fixed indentations and ported python 2 code to python 3
This commit is contained in:
alphataubio
@ -27,17 +27,17 @@ import sys, os, timeit
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from timeit import default_timer as timer
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start_time = timer()
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"""
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Try to import numpy; if failed, import a local version mynumpy
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Try to import numpy; if failed, import a local version mynumpy
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which needs to be provided
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"""
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try:
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import numpy as np
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except:
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print >> sys.stderr, "numpy not found. Exiting."
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print("numpy not found. Exiting.", file=sys.stderr)
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sys.exit(1)
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"""
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Check that the required arguments (box offset and size in simulation units
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Check that the required arguments (box offset and size in simulation units
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and the sequence file were provided
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"""
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try:
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@ -45,8 +45,8 @@ try:
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box_length = float(sys.argv[2])
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infile = sys.argv[3]
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except:
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print >> sys.stderr, "Usage: %s <%s> <%s> <%s>" % (sys.argv[0], \
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"box offset", "box length", "file with sequences")
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print( "Usage: %s <%s> <%s> <%s>" % (sys.argv[0], \
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"box offset", "box length", "file with sequences"), file=sys.stderr)
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sys.exit(1)
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box = np.array ([box_length, box_length, box_length])
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@ -57,8 +57,7 @@ try:
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inp = open (infile, 'r')
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inp.close()
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except:
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print >> sys.stderr, "Could not open file '%s' for reading. \
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Aborting." % infile
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print( "Could not open file '%s' for reading. Aborting." % infile, file=sys.stderr)
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sys.exit(2)
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# return parts of a string
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@ -86,7 +85,7 @@ Define auxiliary variables for the construction of a helix
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# center of the double strand
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CM_CENTER_DS = POS_BASE + 0.2
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# ideal distance between base sites of two nucleotides
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# ideal distance between base sites of two nucleotides
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# which are to be base paired in a duplex
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BASE_BASE = 0.3897628551303122
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@ -118,7 +117,7 @@ strandnum = []
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bonds = []
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"""
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"""
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Convert local body frame to quaternion DOF
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"""
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def exyz_to_quat (mya1, mya3):
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@ -135,25 +134,25 @@ def exyz_to_quat (mya1, mya3):
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# compute other components from it
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if q0sq >= 0.25:
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myquat[0] = np.sqrt(q0sq)
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myquat[1] = (mya2[2] - mya3[1]) / (4.0*myquat[0])
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myquat[2] = (mya3[0] - mya1[2]) / (4.0*myquat[0])
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myquat[3] = (mya1[1] - mya2[0]) / (4.0*myquat[0])
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myquat[0] = np.sqrt(q0sq)
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myquat[1] = (mya2[2] - mya3[1]) / (4.0*myquat[0])
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myquat[2] = (mya3[0] - mya1[2]) / (4.0*myquat[0])
