class PbamAutoParser:
"""ELEC pbam-auto specific tokens/grammars."""
# https://apbs.readthedocs.io/en/latest/using/input/elec/pbam-auto.html
keyword = CLiteral("pbam-auto") | CLiteral("pbam")
# .setParseAction(GenericToken.check_depricated)
grammar = (keyword
& ZeroOrMore(ElecToken.name)
& ZeroOrMore(PbToken.thr3dmap)
& ZeroOrMore(PbToken.diff)
& ZeroOrMore(PbToken.dx)
& ZeroOrMore(PbToken.grid2d)
& ZeroOrMore(PbToken.gridpts)
& ZeroOrMore(GenericToken.mol)
& ZeroOrMore(PbToken.ntraj)
& ZeroOrMore(PbToken.pbc)
& ZeroOrMore(ElecToken.pdie)
& ZeroOrMore(PbToken.randorient)
& ZeroOrMore(PbToken.runname)
& ZeroOrMore(PbToken.runtype)
& ZeroOrMore(PbToken.salt)
& ZeroOrMore(ElecToken.sdie)
& ZeroOrMore(GenericToken.temp)
& ZeroOrMore(PbToken.term)
& ZeroOrMore(PbToken.termcombine)
& ZeroOrMore(PbToken.units)
& ZeroOrMore(PbToken.xyz))
class MgManualParser:
"""ELEC mg-manual specific tokens/grammars."""
# https://apbs.readthedocs.io/en/latest/using/input/elec/mg-manual.html
integer_val = ApbsLegacyInput.get_integer_grammar()
nlev = Group(CLiteral("nlev") - integer_val)
grammar = (CLiteral("mg-manual")
& ZeroOrMore(ElecToken.name)
& ZeroOrMore(ElecToken.bcfl)
& ZeroOrMore(GenericToken.calcenergy)
& ZeroOrMore(GenericToken.calcforce)
& ZeroOrMore(ElecToken.chgm)
& ZeroOrMore(ElecToken.dime)
& ZeroOrMore(ElecToken.etol)
& ZeroOrMore(ElecToken.gcent)
& ZeroOrMore(ElecToken.glen)
& ZeroOrMore(GenericToken.grid)
& ZeroOrMore(ElecToken.ion)
& ZeroOrMore(ElecToken.pbe)
& ZeroOrMore(GenericToken.mol)
& ZeroOrMore(nlev)
& ZeroOrMore(ElecToken.pdie)
& ZeroOrMore(GenericToken.sdens)
& ZeroOrMore(ElecToken.sdie)
& ZeroOrMore(GenericToken.srad)
& ZeroOrMore(ElecToken.srfm)
& ZeroOrMore(GenericToken.swin)
& ZeroOrMore(GenericToken.temp)
& ZeroOrMore(ElecToken.usemap)
& ZeroOrMore(ElecToken.write)
& ZeroOrMore(ElecToken.writemat))
def apolar_parser(self):
"""Setup the tokens and grammar for the APOLAR section.
:return: a dictionary containing the APOLAR section of the input file
:rtype: dict
"""
grammar = (ZeroOrMore(ElecToken.name)
& ZeroOrMore(GenericToken.bconc)
& ZeroOrMore(GenericToken.calcenergy)
& ZeroOrMore(GenericToken.calcforce)
& ZeroOrMore(ApolarToken.dpos)
& ZeroOrMore(GenericToken.gamma)
& ZeroOrMore(GenericToken.grid)
& ZeroOrMore(GenericToken.mol)
& ZeroOrMore(ApolarToken.press)
& ZeroOrMore(GenericToken.sdens)
& ZeroOrMore(GenericToken.srad)
& ZeroOrMore(ApolarToken.srfm)
& ZeroOrMore(GenericToken.swin)
& ZeroOrMore(GenericToken.temp))
def format_apolar(results: ParseResults):
return self.format_section(results, "APOLAR")
return Group(
Suppress(CLiteral("APOLAR")) - grammar -
Suppress(CLiteral("END"))).setParseAction(format_apolar)
class GeoflowAutoParser:
"""ELEC geoflow-auto specific tokens/grammars."""
