def rotamerizeFromAtomSpecs(atomSpec1, atomSpec2, ignoreDensity=False):
"""Rotamerize a stretch of nucleotides
ARGUMENTS:
atomSpec1 - an atom spec specifying the start of the stretch
atomSpec2 - an atom spec specifying the end of the stretch
OPTIONAL ARGUMENTS:
ignoreDensity - ignore the density when performing the minimization
defaults to False
RETURNS:
False if there is a problem with the selected nucleotides
None otherwise
"""
#stop waiting for the user to cancel the rotamerize
__setMenuToRotamerize()
global waitingForClicks
waitingForClicks = False
#print "atom 1 = ", atomSpec1
#print "atom 2 = ", atomSpec2
#unpack the atom descriptions
(mol1, chain1, startResNum, startInsCode, startAtom, alt1) = atomSpec1[1:]
(mol2, chain2, endResNum, endInsCode, endAtom, alt2) = atomSpec2[1:]
#make sure that the picked atoms define a single stretch of RNA
if mol1 != mol2:
print "Rotamerize atoms are not in the same molecule"
add_status_bar_text("Rotamerize atoms are not in the same molecule")
return False
if chain1 != chain2:
print "Rotamerize atoms are not in the same chain"
add_status_bar_text("Rotamerize atoms are not in the same chain")
return False
molNum = mol1
chain = chain1
startResFull = str(startResNum) + str(startInsCode)
endResFull = str(endResNum) + str(endInsCode)
try:
pseudoMol = PseudoMolecule(createFromMolecule=molNum,
chain=chain,
batons=False)
except PseudoMoleculeError, err:
#if creating the PseudoMolecule raises an error, then it means that molecule we clicked on contains
#anisotropic temperature records and we're using a version of Coot that's older than rev 3631
#so clear_and_update_molecule can't handle anisotropic records
print err
#add_status_bar_text(str(err))
#Since this isn't an intuitive problem (i.e. it's far less obvious for the user than "you clicked on
#two different chains"), we create a dialog box instead of a status bar message
createRCraneErrorDialog(str(err) + "\n\nRotamerization canceled.")
return False
def rotamerizeFromAtomSpecs(atomSpec1, atomSpec2, ignoreDensity = False):
"""Rotamerize a stretch of nucleotides
ARGUMENTS:
atomSpec1 - an atom spec specifying the start of the stretch
atomSpec2 - an atom spec specifying the end of the stretch
OPTIONAL ARGUMENTS:
ignoreDensity - ignore the density when performing the minimization
defaults to False
RETURNS:
False if there is a problem with the selected nucleotides
None otherwise
"""
#stop waiting for the user to cancel the rotamerize
__setMenuToRotamerize()
global waitingForClicks
waitingForClicks = False
#print "atom 1 = ", atomSpec1
#print "atom 2 = ", atomSpec2
#unpack the atom descriptions
(mol1, chain1, startResNum, startInsCode, startAtom, alt1) = atomSpec1[1:]
(mol2, chain2, endResNum, endInsCode, endAtom, alt2) = atomSpec2[1:]
#make sure that the picked atoms define a single stretch of RNA
if mol1 != mol2:
print "Rotamerize atoms are not in the same molecule"
add_status_bar_text("Rotamerize atoms are not in the same molecule")
return False
if chain1 != chain2:
print "Rotamerize atoms are not in the same chain"
add_status_bar_text("Rotamerize atoms are not in the same chain")
return False
molNum = mol1
chain = chain1
startResFull = str(startResNum) + str(startInsCode)
endResFull = str(endResNum) + str(endInsCode)
try:
pseudoMol = PseudoMolecule(createFromMolecule = molNum, chain = chain, batons = False)
except PseudoMoleculeError, err:
#if creating the PseudoMolecule raises an error, then it means that molecule we clicked on contains
#anisotropic temperature records and we're using a version of Coot that's older than rev 3631
#so clear_and_update_molecule can't handle anisotropic records
print err
#add_status_bar_text(str(err))
#Since this isn't an intuitive problem (i.e. it's far less obvious for the user than "you clicked on
#two different chains"), we create a dialog box instead of a status bar message
createRCraneErrorDialog(str(err) + "\n\nRotamerization canceled.")
return False
def pickAtoms(ignoreDensity=False):
"""Prompt the user to pick two atoms to rotamerize a stretch of nucleotides. Alternatively, if
we're already waiting for the user to pick atoms, then cancel the pending picks.