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myquat[3] = (mya1[1] - mya2[0]) / (4.0*myquat[0])
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elif q1sq >= 0.25:
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myquat[1] = np.sqrt(q1sq)
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myquat[0] = (mya2[2] - mya3[1]) / (4.0*myquat[1])
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myquat[2] = (mya2[0] + mya1[1]) / (4.0*myquat[1])
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myquat[3] = (mya1[2] + mya3[0]) / (4.0*myquat[1])
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myquat[1] = np.sqrt(q1sq)
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myquat[0] = (mya2[2] - mya3[1]) / (4.0*myquat[1])
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myquat[2] = (mya2[0] + mya1[1]) / (4.0*myquat[1])
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myquat[3] = (mya1[2] + mya3[0]) / (4.0*myquat[1])
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elif q2sq >= 0.25:
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myquat[2] = np.sqrt(q2sq)
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myquat[0] = (mya3[0] - mya1[2]) / (4.0*myquat[2])
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myquat[1] = (mya2[0] + mya1[1]) / (4.0*myquat[2])
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myquat[3] = (mya3[1] + mya2[2]) / (4.0*myquat[2])
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myquat[2] = np.sqrt(q2sq)
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myquat[0] = (mya3[0] - mya1[2]) / (4.0*myquat[2])
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myquat[1] = (mya2[0] + mya1[1]) / (4.0*myquat[2])
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myquat[3] = (mya3[1] + mya2[2]) / (4.0*myquat[2])
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elif q3sq >= 0.25:
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myquat[3] = np.sqrt(q3sq)
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myquat[0] = (mya1[1] - mya2[0]) / (4.0*myquat[3])
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myquat[1] = (mya3[0] + mya1[2]) / (4.0*myquat[3])
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myquat[2] = (mya3[1] + mya2[2]) / (4.0*myquat[3])
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myquat[3] = np.sqrt(q3sq)
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myquat[0] = (mya1[1] - mya2[0]) / (4.0*myquat[3])
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myquat[1] = (mya3[0] + mya1[2]) / (4.0*myquat[3])
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myquat[2] = (mya3[1] + mya2[2]) / (4.0*myquat[3])
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norm = 1.0/np.sqrt(myquat[0]*myquat[0] + myquat[1]*myquat[1] + \
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myquat[2]*myquat[2] + myquat[3]*myquat[3])
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@ -169,62 +168,62 @@ Adds a strand to the system by appending it to the array of previous strands
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"""
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def add_strands (mynewpositions, mynewa1s, mynewa3s):
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overlap = False
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# This is a simple check for each of the particles where for previously
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# placed particles i we check whether it overlaps with any of the
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# This is a simple check for each of the particles where for previously
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# placed particles i we check whether it overlaps with any of the
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# newly created particles j
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print >> sys.stdout, "## Checking for overlaps"
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print( "## Checking for overlaps", file=sys.stdout)
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for i in xrange(len(positions)):
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for i in range(len(positions)):
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p = positions[i]
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pa1 = a1s[i]
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p = positions[i]
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pa1 = a1s[i]
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for j in xrange (len(mynewpositions)):
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for j in range (len(mynewpositions)):
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q = mynewpositions[j]
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qa1 = mynewa1s[j]
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q = mynewpositions[j]
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qa1 = mynewa1s[j]
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# skip particles that are anyway too far away
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dr = p - q
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dr -= box * np.rint (dr / box)
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if np.dot(dr, dr) > RC2:
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continue
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# skip particles that are anyway too far away