# https://apbs.readthedocs.io/en/latest/using/input/elec/geoflow-auto.html
number_val = ApbsLegacyInput.get_number_grammar()
press = Group(CLiteral("press") - number_val)
vdwdisp = Group(CLiteral("vdwdisp") - oneOf("0 1"))
keyword = CLiteral("geoflow-auto") | CLiteral("geoflow")
# .setParseAction(GenericToken.check_depricated)
grammar = (
keyword
& ZeroOrMore(ElecToken.name)
& ZeroOrMore(ElecToken.bcfl)
& ZeroOrMore(GenericToken.bconc)
& ZeroOrMore(ElecToken.etol)
& ZeroOrMore(GenericToken.gamma)
& ZeroOrMore(GenericToken.grid
) # . setParseAction(GenericToken.check_depricated)
& ZeroOrMore(ElecToken.pbe)
& ZeroOrMore(GenericToken.mol)
& ZeroOrMore(ElecToken.pdie)
& ZeroOrMore(press)
& ZeroOrMore(ElecToken.sdie)
& ZeroOrMore(vdwdisp))
def elec_parser(self):
"""Setup the tokens and grammar for the ELEC section.
:return: a dictionary containing the APOLAR section of the input file
:rtype: dict
"""
grammar = (
TabiParser.grammar
| FeManualParser.grammar
| GeoflowAutoParser.grammar
| MgAutoParser.grammar
| MgManualParser.grammar
| MgParaParser.grammar
| MgDummyParser.grammar
| PbamAutoParser.grammar
| PbsamAutoParser.grammar
| PygbeParser.grammar
)
def format_elec(results: ParseResults):
return self.format_section(results, "ELEC")
return Group(
Suppress(CLiteral("ELEC")) - grammar - Suppress(CLiteral("END"))
).setParseAction(format_elec)
def print_parser(self):
"""Setup the tokens and grammar for the PRINT section."""
identifier = ApbsLegacyInput.get_identifier_grammar()
# tokens/grammars:
choices = oneOf("elecEnergy elecForce apolEnergy apolForce",
caseless=True)
expr = identifier + Optional(
OneOrMore(oneOf("+ -") + identifier) +
ZeroOrMore(oneOf("+ -") + identifier))
grammar = Group(choices - expr)
def format_print(results: ParseResults):
"""Format the PRINT section of the APBS input file.
:param results ParseResults: pyparsing results of matching grammar
:return: a dictionary of the PRINT section of the input file
:rtype: dict
Example: Convert the following:
print elecEnergy complex - mol2 - mol1 end
To:
'PRINT': {0: {
'elecenergy':
['complex', '-', 'mol2', '-', 'mol1']
}
}
"""
section = "PRINT"
if section not in self.final_output:
self.final_output[section] = {}
idx = len(self.final_output[section])
self.final_output[section][idx] = {}
for row in results[0]:
LOGGER.debug("TYPE: %s", type(row))
for item in row:
LOGGER.debug("type item: %s, item: %s", type(item), item)
if isinstance(item, str):
key = item.lower()
LOGGER.debug("key: %s", key)
if key not in self.final_output[section][idx].keys():
self.final_output[section][idx][key] = row[1:]
break
else:
# NOTE: UGLY but this is how to break out of the inner and
# outer loop as documented at:
# https://note.nkmk.me/en/python-break-nested-loops
break
break
return self.final_output
value = Group(
Suppress(CLiteral("PRINT")) - grammar -
Suppress(CLiteral("END"))).setParseAction(format_print)
return value
class ApolarToken:
"""APOLAR specific tokens/grammars that can be used by other classes."""
# https://apbs.readthedocs.io/en/latest/using/input/apolar/index.html
number_val = ApbsLegacyInput.get_number_grammar()
dpos = Group(CLiteral("dpos") - number_val)
press = Group(CLiteral("press") - number_val)
srfm = Group(CLiteral("srfm") - oneOf("sacc", caseless=True))
class FeManualParser:
"""ELEC fe-manual specific tokens/grammars."""
