| 1 |
#!@PYTHON_EXECUTABLE@ |
| 2 |
"""Water Quaternion Sampler |
| 3 |
|
| 4 |
Samples water orientations from a list of known good |
| 5 |
orientations |
| 6 |
|
| 7 |
Usage: waterRotator |
| 8 |
|
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Options: |
| 10 |
-h, --help show this help |
| 11 |
-m, --meta-data=... use specified meta-data (.md) file |
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-o, --output-file=... use specified output (.md) file |
| 13 |
|
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|
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Example: |
| 16 |
waterRotator -m basal.md -o basal.new.md |
| 17 |
|
| 18 |
""" |
| 19 |
|
| 20 |
__author__ = "Dan Gezelter (gezelter@nd.edu)" |
| 21 |
__version__ = "$Revision$" |
| 22 |
__date__ = "$Date$" |
| 23 |
__copyright__ = "Copyright (c) 2006 by the University of Notre Dame" |
| 24 |
__license__ = "OpenMD" |
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|
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import sys |
| 27 |
import getopt |
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import string |
| 29 |
import math |
| 30 |
import random |
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|
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_haveMDFileName = 0 |
| 33 |
_haveOutputFileName = 0 |
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|
| 35 |
metaData = [] |
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frameData = [] |
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positions = [] |
| 38 |
velocities = [] |
| 39 |
quaternions = [] |
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angVels = [] |
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indices = [] |
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neighbors = [] |
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DonatingTo = [] |
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AcceptingFrom = [] |
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OldDonor = [] |
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Hmat = [] |
| 47 |
BoxInv = [] |
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#Hmat = zeros([3,3],Float) |
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#BoxInv = zeros([3],Float) |
| 50 |
H1vects = [] |
| 51 |
H2vects = [] |
| 52 |
DipoleVects = [] |
| 53 |
allAcceptors = [] |
| 54 |
availableneighbs = [] |
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surfaceSet = set([-1]) |
| 56 |
|
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|
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|
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def usage(): |
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print __doc__ |
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|
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|
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def readFile(mdFileName): |
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mdFile = open(mdFileName, 'r') |
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# Find OpenMD version info first |
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line = mdFile.readline() |
| 67 |
while 1: |
| 68 |
if '<OOPSE version=' in line or '<OpenMD version=' in line: |
| 69 |
OpenMDversion = line |
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break |
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line = mdFile.readline() |
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|
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# Rewind file and find start of MetaData block |
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|
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mdFile.seek(0) |
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line = mdFile.readline() |
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print "reading MetaData" |
| 78 |
while 1: |
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if '<MetaData>' in line: |
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while 2: |
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metaData.append(line) |
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line = mdFile.readline() |
| 83 |
if '</MetaData>' in line: |
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metaData.append(line) |
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break |
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break |
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line = mdFile.readline() |
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|
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mdFile.seek(0) |
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print "reading Snapshot" |
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line = mdFile.readline() |
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while 1: |
