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Corrected a bug in OPLSAA ("oplsaa.lt") which incorrectly named sever…
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…al angle and dihedral types (@Angle:NB_OA_CR, @Angle:NB_OA_CR, @dihedral:H~_N~_CT_CT).  Those angle and dihedral type names have been restored.  Also: the "oplsaa2lt.py" conversion script has been debugged and cleaned up.  Most users will not be affecgted by this change.
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@jewettaij
jewettaij committed Feb 2, 2025
1 parent a07a385 commit 4d4b105
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173 changes: 109 additions & 64 deletions moltemplate/force_fields/convert_OPLSAA_to_LT/oplsaa2lt.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,8 +17,8 @@
assert version.major > 3 or (version.major == 3 and version.minor >= 7)

__author__ = "Domenico Marson and Andrew Jewett"
__version__ = '1.0.0'
__date__ = '2025-1-31'
__version__ = '1.0.1'
__date__ = '2025-2-01'

g_program_name = __file__.split('/')[-1]

Expand Down Expand Up @@ -168,84 +168,126 @@ def get_dihedrals_and_impropers(input_lines) -> tuple[list[Dihedral], list[Impro
return loaded_dihedrals, loaded_impropers


# NOTE: PROBLEM WITH SAME-TYPES BONDED INTERACTIONS...
# The same dihedral (from atom types POV) can have != parameters, based on comment...
# e.g.:
# 102 0.000 5.500 0.00 0.0 O -C -OH-HO carboxylic acid - aliphatic
# 210 0.000 5.000 0.00 0.0 O -C -OH-HO benzoic acids
# the same problem is observed also for bonds and angles...
def check_uniqueness(
def delete_redundant_duplicates(
interactions: list[Dihedral]|list[Improper]|list[Angle]|list[Bond],
) -> None:
""" OPLSAA files contain many duplicates. Decide which interactions to keep and return the list to the caller."""

##### My apologies for this ugly code. #####
# It wasn't planned that way, but we keep finding
# more special cases that need custom code added.
# PAR and SB files have grown over time and we keep
# finding more redundancy problems that need fixing.

# Step1: Remove duplicate interactions.
# Create a dictionary of all the duplicate interactions
# which share the same atom types and coefficients
# (excluding comments).
typescoeff_to_interaction = defaultdict(dict)
# It wasn't planned that way. The PAR and SB files
# that store OPLSAA parameters have grown messy over time.
# We keep finding more redundancy problems that need fixing.
# That's why this code has so many edge cases.

# ----------- Step 1: ---------------
# Organize interactions according to:
# -atom type strings (a tuple which may include wildcards)
# -force-field parameters (This is called "params" in the code.)
# -the "paramstr" (This is the entire string following the atom type list.
# including the parameters AND comments, if present.)
# The result is stored in a dictionary-of-dictionary-of-dictionaries.
# named "types_to_paraminteractions". Lookup interactions this way:
# types_to_paraminteractions[atomtypes][params][paramstr] --> interaction
#
# Later, during Step2, we will use it to figure out which interactions
# are redundant and can be discarded.
types_to_paraminteractions = {}
for interaction in interactions:
types = tuple(interaction.types)
# Find the text containing the force field parameters ("coeffs")
coeff = interaction.coeff_line
# Typically, this is "angle_coeff @angle:C3_N~_H~ 38. 118.4 # "
# But we only want "38. 118.4 # ".
# Find the text containing the force field parameters ("paramstr")
paramstr = interaction.coeff_line
# Typically, this is "angle_coeff @angle:C3_N~_H~ 38. 118.4 # WJ94"
# But we only want "38. 118.4 # WJ94".
# So we ignore the text before the first two spaces:
ispace1 = coeff.find(" ")
ispace2 = coeff.find(" ", ispace1+1)
ispace1 = paramstr.find(" ")
ispace2 = paramstr.find(" ", ispace1+1)
ispace2 = ispace2+1
coeff = coeff[ispace2:].strip() # eg. "38. 118.4 #"
# Finally, strip off the comment
coeff_no_comment = coeff.lstrip("#").split("#")[0].strip()
# Instead of storing the interaction at (types, coeff_no_comment),
# I store an additional dictionary (whose key is (types, coeff)).
# That way I can keep track of all the different comments that
# were added to this (otherwise identical) interaction.
# We want to keep all of them, but discard the ones that are
# trivially similar to each other.
typescoeff_to_interaction[(types, coeff_no_comment)][(types, coeff)] = interaction
# Copy the the non-redudant entries back into "interactions" again.
i = 0
for coeff_no_comment, coeff_interactions in typescoeff_to_interaction.items():
for typescoeff, interaction in coeff_interactions.items():
# Edge case: We want to ignore interactions if
# they lack a comment and are otherwise identical.
# ...so we also check for (coeff != coeff_no_comment).
coeff = typescoeff[1]
coeff_blank_comment = coeff
i_comment = coeff.find("#")
if i_comment > 0:
coeff_blank_comment = coeff[:i_comment+1]
comment = coeff[i_comment+1:]
if len(coeff_interactions) == 1:
interactions[i] = interaction
i += 1
elif coeff not in (coeff_no_comment, coeff_blank_comment):
# For some reason, a lot of comments only contain ' "'
# We want to skip those too.
if comment.strip() != '"':
interactions[i] = interaction
i += 1