# https://apbs.readthedocs.io/en/latest/using/input/elec/fe-manual.html
identifier = ApbsLegacyInput.get_identifier_grammar()
integer_val = ApbsLegacyInput.get_integer_grammar()
number_val = ApbsLegacyInput.get_number_grammar()
akeyPRE_options = oneOf("unif geom", caseless=True)
akeyPRE = Group(CLiteral("akeyPRE") - akeyPRE_options)
akeySOLVE_options = oneOf("resi", caseless=True)
akeySOLVE = Group(CLiteral("akeySOLVE") - akeySOLVE_options)
domainLength = Group(CLiteral("domainLength") - ElecToken.grid_floats)
ekey_options = oneOf("simp glob global frac", caseless=True)
ekey = Group(CLiteral("ekey") - ekey_options).setParseAction(
GenericToken.check_depricated
)
maxsolve = Group(CLiteral("maxsolve") - number_val)
maxvert = Group(CLiteral("maxvert") - number_val)
targetNum = Group(CLiteral("targetNum") - integer_val)
targetRes = Group(CLiteral("targetRes") - number_val)
usemesh = Group(CLiteral("usemesh") - identifier)
grammar = (
CLiteral("fe-manual")
& ZeroOrMore(ElecToken.name)
& ZeroOrMore(akeyPRE)
& ZeroOrMore(akeySOLVE)
& ZeroOrMore(ElecToken.async_value)
& ZeroOrMore(ElecToken.bcfl)
& ZeroOrMore(GenericToken.calcenergy)
& ZeroOrMore(GenericToken.calcforce)
& ZeroOrMore(ElecToken.chgm)
& ZeroOrMore(domainLength)
& ZeroOrMore(ekey)
& ZeroOrMore(ElecToken.etol)
& ZeroOrMore(ElecToken.ion)
& ZeroOrMore(ElecToken.pbe)
& ZeroOrMore(maxsolve)
& ZeroOrMore(maxvert)
& ZeroOrMore(GenericToken.mol)
& ZeroOrMore(ElecToken.pdie)
& ZeroOrMore(GenericToken.sdens)
& ZeroOrMore(ElecToken.sdie)
& ZeroOrMore(GenericToken.srad)
& ZeroOrMore(ElecToken.srfm)
& ZeroOrMore(GenericToken.swin)
& ZeroOrMore(targetNum)
& ZeroOrMore(targetRes)
& ZeroOrMore(GenericToken.temp)
& ZeroOrMore(ElecToken.usemap)
& ZeroOrMore(usemesh)
& ZeroOrMore(ElecToken.write)
)
def __init__(self):
"""Setup parsing tokens and grammar for the APBS input file format."""
# The FINAL_OUTPUT is a dictionary produced after parsing a file
# using the grammar and processing rules.
self.final_output = {}
# The highest level grammar to parse the READ, ELEC, APOLAR, and
# PRINT sections until the QUIT keyword is found.
self.grammar = OneOrMore(self.read_parser()) + OneOrMore(
self.apolar_parser() | self.elec_parser()
) + ZeroOrMore(self.print_parser()) + Suppress(CLiteral("QUIT")) | (
# The following is one way to "narrow down" errors in an input
# file. It was adopted from:
# https://web.archive.org/web/20160821175151/http://pyparsing.wikispaces.com/share/view/30875955
# The idea is that the parsers above will succeed or the
# following will succeed and set the ParseSyntaxException
# stating that the token in the file is "unknown" and will
# show the line and column where the parser stopped. It does
# not always point out subtle errors like when a key is used
# in a section that does not support it. For example, using
# a keyword from pbam-auto in an ELEC section that specifies
# using tabi-auto type.
empty
- ~Word(printables).setName("<unknown>")
)
class MgAutoParser:
"""ELEC mg-auto specific tokens/grammars."""
