Re: Basic python scripts for File Manipulation

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    • March 15, 2011 at 2:44 am #829
      Anonymous

        Hi,

        I am searching for the following files :-

        File Manipulation

        cat_silent.pl: concatenate silentfiles
        changeChain.pl: change the chain id of a PDB
        compose_score_silent.py: generate a silentfile from a set of PDBs
        createLoop.pl: create a dummy structure from a sequence of amino acids
        createTemplate.pl: create a homology model template from a FASTA file and a homologous structure
        make_coords_file.py: generate .coords format from native pdb (for input to cluster_info_silent.out, see below)
        molecule.exe: generate JUFO file and rename ligand atoms (with addhydrogens.inp, mdl2rosetta.inp, and pdb2mdl.inp)
        pdb_fasta.pl: generate a FASTA from a PDB
        pdb2tag.pl: rename a PDB or set of PDBs to their tag names (as shown in the silentfile)
        reconstruct_PDB_by_index: generate PDBs from abinitio-format silentfile
        renumberPDBandchains.pl: renumber the residues of a PDB sequentially, starting at 1
        renumberPDBatoms.pl: renumber the atoms of a PDB sequentially, starting at 1
        silentDock2pdb.pl: generate PDBs from a docking silentfile

        Evaluation

        TMalign: aligns structures based on CA-CA distances
        VMD: X-Windows molecular graphics viewer
        getColumn.pl: display silentfile and scorefile columns
        gnuplot: graphically display data
        cluster_plot.pl: generate a gnuplot input file to plot the score versus another field
        histogram.pl: generate a quick histogram from STDIN data

        Clustering

        cluster.pl: automatic clustering of an abinitio-format silentfile
        cluster_info_silent.out: fully configurable silentfile clustering
        cluster_pdbs.pl: cluster a set of PDBs
        cluster_variation.pl: find per-residue variation within a cluster
        make_color_trees.py: make a dendrogram of the clusters
        make_new_plot.py: make a contacts plot

        Can anybody tell me where can I find them ??

      • March 15, 2011 at 4:22 pm #5182
        Anonymous

          Some of these are in “BioTools”, which is part of the wider 3.2 package (outside the code itself).

          Some of these don’t have anything to do with Rosetta; notably gnuplot and VMD, which are publically available (probably open-source) software, which you can easily find on the internet.

          You should also try looking through the 2.x releases.

          Let me know where you found this list and I’ll try to track that author down to get them to tell me where it’s supposed to be.

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