Map BEIS and MEGAN species to CRACMM

author: Havala Pye
date: 2024-08-08

updated: Nash Skipper
date: 2024-08-09

updated: Michael Pye
date: 2025-02-27

Notebook Description

This Notebook identifies the CRACMM species for each BEIS/MEGAN species using the mapper. The cracmm_mapper function depends on rdkit .

Download Notebook

Click here to access the Jupyter Notebook file directly in GitHub where it can be downloaded.

Setup

import pandas as pd
import os

## Install rdkit if not already installed

# !python -m pip install --user rdkit

# to install in the current kernel:
# %pip install rdkit

# set location of mapper downloaded from https://github.com/USEPA/CRACMM/
# import sys
# utildir = '/path/to/cracmm/utilities/directory'   
# sys.path.append(utildir)

# Import the python utilities
import cracmm1_mapper as cracmm1   # includes: get_cracmm_roc(smiles,koh,log10cstar) (Version 1)
import cracmm2_mapper as cracmm2   # includes: get_cracmm_roc(smiles,koh,log10cstar) (Version 2)

datadir = '../emissions/BiogenicMappings/'    # data files of mappings
outputdir = os.path.join(os.getcwd(), 'output/')

pd.set_option('display.max_rows', None)
pd.options.mode.copy_on_write = True
csvout_kw = dict(sep=',', na_rep='', float_format=None, columns=None, header=True, index=False)

BEIS

input beis mapping from https://github.com/USEPA/CRACMM/tree/main/emissions/BiogenicMappings

filename = datadir + 'bvoc_beis_tocracmm.csv' 
dfbeis = pd.read_csv(filename)
# for checking if any species mapping changed
orig_map_colname = 'CRACMM1' # an existing version in file to compare to, options: CRACMM1, CRACMM2
dfbeis = dfbeis.rename(columns=dict(CRACMMorig=orig_map_colname))

# run cracmm2 mapper
smiles_k = 'SMILES'
koh_k    = 'ATMOSPHERIC_HYDROXYLATION_RATE_(AOH)_CM3/MOLECULE*SEC_OPERA_PRED'
cstar_k  = 'log10Cstar_ugm3'
dfbeis['CRACMMnew'] = dfbeis.apply(lambda x: cracmm2.get_cracmm_roc(x[smiles_k], x[koh_k], x[cstar_k]), axis=1)

# check if any species mappings changed
dfbeis_checkmatch = dfbeis.eval(f'match = {orig_map_colname}==CRACMMnew')
show_cols = ['SPECIES_NAME',orig_map_colname,'CRACMMnew']
if len(dfbeis_checkmatch[dfbeis_checkmatch.match==False])>0:
    print(f'the species mappings below changed from {orig_map_colname}')
    display(dfbeis_checkmatch[show_cols][dfbeis_checkmatch.match==False])
else:
    print(f'all species matched {orig_map_colname} mapping')

# save output
#dfbeis = dfbeis.drop(columns=orig_map_colname)
dfbeis.to_csv(outputdir+'bvoc_beis_tocracmm.csv', **csvout_kw)

the species mappings below changed from CRACMM1

/work/MOD3DEV/mpye/cracmm_sphinx/utilities/cracmm2_mapper.py:284: UserWarning: Species with SMILES [N]=O is unknown in CRACMM and has been mapped to UNKCRACMM.
  warnings.warn(unkcracmm_msg)
/work/MOD3DEV/mpye/cracmm_sphinx/utilities/cracmm2_mapper.py:284: UserWarning: Species with SMILES [C-]#[O+] is unknown in CRACMM and has been mapped to UNKCRACMM.
  warnings.warn(unkcracmm_msg)

	SPECIES_NAME	CRACMM1	CRACMMnew
1	nitric oxide	UNKKOH	UNKCRACMM
12	para-cymene	ROCP6ARO	VROCP6ARO
32	carbon monoxide	SLOWROC	UNKCRACMM

MEGAN

input megan mapping from https://github.com/USEPA/CRACMM/tree/main/emissions/BiogenicMappings

filename = datadir + 'bvoc_megan_tocracmm.csv'
dfmegan = pd.read_csv(filename)
# for checking if any species mapping changed
orig_map_colname = 'CRACMM1' # an existing version in file to compare to, options: CRACMM1, CRACMM2
dfmegan = dfmegan.rename(columns=dict(CRACMMorig=orig_map_colname))

# run cracmm2 mapper
smiles_k = 'SMILES'
koh_k    = 'ATMOSPHERIC_HYDROXYLATION_RATE_(AOH)_CM3/MOLECULE*SEC_OPERA_PRED'
cstar_k  = 'log10Cstar_ugm3'
dfmegan['CRACMMnew'] = dfmegan.apply(lambda x: cracmm2.get_cracmm_roc(x[smiles_k], x[koh_k], x[cstar_k]), axis=1)

# check if any species mappings changed
dfmegan_checkmatch = dfmegan.eval(f'match = {orig_map_colname}==CRACMMnew')
show_cols = ['REPRESENTATIVE_COMPOUND_NAME',orig_map_colname,'CRACMMnew']
if len(dfmegan_checkmatch[dfmegan_checkmatch.match==False])>0:
    print(f'the species mappings below changed from {orig_map_colname}')
    display(dfmegan_checkmatch[show_cols][dfmegan_checkmatch.match==False])
else:
    print(f'all species matched {orig_map_colname} mapping')