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dr = p - q
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dr -= box * np.rint(dr / box)
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if np.dot(dr, dr) > RC2:
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continue
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# base site and backbone site of the two particles
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# base site and backbone site of the two particles
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p_pos_back = p + pa1 * POS_BACK
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p_pos_base = p + pa1 * POS_BASE
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q_pos_back = q + qa1 * POS_BACK
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q_pos_base = q + qa1 * POS_BASE
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# check for no overlap between the two backbone sites
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# check for no overlap between the two backbone sites
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dr = p_pos_back - q_pos_back
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dr -= box * np.rint (dr / box)
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dr -= box * np.rint(dr / box)
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if np.dot(dr, dr) < RC2_BACK:
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overlap = True
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# check for no overlap between the two base sites
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# check for no overlap between the two base sites
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dr = p_pos_base - q_pos_base
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dr -= box * np.rint (dr / box)
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dr -= box * np.rint(dr / box)
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if np.dot(dr, dr) < RC2_BASE:
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overlap = True
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# check for no overlap between backbone site of particle p
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# with base site of particle q
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# check for no overlap between backbone site of particle p
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# with base site of particle q
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dr = p_pos_back - q_pos_base
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dr -= box * np.rint (dr / box)
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if np.dot(dr, dr) < RC2_BACK_BASE:
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overlap = True
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# check for no overlap between base site of particle p and
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# backbone site of particle q
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# check for no overlap between base site of particle p and
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# backbone site of particle q
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dr = p_pos_base - q_pos_back
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dr -= box * np.rint (dr / box)
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if np.dot(dr, dr) < RC2_BACK_BASE:
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overlap = True
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# exit if there is an overlap
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# exit if there is an overlap
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if overlap:
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return False
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@ -237,10 +236,10 @@ def add_strands (mynewpositions, mynewa1s, mynewa3s):
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a1s.append (p)
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for p in mynewa3s:
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a3s.append (p)
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# calculate quaternion from local body frame and append
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for ia in xrange(len(mynewpositions)):
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mynewquaternions = exyz_to_quat(mynewa1s[ia],mynewa3s[ia])
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quaternions.append(mynewquaternions)
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# calculate quaternion from local body frame and append
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for ia in range(len(mynewpositions)):
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mynewquaternions = exyz_to_quat(mynewa1s[ia],mynewa3s[ia])
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quaternions.append(mynewquaternions)
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return True
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@ -281,7 +280,7 @@ def get_rotation_matrix(axis, anglest):
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[olc*x*z-st*y, olc*y*z+st*x, olc*z*z+ct]])
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"""
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Generates the position and orientation vectors of a
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Generates the position and orientation vectors of a
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(single or double) strand from a sequence string
