PyeMap-2.0.2

Bug fixes:

• Fixed bug associated with sequence alignment when non protein residues are not placed at the end of the chain. Had no effect on the back end, but cause visualization bugs and occasional crashes on the web server.

PyeMap-2.0.1

• Remove CairoSVG dependency
• Make pygraphviz optional
• Remove deprecated Biopython call to MUSCLE, make compatible with new MUSCLE API

PyeMap 2.0

In version 2.0, PyeMap is now capable of mining protein graphs for shared ET pathways/motifs. This is available under the
pyemap.graph_mining modules.

Changelog:

Single Protein

• Automatic identification of redox-active metal ions
• Support for pathway visualization in nglview widget
• New degree-based edge pruning algorithm
• User control over residue depth and RSA thresholds for determining buried/surface exposed

Graph Mining

• gSpan and pattern matching algorithms
• Control over substitutions and edge thresholds
• Sequence and structural based clustering of protein subgraphs
• Support for subgraph visualization in nglview widget

General Improvements

• Improved SMILES strings for standard amino acids and ET active moieties
• Improved visualization of residues using RDKit
• Remove wget dependency, use requests to fetch files

pyemap-1.0.4

Bug fixes:

• Fixed type checking for original atom ID
• Fixed NGL visualization for residues with insertion codes

pyemap-1.0.3.2

Bug fix:
Now correctly draws standard aromatic residues to file and PIL image

pyemap-1.0.3.1

Hot fix for compatibility issues. We now pin to Pillow 7.2.0, and remove some tests which were causing issues with newer RDKit.

pyemap-1.0.3

Minor bug fixes.

1. Remove side chains and cleanup bonding for automatically detected ETA moieties
2. Sanitize custom residue names to fix bug where preceding space would cause errors in web version

pyemap-1.0.2

Minor update

Bug fixes

• Fixed divide by zero error which caused errors when a protein had standard residues lacking side chain atoms. Such residues are now removed from the graph and a warning is displayed
• Non-Side chain atoms are no longer removed from consideration during residue depth calculations, which improves accuracy of solvent exposure criterion

Compatibility notes

• More explicit warnings are included for issues with Mac OS Catalina and MSMS
• Error message from newer RDKit is suppressed

pyemap-1.0.1

Compatible with NetworkX 2.4

pyemap-1.0.0

PyeMap 1.0.0

Not compatible with NetworkX >= 2.4