forked from lijiext/lammps
1009 lines
35 KiB
Python
1009 lines
35 KiB
Python
#! /usr/bin/evn python2
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# This is amber2lammps, a program written by Keir E. Novik to convert
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# Amber files to Lammps files.
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#
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# Copyright 1999, 2000 Keir E. Novik; all rights reserved.
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#
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# Modified by Vikas Varshney, U Akron, 5 July 2005, as described in README
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# Bug Fixed :Third argument in Dihedral Coeffs section is an integer - Ketan S Khare September 26, 2011
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# Modified by Vikas Varshney, Oct 8, 2013 to include additional flags (Atomic_Number, Coulombic and van der Waals 1-4 factors which are included in newer versions of .top and .crd files in amber12.
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#============================================================
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def Pop(S, I=-1):
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'Pop item I from list'
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X = S[I]
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del S[I]
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return X
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#============================================================
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class Lammps:
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#--------------------------------------------------------
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def Dump(self):
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'Write out contents of self (intended for debugging)'
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Name_list = self.__dict__.keys()
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Name_list.sort()
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for Name in Name_list:
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print Name + ':', self.__dict__[Name]
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#--------------------------------------------------------
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def Write_data(self, Basename, Item_list):
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'Write the Lammps data to file (used by Write_Lammps)'
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import os, sys
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Filename = 'data.' + Basename
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Dir_list = os.listdir('.')
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i = 1
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while Filename in Dir_list:
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Filename = 'data' + `i` + '.' + Basename
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i = i +1
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del i
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print 'Writing', Filename + '...',
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sys.stdout.flush()
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try:
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F = open(Filename, 'w')
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except IOError, Detail:
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print '(error:', Detail[1] + '!)'
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return
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try:
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F.writelines(Item_list)
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except IOError, Detail:
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print '(error:', Detail[1] + '!)'
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F.close()
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return
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F.close()
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print 'done.'
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#--------------------------------------------------------
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def Write_Lammps(self, Basename):
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'Write the Lammps data file, ignoring blank sections'
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import string
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L = []
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L.append('LAMMPS data file for ' + self.name + '\n\n')
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L.append(`self.atoms` + ' atoms\n')
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L.append(`self.bonds` + ' bonds\n')
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L.append(`self.angles` + ' angles\n')
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L.append(`self.dihedrals` + ' dihedrals\n')
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L.append(`self.impropers` + ' impropers\n\n')
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L.append(`self.atom_types` + ' atom types\n')
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if self.bonds > 0:
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L.append(`self.bond_types` + ' bond types\n')
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if self.angles > 0:
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L.append(`self.angle_types` + ' angle types\n')
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if self.dihedrals > 0:
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L.append(`self.dihedral_types` + ' dihedral types\n')
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L.append('\n')
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L.append(`self.xlo` + ' ' + `self.xhi` + ' xlo xhi\n')
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L.append(`self.ylo` + ' ' + `self.yhi` + ' ylo yhi\n')
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L.append(`self.zlo` + ' ' + `self.zhi` + ' zlo zhi\n\n')
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if self.atom_types != 0:
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L.append('Masses\n\n')
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for i in range(self.atom_types):
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L.append(`i+1` + ' ' + `self.Masses[i]` + '\n')
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L.append('\n')
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L.append('Pair Coeffs\n\n')
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for i in range(self.atom_types):
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L.append(`i+1`)
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for j in range(len(self.Nonbond_Coeffs[0])):
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L.append(' ' + `self.Nonbond_Coeffs[i][j]`)
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L.append('\n')
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L.append('\n')
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if self.bonds != 0 and self.bond_types != 0:
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L.append('Bond Coeffs\n\n')
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for i in range(self.bond_types):
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L.append(`i+1`)
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for j in range(len(self.Bond_Coeffs[0])):
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L.append(' ' + `self.Bond_Coeffs[i][j]`)
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L.append('\n')
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L.append('\n')
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if self.angles != 0 and self.angle_types != 0:
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L.append('Angle Coeffs\n\n')
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for i in range(self.angle_types):
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L.append(`i+1`)
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for j in range(len(self.Angle_Coeffs[0])):
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L.append(' ' + `self.Angle_Coeffs[i][j]`)
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L.append('\n')
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L.append('\n')
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if self.dihedrals != 0 and self.dihedral_types != 0:
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L.append('Dihedral Coeffs\n\n')
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for i in range(self.dihedral_types):
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L.append(`i+1`)
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for j in range(len(self.Dihedral_Coeffs[0])):
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L.append(' ' + `self.Dihedral_Coeffs[i][j]`)
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L.append('\n')
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L.append('\n')
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if self.atoms != 0:
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L.append('Atoms\n\n')
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for i in range(self.atoms):
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L.append(`i+1`)
