def LookupChargePairs(chargebyatomid,
# bond_ids,
# bond_types,
# bond_pairs,
lines_atoms,
lines_bonds,
lines_bond_list,
lines_chargebybond,
atom_style,
section_name,
prefix='',
suffix=''):
# bond_ids_offset=0):
# report_progress = False):
"""
LookupChargePairs() looks up partial-charge pair contributions from the
types of atoms participating in a bond.
Output:
...It looks up the corresponding change in the partial charges for
each pair of atoms and stores this in the "chargebyatomid" dictionary.
Input (continued):
This function requires:
...a list of bonded pairs of atoms
stored in the lines_bonds variable (from the "Data Bond List"
or "Data Bonds AtomId AtomId" sections)
...and a list of atom types
stored in the lines_atoms variable (from the "Data Atoms" section)
...and a list of charge-pairs-as-a-function-of-atom-types
stored in the lines_chargebybond (from the "Data Bonds By Type" section)
"""
column_names = AtomStyle2ColNames(atom_style)
i_atomid, i_atomtype, i_molid = ColNames2AidAtypeMolid(column_names)
atomids = []
atomtypes = []
atomids2types = {}
for iv in range(0, len(lines_atoms)):
line = lines_atoms[iv].strip()
if '#' in line:
icomment = line.find('#')
line = (line[:icomment]).strip()
if len(line) > 0:
tokens = ttree_lex.SplitQuotedString(line)
if ((len(tokens) <= i_atomid) or (len(tokens) <= i_atomtype)):
sys.stderr.write("\"" + line + "\"\n")
raise(ttree_lex.InputError(
'Error not enough columns on line ' + str(iv + 1) + ' of \"Atoms\" section.'))
tokens = ttree_lex.SplitQuotedString(line)
atomid = ttree_lex.EscCharStrToChar(tokens[i_atomid])
atomids.append(atomid)
atomtype = ttree_lex.EscCharStrToChar(tokens[i_atomtype])
atomtypes.append(atomtype)
atomids2types[atomid] = atomtype
#assert(isinstance(bond_ids, list))
#assert(isinstance(bond_types, list))
#assert(isinstance(bond_pairs, list))
#del bond_ids[:]
#del bond_types[:]
#del bond_pairs[:]
bond_pairs = []
for ie in range(0, len(lines_bond_list)):
line = lines_bond_list[ie].strip()
if '#' in line:
icomment = line.find('#')
line = (line[:icomment]).strip()
if len(line) == 0:
continue
tokens = ttree_lex.SplitQuotedString(line)
if len(tokens) == 3:
# bond_ids.append(ttree_lex.EscCharStrToChar(tokens[0]))
bond_pairs.append((ttree_lex.EscCharStrToChar(tokens[1]),
ttree_lex.EscCharStrToChar(tokens[2])))
else:
raise(ttree_lex.InputError('Incorrect number of columns on line ' +
str(ie + 1) + ' of \"' + section_name + '\" section.'))
for ie in range(0, len(lines_bonds)):
line = lines_bonds[ie].strip()
if '#' in line:
icomment = line.find('#')
line = (line[:icomment]).strip()
if len(line) == 0:
continue
tokens = ttree_lex.SplitQuotedString(line)
if len(tokens) == 4:
# bond_ids.append(ttree_lex.EscCharStrToChar(tokens[0]))
# bond_types.append(ttree_lex.EscCharStrToChar(tokens[1]))
bond_pairs.append((ttree_lex.EscCharStrToChar(tokens[2]),
ttree_lex.EscCharStrToChar(tokens[3])))
else:
raise(ttree_lex.InputError('Incorrect number of columns on line ' +
str(ie + 1) + ' of \"' + section_name + '\" section.'))
