def main():
args = parse_args()
# check if files exist
if not os.path.isfile(args.infile):
raise Exception("File not found: {0}!".format(args.infile))
outdir = os.path.dirname(args.outfile)
if not os.path.exists(outdir):
raise Exception("Output directory not found: {0}!".format(outdir))
# perform conversion
try:
print 'Performing InterMol conversion:'
print ' From: {0}'.format(args.infile)
print ' To: {0}'.format(args.outfile)
name = 'system'
Driver.initSystem(name) # what does this name do?
Driver.load(args.infile)
Driver.write(args.outfile)
except:
print 'Failed at InterMol conversion'
sys.exit(1)
# calc input energies
if args.energy:
e_in, e_infile = evaluate.desmond_energies(args.infile, args.cfgfile, args.despath)
print 'Total energy from %s:' % e_infile
print e_in
e_out, e_outfile = evaluate.desmond_energies(args.outfile, args.cfgfile, args.despath)
print 'Total energy from %s:' % e_outfile
print e_out
def lammps_to_gromacs(name, gropath='', grosuff='', lmppath='', lmpbin='lmp_openmpi',
energy=True, clean=True):
"""Test lammps to gromacs conversion
"""
lmp_in = os.path.join('Inputs/Lammps/', name, 'data.lmp')
if not os.path.isfile(lmp_in):
raise Exception("File not found: {0}!".format(lmp_in))
top_out = os.path.join('Outputs/LammpsToGromacs/', name, 'topol.top')
gro_out = os.path.join('Outputs/LammpsToGromacs/', name, 'conf.gro')
# calc input energies
if energy:
e_in = lammps_energies(name, 'in', lmppath, lmpbin)
# where the magic happens
Driver.initSystem(name)
Driver.load(lmp_in)
Driver.write(top_out, gro_out)
# calc output energies
if energy:
e_out = gromacs_energies(name, top_out, gro_out, 'LtoG', gropath, grosuff)
# delete gromacs backup files
if clean:
import glob
filelist = glob.glob("Inputs/Gromacs/{name}/#*#".format(name=name))
filelist += glob.glob("Outputs/GromacsToGromacs/{name}/#*#".format(name=name))
for f in filelist:
os.remove(f)
if energy:
return combine_energy_results(e_in, e_out)
def lammps_to_lammps(name, lmppath='', lmpbin='lmp_openmpi', energy=True,
verbose=False):
"""Test lammps to lammps conversion
"""
lmp_in = os.path.join('Inputs/Lammps/', name, 'data.lmp')
if not os.path.isfile(lmp_in):
raise Exception("File not found: {0}!".format(lmp_in))
lmp_out = os.path.join('Outputs/LammpsToLammps/', name, 'data.lmp')
# calc input energies
if energy:
e_in = lammps_energies(name, 'in', lmppath, lmpbin, verbose)
# where the magic happens
Driver.initSystem(name)
Driver.load(lmp_in)
Driver.write(lmp_out)
# calc output energies
if energy:
e_out = lammps_energies(name, 'LtoL', lmppath, lmpbin)
if energy:
return combine_energy_results(e_in, e_out)
def gromacs_to_gromacs(name="system2_GMX", top=None, gro=None, gropath="", grosuff="", energy=True, clean=True):
"""Test gromacs to gromacs conversion
"""
if top == None:
top = os.path.join(name, "topol.top")
if gro == None:
gro = os.path.join(name, "conf.gro")
gro_in = os.path.join("Inputs/Gromacs/", gro)
if not os.path.isfile(gro_in):
raise Exception("File not found: {0}!".format(gro_in))
top_in = os.path.join("Inputs/Gromacs/", top)
if not os.path.isfile(top_in):
raise Exception("File not found: {0}!".format(top_in))
top_out = os.path.join("Outputs/GromacsToGromacs/", name, "topol.top")
gro_out = os.path.join("Outputs/GromacsToGromacs/", name, "conf.gro")
# calc input energies
if energy:
e_in = gromacs_energies(name, top_in, gro_in, "in", gropath, grosuff)
# where the magic happens
Driver.initSystem(name)