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for j in range(len(self.Atoms[0])):
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L.append(' ' + `self.Atoms[i][j]`)
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L.append('\n')
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L.append('\n')
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if self.bonds != 0 and self.bond_types != 0:
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L.append('Bonds\n\n')
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for i in range(self.bonds):
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L.append(`i+1`)
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for j in range(len(self.Bonds[0])):
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L.append(' ' + `self.Bonds[i][j]`)
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L.append('\n')
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L.append('\n')
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if self.angles != 0 and self.angle_types != 0:
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L.append('Angles\n\n')
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for i in range(self.angles):
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L.append(`i+1`)
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for j in range(len(self.Angles[0])):
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L.append(' ' + `self.Angles[i][j]`)
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L.append('\n')
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L.append('\n')
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if self.dihedrals != 0 and self.dihedral_types != 0:
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L.append('Dihedrals\n\n')
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for i in range(self.dihedrals):
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L.append(`i+1`)
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for j in range(len(self.Dihedrals[0])):
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L.append(' ' + `self.Dihedrals[i][j]`)
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L.append('\n')
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L.append('\n')
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self.Write_data(Basename, L)
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#============================================================
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class Amber:
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def __init__(self):
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'Initialize the Amber class'
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self.CRD_is_read = 0
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self.TOP_is_read = 0
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#--------------------------------------------------------
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def Dump(self):
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'Write out contents of self (intended for debugging)'
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Name_list = self.__dict__.keys()
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Name_list.sort()
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for Name in Name_list:
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print Name + ':', self.__dict__[Name]
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#--------------------------------------------------------
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def Coerce_to_Lammps(self):
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'Return the Amber data converted to Lammps format'
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import math
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if self.CRD_is_read and self.TOP_is_read:
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l = Lammps()
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print 'Converting...',
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l.name = self.ITITL
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l.atoms = self.NATOM
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l.bonds = self.NBONH + self.MBONA
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l.angles = self.NTHETH + self.MTHETA
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l.dihedrals = self.NPHIH + self.MPHIA
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l.impropers = 0
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l.atom_types = self.NTYPES
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l.bond_types = self.NUMBND
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l.angle_types = self.NUMANG
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l.dihedral_types = self.NPTRA
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Shift = 0
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if self.__dict__.has_key('BOX'):
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l.xlo = 0.0
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l.xhi = self.BOX[0]
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l.ylo = 0.0
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l.yhi = self.BOX[1]
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l.zlo = 0.0
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l.zhi = self.BOX[2]
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if (l.xlo > min(self.X)) or (l.xhi < max(self.X)) or \
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(l.ylo > min(self.Y)) or (l.yhi < max(self.Y)) or \
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(l.zlo > min(self.Z)) or (l.zhi < max(self.Z)):
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# Vikas Modification: Disabling Shifting. This means I am intend to send exact coordinates of each atom and let LAMMPS
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# take care of imaging into periodic image cells. If one wants to shift all atoms in the periodic box,
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# please uncomment the below 2 lines.
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print '(warning: Currently not shifting the atoms to the periodic box)'
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#Shift = 1
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else:
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print '(warning: Guessing at periodic box!)',
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l.xlo = min(self.X)
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l.xhi = max(self.X)
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l.ylo = min(self.Y)
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l.yhi = max(self.Y)
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l.zlo = min(self.Z)
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l.zhi = max(self.Z)
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# This doesn't check duplicate values
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l.Masses = []
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for i in range(l.atom_types):
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l.Masses.append(0)
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for i in range(self.NATOM):
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l.Masses[self.IAC[i] - 1] = self.AMASS[i]
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l.Nonbond_Coeffs = []
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for i in range(self.NTYPES):
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l.Nonbond_Coeffs.append([0,0])
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for i in range(self.NTYPES):
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j = self.ICO[i * (self.NTYPES + 1)] - 1
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if self.CN1[j] == 0.0:
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l.Nonbond_Coeffs[i][0] = 0.0
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else:
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l.Nonbond_Coeffs[i][0] = \
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0.25 * (self.CN2[j])**2 / self.CN1[j]
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if self.CN2[j] == 0.0:
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l.Nonbond_Coeffs[i][1] = 0.0
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else:
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l.Nonbond_Coeffs[i][1] = \
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(self.CN1[j] / self.CN2[j])**(1.0/6.0)
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l.Bond_Coeffs = []
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for i in range(self.NUMBND):
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l.Bond_Coeffs.append([0,0])
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for i in range(self.NUMBND):
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l.Bond_Coeffs[i][0] = self.RK[i]
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l.Bond_Coeffs[i][1] = self.REQ[i]
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l.Angle_Coeffs = []
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for i in range(self.NUMANG):
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l.Angle_Coeffs.append([0,0])
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for i in range(self.NUMANG):
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l.Angle_Coeffs[i][0] = self.TK[i]
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l.Angle_Coeffs[i][1] = (180/math.pi) * self.TEQ[i]