# https://apbs.readthedocs.io/en/latest/using/input/elec/mg-auto.html
grammar = (CLiteral("mg-auto")
& ZeroOrMore(ElecToken.name)
& ZeroOrMore(ElecToken.bcfl)
& ZeroOrMore(GenericToken.calcenergy)
& ZeroOrMore(GenericToken.calcforce)
& ZeroOrMore(ElecToken.cgcent)
& ZeroOrMore(ElecToken.cglen)
& ZeroOrMore(ElecToken.chgm)
& ZeroOrMore(ElecToken.dime)
& ZeroOrMore(ElecToken.etol)
& ZeroOrMore(ElecToken.fgcent)
& ZeroOrMore(ElecToken.fglen)
& ZeroOrMore(ElecToken.ion)
& ZeroOrMore(ElecToken.pbe)
& ZeroOrMore(GenericToken.mol)
& ZeroOrMore(ElecToken.pdie)
& ZeroOrMore(GenericToken.sdens)
& ZeroOrMore(ElecToken.sdie)
& ZeroOrMore(GenericToken.srad)
& ZeroOrMore(ElecToken.srfm)
& ZeroOrMore(GenericToken.swin)
& ZeroOrMore(GenericToken.temp)
& ZeroOrMore(ElecToken.usemap)
& ZeroOrMore(ElecToken.write)
& ZeroOrMore(ElecToken.writemat))
class MgDummyParser:
"""ELEC mg-dummy specific tokens/grammars."""
# https://apbs.readthedocs.io/en/latest/using/input/elec/mg-dummy.html
grammar = (
CLiteral("mg-dummy")
& ZeroOrMore(ElecToken.name)
& ZeroOrMore(ElecToken.bcfl)
& ZeroOrMore(GenericToken.calcenergy
) # .setParseAction(GenericToken.check_depricated)
& ZeroOrMore(GenericToken.calcforce
) # .setParseAction(GenericToken.check_depricated)
& ZeroOrMore(ElecToken.chgm)
& ZeroOrMore(ElecToken.dime)
& ZeroOrMore(ElecToken.gcent)
& ZeroOrMore(ElecToken.glen)
& ZeroOrMore(GenericToken.grid)
& ZeroOrMore(ElecToken.ion)
& ZeroOrMore(
ElecToken.nlev) # .setParseAction(GenericToken.check_depricated)
& ZeroOrMore(ElecToken.pbe)
& ZeroOrMore(GenericToken.mol)
& ZeroOrMore(ElecToken.pdie)
& ZeroOrMore(GenericToken.sdens)
& ZeroOrMore(ElecToken.sdie)
& ZeroOrMore(GenericToken.srad)
& ZeroOrMore(ElecToken.srfm)
& ZeroOrMore(GenericToken.swin)
& ZeroOrMore(GenericToken.temp)
& ZeroOrMore(ElecToken.write))
def read_parser(self):
"""Setup the tokens and grammar for the READ section."""
# https://apbs.readthedocs.io/en/latest/using/input/read.html
path_val = ApbsLegacyInput.get_path_grammar()
# tokens/grammars:
file_fmt = oneOf("dx gz", caseless=True)
charge = Group(CLiteral("charge") - file_fmt - path_val)
diel = Group(
CLiteral("diel") - file_fmt - path_val - path_val - path_val
)
kappa = Group(CLiteral("kappa") - file_fmt - path_val)
mesh = Group(CLiteral("mesh") - CLiteral("mcsf") - path_val)
mol_format = oneOf("pqr pdb", caseless=True)
mol = Group(CLiteral("mol") - mol_format - path_val)
parm_format = oneOf("flat xml", caseless=True)
parm = Group(CLiteral("parm") - parm_format - path_val)
pot = Group(CLiteral("pot") - file_fmt - path_val)
groups = ["charge", "diel", "kappa", "mol", "parm", "pot"]
grammar = Group(
OneOrMore(mol)
& ZeroOrMore(
mesh
) # .setParseAction(GenericToken.check_depricated)
& ZeroOrMore(charge)
& ZeroOrMore(diel)
& ZeroOrMore(kappa)
& ZeroOrMore(parm)
& ZeroOrMore(pot)
)
def format_read(results: ParseResults):
return self.format_read_section(results, groups)
return Group(
Suppress(CLiteral("READ")) - grammar - Suppress(CLiteral("END"))
).setParseAction(format_read)
class MgParaParser:
"""ELEC mg-para specific tokens/grammars."""
