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Commit 20ad26b6 authored by Jason Swails's avatar Jason Swails
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Add some protection against an uncaught exception in the CharmmFile destructor 

Add a test case and example for running with CHARMM files.
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examples/ala_ala_ala.pdb 0 → 100644
View file @ 20ad26b6
REMARK *
REMARK DATE: 8/ 5/ 9 14:44:19 CREATED BY USER: mjw
ATOM 1 N ALA 1 0.024 -0.103 -0.101 1.00 0.00 AAL
ATOM 2 HT1 ALA 1 0.027 -1.132 -0.239 1.00 0.00 AAL
ATOM 3 HT2 ALA 1 -0.805 0.163 0.471 1.00 0.00 AAL
ATOM 4 HT3 ALA 1 -0.059 0.384 -1.019 1.00 0.00 AAL
ATOM 5 CA ALA 1 1.247 0.375 0.636 1.00 0.00 AAL
ATOM 6 HA ALA 1 0.814 0.861 1.495 1.00 0.00 AAL
ATOM 7 CB ALA 1 2.057 -0.772 1.289 1.00 0.00 AAL
ATOM 8 HB1 ALA 1 3.136 -0.752 1.032 1.00 0.00 AAL
ATOM 9 HB2 ALA 1 1.990 -0.641 2.395 1.00 0.00 AAL
ATOM 10 HB3 ALA 1 1.656 -1.782 1.063 1.00 0.00 AAL
ATOM 11 C ALA 1 1.956 1.579 0.036 1.00 0.00 AAL
ATOM 12 O ALA 1 1.219 2.525 -0.201 1.00 0.00 AAL
ATOM 13 N ALA 2 3.289 1.631 -0.202 1.00 0.00 AAL
ATOM 14 HN ALA 2 3.939 0.868 -0.174 1.00 0.00 AAL
ATOM 15 CA ALA 2 3.990 2.909 -0.215 1.00 0.00 AAL
ATOM 16 HA ALA 2 3.742 3.440 0.695 1.00 0.00 AAL
ATOM 17 CB ALA 2 3.662 3.802 -1.434 1.00 0.00 AAL
ATOM 18 HB1 ALA 2 4.192 4.778 -1.358 1.00 0.00 AAL
ATOM 19 HB2 ALA 2 3.956 3.311 -2.382 1.00 0.00 AAL
ATOM 20 HB3 ALA 2 2.577 4.027 -1.467 1.00 0.00 AAL
ATOM 21 C ALA 2 5.487 2.654 -0.128 1.00 0.00 AAL
ATOM 22 O ALA 2 5.889 1.489 -0.137 1.00 0.00 AAL
ATOM 23 N ALA 3 6.275 3.733 -0.037 1.00 0.00 AAL
ATOM 24 HN ALA 3 5.963 4.691 -0.028 1.00 0.00 AAL
ATOM 25 CA ALA 3 7.707 3.802 0.068 1.00 0.00 AAL
ATOM 26 HA ALA 3 8.160 3.418 -0.833 1.00 0.00 AAL
ATOM 27 CB ALA 3 8.233 3.093 1.333 1.00 0.00 AAL
ATOM 28 HB1 ALA 3 9.342 3.149 1.356 1.00 0.00 AAL
ATOM 29 HB2 ALA 3 7.835 3.593 2.240 1.00 0.00 AAL
ATOM 30 HB3 ALA 3 7.923 2.030 1.332 1.00 0.00 AAL
ATOM 31 C ALA 3 8.018 5.323 0.136 1.00 0.00 AAL
ATOM 32 OT1 ALA 3 7.032 6.119 0.127 1.00 0.00 AAL
ATOM 33 OT2 ALA 3 9.219 5.692 0.188 1.00 0.00 AAL
TER 34 ALA 3
END
examples/ala_ala_ala.psf 0 → 100644
View file @ 20ad26b6
PSF CMAP CHEQ
2 !NTITLE
**
* DATE: 8/ 5/ 9 14:44:19 CREATED BY USER: mjw
33 !NATOM
1 AAL 1 ALA N 56 -0.300000 14.0070 0 0.00000 -0.301140E-02
2 AAL 1 ALA HT1 2 0.330000 1.00800 0 0.00000 -0.301140E-02
3 AAL 1 ALA HT2 2 0.330000 1.00800 0 0.00000 -0.301140E-02
4 AAL 1 ALA HT3 2 0.330000 1.00800 0 0.00000 -0.301140E-02
5 AAL 1 ALA CA 22 0.210000 12.0110 0 0.00000 -0.301140E-02
6 AAL 1 ALA HA 6 0.100000 1.00800 0 0.00000 -0.301140E-02
7 AAL 1 ALA CB 24 -0.270000 12.0110 0 0.00000 -0.301140E-02
8 AAL 1 ALA HB1 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