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l.Dihedral_Coeffs = []
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for i in range(self.NPTRA):
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l.Dihedral_Coeffs.append([0,0,0])
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for i in range(self.NPTRA):
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l.Dihedral_Coeffs[i][0] = self.PK[i]
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if self.PHASE[i] == 0:
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l.Dihedral_Coeffs[i][1] = 1
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else:
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l.Dihedral_Coeffs[i][1] = -1
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l.Dihedral_Coeffs[i][2] = int(self.PN[i])
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l.Atoms = []
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for i in range(self.NATOM):
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x = self.X[i]
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y = self.Y[i]
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z = self.Z[i]
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if Shift:
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while x < l.xlo:
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x = x + self.BOX[0]
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while x > l.xhi:
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x = x - self.BOX[0]
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while y < l.ylo:
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y = y + self.BOX[1]
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while y > l.yhi:
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y = y - self.BOX[1]
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while z < l.zlo:
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z = z + self.BOX[2]
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while z > l.zhi:
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z = z - self.BOX[2]
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l.Atoms.append([0, self.IAC[i], self.CHRG[i]/18.2223, \
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x, y, z])
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l.Bonds = []
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for i in range(l.bonds):
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l.Bonds.append([0,0,0])
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for i in range(self.NBONH):
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l.Bonds[i][0] = self.ICBH[i]
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l.Bonds[i][1] = abs(self.IBH[i])/3 + 1
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l.Bonds[i][2] = abs(self.JBH[i])/3 + 1
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for i in range(self.NBONA):
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l.Bonds[self.NBONH + i][0] = self.ICB[i]
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l.Bonds[self.NBONH + i][1] = abs(self.IB[i])/3 + 1
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l.Bonds[self.NBONH + i][2] = abs(self.JB[i])/3 + 1
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l.Angles = []
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for i in range(l.angles):
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l.Angles.append([0,0,0,0])
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for i in range(self.NTHETH):
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l.Angles[i][0] = self.ICTH[i]
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l.Angles[i][1] = abs(self.ITH[i])/3 + 1
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l.Angles[i][2] = abs(self.JTH[i])/3 + 1
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l.Angles[i][3] = abs(self.KTH[i])/3 + 1
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for i in range(self.NTHETA):
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l.Angles[self.NTHETH + i][0] = self.ICT[i]
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l.Angles[self.NTHETH + i][1] = abs(self.IT[i])/3 + 1
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l.Angles[self.NTHETH + i][2] = abs(self.JT[i])/3 + 1
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l.Angles[self.NTHETH + i][3] = abs(self.KT[i])/3 + 1
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l.Dihedrals = []
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for i in range(l.dihedrals):
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l.Dihedrals.append([0,0,0,0,0])
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for i in range(self.NPHIH):
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l.Dihedrals[i][0] = self.ICPH[i]
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l.Dihedrals[i][1] = abs(self.IPH[i])/3 + 1
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l.Dihedrals[i][2] = abs(self.JPH[i])/3 + 1
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l.Dihedrals[i][3] = abs(self.KPH[i])/3 + 1
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l.Dihedrals[i][4] = abs(self.LPH[i])/3 + 1
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for i in range(self.NPHIA):
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l.Dihedrals[self.NPHIH + i][0] = self.ICP[i]
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l.Dihedrals[self.NPHIH + i][1] = abs(self.IP[i])/3 + 1
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l.Dihedrals[self.NPHIH + i][2] = abs(self.JP[i])/3 + 1
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l.Dihedrals[self.NPHIH + i][3] = abs(self.KP[i])/3 + 1
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l.Dihedrals[self.NPHIH + i][4] = abs(self.LP[i])/3 + 1
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print 'done.'
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return l
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else:
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print '(Error: Not all the Amber data has been read!)'
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#--------------------------------------------------------
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def Read_data(self, Filename):
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'Read the filename, returning a list of strings'
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import string, sys
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print 'Reading', Filename + '...',
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sys.stdout.flush()
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try:
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F = open(Filename)
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except IOError, Detail:
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print '(error:', Detail[1] + '!)'
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return
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try:
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Lines = F.readlines()
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except IOError, Detail:
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print '(error:', Detail[1] + '!)'
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F.close()
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return
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F.close()
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# If the first line is empty, use the Basename
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if Filename[-4:] == '.crd':
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if string.split(Lines[0]) == []: # This line corresponds to TITLE name in CRD file
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Basename = Filename[:string.find(Filename, '.')]
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Item_list = [Basename]
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print 'Warning: Title not present... Assigning Basename as Title'
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else:
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Item_list = []
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else:
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if string.split(Lines[3]) == []: # This line corresponds to TITLE name in TOPOLOGY file
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Basename = Filename[:string.find(Filename, '.')]
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Item_list = [Basename]
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print 'Warning: Title not present... Assigning Basename as Title'
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else:
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Item_list = []
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for Line in Lines:
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if Line[0]!='%': #Vikas' Modification: This condition ignores all the lines starting with % in the topology file.
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Item_list.extend(string.split(Line))
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return Item_list
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#--------------------------------------------------------
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def Read_CRD(self, Basename):
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'Read the Amber coordinate/restart (.crd) file'
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# The optional velocities and periodic box size are not yet parsed.
