#!/usr/bin/env python
# cardinal_pythonlib/psychiatry/drugs.py
"""
===============================================================================
Original code copyright (C) 2009-2022 Rudolf Cardinal (rudolf@pobox.com).
This file is part of cardinal_pythonlib.
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
https://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
===============================================================================
**Drug information, with an emphasis on psychotropic drugs, including
translating specific to generic names.**
**Examples**
Test within Python:
.. code-block:: python
from cardinal_pythonlib.psychiatry.drugs import *
drug_name_to_generic("UNKNOWN")
drug_name_to_generic("UNKNOWN", unknown_to_default=True)
drug_names_to_generic([
"citalopram", "Citalopram", "Cipramil", "Celexa",
"olanzepine", # typo
"dextroamphetamine",
"amitryptyline",
])
**Antidepressants**
As of 2018-07-01, this is a functional superset of the SLAM
antidepressant-finding SQL (see ``dep_med_v1``), though mainly a superset in
non-antidepressant respects; the only antidepressants it adds are:
- buproprion, maprotiline
The SLAM antidepressant finder finds:
- tricyclic (category)
- amitriptyline, clomipramine, dosulepin, doxepin, imipramine, lofepramine,
nortriptyline, trimipramine
- mianserin, trazodone, phenelzine, isocarboxazid, tranylcypromine, moclobemide
- citalopram, escitalopram, fluoxetine, fluvoxamine, paroxetine, sertraline
- mirtazapine, reboxetine, venlafaxine, agomelatine, duloxetine
- flupentixol, tryptophan
Sorted, that is:
.. code-block:: none
agomelatine
amitriptyline
citalopram
clomipramine
dosulepin
doxepin
duloxetine
escitalopram
fluoxetine
flupentixol
fluvoxamine
imipramine
isocarboxazid
lofepramine
mianserin
mirtazapine
moclobemide
nortriptyline
paroxetine
phenelzine
reboxetine
sertraline
tranylcypromine
trazodone
tricyclic
trimipramine
tryptophan
venlafaxine
Compare that against the output of:
.. code-block:: python
[x.generic_name for x in all_drugs_where(slam_antidepressant_finder=True,
include_categories=True)]
**Using this code from R via reticulate**
Test within R:
.. code-block:: r
# -------------------------------------------------------------------------
# Load libraries
# -------------------------------------------------------------------------
RUN_ONCE_ONLY <- '
library(devtools)
devtools::install_github("rstudio/reticulate") # get latest version
'
library(data.table)
library(reticulate)
# -------------------------------------------------------------------------
# Set up reticulate
# -------------------------------------------------------------------------
VENV <- "~/dev/venvs/cardinal_pythonlib" # or your preferred virtualenv
PYTHON_EXECUTABLE <- ifelse(
.Platform$OS.type == "windows",
file.path(VENV, "Scripts", "python.exe"), # Windows
file.path(VENV, "bin", "python") # Linux
)
reticulate::use_python(PYTHON_EXECUTABLE, required=TRUE)
# ... it is CRITICAL to use required=TRUE, or it might fail silently
# Unnecessary now reticulate::use_python() works:
#
# PYTHON_VERSION <- "python3.5"
# CARDINAL_PYTHONLIB_BASEDIR <- ifelse(
# .Platform$OS.type == "windows",
# file.path(VENV, "lib", "site-packages/cardinal_pythonlib"),
# file.path(VENV, "lib", PYTHON_VERSION, "site-packages/cardinal_pythonlib")
# )
# reticulate::use_virtualenv(VENV, required=TRUE)
#
# cpl_fileops <- reticulate::import_from_path("fileops", CARDINAL_PYTHONLIB_BASEDIR)
# cpl_drugs <- reticulate::import_from_path("drugs", file.path(CARDINAL_PYTHONLIB_BASEDIR, "psychiatry"))
#
# ... this is NOT WORKING properly; dotted imports via reticulate::import() fail; also, imports from
# within the Python code fail even if you use reticulate::import_from_path(); this suggests the virtualenv is not set up
# properly; use reticulate::use_python() instead.
# -------------------------------------------------------------------------
# Import Python modules
# -------------------------------------------------------------------------
cardinal_pythonlib <- reticulate::import("cardinal_pythonlib")
cpl_fileops <- reticulate::import("cardinal_pythonlib.fileops")
cpl_drugs <- reticulate::import("cardinal_pythonlib.psychiatry.drugs")
# -------------------------------------------------------------------------
# Do something useful
# -------------------------------------------------------------------------
testnames <- c("citalopram", "Cipramil", "Prozac", "fluoxetine")
# Works for simple variables:
cpl_drugs$drug_names_to_generic(testnames)
# Also works for data table replacements:
dt <- data.table(
subject = c("Alice", "Bob", "Charles", "Dawn", "Egbert", "Flora"),
drug = c("citalopram", "Cipramil", "Prozac", "fluoxetine", "Priadel", "Haldol")
)
dt[, drug_generic := cpl_drugs$drug_names_to_generic(drug)]
dt[, is_antidepressant := cpl_drugs$drug_names_match_criteria(
drug_generic,
names_are_generic=TRUE,
antidepressant=TRUE)]
dt[, is_antidepressant_not_ssri := cpl_drugs$drug_names_match_criteria(
drug_generic,
names_are_generic=TRUE,
antidepressant=TRUE,
ssri=FALSE)]
dt[, is_conventional_antidepressant := cpl_drugs$drug_names_match_criteria(
drug_generic,
names_are_generic=TRUE,
conventional_antidepressant=TRUE)]
dt[, slam_antidepressant_finder := cpl_drugs$drug_names_match_criteria(
drug_generic,
names_are_generic=TRUE,
slam_antidepressant_finder=TRUE,
include_categories=TRUE)]
**Use for SQL finding**
.. code-block:: python
from typing import List
from cardinal_pythonlib.psychiatry.drugs import *
colname = "somecol"
antidepressants = all_drugs_where(conventional_antidepressant=True) # type: List[Drug]
antidep_sql_parts = [drug.sql_column_like_drug(colname) for drug in antidepressants]
antidep_sql = " OR ".join(antidep_sql_parts)
antipsychotics = all_drugs_where(antipsychotic=True) # type: List[Drug]
antipsy_sql_parts = [drug.sql_column_like_drug(colname) for drug in antipsychotics]
antipsy_sql = " OR ".join(antipsy_sql_parts)
alldrugs = all_drugs_where()
alldrug_sql_parts = [drug.sql_column_like_drug(colname) for drug in alldrugs]
alldrug_sql = " OR ".join(alldrug_sql_parts)
lithium = get_drug("lithium")
lithium_sql = lithium.sql_column_like_drug(colname)
