cbc-univie · florianjoerg · Sep 22, 2022 · Sep 22, 2022 · Sep 22, 2022 · Sep 22, 2022
diff --git a/docs/documentation_pages/autosummary/protex.system.IonicLiquidSystem.rst b/docs/documentation_pages/autosummary/protex.system.IonicLiquidSystem.rst
@@ -1,4 +1,4 @@
-protex.system.IonicLiquidSystem
+protex.system.IonicLiquidSystem
 ===============================
 
 .. currentmodule:: protex.system
@@ -20,7 +20,6 @@ protex.system.IonicLiquidSystem
  ~IonicLiquidSystem.loadCheckpoint
  ~IonicLiquidSystem.loadState
  ~IonicLiquidSystem.load_updates
- ~IonicLiquidSystem.report_states
  ~IonicLiquidSystem.saveCheckpoint
  ~IonicLiquidSystem.saveState
  ~IonicLiquidSystem.save_updates

diff --git a/docs/documentation_pages/autosummary/protex.system.IonicLiquidTemplates.rst b/docs/documentation_pages/autosummary/protex.system.IonicLiquidTemplates.rst
@@ -1,4 +1,4 @@
-protex.system.IonicLiquidTemplates
+protex.system.IonicLiquidTemplates
 ==================================
 
 .. currentmodule:: protex.system
@@ -16,7 +16,6 @@ protex.system.IonicLiquidTemplates
  .. autosummary::
  :nosignatures:
 
- ~IonicLiquidTemplates.get_canonical_name
  ~IonicLiquidTemplates.get_charge_template_for
  ~IonicLiquidTemplates.get_residue_name_for_coupled_state
  ~IonicLiquidTemplates.get_update_value_for

diff --git a/docs/documentation_pages/autosummary/protex.testsystems.generate_hpts_system.rst b/docs/documentation_pages/autosummary/protex.testsystems.generate_hpts_system.rst
@@ -0,0 +1,6 @@
+protex.testsystems.generate\_hpts\_system
+=========================================
+
+.. currentmodule:: protex.testsystems
+
+.. autofunction:: generate_hpts_system
diff --git a/docs/documentation_pages/autosummary/protex.testsystems.rst b/docs/documentation_pages/autosummary/protex.testsystems.rst
@@ -15,6 +15,7 @@
  :toctree:
  :nosignatures:
 
+ generate_hpts_system
  generate_im1h_oac_system
  generate_single_im1h_oac_system
 

