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added *_driver.p, added main_simple in convert
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Ellen Zhong committed Jun 19, 2014
1 parent 51ffd6a commit ec76b2c
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Showing 5 changed files with 543 additions and 37 deletions.
210 changes: 173 additions & 37 deletions testing/convert.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
import os
import argparse
from warnings import warn
import logging
import traceback
import pdb
import numpy as np
Expand All @@ -11,6 +12,10 @@
from gromacs_energies import gromacs_energies
from lammps_energies import lammps_energies
import helper_functions
from user_exceptions import *
import desmond_driver
import gromacs_driver
import lammps_driver

# global constants

Expand All @@ -19,6 +24,15 @@
LMP_POS = 2
N_FILETYPES = 3

# Make a global logging object.
logger = logging.getLogger('InterMolLog')
logger.setLevel(logging.INFO) # specifies lowest severity log messages to handle (DEBUG will be ignored)
h = logging.StreamHandler()
#f = logging.Formatter("%(levelname)s %(asctime)s %(funcName)s %(lineno)d %(message)s")
f = logging.Formatter("%(levelname)s %(asctime)s %(message)s", "%Y-%m-%d %H:%M:%S")
h.setFormatter(f)
logger.addHandler(h)

def get_parser():
parser = argparse.ArgumentParser(description = 'Perform a file conversion')

Expand Down Expand Up @@ -71,9 +85,128 @@ def get_parser():

return parser

def main(args=''):
def main_simple():
args = get_parser().parse_args()
System._sys = System('InterMol')

# --------------- PROCESS INPUTS ----------------- #

if args.des_in:
prefix = args.des_in[0][args.des_in[0].rfind('/') + 1:-4]
desmond_driver.readFile(args.des_in[0])
elif args.gro_in:
prefix = args.gro_in[0][args.gro_in[0].rfind('/') + 1:-4]
# find the top file since order of inputs is not enforced
top_in = [x for x in args.gro_in if x.endswith('.top')]
assert(len(top_in)==1)
top_in = top_in[0] # now just string instead of list
# find the gro file since order of inputs is not enforced
gro_in = [x for x in args.gro_in if x.endswith('.gro')]
assert(len(gro_in)==1)
gro_in = gro_in[0]
gromacs_driver.readFile(top_in, gro_in, args.gropath)
elif args.lmp_in:
prefix = args.lmp_in[0][args.lmp_in[0].rfind('/') + 1:-4]
lammps_driver.readFile(args.lmp_in[0])
else:
logger.error('No input file')
sys.exit(1)

# --------------- WRITE OUTPUTS ----------------- #

if not args.oname: # default is to append _converted to the input prefix
oname = '%s_converted' % prefix
else:
oname = args.oname
oname = os.path.join(args.odir, oname) # prepend output directory to oname

status = [-1]*N_FILETYPES # records status of conversion
if args.desmond:
try:
desmond_driver.writeFile('{0}.cms'.format(oname))
status[DES_POS] = 0
except Exception as e: # other output types will still be attempted
logger.exception(e) # reports the supressed exception
if args.gromacs:
try:
gromacs_driver.writeFile('{0}.top'.format(oname), '{0}.gro'.format(oname))
status[GRO_POS] = 0
except Exception as e:
logger.exception(e)
if args.lammps:
try:
lammps_driver.writeFile('{0}.lmp'.format(oname))
status[LMP_POS] = 0
except Exception as e:
logger.exception(e)

if args.energy:
# evaluate input energy
if args.des_in:
input_type = 'Desmond' # used for displaying results
e_in, e_infile = desmond_driver.desmond_energies(args.des_in[0],
'Inputs/Desmond/onepoint.cfg', args.despath)
elif args.gro_in:
input_type = 'Gromacs'
e_in, e_infile = gromacs_driver.gromacs_energies(top_in, gro_in,
'Inputs/Gromacs/grompp.mdp', args.gropath, '')
elif args.lmp_in:
input_type = 'Lammps'
# TODO: fix this when --lmp_in gets changed to read input files
temp = args.lmp_in[0].split('.')[0] + '.input'
e_in, e_infile = lammps_driver.lammps_energies(temp, args.lmppath)
else:
warn('Something weird went wrong! Code should have never made it here.')
pass # should never reach here

