Metadata-Version: 2.4
Name: chemdiagrams
Version: 0.1.0
Summary: Publication-quality reaction energy diagrams for computational chemistry
Author-email: Tim Bastian Enders <chemistry.tim.enders@gmail.com>
License: MIT License
        
        Copyright (c) 2026 Tim Bastian Enders
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
        copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
        SOFTWARE.
        
Project-URL: Repository, https://github.com/Tonner-Zech-Group/chem-diagrams
Project-URL: Bug Tracker, https://github.com/Tonner-Zech-Group/chem-diagrams/issues
Project-URL: Homepage, https://github.com/Tonner-Zech-Group
Keywords: chemistry,energy diagram,reaction profile,potential energy surface,matplotlib,computational chemistry,theoretical chemistry,visualization
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Scientific/Engineering :: Visualization
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: matplotlib>=3.7
Requires-Dist: numpy>=1.23
Provides-Extra: dev
Requires-Dist: pytest; extra == "dev"
Requires-Dist: mypy; extra == "dev"
Requires-Dist: ruff; extra == "dev"
Dynamic: license-file

# chemdiagrams

[![PyPI version](https://img.shields.io/pypi/v/chemdiagrams.svg)](https://pypi.org/project/chemdiagrams/)
[![Python versions](https://img.shields.io/pypi/pyversions/chemdiagrams.svg)](https://pypi.org/project/chemdiagrams/)
[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](LICENSE)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.ZENODO_DOI.svg)](https://doi.org/10.5281/zenodo.ZENODO_DOI)

A Python package for creating publication-quality reaction energy diagrams with Matplotlib.

```python
from chemdiagrams import EnergyDiagram

dia = EnergyDiagram(
    style="twosided",
    dpi=250,
    extra_y_margin=(0,0.25),
)

dia.draw_path(
    [0,1,2], [-32, 18, 0], "blue",
    path_name="Blue path",   
)

dia.draw_path(
    [2,3,4], [0, 25, -42], "red",
    path_name="Red path",
)

dia.draw_difference_bar(
    2, (-32, -42),
    r"$\Delta E_\mathrm{R}$: ",
    left_side=True,
    x_whiskers=(0,4),
    whiskercolor="red"
)
dia.bars[0].whisker_1.set_color("blue")

dia.add_image_series_in_plot(
    [penguin_II, penguin_TS, penguin, penguin_TS, penguin_II],
    y_placement="top",
    y_offsets=2
)

dia.add_numbers_average(color="black")
dia.merge_plateaus(2, "Blue path", "Red path")
dia.add_xaxis_break(2)
dia.set_xlabels(["P1", "TS1", "E", "TS2", "P2"])
dia.ax.set_ylabel(r"$\Delta E$ in kJ mol$^{-1}$", fontsize=8)
dia.legend(fontsize=5)

dia.show()
```

![Complex diagram](https://raw.githubusercontent.com/Tonner-Zech-Group/chem-diagrams/main/docs/img/example_complex.png)

## Installation

You can use the latest release by installing it from PyPi:

```bash
pip install chemdiagrams
```

**Requirements:** Python ≥ 3.10, Matplotlib ≥ 3.7, NumPy ≥ 1.23

## Features

- Multiple reaction paths on a single diagram
- Five connector styles: dotted, solid, broken dotted, broken solid, or none
- Four diagram styles: `open`, `halfboxed`, `boxed`, `twosided`
- Automatic, stacked, naïve, and averaged energy label placement
- Energy difference bars with optional whiskers
- Axis break markers for both x and y axes
- Image placement along the diagram, with automatic collision avoidance
- Full access to the underlying Matplotlib objects for fine-grained customisation
- Method chaining for compact, readable diagram construction

## Methods

| Method | Description |
|--------|-------------|
| `draw_path()` | Add a reaction pathway to the diagram |
| `draw_difference_bar()` | Draw a vertical energy difference arrow between two levels |
| `merge_plateaus()` | Visually merge two coincident energy levels at a shared x-position |
| `set_xlabels()` | Set text labels for the reaction states along the x-axis |
| `set_diagram_style()` | Change the overall visual style (`open`, `boxed`, `halfboxed`, `twosided`) |
| `add_numbers_naive()` | Annotate each energy level directly above its bar |
| `add_numbers_stacked()` | Stack labels above the highest state to avoid overlap |
| `add_numbers_auto()` | Automatically distribute labels to minimise clutter (recommended) |
| `add_numbers_average()` | Annotate with the mean energy across all paths at each x-position |
| `add_xaxis_break()` | Add a break marker on the x-axis |
| `add_yaxis_break()` | Add a break marker on the y-axis |
| `add_image_in_plot()` | Place a single image at an explicit data-coordinate position |
| `add_image_series_in_plot()` | Place a series of images along the diagram with automatic collision avoidance |
| `legend()` | Add a legend for all named paths |
| `show()` | Display the figure |

