Tools in MCCE4-Tools - Last updated: 10/22/25: * Tools without description: awaiting authors input. ================================================================================================== cif2pdb :: Convert cif to pdb -------------------------------------------------------------------------------------------------- clear_mcce_folder :: Delete all MCCE outputs from a folder. Kept: run.prm, original pdb and prot.pdb, as well as any non-MCCE files. -------------------------------------------------------------------------------------------------- detect_hbonds :: Detect h-bonds in a mcce pdb file. -------------------------------------------------------------------------------------------------- filesdiff :: Obtain the column difference between two mcce files, or diff all files in two mcce output folders. The difference file is saved with the 'diff_' prefix. Applicable to these files: all_pK.out, all_sum_crg.out, entropy.out, fort.38, head3.lst, pK.out, residues_stats.txt, sum_crg.out, vdw0.lst. -------------------------------------------------------------------------------------------------- get_aver_pqr :: Obtain an occupancy-weighted charge pqr file using the occupancy table (fort.38) and step2_out.pdb data. Minimal usage: get_aver_pqr get_aver_pqr --most_occ_pqr # to obtain the pqr of the most occupied conformers -------------------------------------------------------------------------------------------------- getpdb :: Download one or more (bioassembly) pdb files from the RSCB Protein Data Bank. -------------------------------------------------------------------------------------------------- Tools for molecular dynamics: "md_" prefix. ........................................... md_clustering :: Given a topology file and one or more trajectories, save the pdbs of the clusters elements in the topology file's parent directory. -------------------------------------------------------------------------------------------------- md_extract_frames :: Extract a trajectory's frames with the given indices into pdb files with options to select segment and cofactors, and print the structure segments parsed by MDAnalysis. -------------------------------------------------------------------------------------------------- md_fix_psf_mdanalysis :: Test the instantiation of a MDAnalysis.Universe given a PSF topology and its associated DCD trajectory file. Upon failure, a new psf file is created using `parmed`, which is then used as the topology file in a new MDAnalysis.Universe instantiation attempt. - If that attempt is successfull, the user is notified that the new psf file is to be used; - If not: the new psf file is deleted and the user is notified that the problem could not be resolved. -------------------------------------------------------------------------------------------------- Tools for mcce microstates processing: "ms_" prefix. .................................................... ms_hbnets :: Using the outut of detect_hbonds, obtain the count and occupancy of H-bonding pairs or microstates via efficient processing of the 'msout file'. Minimal usage examples: ms_hbnets; ms_hbnets -n_states 30000 -------------------------------------------------------------------------------------------------- ms_hbnets1_mspdbs :: Generate a random sample of MCCE microstates in pdb format. Minimal usage: ms_hbnets1_mspdbs -------------------------------------------------------------------------------------------------- ms_hbnets2_hah :: Compute all possible hbonds over a collection directory of step2_out formatted pdbs using the MCCE_bin.detect_hbonds.detect_hbonds function. Each pdb will have its own associated txt file containing their hbond donors, acceptors, distances and angles. -------------------------------------------------------------------------------------------------- ms_hbnets3_nets :: list_hbond_networks -------------------------------------------------------------------------------------------------- ms_hbnets4_stats :: Analyze network similarites/statistics across a collection directory of microstate associated network files. -------------------------------------------------------------------------------------------------- ms_hbond_percentages :: -------------------------------------------------------------------------------------------------- ms_plot_energies.py :: -------------------------------------------------------------------------------------------------- ms_protonation :: Obtain Protonation Microstates Analysis with Weighted Correlation The requied input is a parameter file of which two examples can be found in MCCE4-Tools/mcce4_tools/tool_param/: 'params.crgms' and 'minimal_no_bounds.crgms'. Make a local copy to your working dir 'some_dir': cd some_dir cp /home//path_to_clone/MCCE4-Tools/mcce4_tools/tool_param/params.crgms . # Edit the file, then run the full command: ms_protonation params.crgms -------------------------------------------------------------------------------------------------- ms_sample2pdbs :: Generate a random sample of MCCE microstates in mcce pdb format. Minimal usage: ms_sample_to_pdbs -------------------------------------------------------------------------------------------------- ms_top2pdbs :: Create pdb & pqr files for the topN tautomeric protonation microstates, along with a summary file & a listing of the N charge vectors. Files in an existing output folder are overwritten. Defaults: pH=7.0; n_top=5; min_occ=0.0; residue_kinds=mcce4.constants.IONIZABLE_RES Examples: > ms_top2pdbs # use all defaults > ms_top2pdbs -eh 30 # Eh titration at ph7 Passing residues kinds: comma-separated; order & case insensitive: > ms_top2pdbs -residue_kinds _CL,his,GLU Note: residue_kinds not in the default list are appended to it. -------------------------------------------------------------------------------------------------- ms_split_msout :: Obtain a reduced msout file, preserving the original as all_. Minimal usage: ms_split_msout # ph=7, eh=0, mc_range=2 (2nd MC run) ms_split_msout --reset_master -ph 5 # ph needed if not 7 options: -h, --help show this help message and exit -mcce_dir MCCE_DIR The mcce run or ms_out folder; required. (default: ./) -ph PH pH point (e.g.: 7, 7.5) of the msout file; Default: 7. -eh EH pH point (e.g.: 200, 200.5) of the msout file; Default: 0. -mc_range [MC_RANGE ...] Which MC run data to extract. One integer for a single run, e.g. 1 for the 1st MC run, or two for an inclusive range, e.g. 3 6. Default: 2. --reset_master Rename the copy of the original file 'all_', to the original msout file name, ''. -------------------------------------------------------------------------------------------------- pdbs2pse :: Bundle a list of pdbs into a Pymol seesion. -------------------------------------------------------------------------------------------------- pI :: Obtain the pI theoretical pI of the input protein pdb file (standard or mcce). If 'sum_crg.out' exists in the pdb parent folder, then the protein pI is also calculated, along with the delta pI (protein pI - theoretical pI). Usage: pI 4lzt.pdb; pI step2_out.pdb -------------------------------------------------------------------------------------------------- postrun :: Flags problem residues: non-canonical charge, high chi^2 or no fit. -------------------------------------------------------------------------------------------------- ================================================================================================== Tools help: For information and usage on each tool, run: -h OR -h Post problems, questions, bugs or feature requests to: https://github.com/GunnerLab/MCCE4-Tools/issues