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Item_list = self.Read_data(Basename + '.crd')
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if Item_list == None:
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return
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elif len(Item_list) < 2:
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print '(error: File too short!)'
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return
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# Parse the data
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if self.__dict__.has_key('ITITL'):
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if Pop(Item_list,0) != self.ITITL:
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print '(warning: ITITL differs!)',
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else:
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self.ITITL = Pop(Item_list,0)
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print self.ITITL #Vikas Modification : Priting the Title
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if self.__dict__.has_key('NATOM'):
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if eval(Pop(Item_list,0)) != self.NATOM:
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print '(error: NATOM differs!)'
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return
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else:
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self.NATOM = eval(Pop(Item_list,0))
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print self.NATOM # Vikas' Modification: Printing number of atoms just to make sure that the program is reading the correct value.
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#if len(Item_list) == 1 + 3 * self.NATOM:
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# Vikas' Modification: I changed the condition.
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if (len(Item_list)%3) != 0:
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self.TIME = eval(Pop(Item_list,0))
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else:
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self.TIME = 0
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print self.TIME # Vikas' Modification : Printing simulation time, just to make sure that the program is readint the correct value.
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if len(Item_list) < 3 * self.NATOM:
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print '(error: File too short!)'
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return
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self.X = []
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self.Y = []
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self.Z = []
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for i in range(self.NATOM):
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self.X.append(eval(Pop(Item_list,0)))
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self.Y.append(eval(Pop(Item_list,0)))
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self.Z.append(eval(Pop(Item_list,0)))
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if (self.NATOM == 1) and len(Item_list):
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print '(warning: Ambiguity!)',
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if len(Item_list) >= 3 * self.NATOM:
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self.VX = []
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self.VY = []
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self.VZ = []
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for i in range(self.NATOM):
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|
self.VX.append(eval(Pop(Item_list,0)))
|
|
self.VY.append(eval(Pop(Item_list,0)))
|
|
self.VZ.append(eval(Pop(Item_list,0)))
|
|
|
|
if len(Item_list) >= 3:
|
|
self.BOX = []
|
|
for i in range(3):
|
|
self.BOX.append(eval(Pop(Item_list,0)))
|
|
|
|
if len(Item_list):
|
|
print '(warning: File too large!)',
|
|
|
|
print 'done.'
|
|
self.CRD_is_read = 1
|
|
|
|
#--------------------------------------------------------
|
|
|
|
def Read_TOP(self, Basename):
|
|
'Read the Amber parameter/topology (.top) file'
|
|
Item_list = self.Read_data(Basename + '.top')
|
|
|
|
if Item_list == None:
|
|
return
|
|
elif len(Item_list) < 31:
|
|
print '(error: File too short!)'
|
|
return
|
|
|
|
# Parse the data
|
|
if self.__dict__.has_key('ITITL'):
|
|
if Pop(Item_list,0) != self.ITITL:
|
|
print '(warning: ITITL differs!)'
|
|
else:
|
|
self.ITITL = Pop(Item_list,0)
|
|
print self.ITITL # Printing Self Title
|
|
|
|
if self.__dict__.has_key('NATOM'):
|
|
if eval(Pop(Item_list,0)) != self.NATOM:
|
|
print '(error: NATOM differs!)'
|
|
return
|
|
else:
|
|
self.NATOM = eval(Pop(Item_list,0))
|
|
print self.NATOM # Printing total number of atoms just to make sure that thing are going right
|
|
self.NTYPES = eval(Pop(Item_list,0))
|
|
self.NBONH = eval(Pop(Item_list,0))
|
|
self.MBONA = eval(Pop(Item_list,0))
|
|
self.NTHETH = eval(Pop(Item_list,0))
|
|
self.MTHETA = eval(Pop(Item_list,0))
|
|
self.NPHIH = eval(Pop(Item_list,0))
|
|
self.MPHIA = eval(Pop(Item_list,0))
|
|
self.NHPARM = eval(Pop(Item_list,0))
|
|
self.NPARM = eval(Pop(Item_list,0))
|
|
self.NEXT = eval(Pop(Item_list,0))
|
|
self.NRES = eval(Pop(Item_list,0))
|
|
self.NBONA = eval(Pop(Item_list,0))
|
|
self.NTHETA = eval(Pop(Item_list,0))
|
|
self.NPHIA = eval(Pop(Item_list,0))
|
|
self.NUMBND = eval(Pop(Item_list,0))
|
|
self.NUMANG = eval(Pop(Item_list,0))
|
|
self.NPTRA = eval(Pop(Item_list,0))
|
|
self.NATYP = eval(Pop(Item_list,0))
|
|
self.NPHB = eval(Pop(Item_list,0))
|
|
self.IFPERT = eval(Pop(Item_list,0))
|
|
self.NBPER = eval(Pop(Item_list,0))
|
|
self.NGPER = eval(Pop(Item_list,0))
|
|
self.NDPER = eval(Pop(Item_list,0))
|
|
self.MBPER = eval(Pop(Item_list,0))
|
|
self.MGPER = eval(Pop(Item_list,0))
|
|
self.MDPER = eval(Pop(Item_list,0))
|
|
self.IFBOX = eval(Pop(Item_list,0))
|
|
self.NMXRS = eval(Pop(Item_list,0))
|
|
self.IFCAP = eval(Pop(Item_list,0))
|
|
|
|
#....................................................
