| 1 |
#!@PYTHON_EXECUTABLE@ |
| 2 |
"""MD Solvator |
| 3 |
|
| 4 |
Opens two md files, one with a solute structure and one with a solvent |
| 5 |
structure. Deletes any solvent molecules that overlap with solute |
| 6 |
molecules and produces a new combined md file. The md file must be |
| 7 |
edited to run properly in OpenMD. Note that the two boxes must have |
| 8 |
identical box geometries (specified on the Hmat line). |
| 9 |
|
| 10 |
Usage: md-solvator |
| 11 |
|
| 12 |
Options: |
| 13 |
-h, --help show this help |
| 14 |
-u, --solute=... use specified meta-data (.md) file as the solute |
| 15 |
-v, --solvent=... use specified meta-data (.md) file as the solvent |
| 16 |
-r, --rcut=... specify the cutoff radius for deleting solvent |
| 17 |
-o, --output-file=... use specified output (.md) file |
| 18 |
-n, --nSoluteAtoms=... Number of atoms in solute molecule, |
| 19 |
default is 1 atom. |
| 20 |
-p, --nSolventAtoms=... Number of atoms in solvent molecule, |
| 21 |
default is 1 atom. |
| 22 |
|
| 23 |
Example: |
| 24 |
md-solvator -u solute.md -v solvent.md -n 3 -p 3 -r 4.0 -o combined.md |
| 25 |
|
| 26 |
""" |
| 27 |
|
| 28 |
__author__ = "Charles Vardeman (cvardema@nd.edu)" |
| 29 |
__version__ = "$Revision$" |
| 30 |
__date__ = "$Date$" |
| 31 |
__copyright__ = "Copyright (c) 2008 by the University of Notre Dame" |
| 32 |
__license__ = "OpenMD" |
| 33 |
|
| 34 |
import sys |
| 35 |
import getopt |
| 36 |
import string |
| 37 |
import math |
| 38 |
import random |
| 39 |
from sets import * |
| 40 |
#from Numeric import * |
| 41 |
|
| 42 |
_haveMDFileName1 = 0 |
| 43 |
_haveMDFileName2 = 0 |
| 44 |
_haveRcut = 0 |
| 45 |
_haveOutputFileName = 0 |
| 46 |
_haveNSoluteAtoms = 0 |
| 47 |
_haveNSolventAtoms = 0 |
| 48 |
|
| 49 |
metaData1 = [] |
| 50 |
frameData1 = [] |
| 51 |
positions1 = [] |
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velocities1 = [] |
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quaternions1 = [] |
| 54 |
angVels1 = [] |
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indices1 = [] |
| 56 |
Hmat1 = [] |
| 57 |
BoxInv1 = [] |
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pvqj1 = [] |
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|
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metaData2 = [] |
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frameData2 = [] |
| 62 |
positions2 = [] |
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velocities2 = [] |
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quaternions2 = [] |
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angVels2 = [] |
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indices2 = [] |
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Hmat2 = [] |
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BoxInv2 = [] |
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pvqj2 = [] |
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|
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keepers = [] |
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|
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soluteTypeLine = str() |
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solventTypeLine = str() |
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soluteMolLine = str() |
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nSolvents = 0 |
| 77 |
|
| 78 |
def usage(): |
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print __doc__ |
| 80 |
|
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def readFile1(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() |
| 85 |
while 1: |
| 86 |
if '<OpenMD version=' in line or '<OOPSE version=' in line: |
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OpenMDversion = line |
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break |
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line = mdFile.readline() |
| 90 |
|
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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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|
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print "reading solute MetaData" |
