diff --git a/docs/getting_started.md b/docs/getting_started.md
index 73cbd5f0..78163ac2 100644
--- a/docs/getting_started.md
+++ b/docs/getting_started.md
@@ -81,9 +81,12 @@ This model file or a custom one can then be specified using the `--model` comman
Not all releases will have a model file included on the [Releases page](https://github.com/Noble-Lab/casanovo/releases), in which case model weights for alternative releases with the same major version number can be used.
-The most recent model weights for Casanovo version 3.x are currently provided under [Casanovo v3.0.0](https://github.com/Noble-Lab/casanovo/releases/tag/v3.0.0):
-- `casanovo_massivekb.ckpt`: Default Casanovo weights to use when analyzing tryptic data. These weights will be downloaded automatically if no weights are explicitly specified.
-- `casanovo_non-enzy.checkpt`: Casanovo weights to use when analyzing non-tryptic data, obtained by fine-tuning the tryptic model on multi-enzyme data. These weights need to be downloaded manually.
+The most recent model weights for Casanovo version 4.2 and above are currently provided under [Casanovo v4.2.0](https://github.com/Noble-Lab/casanovo/releases/tag/v4.2.0):
+- `casanovo_v4_2_0.ckpt`: Default Casanovo weights to use as described in [Melendez et al.](https://pubs.acs.org/doi/full/10.1021/acs.jproteome.4c00422). These weights will be downloaded automatically if no weights are explicitly specified.
+
+Alternatively, model weigths for Casanovo version 4.x as described in [Yilmaz et al.](https://www.nature.com/articles/s41467-024-49731-x) are currently provided under [Casanovo v4.0.0](https://github.com/Noble-Lab/casanovo/releases/tag/v4.0.0):
+- `casanovo_massivekb.ckpt`: Casanovo weights to use when analyzing tryptic data. These weights need to be downloaded manually.
+- `casanovo_nontryptic.ckpt`: Casanovo weights to use when analyzing non-tryptic data, obtained by fine-tuning the tryptic model on multi-enzyme data. These weights need to be downloaded manually.
## Running Casanovo
diff --git a/docs/images/configure-help.svg b/docs/images/configure-help.svg
index 0822927a..b1fcce10 100644
--- a/docs/images/configure-help.svg
+++ b/docs/images/configure-help.svg
@@ -19,57 +19,63 @@
font-weight: 700;
}
- .terminal-3936755216-matrix {
+ .terminal-2766440694-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-3936755216-title {
+ .terminal-2766440694-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-3936755216-r1 { fill: #c5c8c6 }
+ .terminal-2766440694-r1 { fill: #c5c8c6 }
+.terminal-2766440694-r2 { fill: #d0b344 }
+.terminal-2766440694-r3 { fill: #c5c8c6;font-weight: bold }
+.terminal-2766440694-r4 { fill: #68a0b3;font-weight: bold }
+.terminal-2766440694-r5 { fill: #868887 }
+.terminal-2766440694-r6 { fill: #98a84b;font-weight: bold }
+.terminal-2766440694-r7 { fill: #d0b344;font-weight: bold }
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-
+
-
- $ casanovo configure --help
-
- Usage: casanovo configure [OPTIONS]
-
- Generate a Casanovo configuration file to customize.
- The casanovo configuration file is in the YAML format.
-
-╭─ Options ────────────────────────────────────────────────────────────────────╮
-│ --output -o FILE The output configuration file. │
-│ --help -h Show this message and exit. │
-╰──────────────────────────────────────────────────────────────────────────────╯
-
+
+ $ casanovo configure --help
+
+Usage:casanovo configure [OPTIONS]
+
+ Generate a Casanovo configuration file to customize.
+ The casanovo configuration file is in the YAML format.
