def getCoordsFromInp( oldInput ):
oldFile = open(oldInput, 'r')
line = oldFile.readline()
#route section
while not isBlankLine(line):
line = oldFile.readline()
line = oldFile.readline()
#comment
while not isBlankLine(line):
line = oldFile.readline()
line = oldFile.readline() #charges and multiplicity
line = oldFile.readline()
coords = []
while not isBlankLine(line):
lineSpl = line.split()
coordInd = floatInList(lineSpl)[-3:]
newCoords = [ float(lineSpl[c]) for c in coordInd]
coords.append(newCoords)
line = oldFile.readline()
oldFile.close()
return coords
def readHighLayerIndexesFromInput(oldInput):
oldFile = open(oldInput, 'r')
line = oldFile.readline()
#route section
while not isBlankLine(line):
line = oldFile.readline()
line = oldFile.readline()
#comment
while not isBlankLine(line):
line = oldFile.readline()
line = oldFile.readline() #charges and multiplicity
line = oldFile.readline()
indexes = []
actualIndex = 0
while not isBlankLine(line):
lineSpl = line.split()
coordInd = getCoordInd(lineSpl)
layerInd = lineSpl[coordInd[-1] + 1]
if "H" == layerInd.upper():
indexes.append(actualIndex)
line = oldFile.readline()
actualIndex += 1
oldFile.close()
return indexes
def writeNewInput ( oldInput, newCoords, newInputName, modredundantLines ):
oldFile = open(oldInput, 'r')
beginning = ""
line = oldFile.readline()
destiny = open(newInputName, 'w')
#route section
while not isBlankLine(line):
beginning += line
line = oldFile.readline()
beginning += line
line = oldFile.readline()
#comment
while not isBlankLine(line):
beginning += line
line = oldFile.readline()
beginning += line
line = oldFile.readline()
beginning += line
destiny.write(beginning)
for coord in newCoords:
line = oldFile.readline()
lineSpl = line.split()
coordInd = floatInList(lineSpl)[-3:]
for ci, crd in zip(coordInd, coord):
lineSpl[ci] = str(crd)
destiny.write("\t".join(lineSpl)+"\n")
line = oldFile.readline()
nonBondParameters = False
while line:
if "NonBon" in line and modredundantLines:
destiny.write(modredundantLines)
destiny.write("\n\n")
nonBondParameters = True
destiny.write(line)
line = oldFile.readline()
if not nonBondParameters:
destiny.write(modredundantLines)
destiny.write("\n")
destiny.close()
oldFile.close()
def writeNewInput(oldInput, newCoords, newInputName, indexes):
oldFile = open(oldInput, 'r')
beginning = ""
line = oldFile.readline()
destiny = open(newInputName, 'w')
#route section
while not isBlankLine(line):
beginning += line
line = oldFile.readline()
beginning += line
line = oldFile.readline()
#comment
while not isBlankLine(line):
beginning += line
line = oldFile.readline()
#charge and multiplicity
beginning += line
line = oldFile.readline()
beginning += line
destiny.write(beginning)
fullCoordsIndex = 0
newCoordsIndex = 0
while not isBlankLine(line):
line = oldFile.readline()
lineSpl = line.split()
coordInd = floatInList(lineSpl)[-3:]
if fullCoordsIndex in indexes:
coord = newCoords[newCoordsIndex]
for ci, crd in zip(coordInd, coord):
lineSpl[ci] = str(crd)
newCoordsIndex += 1
destiny.write("\t".join(lineSpl) + "\n")
fullCoordsIndex += 1
line = oldFile.readline()
while line:
destiny.write(line)
line = oldFile.readline()
destiny.close()
oldFile.close()
def writeNewInput(oldInput, newCoords, newInputName):
oldFile = open(oldInput, 'r')
beginning = ""
line = oldFile.readline()
destiny = open(newInputName, 'w')
#route section
while not isBlankLine(line):
beginning += line
line = oldFile.readline()
beginning += line
line = oldFile.readline()
#comment
while not isBlankLine(line):
beginning += line
line = oldFile.readline()
beginning += line
line = oldFile.readline()
beginning += line
destiny.write(beginning)
for coord in newCoords:
line = oldFile.readline()
lineSpl = line.split()
coordInd = floatInList(lineSpl)[-3:]
for ci, crd in zip(coordInd, coord):
lineSpl[ci] = str(crd)
destiny.write("\t".join(lineSpl) + "\n")
line = oldFile.readline()
while line:
destiny.write(line)
line = oldFile.readline()
destiny.close()
oldFile.close()
def getFrozenIndexes(oldInput):
oldFile = open(oldInput, 'r')
line = oldFile.readline()
#route section
while not isBlankLine(line):
line = oldFile.readline()
line = oldFile.readline()
#comment
while not isBlankLine(line):
line = oldFile.readline()
line = oldFile.readline() #charges and multiplicity
line = oldFile.readline()
indexes = []
ind = 0
coords = []
elements = []
while not isBlankLine(line):
lineSpl = line.split()
if lineSpl[1] == "-1":
indexes.append(ind)
coordInd = floatInList(lineSpl)[-3:]
newCoords = [float(lineSpl[c]) for c in coordInd]
coords.append(newCoords)
elements.append(lineSpl[0])
line = oldFile.readline()
ind += 1
oldFile.close()
return indexes, coords, elements
def readHighLayerFromInput(oldInput):
oldFile = open(oldInput, 'r')
line = oldFile.readline()
#route section
while not isBlankLine(line):
line = oldFile.readline()
line = oldFile.readline()
#comment
while not isBlankLine(line):
line = oldFile.readline()
line = oldFile.readline() #charges and multiplicity
line = oldFile.readline()
coords = []
elements = []
while not isBlankLine(line):
lineSpl = line.split()
coordInd = floatInList(lineSpl)[-3:]
newCoords = [float(lineSpl[c]) for c in coordInd]
layerInd = lineSpl[coordInd[-1] + 1]
if "H" == layerInd.upper():
coords.append(newCoords)
element = lineSpl[0][0]
elements.append(element)
line = oldFile.readline()
oldFile.close()
return elements, coords