|
|
|
|
if len(Item_list) < 5 * self.NATOM + self.NTYPES**2 + \
|
|
2*(self.NRES + self.NUMBND + self.NUMANG) + \
|
|
3*self.NPTRA + self.NATYP:
|
|
print '(error: File too short!)'
|
|
return -1
|
|
|
|
self.IGRAPH = []
|
|
Pop(Item_list,0)
|
|
|
|
# A little kludge is needed here, since the IGRAPH strings are
|
|
# not separated by spaces if 4 characters in length.
|
|
for i in range(self.NATOM):
|
|
if len(Item_list[0]) > 4:
|
|
Item_list.insert(1, Item_list[0][4:])
|
|
Item_list.insert(1, Item_list[0][0:4])
|
|
del Item_list[0]
|
|
self.IGRAPH.append(Pop(Item_list,0))
|
|
|
|
# Vikas' Modification : In the following section, I am printing out each quantity which is currently being read from the topology file.
|
|
print 'Reading Charges...'
|
|
self.CHRG = []
|
|
for i in range(self.NATOM):
|
|
self.CHRG.append(eval(Pop(Item_list,0)))
|
|
|
|
print 'Reading Atomic Number...'
|
|
self.ANUMBER = []
|
|
for i in range(self.NATOM):
|
|
self.ANUMBER.append(eval(Pop(Item_list,0)))
|
|
|
|
print 'Reading Atomic Masses...'
|
|
self.AMASS = []
|
|
for i in range(self.NATOM):
|
|
self.AMASS.append(eval(Pop(Item_list,0)))
|
|
|
|
print 'Reading Atom Types...'
|
|
self.IAC = []
|
|
for i in range(self.NATOM):
|
|
self.IAC.append(eval(Pop(Item_list,0)))
|
|
|
|
print 'Reading Excluded Atoms...'
|
|
self.NUMEX = []
|
|
for i in range(self.NATOM):
|
|
self.NUMEX.append(eval(Pop(Item_list,0)))
|
|
|
|
print 'Reading Non-bonded Parameter Index...'
|
|
self.ICO = []
|
|
for i in range(self.NTYPES**2):
|
|
self.ICO.append(eval(Pop(Item_list,0)))
|
|
|
|
print 'Reading Residue Labels...'
|
|
self.LABRES = []
|
|
for i in range(self.NRES):
|
|
self.LABRES.append(Pop(Item_list,0))
|
|
|
|
print 'Reading Residues Starting Pointers...'
|
|
self.IPRES = []
|
|
for i in range(self.NRES):
|
|
self.IPRES.append(eval(Pop(Item_list,0)))
|
|
|
|
print 'Reading Bond Force Constants...'
|
|
self.RK = []
|
|
for i in range(self.NUMBND):
|
|
self.RK.append(eval(Pop(Item_list,0)))
|
|
|
|
print 'Reading Equilibrium Bond Values...'
|
|
self.REQ = []
|
|
for i in range(self.NUMBND):
|
|
self.REQ.append(eval(Pop(Item_list,0)))
|
|
|
|
print 'Reading Angle Force Constants...'
|
|
self.TK = []
|
|
for i in range(self.NUMANG):
|
|
self.TK.append(eval(Pop(Item_list,0)))
|
|
|
|
print 'Reading Equilibrium Angle Values...'
|
|
self.TEQ = []
|
|
for i in range(self.NUMANG):
|
|
self.TEQ.append(eval(Pop(Item_list,0)))
|
|
|
|
print 'Reading Dihedral Force Constants...'
|
|
self.PK = []
|
|
for i in range(self.NPTRA):
|
|
self.PK.append(eval(Pop(Item_list,0)))
|
|
|
|
print 'Reading Dihedral Periodicity...'
|
|
self.PN = []
|
|
for i in range(self.NPTRA):
|
|
self.PN.append(eval(Pop(Item_list,0)))
|
|
|
|
print 'Reading Dihedral Phase...'
|
|
self.PHASE = []
|
|
for i in range(self.NPTRA):
|
|
self.PHASE.append(eval(Pop(Item_list,0)))
|
|
|
|
print 'Reading 1-4 Electrostatic Scaling Factor...'
|
|
self.SCEEFAC = []
|
|
for i in range(self.NPTRA):
|
|
self.SCEEFAC.append(eval(Pop(Item_list,0)))
|
|
|
|
print 'Reading 1-4 Van der Waals Scaling Factor...'
