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generate_README.sh Helper to generate this beautiful README file .gitignore Self explained ! latex/beamer_header.sty latex/spherical_coordinates.tex latex/tikz/amino_acid.tex Simple amino acid drawing in LaTeX TikZ latex/tikz/peptidic_chain.tex latex/tikz/perpendicular.tex latex/tikz/phenylalanine_channels.tex Drawing grid and skewed grids with perspective in TikZ latex/tikz/phenylalanine.tex Phe drawing in LaTeX TikZ latex/tikz/RL.tex python/basis.py python/Clustering.py python/echo.py python/Grid3/adjmat.py Adjacency matrix of a 3D grid and flooding algorithm using Dijkstra python/Grid3/align.py Align by translation density mrc files using 3D convolution. python/Grid3/data/1igd.mrc python/Grid3/data/1igd_translate.mrc python/Grid3/gaussian_grid3.py Generate a random 3D grid filled with Gaussians python/Grid3/gradient.py python/Grid3/line.py python/Grid3/mrc.py Save a 3D grid as a mrc density file python/hierarchical_sort_pairwise_matrix.py Sort hierarchicaly a pairwise --distance-- matrix python/__init__.py python/kabsch.py Kabsch algorithm for rigid body structure alignment python/kde.py Kernel Density Estimation python/list_utils.py Utilities for lists. merge_lists python/match3d.py Use MODELLER to transfer coordinates from one PDB to the other keeping sequence and numbering python/modeller/align_pdb_seq.py python/modeller/build.py Use MODELLER to generate extended peptide conformation of a given sequence python/modeller/repair_protein.py python/mols/mol2topdbqt.py Convert a mol2 to a pdbqt file python/mols/molconvert.py Convert between molecular file formats using PyMol python/mols/rdkit_fix.py Build a 3D structure from a flat mol file or from a SMILES. Fix a molecule using rdkit python/mols/rdkit_fix.sh Helper for rdkit_fix.py python/mols/splitmol.py Split molecular file in multiple files python/multiprocessing_lock_file.py Using lock files for multiprocess in python python/openmm/topology.py python/pairwise-rmsds.py Compute RMSD pairwisely between pdb files python/pdbs_to_dcd.py Convert a set of PDB files to a DCD trajectory file python/pdbsurf.py Generate surface points from a PDB file python/projection.py Miller projection of protein surfaces python/protein/data/1igd.pdb python/protein_roll.py Apply rotation to a protein and save a dcd trajectory file python/protein/rotate.py python/protein/spherical.py python/protein/test.sh python/pymol/cgo_arrow.py python/pytorch/Dataset.py python/recutils.py Python utility to handle recfiles python/rmsd_traj_multiref.py Compute the RMSD between a traj and multiple external reference PDB files python/struct_align.py Align protein structures python/struct_distance.py Compute distance in a trajectory file python/xonsh/events.py Events for xonsh (see: https://xon.sh/events.html) README shell/bsync.sh Bidirectional directory sync based on rsync shell/hview.sh Keep the first line visible (using vim) shell/pdb_batch_download.sh Download batch of PDB files shell/tmscore/np.py Helper function for tmscore utilities shell/tmscore/tmscore_cluster.py Cluster PDB files based on TMscore or RMSD shell/tmscore/tmscore_format.sh Helper script for shell/tmscore/tmscore-multi.sh shell/tmscore/tmscore-max.sh Find the maximum TMscore for each entry shell/tmscore/tmscore-multi.sh Compute TM-score on multiple PDB files shell/tmscore/tmscore_plot.py Plot TMscore pairwise matrix
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