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protein_build_script.py
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protein_build_script.py
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import sys;
import subprocess;
import math;
class Atom:
Symbol = "";
AminoAcidAtomName = "";
AminoAcidName = "";
AminoAcidIdx = -1;
Position = (0,0,0);
AtomIdx = -1;
def __init__(self, symbol, name, atomIdx, x, y, z):
self.Symbol = symbol;
self.AminoAcidAtomName = name;
self.Position = (x,y,z);
self.AtomIdx = atomIdx;
def __repr__(self):
return self.AminoAcidAtomName;
def __str__(self):
return self.AminoAcidAtomName;
def magnitude(v):
return math.sqrt(sum(v[i]*v[i] for i in range(len(v))))
def add(u, v):
return [ u[i]+v[i] for i in range(len(u)) ]
def subtract(u, v):
return [ u[i]-v[i] for i in range(len(u)) ]
def scalarMultiply(scalar, v):
return [ scalar*v[i] for i in range(len(v)) ]
def dot(u, v):
return sum(u[i]*v[i] for i in range(len(u)))
def normalize(v):
vmag = magnitude(v)
return [ v[i]/vmag for i in range(len(v)) ]
def addAminoAcidToPdb(inputFileName, outputFileName, aminoAcidCode):
if len(aminoAcidCode) == 1:
aminoAcidCode = mapOneLetterToThreeLetterAminoAcidCode(aminoAcidCode);
inFile = open(inputFileName,"r");
outFile = open(outputFileName,"w");
lastLine = "";
lastBackboneNitrogen = None;
lastBackboneCarbon = None;
newPeptideLength = None;
for line in inFile:
if lastLine.startswith("SEQRES"):
[ aminoAcids, peptideLength, lineIdx ] = parseSequence(lastLine);
if newPeptideLength is None:
newPeptideLength = peptideLength+1;
if line.startswith("SEQRES"):
seqresLine = generateSeqresLine(aminoAcids, newPeptideLength, lineIdx);
outFile.write(seqresLine);
else:
if len(aminoAcids) < 13:
aminoAcids.append(aminoAcidCode);
seqresLine = generateSeqresLine(aminoAcids, newPeptideLength, lineIdx);
outFile.write(seqresLine);
else:
seqresLine = generateSeqresLine(aminoAcids, newPeptideLength, lineIdx);
outputFile.write(lastLine);
seqresLine = generateSeqresLine([aminoAcidCode], newPeptideLength, lineIdx+1);
outFile.write(seqresLine);
outFile.write(line);
elif line.startswith("TER"):
lastAtom = parseAtom(lastLine);
lastAtomIdx = lastAtom.AtomIdx;
outFile.write(lastLine);
aminoAcidAtoms = getAminoAcidAtoms(aminoAcidCode, newPeptideLength);
positionAminoAcid(aminoAcidAtoms, lastBackboneNitrogen, lastBackboneCarbon);
atomLines = generateAtomLines(aminoAcidAtoms, lastAtomIdx+1);
for i in range(len(atomLines)):
outFile.write(atomLines[i]);
terminalLine = generateTerminalLine();
outFile.write(terminalLine);
elif not lastLine.startswith("TER"):
outFile.write(lastLine);
if line.startswith("ATOM"):
atom = parseAtom(line);
if atom.AminoAcidAtomName == "N":
lastBackboneNitrogen = atom;
elif atom.AminoAcidAtomName == "C":
lastBackboneCarbon = atom;
lastLine = line;
outFile.write(lastLine);
outFile.close();
inFile.close();
def generateSeqresLine(aminoAcids, peptideLength, lineIdx):
seqresLine = "SEQRES {:3} A {:4} {}".format(lineIdx,peptideLength," ".join(aminoAcids));
return seqresLine.ljust(80) + "\n";
def getAminoAcidAtoms(aminoAcidCode, aminoAcidIdx):
aminoAcidFileName = "../AminoAcids/" + aminoAcidCode + ".txt";
file = open(aminoAcidFileName,"r");
atoms = [];
for line in file:
atom = parseAtom(line);
atom.AminoAcidName = aminoAcidCode;
atom.AminoAcidIdx = aminoAcidIdx;
atoms.append(atom);
return atoms;
def positionAminoAcid(aminoAcidAtoms, lastBackboneNitrogen, lastBackboneCarbon):
lastBackboneDirection = subtract(lastBackboneCarbon.Position, lastBackboneNitrogen.Position);
normalizedBackboneDirection = normalize(lastBackboneDirection);
[ rBB, thetaBB, phiBB ] = calculateSphericalCoordinates(normalizedBackboneDirection);
aminoAcidNitrogen = None;
aminoAcidCarbon = None;
for i in range(len(aminoAcidAtoms)):
atom = aminoAcidAtoms[i];
if atom.AminoAcidAtomName == "N":