del interactions[i:]
paramstr = paramstr[ispace2:].strip() # eg. "38. 118.4 # WJ94"
# Finally, strip off the comment, leaving only the parameters
params = paramstr.lstrip("#").split("#")[0].strip() # eg. "38. 118.4"
if types not in types_to_paraminteractions:
# Multiple interactions can exist for these same atom types
# differing by either the parameters, or comments, or both.
# Store a dictionary that looks up the interaction between these
# atoms according to their params (without comments).
types_to_paraminteractions[types] = {} # We will use this below

# Create a dictionary that looks up all the interactions
# which share the same types and parameters (.ie params), but may
# have different comments. We might want to delete these duplicates
# later, but for now, we keep track of all of them.
params_to_interactions = types_to_paraminteractions[types]
if params not in params_to_interactions:
params_to_interactions[params] = {}
paramstr_to_interactions = params_to_interactions[params]

# For these interactions, its possible that multiple interactions
# may exist in the file with identical atom types, parameters (coeffs)
# AND comments. To get rid of these trivial duplicates, we store them in
# a dictionary, indexed by the original paramstr (including comments).
paramstr_to_interactions[paramstr] = interaction

# ----------- Step 2: ---------------
# Decide which of these interactions should be discarded.
# (The interactions we want to keep will be stored in
# out_interactions, which will be returned to the caller.)
del interactions[:]
for types, params_to_interactions in types_to_paraminteractions.items():
for params, paramstr_to_interactions in params_to_interactions.items():
for paramstr, interaction in paramstr_to_interactions.items():
discarded = True
paramstr_blank_comment = paramstr
i_comment = paramstr.find("#")
if i_comment > 0:
paramstr_blank_comment = paramstr[:i_comment+1]
comment = paramstr[i_comment+1:]
if len(paramstr_to_interactions) == 1:
interactions.append(interaction)
discarded = False
elif (
paramstr not in (params, paramstr_blank_comment) # case 1
and (comment.strip() != '"') # case 2 (see below)
):
# Edge Case 1:
# We want to ignore interactions if
# they lack a comment but they are otherwise identical.
# ...so we also check to make sure that paramstr != params.
# (and also paramstr != paramstr_blank_comment)
#
# Edge Case 2:
# For some reason, a lot of comments only contain '"'. We
# want to skip those too (since they are otherwise identical)
#
# If none of these edge-cases are true,
# then we don't discard the interaction.
interactions.append(interaction)
discarded = False
# If all of the duplicate interactions are identical except for
# the comments following the params, then throw away these
# duplicates (merge them into a single interaction).
if (len(params_to_interactions) == 1) and (not discarded):
break # skip the remaining duplicates for these atoms