# HOWEVER, NOTE THAT LITHIUM IS CURRENTLY OVER-INCLUSIVE and will include
# lithium chloride for LiDCO measurement.
""" # noqa
import re
from typing import Dict, List, Optional, Pattern, Union
from cardinal_pythonlib.sql.literals import sql_string_literal
# =============================================================================
# Regex constants
# =============================================================================
WILDCARD = ".*" # if re.DOTALL is set, this also matches newlines
WB = WORD_BOUNDARY = r"\b"
# =============================================================================
# Class to capture drug information
# =============================================================================
[docs]class Drug(object):
"""
Class to describe a specific drug, or a drug category.
Also embodies knowledge about brand names and common misspellings.
See the :const:`DRUGS` list for example of use.
"""
def __init__(
self,
# Names
generic: Union[str, List[str]],
alternatives: List[str] = None,
category_not_drug: bool = False,
add_preceding_wildcards: bool = True,
add_preceding_word_boundary: bool = True,
add_following_wildcards: bool = True,
# Psychiatry
psychotropic: bool = None, # special; can be used as override if False # noqa
antidepressant: bool = False,
conventional_antidepressant: bool = False,
ssri: bool = False,
non_ssri_modern_antidepressant: bool = False,
tricyclic_antidepressant: bool = False,
tetracyclic_and_related_antidepressant: bool = False,
monoamine_oxidase_inhibitor: bool = False,
antipsychotic: bool = False,
first_generation_antipsychotic: bool = False,
second_generation_antipsychotic: bool = False,
stimulant: bool = False,
anticholinergic: bool = False,
benzodiazepine: bool = False,
z_drug: bool = False,
non_benzodiazepine_anxiolytic: bool = False,
gaba_a_functional_agonist: bool = False,
gaba_b_functional_agonist: bool = False,
mood_stabilizer: bool = False,
# Endocrinology
antidiabetic: bool = False,
sulfonylurea: bool = False,
biguanide: bool = False,
glifozin: bool = False,
glp1_agonist: bool = False,
dpp4_inhibitor: bool = False,
meglitinide: bool = False,
thiazolidinedione: bool = False,
# Cardiovascular
cardiovascular: bool = False,
beta_blocker: bool = False,
ace_inhibitor: bool = False,
statin: bool = False,
# Respiratory
respiratory: bool = False,
beta_agonist: bool = False,
# Gastrointestinal
gastrointestinal: bool = False,
proton_pump_inhibitor: bool = False,
nonsteroidal_anti_inflammatory: bool = False,
# Nutritional
vitamin: bool = False,
# Special flags:
slam_antidepressant_finder: bool = False,
) -> None:
# noinspection PyUnresolvedReferences
"""
Initialize and determine/store category knowledge.
``alternatives`` can include regexes (as text).
We add front/back wildcards by default; this handles all situations
like "depot X", etc. We also add a preceding word boundary (after the
wildcard); thus the usual transformation is ``XXX`` -> ``.*\bXXX.*``.
Args:
generic: generic name, or list of names
alternatives: can include regexes (as text)
category_not_drug: is this a drug category, not a specific drug?
add_preceding_wildcards: when making a regex (etc.), add a wildcard
to the start of all possibilities (generic + alternative names)
that don't already have one?
add_preceding_word_boundary: when making a regex (etc.), add word
boundaries to the start of all possibilities (generic +
alternative names) that don't already have one?
add_following_wildcards: when making a regex (etc.), add a wildcard
to the end of all possibilities (generic + alternative names)
that don't already have one?
psychotropic: a psychotropic drug?
antidepressant: an antidepressant?
conventional_antidepressant: a traditional antidepressant?
ssri: a selective serotonin reuptake inhibitor (SSRI)?
non_ssri_modern_antidepressant: a non-SSRI "modern" antidepressant?
tricyclic_antidepressant: a tricyclic?
tetracyclic_and_related_antidepressant: a tetracyclic or related?
monoamine_oxidase_inhibitor: a MAO-I?
antipsychotic: an antipsychotic?
first_generation_antipsychotic: an FGA?
second_generation_antipsychotic: an SGA?
stimulant: a psychostimulant?
anticholinergic: an anticholinergic?
benzodiazepine: a benzodiazepine?
z_drug: a "Z" drug (e.g. zopiclone, zolpidem, ...)
non_benzodiazepine_anxiolytic: a non-BZ anxiolytic?
gaba_a_functional_agonist: a GABA-A functional agonist?
gaba_b_functional_agonist: a GABA-B functional agonist?
mood_stabilizer: a "mood stabilizer"?
antidiabetic: treats diabetes?
sulfonylurea: a sulfonylurea (sulphonylurea), for diabetes?
biguanide: a biguanide, for diabetes?
glifozin: a glifozin, for diabetes?
glp1_agonist: a GLP-1 agonist, for diabetes?
dpp4_inhibitor: a DPP4 inhibitor, for diabetes?
meglitinide: a meglitinide, for diabetes?
thiazolidinedione: a thiazolidinedione, for diabetes?
cardiovascular: a cardiovascular drug?
beta_blocker: a beta adrenoceptor antagonist?
ace_inhibitor: an ACE inhibitor?
statin: a statin?
respiratory: a respiratory drug?
beta_agonist: a beta adrenoceptor agonist?
gastrointestinal: a gastrointestinal drug?
proton_pump_inhibitor: a PPI?
nonsteroidal_anti_inflammatory: an NSAID?
vitamin: a vitamin?
slam_antidepressant_finder: a drug found by the SLAM
antidepressant-finding code? (A bit specialized, this one!)