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"""
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def generate_strand(bp, sequence=None, start_pos=np.array([0, 0, 0]), \
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@ -295,76 +294,75 @@ def generate_strand(bp, sequence=None, start_pos=np.array([0, 0, 0]), \
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# overall direction of the helix
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dir = np.array(dir, dtype=float)
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if sequence == None:
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sequence = np.random.randint(1, 5, bp)
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sequence = np.random.randint(1, 5, bp)
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# the elseif here is most likely redundant
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# the elseif here is most likely redundant
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elif len(sequence) != bp:
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n = bp - len(sequence)
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sequence += np.random.randint(1, 5, n)
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print >> sys.stderr, "sequence is too short, adding %d random bases" % n
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n = bp - len(sequence)
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sequence += np.random.randint(1, 5, n)
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print( "sequence is too short, adding %d random bases" % n, file=sys.stderr)
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# normalize direction
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dir_norm = np.sqrt(np.dot(dir,dir))
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if dir_norm < 1e-10:
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print >> sys.stderr, "direction must be a valid vector, \
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defaulting to (0, 0, 1)"
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dir = np.array([0, 0, 1])
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print( "direction must be a valid vector, defaulting to (0, 0, 1)", file=sys.stderr)
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dir = np.array([0, 0, 1])
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else: dir /= dir_norm
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# find a vector orthogonal to dir to act as helix direction,
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# if not provided switch off random orientation
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if perp is None or perp is False:
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v1 = np.random.random_sample(3)
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v1 -= dir * (np.dot(dir, v1))
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v1 /= np.sqrt(sum(v1*v1))
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v1 = np.random.random_sample(3)
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v1 -= dir * (np.dot(dir, v1))
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v1 /= np.sqrt(sum(v1*v1))
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else:
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v1 = perp;
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v1 = perp;
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# generate rotational matrix representing the overall rotation of the helix
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R0 = get_rotation_matrix(dir, rot)
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# rotation matrix corresponding to one step along the helix
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R = get_rotation_matrix(dir, [1, "bp"])
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# set the vector a1 (backbone to base) to v1
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# set the vector a1 (backbone to base) to v1
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a1 = v1
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# apply the global rotation to a1
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# apply the global rotation to a1
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a1 = np.dot(R0, a1)
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# set the position of the fist backbone site to start_pos
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rb = np.array(start_pos)
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# set a3 to the direction of the helix
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a3 = dir
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for i in range(bp):
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# work out the position of the centre of mass of the nucleotide
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rcdm = rb - CM_CENTER_DS * a1
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# append to newpositions
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mynewpositions.append(rcdm)
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mynewa1s.append(a1)
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mynewa3s.append(a3)
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# if we are not at the end of the helix, we work out a1 and rb for the
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# next nucleotide along the helix