ARGUMENTS:
None
OPTIONAL ARGUMENTS:
ignoreDensity - ignore the density when performing the minimization
defaults to False
RETURNS:
None
"""
#create the citation pop-up if necessary
createCitationPopup()
global waitingForClicks
#make sure that we're not waiting on a pending extendChain call
extendChain.clearPendingExtendChain()
if waitingForClicks:
#if we're already in the middle of a rotamerize call, then cancel the pending rotamerize
print "Rotamerize cancelled"
add_status_bar_text("Rotamerize cancelled")
clear_pending_picks(
) #tell Coot to stop waiting for the user to click on atoms
__setMenuToRotamerize()
waitingForClicks = False
else:
#if we're not in the middle of a rotamerize call, then start one
#make sure that there is a refinement map set
if not ignoreDensity and imol_refinement_map() == -1:
print "No refinement map set for RCrane rotamerize"
selectMapDialog(pickAtoms)
return
print "Click on 2 atoms (in the same molecule)"
add_status_bar_text(
"Pick 2 atoms [Ctrl Left-mouse rotates the view]...")
__setMenuToCancel()
waitingForClicks = True
user_defined_click(
2, lambda atomSpec1, atomSpec2: rotamerizeFromAtomSpecs(
atomSpec1, atomSpec2, ignoreDensity))
def pickAtoms(ignoreDensity = False):
"""Prompt the user to pick two atoms to rotamerize a stretch of nucleotides. Alternatively, if
we're already waiting for the user to pick atoms, then cancel the pending picks.
ARGUMENTS:
None
OPTIONAL ARGUMENTS:
ignoreDensity - ignore the density when performing the minimization
defaults to False
RETURNS:
None
"""
#create the citation pop-up if necessary
createCitationPopup()
global waitingForClicks
#make sure that we're not waiting on a pending extendChain call
extendChain.clearPendingExtendChain()
if waitingForClicks:
#if we're already in the middle of a rotamerize call, then cancel the pending rotamerize
print "Rotamerize cancelled"
add_status_bar_text("Rotamerize cancelled")
clear_pending_picks() #tell Coot to stop waiting for the user to click on atoms
__setMenuToRotamerize()
waitingForClicks = False
else:
#if we're not in the middle of a rotamerize call, then start one
#make sure that there is a refinement map set
if not ignoreDensity and imol_refinement_map() == -1:
print "No refinement map set for RCrane rotamerize"
selectMapDialog(pickAtoms)
return
print "Click on 2 atoms (in the same molecule)"
add_status_bar_text("Pick 2 atoms [Ctrl Left-mouse rotates the view]...")
__setMenuToCancel()
waitingForClicks = True
user_defined_click(2, lambda atomSpec1, atomSpec2: rotamerizeFromAtomSpecs(atomSpec1, atomSpec2, ignoreDensity))
def pickAtoms():
"""Prompt the user to pick an atoms to extend a stretch of nucleotides. Alternatively, if
we're already waiting for the user to pick an atom, then cancel the pending pick.
ARGUMENTS:
None
RETURNS:
None
"""
#create the citation pop-up if necessary
createCitationPopup()
#make sure that we're not waiting on a pending rotamerize call
rotamerize.clearPendingRotamerize()
global waitingForClicks
if waitingForClicks:
#if we're already in the middle of an extend chain call, then cancel the pending call
print "Rotamerize cancelled"
add_status_bar_text("Extend chain cancelled")
clear_pending_picks(
) #tell Coot to stop waiting for the user to click on atoms
__setMenuToExtendChain()
waitingForClicks = False
else:
#if we're not in the middle of a extend chain call, then start one
#make sure that there is a refinement map set
if imol_refinement_map() == -1:
print "No refinement map set for RCrane extend chain"
selectMapDialog(pickAtoms)
return
print "Click on a nucleotide to extend"
add_status_bar_text(
"Pick a nucleotide [Ctrl Left-mouse rotates the view]...")