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if '<Snapshot>' in line: |
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line = mdFile.readline() |
| 95 |
while 1: |
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print "reading FrameData" |
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if '<FrameData>' in line: |
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while 2: |
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frameData.append(line) |
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if 'Hmat:' in line: |
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L = line.split() |
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Hxx = float(L[2].strip(',')) |
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Hxy = float(L[3].strip(',')) |
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Hxz = float(L[4].strip(',')) |
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Hyx = float(L[7].strip(',')) |
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Hyy = float(L[8].strip(',')) |
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Hyz = float(L[9].strip(',')) |
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Hzx = float(L[12].strip(',')) |
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Hzy = float(L[13].strip(',')) |
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Hzz = float(L[14].strip(',')) |
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Hmat.append([Hxx, Hxy, Hxz]) |
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Hmat.append([Hyx, Hyy, Hyz]) |
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Hmat.append([Hzx, Hzy, Hzz]) |
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print Hmat |
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BoxInv.append(1.0/Hxx) |
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BoxInv.append(1.0/Hyy) |
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BoxInv.append(1.0/Hzz) |
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print BoxInv |
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line = mdFile.readline() |
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if '</FrameData>' in line: |
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frameData.append(line) |
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break |
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break |
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|
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line = mdFile.readline() |
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while 1: |
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if '<StuntDoubles>' in line: |
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line = mdFile.readline() |
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while 2: |
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L = line.split() |
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myIndex = int(L[0]) |
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indices.append(myIndex) |
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pvqj = L[1] |
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x = float(L[2]) |
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y = float(L[3]) |
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z = float(L[4]) |
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positions.append([x, y, z]) |
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vx = float(L[5]) |
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vy = float(L[6]) |
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vz = float(L[7]) |
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velocities.append([vx, vy, vz]) |
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qw = float(L[8]) |
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qx = float(L[9]) |
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qy = float(L[10]) |
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qz = float(L[11]) |
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quaternions.append([qw, qx, qy, qz]) |
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jx = float(L[12]) |
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jy = float(L[13]) |
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jz = float(L[14]) |
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angVels.append([jx, jy, jz]) |
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line = mdFile.readline() |
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if '</StuntDoubles>' in line: |
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break |
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break |
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line = mdFile.readline() |
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if not line: break |
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|
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mdFile.close() |
