def main():
    parser = argparse.ArgumentParser(description=desc, 
                                     formatter_class=argparse.RawDescriptionHelpFormatter)
    
#    parser.add_argument('--ndof', help='Number of total degrees of freedom (e.g. 3*number of atoms).  This is simply the length of a coordinates vector.', 
#                        type=int, default=1)
#    parser.add_argument('--Database','-d', help = 'Name of database to write into', type = str, default="optimdb.sqlite")
#    parser.add_argument('--Mindata','-m', help = 'Name of min.data file', type = str, default="min.data")
#    parser.add_argument('--Tsdata','-t', help = 'Name of ts.data file', type = str, default="ts.data")
#    parser.add_argument('--Pointsmin','-p', help = 'Name of points.min file', type = str, default="points.min")
#    parser.add_argument('--Pointsts','-q', help = 'Name of points.ts file', type = str, default="points.ts")
    parser.add_argument('--endianness', help = 'set the endianness of the binary data.  Can be "<" for little-endian or ">" for big-endian', type = str, default="=")
    args = parser.parse_args()
    
    system = AMBERSystem(prmtopFname="coords.prmtop", inpcrdFname="coords.inpcrd")
    db = system.create_database()
    converter = OptimDBConverter(db, mindata="min.data", 
                 tsdata="ts.data", pointsmin="points.min", pointsts="points.ts",
                 endianness=args.endianness)
    converter.convert()
    
#    system.get_ndof = lambda : args.ndof
    run_gui(system, db=db)
    
    print db.number_of_minima()
Beispiel #2
0
def main():
    parser = argparse.ArgumentParser(
        description=desc, formatter_class=argparse.RawDescriptionHelpFormatter)

    #    parser.add_argument('--ndof', help='Number of total degrees of freedom (e.g. 3*number of atoms).  This is simply the length of a coordinates vector.',
    #                        type=int, default=1)
    #    parser.add_argument('--Database','-d', help = 'Name of database to write into', type = str, default="optimdb.sqlite")
    #    parser.add_argument('--Mindata','-m', help = 'Name of min.data file', type = str, default="min.data")
    #    parser.add_argument('--Tsdata','-t', help = 'Name of ts.data file', type = str, default="ts.data")
    #    parser.add_argument('--Pointsmin','-p', help = 'Name of points.min file', type = str, default="points.min")
    #    parser.add_argument('--Pointsts','-q', help = 'Name of points.ts file', type = str, default="points.ts")
    parser.add_argument(
        '--endianness',
        help=
        'set the endianness of the binary data.  Can be "<" for little-endian or ">" for big-endian',
        type=str,
        default="=")
    args = parser.parse_args()

    system = AMBERSystem(prmtopFname="coords.prmtop",
                         inpcrdFname="coords.inpcrd")
    db = system.create_database()
    converter = OptimDBConverter(db,
                                 mindata="min.data",
                                 tsdata="ts.data",
                                 pointsmin="points.min",
                                 pointsts="points.ts",
                                 endianness=args.endianness)
    converter.convert()

    #    system.get_ndof = lambda : args.ndof
    run_gui(system, db=db)

    print db.number_of_minima()
Beispiel #3
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print e 
print 'Analytic Gradient = '
print g[60:65] 
print 'Numerical Gradient = '
print gnum[60:65] 

import numpy as np 
print 'Num vs Analytic Gradient =' 
print np.max(np.abs(gnum-g)), np.max(np.abs(gnum))
print np.max(np.abs(gnum-g)) / np.max(np.abs(gnum))

# --- Test  AMBERSystem class 
from pele.amber.amberSystem import AMBERSystem 

# create new amber system    
sysAmb  = AMBERSystem('../aladipep/coords.prmtop', '../aladipep/coords.inpcrd')
    
# load existing database 
from pele.storage import Database
dbcurr = Database(db="../aladipep/aladipep.db")
                            
# ------ Test potential 
print 'testing potential in ambSystem' 
sysAmb.test_potential("../aladipep/coords.pdb")
    
# ------ BH 
print 'testing BH' 
nsteps = 1
sysAmb.test_BH(dbcurr, nsteps)

for minimum in dbcurr.minima():
Beispiel #4
0
from pele.amber.amberSystem import AMBERSystem 
from pele.gui import run as gr    

sysAmb  = AMBERSystem('coords.prmtop', 'coords.inpcrd')
gr.run_gui(sysAmb, db="optimdb.sqlite")