Attributes:
mixture (bool): is this a mixture of more than one drug?
Will be set if more than one generic name is given.
all_generics (List[str]): list of all generic names in lower case
generic_name: generic name (or combination name like ``a_with_b``
for mixtures of ``a`` and ``b``)
regex: compiled case-insensitive regular expression to match
possible names
"""
self.add_preceding_word_boundary = add_preceding_word_boundary
self.add_preceding_wildcards = add_preceding_wildcards
self.add_following_wildcards = add_following_wildcards
# ---------------------------------------------------------------------
# Name handling
# ---------------------------------------------------------------------
if isinstance(generic, list):
self.mixture = True
self.all_generics = [x.lower().strip() for x in generic]
self.generic_name = "_with_".join(self.all_generics)
elif isinstance(generic, str):
self.mixture = False
self.generic_name = generic.lower().strip()
self.all_generics = [self.generic_name]
else:
raise ValueError(f"Bad generic_name: {generic!r}")
self.alternatives = alternatives or [] # type: List[str]
self._regex_text = None # type: Optional[str]
self._regex = None # type: Optional[Pattern]
self._sql_like_fragments = None # type: Optional[List[str]]
# ---------------------------------------------------------------------
# Things we know about psychotropics
# ---------------------------------------------------------------------
if (
ssri
or non_ssri_modern_antidepressant
or tricyclic_antidepressant
or tetracyclic_and_related_antidepressant
or monoamine_oxidase_inhibitor
):
conventional_antidepressant = True
if conventional_antidepressant:
antidepressant = True
if first_generation_antipsychotic or second_generation_antipsychotic:
antipsychotic = True
if benzodiazepine or z_drug:
gaba_a_functional_agonist = True
if (
antidepressant
or antipsychotic
or stimulant
or anticholinergic
or gaba_a_functional_agonist
or gaba_b_functional_agonist
or mood_stabilizer
) and (psychotropic is not False):
psychotropic = True
if psychotropic is None:
psychotropic = False
# ---------------------------------------------------------------------
# Things we know about other drugs
# ---------------------------------------------------------------------
if (
sulfonylurea
or biguanide
or glifozin
or glp1_agonist
or dpp4_inhibitor
or meglitinide
or thiazolidinedione
):
antidiabetic = True
if beta_blocker or ace_inhibitor:
cardiovascular = True
# ---------------------------------------------------------------------
# Store category knowledge
# ---------------------------------------------------------------------
self.category_not_drug = category_not_drug
self.psychotropic = psychotropic
self.antidepressant = antidepressant
self.conventional_antidepressant = conventional_antidepressant
self.ssri = ssri
self.non_ssri_modern_antidepressant = non_ssri_modern_antidepressant
self.tricyclic = tricyclic_antidepressant
self.tetracyclic_and_related_antidepressant = (
tetracyclic_and_related_antidepressant
)
self.monoamine_oxidase_inhibitor = monoamine_oxidase_inhibitor
self.antipsychotic = antipsychotic
self.first_generation_antipsychotic = first_generation_antipsychotic
self.second_generation_antipsychotic = second_generation_antipsychotic
self.stimulant = stimulant
self.anticholinergic = anticholinergic
self.benzodiazepine = benzodiazepine
self.z_drug = z_drug
self.gaba_a_functional_agonist = gaba_a_functional_agonist
self.gaba_b_functional_agonist = gaba_b_functional_agonist
self.non_benzodiazepine_anxiolytic = non_benzodiazepine_anxiolytic
self.mood_stabilizer = mood_stabilizer
self.antidiabetic = antidiabetic
self.sulfonylurea = sulfonylurea
self.biguanide = biguanide
self.cardiovascular = cardiovascular
self.beta_blocker = beta_blocker
self.ace_inhibitor = ace_inhibitor
self.statin = statin
self.respiratory = respiratory
self.beta_agonist = beta_agonist
self.gastrointestinal = gastrointestinal
self.proton_pump_inhibitor = proton_pump_inhibitor
self.nonsteroidal_anti_inflammatory = nonsteroidal_anti_inflammatory
self.vitamin = vitamin
# ---------------------------------------------------------------------
# Store other flags
# ---------------------------------------------------------------------
self.slam_antidepressant_finder = slam_antidepressant_finder
@property
def regex_text(self) -> str:
"""
Return regex text (yet to be compiled) for this drug.
"""
if self._regex_text is None:
possibilities = [] # type: List[str]
for p in list(set(self.all_generics + self.alternatives)):
if self.add_preceding_word_boundary and not p.startswith(WB):
p = WB + p
if self.add_preceding_wildcards and not p.startswith(WILDCARD):
p = WILDCARD + p
if self.add_following_wildcards and not p.endswith(WILDCARD):
p = p + WILDCARD
possibilities.append(p)
self._regex_text = "|".join("(?:" + x + ")" for x in possibilities)
return self._regex_text
@property
def regex(self) -> Pattern:
"""
Returns a compiled regex for this drug.
"""
if self._regex is None:
self._regex = re.compile(
self.regex_text, re.IGNORECASE | re.DOTALL
)
return self._regex
[docs] @staticmethod
def regex_to_sql_like(
regex_text: str,
single_wildcard: str = "_",
zero_or_more_wildcard: str = "%",
) -> List[str]:
"""
Converts regular expression text to a reasonably close fragment
for the SQL ``LIKE`` operator.
NOT PERFECT, but works for current built-in regular expressions.