# for ie in range(0, len(lines_bonds_atomid_atomid)):
# line = lines_bonds_atomid_atomid[ie].strip()
# if '#' in line:
# icomment = line.find('#')
# line = (line[:icomment]).strip()
# if len(line) == 0:
# continue
# tokens = ttree_lex.SplitQuotedString(line)
# if len(tokens) == 2:
# #bondid_n = bond_ids_offset + len(bond_ids) + 1
# #bond_ids.append(prefix+str(bondid_n)+suffix)
# bond_pairs.append( (ttree_lex.EscCharStrToChar(tokens[0]),
# ttree_lex.EscCharStrToChar(tokens[1])) )
# else:
# raise(ttree_lex.InputError('Incorrect number of columns on line '+str(ie+1)+' of \"'+section_name+'\" section.'))
#assert(len(bond_types) == 0)
typepattern_to_chargepairs = []
warning_unassigned_chargepairs = None
for i in range(0, len(lines_chargebybond)):
line = lines_chargebybond[i].strip()
if '#' in line:
icomment = line.find('#')
line = (line[:icomment]).strip()
if len(line) > 0:
tokens = ttree_lex.SplitQuotedString(line)
if (len(tokens) != 4):
raise(ttree_lex.InputError('Error: Wrong number of columns in the \"Charge Pairs By Type\" section of data file.\n'
'Offending line:\n' +
'\"' + line + '\"\n'
'Expected 4 columns\n'))
chargepair = (float(tokens[2]),
float(tokens[3]))
typepattern = []
for typestr in tokens[:2]:
if ttree_lex.HasRE(typestr):
regex_str = typestr[3:]
typepattern.append(re.compile(regex_str))
else:
typepattern.append(ttree_lex.EscCharStrToChar(typestr))
typepattern_to_chargepairs.append([typepattern, chargepair])
for atomid1, atomid2 in bond_pairs:
if atomid1 not in atomids2types:
raise ttree_lex.InputError('Error: atom \"' + atomid1 + '\" not defined in \"Data Atoms\".\n'
' This usually happens when the user mistypes one of the names of the\n'
' $atoms in either a \"Data Atoms\" or \"Data Bond List\" section.\n'
' To find out where the mistake occured, search the \n'
' \"ttree_assignments.txt\" file for:\n'
' \"' + atomid1 + '\"\n')
if atomid2 not in atomids2types:
raise ttree_lex.InputError('Error: atom \"' + atomid2 + '\" not defined in \"Data Atoms\".\n'
' This usually happens when the user mistypes one of the names of the\n'
' $atoms in either a \"Data Atoms\" or \"Data Bond List\" section.\n'
' To find out where the mistake occured, search the \n'
' \"ttree_assignments.txt\" file for:\n'
' \"' + atomid2 + '\"\n')
atomtype1 = atomids2types[atomid1]
atomtype2 = atomids2types[atomid2]
found = False
for typepattern, chargepair in typepattern_to_chargepairs:
# use string comparisons to check if atom types match the pattern
if ttree_lex.MatchesAll((atomtype1, atomtype2), typepattern):
# ("MatchesAll()" defined in "ttree_lex.py")
chargebyatomid[atomid1] += chargepair[0]
chargebyatomid[atomid2] += chargepair[1]
found = True
elif ttree_lex.MatchesAll((atomtype2, atomtype1), typepattern):
chargebyatomid[atomid1] += chargepair[1]
chargebyatomid[atomid2] += chargepair[0]
found = True
if (not found) and (not warning_unassigned_chargepairs):
warning_unassigned_chargepairs = (atomid1, atomid2)
if warning_unassigned_chargepairs:
sys.stderr.write('---------------------------------------------------------------------------\n'
'Warning: bonds found between atoms with no partial-charge rules.\n'
' This means that somewhere you are using a force-field\n'
' which assigns atomic charge according to the bonds these atoms\n'
' participate in, AND at least one pair of bonded atoms does NOT have\n'
' a rule defined to assign charges to that pair of atoms.\n'
' This can happen if there is a problem with the force-field file\n'
' OR if you are defining the charges for these atoms manually\n'
' In the later case, it is not a problem.\n'
' The first bond with this problem is between this pair of atoms:\n'
' ' +
str(warning_unassigned_chargepairs[0]) + '\n'
' ' +
str(warning_unassigned_chargepairs[1]) + '\n'
'---------------------------------------------------------------------------\n')
def LookupBondTypes(bond_types,
bond_ids,
bond_pairs,
lines_atoms,
lines_bonds,
lines_bondsbytype,
atom_style,
section_name,
prefix='',
suffix='',
bond_ids_offset=0):
#report_progress = False):
"""
LookupBondTypes() looks up bond types.
Output:
...It looks up the corresponding type of each bond and store it in the
"bond_types" list. (If the bond_ids were not specified by the user,
generate them and store them in the bond_ids list.)
Input (continued):
This function requires:
...a list of bonded pairs of atoms
stored in the lines_bonds variable (from the "Data Bond List"
or "Data Bonds AtomId AtomId" sections)
...and a list of atom types
stored in the lines_atoms variable (from the "Data Atoms" section)
...and a list of bond-types-as-a-function-of-atom-types
stored in the lines_bondsbytype (from the "Data Bonds By Type" section)
Generated bond_ids (if applicable) are of the form
prefix + str(number) + suffix
(where "number" begins at bond_ids_offset+1)
"""
column_names = AtomStyle2ColNames(atom_style)
i_atomid, i_atomtype, i_molid = ColNames2AidAtypeMolid(column_names)
atomids = []
atomtypes = []
atomids2types = {}
for iv in range(0, len(lines_atoms)):
line = lines_atoms[iv].strip()
if '#' in line:
icomment = line.find('#')
line = (line[:icomment]).strip()
if len(line) > 0:
tokens = ttree_lex.SplitQuotedString(line)
if ((len(tokens) <= i_atomid) or (len(tokens) <= i_atomtype)):
sys.stderr.write("\""+line+"\"\n")
raise(ttree_lex.InputError('Error not enough columns on line '+str(iv+1)+' of \"Atoms\" section.'))
