu.Clear()
self.resMenu.AppendItems(self.unrecognized_types.keys())
self.removeMenu.Append(self.selectedType)
return
# First we have to create a temporary PDB file that contains only the ATOM/HETATM
# records for the selected unrecognized residue type
for aline in self.unrecognized_types[self.selectedType]:
if (aline[0:4] == "ATOM" or aline[0:6] == "HETATM"):
self.seqpos = int(aline[22:26])
self.chainID = aline[21].strip()
break
f = open("params.pdb", "w")
for aline in self.unrecognized_types[self.selectedType]:
f.write(aline + "\n")
f.close()
self.txtCode.SetValue(str(self.selectedType))
# Now use openbabel to convert this PDB file to a mol2 file
obConversion = openbabel.OBConversion()
obConversion.SetInAndOutFormats("pdb", "mol2")
mol = openbabel.OBMol()
obConversion.ReadFile(mol, "params.pdb")
obConversion.WriteFile(mol, 'params.mol2')
obConversion.CloseOutFile()
# Now read the mol2 file as usual
# Attempt to generate the params file
try:
if (os.path.isfile("LG.params")):
os.remove("LG.params")
if (os.path.isfile("LG.fa.params")):
os.remove("LG.fa.params")
if (os.path.isfile("LG.cen.params")):
os.remove("LG.cen.params")
#molfile_to_params.main(["params.mol2", "--no-pdb", "--keep-names"])
molfile_to_params.main(
["params.mol2", "--no-pdb", "--keep-names", "-c"])
except:
if (platform.system() == "Windows"):
dlg = wx.MessageDialog(
self,
"OpenBabel was not able to convert this residue to a mol2 file!\n\nDid you install OpenBabel separately? If not, would you like to view the download page?",
"Params File Found",
wx.YES_NO | wx.ICON_EXCLAMATION | wx.CENTRE)
if (dlg.ShowModal() == wx.ID_YES):
webbrowser.open(
"http://sourceforge.net/projects/openbabel/files/openbabel/2.3.2/OpenBabel2.3.2a_Windows_Installer.exe/download"
)
dlg.Destroy()
else:
wx.MessageBox(
"OpenBabel was not able to convert this residue to a mol2 file!",
"File Cannot Be Processed", wx.OK | wx.ICON_EXCLAMATION)
return
logInfo("Params file created successfully")
# Now read the LG.params file and grab out the atom names and their assigned types
# so the user can see them and modify them if desired
f = open("LG.fa.params", "r")
if (self.grdParamsAtoms.NumberRows > 0):
self.grdParamsAtoms.DeleteRows(0, self.grdParamsAtoms.NumberRows)
self.atomnames = []
atomtypes = []
for aline in f:
if (aline[0:4] == "ATOM"):
atomname = aline.split()[1]
atomtype = aline.split()[2]
self.atomnames.append(atomname)
atomtypes.append(atomtype)
f.close()
# Sort the atomnames to make it easier for the user to find things
for i in range(0, len(self.atomnames) - 1):
lowest = i
for j in range(i + 1, len(self.atomnames)):
if (self.atomnames[j] < self.atomnames[lowest]):
lowest = j
temp = self.atomnames[i]
self.atomnames[i] = self.atomnames[lowest]
self.atomnames[lowest] = temp
temp = atomtypes[i]
atomtypes[i] = atomtypes[lowest]
atomtypes[lowest] = temp
# Now add things to the grid
for i in range(0, len(self.atomnames)):
self.grdParamsAtoms.AppendRows(1)
self.grdParamsAtoms.SetRowLabelValue(i, self.atomnames[i])
self.grdParamsAtoms.SetCellValue(i, 0, atomtypes[i])
self.grdParamsAtoms.SetCellAlignment(i, 0, wx.ALIGN_CENTRE,
wx.ALIGN_CENTRE)
readOnly = wx.grid.GridCellAttr()
readOnly.SetReadOnly(True)
self.grdParamsAtoms.SetRowAttr(i, readOnly)
# Update some of the atom selection menus with the list of atomnames
self.atomMenu.Clear()
self.atomMenu.AppendItems(self.atomnames)
self.NtermMenu.Clear()
self.NtermMenu.AppendItems(self.atomnames)
self.CtermMenu.Clear()
self.CtermMenu.AppendItems(self.atomnames)
self.btnAdd.Enable()