| 97 |
while 1: |
| 98 |
if '<MetaData>' in line: |
| 99 |
while 2: |
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metaData1.append(line) |
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line = mdFile.readline() |
| 102 |
if 'type' in line: |
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global soluteTypeLine |
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soluteTypeLine = line |
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if 'nMol' in line: |
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global soluteMolLine |
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soluteMolLine = line |
| 108 |
if '</MetaData>' in line: |
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metaData1.append(line) |
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break |
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break |
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line = mdFile.readline() |
| 113 |
|
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mdFile.seek(0) |
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print "reading solute Snapshot" |
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line = mdFile.readline() |
| 117 |
while 1: |
| 118 |
if '<Snapshot>' in line: |
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line = mdFile.readline() |
| 120 |
while 1: |
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print "reading solute FrameData" |
| 122 |
if '<FrameData>' in line: |
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while 2: |
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frameData1.append(line) |
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if 'Hmat:' in line: |
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L = line.split() |
| 127 |
Hxx = float(L[2].strip(',')) |
| 128 |
Hxy = float(L[3].strip(',')) |
| 129 |
Hxz = float(L[4].strip(',')) |
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Hyx = float(L[7].strip(',')) |
| 131 |
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(',')) |
| 135 |
Hzz = float(L[14].strip(',')) |
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Hmat1.append([Hxx, Hxy, Hxz]) |
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Hmat1.append([Hyx, Hyy, Hyz]) |
| 138 |
Hmat1.append([Hzx, Hzy, Hzz]) |
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BoxInv1.append(1.0/Hxx) |
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BoxInv1.append(1.0/Hyy) |
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BoxInv1.append(1.0/Hzz) |
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line = mdFile.readline() |
| 143 |
if '</FrameData>' in line: |
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frameData1.append(line) |
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break |
| 146 |
break |
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|
| 148 |
line = mdFile.readline() |
| 149 |
while 1: |
| 150 |
if '<StuntDoubles>' in line: |
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line = mdFile.readline() |
| 152 |
while 2: |
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L = line.split() |
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myIndex = int(L[0]) |
| 155 |
indices1.append(myIndex) |
| 156 |
pvqj1.append(L[1]) |
| 157 |
x = float(L[2]) |
| 158 |
y = float(L[3]) |
| 159 |
z = float(L[4]) |
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positions1.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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velocities1.append([vx, vy, vz]) |
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if 'pvqj' in L[1]: |
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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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quaternions1.append([qw, qx, qy, qz]) |
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jx = float(L[12]) |
| 172 |
jy = float(L[13]) |
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jz = float(L[14]) |
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angVels1.append([jx, jy, jz]) |