# https://apbs.readthedocs.io/en/latest/using/input/elec/mg-para.html
number_val = ApbsLegacyInput.get_number_grammar()
pdime = Group(CLiteral("pdime") - ElecToken.grid_floats)
ofrac = Group(CLiteral("ofrac") - number_val)
grammar = (
CLiteral("mg-para")
& ZeroOrMore(ElecToken.name)
& ZeroOrMore(ElecToken.async_value)
& ZeroOrMore(ElecToken.bcfl)
& ZeroOrMore(GenericToken.calcenergy)
& ZeroOrMore(GenericToken.calcforce)
& ZeroOrMore(ElecToken.cgcent)
& ZeroOrMore(ElecToken.cglen)
& ZeroOrMore(ElecToken.chgm)
& ZeroOrMore(ElecToken.dime)
& ZeroOrMore(ElecToken.etol)
& ZeroOrMore(ElecToken.fgcent)
& ZeroOrMore(ElecToken.fglen)
& ZeroOrMore(ElecToken.ion)
& ZeroOrMore(ElecToken.pbe)
& ZeroOrMore(GenericToken.mol)
& ZeroOrMore(ofrac)
& ZeroOrMore(ElecToken.pdie)
& ZeroOrMore(pdime)
& ZeroOrMore(GenericToken.sdens)
& ZeroOrMore(ElecToken.sdie)
& ZeroOrMore(GenericToken.srad)
& ZeroOrMore(ElecToken.srfm)
& ZeroOrMore(GenericToken.swin)
& ZeroOrMore(GenericToken.temp)
& ZeroOrMore(ElecToken.usemap)
& ZeroOrMore(ElecToken.write)
& ZeroOrMore(ElecToken.writemat)
)
class TabiParser:
"""ELEC tabi specific tokens/grammars."""
# https://apbs.readthedocs.io/en/latest/using/input/elec/tabi.html
integer_val = ApbsLegacyInput.get_integer_grammar()
number_val = ApbsLegacyInput.get_number_grammar()
# TODO: Should this be replaced which a check to make
# sure that "number_val is between 0.0 and 1.0"
mac = Group(CLiteral("mac") - number_val)
mesh = Group(CLiteral("mesh") - oneOf("0 1 2 ses skin"))
outdata = Group(CLiteral("outdata") - oneOf("0 1"))
tree_n0 = Group(CLiteral("tree_n0") - integer_val)
tree_order = Group(CLiteral("tree_order") - integer_val)
grammar = (CLiteral("tabi")
& ZeroOrMore(ElecToken.name)
& ZeroOrMore(ElecToken.ion)
& ZeroOrMore(mac)
& ZeroOrMore(mesh)
& ZeroOrMore(GenericToken.mol)
& ZeroOrMore(outdata)
& ZeroOrMore(ElecToken.pdie)
& ZeroOrMore(GenericToken.sdens)
& ZeroOrMore(ElecToken.sdie)
& ZeroOrMore(GenericToken.srad)
& ZeroOrMore(GenericToken.temp)
& ZeroOrMore(tree_n0)
& ZeroOrMore(tree_order))
class PbsamAutoParser:
"""ELEC pbsam-auto specific tokens/grammars."""
# https://apbs.readthedocs.io/en/latest/using/input/elec/pbsam-auto.html
number_val = ApbsLegacyInput.get_number_grammar()
path_val = ApbsLegacyInput.get_path_grammar()
# pbsam-auto specific Keywords
exp = Group(CLiteral("exp") - path_val)
imat = Group(CLiteral("imat") - path_val)
surf = Group(CLiteral("surf") - path_val)
tolsp = Group(CLiteral("tolsp") - number_val)
keyword = CLiteral("pbsam-auto") | CLiteral("pbsam")
# .setParseAction(GenericToken.check_depricated)
grammar = (
keyword
& ZeroOrMore(ElecToken.name)
& ZeroOrMore(PbToken.thr3dmap)
& ZeroOrMore(PbToken.diff)
& ZeroOrMore(PbToken.dx)
& ZeroOrMore(exp)
& ZeroOrMore(PbToken.grid2d)
& ZeroOrMore(imat)
& ZeroOrMore(PbToken.ntraj)
& ZeroOrMore(PbToken.pbc)
& ZeroOrMore(ElecToken.pdie)
& ZeroOrMore(PbToken.randorient)
& ZeroOrMore(PbToken.runname)
& ZeroOrMore(PbToken.runtype)
& ZeroOrMore(PbToken.salt)
& ZeroOrMore(ElecToken.sdie)
& ZeroOrMore(surf)
& ZeroOrMore(GenericToken.temp)
& ZeroOrMore(PbToken.term)
& ZeroOrMore(PbToken.termcombine)
& ZeroOrMore(tolsp)
& ZeroOrMore(PbToken.units)
& ZeroOrMore(PbToken.xyz)
)
class PbToken:
"""ELEC pbam-auto and pbsam-auto specific tokens/grammars."""
