A collection of the various scripts I wrote during my PhD to assist in multiple tasks.

Directory Listing /amber /average_bond_trajectory AvgBond.py/AvgBond.sh - mean length of a bond in a crystal simulation over all copies of asymmetric unit and several trajectory intervals BondPerASU.sh - a bond length in each copy of the asymmetric unit in one trajectory frame BondPerASU2.sh - like BonPerASU.sh but on reversed symmetry trajectories

/bfactors select_bfacs_byname.py - select subset of B factors based on atom names

/cpptraj checkZN.sh - cpptraj.hbond.in - cpptraj.rmsd_active - cpptraj_nowat_merge.in - ctraj_chiangles - ctraj_cluster12 - ctraj_distmatrix - ctraj_nmwiz_quasi - ctraj_quasi - ctraj_quasi1 - ptraj_01_01 - ptraj_bfactor - ptraj_CalcAvgesAvg - ptraj_CalcAvgesbfactor - ptraj_CalcLatRmsd - ptraj_CalcUCbfactor - ptraj_CalcUCRMSD - ptraj_CreateAvgUC - ptraj_density - ptraj_densitymatrix - ptraj_imageWat1 - ptraj_mergetrajectory - ptraj_rmsd - ptraj_supercell_imageWat - ptraj_translate - runquasi.sh - StripMerge.sh -

/dihedral_analysis dihedralX.py -

/equilibration_hairpin MakeEqFile.sh - MakeRestraints.py -

/forceCalc LoadHairpin.m TestForces.m

/other check_com.py check_mask.py check_mergetraj.py

/parametrize_torsion check_CAC.sh makeAmatBvec_byhand.py mk_files_CAC.sh runllsp.m

/prep DOALL.sh prepscript_nowat.sh prepscritp_UC.sh prepscript1rpgK.sh prepscriptH_NVT.sh prepscriptHIS.sh prepscriptsIe.sh

/rmsd make_rmsd_table.py

/rmsd_averages averages.py makesummary.sh

/run 1p7e_prep_min_dynamics.sh equil_cdpa_nvt.sh equil_cdpa_restraints.sh run_cdpa_restraints.sh

/volume cellvolume.m makepercentvolume.m process_mdout.perl volcheck.sh

/waters uc_water.py

/awk awk_examples.py heatcapacity.awk jigglepdb.awk.txt md2map.sh pressure.sh

/bash AbsPath.sh bashrc_casegroup convert_wma2mp3.sh CorrelateRst.sh cp_nc_from_Dave.sh fix_numbering_pdb.csh fix_numbering_pdb_2.csh masterRun.sh meldwrap.sh minimizeEx_tyr.sh mov2avi.sh pdbget prepscript.sh print_array.sh renumber.sh rsync.sh run_gyges.sh runObelix.sh runObelix_mod2.sh runObelix_mod3.sh runObelix_NVE.sh scan_dihedral_amber.sh scan_torsions.sh

/bioinfo kmeans.py NeedlemanWunsh_affine.py

/crystallography align_two_maps.sh cif_intensity_2_mtz_fobs.sh cif2mtzExScrpt.sh converst_maps.sh density_eds.csh diff_maps.sh fft.sh filter_mtz.py frac_translate.sh get_r.sh get_r_entre_fobs.sh hlify.sh pdbset.sh sfall2.sh sfallExScrpt.sh unique.sh

/latex midterm2.tex Duff_Abstract.tex latex_subfloats.tex phenix-afitt.tex research_summary.tex SummaryStructures.tex

/matlab ErrorFun.m RunOpt.m FourierT.m blackjack.m blackjacksim.m CellParams.m cellvolume.m CompAutoCorr.m CompXfrmPawel.m createFit2.m derive_TLS_eq.m diffusion_fit.m DotProduct.m em_1dim.m funcs.m functionplot.m GMM InterpDih.m Line2Tenso.m linearfitplot.m MakeGraphs.m matave.m matconv.m matcpy.m matrices.m matrixdata.m MeanSquareDispFrom2Files.m MeanSquareDispFromNetCDF.m MetricTensor.m overfitting_example.m peakfitter.m plot_latex_title.m Recip.m restart_volumes.m sine_plot.m smoothNrg.m SmoothRMS.m smoothVol.m SmoothWatRMS.m TLS_cross.m Uequiv.m vectorization2.m VectorLength.m