__setMenuToCancel()
waitingForClicks = True
user_defined_click(1, extendChainFromAtomSpec)
def pickAtoms():
"""Prompt the user to pick an atoms to extend a stretch of nucleotides. Alternatively, if
we're already waiting for the user to pick an atom, then cancel the pending pick.
ARGUMENTS:
None
RETURNS:
None
"""
#create the citation pop-up if necessary
createCitationPopup()
#make sure that we're not waiting on a pending rotamerize call
rotamerize.clearPendingRotamerize()
global waitingForClicks
if waitingForClicks:
#if we're already in the middle of an extend chain call, then cancel the pending call
print "Rotamerize cancelled"
add_status_bar_text("Extend chain cancelled")
clear_pending_picks() #tell Coot to stop waiting for the user to click on atoms
__setMenuToExtendChain()
waitingForClicks = False
else:
#if we're not in the middle of a extend chain call, then start one
#make sure that there is a refinement map set
if imol_refinement_map() == -1:
print "No refinement map set for RCrane extend chain"
selectMapDialog(pickAtoms)
return
print "Click on a nucleotide to extend"
add_status_bar_text("Pick a nucleotide [Ctrl Left-mouse rotates the view]...")
__setMenuToCancel()
waitingForClicks = True
user_defined_click(1, extendChainFromAtomSpec)
def __decideDirectionFromAtom(atomName, resNum):
"""Determine the direction to extend the chain based on the atom name (for use with isolated nuclotides)
ARGUMENTS:
atomName - the atom name
resNum - the residue number of the current nucleotide (used in reporting errors)
RETURNS:
False if the direction cannot be determined from the atom name
3 or 5 otherwise
EFFECTS:
if the direction cannot be determined from the atom name, an error will be reported to the user
(and False will be returned)
"""
if atomName in ATOMS3P:
return 3
elif atomName in ATOMS5P:
return 5
else:
print "Nucleotide " + resNum + " is an isolated nucleotide. Please select either the O5' or"
print "O3' atom to extend in the 5' or 3' direction, respectively."
add_status_bar_text("Must select either O5' or O3' of isolated nucleotides.")
return False
def __decideDirectionFromAtom(atomName, resNum):
"""Determine the direction to extend the chain based on the atom name (for use with isolated nuclotides)
ARGUMENTS:
atomName - the atom name
resNum - the residue number of the current nucleotide (used in reporting errors)
RETURNS:
False if the direction cannot be determined from the atom name
3 or 5 otherwise
EFFECTS:
if the direction cannot be determined from the atom name, an error will be reported to the user
(and False will be returned)
"""
if atomName in ATOMS3P:
return 3
elif atomName in ATOMS5P:
return 5
else:
print "Nucleotide " + resNum + " is an isolated nucleotide. Please select either the O5' or"
print "O3' atom to extend in the 5' or 3' direction, respectively."
add_status_bar_text(
"Must select either O5' or O3' of isolated nucleotides.")
return False
#starting suite of this residue, then start the minimization at the previous nucleotide
startIndex -= 1
startResFull = pseudoMol.resNumFull(startIndex)
if ((endIndex + 1) < pseudoMol.getNumNts() and endAtom.strip() == "O3'"
and pseudoMol.connectedToNextFromIndex(endIndex)):
#if we're not at the last nucleotide and the user clicked on an atom belonging exclusively to the
#ending suite of this residue, then include the next residue in the minimization
endIndex += 1
endResFull = pseudoMol.resNumFull(endIndex)
#warn the user if they haven't selected an entire suite
if startIndex == endIndex:
print "You must select at least one suite (two residues) to rotamerize."
add_status_bar_text(
"You must select at least one suite (two residues) to rotamerize.")
return False
#make sure that the selected residues are all connected
for curIndex in range(startIndex, endIndex):
if not pseudoMol.connectedToNextFromIndex(curIndex):
print "Nucleotides " + pseudoMol.resNumFull(
curIndex) + " and " + pseudoMol.resNumFull(
curIndex + 1) + " are not connected. Cannot rotamerize."
