Refactor pdb_edit.py

[fsimkovic]

The purpose of this issue is for me to keep track of the refactored functions. A list of currently implemented functions is below:

All ticked methods contain docstrings, were modified and only require final checks.

• def backbone(inpath=None, outpath=None):
• def calpha_only(inpdb, outpdb):
• def check_pdb_directory(directory,single=True,allsame=True,sequence=None):
• def check_pdbs(models,single=True,allsame=True,sequence=None):
• def extract_chain(inpdb, outpdb, chainID=None, newChainID=None, cAlphaOnly=False, renumber=True ):
• def extract_model(inpdb, outpdb, modelID ):
• def keep_matching(refpdb=None, targetpdb=None, outpdb=None, resSeqMap=None ):
• def _keep_matching(refpdb=None, targetpdb=None, outpdb=None, resSeqMap=None ):
• def get_info(inpath):
• def match_resseq(targetPdb=None, outPdb=None, resMap=None, sourcePdb=None ):
• def merge(pdb1=None, pdb2=None, pdbout=None ):
• def molecular_weight(pdbin):
• def most_prob(hierarchy, always_keep_one_conformer=True):
• def num_atoms_and_residues(pdbin,first=False):
• def _parse_modres(modres_text):
• def prepare_nmr_model(nmr_model_in,models_dir):
• def reliable_sidechains(inpath=None, outpath=None ):
• def rename_chains(inpdb=None, outpdb=None, fromChain=None, toChain=None ):
• def resseq(pdbin):
• def _resseq(hierarchy):
• def renumber_residues(pdbin, pdbout, start=1):
• def _renumber(hierarchy, start):
• def renumber_residues_gaps(pdbin, pdbout, gaps, start=1):
• def _rog_side_chain_treatment(hierarchy, scores, del_orange):
• def rog_side_chain_treatment(pdbin, pdbout, rog_data, del_orange=False):
• def select_residues(pdbin, pdbout, chain_id=None, delete=None, tokeep=None, delete_idx=None, tokeep_idx=None, raw=False):
• def sequence(pdbin):
• def _sequence(hierarchy):
• def _sequence1(hierarchy):
• def sequence_data(pdbin):
• def _sequence_data(hierarchy):
• def split_pdb(pdbin, directory=None):
• def split_into_chains(pdbin, chain=None, directory=None):
• def standardise(pdbin, pdbout, chain=None, del_hetatm=False):
• def std_residues_cctbx(pdbin, pdbout, del_hetatm=False): --> def std_residues(pdbin, pdbout, del_hetatm=False):
• def strip(pdbin, pdbout, hetatm=False, hydrogen=False, atom_types=[]):
• def _strip(hierachy, hetatm=False, hydrogen=False, atom_types=[]):
• def to_single_chain(inpath, outpath):
• def translate(inpdb=None, outpdb=None, ftranslate=None):

Deleted functions

• def extract_header_pdb_code(pdb_input):
• def extract_header_title(pdb_input):
• def _parse_rwcontents(logfile):
• def _run_rwcontents(pdbin, logfile):
• def reliable_sidechains_cctbx(pdbin=None, pdbout=None ):
• def Xselect_residues(inpath=None, outpath=None, residues=None):
• def Xsplit(pdbin):
• def Xstd_residues(pdbin, pdbout ):
• def xyz_coordinates(pdbin):
• def _xyz_coordinates(hierarchy):
• def xyz_cb_coordinates(pdbin):
• def _xyz_cb_coordinates(hierarchy):
• def _xyz_atom_coords(atom_group):