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|
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def writeFile(outputFileName): |
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outputFile = open(outputFileName, 'w') |
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|
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outputFile.write("<OpenMD version=1>\n"); |
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|
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for metaline in metaData: |
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outputFile.write(metaline) |
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|
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outputFile.write(" <Snapshot>\n") |
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|
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for frameline in frameData: |
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outputFile.write(frameline) |
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|
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outputFile.write(" <StuntDoubles>\n") |
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|
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sdFormat = 'pvqj' |
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for i in range(len(indices)): |
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|
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outputFile.write("%10d %7s %18.10g %18.10g %18.10g %13e %13e %13e %13e %13e %13e %13e %13e %13e %13e\n" % (indices[i], sdFormat, positions[i][0], positions[i][1], positions[i][2], velocities[i][0], velocities[i][1], velocities[i][2], quaternions[i][0], quaternions[i][1], quaternions[i][2], quaternions[i][3], angVels[i][0], angVels[i][1], angVels[i][2])) |
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|
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outputFile.write(" </StuntDoubles>\n") |
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outputFile.write(" </Snapshot>\n") |
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outputFile.write("</OpenMD>\n") |
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outputFile.close() |
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|
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def roundMe(x): |
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if (x >= 0.0): |
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return math.floor(x + 0.5) |
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else: |
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return math.ceil(x - 0.5) |
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|
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def wrapVector(myVect): |
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scaled = [0.0, 0.0, 0.0] |
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for i in range(3): |
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scaled[i] = myVect[i] * BoxInv[i] |
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scaled[i] = scaled[i] - roundMe(scaled[i]) |
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myVect[i] = scaled[i] * Hmat[i][i] |
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return myVect |
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|
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def dot(L1, L2): |
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myDot = 0.0 |
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for i in range(len(L1)): |
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myDot = myDot + L1[i]*L2[i] |
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return myDot |
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|
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def normalize(L1): |
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L2 = [] |
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myLength = math.sqrt(dot(L1, L1)) |
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for i in range(len(L1)): |
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L2.append(L1[i] / myLength) |
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return L2 |
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|
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def cross(L1, L2): |
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# don't call this with anything other than length 3 lists please |
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# or you'll be sorry |
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L3 = [0.0, 0.0, 0.0] |
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L3[0] = L1[1]*L2[2] - L1[2]*L2[1] |
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L3[1] = L1[2]*L2[0] - L1[0]*L2[2] |
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L3[2] = L1[0]*L2[1] - L1[1]*L2[0] |