# NOTE: PROBLEM WITH SAME-TYPES BONDED INTERACTIONS...
# The same dihedral (from atom types POV) can have != parameters, based on comment...
# e.g.:
# 102 0.000 5.500 0.00 0.0 O -C -OH-HO carboxylic acid - aliphatic
# 210 0.000 5.000 0.00 0.0 O -C -OH-HO benzoic acids
# the same problem is observed also for bonds and angles...
def count_nonredundant_duplicates(
interactions: list[Dihedral]|list[Improper]|list[Angle]|list[Bond],
) -> None:
for idx, it1 in enumerate(interactions):
for it2 in interactions[idx+1:]:
if it1.types == it2.types:
it1_coeff = it1.coeff_line.lstrip("#").split("#")[0]
it2_coeff = it2.coeff_line.lstrip("#").split("#")[0]
# If we are not skipping this interaction, then
# keep track of the number of duplicate interactions of this type
if it1.duplicate_count == 0:
it1.duplicate_count = 1
it2.duplicate_count = it1.duplicate_count + 1




def sort_duplicates(
interactions: list[Dihedral]|list[Improper]|list[Angle]|list[Bond],
) -> None:
Expand Down Expand Up @@ -335,10 +377,13 @@ def main(argv):
dihedrals, impropers = get_dihedrals_and_impropers(lines_par)


# Now, let's cleanup all the lists of bonded interactions.
# (Remove redundant entries, and sort by atom-type)
for interactions in [bonds, angles, dihedrals, impropers]:
interactions.sort(key=lambda x: x.typename)
interactions.sort(key=lambda x: x.sort_key)
check_uniqueness(interactions)
delete_redundant_duplicates(interactions)
count_nonredundant_duplicates(interactions)
sort_duplicates(interactions)


