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color backbone contacts green
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@JenkeScheen
JenkeScheen committed Apr 10, 2024
1 parent 833b3e7 commit b4c8eba
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184 changes: 28 additions & 156 deletions choppa/render/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,13 +25,11 @@ def show_contacts(
selection_residues,
selection_lig,
contact_color,
cutoff=3.6,
bigcutoff=4.0,
):
"""
PyMOL plugin that provides show_contacts command and GUI for highlighting good and bad
polar contacts. Factored out of clustermols by Matthew Baumgartner. The advantage of this
package is it requires many fewer dependencies.
Heavily reduced PyMOL plugin that provides show_contacts command and GUI for highlighting good and bad
polar contacts. Factored out of clustermols by Matthew Baumgartner.
Returns:
List of contacts
Expand All @@ -41,160 +39,34 @@ def show_contacts(

# ensure only N and O atoms are in the selection
all_don_acc_lig = selection_lig + " and (donor or acceptor)"
all_don_acc_res = selection_residues + " and (donor or acceptor)"
all_don_acc_res = selection_residues + " and (donor or acceptor) and sidechain"
all_don_acc_res_backbone = selection_residues + " and (donor or acceptor) and backbone"

# if theses selections turn out not to have any atoms in them, pymol throws cryptic errors when calling the dist function like:
# 'Selector-Error: Invalid selection name'
# So for each one, manually perform the selection and then pass the reference to the distance command and at the end, clean up the selections
# the return values are the count of the number of atoms
all1_sele_count = pymol_instance.cmd.select("all_don_acc1_sele", all_don_acc_lig)
all2_sele_count = pymol_instance.cmd.select("all_don_acc2_sele", all_don_acc_res)

########################################
contacts_name = f"{selection_residues}_contacts"
if all1_sele_count and all2_sele_count:
pymol_instance.cmd.distance(
contacts_name, "all_don_acc1_sele", "all_don_acc2_sele", bigcutoff, mode=0
)
pymol_instance.cmd.set("dash_radius", "0.09", contacts_name)
pymol_instance.cmd.set("dash_color", contact_color, contacts_name)
pymol_instance.cmd.hide("labels", contacts_name)





# ########################################
# # compute good polar interactions according to pymol
# polres = result + "_polar"
# if all1_sele_count and all2_sele_count:
# pymol_instance.cmd.distance(
# polres, "all_don_acc1_sele", "all_don_acc2_sele", cutoff, mode=2
# ) # hopefully this checks angles? Yes
# pymol_instance.cmd.set("dash_radius", "0.126", polres)

# ########################################
# # When running distance in mode=2, the cutoff parameter is ignored if set higher then the default of 3.6
# # so set it to the passed in cutoff and change it back when you are done.
# old_h_bond_cutoff_center = pymol_instance.cmd.get(
# "h_bond_cutoff_center"
# ) # ideal geometry
# old_h_bond_cutoff_edge = pymol_instance.cmd.get(
# "h_bond_cutoff_edge"
# ) # minimally acceptable geometry
# pymol_instance.cmd.set("h_bond_cutoff_center", bigcutoff)
# pymol_instance.cmd.set("h_bond_cutoff_edge", bigcutoff)

# # compute possibly suboptimal polar interactions using the user specified distance
# pol_ok_res = result + "_polar_ok"
# if all1_sele_count and all2_sele_count:
# pymol_instance.cmd.distance(
# pol_ok_res, "all_don_acc1_sele", "all_don_acc2_sele", bigcutoff, mode=2
# )
# pymol_instance.cmd.set("dash_radius", "0.06", pol_ok_res)

# # now reset the h_bond cutoffs
# pymol_instance.cmd.set("h_bond_cutoff_center", old_h_bond_cutoff_center)
# pymol_instance.cmd.set("h_bond_cutoff_edge", old_h_bond_cutoff_edge)

# ########################################

# onlyacceptors1 = selection + " and (acceptor and !donor)"
# onlyacceptors2 = selection2 + " and (acceptor and !donor)"
# onlydonors1 = selection + " and (!acceptor and donor)"
# onlydonors2 = selection2 + " and (!acceptor and donor)"

# # perform the selections
# onlyacceptors1_sele_count = pymol_instance.cmd.select(
# "onlyacceptors1_sele", onlyacceptors1
# )
# onlyacceptors2_sele_count = pymol_instance.cmd.select(
# "onlyacceptors2_sele", onlyacceptors2
# )
# onlydonors1_sele_count = pymol_instance.cmd.select("onlydonors1_sele", onlydonors1)
# onlydonors2_sele_count = pymol_instance.cmd.select("onlydonors2_sele", onlydonors2)

# # print out some warnings
# if SC_DEBUG > 2:
# if not onlyacceptors1_sele_count:
# print("Warning: onlyacceptors1 selection empty!")
# if not onlyacceptors2_sele_count:
# print("Warning: onlyacceptors2 selection empty!")
# if not onlydonors1_sele_count:
# print("Warning: onlydonors1 selection empty!")
# if not onlydonors2_sele_count:
# print("Warning: onlydonors2 selection empty!")