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return L3 |
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|
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def f(x): |
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return x |
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|
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def findNeighbors(): |
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|
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for i in range(len(indices)): |
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neighbors.append(list()) |
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|
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|
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for i in range(len(indices)-1): |
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iPos = positions[i] |
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for j in range(i+1, len(indices)): |
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jPos = positions[j] |
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|
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dpos = [jPos[0] - iPos[0], jPos[1]-iPos[1], jPos[2]-iPos[2]] |
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dpos = wrapVector(dpos) |
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dist2 = dot(dpos,dpos) |
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|
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if (dist2 < 9.0): |
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neighbors[i].append(j) |
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neighbors[j].append(i) |
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|
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if (len(neighbors[i]) == 4): |
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break |
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|
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surfaceCount = 0 |
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for i in range(len(indices)): |
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if (len(neighbors[i]) < 4): |
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neighbors[i].append(-1) |
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surfaceCount = surfaceCount + 1 |
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|
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print "surfaceCount = %d" % surfaceCount |
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|
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def randomizeProtons(): |
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|
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# do 10 proton bucket brigades: |
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for i in range(10): |
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origPoint = random.randint(0,len(indices)) |
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protonBucketBrigade(origPoint) |
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|
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# check to make sure everyone has a happy proton set: |
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|
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for j in range(len(indices)): |
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if (len(DonatingTo[j]) != 2): |
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# print "first round to fix molecule %d" % j |
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protonBucketBrigade(j) |
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|
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# check to make sure everyone has a happy proton set: |
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|
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for j in range(len(indices)): |
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if (len(DonatingTo[j]) != 2): |
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print "second round to fix molecule %d" % j |
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protonBucketBrigade(j) |
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|
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for j in range(len(indices)): |
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if (len(DonatingTo[j]) != 2): |
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print "unfilled proton donor list for molecule %d" % j |
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|
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|
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|
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def protonBucketBrigade(origPoint): |
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|
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for i in range(len(indices)): |