Args:
regex_text: regular expression text to work with
single_wildcard: SQL single wildcard, typically an underscore
zero_or_more_wildcard: SQL "zero/one/many" wildcard, probably always
a percent symbol
Returns:
string for an SQL string literal
Raises:
:exc:`ValueError` for some regex text that it doesn't understand
properly
"""
def append_to_all(new_content: str) -> None:
nonlocal results
results = [r + new_content for r in results]
def split_and_append(new_options: List[str]) -> None:
nonlocal results
newresults = [] # type: List[str]
for option in new_options:
newresults.extend([r + option for r in results])
results = newresults
def deduplicate_wildcards(text: str) -> str:
while zero_or_more_wildcard + zero_or_more_wildcard in text:
text = text.replace(
zero_or_more_wildcard + zero_or_more_wildcard,
zero_or_more_wildcard,
)
return text
# Basic processing
working = regex_text # strings are immutable
results = [zero_or_more_wildcard] # start with a wildcard
while working:
if working.startswith(".*"):
# e.g. ".*ozapi"
append_to_all(zero_or_more_wildcard)
working = working[2:]
elif working.startswith("["):
# e.g. "[io]peridol"
close_bracket = working.index("]") # may raise
bracketed = working[1:close_bracket]
option_groups = bracketed.split("|")
options = [c for group in option_groups for c in group]
split_and_append(options)
working = working[close_bracket + 1 :]
elif len(working) > 1 and working[1] == "?":
# e.g. "r?azole"
split_and_append(["", working[0]])
# ... regex "optional character"
# ... SQL: some results with a single wildcard, some without
working = working[2:]
elif working.startswith("."):
# single character wildcard
append_to_all(single_wildcard)
working = working[1:]
else:
append_to_all(working[0])
working = working[1:]
append_to_all(zero_or_more_wildcard) # end with a wildcard
# Remove any duplicate (consecutive) % wildcards:
results = [deduplicate_wildcards(r) for r in results]
# Done
return results
@property
def sql_like_fragments(self) -> List[str]:
"""
Returns all the string literals to which a database column should be
compared using the SQL ``LIKE`` operator, to match this drug.
This isn't as accurate as the regex, but ``LIKE`` can do less.
``LIKE`` uses the wildcards ``?`` and ``%``.
"""
if self._sql_like_fragments is None:
self._sql_like_fragments = []
for p in list(set(self.all_generics + self.alternatives)):
self._sql_like_fragments.extend(self.regex_to_sql_like(p))
return self._sql_like_fragments
[docs] def name_matches(self, name: str) -> bool:
"""
Detects whether the name that's passed matches our knowledge of any of
things that this drug might be called: generic name, brand name(s),
common misspellings.
The parameter should be pre-stripped of edge whitespace.
"""
return bool(self.regex.match(name))
[docs] def sql_column_like_drug(self, column_name: str) -> str:
"""
Returns SQL like
.. code-block:: sql
(column_name LIKE '%drugname1%' OR
column_name LIKE '%drugname2%')
for the drug names that this Drug object knows about.
Args:
column_name: column name, pre-escaped if necessary
Returns:
SQL fragment as above
"""
clauses = [
f"{column_name} LIKE {sql_string_literal(f)}"
for f in self.sql_like_fragments
]
return f"({' OR '.join(clauses)})"
# Source data.
DRUGS = [
# In comments below: (*) misspelling, capitalized for brand name, (~)
# hybrid generic/brand name, (+) old name.
# -------------------------------------------------------------------------
# SSRIs
# -------------------------------------------------------------------------
Drug(
"citalopram",
["Cipramil", "Celexa"],
ssri=True,
slam_antidepressant_finder=True,
),
Drug(
"escitalopram",
["Cipralex", "Lexapro"],
ssri=True,
slam_antidepressant_finder=True,
),
Drug(
"fluoxetine",
["Prozac", "Bellzac", "Oxactin", "Prozep", "Sarafem", "fluox.*"],
# CPFT 2013: "fluoxetine Dec"
ssri=True,
slam_antidepressant_finder=True,
),
Drug(
"fluvoxamine",
["Luvox", "Faverin", "fluvoxamine.*"], # e.g. "fluvoxamine maleate"
ssri=True,
slam_antidepressant_finder=True,
),
Drug(
"paroxetine",
["Seroxat", "Paxil"], # there are other brands elsewhere...