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if i != bp - 1:
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a1 = np.dot(R, a1)
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rb += a3 * BASE_BASE
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rcdm = rb - CM_CENTER_DS * a1
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# if we are working on a double strand, we do a cycle similar
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# append to newpositions
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mynewpositions.append(rcdm)
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mynewa1s.append(a1)
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mynewa3s.append(a3)
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# if we are not at the end of the helix, we work out a1 and rb for the
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# next nucleotide along the helix
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if i != bp - 1:
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a1 = np.dot(R, a1)
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rb += a3 * BASE_BASE
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# if we are working on a double strand, we do a cycle similar
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# to the previous one but backwards
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if double == True:
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a1 = -a1
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a3 = -dir
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R = R.transpose()
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for i in range(bp):
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rcdm = rb - CM_CENTER_DS * a1
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mynewpositions.append (rcdm)
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mynewa1s.append (a1)
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mynewa3s.append (a3)
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a1 = np.dot(R, a1)
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rb += a3 * BASE_BASE
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a1 = -a1
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a3 = -dir
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R = R.transpose()
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for i in range(bp):
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rcdm = rb - CM_CENTER_DS * a1
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mynewpositions.append (rcdm)
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mynewa1s.append (a1)
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mynewa3s.append (a3)
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a1 = np.dot(R, a1)
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rb += a3 * BASE_BASE
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assert (len (mynewpositions) > 0)
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@ -391,10 +389,10 @@ def read_strands(filename):
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try:
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infile = open (filename)
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except:
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print >> sys.stderr, "Could not open file '%s'. Aborting." % filename
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print( "Could not open file '%s'. Aborting." % filename, file=sys.stderr )
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sys.exit(2)
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# This block works out the number of nucleotides and strands by reading
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# This block works out the number of nucleotides and strands by reading
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# the number of non-empty lines in the input file and the number of letters,
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# taking the possible DOUBLE keyword into account.
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nstrands, nnucl, nbonds = 0, 0, 0
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@ -406,30 +404,29 @@ def read_strands(filename):
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if line[:6] == 'DOUBLE':
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line = line.split()[1]
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length = len(line)
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print >> sys.stdout, "## Found duplex of %i base pairs" % length
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print( "## Found duplex of %i base pairs" % length, file=sys.stdout)
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nnucl += 2*length
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nstrands += 2
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nbonds += (2*length-2)
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nbonds += (2*length-2)
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else:
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line = line.split()[0]
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length = len(line)
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print >> sys.stdout, \
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"## Found single strand of %i bases" % length