## Usage

### Drawing paths

Each call to `draw_path` adds one reaction pathway. Paths can span different x-ranges, allowing branching or incomplete pathways.

```python
dia = EnergyDiagram()

dia.draw_path(
    x_data=[0, 1, 2, 3, 4, 5],
    y_data=[0, -13, 22, 75, 39, 20],
    color="blue",
    path_name="Pathway A",      # name appears in the legend
    linetypes=[1, 1, 2, -1, 0], # connector style per segment
)

dia.draw_path(
    x_data=[0, 1, 2, 3, 5],
    y_data=[0, -25, 20, 50, 6],
    color="red",
    path_name="Pathway B",
)

dia.legend(fontsize=7)
dia.add_numbers_auto()
dia.set_xlabels(["A", "B", "C", "D", "E", "F"])
dia.ax.set_ylabel("Energy / kJ mol$^{-1}$", fontsize=8)

dia.show()
```

![Multiple paths](https://raw.githubusercontent.com/Tonner-Zech-Group/chem-diagrams/main/docs/img/example_multipaths.png)

**Connector styles** (`linetypes`):

| Value | Style |
|-------|-------|
| `1` | dotted line (default) |
| `-1` | dotted line with gap |
| `2` | solid line |
| `-2` | solid line with gap |
| `0` | no connector |

A single integer applies the same style to all segments. A list applies styles individually.

### Diagram styles

```python
dia.set_diagram_style("halfboxed")  # open | halfboxed | boxed | twosided
```

The style can be set at construction via `EnergyDiagram(style="boxed")` or changed afterwards with `set_diagram_style`.

![Diagram styles](https://raw.githubusercontent.com/Tonner-Zech-Group/chem-diagrams/main/docs/img/example_styles.png)

### X-axis labels

By default labels are placed **below** the x-axis:
```python
dia.set_xlabels(["A", "TS", "B"], fontsize=8, weight="normal")
```

Pass `in_plot=True` to render them **inside** the plot area, directly below the lowest energy state.
```python
dia.set_xlabels(["A", "TS", "B"], in_plot=True)
```

Use `labelplaces` to set explicit x-coordinates instead of the default sequential placement:
```python
dia.set_xlabels(["A", "TS", "B"], labelplaces=[0, 2, 3])
```

### Energy labels

Four numbering strategies are available. Call them after all paths have been drawn.

```python
dia.add_numbers_auto()                   # distributes labels to avoid overlaps (recommended)
dia.add_numbers_stacked()                # stacks all labels above the highest state
dia.add_numbers_naive()                  # places each label directly above its bar
dia.add_numbers_average()                # displays the mean energy across all paths

# Restrict to a range of x-values
dia.add_numbers_auto(x_min_max=(1, 4))

# Exclude a path from labelling
dia.draw_path(..., show_numbers=False)
```

### Energy difference bars

```python
dia = EnergyDiagram(style="halfboxed")
dia.draw_path(x_data=[0,1,2,3,4,5], y_data=[0,-13,22,75,39,-25], color="blue")

dia.draw_difference_bar(
    x=3,
    y_start_end=(-25, 0),
    description=r"$\Delta E_\mathrm{R}$: ",
    color="black",
    x_whiskers=(5, 0),       # draw horizontal whiskers from x=5 and x=0
    whiskercolor="blue",
    left_side=True           # text on the left
)
dia.set_xlabels(["A", "B", "C", "D", "E", "F"])
dia.add_numbers_auto()
dia.show()
```

![Difference bar](https://raw.githubusercontent.com/Tonner-Zech-Group/chem-diagrams/main/docs/img/example_diffbar.png)

### Axis breaks

```python
dia = EnergyDiagram(style="twosided")
dia.draw_path(...)

dia.add_yaxis_break(y=5)
dia.add_xaxis_break(x=2, gap_scale=2, stopper_scale=1.5, angle=60)

dia.show()
```

Note: x-axis breaks are not compatible with the `"open"` style.

### Merging degenerate plateaus

When two paths share the same energy level at the same x-position, `merge_plateaus`
replaces both full-width bars with two shorter half-bars separated by a gap, with
diagonal tick marks to indicate degeneracy.
```python
dia = EnergyDiagram()
dia.draw_path(x_data=[0, 1, 2], y_data=[0, 50, 10], color="blue", path_name="Path A")
dia.draw_path(x_data=[0, 1, 2], y_data=[0, 50, -5], color="red",  path_name="Path B")

# Both paths share y=50 at x=1
dia.merge_plateaus(
    x=1,
    path_name_left="Path A",
    path_name_right="Path B",
    gap_scale=1.0,       # width of the gap between the two half-bars
    stopper_scale=1.0,   # size of the diagonal tick marks
    angle=30,            # angle of the tick marks in degrees
)

dia.add_numbers_auto()
dia.show()
```

Both paths must already be drawn and must have exactly the same y-value at `x`.

