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modernize tinker2lmp scripts so they run with both python2.7 and python3.x

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This commit is contained in:
Axel Kohlmeyer
2022-07-05 08:02:34 -04:00
parent 89e0989522
commit 212048d4cc
2 changed files with 130 additions and 129 deletions
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146
tools/tinker/data.py
View File

@ -3,16 +3,17 @@
# #
# Copyright (2005) Sandia Corporation. Under the terms of Contract # Copyright (2005) Sandia Corporation. Under the terms of Contract
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains # DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
# certain rights in this software. This software is distributed under # certain rights in this software. This software is distributed under
# the GNU General Public License. # the GNU General Public License.
# data tool # data tool
from __future__ import print_function
oneline = "Read, write, manipulate LAMMPS data files" oneline = "Read, write, manipulate LAMMPS data files"
docstr = """ docstr = """
d = data("data.poly") read a LAMMPS data file, can be gzipped d = data("data.poly") read a LAMMPS data file, can be gzipped
d = data() create an empty data file d = data() create an empty data file
d.map(1,"id",3,"x") assign names to atom columns (1-N) d.map(1,"id",3,"x") assign names to atom columns (1-N)
@ -26,17 +27,17 @@ d.reorder("Atoms",1,3,2,4,5) reorder columns (1-N) in a data file section
1,3,2,4,5 = new order of previous columns, can delete columns this way 1,3,2,4,5 = new order of previous columns, can delete columns this way
d.title = "My LAMMPS data file" set title of the data file d.title = "My LAMMPS data file" set title of the data file
d.headers["atoms"] = 1500 set a header value d.headers["atoms"] = 1500 set a header value
d.sections["Bonds"] = lines set a section to list of lines (with newlines) d.sections["Bonds"] = lines set a section to list of lines (with newlines)
d.delete("bonds") delete a keyword or section of data file d.delete("bonds") delete a keyword or section of data file
d.delete("Bonds") d.delete("Bonds")
d.replace("Atoms",5,vec) replace Nth column of section with vector d.replace("Atoms",5,vec) replace Nth column of section with vector
d.newxyz(dmp,1000) replace xyz in Atoms with xyz of snapshot N d.newxyz(dmp,1000) replace xyz in Atoms with xyz of snapshot N
newxyz assumes id,x,y,z are defined in both data and dump files newxyz assumes id,x,y,z are defined in both data and dump files
also replaces ix,iy,iz if they are defined also replaces ix,iy,iz if they are defined
index,time,flag = d.iterator(0/1) loop over single data file snapshot index,time,flag = d.iterator(0/1) loop over single data file snapshot
time,box,atoms,bonds,tris,lines = d.viz(index) return list of viz objects time,box,atoms,bonds,tris,lines = d.viz(index) return list of viz objects
@ -53,7 +54,7 @@ time,box,atoms,bonds,tris,lines = d.viz(index) return list of viz objects
NULL if bonds do not exist NULL if bonds do not exist
tris = NULL tris = NULL
lines = NULL lines = NULL
d.write("data.new") write a LAMMPS data file d.write("data.new") write a LAMMPS data file
""" """
@ -65,7 +66,7 @@ d.write("data.new") write a LAMMPS data file
# Variables # Variables
# title = 1st line of data file # title = 1st line of data file
# names = dictionary with atom attributes as keys, col #s as values # names = dictionary with atom attributes as keys, col #s as values
# headers = dictionary with header name as key, value or tuple as values # headers = dictionary with header name as key, value or tuple as values
# sections = dictionary with section name as key, array of lines as values # sections = dictionary with section name as key, array of lines as values
# nselect = 1 = # of snapshots # nselect = 1 = # of snapshots
@ -79,13 +80,13 @@ except: PIZZA_GUNZIP = "gunzip"
# Class definition # Class definition
class data: class data(object):