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DonatingTo.append(list()) |
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AcceptingFrom.append(list()) |
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OldDonor.append(list()) |
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|
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donor = origPoint |
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# pick unreasonable start values (that don't match surface atom |
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# unreasonable values) |
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acceptor = -10 |
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|
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for i in range(50000): |
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#while (acceptor != origPoint): |
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myNeighbors = set(neighbors[donor]) |
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|
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# can't pick a proton choice from one of my current protons: |
| 298 |
badChoices = set(DonatingTo[donor]).union(set(OldDonor[acceptor])) |
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# can't send a proton back to guy who sent one to me (no give-backs): |
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#badChoices.add(set(OldDonor[acceptor])) |
| 301 |
# can't send a proton to anyone who is already taking 2: |
| 302 |
for j in myNeighbors.difference(surfaceSet): |
| 303 |
if (len(AcceptingFrom[j]) == 2): |
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badChoices.add(j) |
| 305 |
|
| 306 |
nDonors = len(DonatingTo[donor]) |
| 307 |
|
| 308 |
if (nDonors <= 1): |
| 309 |
|
| 310 |
if (len(myNeighbors.difference(badChoices)) != 0): |
| 311 |
acceptor = random.choice(list(myNeighbors.difference(badChoices))) |
| 312 |
else: |
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acceptor = -1 |
| 314 |
|
| 315 |
DonatingTo[donor].append(acceptor) |
| 316 |
|
| 317 |
if (acceptor != -1): |
| 318 |
AcceptingFrom[acceptor].append(donor) |
| 319 |
OldDonor[acceptor].append(donor) |
| 320 |
elif (nDonors == 2): |
| 321 |
acceptor = random.choice(DonatingTo[donor]) |
| 322 |
else: |
| 323 |
print "Whoah! How'd we get here?" |
| 324 |
|
| 325 |
donor = acceptor |
| 326 |
if (acceptor == -1): |
| 327 |
# surface atoms all have a -1 neighbor, but that's OK. A proton |
| 328 |
# is allowed to point out of the surface, but it does break the |
| 329 |
# proton chain letter |
| 330 |
# print "surface atom found, starting over from origPoint" |
| 331 |
donor = origPoint |
| 332 |
# break |
| 333 |
|
| 334 |
def computeQuats(): |
| 335 |
|
| 336 |
for i in range(len(indices)): |
| 337 |
DonatingTo.append(list()) |
| 338 |
AcceptingFrom.append(list()) |
| 339 |
OldDonor.append(list()) |
| 340 |
# print "Computing Quaternions" |
| 341 |
ux = [0.0, 0.0, 0.0] |
| 342 |
uy = [0.0, 0.0, 0.0] |
| 343 |
uz = [0.0, 0.0, 0.0] |
| 344 |
RotMat = [ux, uy, uz] |
| 345 |
totalDipole = [0.0, 0.0, 0.0] |
| 346 |
for i in range(len(indices)): |
| 347 |
# print "doing quats for molecule %d" % i |
| 348 |
# print "Dlen = %d " % len(DonatingTo[i]) |
| 349 |
# print DonatingTo[i] |
| 350 |
|
| 351 |
|
| 352 |
myPos = positions[i] |
| 353 |
|
| 354 |
acceptor1 = DonatingTo[i][0] |
| 355 |
acceptor2 = DonatingTo[i][1] |
| 356 |
if (acceptor1 == -1 and acceptor2 == -1): |
| 357 |
donor1 = AcceptingFrom[i][0] |
| 358 |
donor2 = AcceptingFrom[i][1] |
| 359 |
npos = positions[donor1] |
| 360 |
apos1 = [npos[0] - myPos[0], npos[1] - myPos[1], npos[2] - myPos[2]] |
| 361 |
apos1 = wrapVector(apos1) |
| 362 |
npos = positions[donor2] |
| 363 |
apos2 = [npos[0] - myPos[0], npos[1] - myPos[1], npos[2] - myPos[2]] |
| 364 |
apos2 = wrapVector(apos2) |
| 365 |
tempX = [0.0, 0.0, 0.0] |
| 366 |
tempY = [0.0, 0.0, 0.0] |
| 367 |
tempZ = [0.0, 0.0, 0.0] |
| 368 |
tempZ[0] = 0.5*(apos1[0] + apos2[0]) |
| 369 |
tempZ[1] = 0.5*(apos1[1] + apos2[1]) |
| 370 |
tempZ[2] = 0.5*(apos1[2] + apos2[2]) |
| 371 |
tempX[0] = (apos2[0] - apos1[0]) |
| 372 |
tempX[1] = (apos2[1] - apos1[1]) |
| 373 |
tempX[2] = (apos2[2] - apos1[2]) |
| 374 |
tempZ = normalize(tempZ) |
| 375 |
tempX = normalize(tempX) |
| 376 |
tempY = cross(tempX, tempZ) |
| 377 |
dpos1[0] = tempZ[0] - 0.5*tempY[0] |
| 378 |
dpos1[1] = tempZ[1] - 0.5*tempY[1] |
| 379 |
dpos1[2] = tempZ[2] - 0.5*tempY[2] |
| 380 |
dpos2[0] = tempZ[0] + 0.5*tempY[0] |
| 381 |
dpos2[1] = tempZ[1] + 0.5*tempY[1] |
| 382 |
dpos2[2] = tempZ[2] + 0.5*tempY[2] |
| 383 |
|
| 384 |
else: |
| 385 |
if (acceptor1 == -1): |
| 386 |
tempVec = [0.0, 0.0, 0.0] |
| 387 |
for j in range(3): |
| 388 |
thisNeighbor = neighbors[i][j] |
| 389 |
npos = positions[thisNeighbor] |
| 390 |
npos1 = [npos[0] - myPos[0], npos[1] - myPos[1], npos[2] - myPos[2]] |
| 391 |
npos1 = wrapVector(npos1) |
| 392 |
tempVec[0] = tempVec[0] + npos1[0] |