Expand Down
18 changes: 6 additions & 12 deletions moltemplate/force_fields/oplsaa.lt
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Original file line number Diff line number Diff line change
Expand Up @@ -5731,8 +5731,7 @@ OPLSAA {
angle_coeff @angle:CT_CT_CZ 58.35 112.7 # wlj
angle_coeff @angle:CT_CT_Cl 69. 109.8 # wlj - from MM2
angle_coeff @angle:CT_CT_F~ 50. 109.5 # PAK F-CT-HC (emd 5-09-94)
angle_coeff @angle:CT_CT_HC__2 37.5 110.7 # CHARMM 22 parameter file
angle_coeff @angle:CT_CT_HC__1 37.5 110.7 # CHARMM 22
angle_coeff @angle:CT_CT_HC 37.5 110.7 # CHARMM 22
angle_coeff @angle:CT_CT_I~ 75. 112.0 # wlj
angle_coeff @angle:CT_CT_N2 80.0 111.2 # ARG JCP 76, 1439
angle_coeff @angle:CT_CT_N3 80.0 111.2 # LYS(OL) JCP 76, 1439
Expand Down Expand Up @@ -6296,8 +6295,7 @@ OPLSAA {
angle_coeff @angle:NB_NB_OA 70. 110.0 # JT-R oxatriazoles
angle_coeff @angle:NB_NB_SA 70. 114.0 # JT-R thiatriazole
angle_coeff @angle:NB_NX_CW 56. 113.1 # MKD synonym for NB-NA-CW
angle_coeff @angle:NB_OA_CR__2 70. 101.3 # JT-R oxatriazole
angle_coeff @angle:NB_OA_CR__1 70. 101.3 # JT-R oxatriazoles
angle_coeff @angle:NB_OA_CR 70. 101.3 # JT-R oxatriazoles
angle_coeff @angle:NB_OA_NB 70. 103.4 # JT-R oxatriazole
angle_coeff @angle:NB_OS_CR 70. 101.3 # JT-R oxatriazoles
angle_coeff @angle:NB_OS_DM 10.0 125. # wlj
Expand Down Expand Up @@ -7166,8 +7164,7 @@ OPLSAA {
@angle:CT_CT_CZ @atom:*_b*_aCT*_d*_i* @atom:*_b*_aCT*_d*_i* @atom:*_b*_aCZ*_d*_i*
@angle:CT_CT_Cl @atom:*_b*_aCT*_d*_i* @atom:*_b*_aCT*_d*_i* @atom:*_b*_aCl*_d*_i*
@angle:CT_CT_F~ @atom:*_b*_aCT*_d*_i* @atom:*_b*_aCT*_d*_i* @atom:*_b*_aF~*_d*_i*
@angle:CT_CT_HC__2 @atom:*_b*_aCT*_d*_i* @atom:*_b*_aCT*_d*_i* @atom:*_b*_aHC*_d*_i*
@angle:CT_CT_HC__1 @atom:*_b*_aCT*_d*_i* @atom:*_b*_aCT*_d*_i* @atom:*_b*_aHC*_d*_i*
@angle:CT_CT_HC @atom:*_b*_aCT*_d*_i* @atom:*_b*_aCT*_d*_i* @atom:*_b*_aHC*_d*_i*
@angle:CT_CT_I~ @atom:*_b*_aCT*_d*_i* @atom:*_b*_aCT*_d*_i* @atom:*_b*_aI~*_d*_i*
@angle:CT_CT_N2 @atom:*_b*_aCT*_d*_i* @atom:*_b*_aCT*_d*_i* @atom:*_b*_aN2*_d*_i*
@angle:CT_CT_N3 @atom:*_b*_aCT*_d*_i* @atom:*_b*_aCT*_d*_i* @atom:*_b*_aN3*_d*_i*
Expand Down Expand Up @@ -7731,8 +7728,7 @@ OPLSAA {
@angle:NB_NB_OA @atom:*_b*_aNB*_d*_i* @atom:*_b*_aNB*_d*_i* @atom:*_b*_aOA*_d*_i*
@angle:NB_NB_SA @atom:*_b*_aNB*_d*_i* @atom:*_b*_aNB*_d*_i* @atom:*_b*_aSA*_d*_i*
@angle:NB_NX_CW @atom:*_b*_aNB*_d*_i* @atom:*_b*_aNX*_d*_i* @atom:*_b*_aCW*_d*_i*
@angle:NB_OA_CR__2 @atom:*_b*_aNB*_d*_i* @atom:*_b*_aOA*_d*_i* @atom:*_b*_aCR*_d*_i*
@angle:NB_OA_CR__1 @atom:*_b*_aNB*_d*_i* @atom:*_b*_aOA*_d*_i* @atom:*_b*_aCR*_d*_i*
@angle:NB_OA_CR @atom:*_b*_aNB*_d*_i* @atom:*_b*_aOA*_d*_i* @atom:*_b*_aCR*_d*_i*
@angle:NB_OA_NB @atom:*_b*_aNB*_d*_i* @atom:*_b*_aOA*_d*_i* @atom:*_b*_aNB*_d*_i*