# -------------------------------------------------------------------- # --------------------------------------------------------------------
def __init__(self,*list): def __init__(self,*list):
self.nselect = 1 self.nselect = 1
if len(list) == 0: if len(list) == 0:
self.title = "LAMMPS data file" self.title = "LAMMPS data file"
self.names = {} self.names = {}
@ -99,7 +100,7 @@ class data:
self.title = f.readline() self.title = f.readline()
self.names = {} self.names = {}
headers = {} headers = {}
while 1: while 1:
line = f.readline() line = f.readline()
@ -109,16 +110,16 @@ class data:
found = 0 found = 0
for keyword in hkeywords: for keyword in hkeywords:
if line.find(keyword) >= 0: if line.find(keyword) >= 0:
found = 1 found = 1
words = line.split() words = line.split()
if keyword == "xlo xhi" or keyword == "ylo yhi" or \ if keyword == "xlo xhi" or keyword == "ylo yhi" or \
keyword == "zlo zhi": keyword == "zlo zhi":
headers[keyword] = (float(words[0]),float(words[1])) headers[keyword] = (float(words[0]),float(words[1]))
elif keyword == "xy xz yz": elif keyword == "xy xz yz":
headers[keyword] = \ headers[keyword] = \
(float(words[0]),float(words[1]),float(words[2])) (float(words[0]),float(words[1]),float(words[2]))
else: else:
headers[keyword] = int(words[0]) headers[keyword] = int(words[0])
if not found: if not found:
break break
@ -128,22 +129,21 @@ class data:
for pair in skeywords: for pair in skeywords:
keyword,length = pair[0],pair[1] keyword,length = pair[0],pair[1]
if keyword == line: if keyword == line:
found = 1 found = 1
if not headers.has_key(length): if length not in headers:
raise StandardError, \ raise (Exception, "data section %s has no matching header value" % line)
"data section %s has no matching header value" % line f.readline()
f.readline()
list = [] list = []
for i in xrange(headers[length]): list.append(f.readline()) for i in range(headers[length]): list.append(f.readline())
sections[keyword] = list sections[keyword] = list
if not found: if not found:
raise StandardError,"invalid section %s in data file" % line raise (Exception,"invalid section %s in data file" % line)
f.readline() f.readline()
line = f.readline() line = f.readline()
if not line: if not line:
break break
line = line.strip() line = line.strip()
f.close() f.close()
self.headers = headers self.headers = headers
self.sections = sections self.sections = sections
@ -153,7 +153,7 @@ class data:
def map(self,*pairs): def map(self,*pairs):
if len(pairs) % 2 != 0: if len(pairs) % 2 != 0:
raise StandardError, "data map() requires pairs of mappings" raise Exception("data map() requires pairs of mappings")
for i in range(0,len(pairs),2): for i in range(0,len(pairs),2):
j = i + 1 j = i + 1
self.names[pairs[j]] = pairs[i]-1 self.names[pairs[j]] = pairs[i]-1
@ -168,7 +168,7 @@ class data:
lines = self.sections[field] lines = self.sections[field]
for line in lines: for line in lines:
words = line.split() words = line.split()
values = map(float,words) values = list(map(float,words))
array.append(values) array.append(values)
return array return array
elif len(list) == 2: elif len(list) == 2:
@ -181,7 +181,7 @@ class data:
vec.append(float(words[n])) vec.append(float(words[n]))
return vec return vec
else: else:
raise StandardError, "invalid arguments for data.get()" raise Exception("invalid arguments for data.get()")
# -------------------------------------------------------------------- # --------------------------------------------------------------------
# reorder columns in a data file field # reorder columns in a data file field
@ -192,10 +192,10 @@ class data:
oldlines = self.sections[name] oldlines = self.sections[name]
newlines = natoms*[""] newlines = natoms*[""]
for index in order: for index in order:
for i in xrange(len(newlines)): for i in range(len(newlines)):
words = oldlines[i].split() words = oldlines[i].split()
newlines[i] += words[index-1] + " " newlines[i] += words[index-1] + " "
for i in xrange(len(newlines)): for i in range(len(newlines)):
newlines[i] += "\n" newlines[i] += "\n"
self.sections[name] = newlines self.sections[name] = newlines
@ -206,7 +206,7 @@ class data:
lines = self.sections[name] lines = self.sections[name]
newlines = [] newlines = []
j = icol - 1 j = icol - 1
for i in xrange(len(lines)): for i in range(len(lines)):
line = lines[i] line = lines[i]
words = line.split() words = line.split()
words[j] = str(vector[i]) words[j] = str(vector[i])
@ -228,48 +228,48 @@ class data:
self.replace("Atoms",self.names['x']+1,x) self.replace("Atoms",self.names['x']+1,x)
self.replace("Atoms",self.names['y']+1,y) self.replace("Atoms",self.names['y']+1,y)
self.replace("Atoms",self.names['z']+1,z) self.replace("Atoms",self.names['z']+1,z)
if dm.names.has_key("ix") and self.names.has_key("ix"): if "ix" in dm.names and "ix" in self.names:
ix,iy,iz = dm.vecs(ntime,"ix","iy","iz") ix,iy,iz = dm.vecs(ntime,"ix","iy","iz")
self.replace("Atoms",self.names['ix']+1,ix) self.replace("Atoms",self.names['ix']+1,ix)
self.replace("Atoms",self.names['iy']+1,iy) self.replace("Atoms",self.names['iy']+1,iy)
self.replace("Atoms",self.names['iz']+1,iz) self.replace("Atoms",self.names['iz']+1,iz)
# -------------------------------------------------------------------- # --------------------------------------------------------------------
# delete header value or section from data file # delete header value or section from data file
def delete(self,keyword): def delete(self,keyword):
if self.headers.has_key(keyword): del self.headers[keyword] if keyword in self.headers: del self.headers[keyword]
elif self.sections.has_key(keyword): del self.sections[keyword] elif keyword in self.sections: del self.sections[keyword]
else: raise StandardError, "keyword not found in data object" else: raise Exception("keyword not found in data object")
# -------------------------------------------------------------------- # --------------------------------------------------------------------
# write out a LAMMPS data file # write out a LAMMPS data file
def write(self,file): def write(self,file):
f = open(file,"w") f = open(file,"w")
print >>f,self.title print(self.title, file=f)
# write any keywords in standard list hkeywords # write any keywords in standard list hkeywords
# in the order they are in hkeywords # in the order they are in hkeywords
# then write any extra keywords at end of header section # then write any extra keywords at end of header section
for keyword in hkeywords: for keyword in hkeywords:
if self.headers.has_key(keyword): if keyword in self.headers:
if keyword == "xlo xhi" or keyword == "ylo yhi" or \ if keyword == "xlo xhi" or keyword == "ylo yhi" or \
keyword == "zlo zhi": keyword == "zlo zhi":
pair = self.headers[keyword] pair = self.headers[keyword]
print >>f,pair[0],pair[1],keyword print(pair[0],pair[1],keyword, file=f)
elif keyword == "xy xz yz": elif keyword == "xy xz yz":
triple = self.headers[keyword] triple = self.headers[keyword]
print >>f,triple[0],triple[1],triple[2],keyword print(triple[0],triple[1],triple[2],keyword, file=f)
else: else:
print >>f,self.headers[keyword],keyword print(self.headers[keyword],keyword, file=f)
for keyword in self.headers.keys(): for keyword in list(self.headers.keys()):
if keyword not in hkeywords: if keyword not in hkeywords:
print >>f,self.headers[keyword],keyword print(self.headers[keyword],keyword, file=f)
# write any sections in standard list skeywords # write any sections in standard list skeywords
# in the order they are in skeywords # in the order they are in skeywords
@ -277,18 +277,18 @@ class data:
for pair in skeywords: for pair in skeywords:
keyword = pair[0] keyword = pair[0]
if self.sections.has_key(keyword): if keyword in self.sections:
print >>f,"\n%s\n" % keyword print("\n%s\n" % keyword, file=f)
for line in self.sections[keyword]: for line in self.sections[keyword]:
print >>f,line, print(line, end='', file=f)
skeyfirst = [pair[0] for pair in skeywords] skeyfirst = [pair[0] for pair in skeywords]
for keyword in self.sections.keys(): for keyword in list(self.sections.keys()):
if keyword not in skeyfirst: if keyword not in skeyfirst:
print >>f,"\n%s\n" % keyword print("\n%s\n" % keyword, file=f)
for line in self.sections[keyword]: for line in self.sections[keyword]:
print >>f,line, print(line, end='', file=f)
f.close() f.close()
@ -304,20 +304,20 @@ class data:
def findtime(self,n): def findtime(self,n):
if n == 0: return 0 if n == 0: return 0
raise StandardError, "no step %d exists" % (n) raise(Exception, "no step %d exists" % (n))
# -------------------------------------------------------------------- # --------------------------------------------------------------------
# return list of atoms and bonds to viz for data object # return list of atoms and bonds to viz for data object
def viz(self,isnap): def viz(self,isnap):
if isnap: raise StandardError, "cannot call data.viz() with isnap != 0" if isnap: raise Exception("cannot call data.viz() with isnap != 0")
id = self.names["id"] id = self.names["id"]
type = self.names["type"] type = self.names["type"]
x = self.names["x"] x = self.names["x"]
y = self.names["y"] y = self.names["y"]
z = self.names["z"] z = self.names["z"]
xlohi = self.headers["xlo xhi"] xlohi = self.headers["xlo xhi"]
ylohi = self.headers["ylo yhi"] ylohi = self.headers["ylo yhi"]
zlohi = self.headers["zlo zhi"] zlohi = self.headers["zlo zhi"]
@ -336,7 +336,7 @@ class data:
# assumes atoms are sorted so can lookup up the 2 atoms in each bond # assumes atoms are sorted so can lookup up the 2 atoms in each bond
bonds = [] bonds = []
if self.sections.has_key("Bonds"): if "Bonds" in self.sections:
bondlines = self.sections["Bonds"] bondlines = self.sections["Bonds"]
for line in bondlines: for line in bondlines:
words = line.split() words = line.split()
@ -349,8 +349,8 @@ class data:
float(atom1words[z]), float(atom1words[z]),
float(atom2words[x]),float(atom2words[y]), float(atom2words[x]),float(atom2words[y]),
float(atom2words[z]), float(atom2words[z]),
float(atom1words[type]),float(atom2words[type])]) float(atom1words[type]),float(atom2words[type])])
tris = [] tris = []
lines = [] lines = []
return 0,box,atoms,bonds,tris,lines return 0,box,atoms,bonds,tris,lines
@ -375,8 +375,8 @@ class data:
hkeywords = ["atoms","ellipsoids","lines","triangles","bodies", hkeywords = ["atoms","ellipsoids","lines","triangles","bodies",
"bonds","angles","dihedrals","impropers", "bonds","angles","dihedrals","impropers",
"atom types","bond types","angle types","dihedral types", "atom types","bond types","angle types","dihedral types",
"improper types", "improper types",
"xlo xhi","ylo yhi","zlo zhi","xy xz yz"] "xlo xhi","ylo yhi","zlo zhi","xy xz yz"]
skeywords = [["Masses","atom types"], skeywords = [["Masses","atom types"],
@ -384,14 +384,14 @@ skeywords = [["Masses","atom types"],
["Lines","lines"],["Triangles","triangles"],["Bodies","bodies"], ["Lines","lines"],["Triangles","triangles"],["Bodies","bodies"],
["Velocities","atoms"], ["Velocities","atoms"],
["Bonds","bonds"], ["Bonds","bonds"],
["Angles","angles"], ["Angles","angles"],
["Dihedrals","dihedrals"], ["Dihedrals","dihedrals"],
["Impropers","impropers"], ["Impropers","impropers"],
["Pair Coeffs","atom types"], ["Pair Coeffs","atom types"],
["Bond Coeffs","bond types"], ["Bond Coeffs","bond types"],
["Angle Coeffs","angle types"], ["Angle Coeffs","angle types"],
["Dihedral Coeffs","dihedral types"], ["Dihedral Coeffs","dihedral types"],
["Improper Coeffs","improper types"], ["Improper Coeffs","improper types"],
["BondBond Coeffs","angle types"], ["BondBond Coeffs","angle types"],
["BondAngle Coeffs","angle types"], ["BondAngle Coeffs","angle types"],
["MiddleBondTorsion Coeffs","dihedral types"], ["MiddleBondTorsion Coeffs","dihedral types"],

113
tools/tinker/tinker2lmp.py
View File

@ -15,6 +15,7 @@
# Author: Steve Plimpton # Author: Steve Plimpton
from __future__ import print_function
import sys,os,math import sys,os,math
from data import data from data import data
@ -29,20 +30,20 @@ DELTA = 0.001 # delta on LAMMPS shrink-wrap box size, in Angstroms
def error(txt=""): def error(txt=""):
if not txt: if not txt:
print "Syntax: tinker2lmp.py -switch args ..." print("Syntax: tinker2lmp.py -switch args ...")
print " -xyz file" print(" -xyz file")
print " -amoeba file" print(" -amoeba file")
print " -hippo file" print(" -hippo file")
print " -data file" print(" -data file")
print " -bitorsion file" print(" -bitorsion file")
print " -nopbc" print(" -nopbc")
print " -pbc xhi yhi zhi" print(" -pbc xhi yhi zhi")
else: print "ERROR:",txt else: print("ERROR:",txt)
#sys.exit() #sys.exit()
# read and store values from a Tinker xyz file # read and store values from a Tinker xyz file
class XYZfile: class XYZfile(object):
def __init__(self,file): def __init__(self,file):
lines = open(file,'r').readlines() lines = open(file,'r').readlines()
header = lines[0] header = lines[0]
@ -212,7 +213,7 @@ class XYZfile:
def output(self,outfile): def output(self,outfile):
fp = open(outfile,'w') fp = open(outfile,'w')
words = self.header.split() words = self.header.split()
print >>fp,self.natoms,"replicated",' '.join(words[1:]) print(self.natoms,"replicated",' '.join(words[1:]), file=fp)
id = self.id id = self.id
label = self.label label = self.label
@ -225,9 +226,9 @@ class XYZfile:
# NOTE: worry about formatting of line # NOTE: worry about formatting of line
for i in range(self.natoms): for i in range(self.natoms):
print >>fp,i+1,label[i],x[i],y[i],z[i],type[i], print(i+1,label[i],x[i],y[i],z[i],type[i], end=' ', file=fp)
for j in bonds[i]: print >>fp,j, for j in bonds[i]: print(j, end=' ', file=fp)
print >>fp print(file=fp)
fp.close() fp.close()
@ -255,7 +256,7 @@ class XYZfile:
# scalar force field params in Force Field Definition section # scalar force field params in Force Field Definition section
# bond, angle, dihedral coeffs indexed by Tinker classes # bond, angle, dihedral coeffs indexed by Tinker classes
class PRMfile: class PRMfile(object):
def __init__(self,file): def __init__(self,file):
lines = open(file,'r').readlines() lines = open(file,'r').readlines()
self.nlines = len(lines) self.nlines = len(lines)
@ -519,7 +520,7 @@ class PRMfile:
error("torsion does not have triplets of params: %d %d %d %d" % \ error("torsion does not have triplets of params: %d %d %d %d" % \
(class1,class2,class3,class4)) (class1,class2,class3,class4))
mfourier = (len(words)-5) / 3 mfourier = int((len(words)-5)/3)
oneparams = [class1,class2,class3,class4,mfourier] oneparams = [class1,class2,class3,class4,mfourier]
for iset in range(mfourier): for iset in range(mfourier):
@ -743,7 +744,7 @@ if pbcflag:
else: else:
xlo = ylo = zlo = BIG xlo = ylo = zlo = BIG
xhi = yhi = zhi = -BIG xhi = yhi = zhi = -BIG
for i in xrange(natoms): for i in range(natoms):
xlo = min(xlo,float(x[i])) xlo = min(xlo,float(x[i]))
ylo = min(ylo,float(y[i])) ylo = min(ylo,float(y[i]))
zlo = min(zlo,float(z[i])) zlo = min(zlo,float(z[i]))
@ -1097,11 +1098,11 @@ for i,one in enumerate(alist):
nbonds,hcount = xyz.angle_hbond_count(atom1,atom2,atom3,lmptype,lmpmass) nbonds,hcount = xyz.angle_hbond_count(atom1,atom2,atom3,lmptype,lmpmass)
if nbonds != 3: if nbonds != 3:
print "Center angle atom has wrong bond count" print("Center angle atom has wrong bond count")
print " angle atom IDs:",atom1,atom2,atom3 print(" angle atom IDs:",atom1,atom2,atom3)
print " angle atom classes:",c1,c2,c3 print(" angle atom classes:",c1,c2,c3)
print " Tinker FF file param options:",len(params[3]) print(" Tinker FF file param options:",len(params[3]))
print " Nbonds and hydrogen count:",nbonds,hcount print(" Nbonds and hydrogen count:",nbonds,hcount)
#sys.exit() NOTE: allow this for now #sys.exit() NOTE: allow this for now
if hcount == 0: which = 1 if hcount == 0: which = 1
@ -1109,22 +1110,22 @@ for i,one in enumerate(alist):
which = 2 which = 2
m += 1 m += 1
print "3-bond angle" print("3-bond angle")
print " angle atom IDs:",atom1,atom2,atom3 print(" angle atom IDs:",atom1,atom2,atom3)
print " angle atom classes:",c1,c2,c3 print(" angle atom classes:",c1,c2,c3)
print " Tinker FF file param options:",len(params[3]) print(" Tinker FF file param options:",len(params[3]))
print " Nbonds and hydrogen count:",nbonds,hcount print(" Nbonds and hydrogen count:",nbonds,hcount)
print " which:",which,m print(" which:",which,m)
elif len(params[3]) == 3: elif len(params[3]) == 3:
nbonds,hcount = xyz.angle_hbond_count(atom1,atom2,atom3,lmptype,lmpmass) nbonds,hcount = xyz.angle_hbond_count(atom1,atom2,atom3,lmptype,lmpmass)
if nbonds != 4: if nbonds != 4:
print "Center angle atom has wrong bond count" print("Center angle atom has wrong bond count")
print " angle atom IDs:",atom1,atom2,atom3 print(" angle atom IDs:",atom1,atom2,atom3)
print " angle atom classes:",c1,c2,c3 print(" angle atom classes:",c1,c2,c3)
print " Tinker FF file param options:",len(params[3]) print(" Tinker FF file param options:",len(params[3]))
print " Nbonds and hydrogen count:",nbonds,hcount print(" Nbonds and hydrogen count:",nbonds,hcount)
#sys.exit() NOTE: allow this for now #sys.exit() NOTE: allow this for now
if hcount == 0: which = 1 if hcount == 0: which = 1
@ -1170,7 +1171,7 @@ for itype in range(len(aparams)):
elif (c3,c2,c1) in badict: elif (c3,c2,c1) in badict:
n1,n2,r1,r2 = badict[(c3,c2,c1)] n1,n2,r1,r2 = badict[(c3,c2,c1)]
else: else:
print "Bond-stretch angle triplet not found: %d %d %d" % (c1,c2,c3) print("Bond-stretch angle triplet not found: %d %d %d" % (c1,c2,c3))
n1,n2,r1,r2 = 4*[0.0] n1,n2,r1,r2 = 4*[0.0]
baparams.append((n1,n2,r1,r2)) baparams.append((n1,n2,r1,r2))
@ -1600,17 +1601,17 @@ if nbitorsions:
nbitorsions) nbitorsions)
fp = open(bitorsionfile,'w') fp = open(bitorsionfile,'w')
print >>fp,"Tinker BiTorsion parameter file for fix bitorsion\n" print("Tinker BiTorsion parameter file for fix bitorsion\n", file=fp)
print >>fp,"%d bitorsion types" % len(bitorsionparams) print("%d bitorsion types" % len(bitorsionparams), file=fp)
itype = 0 itype = 0
for nx,ny,array in bitorsionparams: for nx,ny,array in bitorsionparams:
itype += 1 itype += 1
print >>fp print(file=fp)
print >>fp,itype,nx,ny print(itype,nx,ny, file=fp)
for ix in range(nx): for ix in range(nx):
for iy in range(ny): for iy in range(ny):
xgrid,ygrid,value = array[ix][iy] xgrid,ygrid,value = array[ix][iy]
print >>fp," ",xgrid,ygrid,value print(" ",xgrid,ygrid,value, file=fp)
fp.close() fp.close()
lines = [] lines = []
@ -1624,21 +1625,21 @@ d.write(datafile)
# print stats to screen # print stats to screen
print "Natoms =",natoms print("Natoms =",natoms)
print "Ntypes =",ntypes print("Ntypes =",ntypes)
print "Tinker XYZ types =",len(tink2lmp) print("Tinker XYZ types =",len(tink2lmp))
print "Tinker PRM types =",prm.ntypes print("Tinker PRM types =",prm.ntypes)
#print "Tinker groups =",ngroups #print "Tinker groups =",ngroups
print "Nmol =",nmol print("Nmol =",nmol)
print "Nbonds =",nbonds print("Nbonds =",nbonds)
print "Nangles =",nangles print("Nangles =",nangles)
print "Ndihedrals =",ndihedrals print("Ndihedrals =",ndihedrals)
print "Nimpropers =",nimpropers print("Nimpropers =",nimpropers)
print "Npitorsions =",npitorsions print("Npitorsions =",npitorsions)
print "Nbitorsions =",nbitorsions print("Nbitorsions =",nbitorsions)
print "Nbondtypes =",len(bparams) print("Nbondtypes =",len(bparams))
print "Nangletypes =",len(aparams) print("Nangletypes =",len(aparams))
print "Ndihedraltypes =",len(dparams) print("Ndihedraltypes =",len(dparams))
print "Nimpropertypes =",len(oparams) print("Nimpropertypes =",len(oparams))
print "Npitorsiontypes =",len(pitorsionparams) print("Npitorsiontypes =",len(pitorsionparams))
print "Nbitorsiontypes =",len(bitorsionparams) print("Nbitorsiontypes =",len(bitorsionparams))