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:
reportModifiedNucError(pseudoMol.resNumFull(curIndex), curResType)
return False
#make sure that all selected residues have phosphates and glycosidic bonds
missingAtom = pseudoMol.checkPhosAndGlycosidicFromIndex(curIndex)
if missingAtom is not None:
print "Nucleotide " + pseudoMol.resNumFull(
curIndex
) + " is missing " + missingAtom + " atom. Cannot rotamerize without phosphate and glycosidic bond coordinates."
add_status_bar_text(
"Nucleotide " + pseudoMol.resNumFull(curIndex) +
" is missing " + missingAtom +
" atom. Cannot rotamerize without phosphate and glycosidic bond coordinates."
)
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
#make sure that this nucleotide isn't mdofied
resType = pseudoMol.resTypeFromIndex(resIndexToCheck)
if resType not in STANDARD_BASES:
reportModifiedNucError(resNumFullToCheck, resType)
return False
#make sure that the molecule (or at least the end of it we're going to be building on) uses PDB3 atom naming
if pseudoMol.checkPDB2FromIndex(resIndexToCheck):
reportPDB2Error(resNumFullToCheck)
return False
#the current residue must have a glycosidic bond
baseType = pseudoMol.resTypeFromIndex(resIndexToCheck)
if baseType == "A" or baseType == "G":
glyN = "N9"
else:
#we already know that the base isn't modified because we checked above
glyN = "N1"
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
#make sure that this nucleotide isn't mdofied
resType = pseudoMol.resTypeFromIndex(resIndexToCheck)
if resType not in STANDARD_BASES:
reportModifiedNucError(resNumFullToCheck, resType)
return False
#make sure that the molecule (or at least the end of it we're going to be building on) uses PDB3 atom naming
if pseudoMol.checkPDB2FromIndex(resIndexToCheck):
reportPDB2Error(resNumFullToCheck)
return False
#the current residue must have a glycosidic bond
baseType = pseudoMol.resTypeFromIndex(resIndexToCheck)
if baseType == "A" or baseType== "G":
glyN = "N9"
else:
#we already know that the base isn't modified because we checked above
glyN = "N1"
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:
reportModifiedNucError(pseudoMol.resNumFull(curIndex), curResType)
return False
#make sure that all selected residues have phosphates and glycosidic bonds
missingAtom = pseudoMol.checkPhosAndGlycosidicFromIndex(curIndex)
if missingAtom is not None:
print "Nucleotide " + pseudoMol.resNumFull(curIndex) + " is missing " + missingAtom + " atom. Cannot rotamerize without phosphate and glycosidic bond coordinates."
add_status_bar_text("Nucleotide " + pseudoMol.resNumFull(curIndex) + " is missing " + missingAtom + " atom. Cannot rotamerize without phosphate and glycosidic bond coordinates.")
return False
#if the ending res is the last residue of the chain, then change it to the second to last residue
#since we need a terminal 3' phosphate
#(Note that createPartialChainObject will then add the extra 3' phosphate)
if (endIndex + 1) >= pseudoMol.getNumNts() or not pseudoMol.connectedToNextFromIndex(endIndex):
endIndex -= 1
endResFull = pseudoMol.resNumFull(endIndex)