+
+╭─ Options ────────────────────────────────────────────────────────────────────╮
+│--output-oFILE The output configuration file. │
+│--help-h Show this message and exit. │
+╰──────────────────────────────────────────────────────────────────────────────╯
+
diff --git a/docs/images/evaluate-help.svg b/docs/images/evaluate-help.svg
index b16c4ffd..2f770e2e 100644
--- a/docs/images/evaluate-help.svg
+++ b/docs/images/evaluate-help.svg
@@ -19,99 +19,108 @@
font-weight: 700;
}
- .terminal-1284026435-matrix {
+ .terminal-2215953096-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-1284026435-title {
+ .terminal-2215953096-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-1284026435-r1 { fill: #c5c8c6 }
+ .terminal-2215953096-r1 { fill: #c5c8c6 }
+.terminal-2215953096-r2 { fill: #d0b344 }
+.terminal-2215953096-r3 { fill: #c5c8c6;font-weight: bold }
+.terminal-2215953096-r4 { fill: #68a0b3;font-weight: bold }
+.terminal-2215953096-r5 { fill: #868887 }
+.terminal-2215953096-r6 { fill: #cc555a }
+.terminal-2215953096-r7 { fill: #d0b344;font-weight: bold }
+.terminal-2215953096-r8 { fill: #8a4346 }
+.terminal-2215953096-r9 { fill: #98a84b;font-weight: bold }
+.terminal-2215953096-r10 { fill: #8d7b39;font-weight: bold }
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@@ -123,35 +132,35 @@
-
+
-
- $ casanovo evaluate --help
-
- Usage: casanovo evaluate [OPTIONS] ANNOTATED_PEAK_PATH...
-
- Evaluate de novo peptide sequencing performance.
- ANNOTATED_PEAK_PATH must be one or more annoated MGF files, such as those
- provided by MassIVE-KB.
-
-╭─ Arguments ──────────────────────────────────────────────────────────────────╮
-│ * ANNOTATED_PEAK_PATH FILE [required] │
-╰──────────────────────────────────────────────────────────────────────────────╯
-╭─ Options ────────────────────────────────────────────────────────────────────╮
-│ --model -m FILE The model weights (.ckpt file). │
-│ If not provided, Casanovo will │
-│ try to download the latest │
-│ release. │
-│ --output -o FILE The mzTab file to which results │
-│ will be written. │
-│ --config -c FILE The YAML configuration file │
-│ overriding the default options. │
-│ --verbosity -v [debug|info|warning|error] Set the verbosity of console │
-│ logging messages. Log files are │
-│ always set to 'debug'. │
-│ --help -h Show this message and exit. │
-╰──────────────────────────────────────────────────────────────────────────────╯
-
+
+ $ casanovo evaluate --help
+
+Usage:casanovo evaluate [OPTIONS] ANNOTATED_PEAK_PATH...
+
+ Evaluate de novo peptide sequencing performance.
+ ANNOTATED_PEAK_PATH must be one or more annoated MGF files, such as those
+ provided by MassIVE-KB.
+
+╭─ Arguments ──────────────────────────────────────────────────────────────────╮
+│* ANNOTATED_PEAK_PATH FILE[required]│
+╰──────────────────────────────────────────────────────────────────────────────╯
+╭─ Options ────────────────────────────────────────────────────────────────────╮
+│--model-mFILE The model weights (.ckpt file). │
+│ If not provided, Casanovo will │
+│ try to download the latest │
+│ release. │
+│--output-oFILE The mzTab file to which results │
+│ will be written. │
+│--config-cFILE The YAML configuration file │
+│ overriding the default options. │
+│--verbosity-v[debug|info|warning|error] Set the verbosity of console │
+│ logging messages. Log files are │
+│ always set to 'debug'. │
+│--help-h Show this message and exit. │
+╰──────────────────────────────────────────────────────────────────────────────╯
+
diff --git a/docs/images/help.svg b/docs/images/help.svg
index 2e22e2d3..eae8e93d 100644
--- a/docs/images/help.svg
+++ b/docs/images/help.svg
@@ -19,126 +19,133 @@
font-weight: 700;
}
- .terminal-100512290-matrix {
+ .terminal-771077830-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-100512290-title {
+ .terminal-771077830-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-100512290-r1 { fill: #c5c8c6 }
+ .terminal-771077830-r1 { fill: #c5c8c6 }
+.terminal-771077830-r2 { fill: #d0b344 }
+.terminal-771077830-r3 { fill: #c5c8c6;font-weight: bold }
+.terminal-771077830-r4 { fill: #68a0b3;font-weight: bold }
+.terminal-771077830-r5 { fill: #d0b344;font-weight: bold }
+.terminal-771077830-r6 { fill: #608ab1;text-decoration: underline; }
+.terminal-771077830-r7 { fill: #868887 }
+.terminal-771077830-r8 { fill: #98a84b;font-weight: bold }
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@@ -150,44 +157,44 @@
-
+
-
- $ casanovo --help
-
- Usage: casanovo [OPTIONS] COMMAND [ARGS]...
