pyplogo 0.1.6

# pyplogo-toolkit

PyPLogo工具包：专业的蛋白质二级结构分析可视化工具。提供从结构提取、多主题定制到高质量出版级绘图的完整解决方案。

PyPLogo Toolkit: A professional tool for protein secondary structure analysis and visualization. Offers a complete solution from structure extraction, multi-theme customization to high-quality publication-ready plotting.

Multiple-sequence alignment with secondary structure

Version 0.1.6 adds compact multi-line alignments with a selectable structure sequence, DSSP structure glyphs, disulfide markers, and residue-level annotation tracks.

from pyplogo import SecondaryStructureVisualizer

alignment = {
    "reference": "MK--TAACDEFG",
    "homolog":   "MKQ-TAACDEFG",
}

visualizer = SecondaryStructureVisualizer(
    colors={
        "H": "#59B97B",
        "G": "#D38AAA",
        "I": "#7668B5",
        "E": "#D6A15E",
        "T": "#9D8BC5",
        "structure_label": "#B27A3D",
    }
)

fig = visualizer.create_alignment_figure(
    alignment,
    structure_sequence="reference",
    secondary_structure="HHTTEEECCC",
    structure_label="reference structure",
    amino_acids_per_line=60,
    structure_mode="major",  # H/G/I/E/T; use "all" for S and coil too
    sequence_colors={"reference": "#B27A3D", "homolog": "#7668B5"},
    disulfide_bonds=[(7, 10)],  # 1-based ungapped residue positions
    epitope_annotations={
        "antibody A epitope": [7, 9, 10],
        "antibody B epitope": [8, 11],
    },
    epitope_colors={
        "antibody A epitope": "#8FB9DB",
        "antibody B epitope": "#D39A9B",
    },
)
fig.savefig("alignment.svg", bbox_inches="tight")

Frequently used style controls include:

• show_legend, legend_position, legend_columns, legend_font_size
• show_epitope_legend, epitope_marker, epitope_marker_size
• sequence_font_size, label_font_size, sequence_pitch
• show_residue_numbers, show_conservation, conservation_threshold
• disulfide_color, disulfide_text_color, disulfide_line_width
• annotation_offset, annotation_track_spacing, structure_offset