# accres = result + "_aa"
# if onlyacceptors1_sele_count and onlyacceptors2_sele_count:
# aa_dist_out = pymol_instance.cmd.distance(
# accres, "onlyacceptors1_sele", "onlyacceptors2_sele", cutoff, 0
# )

# if aa_dist_out < 0:
# print(
# "\n\nCaught a pymol selection error in acceptor-acceptor selection of show_contacts"
# )
# print("accres:", accres)
# print("onlyacceptors1", onlyacceptors1)
# print("onlyacceptors2", onlyacceptors2)
# return False

# pymol_instance.cmd.set("dash_color", "red", accres)
# pymol_instance.cmd.set("dash_radius", "0.125", accres)

# ########################################

# donres = result + "_dd"
# if onlydonors1_sele_count and onlydonors2_sele_count:
# dd_dist_out = pymol_instance.cmd.distance(
# donres, "onlydonors1_sele", "onlydonors2_sele", cutoff, 0
# )

# # try to catch the error state
# if dd_dist_out < 0:
# print("\n\nCaught a pymol selection error in dd selection of show_contacts")
# print("donres:", donres)
# print("onlydonors1", onlydonors1)
# print("onlydonors2", onlydonors2)
# print(
# "pymol_instance.cmd.distance('"
# + donres
# + "', '"
# + onlydonors1
# + "', '"
# + onlydonors2
# + "', "
# + str(cutoff)
# + ", 0)"
# )
# return False

# pymol_instance.cmd.set("dash_color", "red", donres)
# pymol_instance.cmd.set("dash_radius", "0.125", donres)

# ##################################################
# # find the buried unpaired atoms of the receptor #
# ##################################################

# # initialize the variable for when CALC_SASA is False
# unpaired_atoms = ""

# # Group
# pymol_instance.cmd.group(
# result,
# "%s %s %s %s %s %s"
# % (polres, allres, accres, donres, pol_ok_res, unpaired_atoms),
# )

# # Clean up the selection objects
# # if the show_contacts debug level is high enough, don't delete them.
# if SC_DEBUG < 5:
# pymol_instance.cmd.delete("all_don_acc1_sele")
# pymol_instance.cmd.delete("all_don_acc2_sele")
# pymol_instance.cmd.delete("onlyacceptors1_sele")
# pymol_instance.cmd.delete("onlyacceptors2_sele")
# pymol_instance.cmd.delete("onlydonors1_sele")
# pymol_instance.cmd.delete("onlydonors2_sele")
all_lig_sele_count = pymol_instance.cmd.select("all_don_acc_lig_sele", all_don_acc_lig)
all_res_sele_count = pymol_instance.cmd.select("all_don_acc_res_sele", all_don_acc_res)
_ = pymol_instance.cmd.select("all_don_acc_res_bb_sele", all_don_acc_res_backbone) # not sure if we need to check for this backbone one?
if not all_lig_sele_count and all_res_sele_count:
return False

# now make the actual contacts
# first with sidechains, color as requested
contacts_name = f"{selection_residues}_contacts_sc"
pymol_instance.cmd.distance(
contacts_name, "all_don_acc_lig_sele", "all_don_acc_res_sele", bigcutoff, mode=0
)
pymol_instance.cmd.set("dash_radius", "0.09", contacts_name)
pymol_instance.cmd.set("dash_color", contact_color, contacts_name)
pymol_instance.cmd.hide("labels", contacts_name)

# now contacts with backbone, color these green
contacts_name = f"{selection_residues}_contacts_bb"
pymol_instance.cmd.distance(
contacts_name, "all_don_acc_lig_sele", "all_don_acc_res_bb_sele", bigcutoff, mode=0
)
pymol_instance.cmd.set("dash_radius", "0.09", contacts_name)
pymol_instance.cmd.set("dash_color", "green", contacts_name)
pymol_instance.cmd.hide("labels", contacts_name)

return True

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