-
- ┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
- ┃ Casanovo ┃
- ┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛
- Casanovo de novo sequences peptides from tandem mass spectra using a
- Transformer model. Casanovo currently supports mzML, mzXML, and MGF files for
- de novo sequencing and annotated MGF files, such as those from MassIVE-KB, for
- training new models.
-
- Links:
-
- • Documentation: https://casanovo.readthedocs.io
- • Official code repository: https://github.com/Noble-Lab/casanovo
-
- If you use Casanovo in your work, please cite:
-
- • Yilmaz, M., Fondrie, W. E., Bittremieux, W., Oh, S. & Noble, W. S. De novo
- mass spectrometry peptide sequencing with a transformer model. Proceedings
- of the 39th International Conference on Machine Learning - ICML '22 (2022)
- doi:10.1101/2022.02.07.479481.
-
-╭─ Options ────────────────────────────────────────────────────────────────────╮
-│ --help -h Show this message and exit. │
-╰──────────────────────────────────────────────────────────────────────────────╯
-╭─ Commands ───────────────────────────────────────────────────────────────────╮
-│ configure Generate a Casanovo configuration file to customize. │
-│ evaluate Evaluate de novo peptide sequencing performance. │
-│ sequence De novo sequence peptides from tandem mass spectra. │
-│ train Train a Casanovo model on your own data. │
-│ version Get the Casanovo version information │
-╰──────────────────────────────────────────────────────────────────────────────╯
-
+
+ $ casanovo --help
+
+Usage:casanovo [OPTIONS] COMMAND [ARGS]...
+
+ ┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
+ ┃ Casanovo ┃
+ ┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛
+ Casanovo de novo sequences peptides from tandem mass spectra using a
+ Transformer model. Casanovo currently supports mzML, mzXML, and MGF files for
+ de novo sequencing and annotated MGF files, such as those from MassIVE-KB, for
+ training new models.
+
+ Links:
+
+ • Documentation: https://casanovo.readthedocs.io
+ • Official code repository: https://github.com/Noble-Lab/casanovo
+
+ If you use Casanovo in your work, please cite:
+
+ • Yilmaz, M., Fondrie, W. E., Bittremieux, W., Oh, S. & Noble, W. S. De novo
+mass spectrometry peptide sequencing with a transformer model. Proceedings
+of the 39th International Conference on Machine Learning - ICML '22 (2022)
+doi:10.1101/2022.02.07.479481.