diff --git a/protex/forcefield/im1h_oac_150_im1_hoac_350_init.crd b/protex/forcefield/im1h_oac_150_im1_hoac_350_init.crd
diff --git a/protex/forcefield/initialize.sh b/protex/forcefield/initialize.sh
diff --git a/protex/single_pairs/im1_hoac_1.crd → ...ex/forcefield/single_pairs/im1_hoac_1.crd b/protex/single_pairs/im1_hoac_1.crd → ...ex/forcefield/single_pairs/im1_hoac_1.crd
diff --git a/protex/single_pairs/im1_hoac_1.psf → ...ex/forcefield/single_pairs/im1_hoac_1.psf b/protex/single_pairs/im1_hoac_1.psf → ...ex/forcefield/single_pairs/im1_hoac_1.psf
diff --git a/protex/single_pairs/im1_hoac_1_init.crd → ...rcefield/single_pairs/im1_hoac_1_init.crd b/protex/single_pairs/im1_hoac_1_init.crd → ...rcefield/single_pairs/im1_hoac_1_init.crd
diff --git a/protex/single_pairs/im1h_oac_1.crd → ...ex/forcefield/single_pairs/im1h_oac_1.crd b/protex/single_pairs/im1h_oac_1.crd → ...ex/forcefield/single_pairs/im1h_oac_1.crd
diff --git a/protex/single_pairs/im1h_oac_1.psf → ...ex/forcefield/single_pairs/im1h_oac_1.psf b/protex/single_pairs/im1h_oac_1.psf → ...ex/forcefield/single_pairs/im1h_oac_1.psf
diff --git a/...ex/single_pairs/im1h_oac_1_im1_hoac_1.crd → ...ld/single_pairs/im1h_oac_1_im1_hoac_1.crd b/...ex/single_pairs/im1h_oac_1_im1_hoac_1.crd → ...ld/single_pairs/im1h_oac_1_im1_hoac_1.crd
diff --git a/...ex/single_pairs/im1h_oac_1_im1_hoac_1.psf → ...ld/single_pairs/im1h_oac_1_im1_hoac_1.psf b/...ex/single_pairs/im1h_oac_1_im1_hoac_1.psf → ...ld/single_pairs/im1h_oac_1_im1_hoac_1.psf
diff --git a/...ngle_pairs/im1h_oac_1_im1_hoac_1_init.crd → ...ngle_pairs/im1h_oac_1_im1_hoac_1_init.crd b/...ngle_pairs/im1h_oac_1_im1_hoac_1_init.crd → ...ngle_pairs/im1h_oac_1_im1_hoac_1_init.crd
diff --git a/...ingle_pairs/im1h_oac_1_im1_hoac_1_neu.crd → ...ingle_pairs/im1h_oac_1_im1_hoac_1_neu.crd b/...ingle_pairs/im1h_oac_1_im1_hoac_1_neu.crd → ...ingle_pairs/im1h_oac_1_im1_hoac_1_neu.crd
diff --git a/protex/single_pairs/im1h_oac_1_init.crd → ...rcefield/single_pairs/im1h_oac_1_init.crd b/protex/single_pairs/im1h_oac_1_init.crd → ...rcefield/single_pairs/im1h_oac_1_init.crd
diff --git a/...e_pairs/im1h_oac_im1_hoac_1_secondtry.crd → ...e_pairs/im1h_oac_im1_hoac_1_secondtry.crd b/...e_pairs/im1h_oac_im1_hoac_1_secondtry.crd → ...e_pairs/im1h_oac_im1_hoac_1_secondtry.crd
diff --git a/...e_pairs/im1h_oac_im1_hoac_1_secondtry.psf → ...e_pairs/im1h_oac_im1_hoac_1_secondtry.psf b/...e_pairs/im1h_oac_im1_hoac_1_secondtry.psf → ...e_pairs/im1h_oac_im1_hoac_1_secondtry.psf
diff --git a/...le_pairs/im1h_oac_im_hoac_1_secondtry.crd → ...le_pairs/im1h_oac_im_hoac_1_secondtry.crd b/...le_pairs/im1h_oac_im_hoac_1_secondtry.crd → ...le_pairs/im1h_oac_im_hoac_1_secondtry.crd
diff --git a/protex/single_pairs/initialize_im1_hoac.sh → ...field/single_pairs/initialize_im1_hoac.sh b/protex/single_pairs/initialize_im1_hoac.sh → ...field/single_pairs/initialize_im1_hoac.sh
diff --git a/protex/single_pairs/initialize_im1h_oac.sh → ...field/single_pairs/initialize_im1h_oac.sh b/protex/single_pairs/initialize_im1h_oac.sh → ...field/single_pairs/initialize_im1h_oac.sh
diff --git a/...pairs/initialize_im1h_oac_1_im1_hoac_1.sh → ...pairs/initialize_im1h_oac_1_im1_hoac_1.sh b/...pairs/initialize_im1h_oac_1_im1_hoac_1.sh → ...pairs/initialize_im1h_oac_1_im1_hoac_1.sh
