Python fileOut Examples

Example #1

File: 07-helixEg.py Project: dspivak/Matriarch

# -*- coding: utf-8 -*-
"""
Created on Mon Apr 13 10:21:53 2015
@author: Tristan Giesa, David I. Spivak, Ravi Jagadeesan
"""
import matriarch
from math import *
mySeqA = 'AAAAAAAAAAAAAAAAAAAA'
myChainA = matriarch.chain(mySeqA)
def parameterizedHelix(t):
    return [4*cos(2*pi*t),-4*sin(2*pi*t),8*t]
W = matriarch.buildAxisTwister(parameterizedHelix)
myHelix = matriarch.twist(myChainA, W)
matriarch.fileOut(myHelix, '07-helixEg.pdb')

Example #2

File: 06-warpedBlock.py Project: dspivak/Matriarch

# -*- coding: utf-8 -*-
"""
Created on Mon Apr 13 10:21:53 2015
@author: Tristan Giesa, David I. Spivak, Ravi Jagadeesan
"""
import matriarch
mySeq = 'AAAPPY'
myChain = matriarch.chain(mySeq)

def F(x):
    return [-x[2], x[1], x[0] - 25]

def FPrime(x):
    return [-x[2], x[1], x[0]]

g = [F, FPrime]
myChain_newAxis = matriarch.moveOrbs(myChain, g)

def parabola(t):
    return [-t * t, 0, 10 * t]

Rout = matriarch.Ray([18, 0, 0], [0, 0, 0])
W = matriarch.buildAxisTwister(parabola, Rout)
warpedBlock = matriarch.twist(myChain_newAxis, W)
matriarch.fileOut(warpedBlock, '06-warpedBlock.pdb')

Example #3

# -*- coding: utf-8 -*-
"""
Created on Mon Apr 13 10:21:53 2015
@author: Tristan Giesa, David I. Spivak, Ravi Jagadeesan
"""
import matriarch
from math import *
mySeqA = 'AAAAAAAAAAAAAAAAAAAA'
myChainA = matriarch.chain(mySeqA)

def parameterizedHelix(t):
    return [4 * cos(2 * pi * t), -4 * sin(2 * pi * t), 8 * t]

W = matriarch.buildAxisTwister(parameterizedHelix)
myHelix = matriarch.twist(myChainA, W)
matriarch.fileOut(myHelix, '07-helixEg.pdb')

Example #4

# -*- coding: utf-8 -*-
"""
Created on Mon Apr 13 10:21:53 2015
@author: Tristan Giesa, David I. Spivak, Ravi Jagadeesan
"""
import matriarch
mySeq = 'AAAPPY'
myChain = matriarch.chain(mySeq)

def parabola(t):
    return [-t * t, 0, 10 * t]

Rout = matriarch.Ray([18, 0, 0], [0, 0, 0])
W = matriarch.buildAxisTwister(parabola, Rout)
twistedBlock = matriarch.twist(myChain, W)
matriarch.fileOut(twistedBlock, '05-twistedBlock.pdb')

Example #5

File: 05-twistedBlock.py Project: dspivak/Matriarch

# -*- coding: utf-8 -*-
"""
Created on Mon Apr 13 10:21:53 2015
@author: Tristan Giesa, David I. Spivak, Ravi Jagadeesan
"""
import matriarch
mySeq = 'AAAPPY'
myChain = matriarch.chain(mySeq)
def parabola(t):
     return [-t*t, 0, 10*t]
Rout = matriarch.Ray([18,0,0],[0,0,0])
W = matriarch.buildAxisTwister(parabola, Rout)
twistedBlock = matriarch.twist(myChain, W)
matriarch.fileOut(twistedBlock,'05-twistedBlock.pdb')

Example #6

File: 06-warpedBlock.py Project: dspivak/Matriarch

# -*- coding: utf-8 -*-
"""
Created on Mon Apr 13 10:21:53 2015
@author: Tristan Giesa, David I. Spivak, Ravi Jagadeesan
"""
import matriarch
mySeq = 'AAAPPY'
myChain = matriarch.chain(mySeq)
def F(x):
	return [-x[2], x[1], x[0]-25]
def FPrime(x):
	return [-x[2], x[1], x[0]]
g = [F, FPrime]
myChain_newAxis = matriarch.moveOrbs(myChain, g)
def parabola(t):
     return [-t*t, 0, 10*t]
Rout = matriarch.Ray([18,0,0],[0,0,0])
W = matriarch.buildAxisTwister(parabola,Rout)
warpedBlock = matriarch.twist(myChain_newAxis, W)
matriarch.fileOut(warpedBlock,'06-warpedBlock.pdb')