identifier = ApbsLegacyInput.get_identifier_grammar()
integer_val = ApbsLegacyInput.get_integer_grammar()
number_val = ApbsLegacyInput.get_number_grammar()
path_val = ApbsLegacyInput.get_path_grammar()
thr3dmap = Group(CLiteral("3dmap") - path_val)
diff = Group(
CLiteral("diff") -
(CLiteral("stat")
| Group(CLiteral("move") - number_val - number_val)
| CLiteral("rot") - number_val))
dx = Group(CLiteral("dx") - path_val)
grid2d = Group(
CLiteral("grid2d") - Group(path_val - oneOf("x y z", caseless=True) -
number_val)) # .setDebug()
gridpts = Group(CLiteral("gridpts") - integer_val)
ntraj = Group(CLiteral("ntraj") - integer_val)
pbc = Group(CLiteral("pbc") - number_val)
randorient = CLiteral("randorient")
runname = Group(CLiteral("runname") - Word(alphanums + "_"))
runtype_options = oneOf("energyforce electrostatics dynamics",
caseless=True)
runtype = Group(CLiteral("runtype") - runtype_options)
# TODO: value of number_val should be 0.00 to 0.15?
salt = Group(CLiteral("salt") - number_val)
term_pos_options = oneOf("x<= x>= y<= y>= z<= z>= r<= r>=", caseless=True)
term_contact = Group(CLiteral("contact") - path_val)
term_pos = Group(term_pos_options - number_val - identifier)
term_time = Group(CLiteral("time") - number_val)
term = Group(CLiteral("term") +
(term_contact | term_pos | term_time)) # .setDebug()
termcombine = Group(
CLiteral("termcombine") - oneOf("and or", caseless=True))
units = Group(CLiteral("units") - oneOf("kcalmol jmol kT", caseless=True))
xyz = Group(CLiteral("xyz") - Group(identifier - path_val))
class PygbeParser:
"""ELEC pygbe specific tokens/grammars."""
# https://apbs.readthedocs.io/en/latest/using/input/elec/pygbe.html
grammar = CLiteral("pygbe") & ZeroOrMore(ElecToken.name)
class ElecToken:
"""ELEC specific tokens/grammars that can be used by other classes."""
# https://apbs.readthedocs.io/en/latest/using/input/elec/index.html
# The following tokens are used by at least 2 of the parser types with
# the same format and rules
identifier = ApbsLegacyInput.get_identifier_grammar()
integer_val = ApbsLegacyInput.get_integer_grammar()
number_val = ApbsLegacyInput.get_number_grammar()
path_val = ApbsLegacyInput.get_path_grammar()
name = Group(CLiteral("name") - identifier)
grid_floats = Group(number_val * 3)
grid_ints = Group(integer_val * 3)
mol_id = Group(CLiteral("mol") - integer_val)
async_value = Group(CLiteral("async") - integer_val)
bcfl_options = oneOf("focus map mdh mem sdh zero", caseless=True)
bcfl = Group(CLiteral("bcfl") - bcfl_options)
cgcent = Group(CLiteral("cgcent") - (mol_id | grid_floats))
cglen = Group(CLiteral("cglen") - grid_floats)
chgm_options = oneOf("spl0 spl2", caseless=True)
chgm = Group(CLiteral("chgm") - chgm_options)
dime = Group(CLiteral("dime") - grid_ints)
etol = Group(CLiteral("etol") - number_val)
fgcent = Group(CLiteral("fgcent") - (mol_id | grid_floats))
fglen = Group(CLiteral("fglen") - grid_floats)
gcent = Group(CLiteral("gcent") - (mol_id | grid_floats))
glen = Group(CLiteral("glen") - grid_floats)