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else: |
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quaternions1.append([0.0, 0.0, 0.0, 0.0]) |
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angVels1.append([0.0, 0.0, 0.0]) |
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|
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line = mdFile.readline() |
| 180 |
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 readFile2(mdFileName): |
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mdFile = open(mdFileName, 'r') |
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# Find OpenMD version info first |
| 191 |
line = mdFile.readline() |
| 192 |
while 1: |
| 193 |
if '<OpenMD version=' in line or '<OOPSE version=': |
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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 |
| 199 |
|
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mdFile.seek(0) |
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line = mdFile.readline() |
| 202 |
print "reading solvent MetaData" |
| 203 |
while 1: |
| 204 |
if '<MetaData>' in line: |
| 205 |
while 2: |
| 206 |
if 'type' in line: |
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global solventTypeLine |
| 208 |
solventTypeLine = line |
| 209 |
metaData2.append(line) |
| 210 |
line = mdFile.readline() |
| 211 |
if '</MetaData>' in line: |
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metaData2.append(line) |
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break |
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break |
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line = mdFile.readline() |
| 216 |
|
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mdFile.seek(0) |
| 218 |
print "reading solvent Snapshot" |
| 219 |
line = mdFile.readline() |
| 220 |
while 1: |
| 221 |
if '<Snapshot>' in line: |
| 222 |
line = mdFile.readline() |
| 223 |
while 1: |
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print "reading solvent FrameData" |
| 225 |
if '<FrameData>' in line: |
| 226 |
while 2: |
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frameData2.append(line) |
| 228 |
if 'Hmat:' in line: |
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L = line.split() |
| 230 |
Hxx = float(L[2].strip(',')) |
| 231 |
Hxy = float(L[3].strip(',')) |
| 232 |
Hxz = float(L[4].strip(',')) |
| 233 |
Hyx = float(L[7].strip(',')) |
| 234 |
Hyy = float(L[8].strip(',')) |
| 235 |
Hyz = float(L[9].strip(',')) |
| 236 |
Hzx = float(L[12].strip(',')) |
| 237 |
Hzy = float(L[13].strip(',')) |
| 238 |
Hzz = float(L[14].strip(',')) |
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Hmat2.append([Hxx, Hxy, Hxz]) |
| 240 |
Hmat2.append([Hyx, Hyy, Hyz]) |
| 241 |
Hmat2.append([Hzx, Hzy, Hzz]) |
| 242 |
BoxInv2.append(1.0/Hxx) |
| 243 |
BoxInv2.append(1.0/Hyy) |
| 244 |
BoxInv2.append(1.0/Hzz) |
| 245 |
line = mdFile.readline() |
| 246 |
if '</FrameData>' in line: |
| 247 |
frameData2.append(line) |
| 248 |
break |
| 249 |
break |
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|
| 251 |
line = mdFile.readline() |
| 252 |
while 1: |
| 253 |
if '<StuntDoubles>' in line: |
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line = mdFile.readline() |
| 255 |
while 2: |
| 256 |
L = line.split() |
| 257 |
myIndex = int(L[0]) |
| 258 |
indices2.append(myIndex) |
| 259 |
pvqj2.append(L[1]) |
| 260 |
x = float(L[2]) |
| 261 |
y = float(L[3]) |
| 262 |
z = float(L[4]) |
| 263 |
positions2.append([x, y, z]) |
| 264 |
vx = float(L[5]) |
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vy = float(L[6]) |
| 266 |
vz = float(L[7]) |
| 267 |
velocities2.append([vx, vy, vz]) |
| 268 |
if 'pvqj' in L[1]: |
| 269 |
qw = float(L[8]) |
| 270 |
qx = float(L[9]) |
| 271 |
qy = float(L[10]) |
| 272 |
qz = float(L[11]) |
| 273 |
quaternions2.append([qw, qx, qy, qz]) |
| 274 |
jx = float(L[12]) |
| 275 |
jy = float(L[13]) |
| 276 |
jz = float(L[14]) |
| 277 |
angVels2.append([jx, jy, jz]) |
| 278 |
else: |
| 279 |
quaternions1.append([0.0, 0.0, 0.0, 0.0]) |
| 280 |
angVels1.append([0.0, 0.0, 0.0]) |
| 281 |
|
| 282 |
line = mdFile.readline() |
| 283 |