9 AAL 1 ALA HB2 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
10 AAL 1 ALA HB3 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
11 AAL 1 ALA C 20 0.510000 12.0110 0 0.00000 -0.301140E-02
12 AAL 1 ALA O 70 -0.510000 15.9990 0 0.00000 -0.301140E-02
13 AAL 2 ALA N 54 -0.470000 14.0070 0 0.00000 -0.301140E-02
14 AAL 2 ALA HN 1 0.310000 1.00800 0 0.00000 -0.301140E-02
15 AAL 2 ALA CA 22 0.700000E-01 12.0110 0 0.00000 -0.301140E-02
16 AAL 2 ALA HA 6 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
17 AAL 2 ALA CB 24 -0.270000 12.0110 0 0.00000 -0.301140E-02
18 AAL 2 ALA HB1 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
19 AAL 2 ALA HB2 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
20 AAL 2 ALA HB3 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
21 AAL 2 ALA C 20 0.510000 12.0110 0 0.00000 -0.301140E-02
22 AAL 2 ALA O 70 -0.510000 15.9990 0 0.00000 -0.301140E-02
23 AAL 3 ALA N 54 -0.470000 14.0070 0 0.00000 -0.301140E-02
24 AAL 3 ALA HN 1 0.310000 1.00800 0 0.00000 -0.301140E-02
25 AAL 3 ALA CA 22 0.700000E-01 12.0110 0 0.00000 -0.301140E-02
26 AAL 3 ALA HA 6 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
27 AAL 3 ALA CB 24 -0.270000 12.0110 0 0.00000 -0.301140E-02
28 AAL 3 ALA HB1 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
29 AAL 3 ALA HB2 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
30 AAL 3 ALA HB3 3 0.900000E-01 1.00800 0 0.00000 -0.301140E-02
31 AAL 3 ALA C 32 0.340000 12.0110 0 0.00000 -0.301140E-02
32 AAL 3 ALA OT1 72 -0.670000 15.9990 0 0.00000 -0.301140E-02
33 AAL 3 ALA OT2 72 -0.670000 15.9990 0 0.00000 -0.301140E-02
32 !NBOND: bonds
2 1 3 1 4 1 7 5
1 5 11 5 11 13 5 6
7 8 7 9 7 10 12 11
17 15 13 14 13 15 21 15
21 23 15 16 17 18 17 19
17 20 22 21 27 25 23 24
23 25 31 25 25 26 27 28
27 29 27 30 31 33 31 32
57 !NTHETA: angles
2 1 3 2 1 4 2 1 5
3 1 4 3 1 5 4 1 5
1 5 6 1 5 7 1 5 11
6 5 7 6 5 11 7 5 11
5 7 8 5 7 9 5 7 10
8 7 9 8 7 10 9 7 10
5 11 12 5 11 13 12 11 13
11 13 14 11 13 15 14 13 15
13 15 16 13 15 17 13 15 21
16 15 17 16 15 21 17 15 21
15 17 18 15 17 19 15 17 20
18 17 19 18 17 20 19 17 20
15 21 22 15 21 23 22 21 23
21 23 24 21 23 25 24 23 25
23 25 26 23 25 27 23 25 31
26 25 27 26 25 31 27 25 31
25 27 28 25 27 29 25 27 30
28 27 29 28 27 30 29 27 30
25 31 32 25 31 33 32 31 33
74 !NPHI: dihedrals
1 5 7 8 1 5 7 9
1 5 7 10 1 5 11 12
1 5 11 13 2 1 5 6
2 1 5 7 2 1 5 11
3 1 5 6 3 1 5 7
3 1 5 11 4 1 5 6
4 1 5 7 4 1 5 11
5 11 13 14 5 11 13 15
6 5 7 8 6 5 7 9
6 5 7 10 6 5 11 12
6 5 11 13 7 5 11 12
7 5 11 13 8 7 5 11
9 7 5 11 10 7 5 11
11 13 15 16 11 13 15 17
11 13 15 21 12 11 13 14
12 11 13 15 13 15 17 18
13 15 17 19 13 15 17 20
13 15 21 22 13 15 21 23
14 13 15 16 14 13 15 17
14 13 15 21 15 21 23 24
15 21 23 25 16 15 17 18
16 15 17 19 16 15 17 20
16 15 21 22 16 15 21 23
17 15 21 22 17 15 21 23