ssri=True,
slam_antidepressant_finder=True,
),
Drug(
"sertraline",
["Lustral", "Zoloft", "Bellsert"],
# NOT Seretra (cf. SLAM code, see email to self 2016-12-02); Seretra =
# seratrodast = for asthma
ssri=True,
slam_antidepressant_finder=True,
),
# -------------------------------------------------------------------------
# FIRST-GENERATION ANTIPSYCHOTICS
# -------------------------------------------------------------------------
Drug("benperidol", ["Anquil"], first_generation_antipsychotic=True),
Drug("chlorpromazine", ["Largactil"], first_generation_antipsychotic=True),
Drug(
"flupentixol",
["Depixol", "Fluanxol", "flupent.*", "Depixol.*"],
# e.g. flupenthixol, flupenthixol decanoate, flupentixol decanoate
first_generation_antipsychotic=True,
antidepressant=True,
slam_antidepressant_finder=True,
),
Drug(
"fluphenazine",
["Modecate", "fluphen.*", "Modecate.*"],
first_generation_antipsychotic=True,
),
Drug(
"haloperidol",
[
"Haldol",
"Serenase",
"hal[io]p.*",
"Dozi.*",
"Hald.*",
"Serena.*",
# NB Serenase, Serenace.
# CPFT 2013: haloperidol, haloperidol decanoate, Haldol, Haldol
# decanoate, Serenase.
],
first_generation_antipsychotic=True,
),
Drug("levomepromazine", ["Nozinan"], first_generation_antipsychotic=True),
Drug("pericyazine", first_generation_antipsychotic=True),
Drug("perphenazine", ["Fentazin"], first_generation_antipsychotic=True),
Drug(
["amitriptyline", "perphenazine"],
["Triptafen"], # special
tricyclic_antidepressant=True,
slam_antidepressant_finder=True,
),
Drug("pimozide", ["Orap"], first_generation_antipsychotic=True),
Drug(
"pipotiazine",
["pipot.*", "Piport.*"],
# ... actually (CPFT 2013): pipotiazine, Piportil
first_generation_antipsychotic=True,
),
Drug(
"prochlorperazine", ["Stemetil"], first_generation_antipsychotic=True
),
Drug("promazine", first_generation_antipsychotic=True),
Drug(
"sulpiride",
["Dolmatil", "Sulpor"],
first_generation_antipsychotic=True,
),
Drug(
"trifluoperazine", ["Stelazine"], first_generation_antipsychotic=True
),
Drug(
"zuclopenthixol",
["zuclop.*", "Clopix.*", "Acc?uphase"],
# ... actually (CPFT 2013): zuclopenthixol, zuclopenthixol acetate,
# zuclopenthixol decanoate, Clopixol, Clopixol Decanoate, Acuphase
first_generation_antipsychotic=True,
),
# -------------------------------------------------------------------------
# SECOND-GENERATION ANTIPSYCHOTICS
# -------------------------------------------------------------------------
Drug(
"amisulpride",
["amisulp.*", "Solian"],
# ... actually (CPFT 2013): amisulpiride(*), amisulpride, Solian
second_generation_antipsychotic=True,
),
Drug(
"aripiprazole",
["Abilify", "ari?pr?ipr?azol.*"],
second_generation_antipsychotic=True,
),
Drug(
"asenapine",
["Saphris", "Sycrest"],
second_generation_antipsychotic=True,
),
Drug(
"clozapine",
["cloz.*", "Denz.*", "Zapon.*"],
# ... actually (CPFT 2013): clozapine, Clozaril, clozepine(*)
second_generation_antipsychotic=True,
),
Drug(
"iloperidone",
["Fanapt", "Fanapta", "Zomaril"],
second_generation_antipsychotic=True,
),
Drug("lurasidone", ["Latuda"], second_generation_antipsychotic=True),
Drug(
"olanzapine",
["olanz.*", "Zalast.*", "Zyprex.*", "Zypad.*"],
# ... actually (CPFT 2013): olanzapine, olanzapine embonate,
# olanz(*), olanzepine(*), olanzapin(*), Zyprexa
second_generation_antipsychotic=True,
),
Drug(
"paliperidone",
["Invega", "Xeplion"],
second_generation_antipsychotic=True,
),
Drug(
"quetiapine",
["quet.*", "Seroquel"],
# ... actually (CPFT 2013): quetiapine, quetiepine(*), Seroquel
second_generation_antipsychotic=True,
),
Drug(
"risperidone",
["risp.*", "Consta"],
# ... actually (CPFT 2013): risperidone, risperadone(*), Risperidone
# Consta (~), Risperdal, Risperdal Consta
second_generation_antipsychotic=True,
),
Drug(
"sertindole",
["Serdolect", "Serlect"],
second_generation_antipsychotic=True,
),
Drug("ziprasidone", second_generation_antipsychotic=True),
Drug(
"zotepine", # not in UK
["Nipolept", "Losizopilon", "Lodopin", "Setous"],
second_generation_antipsychotic=True,
),
# -------------------------------------------------------------------------
# STIMULANTS
# -------------------------------------------------------------------------
Drug(
"amfetamine",
[".*am[ph|f]etamine.*", "Adderall"],
# ... actually (CPFT 2013): dextroamphetamine(+), dexamfetamine
stimulant=True,
),
Drug(
"methylphenidate",
["Ritalin", "Concerta.*", "Equasym.*", "Medikinet.*"],
# ... actually (CPFT 2013): methylphenidate, Ritalin, Concerta
stimulant=True,
),
Drug("modafinil", ["Provigil"], stimulant=True),
# -------------------------------------------------------------------------
# ANTICHOLINERGICS
# -------------------------------------------------------------------------
Drug("benztropine", ["benzatropine"], anticholinergic=True),
Drug("orphenadrine", ["Biorphen", "Disipal"], anticholinergic=True),
Drug("procyclidine", ["Arpicolin", "Kemadrin"], anticholinergic=True),
Drug("trihexyphenidyl", ["Broflex"], anticholinergic=True),
# -------------------------------------------------------------------------
# OTHER MODERN ANTIDEPRESSANTS
# -------------------------------------------------------------------------
Drug(
"agomelatine",
["Valdoxan"],
non_ssri_modern_antidepressant=True,
slam_antidepressant_finder=True,
),
Drug(
"bupropion",
["Zyban"],
non_ssri_modern_antidepressant=True
# antidepressant license in US, smoking cessation in UK
),
Drug(
"duloxetine",
["Cymbalta", "Yentreve", "duloxat.*"],
non_ssri_modern_antidepressant=True,
slam_antidepressant_finder=True,
),
Drug(
"mirtazapine",
["mirtaz.*", "mirtazepine", "Zispin", "Mirza"],
# ... actually (CPFT 2013): mirtazapine, mirtazepine(*), "mirtazapine
# Dec" (?)
non_ssri_modern_antidepressant=True,
slam_antidepressant_finder=True,
),
Drug(
"reboxetine",
["Edronax", "reboxat.*"],
non_ssri_modern_antidepressant=True,
slam_antidepressant_finder=True,
),
Drug(
"tryptophan",
["Optimax"],
non_ssri_modern_antidepressant=True,
slam_antidepressant_finder=True,
),
Drug(
"venlafaxine",
["venla.*", "Eff?exor.*"],
# ... actually (CPFT 2013): venlafaxine, venlafaxine XL,
non_ssri_modern_antidepressant=True, # though obviously an SSRI too...