# Are charge, conc, and radius ALL required?
ion_charge = Group(CLiteral("charge") - number_val)
ion_conc = Group(CLiteral("conc") - number_val)
ion_radius = Group(CLiteral("radius") - number_val)
ion = Group(CLiteral("ion") - ion_charge & ion_conc & ion_radius)
nlev = Group(CLiteral("nlev") - number_val)
# TODO: I think only 1 of these are allowed (not ZeroOrMore)
pbe = Group(oneOf("lpbe lrpbe npbe nrpbe", caseless=True))
# TODO: Number must be >= 1
pdie = Group(CLiteral("pdie") - number_val).setParseAction(
check_range(1.0))
# NOTE: Should be a value between 78-80?
sdie = Group(CLiteral("sdie") - number_val)
srfm_options = oneOf("mol smol spl2", caseless=True)
srfm = Group(CLiteral("srfm") - srfm_options)
usemap_options = oneOf("diel kappa charge", caseless=True)
usemap = Group(CLiteral("usemap") - Group(usemap_options - integer_val))
write_type_options = oneOf(
"charge "
"pot "
"smol "
"sspl "
"vdw "
"ivdw "
"lap "
"edens "
"ndens "
"qdens "
"dielx "
"diely "
"dielz "
"kappa",
caseless=True,
)
write_format_options = oneOf("avs dx flat gz uhbd", caseless=True)
write = Group(
CLiteral("write") -
Group(write_type_options - write_format_options - path_val))
writemat = Group(
CLiteral("writemat") - oneOf("poisson", caseless=True) - path_val)
class GenericToken:
"""Generic tokens/grammars that can be used by other classes."""
@staticmethod
def check_depricated(instring: str, loc: int,
tokenlist: ParseResults) -> ParseResults:
"""Possibly using a depricated keyword or value.
Try to be produce a helpful error messsage.
:param instring str: the string that may be using a depricated value
:param loc int: the character offset into string
:return: the original or updated ParseResults
:rtype: ParseResults
"""
depricated_values = {"ekey": "glob", "bcfl": "mem"}
substitute_values = {"glob": "global", "mem": "mdh"}
if isinstance(tokenlist, ParseResults):
if (isinstance(tokenlist[0], ParseResults)
and len(tokenlist[0]) == 2):
# We have a key and value
key = tokenlist[0][0]
value = tokenlist[0][1]
if key in depricated_values:
LOGGER.warning(
"WARNING: Depricated value (%s) for key "
"(%s) at offset (%s)",
value,
key,
loc,
)
if value in substitute_values:
new_value = substitute_values[value]
# NOTE: Unfortunatly, the location is the
# offset from the begining of instring
# so we don't have a line count.
# Find the line number, column, and
# offending line with this hack :-(
count = 0
idx = 1
lineno = 0
column = 0
line = ""
for data in instring.splitlines():
if count > loc:
break
if key in data and value in data:
line = data
lineno = idx
column = data.find(value) + 1
count += len(data) + 1
idx += 1
LOGGER.warning(
ApbsLegacyInput.banner_message(
lineno,
column,
line,
f"WARNING: Substituting new value, {new_value}"
f", for {value}",
))
# Substitute the depricated value with correct value
tokenlist[0][1] = new_value
return tokenlist
number_val = ApbsLegacyInput.get_number_grammar()
bconc = Group(CLiteral("bconc") - number_val)
calc_options = oneOf("no total comps", caseless=True)
calcenergy = Group(CLiteral("calcenergy") - calc_options)
calcforce = Group(CLiteral("calcforce") - calc_options)
gamma = Group(CLiteral("gamma") - number_val)
grid_coord = Group(number_val * 3)
grid = Group(CLiteral("grid") - grid_coord)
mol = Group(CLiteral("mol") - number_val)
sdens = Group(CLiteral("sdens") - number_val)
srad = Group(CLiteral("srad") - number_val)
swin = Group(CLiteral("swin") - number_val)
temp = Group(CLiteral("temp") - number_val)