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print( "## Found single strand of %i bases" % length, file=sys.stdout)
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nnucl += length
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nstrands += 1
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nbonds += length-1
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nbonds += length-1
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# rewind the sequence input file
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infile.seek(0)
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print >> sys.stdout, "## nstrands, nnucl = ", nstrands, nnucl
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print( "## nstrands, nnucl = ", nstrands, nnucl, file=sys.stdout)
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# generate the data file in LAMMPS format
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try:
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out = open ("data.oxdna", "w")
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except:
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print >> sys.stderr, "Could not open data file for writing. Aborting."
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print( "Could not open data file for writing. Aborting.", file=sys.stderr)
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sys.exit(2)
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lines = infile.readlines()
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nlines = len(lines)
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i = 1
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@ -440,115 +437,114 @@ def read_strands(filename):
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line = line.upper().strip()
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# skip empty lines
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if len(line) == 0:
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i += 1
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continue
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if len(line) == 0:
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i += 1
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continue
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# block for duplexes: last argument of the generate function
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# is set to 'True'
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# block for duplexes: last argument of the generate function
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# is set to 'True'
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if line[:6] == 'DOUBLE':
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line = line.split()[1]
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length = len(line)
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seq = [(base_to_number[x]) for x in line]
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myns += 1
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for b in xrange(length):
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basetype.append(seq[b])
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strandnum.append(myns)
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myns += 1
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for b in range(length):
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basetype.append(seq[b])
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strandnum.append(myns)
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for b in xrange(length-1):
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bondpair = [noffset + b, noffset + b + 1]
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bonds.append(bondpair)
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noffset += length
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for b in range(length-1):
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bondpair = [noffset + b, noffset + b + 1]
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bonds.append(bondpair)
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noffset += length
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# create the sequence of the second strand as made of
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# complementary bases
|
||||
seq2 = [5-s for s in seq]
|
||||
seq2.reverse()
|
||||
# create the sequence of the second strand as made of
|
||||
# complementary bases
|
||||
seq2 = [5-s for s in seq]
|
||||
seq2.reverse()
|
||||
|
||||
myns += 1
|
||||
for b in xrange(length):
|
||||
basetype.append(seq2[b])
|
||||
strandnum.append(myns)
|
||||
myns += 1
|
||||
for b in range(length):
|
||||
basetype.append(seq2[b])
|
||||
strandnum.append(myns)
|
||||
|
||||
for b in xrange(length-1):
|
||||
bondpair = [noffset + b, noffset + b + 1]
|
||||
bonds.append(bondpair)
|
||||
noffset += length
|
||||
|
||||
print >> sys.stdout, "## Created duplex of %i bases" % (2*length)
|
||||
for b in range(length-1):
|
||||
bondpair = [noffset + b, noffset + b + 1]
|
||||
bonds.append(bondpair)
|
||||
noffset += length
|
||||
|
||||
# generate random position of the first nucleotide
|
||||
print( "## Created duplex of %i bases" % (2*length), file=sys.stdout)
|
||||
|
||||
# generate random position of the first nucleotide
|
||||
cdm = box_offset + np.random.random_sample(3) * box
|
||||
|
||||
# generate the random direction of the helix
|
||||
# generate the random direction of the helix
|
||||