# evaluate output energy
output_type = []
e_outfile = []
e_out = []
if args.desmond and status[DES_POS] == 0:
output_type.append('Desmond')
try:
out, outfile = desmond_driver.desmond_energies('%s.cms' % oname,
'Inputs/Desmond/onepoint.cfg', args.despath)
e_out.append(out)
e_outfile.append(outfile)
except Exception as e:
logger.exception(e) #reports the supressed exception
e_out.append(-1)
e_outfile.append(-1)

if args.gromacs and status[GRO_POS] == 0:
output_type.append('Gromacs')
try:
out, outfile = gromacs_driver.gromacs_energies('%s.top' % oname,
'%s.gro' % oname, 'Inputs/Gromacs/grompp.mdp', args.gropath, '')
e_out.append(out)
e_outfile.append(outfile)
except Exception as e:
logger.exception(e)
e_out.append(-1)
e_outfile.append(-1)

if args.lammps and status[LMP_POS] == 0:
output_type.append('Lammps')
try:
out, outfile = lammps_driver.lammps_energies('%s.input' % oname,
args.lmppath)
e_out.append(out)
e_outfile.append(outfile)
except Exception as e:
logger.exception(e)
e_out.append(-1)
e_outfile.append(-1)

#TODO: fix verbosity
# display energy comparison results
print ''
print '{0} input energy file: {1}'.format(input_type, e_infile)
for type, file in zip(output_type, e_outfile):
print '{0} output energy file: {1}'.format(type, file)
helper_functions.print_multiple_energy_results(e_in, e_out, input_type, output_type)

def main(args=''):

parser = get_parser() # returns parser object
if not args: # args automatically obtained from sys.argv
Expand All @@ -84,42 +217,40 @@ def main(args=''):

# check to make sure output directory exists before doing anything
if not os.path.exists(args.odir):
raise Exception('Output directory not found: {0}'.format(args.odir))
logger.error('Output directory not found: {0}'.format(args.odir))
sys.exit(1)

# check to make sure a conversion type is selected before doing anything
if not args.desmond and not args.gromacs and not args.lammps:
print 'ERROR: no conversion type selected'
logger.error('no conversion type selected')
sys.exit(1)

print 'Performing InterMol conversion...'
System._sys = System('InterMol')
print 'System initialized'

# --------------- PROCESS INPUTS ----------------- #

results = [1]*N_FILETYPES # failed on read, used in UnitTest.py
if args.des_in: # input type is desmond
# check if input exists
if not os.path.isfile(args.des_in[0]):
raise Exception('File not found: {0}'.format(args.des_in[0]))
logger.error('File not found: {0}'.format(args.des_in[0]))
raise ReadError('File not found')
prefix = args.des_in[0][args.des_in[0].rfind('/') + 1:-4]
from intermol.DesmondExt.DesmondParser import DesmondParser as DesmondParser
DesmondParser = DesmondParser()
print 'Reading in Desmond structure {0}...'.format(args.des_in[0])
logger.info('Reading in Desmond structure {0}...'.format(args.des_in[0]))
try:
DesmondParser.readFile(args.des_in[0], args.verbose)
results = [0]*N_FILETYPES # OK so far
print 'Sructure loaded\n'
logger.info('Sructure loaded')
except Exception as err:
print 'Failed on read'
print traceback.format_exc()
return results
logger.exception(err)
raise ReadError('Failed on read')

elif args.gro_in: # input type is gromacs
# check if input exists
for f in args.gro_in:
if not os.path.isfile(f):
raise Exception('File not found: {0}'.format(f))
logger.exception('File not found: {0}'.format(f))
raise ReadError('File not found')
# find the top file since order of inputs is not enforced
top_in = [x for x in args.gro_in if x.endswith('.top')]
assert(len(top_in)==1)
Expand All @@ -130,59 +261,62 @@ def main(args=''):
gro_in = gro_in[0]
prefix = args.gro_in[0][args.gro_in[0].rfind('/') + 1:-4]
# ensure .gro and .top are a valid match
_ = gromacs_energies(top_in, gro_in,
try:
gromacs_energies(top_in, gro_in,
'Inputs/Gromacs/grompp.mdp', args.gropath, '',
grompp_check=True)
except Exception as err:
logger.exception(err)
raise ReadError('grompp check failed')