/matplotlib analyze_refines.py - includes seabron KDE distribution, violin, box and scatter plots axes.py axes_legend.py axes2.py bargraph.py broken_axes.py centercolormapatzero.py fromgroup.py histogram.py kmeans_plot.py legend.py plot_benchmarks.py plot_chi.py plot_comshifts_3Dscatter.py plot_energy_r_pub.py plot_histograms_pub.py plot_mogul.py plot_PheTorsions.py plot_PhiPsi.py plot_UC_hist.py plot_UC_series.py plotAutoCorr.py plotpy.py quickplotsmth.py scatter_plot_bug.py scatter_seaborn.py secondary_structure_color_bar.py simpleplot.py tickmarks.py

/namd clean_prmtop_namd.sh namdcheck.sh tyr_namd_min.sh tyr_namd_run.sh

/pandas analyze_pandas.py analyze_refines.py data_reduce.py process_songs_clean.py taxi.py

/PBS gordonequil1.sh gordonMasterEquil_1.sh gordonMasterEquil_1_S.sh gordonMasterEquil_2_S.sh gordonMasterEquil_S.sh gygesmin.sh kraken_multiple_jobs_maria.sh kraken_namd.sh krakenequil.sh krakenMasterEquil.sh krakenMasterRun.sh krakenMasterRun_namd.sh krakenrun.sh minimize_krakow.sh ranger_masterRun.sh rangerrun.sh run_casegroup3.sh run_gordon.sh run_Gyges.sh run_tyr.sh run_tyr_1rpg.sh run_tyr_4lzt.sh run_tyr_namd.sh runRangerEx1.sh runRangerEx2.sh

/phenix /afitt afitt.py afitt_fd.py /amber_adaptbx init.py amber_geometry_minimization.py amber_library_server.py fix_ambpdb.py get_candidates.py get_charge_and_multiplicity.py getmdgxfrc.c getmdgxfrc.h lbfgs.py pdb4amber.py restraints.py tst_minimization.py tst_refinement.py AmberPrep.py /cci_scripts crawl_results.py get_clash.py getfiles.py run_tests.py test_amber_hydrogens.py /Tom_SF_from_MD run_demo.csh analyze_pandas.py changeHIS.py check_failed_volumes.py check_special_pos.py cif_read.py crawl_refines_print_Rfactor.py file_setup_for_refine.py filter_mtz.py find_ligands.py find_success_pdb.py gather_analyze_plot.py get_candidates.py get_clashscores.py get_CRYST1.py get_nsymops.py make_SMTRY.py map_info.py mine_refine_100.py molprobity_coot.py pavel_examples.py pbd_hier_sg.py phenix_sander_api.py phenix_unitcell.py refine_ligandme_errors.py restr_from_pdb_cif.py rism_vs_bulk_2g04.py run_check_weights.py run_ratio_tests.py run_refine.py run_refine_100.py run_refine_doover.py run_refine_elbow.py run_refine_nigel.py sander_api2.py special_pos_test.py test_hierarcy.py testcart.py tst_steepest.py vector_to_list.cpp

/pymol movie_fade.py mk_movei.pml mk_movie1.pml mk_movie2.pml mk_movie3.pml align_rmsd.pml arrow.py axes.py draw_supercell_xy.py draw_supercell_yz.py electron_density_mesh.pml get_rmsd_pymol.py nm_original.py nmodes.py pmlrc.py pymol_axes.py pymol_EDmesh.pml states_nmd1.py states_nmd2.py supercell.py SuperSymPlugin12.py update_pymol.sh

/python /com bfacs_com.py bfacs_RevSymm.py com.py select_bfacs_byname.py

/comshifts analyze_com_shifts.py checkcom.py comshifts_fixed.py plot_comshifts.py plotcom.py traj_com_scatter.py

/contacts contacts.py getTrajContacts.py plot_contacts.py plot_TrajContacts.py run_getTrajContacts.py summarize_contacts.py sumTrajContacts.py

/fav8 avgmatrix.py avgwaterstate.py avgwaterstate2.py bigmatrix.py dihedral.py dihedral2.py dihedralfirstframe.py dssp.py dssp4corr.py makedistancegraphs.py mat2bin.py matrix_dist.py percentage.py waterdistance.py waterstateshift.py