| 393 |
tempVec[1] = tempVec[1] + npos1[1] |
| 394 |
tempVec[2] = tempVec[2] + npos1[2] |
| 395 |
dpos1 = [-tempVec[0]/3.0, -tempVec[1]/3.0, -tempVec[2]/3.0] |
| 396 |
dpos1 = normalize(dpos1) |
| 397 |
else: |
| 398 |
a1pos = positions[acceptor1] |
| 399 |
dpos1 = [a1pos[0] - myPos[0], a1pos[1] - myPos[1], a1pos[2] - myPos[2]] |
| 400 |
dpos1 = wrapVector(dpos1) |
| 401 |
dpos1 = normalize(dpos1) |
| 402 |
|
| 403 |
|
| 404 |
if (acceptor2 == -1): |
| 405 |
tempVec = [0.0, 0.0, 0.0] |
| 406 |
for j in range(3): |
| 407 |
thisNeighbor = neighbors[i][j] |
| 408 |
npos = positions[thisNeighbor] |
| 409 |
npos1 = [npos[0] - myPos[0], npos[1] - myPos[1], npos[2] - myPos[2]] |
| 410 |
npos1 = wrapVector(npos1) |
| 411 |
tempVec[0] = tempVec[0] + npos1[0] |
| 412 |
tempVec[1] = tempVec[1] + npos1[1] |
| 413 |
tempVec[2] = tempVec[2] + npos1[2] |
| 414 |
dpos2 = [-tempVec[0]/3.0, -tempVec[1]/3.0, -tempVec[2]/3.0] |
| 415 |
dpos2 = normalize(dpos2) |
| 416 |
else: |
| 417 |
a2pos = positions[acceptor2] |
| 418 |
dpos2 = [a2pos[0] - myPos[0], a2pos[1] - myPos[1], a2pos[2] - myPos[2]] |
| 419 |
dpos2 = wrapVector(dpos2) |
| 420 |
dpos2 = normalize(dpos2) |
| 421 |
|
| 422 |
for j in range(3): |
| 423 |
uz[j] = (dpos1[j] + dpos2[j])/2.0 |
| 424 |
uz = normalize(uz) |
| 425 |
for j in range(3): |
| 426 |
uy[j] = dpos2[j] - dpos1[j] |
| 427 |
uy = normalize(uy) |
| 428 |
ux = cross(uy, uz) |
| 429 |
ux = normalize(ux) |
| 430 |
|
| 431 |
q = [0.0, 0.0, 0.0, 0.0] |
| 432 |
|
| 433 |
# RotMat to Quat code is out of OpenMD's SquareMatrix3.hpp code: |
| 434 |
|
| 435 |
RotMat[0] = ux |
| 436 |
RotMat[1] = uy |
| 437 |
RotMat[2] = uz |
| 438 |
|
| 439 |
t = RotMat[0][0] + RotMat[1][1] + RotMat[2][2] + 1.0 |
| 440 |
|
| 441 |
if( t > 1e-6 ): |
| 442 |
s = 0.5 / math.sqrt( t ) |
| 443 |
q[0] = 0.25 / s |
| 444 |
q[1] = (RotMat[1][2] - RotMat[2][1]) * s |
| 445 |
q[2] = (RotMat[2][0] - RotMat[0][2]) * s |
| 446 |
q[3] = (RotMat[0][1] - RotMat[1][0]) * s |
| 447 |
else: |
| 448 |
ad1 = RotMat[0][0] |
| 449 |
ad2 = RotMat[1][1] |
| 450 |
ad3 = RotMat[2][2] |
| 451 |
|
| 452 |
if( ad1 >= ad2 and ad1 >= ad3 ): |
| 453 |
s = 0.5 / math.sqrt( 1.0 + RotMat[0][0] - RotMat[1][1] - RotMat[2][2] ) |
| 454 |
q[0] = (RotMat[1][2] - RotMat[2][1]) * s |
| 455 |
q[1] = 0.25 / s |
| 456 |
q[2] = (RotMat[0][1] + RotMat[1][0]) * s |
| 457 |
q[3] = (RotMat[0][2] + RotMat[2][0]) * s |
| 458 |
elif ( ad2 >= ad1 and ad2 >= ad3 ): |
| 459 |
s = 0.5 / math.sqrt( 1.0 + RotMat[1][1] - RotMat[0][0] - RotMat[2][2] ) |
| 460 |
q[0] = (RotMat[2][0] - RotMat[0][2] ) * s |
| 461 |
q[1] = (RotMat[0][1] + RotMat[1][0]) * s |
| 462 |
q[2] = 0.25 / s |
| 463 |
q[3] = (RotMat[1][2] + RotMat[2][1]) * s |
| 464 |
else: |
| 465 |
s = 0.5 / math.sqrt( 1.0 + RotMat[2][2] - RotMat[0][0] - RotMat[1][1] ) |
| 466 |
q[0] = (RotMat[0][1] - RotMat[1][0]) * s |
| 467 |
q[1] = (RotMat[0][2] + RotMat[2][0]) * s |
| 468 |
q[2] = (RotMat[1][2] + RotMat[2][1]) * s |
| 469 |
q[3] = 0.25 / s |
| 470 |
|
| 471 |
quaternions[i] = q |
| 472 |
totalDipole = [totalDipole[0] + uz[0], totalDipole[1] + uz[1], totalDipole[2] + uz[2]] |
| 473 |
totalDipole = [-totalDipole[0], -totalDipole[1], -totalDipole[2]] |
| 474 |
print totalDipole |
| 475 |
Dipole = math.sqrt(dot(totalDipole, totalDipole)) |
| 476 |
print 'Total Dipole Moment = %d' % Dipole |
| 477 |
if (Dipole > 40 or Dipole < -40): |
| 478 |
print "Bad Dipole, starting over" |
| 479 |
for i in range(len(indices)): |
| 480 |
del OldDonor[:] |
| 481 |
del AcceptingFrom[:] |
| 482 |
del DonatingTo[:] |
| 483 |
# del badChoices[:] |
| 484 |
randomizeProtons() |
| 485 |
computeQuats() |
| 486 |
else: |
| 487 |
print "All Done!" |
| 488 |
|
| 489 |
|
| 490 |
|
| 491 |
def main(argv): |
| 492 |
try: |
| 493 |
opts, args = getopt.getopt(argv, "hm:o:", ["help", "meta-data=", "output-file="]) |
| 494 |
except getopt.GetoptError: |
| 495 |
usage() |
| 496 |
sys.exit(2) |
| 497 |
for opt, arg in opts: |
| 498 |
if opt in ("-h", "--help"): |
| 499 |
usage() |
| 500 |
sys.exit() |
| 501 |
elif opt in ("-m", "--meta-data"): |
| 502 |
mdFileName = arg |
| 503 |
global _haveMDFileName |
| 504 |
_haveMDFileName = 1 |
| 505 |
elif opt in ("-o", "--output-file"): |
| 506 |
outputFileName = arg |
| 507 |
global _haveOutputFileName |
| 508 |
_haveOutputFileName = 1 |
| 509 |
if (_haveMDFileName != 1): |
| 510 |
usage() |
| 511 |
print "No meta-data file was specified" |
| 512 |
sys.exit() |
| 513 |
if (_haveOutputFileName != 1): |
| 514 |
usage() |
| 515 |
print "No output file was specified" |
| 516 |
sys.exit() |
| 517 |
readFile(mdFileName) |
| 518 |
# analyzeQuats() |
| 519 |
findNeighbors() |
| 520 |
randomizeProtons() |
| 521 |
computeQuats() |
| 522 |
writeFile(outputFileName) |
| 523 |
|
| 524 |
if __name__ == "__main__": |
| 525 |
if len(sys.argv) == 1: |
| 526 |
usage() |
| 527 |
sys.exit() |
| 528 |
main(sys.argv[1:]) |