### Figure settings

```python
dia = EnergyDiagram(
    extra_x_margin=(0, 0.5),   # additional margin in x (axis units)
    extra_y_margin=(0, 0.2),   # additional margin in y (relative units)
    figsize=(6, 4),            # explicit figure size in inches
    width_limit=7,             # maximum auto-scaled width in inches
    fontsize=10,
    style="halfboxed",
    dpi=150,
)
```

### Placing images

`add_image_in_plot` places a single image at an explicit position in data coordinates.

```python
# Single image at a fixed position
dia.add_image_in_plot(
    "path/to/image.png",
    position=(2, 30),               # (x, y) in data coordinates
    img_name="my_image",            # optional name to access the artist later via dia.images
    width=0.5,                      # width in axis units; 
                                    # if omitted, height is used to scale or width is set automatically
    height=None,                    # height in axis units
    horizontal_alignment="center",  # "center", "left", or "right" relative to position
    vertical_alignment="center",    # "center", "top", or "bottom" relative to position
    framed=True,                    # draw a border rectangle around the image
    frame_color="black",            # color of the border
)
```

`add_image_series_in_plot` places one image per reaction state, with automatic collision avoidance against energy numbers and x-axis labels.

```python
# Series of images distributed automatically along the diagram
dia.add_image_series_in_plot(
    ["img0.png", "img1.png", "img2.png", "img3.png", "img4.png"],
    img_x_places=[0, 1, 2, 3, 4],        # which x positions to place images at;
                                         # defaults to 0,1,2,... if omitted
    y_placement="auto",                  # "auto", "top", or "bottom" — can also be a list
                                         # per image, e.g. ["auto", "top", "auto", "bottom", "auto"]
                                         # "auto" automatically decides whether it is placed on top or bottom
    y_offsets=5,                         # additional vertical offset in data units, scalar or per-image list
    img_series_name="my_series",         # optional name to access artists later via dia.images
    width=0.6,                           # scalar applies to all; pass a list for per-image widths
                                         # if omitted, height is used to scale or width is set automatically
    height=None,                         # scalar applies to all; pass a list for per-image heights
    framed=False,                        # scalar or per-image list of bools
    frame_colors="black",                # scalar or per-image list of color strings
)
```

SVG and EPS formats are not supported; PNG and JPEG work best.

### Saving figures

```python
dia.fig.savefig("diagram.png", dpi=300, bbox_inches="tight")
dia.fig.savefig("diagram.pdf", bbox_inches="tight")
```

### Accessing Matplotlib objects

All artists are accessible after drawing for direct Matplotlib customisation.

```python
dia.draw_path(..., path_name="My Path")
dia.add_numbers_auto()

# Plateau and connector lines
# Keys are x-positions formatted to one decimal place
plateau   = dia.lines["My Path"].plateaus["2.0"]     # x=2
connector = dia.lines["My Path"].connections["1.5"]  # midpoint between x=1 and x=2
plateau.set_color("green")

# Energy labels
label = dia.numbers["My Path"]["2.0"]                # x=2
label.set_color("red")
label.set_fontsize(12)

# Difference bar components
dia.bars[0].text.set_color("red")
dia.bars[0].bar.arrow_patch.set_color("green")
dia.bars[0].whisker_2.set_linestyle("--")

# Style objects (axes, arrows, x-labels)
dia.ax_objects.x_labels["2.0"].set_color("purple")

# Axis arrows (twosided/open/halfopen styles)
dia.ax_objects.arrows["x_arrow"].set_color("gray")

# Axis break artists
dia.ax_objects.xaxis_breaks["2.0"].stopper_1.set_color("red")
dia.ax_objects.yaxis_breaks["5.0"].whitespace.set_facecolor("lightyellow")

# Direct Matplotlib axes access
dia.ax.set_ylabel("Energy / kJ mol$^{-1}$", fontsize=10)
dia.fig.savefig("diagram.png", dpi=300, bbox_inches="tight")

# Access a single image artist added with add_image_in_plot
img_object = dia.images["my_image"]                  # ImageObject
img_object.image.set_alpha(0.8)                      # AxesImage — any matplotlib imshow property
img_object.borders["top"].set_color("red")           # frame border lines, keyed by "top",
img_object.borders["left"].set_linewidth(2)          # "bottom", "top", "left", "right"

# Access images added with add_image_series_in_plot
series = dia.images["my_series"]                     # dict keyed by x-position as "x.x" string
img_at_x1 = series["1.0"]                            # ImageObject at x=1
img_at_x1.image.set_alpha(0.5)
img_at_x1.borders["bottom"].set_linestyle("--")

```

## Examples

A full set of examples covering all features is available in [`examples/example_use.ipynb`](https://github.com/Tonner-Zech-Group/chem-diagrams/blob/main/examples/example_use.ipynb).

## Citation

If you use chemdiagrams in published work, please consider citing the repository:

```
Tim Bastian Enders, chemdiagrams, https://github.com/Tonner-Zech-Group/chem-diagrams
```

## License

MIT — see [LICENSE](LICENSE) for details.