if '</StuntDoubles>' in line: |
| 284 |
break |
| 285 |
break |
| 286 |
line = mdFile.readline() |
| 287 |
if not line: break |
| 288 |
|
| 289 |
mdFile.close() |
| 290 |
|
| 291 |
def writeFile(outputFileName): |
| 292 |
outputFile = open(outputFileName, 'w') |
| 293 |
|
| 294 |
outputFile.write("<OpenMD version=1>\n") |
| 295 |
|
| 296 |
# for metaline in metaData1: |
| 297 |
# outputFile.write(metaline) |
| 298 |
outputFile.write(" <MetaData>\n") |
| 299 |
outputFile.write("\n\n") |
| 300 |
outputFile.write("component{\n") |
| 301 |
outputFile.write(soluteTypeLine) |
| 302 |
outputFile.write(soluteMolLine) |
| 303 |
outputFile.write("}\n") |
| 304 |
|
| 305 |
outputFile.write("component{\n") |
| 306 |
outputFile.write(solventTypeLine) |
| 307 |
outputFile.write("nMol = %d;\n" % (nSolvents)) |
| 308 |
outputFile.write("}\n") |
| 309 |
outputFile.write("\n\n") |
| 310 |
outputFile.write(" </MetaData>\n") |
| 311 |
outputFile.write(" <Snapshot>\n") |
| 312 |
|
| 313 |
for frameline in frameData1: |
| 314 |
outputFile.write(frameline) |
| 315 |
|
| 316 |
outputFile.write(" <StuntDoubles>\n") |
| 317 |
|
| 318 |
|
| 319 |
newIndex = 0 |
| 320 |
for i in range(len(indices1)): |
| 321 |
if (pvqj1[i] == 'pv'): |
| 322 |
outputFile.write("%10d %7s %18.10g %18.10g %18.10g %14e %13e %13e\n" % (newIndex, pvqj1[i], positions1[i][0], positions1[i][1], positions1[i][2], velocities1[i][0], velocities1[i][1], velocities1[i][2])) |
| 323 |
elif(pvqj1[i] == 'pvqj'): |
| 324 |
outputFile.write("%10d %7s %18.10g %18.10g %18.10g %13e %13e %13e %13e %13e %13e %13e %13e %13e %13e\n" % (newIndex, pvqj1[i], positions1[i][0], positions1[i][1], positions1[i][2], velocities1[i][0], velocities1[i][1], velocities1[i][2], quaternions1[i][0], quaternions1[i][1], quaternions1[i][2], quaternions1[i][3], angVels1[i][0], angVels1[i][1], angVels1[i][2])) |
| 325 |
|
| 326 |
newIndex = newIndex + 1 |
| 327 |
|
| 328 |
outputFile.write(" </StuntDoubles>\n") |
| 329 |
outputFile.write(" </Snapshot>\n") |
| 330 |
outputFile.write("</OpenMD>\n") |
| 331 |
outputFile.close() |
| 332 |
|
| 333 |
def checkBoxes(): |
| 334 |
boxTolerance = 1.0e-3 |
| 335 |
maxDiff = 0.0 |
| 336 |
for i in range(3): |
| 337 |
for j in range(3): |
| 338 |
diff = math.fabs( Hmat1[i][j] - Hmat2[i][j]) |
| 339 |
if (diff > maxDiff): |
| 340 |
maxDiff = diff |
| 341 |
if (maxDiff > boxTolerance): |
| 342 |
print "The solute and solvent boxes have different geometries:" |
| 343 |
print " Solute | Solvent" |
| 344 |
print " -------------------------------------|------------------------------------" |
| 345 |
for i in range(3): |
| 346 |
print( "| %10.4g %10.4g %10.4g | %10.4g %10.4g %10.4g |" % (Hmat1[i][0], Hmat1[i][1], Hmat1[i][2], Hmat2[i][0], Hmat2[i][1], Hmat2[i][2])) |
| 347 |
|
| 348 |
print " -------------------------------------|------------------------------------" |
| 349 |
sys.exit() |
| 350 |
|
| 351 |
|
| 352 |
def roundMe(x): |
| 353 |
if (x >= 0.0): |
| 354 |
return math.floor(x + 0.5) |
| 355 |
else: |
| 356 |
return math.ceil(x - 0.5) |
| 357 |
|
| 358 |
def frange(start,stop,step=1.0): |
| 359 |
while start < stop: |
| 360 |
yield start |
| 361 |
start += step |
| 362 |
|
| 363 |
|
| 364 |
def wrapVector(myVect): |
| 365 |
scaled = [0.0, 0.0, 0.0] |
| 366 |
for i in range(3): |
| 367 |
scaled[i] = myVect[i] * BoxInv1[i] |
| 368 |
scaled[i] = scaled[i] - roundMe(scaled[i]) |
| 369 |
myVect[i] = scaled[i] * Hmat1[i][i] |
| 370 |
return myVect |
| 371 |
|
| 372 |
def dot(L1, L2): |
| 373 |
myDot = 0.0 |
| 374 |
for i in range(len(L1)): |
| 375 |
myDot = myDot + L1[i]*L2[i] |
| 376 |
return myDot |
| 377 |
|
| 378 |
def normalize(L1): |
| 379 |
L2 = [] |
| 380 |
myLength = math.sqrt(dot(L1, L1)) |
| 381 |
for i in range(len(L1)): |
| 382 |
L2.append(L1[i] / myLength) |
| 383 |
return L2 |
| 384 |
|
| 385 |
def cross(L1, L2): |
| 386 |
# don't call this with anything other than length 3 lists please |
| 387 |
# or you'll be sorry |
| 388 |
L3 = [0.0, 0.0, 0.0] |
| 389 |
L3[0] = L1[1]*L2[2] - L1[2]*L2[1] |
| 390 |
L3[1] = L1[2]*L2[0] - L1[0]*L2[2] |
| 391 |
L3[2] = L1[0]*L2[1] - L1[1]*L2[0] |
| 392 |