18 17 15 21 19 17 15 21
20 17 15 21 21 23 25 26
21 23 25 27 21 23 25 31
22 21 23 24 22 21 23 25
23 25 27 28 23 25 27 29
23 25 27 30 23 25 31 32
23 25 31 33 24 23 25 26
24 23 25 27 24 23 25 31
26 25 27 28 26 25 27 29
26 25 27 30 26 25 31 32
26 25 31 33 27 25 31 32
27 25 31 33 28 27 25 31
29 27 25 31 30 27 25 31
5 !NIMPHI: impropers
11 5 13 12 13 11 15 14
21 15 23 22 23 21 25 24
31 25 33 32
5 !NDON: donors
1 2 1 3 1 4 13 14
23 24
4 !NACC: acceptors
12 11 22 21 32 31 33 31
0 !NNB
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0
0
9 0 !NGRP NST2
0 2 0 6 1 0 10 1 0
12 1 0 16 1 0 20 1 0
22 1 0 26 1 0 30 2 0
1 !MOLNT
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1
0 0 !NUMLP NUMLPH
1 !NCRTERM: cross-terms
11 13 15 21 13 15 21 23
examples/charmm22.par 0 → 100644
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examples/charmm22.rtf 0 → 100644
View file @ 20ad26b6
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examples/simulateCharmm.py 0 → 100644
View file @ 20ad26b6
from simtk.openmm.app import *
from simtk.openmm import *
from simtk.unit import *
from sys import stdout
# Read the PSF
psf = CharmmPSF.load_from_psf('ala_ala_ala.psf')
# Get the coordinates from the PDB
pdb = PDBFile('ala_ala_ala.pdb')
# Read and condense the parameter set
params = CharmmParameterSet.load_set(tfile='charmm22.rtf',
pfile='charmm22.par').condense()
# Load the parameter set !! do not forget this !!
psf.load_parameters(params)
# Instantiate the system
system = psf.createSystem(nonbondedMethod=NoCutoff, nonbondedCutoff=None)
integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds)
simulation = Simulation(psf.topology, system, integrator)
simulation.context.setPositions(pdb.getPositions())
simulation.minimizeEnergy()
simulation.reporters.append(PDBReporter('ch_output.pdb', 1000))
simulation.reporters.append(
StateDataReporter(stdout, 1000, step=True, potentialEnergy=True,
temperature=True)
)
simulation.step(10000)
wrappers/python/simtk/openmm/app/charmm/_charmmfile.py
View file @ 20ad26b6
......@@ -21,6 +21,7 @@ class CharmmFile(object):
"""
def __init__(self, fname, mode='r'):
self.closed = False
if mode not in ('r', 'w'):
raise ValueError('Cannot open CharmmFile with mode "%s"' % mode)
if mode == 'r':
......@@ -31,7 +32,6 @@ class CharmmFile(object):
self._handle = open(fname, mode)
except IOError, e:
raise CharmmFileError(str(e))
self.closed = False
self.line_number = 0
def write(self, *args, **kwargs):
......@@ -75,7 +75,11 @@ class CharmmFile(object):
self._handle.seek(0)
def __del__(self):
self.closed or self._handle.close()
try:
self.closed or self._handle.close()
except AttributeError:
# It didn't make it out of the constructor
pass
# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
......
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