Matriarch

Authors: Ravi Jagadeesan, David Spivak, Tristan Giesa, and Markus Buehler.

On this page, we show some sample python scripts, written in Matriarch, along with visualizations of the .pdb (Protein Data Bank) files that they produce. These include a collagen molecule, a triangular helix, the spherical spiral shown to the right, and an array of spaced chains. More information on the Matriarch programs shown below can be found in the User's Guide.

Collagen

from matriarch import *
from math import *

def collagen(seq1, seq2): 
    a1 = chain(seq1) 
    a2 = chain(seq2)
    hel1 = helixBuilder(a1,1.5,9.5238,'L') 
    hel2 = helixBuilder(a2,1.5,9.5238,'L')
    helhel1 = helixBuilder(hel1,4,85.5,'L') 
    helhel2 = helixBuilder(hel2,4,85.5,'L')
    helhel1rot = shiftOrbs(rotateOrbs(helhel1,2*pi/3),2.8)
    helhel2rot = shiftOrbs(rotateOrbs(helhel2,4*pi/3),5.6)
    homodimer = overlay(helhel1,helhel1rot) 
    output = overlay(homodimer,helhel2rot)
    return output

def helixBuilder(myBB,rad,pitch,handed):
    scale = sqrt(rad*rad + pitch*pitch/(4*pi*pi))
    if handed=='R':
        sign=1
    elif handed=='L':
        sign=-1
    else: 
        print handed,' should be L or R.'
    def parameterizedHelix(t):
        sc = sign/scale
        return [rad*cos(sc*t),-rad*sin(sc*t),pitch*t/(2*pi*scale)]
    W = buildAxisTwister(parameterizedHelix)
    return twist(myBB, W)

seq1 = 'GFZGPKGTAGEZGKAGERGVZGPZGAVGPAGKDGEAGAQGAZGPAGPAGERGEQGPA'
seq2 = 'GFZGPKGPSGDZGKZGEKGHPGLAGARGAZGPDGNNGAQGPZGPQGVQGGKGEQGPA'
collgn = collagen(seq1,seq2)
fileOut(collgn,'collgn.pdb')

Triangular helix

from matriarch import * 
from math import *

def triangleTwister(side, pitch, length, smoothingFactor):
    iterations = int(length/(3*side)) + 2
    const = sqrt(3)/6
    def loop(Z0):
        return [[side*2*const,0,Z0],[-side*const,side/2.0,Z0+pitch/3.0],[-side*const,-side/2.0,Z0+pitch*2/3.0]]
    PList = []
    for n in range(0,iterations):
        PList.extend(loop(pitch*n))
    Rout = Ray([0,0,0],[0,0,1])
    provideTheta = []
    return smoothedPieceWiseLinear(PList, Rout, provideTheta, smoothingFactor)

aminoLength=3.4

actualSeq ='TNVIIEGNVTLGHRVKIGTGCVIKNSVIGDDCEISP'
Mult=3
Side=9*aminoLength
Pitch=7
SmthFact = 0.33
totalLen=Mult*aminoLength*len(actualSeq)
myChain = attachSeries(chain(actualSeq),Mult)
myTriangle = twist(myChain, triangleTwister(Side, Pitch, totalLen, SmthFact))

fileOut(myTriangle,'triangleHelix.pdb')

Spherical spiral

from matriarch import *
from math import *

seq1 = 'AAAAGGPGGYGGPGGAAAA'
a = chain(seq1)
ser = attachSeries(a,25)

def SphSprl(k,Rout):
    def curve(t):
        return [k*sin(t)*cos(20*t), k*sin(t)*sin(20*t), k*cos(t)]
    tmax=pi
    Thetaspec=0
    return buildAxisTwister(curve,Rout,Thetaspec,tmax)

Rout = Ray([0,0,0], [0,0,0])
k1 = 1        #first try
W1 = SphSprl(k1,Rout)

contourLength = length(ser)
lengthOfCurveWithKEquals1 = W1[0].length
knew = contourLength / lengthOfCurveWithKEquals1

SphSprlTwister = SphSprl(knew + 0.001,Rout)
output = twist(ser, SphSprlTwister)

fileOut(output,'sphericalSpiral.pdb')

Array of spaced chains

from matriarch import *

mySeqG = 'GGGGGGGGG'
mySeqA = 'AAA'
myChainG = chain(mySeqG)
myChainA = chain(mySeqA)
spacedBlock = space(myChainG, myChainA, 10)
array = makeArray(spacedBlock, 10, 15, 4, 6, True)
fileOut(array, 'arraySpaced.pdb')

Matriarch by Jagadeesan, Spivak, Giesa, and Buehler is licensed under a Creative Commons Attribution 4.0 International License.