|
|
self.SCNBFAC = []
|
|
for i in range(self.NPTRA):
|
|
self.SCNBFAC.append(eval(Pop(Item_list,0)))
|
|
|
|
print 'Reading Solty...' #I think this is currently not used in AMBER. Check it out, though
|
|
self.SOLTY = []
|
|
for i in range(self.NATYP):
|
|
self.SOLTY.append(eval(Pop(Item_list,0)))
|
|
|
|
#....................................................
|
|
|
|
if len(Item_list) < 2 * self.NTYPES * (self.NTYPES + 1) / 2:
|
|
print '(error: File too short!)'
|
|
return -1
|
|
|
|
print 'Reading LJ A Coefficient...'
|
|
self.CN1 = []
|
|
for i in range(self.NTYPES * (self.NTYPES + 1) / 2):
|
|
self.CN1.append(eval(Pop(Item_list,0)))
|
|
|
|
print 'Reading LJ B Coefficient...'
|
|
self.CN2 = []
|
|
for i in range(self.NTYPES * (self.NTYPES + 1) / 2):
|
|
self.CN2.append(eval(Pop(Item_list,0)))
|
|
|
|
#....................................................
|
|
|
|
if len(Item_list) < 3 * (self.NBONH + self.NBONA) + \
|
|
4 * (self.NTHETH + self.NTHETA) + 5 * (self.NPHIH + self.NPHIA):
|
|
print '(error: File too short!)'
|
|
return -1
|
|
|
|
print 'Reading Bonds which include hydrogen...'
|
|
self.IBH = []
|
|
self.JBH = []
|
|
self.ICBH = []
|
|
for i in range(self.NBONH):
|
|
self.IBH.append(eval(Pop(Item_list,0)))
|
|
self.JBH.append(eval(Pop(Item_list,0)))
|
|
self.ICBH.append(eval(Pop(Item_list,0)))
|
|
|
|
print 'Reading Bonds which dont include hydrogen...'
|
|
self.IB = []
|
|
self.JB = []
|
|
self.ICB = []
|
|
for i in range(self.NBONA):
|
|
self.IB.append(eval(Pop(Item_list,0)))
|
|
self.JB.append(eval(Pop(Item_list,0)))
|
|
self.ICB.append(eval(Pop(Item_list,0)))
|
|
|
|
print 'Reading Angles which include hydrogen...'
|
|
self.ITH = []
|
|
self.JTH = []
|
|
self.KTH = []
|
|
self.ICTH = []
|
|
for i in range(self.NTHETH):
|
|
self.ITH.append(eval(Pop(Item_list,0)))
|
|
self.JTH.append(eval(Pop(Item_list,0)))
|
|
self.KTH.append(eval(Pop(Item_list,0)))
|
|
self.ICTH.append(eval(Pop(Item_list,0)))
|
|
|
|
print 'Reading Angles which dont include hydrogen...'
|
|
self.IT = []
|
|
self.JT = []
|
|
self.KT = []
|
|
self.ICT = []
|
|
for i in range(self.NTHETA):
|
|
self.IT.append(eval(Pop(Item_list,0)))
|
|
self.JT.append(eval(Pop(Item_list,0)))
|
|
self.KT.append(eval(Pop(Item_list,0)))
|
|
self.ICT.append(eval(Pop(Item_list,0)))
|
|
|
|
print 'Reading Dihedrals which include hydrogen...'
|
|
self.IPH = []
|
|
self.JPH = []
|
|
self.KPH = []
|
|
self.LPH = []
|
|
self.ICPH = []
|
|
for i in range(self.NPHIH):
|
|
self.IPH.append(eval(Pop(Item_list,0)))
|
|
self.JPH.append(eval(Pop(Item_list,0)))
|
|
self.KPH.append(eval(Pop(Item_list,0)))
|
|
self.LPH.append(eval(Pop(Item_list,0)))
|
|
self.ICPH.append(eval(Pop(Item_list,0)))
|
|
|
|
print 'Reading Dihedrals which dont include hydrogen...'
|
|
self.IP = []
|
|
self.JP = []
|
|
self.KP = []
|
|
self.LP = []
|
|
self.ICP = []
|
|
for i in range(self.NPHIA):
|
|
self.IP.append(eval(Pop(Item_list,0)))
|
|
self.JP.append(eval(Pop(Item_list,0)))
|
|
self.KP.append(eval(Pop(Item_list,0)))
|
|
self.LP.append(eval(Pop(Item_list,0)))
|
|
self.ICP.append(eval(Pop(Item_list,0)))
|
|
|
|
#....................................................
|
|
|
|
if len(Item_list) < self.NEXT + 3 * self.NPHB + 4 * self.NATOM:
|
|
print '(error: File too short!)'
|
|
return -1
|
|
|
|
print 'Reading Excluded Atom List...'
|
|
self.NATEX = []
|
|
for i in range(self.NEXT):
|
|
self.NATEX.append(eval(Pop(Item_list,0)))
|
|
|
|
print 'Reading H-Bond A Coefficient, corresponding to r**12 term for all possible types...'
|
|
self.ASOL = []
|
|
for i in range(self.NPHB):
|
|
self.ASOL.append(eval(Pop(Item_list,0)))
|
|
|
|
print 'Reading H-Bond B Coefficient, corresponding to r**10 term for all possible types...'
