startIndex = pseudoMol.resIndex(startResFull)
endIndex = pseudoMol.resIndex(endResFull)
if (startIndex > endIndex):
#make sure that the starting atom is before the ending atom
#if it isn't, swap them
(startResFull, endResFull) = (endResFull, startResFull)
(startIndex, endIndex) = (endIndex, startIndex)
(startAtom, endAtom) = (startAtom, endAtom)
#make sure that the molecule using PDB3 naming (as oppsed to PDB2)
#TODO: check all residues for PDB3 naming instead of just the first one in case the molecule uses a mix of PDB2 and PDB3 naming
# this seems like an unlikely problem, but it can't hurt to double check
if pseudoMol.checkPDB2FromIndex(startIndex):
reportPDB2Error(startResFull)
return False
if (startIndex > 0 and startAtom.strip() in frozenset(
["P", "OP1", "OP2", "O5'", "C5'"])
and pseudoMol.connectedToPrevFromIndex(startIndex)):
#if we're not at the first nucleotide and the user clicked on an atom belonging exclusively to the
#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
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 pseudoMol.getAtomCoordsFromIndex("C1'", resIndexToCheck) is None:
print "Nucleotide " + resNumFullToCheck + " does not have a C1' atom. Cannot extend chain."
add_status_bar_text("Nucleotide " + resNumFullToCheck +
" does not have a C1' atom. Cannot extend chain.")
return False
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 pseudoMol.getAtomCoordsFromIndex("C1'", resIndexToCheck) is None:
print "Nucleotide " + resNumFullToCheck + " does not have a C1' atom. Cannot extend chain."
add_status_bar_text("Nucleotide " + resNumFullToCheck + " does not have a C1' atom. Cannot extend chain.")
return False
if pseudoMol.getAtomCoordsFromIndex(glyN, resIndexToCheck) is None:
startIndex = pseudoMol.resIndex(startResFull)
endIndex = pseudoMol.resIndex(endResFull)
if (startIndex > endIndex):
#make sure that the starting atom is before the ending atom
#if it isn't, swap them
(startResFull, endResFull) = (endResFull, startResFull)
(startIndex, endIndex) = (endIndex, startIndex)
(startAtom, endAtom) = (startAtom, endAtom)
#make sure that the molecule using PDB3 naming (as oppsed to PDB2)
#TODO: check all residues for PDB3 naming instead of just the first one in case the molecule uses a mix of PDB2 and PDB3 naming
# this seems like an unlikely problem, but it can't hurt to double check
if pseudoMol.checkPDB2FromIndex(startIndex):
reportPDB2Error(startResFull)
return False
if (startIndex > 0
and startAtom.strip() in frozenset(["P", "OP1", "OP2", "O5'", "C5'"])
and pseudoMol.connectedToPrevFromIndex(startIndex)):
#if we're not at the first nucleotide and the user clicked on an atom belonging exclusively to the
#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
