Merge pull request #8 from compomics/multiprediction

Addition of multiconformer prediction model and functionality

Author: rodvrees

.gitignore

@@ -111,3 +111,4 @@ IM2Deep.code-workspace
 
 # Testing
 test_data/
+test.ipynb

README.md

@@ -11,14 +11,17 @@ It is able to accurately predict CCS for modified peptides, even if the modifica
 Install with pip:
 `pip install im2deep`
 
+If you want to use the multi-output model for CCS prediction of multiconformational peptide ions, use the following installation command:
+`pip install 'im2deep[er]'`
+
 ## Usage
 ### Basic CLI usage:
 ```sh
 im2deep <path/to/peptide_file.csv>
 ```
 If you want to calibrate your predictions (HIGHLY recommended), please provide a calibration file:
 ```sh
-im2deep <path/to/peptide_file.csv> --calibration_file <path/to/peptide_file_with_CCS.csv>
+im2deep <path/to/peptide_file.csv> --calibration-file <path/to/peptide_file_with_CCS.csv>
 ```
 For an overview of all CLI arguments, run `im2deep --help`.
 

im2deep/__init__.py

@@ -1,3 +1,3 @@
 """IM2Deep: Deep learning framework for peptide collisional cross section prediction."""
 
-__version__ = "0.3.1"
+__version__ = "1.0.0"