slam_antidepressant_finder=True,
),
# -------------------------------------------------------------------------
# TRICYCLIC AND RELATED ANTIDEPRESSANTS
# -------------------------------------------------------------------------
Drug(
"tricyclic_antidepressant",
["tricyclic.*", "tca" + WB],
tricyclic_antidepressant=True,
slam_antidepressant_finder=True,
category_not_drug=True,
),
Drug(
"amitriptyline",
["amitr[i|y]pt[i|y]l[i|y]n.*", "Vanatrip", "Elavil", "Endep"],
# ... actually (CPFT 2013): amitriptyline, amitriptiline(*),
# amitryptyline(*)
# Triptafen = amitriptyline + perphenazine; see above.
tricyclic_antidepressant=True,
slam_antidepressant_finder=True,
),
Drug(
"clomipramine",
["Anafranil.*"],
tricyclic_antidepressant=True,
slam_antidepressant_finder=True,
),
Drug(
"dosulepin",
["dothiepin", "Prothiaden"],
# ... actually (CPFT 2013): dosulepin, dothiepin(+)
tricyclic_antidepressant=True,
slam_antidepressant_finder=True,
),
Drug(
"doxepin",
["Sinepin", "Sinequan", "Sinepin", "Xepin"],
# Xepin is cream only
tricyclic_antidepressant=True,
slam_antidepressant_finder=True,
),
Drug(
"imipramine",
["Tofranil"],
tricyclic_antidepressant=True,
slam_antidepressant_finder=True,
),
Drug(
"lofepramine",
["Lomont"],
tricyclic_antidepressant=True,
slam_antidepressant_finder=True,
),
Drug(
"nortriptyline",
["nortr.*", "Allegron", "Pamelor", "Aventyl"],
# ... actually (CPFT 2013): nortriptyline, nortryptiline(*)
tricyclic_antidepressant=True,
slam_antidepressant_finder=True,
),
Drug(
"trimipramine",
["Surmontil"],
tricyclic_antidepressant=True,
slam_antidepressant_finder=True,
),
# -------------------------------------------------------------------------
# TETRACYCLIC-RELATED ANTIDEPRESSANTS
# -------------------------------------------------------------------------
Drug(
"mianserin",
tetracyclic_and_related_antidepressant=True,
slam_antidepressant_finder=True,
),
Drug(
"trazodone",
["Molipaxin"],
tetracyclic_and_related_antidepressant=True,
slam_antidepressant_finder=True,
),
Drug(
"nefazodone",
# discontinued for hepatotoxicity? But apparently still used in 2014
# in the UK: http://www.bbc.co.uk/news/uk-25745824
["Dutonin", "Nefadar", "Serzone"],
tetracyclic_and_related_antidepressant=True
# brand names from https://en.wikipedia.org/wiki/Nefazodone
# ... yup, still a trickle, mostly from Islington:
# https://openprescribing.net/chemical/0403040T0/
),
Drug(
"maprotiline",
["Ludiomil"],
tetracyclic_and_related_antidepressant=True,
),
# -------------------------------------------------------------------------
# MAOIs
# -------------------------------------------------------------------------
Drug(
"phenelzine",
["phenylethylhydrazine", "Alazin", "Nardil"],
monoamine_oxidase_inhibitor=True,
slam_antidepressant_finder=True
# - SLAM code (see e-mail to self 2016-12-02) also has %Alazin%; not sure # noqa
# that's right; see also
# http://www.druglib.com/activeingredient/phenelzine/
# - oh, yes, it is right:
# https://www.pharmacompass.com/active-pharmaceutical-ingredients/alazin # noqa
# - phenylethylhydrazine is a synonym; see
# http://www.minclinic.ru/drugs/drugs_eng/B/Beta-phenylethylhydrazine.html # noqa
),
# not included: pheniprazine
Drug(
"isocarboxazid",
monoamine_oxidase_inhibitor=True,
slam_antidepressant_finder=True,
),
Drug(
"moclobemide",
["Manerix"],
monoamine_oxidase_inhibitor=True,
slam_antidepressant_finder=True,
),
Drug(
"tranylcypromine",
["Parnate"],
monoamine_oxidase_inhibitor=True,
slam_antidepressant_finder=True,
),
# -------------------------------------------------------------------------
# BENZODIAZEPINES
# -------------------------------------------------------------------------
Drug(
"benzodiazepine",
["benzodiazepine.*"],
benzodiazepine=True,
category_not_drug=True,
),
Drug("alprazolam", benzodiazepine=True),
Drug("chlordiazepoxide", benzodiazepine=True),
Drug("clobazam", benzodiazepine=True),
Drug("clonazepam", ["Rivotril"], benzodiazepine=True),
Drug(
"diazepam",
["diaz.*", "Valium"],
# ... actually (CPFT 2013): diazepam, diazapam(*), diazapem(*), Valium
benzodiazepine=True,
),
Drug("flurazepam", ["Dalmane"], benzodiazepine=True),
Drug("loprazolam", benzodiazepine=True),
Drug("lorazepam", ["Ativan"], benzodiazepine=True),
Drug("lormetazepam", benzodiazepine=True),
Drug("midazolam", ["Hypnovel"], benzodiazepine=True),
Drug("nitrazepam", benzodiazepine=True),
Drug("oxazepam", benzodiazepine=True),
Drug("temazepam", benzodiazepine=True),
# -------------------------------------------------------------------------
# Z-DRUGS
# -------------------------------------------------------------------------
Drug("zaleplon", ["Sonata"], z_drug=True),
Drug(
"zolpidem",
["zolpidem.*", "Stilnoct"],
# ... actually (CPFT 2013): zolpidem, zolpidem tartrate
z_drug=True,
),
Drug("zopiclone", ["Zimovane"], z_drug=True),
# -------------------------------------------------------------------------
# OTHER GABA MODULATORS
# -------------------------------------------------------------------------
Drug(
"baclofen",
[
"Lioresal",
"Lyflex",
"Bacfen",
"Baclof",
"Bacmax",
"Chinofen",
"Parafon",
"Riclofen",
"Spinofen",
"Spinospas",
"Tefsole",
"Gablofen",
"Kemstro",
],
gaba_b_functional_agonist=True,
),
# -------------------------------------------------------------------------
# OTHER ANXIOLYTICS
# -------------------------------------------------------------------------
Drug("buspirone", ["Buspar"], non_benzodiazepine_anxiolytic=True),
# -------------------------------------------------------------------------
# OTHER ANTIMANIC
# -------------------------------------------------------------------------
Drug(
"carbamazepine",
["Carbagen.*", "Tegretol.*"],
# also Tegretol Prolonged Release (formerly Tegretol Retard)
# ... actually (CPFT 2013): carbamazepine, Tegretol
mood_stabilizer=True,
),
Drug(
"valproate",
[".*valp.*", "Epilim.*", "Episenta", "Epival", "Convulex", "Depakote"],