|
|
self.BSOL = []
|
|
for i in range(self.NPHB):
|
|
self.BSOL.append(eval(Pop(Item_list,0)))
|
|
|
|
print 'Reading H-Bond Cut...' # I think it is not being used nowadays
|
|
self.HBCUT = []
|
|
for i in range(self.NPHB):
|
|
self.HBCUT.append(eval(Pop(Item_list,0)))
|
|
|
|
print 'Reading Amber Atom Types for each atom...'
|
|
self.ISYMBL = []
|
|
for i in range(self.NATOM):
|
|
self.ISYMBL.append(Pop(Item_list,0))
|
|
|
|
print 'Reading Tree Chain Classification...'
|
|
self.ITREE = []
|
|
for i in range(self.NATOM):
|
|
self.ITREE.append(Pop(Item_list,0))
|
|
|
|
print 'Reading Join Array: Tree joining information' # Currently unused in Sander, an AMBER module
|
|
self.JOIN = []
|
|
for i in range(self.NATOM):
|
|
self.JOIN.append(eval(Pop(Item_list,0)))
|
|
|
|
print 'Reading IRotate...' # Currently unused in Sander and Gibbs
|
|
self.IROTAT = []
|
|
for i in range(self.NATOM):
|
|
self.IROTAT.append(eval(Pop(Item_list,0)))
|
|
|
|
#....................................................
|
|
|
|
if self.IFBOX > 0:
|
|
if len(Item_list) < 3:
|
|
print '(error: File too short!)'
|
|
return -1
|
|
|
|
print 'Reading final residue which is part of solute...'
|
|
self.IPTRES = eval(Pop(Item_list,0))
|
|
print 'Reading total number of molecules...'
|
|
self.NSPM = eval(Pop(Item_list,0))
|
|
print 'Reading first solvent moleule index...'
|
|
self.NSPSOL = eval(Pop(Item_list,0))
|
|
|
|
if len(Item_list) < self.NSPM + 4:
|
|
print '(error: File too short!)'
|
|
return -1
|
|
|
|
print 'Reading atom per molecule...'
|
|
self.NSP = []
|
|
for i in range(self.NSPM):
|
|
self.NSP.append(eval(Pop(Item_list,0)))
|
|
|
|
self.BETA = eval(Pop(Item_list,0))
|
|
|
|
print 'Reading Box Dimensions...'
|
|
if self.__dict__.has_key('BOX'):
|
|
BOX = []
|
|
for i in range(3):
|
|
BOX.append(eval(Pop(Item_list,0)))
|
|
for i in range(3):
|
|
if BOX[i] != self.BOX[i]:
|
|
print '(warning: BOX differs!)',
|
|
break
|
|
del BOX
|
|
else:
|
|
self.BOX = []
|
|
for i in range(3):
|
|
self.BOX.append(eval(Pop(Item_list,0)))
|
|
|
|
#....................................................
|
|
|
|
if self.IFCAP > 0:
|
|
if len(Item_list) < 5:
|
|
print '(error: File too short!)'
|
|
return -1
|
|
print 'Reading ICAP variables::: For details, refer to online AMBER format manual'
|
|
self.NATCAP = eval(Pop(Item_list,0))
|
|
self.CUTCAP = eval(Pop(Item_list,0))
|
|
self.XCAP = eval(Pop(Item_list,0))
|
|
self.YCAP = eval(Pop(Item_list,0))
|
|
self.ZCAP = eval(Pop(Item_list,0))
|
|
|
|
#....................................................
|
|
|
|
if self.IFPERT > 0:
|
|
if len(Item_list) < 4 * self.NBPER + 5 * self.NGPER + \
|
|
6 * self.NDPER + self.NRES + 6 * self.NATOM:
|
|
print '(error: File too short!)'