return L3 |
| 393 |
|
| 394 |
def removeOverlaps(rcut,nSolventAtoms,nSoluteAtoms): |
| 395 |
|
| 396 |
rcut2 = rcut*rcut |
| 397 |
nextMol = 0 |
| 398 |
for i in range(0,len(indices2),nSolventAtoms): |
| 399 |
keepThisMolecule = 1 |
| 400 |
for atom1 in range (i, (i+nSolventAtoms)): |
| 401 |
|
| 402 |
iPos = positions2[atom1] |
| 403 |
for j in range(0,len(indices1)): |
| 404 |
for atom2 in range (j, (j+nSoluteAtoms), nSoluteAtoms): |
| 405 |
jPos = positions1[atom2] |
| 406 |
dpos = [jPos[0]-iPos[0], jPos[1]-iPos[1], jPos[2]-iPos[2]] |
| 407 |
dpos = wrapVector(dpos) |
| 408 |
dist2 = dot(dpos,dpos) |
| 409 |
|
| 410 |
|
| 411 |
if (dist2 < rcut2): |
| 412 |
keepThisMolecule = 0 |
| 413 |
break |
| 414 |
if (keepThisMolecule == 0): |
| 415 |
break |
| 416 |
|
| 417 |
keepers.append(keepThisMolecule) |
| 418 |
|
| 419 |
|
| 420 |
global nSolvents |
| 421 |
myIndex = len(indices2) - 1 |
| 422 |
for i in range(0,len(keepers)): |
| 423 |
|
| 424 |
if (keepers[i] == 1): |
| 425 |
nSolvents = nSolvents + 1 |
| 426 |
atomStartIndex = i * nSolventAtoms |
| 427 |
for j in range (atomStartIndex, (atomStartIndex+nSolventAtoms)): |
| 428 |
indices1.append(myIndex) |
| 429 |
pvqj1.append(pvqj2[j]) |
| 430 |
if (pvqj2[j] == 'pv'): |
| 431 |
positions1.append(positions2[j]) |
| 432 |
velocities1.append(velocities2[j]) |
| 433 |
quaternions1.append([0.0, 0.0, 0.0, 0.0]) |
| 434 |
angVels1.append([0.0, 0.0, 0.0]) |
| 435 |
else: |
| 436 |
positions1.append(positions2[j]) |
| 437 |
velocities1.append(velocities2[j]) |
| 438 |
quaternions1.append(quaternions2[j]) |
| 439 |
angVels1.append(angVels2[j]) |
| 440 |
# indices1.append(indices2[j]) |
| 441 |
myIndex = myIndex +1 |
| 442 |
|
| 443 |
def main(argv): |
| 444 |
try: |
| 445 |
opts, args = getopt.getopt(argv, "hu:v:n:p:r:o:", ["help", "solute=","solvent=","nSoluteAtoms=","nSolventAtoms=", "rcut=" "output-file="]) |
| 446 |
except getopt.GetoptError: |
| 447 |
usage() |
| 448 |
sys.exit(2) |
| 449 |
for opt, arg in opts: |
| 450 |
if opt in ("-h", "--help"): |
| 451 |
usage() |
| 452 |
sys.exit() |
| 453 |
elif opt in ("-u", "--solute"): |
| 454 |
mdFileName1 = arg |
| 455 |
global _haveMDFileName1 |
| 456 |
_haveMDFileName1 = 1 |
| 457 |
elif opt in ("-v", "--solvent"): |
| 458 |
mdFileName2 = arg |
| 459 |
global _haveMDFileName2 |
| 460 |
_haveMDFileName2 = 1 |
| 461 |
elif opt in ("-n", "--nSoluteAtoms"): |
| 462 |
nSoluteAtoms = int(arg) |
| 463 |
global _haveNSoluteAtoms |
| 464 |
_haveNSoluteAtoms = 1 |
| 465 |
elif opt in ("-p", "--nSolventAtoms"): |
| 466 |
nSolventAtoms = int(arg) |
| 467 |
global _haveNSolventAtoms |
| 468 |
_haveNSolventAtoms = 1 |
| 469 |
elif opt in ("-r", "--rcut"): |
| 470 |
rcut = float(arg) |
| 471 |
global _haveRcut |
| 472 |
_haveRcut = 1 |
| 473 |
elif opt in ("-o", "--output-file"): |
| 474 |
outputFileName = arg |
| 475 |
global _haveOutputFileName |
| 476 |
_haveOutputFileName = 1 |
| 477 |
|
| 478 |
if (_haveMDFileName1 != 1): |
| 479 |
usage() |
| 480 |
print "No meta-data file was specified for the solute" |
| 481 |
sys.exit() |
| 482 |
|
| 483 |
if (_haveMDFileName2 != 1): |
| 484 |
usage() |
| 485 |
print "No meta-data file was specified for the solvent" |
| 486 |
sys.exit() |
| 487 |
|
| 488 |
if (_haveOutputFileName != 1): |
| 489 |
usage() |
| 490 |
print "No output file was specified" |
| 491 |
sys.exit() |
| 492 |
|
| 493 |
if (_haveRcut != 1): |
| 494 |
print "No cutoff radius was specified, using 4 angstroms" |
| 495 |
rcut =4.0 |
| 496 |
|
| 497 |
if (_haveNSoluteAtoms != 1): |
| 498 |
print "Number of solute atoms was not specified. Using 1 atom." |
| 499 |
nSoluteAtoms = 1 |
| 500 |
|
| 501 |
if (_haveNSolventAtoms != 1): |
| 502 |
print "Number of solute atoms was not specified. Using 1 atom." |
| 503 |
nSolventAtoms = 1 |
| 504 |
|
| 505 |
readFile1(mdFileName1) |
| 506 |
readFile2(mdFileName2) |
| 507 |
checkBoxes() |
| 508 |
removeOverlaps(rcut,nSolventAtoms,nSoluteAtoms) |
| 509 |
writeFile(outputFileName) |
| 510 |
|
| 511 |
if __name__ == "__main__": |
| 512 |
if len(sys.argv) == 1: |
| 513 |
usage() |
| 514 |
sys.exit() |
| 515 |
main(sys.argv[1:]) |