axis = np.random.random_sample(3)
|
||||
axis /= np.sqrt(np.dot(axis, axis))
|
||||
|
||||
# use the generate function defined above to create
|
||||
# the position and orientation vector of the strand
|
||||
# use the generate function defined above to create
|
||||
# the position and orientation vector of the strand
|
||||
newpositions, newa1s, newa3s = generate_strand(len(line), \
|
||||
sequence=seq, dir=axis, start_pos=cdm, double=True)
|
||||
sequence=seq, dir=axis, start_pos=cdm, double=True)
|
||||
|
||||
# generate a new position for the strand until it does not overlap
|
||||
# with anything already present
|
||||
start = timer()
|
||||
# with anything already present
|
||||
start = timer()
|
||||
while not add_strands(newpositions, newa1s, newa3s):
|
||||
cdm = box_offset + np.random.random_sample(3) * box
|
||||
axis = np.random.random_sample(3)
|
||||
axis /= np.sqrt(np.dot(axis, axis))
|
||||
newpositions, newa1s, newa3s = generate_strand(len(line), \
|
||||
sequence=seq, dir=axis, start_pos=cdm, double=True)
|
||||
print >> sys.stdout, "## Trying %i" % i
|
||||
end = timer()
|
||||
print >> sys.stdout, "## Added duplex of %i bases (line %i/%i) in %.2fs, now at %i/%i" % \
|
||||
(2*length, i, nlines, end-start, len(positions), nnucl)
|
||||
sequence=seq, dir=axis, start_pos=cdm, double=True)
|
||||
print( "## Trying %i" % i, file=sys.stdout)
|
||||
end = timer()
|
||||
print( "## Added duplex of %i bases (line %i/%i) in %.2fs, now at %i/%i" % \
|
||||
(2*length, i, nlines, end-start, len(positions), nnucl), file=sys.stdout)
|
||||
|
||||
# block for single strands: last argument of the generate function
|
||||
# is set to 'False'
|
||||
# block for single strands: last argument of the generate function
|
||||
# is set to 'False'
|
||||
else:
|
||||
length = len(line)
|
||||
seq = [(base_to_number[x]) for x in line]
|
||||
|
||||
myns += 1
|
||||
for b in xrange(length):
|
||||
basetype.append(seq[b])
|
||||
strandnum.append(myns)
|
||||
myns += 1
|
||||
for b in range(length):
|
||||
basetype.append(seq[b])
|
||||
strandnum.append(myns)
|
||||
|
||||
for b in xrange(length-1):
|
||||
bondpair = [noffset + b, noffset + b + 1]
|
||||
bonds.append(bondpair)
|
||||
noffset += length
|
||||
for b in range(length-1):
|
||||
bondpair = [noffset + b, noffset + b + 1]
|
||||
bonds.append(bondpair)
|
||||
noffset += length
|
||||
|
||||
# generate random position of the first nucleotide
|
||||
# generate random position of the first nucleotide
|
||||
cdm = box_offset + np.random.random_sample(3) * box
|
||||
|
||||
# generate the random direction of the helix
|
||||
# generate the random direction of the helix
|
||||
axis = np.random.random_sample(3)
|
||||
axis /= np.sqrt(np.dot(axis, axis))
|
||||
|
||||
print >> sys.stdout, \
|
||||
"## Created single strand of %i bases" % length
|
||||
print("## Created single strand of %i bases" % length, file=sys.stdout)
|
||||
|
||||
newpositions, newa1s, newa3s = generate_strand(length, \
|
||||
sequence=seq, dir=axis, start_pos=cdm, double=False)
|
||||
start = timer()
|
||||
start = timer()
|
||||
while not add_strands(newpositions, newa1s, newa3s):
|
||||
cdm = box_offset + np.random.random_sample(3) * box
|
||||
axis = np.random.random_sample(3)
|
||||
axis /= np.sqrt(np.dot(axis, axis))
|
||||
axis /= np.sqrt(np.dot(axis, axis))
|
||||
newpositions, newa1s, newa3s = generate_strand(length, \
|
||||
sequence=seq, dir=axis, start_pos=cdm, double=False)
|
||||
sequence=seq, dir=axis, start_pos=cdm, double=False)
|
||||
print >> sys.stdout, "## Trying %i" % (i)
|
||||
end = timer()
|
||||
print >> sys.stdout, "## Added single strand of %i bases (line %i/%i) in %.2fs, now at %i/%i" % \
|
||||
(length, i, nlines, end-start,len(positions), nnucl)
|
||||
end = timer()
|
||||
print( "## Added single strand of %i bases (line %i/%i) in %.2fs, now at %i/%i" % \
|
||||
(length, i, nlines, end-start,len(positions), nnucl), file=sys.stdout)
|
||||
|
||||
i += 1
|
||||
|
||||
# sanity check
|
||||
if not len(positions) == nnucl:
|
||||
print len(positions), nnucl
|
||||
print( len(positions), nnucl )
|
||||
raise AssertionError
|
||||
|
||||
out.write('# LAMMPS data file\n')
|
||||
@ -580,44 +576,41 @@ def read_strands(filename):
|
||||
out.write('Atoms\n')
|
||||
out.write('\n')
|
||||
|
||||
for i in xrange(nnucl):
|
||||
out.write('%d %d %22.15le %22.15le %22.15le %d 1 1\n' \
|
||||
% (i+1, basetype[i], \
|
||||
positions[i][0], positions[i][1], positions[i][2], \
|
||||
strandnum[i]))
|
||||
for i in range(nnucl):
|
||||
out.write('%d %d %22.15le %22.15le %22.15le %d 1 1\n' \
|
||||
% (i+1, basetype[i], positions[i][0], positions[i][1], positions[i][2], strandnum[i]))
|
||||
|
||||
out.write('\n')
|
||||
out.write('# Atom-ID, translational, rotational velocity\n')
|
||||
out.write('Velocities\n')
|
||||
out.write('\n')
|
||||
|
||||
for i in xrange(nnucl):
|
||||
out.write("%d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le\n" \
|
||||
% (i+1,0.0,0.0,0.0,0.0,0.0,0.0))
|
||||
for i in range(nnucl):
|
||||
out.write("%d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le\n" \
|
||||
% (i+1,0.0,0.0,0.0,0.0,0.0,0.0))
|
||||
|
||||
out.write('\n')
|
||||
out.write('# Atom-ID, shape, quaternion\n')
|
||||
out.write('Ellipsoids\n')
|
||||
out.write('\n')
|
||||
|
||||
for i in xrange(nnucl):
|
||||
out.write(\
|
||||
"%d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le\n" \
|
||||
% (i+1,1.1739845031423408,1.1739845031423408,1.1739845031423408, \