|
|
return -1
|
|
|
|
print 'Reading perturb variables, 1. Bond, 2. Angles, 3. Dihedrals, etc etc.::: For details, refer to online AMBER format manual'
|
|
self.IBPER = []
|
|
self.JBPER = []
|
|
for i in range(self.NBPER):
|
|
self.IBPER.append(eval(Pop(Item_list,0)))
|
|
self.JBPER.append(eval(Pop(Item_list,0)))
|
|
|
|
self.ICBPER = []
|
|
for i in range(2 * self.NBPER):
|
|
self.ICBPER.append(eval(Pop(Item_list,0)))
|
|
|
|
self.ITPER = []
|
|
self.JTPER = []
|
|
self.KTPER = []
|
|
for i in range(self.NGPER):
|
|
self.ITPER.append(eval(Pop(Item_list,0)))
|
|
self.JTPER.append(eval(Pop(Item_list,0)))
|
|
self.KTPER.append(eval(Pop(Item_list,0)))
|
|
|
|
self.ICTPER = []
|
|
for i in range(2 * self.NGPER):
|
|
self.ICTPER.append(eval(Pop(Item_list,0)))
|
|
|
|
self.IPPER = []
|
|
self.JPPER = []
|
|
self.KPPER = []
|
|
self.LPPER = []
|
|
for i in range(self.NDPER):
|
|
self.IPPER.append(eval(Pop(Item_list,0)))
|
|
self.JPPER.append(eval(Pop(Item_list,0)))
|
|
self.KPPER.append(eval(Pop(Item_list,0)))
|
|
self.LPPER.append(eval(Pop(Item_list,0)))
|
|
|
|
self.ICPPER = []
|
|
for i in range(2 * self.NDPER):
|
|
self.ICPPER.append(eval(Pop(Item_list,0)))
|
|
|
|
LABRES = []
|
|
for i in range(self.NRES):
|
|
LABRES.append(Pop(Item_list,0))
|
|
for i in range(self.NRES):
|
|
if LABRES[i] != self.LABRES[i]:
|
|
print '(warning: BOX differs!)',
|
|
break
|
|
|
|
self.IGRPER = []
|
|
for i in range(self.NATOM):
|
|
self.IGRPER.append(eval(Pop(Item_list,0)))
|
|
|
|
self.ISMPER = []
|
|
for i in range(self.NATOM):
|
|
self.ISMPER.append(eval(Pop(Item_list,0)))
|
|
|
|
self.ALMPER = []
|
|
for i in range(self.NATOM):
|
|
self.ALMPER.append(eval(Pop(Item_list,0)))
|
|
|
|
self.IAPER = []
|
|
for i in range(self.NATOM):
|
|
self.IAPER.append(eval(Pop(Item_list,0)))
|
|
|
|
self.IACPER = []
|
|
for i in range(self.NATOM):
|
|
self.IACPER.append(eval(Pop(Item_list,0)))
|
|
|
|
self.CGPER = []
|
|
for i in range(self.NATOM):
|
|
self.CGPER.append(eval(Pop(Item_list,0)))
|
|
|
|
#....................................................
|
|
|
|
self.IPOL = 0
|
|
if self.IPOL == 1:
|
|
if len(Item_list) < self.NATOM:
|
|
print '(error: File too short!)'
|
|
return -1
|
|
print 'Reading Polarizability Data. For details, refer to online AMBER format manual'
|
|
self.ATPOL = []
|
|
for i in range(self.NATOM):
|
|
self.ATPOL.append(eval(Pop(Item_list,0)))
|
|
|
|
if self.IFPERT == 1:
|
|
if len(Item_list) < self.NATOM:
|
|
print '(error: File too short!)'
|
|
return -1
|
|
self.ATPOL1 = []
|
|
for i in range(self.NATOM):
|
|
self.ATPOL1.append(eval(Pop(Item_list,0)))
|
|
|
|
#....................................................
|
|
|
|
if len(Item_list):
|
|
print '(warning: File too large!)',
|
|
|
|
print 'done.'
|
|
self.TOP_is_read = 1
|
|
|
|
#============================================================
|
|
|
|
def Find_Amber_files():
|
|
'Look for sets of Amber files to process'
|
|
'''If not passed anything on the command line, look for pairs of
|
|
Amber files (.crd and .top) in the current directory. For
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each set if there is no corresponding Lammps file (data.), or it is
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older than any of the Amber files, add its basename to a list of
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strings. This list is returned by the function'''
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# Date and existence checks not yet implemented
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import os, sys
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Basename_list = []
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# Extract basenames from command line
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for Name in sys.argv[1:]:
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if Name[-4:] == '.crd':
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Basename_list.append(Name[:-4])
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else:
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if Name[-4:] == '.top':
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Basename_list.append(Name[:-4])
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else:
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Basename_list.append(Name)
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# Remove duplicate basenames
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for Basename in Basename_list[:]:
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while Basename_list.count(Basename) > 1:
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Basename_list.remove(Basename)
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if Basename_list == []:
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print 'Looking for Amber files...',
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Dir_list = os.listdir('.')
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Dir_list.sort()
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for File in Dir_list:
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if File[-4:] == '.top':
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Basename = File[:-4]
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if (Basename + '.crd') in Dir_list:
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Basename_list.append(Basename)
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if Basename_list != []:
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print 'found',
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for i in range(len(Basename_list)-1):
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print Basename_list[i] + ',',
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print Basename_list[-1] + '\n'
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if Basename_list == []:
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print 'none.\n'
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return Basename_list
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#============================================================
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def Convert_Amber_files():
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'Handle the whole conversion process'
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print
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print 'Welcome to amber2lammps, a program to convert Amber files to Lammps format!'
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print
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Basename_list = Find_Amber_files()
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for Basename in Basename_list:
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a = Amber()
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a.Read_CRD(Basename)
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if a.CRD_is_read:
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a.Read_TOP(Basename)
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if a.TOP_is_read:
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l = a.Coerce_to_Lammps()
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l.Write_Lammps(Basename)
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del l
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del a
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print
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#============================================================
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Convert_Amber_files()
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