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()
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()
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():
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")