/quasiharmonics make_nmd.py make_nmd_bynumber.py

/sasa asa.py molecule.py vector3d.py

/toolpy_huanwang pdb_stat.py tools_v100.py util.py

addwaters2.py adp2tls.py adp2tls_cov.py adp_analyze.py analyse_supercell.py analyze_geo_min.py anisotropic.py asu_res.py bfactor_correlation.py bond_angle_rmsd.py broken_axes.py cc_std_dev.py channelProfile.py channelProfile3.py checkcom.py check_com.py check_memory.py check_mergetraj.py clean_bibliography.py clean_prmtop_namd.sh cluster_freq.py comparepdb.py convert_string_array.py cpptraj_quasih_play.py crawl_results.py ctraj_cluster.py dbscan.py decorator_howmanytimes.py density.py difference_vector.py dssp.py fileread_Raik_Grunberg.py find_successful_pdbs.py fix_ambpdb.py flatten.py gather_pickle.py getatoms.sh GetBfacsFromCif4SupCell.py GetBfacsfromPdb2Pdb.py getbfactors.py GetBox.py GetFracCoordArray.py getTrajContacts.py GetVolume.py get_amber_email_stats.py GMM.py hbond_diff.py hbond_summary.py heatmap.py histogramathome.py imit_cpptraj_quasiharm.py journal_abbreviations.txt kabsch.py kabsch2.py ls.py MakeRestraints.py mergepdbs.py misc.py MolProb_Trajalyze.py my_run_transfer_adps.py nccoords ncframes NeedlemanWunsch.py new_template.py NS_SmithWaterman.py numberlines.py parsedata.py pdb2rst7.py pdb4amber.py pdb_chain.py PermanenceTimes2.py phipsi.py pickle_data.py pickle_timings.py play_w_pca.py plotcom.py plotpy.py plot_heatmap.py popen.py python_def.py ReadAmberFiles.py readDCD.py README_python regexp.py removewaters.py remove_waters.py residueContacts.py residueContacts.sh resid_select.py ringer_ne_dist.py rmsd.py roll.py RunTime.py sander_api.py search.py smooth_signal.py smtry_C121.py smtry_P6122.py smtry_P6122_send.py test_rmsd.py timing_decorator.py timing_example.py timing_example2.py trajectoryContacts.py traj_com_scatter.py trans2pdb.py uc_water.py walk.py watersPerCell.py

/R final.tex R1.tex R2.tex R4.tex R6.tex studentst.R

/readmes Amber Bash C++ computer_freeze_restart_notes crystallography GIT lyx matlab matplotlib openmm pandas PBS phenix prmtop_amber_notes pycharm pymol python R TCL VMD

/tcl _sasa_res.tcl analyze_1aho_contacts.tcl calculatetransformationmatrixnottcl change_beta_occupancy.tcl COM.tcl difference_matrix.tcl diffusion_constant.tcl frame_rmsd.tcl ftomek_atom_interaction.tcl Script_S2_calc_Brushweiler.tcl tomek_atom_interaction.tcl vmd_monomers.tcl vmdview.tcl vmdview2.tcl

/xtalutil /Analyze AnalyzeIndivASU.py AnalyzeRevSym.py GetBfactors.py GetSym.py GetTrajContacts.py GetVolume.py MakeASU.py MakePDB4Map.py md2map.sh NoStripMerge.sh plotBfac.sh plotIndivASU.py plotRMSD.py plotRMSD_v4.py plotRMSDPerASU.py plotVolume.py ReadAmberFiles.py RevSym.py RevSym_com.py SplitTrajectory.py XtalAnalyze.sh XtalPlot.sh

/Auxiliary adp.py adp_flex.py adp2tls.py compare_adp.py density.py difference_vector.py distance_matrix.py filter_mtz.py fit_supercell_com.py make_nmd.py MolProb_Trajalyze.py ncframes prepscript_asu.sh prepscript_nowat.sh pressure.sh process_mdout.perl pymol_nmodes.py StripMerge.sh

/Phenix amber.py compile.sh getmdgxfrc.{c,h} Makefile phenix_amber_interface.cpp ReadAmberFilesLight.py tst_steepest.py