endIndex -= 1
endResFull = pseudoMol.resNumFull(endIndex)
#make sure that we're not now down to a single residue
if startIndex >= endIndex:
print "Cannot rotamerize this suite without a 3' phosphate."
add_status_bar_text(
"Cannot rotamerize this suite without a 3' phosphate.")
return False
#make sure that there are no insertion codes (since Coot's refine_zone can't handle these)
#ideally, refine_zone will eventually get fixed and I can remove this check
for curIndex in range(startIndex, endIndex + 2):
#we need to check the last residue and the one after that, since createPartialChainObject will add on the 3' phosphate
if pseudoMol.resNum(curIndex)[1] != "":
reportInsCodeError(pseudoMol.resNumFull(curIndex))
return False
#make sure that the user hasn't tried to rotamerize too many nucleotides
#If they have, it's likely due to misclicking, so we don't want to force them to sit through rotamerizing hundreds of nucleotides
numNucsToRotamerize = endIndex - startIndex + 1
if (MAX_NUCLEOTIDES_TO_ROTAMERIZE > 0) and (numNucsToRotamerize >
MAX_NUCLEOTIDES_TO_ROTAMERIZE):
print "Warning: Too many nucleotides to rotamerize."
print " Trying to rotamerize", numNucsToRotamerize, "nucleotides and your current maximum is", MAX_NUCLEOTIDES_TO_ROTAMERIZE
print " To increase the maximum, go to Calculate -> Scripting -> Python"
print " and type rcrane.setRotamerizeMaxNucleotides(" + str(
numNucsToRotamerize) + ")"
print " or type rcrane.setRotamerizeMaxNucleotides(-1) to remove the limit."
add_status_bar_text(
return False
elif connectedToNext:
extendDir = 5
elif connectedToPrev:
extendDir = 3
else:
#we're dealing with a single nt not 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
#make sure that the residue we're going to extend doesn't have an insertion code
# (also check the next and previous residues)
if pseudoMol.resNum(resIndex)[1] != "":
reportInsCodeError(resNumFull)
return False
if connectedToNext and pseudoMol.resNum(resIndex + 1)[1] != "":
reportInsCodeError(pseudoMol.resNumFull(resIndex + 1))
return False
if connectedToPrev and pseudoMol.resNum(resIndex - 1)[1] != "":
reportInsCodeError(pseudoMol.resNumFull(resIndex - 1))
return False
#figure out which residue we should be checking for PDB2 naming and missing glycosidic bond atoms
if curResIsPhosOnly:
resIndexToCheck = resIndex - 1
resNumFullToCheck = pseudoMol.resNumFull(resIndex - 1)
else:
resIndexToCheck = resIndex
resNumFullToCheck = resNumFull
elif connectedToNext:
extendDir = 5
elif connectedToPrev:
extendDir = 3
else:
#we're dealing with a single nt not 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
#make sure that the residue we're going to extend doesn't have an insertion code
# (also check the next and previous residues)
if pseudoMol.resNum(resIndex)[1] != "":
reportInsCodeError(resNumFull)
return False
if connectedToNext and pseudoMol.resNum(resIndex+1)[1] != "":
reportInsCodeError(pseudoMol.resNumFull(resIndex+1))
return False
if connectedToPrev and pseudoMol.resNum(resIndex-1)[1] != "":
reportInsCodeError(pseudoMol.resNumFull(resIndex-1))
return False
#figure out which residue we should be checking for PDB2 naming and missing glycosidic bond atoms
if curResIsPhosOnly:
resIndexToCheck = resIndex - 1
resNumFullToCheck = pseudoMol.resNumFull(resIndex - 1)
else:
resIndexToCheck = resIndex
resNumFullToCheck = resNumFull
endIndex -= 1
endResFull = pseudoMol.resNumFull(endIndex)
#make sure that we're not now down to a single residue
if startIndex >= endIndex:
print "Cannot rotamerize this suite without a 3' phosphate."
add_status_bar_text("Cannot rotamerize this suite without a 3' phosphate.")
return False
#make sure that there are no insertion codes (since Coot's refine_zone can't handle these)
#ideally, refine_zone will eventually get fixed and I can remove this check
for curIndex in range(startIndex, endIndex+2):
#we need to check the last residue and the one after that, since createPartialChainObject will add on the 3' phosphate
if pseudoMol.resNum(curIndex)[1] != "":
reportInsCodeError(pseudoMol.resNumFull(curIndex))
return False
#make sure that the user hasn't tried to rotamerize too many nucleotides
#If they have, it's likely due to misclicking, so we don't want to force them to sit through rotamerizing hundreds of nucleotides
numNucsToRotamerize = endIndex - startIndex + 1
if (MAX_NUCLEOTIDES_TO_ROTAMERIZE > 0) and (numNucsToRotamerize > MAX_NUCLEOTIDES_TO_ROTAMERIZE):
print "Warning: Too many nucleotides to rotamerize."
print " Trying to rotamerize", numNucsToRotamerize, "nucleotides and your current maximum is", MAX_NUCLEOTIDES_TO_ROTAMERIZE
print " To increase the maximum, go to Calculate -> Scripting -> Python"
print " and type rcrane.setRotamerizeMaxNucleotides(" + str(numNucsToRotamerize) + ")"
print " or type rcrane.setRotamerizeMaxNucleotides(-1) to remove the limit."
add_status_bar_text("Warning: Too many nts to rotamerize. Trying to rotamerize " + str(numNucsToRotamerize) + " nts and your current max is " + str(MAX_NUCLEOTIDES_TO_ROTAMERIZE))
return False