aminoAcidNitrogen = atom;
elif atom.AminoAcidAtomName == "C":
aminoAcidCarbon = atom;
aminoAcidDirection = subtract(aminoAcidCarbon.Position, aminoAcidNitrogen.Position);
normalizedAminoAcidDirection = normalize(aminoAcidDirection);
[ rAA, thetaAA, phiAA ] = calculateSphericalCoordinates(normalizedAminoAcidDirection);
oldNitrogenPosition = aminoAcidNitrogen.Position;
newNitrogenPosition = add(lastBackboneCarbon.Position,\
scalarMultiply(1.32,normalizedBackboneDirection));
dTheta = thetaBB - thetaAA;
dPhi = phiBB - phiAA;
for i in range(len(aminoAcidAtoms)):
atom = aminoAcidAtoms[i];
nitrogenCenteredPosition = subtract(atom.Position, oldNitrogenPosition);
[ r, theta, phi ] = calculateSphericalCoordinates(nitrogenCenteredPosition);
rotatedPosition = calculateCartesianCoordinates(r,theta+dTheta,phi+dPhi);
atom.Position = tuple(add(rotatedPosition,newNitrogenPosition));
def calculateCartesianCoordinates(r,theta,phi):
x = r*math.sin(theta)*math.cos(phi);
y = r*math.sin(theta)*math.sin(phi);
z = r*math.cos(theta);
return [ x, y, z ];
def calculateSphericalCoordinates(v3D):
r = magnitude(v3D);
if r == 0:
return [ r, 0, 0 ];
theta = math.acos(v3D[2]/r);
phi = math.acos(v3D[0]/(r*math.sin(theta)));
if v3D[1] < 0 and phi > 0:
phi = -phi;
return [ r, theta, phi ];
def generateAtomLines(atoms, nextAtomIdx):
atomLines = [];
for idx in range(len(atoms)):
atom = atoms[idx];
atomLine = generateAtomLine(atom, nextAtomIdx);
atomLines.append(atomLine);
nextAtomIdx += 1;
return atomLines;
def generateAtomLine(atom, nextAtomIdx):
return "ATOM {:>5} {:>4} {:3} A{:4} {:8.3f}{:8.3f}{:8.3f}{:6.2f}{:6.2f} {:>2} \n".format(\
nextAtomIdx,\
atom.AminoAcidAtomName,\
atom.AminoAcidName,\
atom.AminoAcidIdx,\
atom.Position[0],\
atom.Position[1],\
atom.Position[2],\
1.0,\
0.0,\
atom.Symbol);
def generateTerminalLine():
return "TER".ljust(80) + "\n";
##def parsePdb(filename):
## file = open(filename, "r");
## atoms = [];
## sequence = [];
## for line in file:
## if line.startswith("SEQRES"):
## aminoAcids = parseSequence(line);
## sequence.extend(aminoAcids);
## elif line.startswith("ATOM"):
## atom = parseAtom(line);
## if type(atom) is Atom:
## print(atom.Position);
## atoms.append(atom);
## return [ sequence, atoms ];
def parseSequence(line):
"Parses PDB SEQRES line"
if line[:6] != "SEQRES":
raise Exception;
lineIdx = int(line[7:10]);
peptideLength = int(line[13:17]);
aminoAcids = line[19:].split();
return [ aminoAcids, peptideLength, lineIdx ];
def parseAtom(line):
"Parses PDB ATOM line"
if line[:4] != "ATOM":
raise Exception;
atomName = line[12:16].strip();
symbol = line[76:78].strip();
atomIdx = int(line[6:11]);
x = float(line[30:38]);
y = float(line[38:46]);
z = float(line[46:54]);
return Atom(symbol,atomName,atomIdx,x,y,z);
def mapOneLetterToThreeLetterAminoAcidCode(oneLetterCode):
if oneLetterCode == "A":
return "ALA";
if oneLetterCode == "G":
return "GLY";
if oneLetterCode == "I":
return "ILE";
if oneLetterCode == "L":
return "LEU";
if oneLetterCode == "P":
return "PRO";
if oneLetterCode == "V":
return "VAL";
if oneLetterCode == "F":
return "PHE";
if oneLetterCode == "W":
return "TRP";
if oneLetterCode == "Y":
return "TYR";
if oneLetterCode == "D":
return "ASP";
if oneLetterCode == "E":
return "GLU";
if oneLetterCode == "R":
return "ARG";
if oneLetterCode == "H":
return "HIS";
if oneLetterCode == "K":
return "LYS";
if oneLetterCode == "S":
return "SER";
if oneLetterCode == "T":
return "THR";
if oneLetterCode == "C":
return "CYS";
if oneLetterCode == "M":
return "MET";
if oneLetterCode == "N":
return "ASN";
if oneLetterCode == "Q":
return "GLN";
def main(argv):
#filename = argv[1];
#aminoAcidCode = argv[2];
inputFileName = "cftr_1_2.pdb";
outputFileName = "cftr_1_3.pdb";
aminoAcidCode = "A";
addAminoAcidToPdb(inputFileName, outputFileName, aminoAcidCode);
if __name__ == "__main__":
main(sys.argv);