Welcome to PDB-numpy’s documentation!

Warning

pdb_numpy is deprecated and no longer actively maintained. Please migrate to pdb_cpp, the successor library which provides improved performance and additional features.

pdb_numpy is a python library designed to facilitate working with coordinates files in the context of structural bioinformatics. The library builds upon the powerful numpy library to provide efficient and easy-to-use tools for reading, manipulating, and analyzing coordinates files.

Table of Contents:

• About PDB-numpy
  • Main features:
  • Installation
  • Dependencies
  • Contributing
  • Author
  • License
• Installation Quick Start
  • Through Pypi
  • Get sources from the GithubRepo
  • Install pdb_numpy
  • Test Installation
• Basic Usage
  • Loading a structure
  • Selection of coordinates subset
• Github project
• PDB_Numpy package
  • Submodules
  • Coor Class
    • Coor
      • Coor.add_symmetry()
      • Coor.alterloc
      • Coor.apply_transformation()
      • Coor.beta
      • Coor.chain
      • Coor.change_order()
      • Coor.com
      • Coor.compute_chains_CA()
      • Coor.copy_box()
      • Coor.elem
      • Coor.field
      • Coor.get_aa_DL_seq()
      • Coor.get_aa_na_seq()
      • Coor.get_aa_seq()
      • Coor.get_index_select()
      • Coor.insertres
      • Coor.len
      • Coor.merge_models()
      • Coor.model_num
      • Coor.name
      • Coor.num
      • Coor.occ
      • Coor.read()
      • Coor.remove_overlap_chain()
      • Coor.reset_residue_index()
      • Coor.resid
      • Coor.residue
      • Coor.resname
      • Coor.select_atoms()
      • Coor.select_index()
      • Coor.total_len
      • Coor.uniq_resid
      • Coor.write()
      • Coor.x
      • Coor.xyz
      • Coor.y
      • Coor.z
  • Model Class
    • Model
      • Model.add_atom()
      • Model.alterloc
      • Model.beta
      • Model.chain
      • Model.dist_under_index()
      • Model.elem
      • Model.field
      • Model.get_index_select()
      • Model.insertres
      • Model.len
      • Model.name
      • Model.num
      • Model.occ
      • Model.resid
      • Model.residue
      • Model.resname
      • Model.select_atoms()
      • Model.select_index()
      • Model.select_tokens()
      • Model.simple_select_atoms()
      • Model.uniq_resid
      • Model.x
      • Model.xyz
      • Model.y
      • Model.z
  • Analysis module
    • compute_pdockQ()
    • compute_pdockQ2()
    • compute_pdockQ_sel()
    • compute_piTM()
    • dockQ()
    • interface_rmsd()
    • native_contact()
    • rmsd()
  • Alignement module
    • pdb_numpy.alignement package
      • Submodules
      • pdb_numpy.alignement.align_cython module
      • pdb_numpy.alignement.profile_cython module
      • Module contents
  • DSSP module
    • add_NH()
    • compute_DSSP()
    • compute_Hbond_matrix()
    • compute_bend()
    • get_NH_xyz()
    • hbond_energy()
  • Geom module
    • angle_vec()
    • atom_dihed_angle()
    • compute_unit_cell_vectors()
    • cryst_convert()
    • cryst_convert_mmCIF()
    • distance_matrix()
    • makeQ()
    • makeW()
    • quaternion_rotate()
    • quaternion_transform()
  • Format module
    • pdb_numpy.format package
      • Submodules
      • pdb_numpy.format.gro module
      • pdb_numpy.format.mmcif module
      • pdb_numpy.format.pdb module
      • pdb_numpy.format.pqr module
      • Module contents

Indices and tables

• Index

• Module Index

• Search Page