add_status_bar_text("Nucleotides " +
pseudoMol.resNumFull(curIndex) + " and " +
pseudoMol.resNumFull(curIndex + 1) +
" are not connected. Cannot rotamerize.")
return False
#note that this loop does not check to see if the last nucleotide is connectedToNext, since that's not required
nextResIsPhosOnly = False
if connectedToNext:
nextResIsPhosOnly = pseudoMol.isOnlyPhosGroupFromIndex(resIndex+1)
extendDir = None #the direction to extend the chain in
if curResIsPhosOnly:
if connectedToPrev:
#we're building on a 3' phosphate
extendDir = 3
else:
#the selected residue is an isolated phosphate group, so we can't do anything
print "Nucleotide " + resNumFull + " is an isolated phosphate group. Cannot extend."
add_status_bar_text("Nucleotide " + resNumFull + " is an isolated phosphate group. Cannot extend.")
return False
elif nextResIsPhosOnly:
if connectedToPrev:
#we're at the 3' end of the chain and there is a 3' phosphate
extendDir = 3
resIndex += 1 #increment the resIndex so that it points to the real last residue of the segment
curResIsPhosOnly = True
resNumFull = pseudoMol.resNumFull(resIndex) #update the residue name in case we need to use it for later error messages
else:
#we're dealing with a single nt containing a 3' phosphate
#we need to decide direction based on the atom clicked
extendDir = __decideDirectionFromAtom(atom, resNumFull)
if not extendDir: return False #if we couldn't determine a direction from the atom, then cancel
nextResIsPhosOnly = False
if connectedToNext:
nextResIsPhosOnly = pseudoMol.isOnlyPhosGroupFromIndex(resIndex + 1)
extendDir = None #the direction to extend the chain in
if curResIsPhosOnly:
if connectedToPrev:
#we're building on a 3' phosphate
extendDir = 3
else:
#the selected residue is an isolated phosphate group, so we can't do anything
print "Nucleotide " + resNumFull + " is an isolated phosphate group. Cannot extend."
add_status_bar_text(
"Nucleotide " + resNumFull +
" is an isolated phosphate group. Cannot extend.")
return False
elif nextResIsPhosOnly:
if connectedToPrev:
#we're at the 3' end of the chain and there is a 3' phosphate
extendDir = 3
resIndex += 1 #increment the resIndex so that it points to the real last residue of the segment
curResIsPhosOnly = True
resNumFull = pseudoMol.resNumFull(
resIndex
) #update the residue name in case we need to use it for later error messages
else:
#we're dealing with a single nt containing a 3' phosphate
#we need to decide direction based on the atom clicked
startIndex -= 1
startResFull = pseudoMol.resNumFull(startIndex)
if ((endIndex + 1) < pseudoMol.getNumNts()
and endAtom.strip() == "O3'"
and pseudoMol.connectedToNextFromIndex(endIndex)):
#if we're not at the last nucleotide and the user clicked on an atom belonging exclusively to the
#ending suite of this residue, then include the next residue in the minimization
endIndex += 1
endResFull = pseudoMol.resNumFull(endIndex)
#warn the user if they haven't selected an entire suite
if startIndex == endIndex:
print "You must select at least one suite (two residues) to rotamerize."
add_status_bar_text("You must select at least one suite (two residues) to rotamerize.")
return False
#make sure that the selected residues are all connected
for curIndex in range(startIndex, endIndex):
if not pseudoMol.connectedToNextFromIndex(curIndex):
print "Nucleotides " + pseudoMol.resNumFull(curIndex) + " and " + pseudoMol.resNumFull(curIndex+1) + " are not connected. Cannot rotamerize."
add_status_bar_text("Nucleotides " + pseudoMol.resNumFull(curIndex) + " and " + pseudoMol.resNumFull(curIndex+1) + " are not connected. Cannot rotamerize.")
return False
#note that this loop does not check to see if the last nucleotide is connectedToNext, since that's not required
for curIndex in range(startIndex, endIndex+1):
#make sure that the selected residues aren't modified nucleotides
curResType = pseudoMol.resTypeFromIndex(curIndex)
if curResType not in STANDARD_BASES: