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lammps/tools/moltemplate/moltemplate/lttree_postprocess.py
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lttree_postprocess.py
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#!/usr/bin/env python
"""
lttree_postprocess.py
This is a stand-alone python script which checks the files created by
lttree.py to insure that the standard instance-variables ($variables)
have all been defined. This script performs a task which is very similar
to the task performed by lttree_check.py. This script attempts to detect
mistakes in the names of $atom, $bond, $angle, $dihedral, $improper, & $mol
variables.
"""
import sys
try:
from .lttree_styles import *
from .ttree_lex import ExtractCatName
except (SystemError, ValueError):
# not installed as a package
from lttree_styles import *
from ttree_lex import ExtractCatName
g_program_name = __file__.split('/')[-1] # = 'lttree_postprocess.py'
g_version_str = '0.5.0'
g_date_str = '2016-12-21'
def main():
atom_style = 'full'
ttree_assignments_fname = 'ttree_assignments.txt'
defined_mols = set([])
defined_atoms = set([])
defined_bonds = set([])
defined_angles = set([])
defined_dihedrals = set([])
defined_impropers = set([])
g_no_check_msg = \
'(To override this error, run moltemplate using the \"-nocheck\" argument.)\n'
if len(sys.argv) > 1:
for i in range(0, len(sys.argv)):
if ((sys.argv[i].lower() == '-atomstyle') or
(sys.argv[i].lower() == '-atom-style') or
(sys.argv[i].lower() == '-atom_style')):
if i + 1 >= len(sys.argv):
raise InputError('Error(' + g_program_name + '): The ' + sys.argv[i] + ' flag should be followed by a LAMMPS\n'
' atom_style name (or single quoted string containing a space-separated\n'
' list of column names such as: atom-ID atom-type q x y z molecule-ID.)\n')
atom_style = sys.argv[i + 1]
elif ((sys.argv[i].lower() == '-ttreeassignments') or
(sys.argv[i].lower() == '-ttree-assignments') or
(sys.argv[i].lower() == '-ttree_assignments')):
if i + 1 >= len(sys.argv):
raise InputError('Error(' + g_program_name + '): The ' + sys.argv[i] + ' flag should be followed by \n'
' a file containing the variable bindings created by ttree/moltemplate.\n')
ttree_assignments_fname = sys.argv[i + 1]
else:
pass # ignore other arguments (they are intended for lttree.py)
atom_column_names = AtomStyle2ColNames(atom_style)
i_atomid = 0
i_molid = -1
for i in range(0, len(atom_column_names)):
if atom_column_names[i].lower() == 'atom-id':
i_atomid = i
elif atom_column_names[i].lower() == 'molecule-id':
i_molid = i
i_max_column = max(i_atomid, i_molid)
# The following variables are defined in "lttree_styles.py"
#data_atoms="Data Atoms"
#data_masses="Data Masses"
#data_velocities="Data Velocities"
#data_bonds="Data Bonds"
#data_angles="Data Angles"
#data_dihedrals="Data Dihedrals"
#data_impropers="Data Impropers"
sys.stderr.write(g_program_name + ' v' +
g_version_str + ' ' + g_date_str + '\n')
try:
# ------------ defined_atoms ------------
try:
f = open(data_atoms + '.template', 'r')
except:
raise InputError('Error(' + g_program_name + '): Unable to open file\n' +
'\"' + data_atoms + '.template\"\n'
' for reading. (Do your files lack a \"' +
data_atoms + '\" section?)\n'
+ g_no_check_msg + '\n')
for line_orig in f:
ic = line_orig.find('#')
if ic != -1:
line = line_orig[:ic]
else:
line = line_orig.rstrip('\n')
tokens = line.strip().split()
if len(tokens) == 0:
pass
elif len(tokens) <= i_max_column:
raise InputError('Error(' + g_program_name + '): The following line from\n'
' "\"' + data_atoms + '.template\" has bad format:\n\n'
+ line_orig + '\n'
' This my probably an internal error. (Feel free to contact the developer.)\n'
+ g_no_check_msg + '\n')
else:
defined_atoms.add(tokens[i_atomid])
if i_molid != -1:
defined_mols.add(tokens[i_molid])
f.close()
# ------------ defined_bonds ------------
try:
f = open(data_bonds + '.template', 'r')
for line_orig in f:
ic = line_orig.find('#')
if ic != -1:
line = line_orig[:ic]
else:
line = line_orig.rstrip('\n')
tokens = line.strip().split()
if len(tokens) == 0:
pass
elif len(tokens) < 4:
raise InputError('Error(' + g_program_name + '): The following line from\n'
' "\"' + data_bonds + '.template\" has bad format:\n\n'
+ line_orig + '\n'
' This my probably an internal error. (Feel free to contact the developer.)\n'
+ g_no_check_msg + '\n')
else:
defined_bonds.add(tokens[0])
f.close()
except:
pass # Defining bonds (stored in the data_bonds file) is optional
# ------------ defined_angles ------------
try:
f = open(data_angles + '.template', 'r')
for line_orig in f:
ic = line_orig.find('#')
if ic != -1:
line = line_orig[:ic]
else:
line = line_orig.rstrip('\n')
tokens = line.strip().split()
if len(tokens) == 0:
pass
elif len(tokens) < 5:
raise InputError('Error(' + g_program_name + '): The following line from\n'
' "\"' + data_angles + '.template\" has bad format:\n\n'
+ line_orig + '\n'
' This my probably an internal error. (Feel free to contact the developer.)\n'
+ g_no_check_msg + '\n')
else:
defined_angles.add(tokens[0])
f.close()
except:
pass # Defining angles (stored in the data_angles file) is optional
# ------------ defined_dihedrals ------------
try:
f = open(data_dihedrals + '.template', 'r')
for line_orig in f:
ic = line_orig.find('#')
if ic != -1:
line = line_orig[:ic]
else:
line = line_orig.rstrip('\n')
tokens = line.strip().split()
if len(tokens) == 0:
pass
elif len(tokens) < 6:
raise InputError('Error(' + g_program_name + '): The following line from\n'
' "\"' + data_dihedrals + '.template\" has bad format:\n\n'
+ line_orig + '\n'
' This my probably an internal error. (Feel free to contact the developer.)\n'
+ g_no_check_msg + '\n')
else:
defined_dihedrals.add(tokens[0])
f.close()
except:
# Defining dihedrals (stored in the data_dihedrals file) is optional
pass
# ------------ defined_impropers ------------
try:
f = open(data_impropers + '.template', 'r')
for line_orig in f:
ic = line_orig.find('#')
if ic != -1:
line = line_orig[:ic]
else:
line = line_orig.rstrip('\n')
tokens = line.strip().split()
if len(tokens) == 0:
pass
elif len(tokens) < 6:
raise InputError('Error(' + g_program_name + '): The following line from\n'
' "\"' + data_impropers + '.template\" has bad format:\n\n'
+ line_orig + '\n'
' This my probably an internal error. (Feel free to contact the developer.)\n'
+ g_no_check_msg + '\n')
else:
defined_impropers.add(tokens[0])
f.close()
except:
# Defining impropers (stored in the data_impropers file) is optional
pass
# ---- Check ttree_assignments to make sure variables are defined ----
try:
f = open(ttree_assignments_fname, 'r')
except:
raise InputError('Error(' + g_program_name + '): Unable to open file\n' +
'\"' + ttree_assignments_fname + '\"\n'
' for reading. (Do your files lack a \"' +
data_atoms + '\" section?)\n'
+ g_no_check_msg + '\n')
for line_orig in f:
ic = line_orig.find('#')
if ic != -1:
line = line_orig[:ic]
usage_location_str = 'near ' + line_orig[ic + 1:]
else:
line = line_orig.rstrip('\n')
usage_location_str = ''
tokens = line.strip().split()
if len(tokens) == 0:
pass
if len(tokens) > 0:
# This file contains a list of variables of the form:
#
# @/atom:MoleculeType1:C 1
# @/atom:MoleculeType1:H 2
# @/atom:MoleculeType2:N 3
# $/atom:molecule1:N1 1
# $/atom:molecule1:C1 2
# :
# $/atom:molecule1141:CH 13578
# $/atom:molecule1142:N3 13579
# :
# We only care about instance variables (which use the '$' prefix)
# Lines corresponding to static variables (which use the '@' prefix)
# are ignored during this pass.
i_prefix = tokens[0].find('$')
if i_prefix != -1:
descr_str = tokens[0][i_prefix + 1:]
cat_name = ExtractCatName(descr_str)
if ((cat_name == 'atom') and
(tokens[0] not in defined_atoms)):
raise InputError('Error(' + g_program_name + '): ' + usage_location_str + '\n' +
' Reference to undefined $atom:\n\n'
' ' + tokens[0] + ' (<--full name)\n\n' +
' (If that atom belongs to a molecule (or other subunit), make sure that\n' +
' you specified the correct path which leads to it (using / and ..))\n\n' +
g_no_check_msg)
elif ((cat_name == 'bond') and
(tokens[0] not in defined_bonds)):
raise InputError('Error(' + g_program_name + '): ' + usage_location_str + '\n' +
' Reference to undefined $bond:\n\n'
' ' + tokens[0] + ' (<--full name)\n\n' +
' (If that bond belongs to a molecule (or other subunit), make sure that\n' +
' you specified the correct path which leads to it (using / and ..))\n\n' +
g_no_check_msg)
elif ((cat_name == 'angle') and
(tokens[0] not in defined_angles)):
raise InputError('Error(' + g_program_name + '): ' + usage_location_str + '\n' +
' Reference to undefined $angle:\n\n' +
' ' + tokens[0] + ' (<--full name)\n\n' +
' (If that angle belongs to a molecule (or other subunit), make sure that\n' +
' you specified the correct path which leads to it (using / and ..))\n\n' +
g_no_check_msg)
elif ((cat_name == 'dihedral') and
(tokens[0] not in defined_dihedrals)):
raise InputError('Error(' + g_program_name + '): ' + usage_location_str + '\n\n' +
' Reference to undefined $dihedral:\n\n'
' ' + tokens[0] + ' (<--full name)\n\n' +
' (If that dihedral belongs to a molecule (or other subunit), make sure that\n' +
' you specified the correct path which leads to it (using / and ..))\n\n' +
g_no_check_msg)
elif ((cat_name == 'improper') and
(tokens[0] not in defined_impropers)):
raise InputError('Error(' + g_program_name + '): ' + usage_location_str + '\n' +
' Reference to undefined $improper:\n\n'
' ' + tokens[0] + ' (<--full name)\n\n' +
' (If that improper belongs to a molecule (or other subunit), make sure that\n' +
' you specified the correct path which leads to it (using / and ..))\n\n' +
g_no_check_msg)
# I used to generate an error when a users defines a $mol
# variable but does not associate any atoms with it (or if the
# user systematically deletes all the atoms in that molecule),
# but I stopped this practice.
# I don't think there is any real need to complain if some
# molecule id numbers are undefined. LAMMPS does not care.
#
# elif ((cat_name == 'mol') and
# (tokens[0] not in defined_mols)):
# raise InputError('Error('+g_program_name+'): '+usage_location_str+'\n'+
# ' Reference to undefined $mol (molecule-ID) variable:\n\n'
# ' '+tokens[0]+' (<--full name)\n\n'+
# ' (If that molecule is part of a larger molecule, then make sure that\n'+
# ' you specified the correct path which leads to it (using / and ..))\n\n'+
# g_no_check_msg)
f.close()
sys.stderr.write(g_program_name + ': -- No errors detected. --\n')
exit(0)
except (ValueError, InputError) as err:
sys.stderr.write('\n' + str(err) + '\n')
sys.exit(1)
return
if __name__ == '__main__':
main()
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