@angle:NB_OS_CR @atom:*_b*_aNB*_d*_i* @atom:*_b*_aOS*_d*_i* @atom:*_b*_aCR*_d*_i*
@angle:NB_OS_DM @atom:*_b*_aNB*_d*_i* @atom:*_b*_aOS*_d*_i* @atom:*_b*_aDM*_d*_i*
Expand Down Expand Up @@ -8915,8 +8911,7 @@ OPLSAA {
dihedral_coeff @dihedral:H~_NT_NT_H~ 0.0 0.0 0.3 0.0 # generic
dihedral_coeff @dihedral:H~_NT_OH_HO 0.0 0.0 0.3 0.0 # generic
dihedral_coeff @dihedral:H~_NT_OS_CT 0.0 0.0 0.3 0.0 # generic
dihedral_coeff @dihedral:H~_N~_CT_CT__2 0.000 0.000 0.000 0.0 # N-ethylformamide
dihedral_coeff @dihedral:H~_N~_CT_CT__1 0.000 0.000 0.000 0.0 # peptides
dihedral_coeff @dihedral:H~_N~_CT_CT 0.000 0.000 0.000 0.0 # peptides
dihedral_coeff @dihedral:H~_N~_CT_C~ 0.000 0.000 0.000 0.0 # peptides
dihedral_coeff @dihedral:H~_N~_C~_C~ 0.000 4.900 0.000 0.0 # dicarbonyls "
dihedral_coeff @dihedral:H~_N~_OH_HO 2.722 -5.154 0.000 0.0 # hydroxamic acids
Expand Down Expand Up @@ -10114,8 +10109,7 @@ OPLSAA {
@dihedral:H~_NT_NT_H~ @atom:*_b*_a*_dH~*_i* @atom:*_b*_a*_dNT*_i* @atom:*_b*_a*_dNT*_i* @atom:*_b*_a*_dH~*_i*
@dihedral:H~_NT_OH_HO @atom:*_b*_a*_dH~*_i* @atom:*_b*_a*_dNT*_i* @atom:*_b*_a*_dOH*_i* @atom:*_b*_a*_dHO*_i*
@dihedral:H~_NT_OS_CT @atom:*_b*_a*_dH~*_i* @atom:*_b*_a*_dNT*_i* @atom:*_b*_a*_dOS*_i* @atom:*_b*_a*_dCT*_i*
@dihedral:H~_N~_CT_CT__2 @atom:*_b*_a*_dH~*_i* @atom:*_b*_a*_dN~*_i* @atom:*_b*_a*_dCT*_i* @atom:*_b*_a*_dCT*_i*
@dihedral:H~_N~_CT_CT__1 @atom:*_b*_a*_dH~*_i* @atom:*_b*_a*_dN~*_i* @atom:*_b*_a*_dCT*_i* @atom:*_b*_a*_dCT*_i*
@dihedral:H~_N~_CT_CT @atom:*_b*_a*_dH~*_i* @atom:*_b*_a*_dN~*_i* @atom:*_b*_a*_dCT*_i* @atom:*_b*_a*_dCT*_i*
@dihedral:H~_N~_CT_C~ @atom:*_b*_a*_dH~*_i* @atom:*_b*_a*_dN~*_i* @atom:*_b*_a*_dCT*_i* @atom:*_b*_a*_dC~*_i*
@dihedral:H~_N~_C~_C~ @atom:*_b*_a*_dH~*_i* @atom:*_b*_a*_dN~*_i* @atom:*_b*_a*_dC~*_i* @atom:*_b*_a*_dC~*_i*
@dihedral:H~_N~_OH_HO @atom:*_b*_a*_dH~*_i* @atom:*_b*_a*_dN~*_i* @atom:*_b*_a*_dOH*_i* @atom:*_b*_a*_dHO*_i*
Expand Down
4 changes: 2 additions & 2 deletions moltemplate/scripts/moltemplate.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -6,8 +6,8 @@
# Copyright (c) 2013

G_PROGRAM_NAME="moltemplate.sh"
G_VERSION="2.22.1"
G_DATE="2025-1-31"
G_VERSION="2.22.2"
G_DATE="2025-2-01"

echo "${G_PROGRAM_NAME} v${G_VERSION} ${G_DATE}" >&2
echo "" >&2
Expand Down
4 changes: 2 additions & 2 deletions setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -45,9 +45,9 @@

url='https://github.com/jewettaij/moltemplate',

download_url='https://github.com/jewettaij/moltemplate/archive/v2.22.1.zip',
download_url='https://github.com/jewettaij/moltemplate/archive/v2.22.2.zip',

version='2.22.1',
version='2.22.2',

keywords=['simulation', 'LAMMPS', 'molecule editor', 'molecule builder',
'ESPResSo'],
Expand Down

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