diff --git a/protex/single_pairs/packmol_im1_hoac_1.inp → ...field/single_pairs/packmol_im1_hoac_1.inp b/protex/single_pairs/packmol_im1_hoac_1.inp → ...field/single_pairs/packmol_im1_hoac_1.inp
diff --git a/protex/single_pairs/packmol_im1h_oac_1.inp → ...field/single_pairs/packmol_im1h_oac_1.inp b/protex/single_pairs/packmol_im1h_oac_1.inp → ...field/single_pairs/packmol_im1h_oac_1.inp
diff --git a/...e_pairs/packmol_im1h_oac_1_im1_hoac_1.inp → ...e_pairs/packmol_im1h_oac_1_im1_hoac_1.inp b/...e_pairs/packmol_im1h_oac_1_im1_hoac_1.inp → ...e_pairs/packmol_im1h_oac_1_im1_hoac_1.inp
diff --git a/protex/single_pairs/toppar/hoac_d.str → ...forcefield/single_pairs/toppar/hoac_d.str b/protex/single_pairs/toppar/hoac_d.str → ...forcefield/single_pairs/toppar/hoac_d.str
diff --git a/...airs/toppar/im1_d_fm_lj_chelpg_withlp.str → ...airs/toppar/im1_d_fm_lj_chelpg_withlp.str b/...airs/toppar/im1_d_fm_lj_chelpg_withlp.str → ...airs/toppar/im1_d_fm_lj_chelpg_withlp.str
diff --git a/...ppar/im1_d_fm_lj_chelpg_withlp_backup.str → ...ppar/im1_d_fm_lj_chelpg_withlp_backup.str b/...ppar/im1_d_fm_lj_chelpg_withlp_backup.str → ...ppar/im1_d_fm_lj_chelpg_withlp_backup.str
diff --git a/...ngle_pairs/toppar/im1h_d_fm_lj_chelpg.str → ...ngle_pairs/toppar/im1h_d_fm_lj_chelpg.str b/...ngle_pairs/toppar/im1h_d_fm_lj_chelpg.str → ...ngle_pairs/toppar/im1h_d_fm_lj_chelpg.str
diff --git a/...irs/toppar/im1h_d_fm_lj_chelpg_backup.str → ...irs/toppar/im1h_d_fm_lj_chelpg_backup.str b/...irs/toppar/im1h_d_fm_lj_chelpg_backup.str → ...irs/toppar/im1h_d_fm_lj_chelpg_backup.str
diff --git a/protex/single_pairs/toppar/oac_d_lj.str → ...rcefield/single_pairs/toppar/oac_d_lj.str b/protex/single_pairs/toppar/oac_d_lj.str → ...rcefield/single_pairs/toppar/oac_d_lj.str
diff --git a/...oppar_drude_master_protein_2013f_lj02.str → ...oppar_drude_master_protein_2013f_lj02.str b/...oppar_drude_master_protein_2013f_lj02.str → ...oppar_drude_master_protein_2013f_lj02.str
diff --git a/protex/single_pairs/toppar/toppar_lj02.str → ...field/single_pairs/toppar/toppar_lj02.str b/protex/single_pairs/toppar/toppar_lj02.str → ...field/single_pairs/toppar/toppar_lj02.str
diff --git a/protex/single_pairs/write_psf_crd.inp → ...forcefield/single_pairs/write_psf_crd.inp b/protex/single_pairs/write_psf_crd.inp → ...forcefield/single_pairs/write_psf_crd.inp
diff --git a/...x/single_pairs/write_psf_crd_im1_hoac.inp → ...d/single_pairs/write_psf_crd_im1_hoac.inp b/...x/single_pairs/write_psf_crd_im1_hoac.inp → ...d/single_pairs/write_psf_crd_im1_hoac.inp
diff --git a/...x/single_pairs/write_psf_crd_im1h_oac.inp → ...d/single_pairs/write_psf_crd_im1h_oac.inp b/...x/single_pairs/write_psf_crd_im1h_oac.inp → ...d/single_pairs/write_psf_crd_im1h_oac.inp
diff --git a/protex/forcefield/toppar/toppar_flo.str b/protex/forcefield/toppar/toppar_flo.str
diff --git a/protex/forcefield/traj/im1h_oac_150_im1_hoac_350_npt_1.rst b/protex/forcefield/traj/im1h_oac_150_im1_hoac_350_npt_1.rst
diff --git a/protex/forcefield/write_psf_crd.inp b/protex/forcefield/write_psf_crd.inp
diff --git a/protex/scripts/charge_changes.json b/protex/scripts/charge_changes.json