+
+╭─ Options ────────────────────────────────────────────────────────────────────╮
+│--help-h Show this message and exit. │
+╰──────────────────────────────────────────────────────────────────────────────╯
+╭─ Commands ───────────────────────────────────────────────────────────────────╮
+│configure Generate a Casanovo configuration file to customize. │
+│evaluate Evaluate de novo peptide sequencing performance. │
+│sequence De novo sequence peptides from tandem mass spectra. │
+│train Train a Casanovo model on your own data. │
+│version Get the Casanovo version information │
+╰──────────────────────────────────────────────────────────────────────────────╯
+
diff --git a/docs/images/sequence-help.svg b/docs/images/sequence-help.svg
index f5799766..6635cfaa 100644
--- a/docs/images/sequence-help.svg
+++ b/docs/images/sequence-help.svg
@@ -19,99 +19,108 @@
font-weight: 700;
}
- .terminal-2359602172-matrix {
+ .terminal-2906046081-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-2359602172-title {
+ .terminal-2906046081-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-2359602172-r1 { fill: #c5c8c6 }
+ .terminal-2906046081-r1 { fill: #c5c8c6 }
+.terminal-2906046081-r2 { fill: #d0b344 }
+.terminal-2906046081-r3 { fill: #c5c8c6;font-weight: bold }
+.terminal-2906046081-r4 { fill: #68a0b3;font-weight: bold }
+.terminal-2906046081-r5 { fill: #868887 }
+.terminal-2906046081-r6 { fill: #cc555a }
+.terminal-2906046081-r7 { fill: #d0b344;font-weight: bold }
+.terminal-2906046081-r8 { fill: #8a4346 }
+.terminal-2906046081-r9 { fill: #98a84b;font-weight: bold }
+.terminal-2906046081-r10 { fill: #8d7b39;font-weight: bold }
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@@ -123,35 +132,35 @@
-
+
-
- $ casanovo sequence --help
-
- Usage: casanovo sequence [OPTIONS] PEAK_PATH...
-
- De novo sequence peptides from tandem mass spectra.
- PEAK_PATH must be one or more mzMl, mzXML, or MGF files from which to sequence
- peptides.
-
-╭─ Arguments ──────────────────────────────────────────────────────────────────╮
-│ * PEAK_PATH FILE [required] │
-╰──────────────────────────────────────────────────────────────────────────────╯
-╭─ Options ────────────────────────────────────────────────────────────────────╮
-│ --model -m FILE The model weights (.ckpt file). │
-│ If not provided, Casanovo will │
-│ try to download the latest │
-│ release. │
-│ --output -o FILE The mzTab file to which results │
-│ will be written. │
-│ --config -c FILE The YAML configuration file │
-│ overriding the default options. │
-│ --verbosity -v [debug|info|warning|error] Set the verbosity of console │
-│ logging messages. Log files are │
-│ always set to 'debug'. │
-│ --help -h Show this message and exit. │
-╰──────────────────────────────────────────────────────────────────────────────╯
-
+
+ $ casanovo sequence --help
+
+Usage:casanovo sequence [OPTIONS] PEAK_PATH...
+
+ De novo sequence peptides from tandem mass spectra.
+ PEAK_PATH must be one or more mzMl, mzXML, or MGF files from which to sequence
+ peptides.
+
+╭─ Arguments ──────────────────────────────────────────────────────────────────╮
+│* PEAK_PATH FILE[required]│
+╰──────────────────────────────────────────────────────────────────────────────╯
+╭─ Options ────────────────────────────────────────────────────────────────────╮
+│--model-mFILE The model weights (.ckpt file). │
+│ If not provided, Casanovo will │
+│ try to download the latest │
+│ release. │
+│--output-oFILE The mzTab file to which results │
+│ will be written. │
+│--config-cFILE The YAML configuration file │
+│ overriding the default options. │
+│--verbosity-v[debug|info|warning|error] Set the verbosity of console │
+│ logging messages. Log files are │
+│ always set to 'debug'. │
+│--help-h Show this message and exit. │
+╰──────────────────────────────────────────────────────────────────────────────╯
+
diff --git a/docs/images/train-help.svg b/docs/images/train-help.svg
index fccd4140..58251215 100644
--- a/docs/images/train-help.svg
+++ b/docs/images/train-help.svg
@@ -19,138 +19,147 @@
font-weight: 700;
}
- .terminal-2430201580-matrix {
+ .terminal-2982408974-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-2430201580-title {
+ .terminal-2982408974-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-2430201580-r1 { fill: #c5c8c6 }
+ .terminal-2982408974-r1 { fill: #c5c8c6 }
+.terminal-2982408974-r2 { fill: #d0b344 }
+.terminal-2982408974-r3 { fill: #c5c8c6;font-weight: bold }
+.terminal-2982408974-r4 { fill: #68a0b3;font-weight: bold }
+.terminal-2982408974-r5 { fill: #868887 }
+.terminal-2982408974-r6 { fill: #cc555a }
+.terminal-2982408974-r7 { fill: #d0b344;font-weight: bold }
+.terminal-2982408974-r8 { fill: #8a4346 }
+.terminal-2982408974-r9 { fill: #98a84b;font-weight: bold }
+.terminal-2982408974-r10 { fill: #8d7b39;font-weight: bold }
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@@ -162,48 +171,48 @@
-
+
-
- $ casanovo train --help
-
- Usage: casanovo train [OPTIONS] TRAIN_PEAK_PATH...