# ... also semisodium valproate
# ... actually (CPFT 2013): sodium valproate [chrono], valproic acid,
# valproate, sodium valproate, sodium valporate(*), sodium valporate(*)
# chrono, Depakote
mood_stabilizer=True,
),
Drug(
"lithium",
["lithium.*", "Camcolit", "Liskonum", "Priadel", "Li-Liquid"],
# ... actually (CPFT 2013): lithium, lithium carbonate, lithium citrate
# (curious: Priadel must be being changed to lithium...)
antidepressant=True,
mood_stabilizer=True,
),
# -------------------------------------------------------------------------
# OTHER FOR BIPOLAR/UNIPOLAR DEPRESSION
# -------------------------------------------------------------------------
Drug(
"lamotrigine",
["lamotrigine.*", "Lamictal"],
mood_stabilizer=True,
antidepressant=True,
),
Drug(
"triiodothyronine",
["tri-iodothyronine", "liothyronine", "Cytomel"],
antidepressant=True,
),
# -------------------------------------------------------------------------
# GENERAL MEDICINE: DIABETES
# -------------------------------------------------------------------------
Drug("glibenclamide", sulfonylurea=True),
Drug(
"gliclazide",
["Zicron", "Diamicron.*", "Dacadis.*", "Vitile.*"],
sulfonylurea=True,
),
Drug("glimepiride", ["Amaryl"], sulfonylurea=True),
Drug("glipizide", ["Minodiab"], sulfonylurea=True),
Drug("tolbutamide", sulfonylurea=True),
Drug("metformin", ["metformin.*", "Glucophage.*"], biguanide=True),
Drug("acarbose", ["Glucobay"], antidiabetic=True),
Drug("dapagliflozin", ["Forxiga"], glifozin=True),
Drug("exenatide", ["Byetta", "Bydureon"], glp1_agonist=True),
Drug("linagliptin", ["Trajenta"], dpp4_inhibitor=True),
Drug(
["linagliptin", "metformin"],
["Jentadueto"],
biguanide=True,
dpp4_inhibitor=True,
),
Drug("liraglutide", ["Victoza"], glp1_agonist=True),
Drug("lixisenatide", ["Lyxumia"], glp1_agonist=True),
Drug("nateglinide", ["Starlix"], meglitinide=True),
Drug("pioglitazone", ["Actos"], thiazolidinedione=True),
Drug(
["pioglitazone", "metformin"],
["Competact"],
thiazolidinedione=True,
biguanide=True,
),
Drug("repaglinide", ["Prandin"], meglitinide=True),
Drug("saxagliptin", ["Onglyza"], dpp4_inhibitor=True),
Drug(
["saxagliptin", "metformin"],
["Komboglyze"],
dpp4_inhibitor=True,
biguanide=True,
),
Drug("sitagliptin", ["Januvia"], dpp4_inhibitor=True),
Drug(
["sitagliptin", "metformin"],
["Janumet"],
dpp4_inhibitor=True,
biguanide=True,
),
Drug("vildagliptin", ["Galvus"], dpp4_inhibitor=True),
Drug(
["vildagliptin", "metformin"],
["Eucreas"],
dpp4_inhibitor=True,
biguanide=True,
),
Drug(
"insulin",
# Insulin. Covering the BNF categories:
# INSULIN
# INSULIN ASPART
# INSULIN GLULISINE
# INSULIN LISPRO
# INSULIN DEGLUDEC
# INSULIN DETEMIR
# INSULIN GLARGINE
# INSULIN ZINC SUSPENSION
# ISOPHANE INSULIN
# PROTAMINE ZINC INSULIN
# BIPHASIC INSULIN ASPART
# BIPHASIC INSULIN LISPRO
# BIPHASIC ISOPHANE INSULIN
[
".*insulin.*",
".*aspart.*",
".*glulisine.*",
".*lispro.*",
".*degludec.*",
".*detemir.*",
".*glargine.*",
".*Hypurin.*",
".*Actrapid.*",
".*Humulin.*",
".*Insuman.*",
".*Novorapid.*",
".*Apidra.*",
".*Humalog.*",
".*Tresiba.*",
".*Levemir.*",
".*Lantus.*",
".*Insulatard.*",
".*NovoMix.*",
],
antidiabetic=True,
),
# -------------------------------------------------------------------------
# GENERAL MEDICINE: CARDIOVASCULAR
# -------------------------------------------------------------------------
Drug("aspirin", cardiovascular=True),
Drug("atenolol", beta_blocker=True),
# ACE inhibitors (selected)
Drug("lisinopril", ace_inhibitor=True),
Drug("ramipril", ace_inhibitor=True),
# Statins
Drug("atorvastatin", ["Lipitor"], statin=True),
Drug("fluvastatin", ["Lescol.*"], statin=True),
Drug("pravastatin", ["Lipostat"], statin=True),
Drug("rosuvastatin", ["Crestor"], statin=True),
Drug("simvastatin", ["Zocor"], statin=True),
Drug(["simvastatin", "ezetimibe"], ["Inegy"], statin=True),
# -------------------------------------------------------------------------
# GENERAL MEDICINE: RESPIRATORY
# -------------------------------------------------------------------------
Drug(
"salbutamol",
["salbut.*", "vent.*"],
# ... actually (CPFT 2013): salbutamol
respiratory=True,
beta_agonist=True,
),
# -------------------------------------------------------------------------
# GENERAL MEDICINE: GASTROINTESTINAL
# -------------------------------------------------------------------------
Drug(
"lactulose",
["lactul.*", "Duphal.*", "Lactug.*", "laevol.*"],
# ... actually (CPFT 2013): lactulose
gastrointestinal=True,
),
Drug("lansoprazole", proton_pump_inhibitor=True),
Drug("omeprazole", proton_pump_inhibitor=True),
Drug("senna", gastrointestinal=True),
# -------------------------------------------------------------------------
# GENERAL MEDICINE: OTHER
# -------------------------------------------------------------------------
Drug("ibuprofen", nonsteroidal_anti_inflammatory=True),
Drug("levothyroxine"),
Drug("paracetamol"),
Drug("thiamine", vitamin=True),
# -------------------------------------------------------------------------
# MAYBE ADD:
# - OPIOIDS
# - clonidine
# - cloral betaine
# - ?domperidone
# - donepezil
# - gabapentin
# - hyoscine
# - Keppra = levetiracetam
# - linezolid (as it's an MAOI)
# - memantine
# - methyldopa
# - ?metoclopramide
# - nicotine
# - pregabalin
# - promethazine
# - ropinirole
# - rotigotine
# - selegiline
# - topiramate
# -------------------------------------------------------------------------
] # type: List[Drug]
# =============================================================================
# High-speed lookup versions of the original constants
# =============================================================================
DRUGS_BY_GENERIC_NAME = {d.generic_name: d for d in DRUGS}
# =============================================================================
# Get drug object by name
# =============================================================================
[docs]def get_drug(
drug_name: str,
name_is_generic: bool = False,
include_categories: bool = False,
) -> Optional[Drug]:
"""
Converts a drug name to a :class:`.Drug` class.