tokens = ttree_lex.SplitQuotedString(line)
atomid = ttree_lex.EscCharStrToChar(tokens[i_atomid])
atomids.append(atomid)
atomtype = ttree_lex.EscCharStrToChar(tokens[i_atomtype])
atomtypes.append(atomtype)
atomids2types[atomid] = atomtype
assert(isinstance(bond_ids, list))
assert(isinstance(bond_types, list))
assert(isinstance(bond_pairs, list))
del bond_ids[:]
del bond_types[:]
del bond_pairs[:]
for ie in range(0, len(lines_bonds)):
line = lines_bonds[ie].strip()
if '#' in line:
icomment = line.find('#')
line = (line[:icomment]).strip()
if len(line) == 0:
continue
tokens = ttree_lex.SplitQuotedString(line)
if section_name == "Data Bonds AtomId AtomId":
if len(tokens) == 2:
bondid_n = bond_ids_offset + len(bond_ids) + 1
bond_ids.append(prefix+str(bondid_n)+suffix)
bond_pairs.append( (ttree_lex.EscCharStrToChar(tokens[0]),
ttree_lex.EscCharStrToChar(tokens[1])) )
else:
raise(ttree_lex.InputError('Incorrect number of columns on line '+str(ie+1)+' of \"'+section_name+'\" section.'))
elif section_name == "Data Bond List":
if len(tokens) == 3:
bond_ids.append(ttree_lex.EscCharStrToChar(tokens[0]))
bond_pairs.append( (ttree_lex.EscCharStrToChar(tokens[1]),
ttree_lex.EscCharStrToChar(tokens[2])) )
else:
raise(ttree_lex.InputError('Incorrect number of columns on line '+str(ie+1)+' of \"'+section_name+'\" section.'))
else:
raise(ttree_lex.InputError('Internal Error ('+g_program_name+'): Unknown section name: \"'+section_name+'\"'))
assert(len(bond_types) == 0)
typepattern_to_coefftypes = []
for i in range(0, len(lines_bondsbytype)):
line = lines_bondsbytype[i].strip()
if '#' in line:
icomment = line.find('#')
line = (line[:icomment]).strip()
if len(line) > 0:
tokens = ttree_lex.SplitQuotedString(line)
if (len(tokens) != 3):
raise(ttree_lex.InputError('Error: Wrong number of columns in the \"Bonds By Type\" section of data file.\n'
'Offending line:\n'+
'\"'+line+'\"\n'
'Expected 3 columns\n'))
coefftype = ttree_lex.EscCharStrToChar(tokens[0])
typepattern = []
for typestr in tokens[1:]:
if ((len(typestr) >= 2) and
(typestr[0] == '/') and (typestr[-1] == '/')):
regex_str = typestr[1:-1]
typepattern.append( re.compile(regex_str) )
else:
typepattern.append(ttree_lex.EscCharStrToChar(typestr))
typepattern_to_coefftypes.append([typepattern, coefftype])
assert(len(bond_ids) == len(bond_pairs))
for ie in range(0,len(bond_ids)):
bond_types.append(None)
for ie in range(0, len(bond_ids)):
bondid = bond_ids[ie]
(atomid1, atomid2) = bond_pairs[ie]
if atomid1 not in atomids2types:
raise ttree_lex.InputError('Error: atom \"'+atomid1+'\" not defined in \"Data Atoms\".\n'
' This usually happens when the user mistypes one of the names of the\n'
' $atoms in either a \"Data Atoms\" or \"Data Bond List\" section.\n'
' To find out where the mistake occured, search the \n'
' \"ttree_assignments.txt\" file for:\n'
' \"'+atomid1+'\"\n')
if atomid2 not in atomids2types:
raise ttree_lex.InputError('Error: atom \"'+atomid2+'\" not defined in \"Data Atoms\".\n'
' This usually happens when the user mistypes one of the names of the\n'
' $atoms in either a \"Data Atoms\" or \"Data Bond List\" section.\n'
' To find out where the mistake occured, search the \n'
' \"ttree_assignments.txt\" file for:\n'
' \"'+atomid2+'\"\n')
atomtype1 = atomids2types[atomid1]
atomtype2 = atomids2types[atomid2]
for typepattern, coefftype in typepattern_to_coefftypes:
# use string comparisons to check if atom types match the pattern
if (ttree_lex.MatchesAll((atomtype1, atomtype2), typepattern) or
ttree_lex.MatchesAll((atomtype2, atomtype1), typepattern)):
# ("MatchesAll()" defined in "ttree_lex.py")
bond_types[ie] = coefftype
for ie in range(0, len(bond_ids)):
if not bond_types[ie]:
(atomid1, atomid2) = bond_pairs[ie]
atomtype1 = atomids2types[atomid1]
atomtype2 = atomids2types[atomid2]
raise ttree_lex.InputError('Error: No bond types defined for the bond between\n'
' atoms '+atomid1+' (type '+atomtype1+')\n'
' and '+atomid2+' (type '+atomtype2+')\n')