# save output
#dfmegan = dfmegan.drop(columns=orig_map_colname)
dfmegan.to_csv(outputdir+'bvoc_beis_tocracmm.csv', **csvout_kw)

the species mappings below changed from CRACMM1

/work/MOD3DEV/mpye/cracmm_sphinx/utilities/cracmm2_mapper.py:284: UserWarning: Species with SMILES S is unknown in CRACMM and has been mapped to UNKCRACMM.
  warnings.warn(unkcracmm_msg)
/work/MOD3DEV/mpye/cracmm_sphinx/utilities/cracmm2_mapper.py:284: UserWarning: Species with SMILES [C-]#[O+] is unknown in CRACMM and has been mapped to UNKCRACMM.
  warnings.warn(unkcracmm_msg)
/work/MOD3DEV/mpye/cracmm_sphinx/utilities/cracmm2_mapper.py:284: UserWarning: Species with SMILES [N]=O is unknown in CRACMM and has been mapped to UNKCRACMM.
  warnings.warn(unkcracmm_msg)

	REPRESENTATIVE_COMPOUND_NAME	CRACMM1	CRACMMnew
23	1-Isopropyl-2-methylbenzene	XYE	XYL
24	p-Cymene	ROCP6ARO	VROCP6ARO
25	m-Cymene	XYE	XYL
26	1-Methyl-4-(prop-1-en-2-yl)benzene	XYM	XYL
27	dl-Borneol	ROCIOXY	VROCIOXY
28	Bornyl acetate	ROCIOXY	VROCIOXY
30	Estragole	ROCP6ARO	VROCP6ARO
32	beta-Ionone	ROCP6ARO	VROCP6ARO
34	6,6-Dimethylbicyclo[3.1.1]heptane-2-carbaldehyde	ROCIOXY	VROCIOXY
35	1-Octanol	ROCIOXY	VROCIOXY
36	1-Octen-3-ol	ROCP6ARO	VROCP6ARO
55	Farnesol	ROCP5ARO	VROCP5ARO
62	cis-Nerolidol	ROCP5ARO	VROCP5ARO
63	trans-Nerolidol	ROCP5ARO	VROCP5ARO
67	2-Ethylhexyl salicylate	ROCP2ALK	VROCP2OXY2
70	(-)-alpha-Cadinol	ROCP5ARO	VROCP5ARO
72	(+)-Cedrol	ROCP5ALK	VROCP5OXY1
77	3,3,5-Trimethylcyclohexyl salicylate	ROCP1ALK	VROCP1OXY1
79	(-)-Kaur-16-ene	ROCP5ARO	VROCP5ARO
86	(+)-Longicyclene	ROCP4ALK	VROCP4ALK
103	Decanal	ROCIOXY	VROCIOXY
104	(E)-6,10-Dimethylundeca-5,9-dien-2-one	ROCP6ARO	VROCP6ARO
105	(E)-6,10-Dimethylundeca-5,9-dien-2-one	ROCP6ARO	VROCP6ARO
108	6,10-Dimethyl-5,9-undecadiene-2-one	ROCP6ARO	VROCP6ARO
109	Nonanal	ROCIOXY	VROCIOXY
110	2-Nonenal	ROCP6ARO	VROCP6ARO
126	7-heptadecene	ROCP5ARO	VROCP5ARO
127	Acetophenone	ROCP6ARO	VROCP6ARO
128	Anisole	XYM	XYL
131	Benzyl benzoate	ROCP5ARO	VROCP5ARO
132	Benzyl acetate	ROCP6ARO	VROCP6ARO
138	Cinnamic acid	ROCP2ALK	VROCP2OXY2
139	Coniferyl alcohol	ROCP1ALK	VROCP1OXY3
142	Ethyl cinnamate	ROCP5ARO	VROCP5ARO
159	Jasmone	ROCP6ARO	VROCP6ARO
162	Linalool oxide pyranoid, cis-(+-)-	ROCP5ARO	VROCP5ARO
163	Linalool oxide pyranoid, cis-(+-)-	ROCP5ARO	VROCP5ARO
165	Methyl benzoate	ROCP6ARO	VROCP6ARO
166	Methyl jasmonate	ROCP5ARO	VROCP5ARO
171	(2E)-3-(4-Hydroxyphenyl)-2-propenoic acid	ROCP1ALK	VROCP1OXY3
174	Safrole	ROCP5ARO	VROCP5ARO
178	m-Xylene	XYM	XYL
181	(Z)-Hex-3-enyl butyrate	ROCP6ARO	VROCP6ARO
187	Diallyl disulfide	ROCP6ARO	VROCP6ARO
190	1-Dodecene	ROCP6ARO	VROCP6ARO
195	Hydrogen sulfide	UNKKOH	UNKCRACMM
196	Indole	ROCP5ARO	VROCP5ARO
204	3-Methylbut-3-en-1-ol	OLI	OLT
207	Allyl propyl disulfide	ROCP6ARO	VROCP6ARO
209	3-Methylindole	ROCP5ARO	VROCP5ARO
210	alpha-Terpinyl acetate	ROCP6ARO	VROCP6ARO
211	alpha-Terpinyl acetate	ROCP6ARO	VROCP6ARO
212	1-Tetradecene	ROCP5ARO	VROCP5ARO
214	Carbon monoxide	SLOWROC	UNKCRACMM
215	Nitric oxide	UNKKOH	UNKCRACMM