Driver.load(top_in, gro_in)
Driver.write(top_out, gro_out)
# calc output energies
if energy:
e_out = gromacs_energies(name, top_out, gro_out, "GtoG", gropath, grosuff)
# delete gromacs backup files
if clean:
import glob
filelist = glob.glob("Inputs/Gromacs/{name}/#*#".format(name=name))
filelist += glob.glob("Outputs/GromacsToGromacs/{name}/#*#".format(name=name))
for f in filelist:
os.remove(f)
if energy:
return combine_energy_results(e_in, e_out)
def desmond_to_desmond(name='2PPN', cms=None, despath=None,
energy=True, clean=True):
"""Test gromacs to gromacs conversion
"""
if cms == None:
cms = os.path.join(name,'desmond.cms')
cms_in = os.path.join('Inputs/Desmond/', cms)
if not os.path.isfile(cms_in):
raise Exception("File not found: {0}!".format(cms_in))
cms_out = os.path.join('Outputs/DesmondToDesmond/', name, 'desmond-converted.cms')
#calc input energies
if energy:
elines_in = desmond_energies(name,cms_in,'in',despath)
Driver.initSystem(name)
Driver.load(cms_in)
Driver.write(cms_out)
# calc output energies
if energy:
elines_out = desmond_energies(name,cms_out,'DtoD',despath)
#MRS: this comparison is not working yet.
e_in = np.zeros([len(elines_in)],float)
e_out = np.zeros([len(elines_out)],float)
for i, e in enumerate(elines_in):
eins = elines_in[i].split()
eouts = elines_out[i].split()
e_in[i] = float(eins[1])
e_out[i] = float(eouts[1])
enames.append()
diff = e_in - e_out
rms = np.sqrt(np.mean(diff ** 2))
return rms, enames, e_in, e_out
else:
return 0,0,0,0
#--- cmd line options ---
parser = OptionParser()
parser.add_option('-p', type='str', dest='top', default='system2_GMX.top',
help="Topology .top file")
parser.add_option('-c', type='str', dest='gro', default='system2_GMX.gro',
help="Structure .gro file")
parser.add_option('-n', type='str', dest='name', default='system',
help="Name of system")
(options, args) = parser.parse_args()
gro = options.gro
gro_in = os.path.join('Inputs/Gromacs/', gro)
if not os.path.isfile(gro_in):
raise Exception("File not found: {0}!".format(gro_in))
top = options.top
top_in = os.path.join('Inputs/Gromacs/', top)
if not os.path.isfile(top_in):
raise Exception("File not found: {0}!".format(top_in))
name = options.name
cms_out = os.path.join('Outputs/GromacsToDesmond/', name + '.cms')
#--- end of options ---
Driver.initSystem(name)
Driver.load(top_in, gro_in)
Driver.write(cms_out)
# get_energy_out
# compare energies
#loop over all test cases for all x_to_y combinations
#List of Desmond files to be converted
filenames = ['a2a_dppc-out', 'protein', 'Rilpivirine', 'simulated_annealing_example', 'lck_Me_Cl_complex_12_1', 'lck_Me_Cl_solvent_12_1']
#Convert Desmond files to Desmond and Gromacs
for name in filenames:
cms_in = os.path.join('Inputs/Desmond/', name, name+ '.cms')
if not os.path.isfile(cms_in):
#raise Exception ("File not found: {0}!".format(cms_in))
error.write('\n(%s) -- File not found: {0}!' %(cms_in))
pass
try:
Driver.load(cms_in)
except:
e = sys.exc_info()
error.write('\n(%s) -- %s--line %s' %(name, e, sys.exc_traceback.tb_lineno))
pass
cms_out = os.path.join('Outputs', 'DesmondToDesmond', name, name+ '_OUT.cms')
try:
Driver.write(cms_out)
except:
e = sys.exc_info()
error.write('\n(%s) -- %s--line %s' %(name, e, sys.exc_traceback.tb_lineno))
pass
gro_out = os.path.join('Outputs', 'DesmondToGromacs', name+ '_OUT.gro')
top_out = os.path.join('Outputs', 'DesmondToGromacs', name+ '_OUT.top')