from intermol.GromacsExt.GromacsTopologyParser import GromacsTopologyParser
import intermol.GromacsExt.GromacsStructureParser as GromacsStructureParser
print "Reading in Gromacs topology {0}...".format(top_in)
logger.info('Reading in Gromacs topology {0}...'.format(top_in))
GromacsTopologyParser._GroTopParser = GromacsTopologyParser()
try:
GromacsTopologyParser._GroTopParser.parseTopology(top_in)
print "Topology loaded\n"
print "Reading in Gromacs structure {0}...".format(gro_in)
logger.info('Topology loaded')
logger.info('Reading in Gromacs structure {0}...'.format(gro_in))
GromacsStructureParser.readStructure(gro_in)
results = [0]*N_FILETYPES # OK so far
print "Structure loaded\n"
logger.info('Structure loaded')
except Exception as err:
print 'Failed on read'
print traceback.format_exc()
return results
logger.exception(err)
raise ReadError('Failed on read')

elif args.lmp_in: # input type is lammps
# check if file exists
if not os.path.isfile(args.lmp_in[0]):
raise Exception('File not found: {0}'.format(args.lmp_in[0]))
logger.exception('File not found: {0}'.format(args.lmp_in[0]))
raise ReadError('File not found')
prefix = args.lmp_in[0][args.lmp_in[0].rfind('/') + 1:-4]
from intermol.lammps_extension.lammps_parser import LammpsParser
print "Reading LAMMPS data & input files..."
logger.info('Reading LAMMPS data & input files...')
try:
lammps_parser = LammpsParser()
lammps_parser.read_system(args.lmp_in[0])
results = [0]*N_FILETYPES # OK so far
print 'Structure loaded\n'
logger.info('Structure loaded')
except Exception as err:
print 'Failed on read'
print traceback.format_exc()
return results
logger.exception(err)
raise ReadError('Failed on read')

else:
print 'No input file'
logger.error('No input file')
sys.exit(1)

# ------------ WRITE OUTPUTS -------------- #

results = [0]*N_FILETYPES #
if not args.oname: # default is to append _converted to the input prefix
oname = '%s_converted' % prefix
else:
oname = args.oname
oname = os.path.join(args.odir, oname) # prepend output directory to oname

if args.desmond and results[DES_POS]==0: # Desmond OK so far
if args.desmond: # Desmond OK so far
results[DES_POS] == 2 # assume bad on write
try:
print 'Converting to Desmond...writing %s.cms...' % oname
logger.info('Converting to Desmond...')
logger.info('Writing %s.cms...' % oname)
from intermol.DesmondExt.DesmondParser import DesmondParser
DesmondParser = DesmondParser()
DesmondParser.writeFile('%s.cms' % oname, args.verbose)
Expand All @@ -191,7 +325,7 @@ def main(args=''):
print 'Failed on write for Desmond'
print traceback.format_exc()

if args.gromacs and results[GRO_POS]==0: #Gromacs OK so far
if args.gromacs: #Gromacs OK so far
results[GRO_POS] == 2 # assume bad on write
try:
print 'Converting to Gromacs...writing %s.gro, %s.top...' % (oname, oname)
Expand All @@ -206,7 +340,7 @@ def main(args=''):
print 'Failed on write for Gromacs'
print traceback.format_exc()

if args.lammps and results[LMP_POS]==0: # LAMMPS OK so far
if args.lammps: # LAMMPS OK so far
results[LMP_POS] == 2 # assume bad on write
try:
print 'Converting to Lammps...writing %s.lmp...' % oname
Expand Down Expand Up @@ -304,4 +438,6 @@ def main(args=''):
return results # converted sucessfully (no energy check)

if __name__ == '__main__':
main()
logger.info('Beginning InterMol conversion')
main_simple()
logger.info('Finished!')
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