|
||||
quaternions[i][0],quaternions[i][1], quaternions[i][2],quaternions[i][3]))
|
||||
|
||||
for i in range(nnucl):
|
||||
out.write("%d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le\n" \
|
||||
% (i+1,1.1739845031423408,1.1739845031423408,1.1739845031423408, \
|
||||
quaternions[i][0],quaternions[i][1], quaternions[i][2],quaternions[i][3]))
|
||||
|
||||
out.write('\n')
|
||||
out.write('# Bond topology\n')
|
||||
out.write('Bonds\n')
|
||||
out.write('\n')
|
||||
|
||||
for i in xrange(nbonds):
|
||||
out.write("%d %d %d %d\n" % (i+1,1,bonds[i][0],bonds[i][1]))
|
||||
for i in range(nbonds):
|
||||
out.write("%d %d %d %d\n" % (i+1,1,bonds[i][0],bonds[i][1]))
|
||||
|
||||
out.close()
|
||||
|
||||
print >> sys.stdout, "## Wrote data to 'data.oxdna'"
|
||||
print >> sys.stdout, "## DONE"
|
||||
print("## Wrote data to 'data.oxdna'", file=sys.stdout)
|
||||
print("## DONE", file=sys.stdout)
|
||||
|
||||
# call the above main() function, which executes the program
|
||||
read_strands (infile)
|
||||
@ -627,4 +620,6 @@ runtime = end_time-start_time
|
||||
hours = runtime/3600
|
||||
minutes = (runtime-np.rint(hours)*3600)/60
|
||||
seconds = (runtime-np.rint(hours)*3600-np.rint(minutes)*60)%60
|
||||
print >> sys.stdout, "## Total runtime %ih:%im:%.2fs" % (hours,minutes,seconds)
|
||||
print( "## Total runtime %ih:%im:%.2fs" % (hours,minutes,seconds), file=sys.stdout)
|
||||
|
||||
|
||||
|
||||
@ -250,59 +250,59 @@ def duplex_array():
|
||||
qrot3=math.sin(0.5*twist)
|
||||
|
||||
for letter in strand[2]:
|
||||
temp1=[]
|
||||
temp2=[]
|
||||
temp1=[]
|
||||
temp2=[]
|
||||
|
||||
temp1.append(nt2num[letter])
|
||||
temp2.append(compnt2num[letter])
|
||||
temp1.append(nt2num[letter])
|
||||
temp2.append(compnt2num[letter])
|
||||
|
||||
temp1.append([posx1,posy1,posz1])
|
||||
temp2.append([posx2,posy2,posz2])
|
||||
temp1.append([posx1,posy1,posz1])
|
||||
temp2.append([posx2,posy2,posz2])
|
||||
|
||||
vel=[0,0,0,0,0,0]
|
||||
temp1.append(vel)
|
||||
temp2.append(vel)
|
||||
vel=[0,0,0,0,0,0]
|
||||
temp1.append(vel)
|
||||
temp2.append(vel)
|
||||
|
||||
temp1.append(shape)
|
||||
temp2.append(shape)
|
||||
temp1.append(shape)
|
||||
temp2.append(shape)
|
||||
|
||||
temp1.append(quat1)
|
||||
temp2.append(quat2)
|
||||
temp1.append(quat1)
|
||||
temp2.append(quat2)
|
||||
|
||||
quat1_0 = quat1[0]*qrot0 - quat1[1]*qrot1 - quat1[2]*qrot2 - quat1[3]*qrot3
|
||||
quat1_1 = quat1[0]*qrot1 + quat1[1]*qrot0 + quat1[2]*qrot3 - quat1[3]*qrot2
|
||||
quat1_2 = quat1[0]*qrot2 + quat1[2]*qrot0 + quat1[3]*qrot1 - quat1[1]*qrot3
|
||||
quat1_3 = quat1[0]*qrot3 + quat1[3]*qrot0 + quat1[1]*qrot2 + quat1[2]*qrot1
|
||||
quat1_0 = quat1[0]*qrot0 - quat1[1]*qrot1 - quat1[2]*qrot2 - quat1[3]*qrot3
|
||||
quat1_1 = quat1[0]*qrot1 + quat1[1]*qrot0 + quat1[2]*qrot3 - quat1[3]*qrot2
|
||||
quat1_2 = quat1[0]*qrot2 + quat1[2]*qrot0 + quat1[3]*qrot1 - quat1[1]*qrot3
|
||||
quat1_3 = quat1[0]*qrot3 + quat1[3]*qrot0 + quat1[1]*qrot2 + quat1[2]*qrot1
|
||||
|
||||
quat1 = [quat1_0,quat1_1,quat1_2,quat1_3]
|
||||
quat1 = [quat1_0,quat1_1,quat1_2,quat1_3]
|
||||
|
||||
posx1=axisx - dcomh*(quat1[0]**2+quat1[1]**2-quat1[2]**2-quat1[3]**2)
|
||||
posy1=axisy - dcomh*(2*(quat1[1]*quat1[2]+quat1[0]*quat1[3]))
|
||||
posz1=posz1+risez
|
||||
posx1=axisx - dcomh*(quat1[0]**2+quat1[1]**2-quat1[2]**2-quat1[3]**2)
|
||||
posy1=axisy - dcomh*(2*(quat1[1]*quat1[2]+quat1[0]*quat1[3]))
|
||||
posz1=posz1+risez
|
||||
|
||||
quat2_0 = quat2[0]*qrot0 - quat2[1]*qrot1 - quat2[2]*qrot2 + quat2[3]*qrot3
|
||||
quat2_1 = quat2[0]*qrot1 + quat2[1]*qrot0 - quat2[2]*qrot3 - quat2[3]*qrot2
|
||||
quat2_2 = quat2[0]*qrot2 + quat2[2]*qrot0 + quat2[3]*qrot1 + quat2[1]*qrot3
|
||||
quat2_3 =-quat2[0]*qrot3 + quat2[3]*qrot0 + quat2[1]*qrot2 + quat2[2]*qrot1
|
||||
quat2_0 = quat2[0]*qrot0 - quat2[1]*qrot1 - quat2[2]*qrot2 + quat2[3]*qrot3
|
||||
quat2_1 = quat2[0]*qrot1 + quat2[1]*qrot0 - quat2[2]*qrot3 - quat2[3]*qrot2
|
||||
quat2_2 = quat2[0]*qrot2 + quat2[2]*qrot0 + quat2[3]*qrot1 + quat2[1]*qrot3
|
||||
quat2_3 =-quat2[0]*qrot3 + quat2[3]*qrot0 + quat2[1]*qrot2 + quat2[2]*qrot1
|
||||
|
||||
quat2 = [quat2_0,quat2_1,quat2_2,quat2_3]
|
||||
quat2 = [quat2_0,quat2_1,quat2_2,quat2_3]
|
||||
|
||||
posx2=axisx + dcomh*(quat1[0]**2+quat1[1]**2-quat1[2]**2-quat1[3]**2)
|
||||
posy2=axisy + dcomh*(2*(quat1[1]*quat1[2]+quat1[0]*quat1[3]))
|
||||
posz2=posz1
|
||||
posx2=axisx + dcomh*(quat1[0]**2+quat1[1]**2-quat1[2]**2-quat1[3]**2)
|
||||
posy2=axisy + dcomh*(2*(quat1[1]*quat1[2]+quat1[0]*quat1[3]))
|
||||
posz2=posz1
|
||||
|
||||
if (len(nucleotide)+1 > strandstart):
|
||||
topology.append([1,len(nucleotide),len(nucleotide)+1])
|
||||
comptopo.append([1,len(nucleotide)+len(strand[2]),len(nucleotide)+len(strand[2])+1])
|
||||
if (len(nucleotide)+1 > strandstart):
|
||||
topology.append([1,len(nucleotide),len(nucleotide)+1])
|
||||
comptopo.append([1,len(nucleotide)+len(strand[2]),len(nucleotide)+len(strand[2])+1])
|
||||
|
||||
nucleotide.append(temp1)
|
||||
compstrand.append(temp2)
|
||||
nucleotide.append(temp1)
|
||||
compstrand.append(temp2)
|
||||
|
||||
for ib in range(len(compstrand)):
|
||||
nucleotide.append(compstrand[len(compstrand)-1-ib])
|
||||
nucleotide.append(compstrand[len(compstrand)-1-ib])
|
||||
|
||||
for ib in range(len(comptopo)):
|
||||
topology.append(comptopo[ib])
|
||||
topology.append(comptopo[ib])
|
||||
|
||||
return
|
||||
|
||||
|
||||
Reference in New Issue
Block a user