labblouin.homology module

labblouin.homology.checkForFileCollision(path, ext)

Ensures a file is not being overwritten. Will recursively keep adding a ‘0’ to end of base filename until a unique filename is found. Returns the path.

labblouin.homology.cleanFastaFile(fname, targetfolder='')

Removes gaps from target FASTA file. Allows for BLAST input using this file. Creates new files for every sequence entry. Returns the filename(s) of the new file(s).

labblouin.homology.cleanModellerFolder(path)

Moves intermediate PDBs to another subfolder in the Modeller folder output from Biskit.

labblouin.homology.compareStructures(foldername1, foldername2, outpath, verbose=False)

Given 2 folders with PDB files, calculates the RMSDs with all possible pairwise combinations of PDBs; writes to file located at path determined by outpath.

labblouin.homology.completePDB(pdbin, pdbout)

Given a PDB, clean/complete the PDB using Modeller’s complete_pdb function.

labblouin.homology.extractRandomFasta(fasta_file, numRandom, dest_file)

Extracts a random number of sequences from a FASTA file. Writes to new FASTA.

class labblouin.homology.fasta(fname, removeGaps=True, allUpper=True)

Open, read, and organize a FASTA file as an object.

read(rgaps, allup)

labblouin.homology.getFirstResidueNumber(pdb)

Gets the FASTA residue number of the first ATOM in a PDB file.

labblouin.homology.getModellerPDB(workflowfolder, targetfile)

Copies the model_00.pdb file from Modeller if present in given workflow directory from homologyWorkflow.

labblouin.homology.getRandomPDBFragment(pdb, k=100)

Given a PDB, get a random fragment of length k.

class labblouin.homology.manualModeller(outfolder, targetfile, templatefldr)

Set up and run Modeller using a given folder of PDB files and a target FASTA sequence.

postProcess()

Make a copy of all found models and rename.

run()

Run, call Modeller.

labblouin.homology.radiusOfGyration(pdbFile, chain, pdb=None)

Returns the approximate radius of gyration of a given PDB molecule. Deprecated; now in PDBnet.

labblouin.homology.rmsd(pdbFile1, pdbFile2)

Returns the RMSD of two PDB files. Requires: Pymol.

labblouin.homology.rrmsd(alignPDB, alignFASTA, rmsd=False, chains=None)

Returns the rRMSD of an aligned pairwise PDB and FASTA file. See Betancourt & Skolnick, “Universal Similarity Measure for Comparison Protein Structures”. Deprecated.

labblouin.homology.startPymol()

Ensures Pymol has been launched.

labblouin.homology.system(instruction)

Executes a system command line instruction. Returns list of stdout, stderr.

labblouin.homology.tmscore(alignPDB, alignFASTA)

Returns the TMscore and associated P-value. See Xu & Zhang, “How significant is a protein structure similarity with TM-score = 0.5?”.

labblouin.homology.writeAlignmentFromFasta(fasta_file, dest_file)

Reads a FASTA file and outputs it to a Clustal-like alignment.

labblouin.homology.writeFirstFromFasta(fasta_file, dest_file)

Extracts first sequence from a FASTA and writes to a new one.

labblouin.homology.writeModellerPIR(pdb_files, seq, dest_file)

labblouin.homology.writeSOAPSSAlignment(fasta_file, pdb1, pdb2, dest_file)

Reads a FASTA file and outputs to a SOAPSS alignment file.