No adduct generation

[samuelcajahuaringa]

Hello Isicle developers,

I try to reproduce the example of collision cross section. The Isicle was installed correctly according to the message

Requirement already satisfied: certifi>=2017.4.17 in /home/oscar.macollunco/anaconda3/envs/isicle/lib/python3.9/site-packages (from requests->snakemake>=6.3.0->isicle==2.0.0) (2024.2.2)
Requirement already satisfied: smmap<6,>=3.0.1 in /home/oscar.macollunco/anaconda3/envs/isicle/lib/python3.9/site-packages (from gitdb<5,>=4.0.1->gitpython->snakemake>=6.3.0->isicle==2.0.0) (5.0.0)
Requirement already satisfied: platformdirs>=2.5 in /home/oscar.macollunco/anaconda3/envs/isicle/lib/python3.9/site-packages (from jupyter-core->nbformat->snakemake>=6.3.0->isicle==2.0.0) (4.2.0)
Installing collected packages: isicle
  Running setup.py develop for isicle
Successfully installed isicle-2.0.0

the structure of example is dimethylglycine.mol

 OpenBabel03092420292D

 16 15  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  8  1  0  0  0  0
  1  9  1  0  0  0  0
  1 10  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  3 11  1  0  0  0  0
  3 12  1  0  0  0  0
  3 13  1  0  0  0  0
  4  5  1  0  0  0  0
  4 14  1  0  0  0  0
  4 15  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  7 16  1  0  0  0  0
M  END

I am trying to get started using isicle but im running into an issue when following the CCS example presented here.

(isicle) oscar.macollunco@sorgan-cpu6:~/isicle$ python
Python 3.9.18 | packaged by conda-forge | (main, Dec 23 2023, 16:33:10) 
[GCC 12.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import isicle
>>> geom = isicle.io.load('dimethylglycine.mol')
>>> geom = geom.initial_optimize(embed=True)
>>> adducts = geom.ionize(method = 'explicit', ion_list = ['H+'], element_list = ['O', 'N'])
>>> adducts = isicle.io.load('ccs_adducts.joblib')
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/oscar.macollunco/isicle/isicle/io.py", line 465, in load
    return load_joblib(path)
  File "/home/oscar.macollunco/isicle/isicle/io.py", line 384, in load_joblib
    with open(path, "rb") as f:
FileNotFoundError: [Errno 2] No such file or directory: 'ccs_adducts.joblib'
>>> 

where i found the 'ccs_adducts.joblib' that is a job submission file? can you send me a example.

Any help would be much appreciated.

[smcolby]

The line adducts = geom.ionize(method = 'explicit', ion_list = ['H+'], element_list = ['O', 'N']) will have generated possible adducts. Downstream activities would include conformational sampling by molecular dynamics, conformer downselection, density functional theory-based geometry optimization, and, finally, CCS prediction.

These tasks have all been developed as snakemake and nextflow workflows, which you found. However, these are intended to be run outside the ISiCLE API. For example, snakemake is invoked as snakemake --snakefile PATH {ARGS}.

We currently do not have documentation detailing the workflow usage, so I would encourage you to familiarize yourself with snakemake and/or nextflow documentation.

[samuelcajahuaringa]

Thanks for the advice @smcolby, if possible use the ccs.nf to test that example, the ccs.bf file that is found in workflows/ccs/nextflow-local/ccs.nf.

[samuelcajahuaringa]

Hello isicle developers

I have installed nextflow and I try to use ccs.nf file but I have the follow problem:

(isicle) oscar.macollunco@sorgan-cpu6:~/isicle/workflows/ccs/nextflow-local$ nextflow run ccs.nf -config nextflow.config N E X T F L O W ~ version 23.10.1 Launching ccs.nf [loving_pauling] DSL2 - revision: 94cf33a3b4 executor > local (1) [b2/140a44] process > adducts (1) [100%] 1 of 1, failed: 1 ✘ [- ] process > conformers - [- ] process > dft - [- ] process > mobility - ERROR ~ Error executing process > 'adducts (1)'

Caused by: Missing output file(s) *.joblib expected by process adducts (1)

Command executed:

!/usr/bin/env python3

import isicle import yaml import os import sys from os.path import *

cwd = "/home/oscar.macollunco/isicle/workflows/ccs/nextflow-local" with open(f"{cwd}/config.yaml", "r") as f: config = yaml.load(f, Loader=yaml.FullLoader)

geom = isicle.io.load("dimethylglycine.mol") geom = geom.initial_optimize(embed=True)

adducts = geom.ionize(ion_list=config['adducts']['ion_list'], element_list=config['adducts']['element_list'], method=config['adducts']['method'])

for add in adducts.adducts: outputpath = f'{add.basename}{add.ion}_{add.adductID}.joblib' isicle.io.save(output_path, add)

Command exit status: 0

Command output: (empty)

Work dir: /home/oscar.macollunco/isicle/workflows/ccs/nextflow-local/work/b2/140a44e0830fd74b84d4de9ef53d4d

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

-- Check '.nextflow.log' file for details

again is the joblib file,

Any help would be much appreciated.

[smcolby]

I am actually not familiar with NextFlow (I've used Snakemake). I'm copying @jessbade here, as she has more experience with NextFlow.