-
- Train a Casanovo model on your own data.
- TRAIN_PEAK_PATH must be one or more annoated MGF files, such as those provided
- by MassIVE-KB, from which to train a new Casnovo model.
-
-╭─ Arguments ──────────────────────────────────────────────────────────────────╮
-│ * TRAIN_PEAK_PATH FILE [required] │
-╰──────────────────────────────────────────────────────────────────────────────╯
-╭─ Options ────────────────────────────────────────────────────────────────────╮
-│ * --validation_peak_pa… -p FILE An annotated MGF file │
-│ for validation, like │
-│ from MassIVE-KB. Use │
-│ this option multiple │
-│ times to specify │
-│ multiple files. │
-│ [required] │
-│ --model -m FILE The model weights │
-│ (.ckpt file). If not │
-│ provided, Casanovo │
-│ will try to download │
-│ the latest release. │
-│ --output -o FILE The mzTab file to │
-│ which results will be │
-│ written. │
-│ --config -c FILE The YAML configuration │
-│ file overriding the │
-│ default options. │
-│ --verbosity -v [debug|info|warning|er Set the verbosity of │
-│ ror] console logging │
-│ messages. Log files │
-│ are always set to │
-│ 'debug'. │
-│ --help -h Show this message and │
-│ exit. │
-╰──────────────────────────────────────────────────────────────────────────────╯
-
+
+ $ casanovo train --help
+
+Usage:casanovo train [OPTIONS] TRAIN_PEAK_PATH...
+
+ Train a Casanovo model on your own data.
+ TRAIN_PEAK_PATH must be one or more annoated MGF files, such as those provided
+ by MassIVE-KB, from which to train a new Casnovo model.
+
+╭─ Arguments ──────────────────────────────────────────────────────────────────╮
+│* TRAIN_PEAK_PATH FILE[required]│
+╰──────────────────────────────────────────────────────────────────────────────╯
+╭─ Options ────────────────────────────────────────────────────────────────────╮
+│*--validation_peak_pa…-pFILE An annotated MGF file │
+│ for validation, like │
+│ from MassIVE-KB. Use │
+│ this option multiple │
+│ times to specify │
+│ multiple files. │
+│[required] │
+│--model-mFILE The model weights │
+│ (.ckpt file). If not │
+│ provided, Casanovo │
+│ will try to download │
+│ the latest release. │
+│--output-oFILE The mzTab file to │
+│ which results will be │
+│ written. │
+│--config-cFILE The YAML configuration │
+│ file overriding the │
+│ default options. │
+│--verbosity-v[debug|info|warning|er Set the verbosity of │
+│ror] console logging │
+│ messages. Log files │
+│ are always set to │
+│ 'debug'. │
+│--help-h Show this message and │
+│ exit. │
+╰──────────────────────────────────────────────────────────────────────────────╯
+