If you already have the generic name, you can get the Drug more
efficiently by setting ``name_is_generic=True``.
Set ``include_categories=True`` to include drug categories (such as
tricyclics) as well as individual drugs.
"""
drug_name = drug_name.strip().lower()
if name_is_generic:
drug = DRUGS_BY_GENERIC_NAME.get(drug_name) # type: Optional[Drug]
if (
drug is not None
and drug.category_not_drug
and not include_categories
):
return None
return drug
else:
for d in DRUGS:
if d.name_matches(drug_name):
return d
return None
# =============================================================================
# Convert drug names to generic equivalents
# =============================================================================
[docs]def drug_name_to_generic(
drug_name: str,
unknown_to_default: bool = False,
default: str = None,
include_categories: bool = False,
) -> str:
"""
Converts a drug name to the name of its generic equivalent.
"""
drug = get_drug(drug_name, include_categories=include_categories)
if drug is not None:
return drug.generic_name
return default if unknown_to_default else drug_name
[docs]def drug_names_to_generic(
drugs: List[str],
unknown_to_default: bool = False,
default: str = None,
include_categories: bool = False,
) -> List[str]:
"""
Converts a list of drug names to their generic equivalents.
The arguments are as for :func:`drug_name_to_generic` but this function
handles a list of drug names rather than a single one.
Note in passing the following conversion of blank-type representations from
R via ``reticulate``, when using e.g. the ``default`` parameter and storing
results in a ``data.table()`` character column:
.. code-block:: none
------------------------------ ----------------
To Python Back from Python
------------------------------ ----------------
[not passed, so Python None] "NULL"
NULL "NULL"
NA_character_ "NA"
NA TRUE (logical)
------------------------------ ----------------
"""
return [
drug_name_to_generic(
drug,
unknown_to_default=unknown_to_default,
default=default,
include_categories=include_categories,
)
for drug in drugs
]
# =============================================================================
# Check drugs against criteria
# =============================================================================
[docs]def drug_matches_criteria(drug: Drug, **criteria: Dict[str, bool]) -> bool:
"""
Determines whether a drug, passed as an instance of :class:`.Drug`, matches
the specified criteria.
Args:
drug: a :class:`.Drug` instance
criteria: ``name=value`` pairs to match against the attributes of
the :class:`Drug` class. For example, you can include keyword
arguments like ``antidepressant=True``.
"""
for attribute, value in criteria.items():
if getattr(drug, attribute) != value:
return False
return True
[docs]def all_drugs_where(
sort=True, include_categories: bool = False, **criteria: Dict[str, bool]
) -> List[Drug]:
"""
Find all drugs matching the specified criteria (see
:func:`drug_matches_criteria`). If ``include_categories`` is true, then
drug categories (like "tricyclics") are included as well as individual
drugs.
Pass keyword arguments such as
.. code-block:: python
from cardinal_pythonlib.psychiatry.drugs import *
non_ssri_antidep = all_drugs_where(antidepressant=True, ssri=False)
print([d.generic_name for d in non_ssri_antidep])
conventional_antidep = all_drugs_where(conventional_antidepressant=True)
print([d.generic_name for d in conventional_antidep])
"""
matching_drugs = [] # type: List[Drug]
for drug in DRUGS:
if drug.category_not_drug and not include_categories:
continue
if drug_matches_criteria(drug, **criteria):
matching_drugs.append(drug)
if sort:
matching_drugs.sort(key=lambda d: d.generic_name)
return matching_drugs
[docs]def drug_name_matches_criteria(
drug_name: str,
name_is_generic: bool = False,
include_categories: bool = False,
**criteria: Dict[str, bool],
) -> bool:
"""
Establish whether a single drug, passed by name, matches the specified
criteria. See :func:`drug_matches_criteria`.
"""
drug = get_drug(drug_name, name_is_generic)
if drug is None:
return False
if drug.category_not_drug and not include_categories:
return False
return drug_matches_criteria(drug, **criteria)
[docs]def drug_names_match_criteria(
drug_names: List[str],
names_are_generic: bool = False,
include_categories: bool = False,
**criteria: Dict[str, bool],
) -> List[bool]:
"""
Establish whether multiple drugs, passed as a list of drug names, each
matches the specified criteria. See :func:`drug_matches_criteria`.
"""
return [
drug_name_matches_criteria(
dn,
name_is_generic=names_are_generic,
include_categories=include_categories,
**criteria,
)
for dn in drug_names
]