reorganize dotfiles

profiles/pymol/.pymol/startup/show_contact_map.py

@@ -0,0 +1,58 @@
+#!/usr/bin/env python
+
+import tkFileDialog
+import tkSimpleDialog
+from pymol import cmd
+import math
+from distutils.util import strtobool
+
+def __init__(self):
+	self.menuBar.addmenuitem('Plugin', 'command', 'Contact map', label='Show contact map', command=lambda s=self: load_map(s))
+
+def load_map(app):
+	contacts_file = tkFileDialog.askopenfile(initialdir=".", title="Load contact map")
+	if contacts_file is None:
+		return
+	show_contact_map(file=contacts_file)
+
+def show_contact_map(selection="all", file=None, as_bonds=1, quiet=0):
+	""" Visualize contact map
+	"""
+	as_bonds = bool(as_bonds)
+	quiet = bool(quiet)
+	contacts = read_contacts(file)
+
+	for contact in contacts:	
+		name = "contact{}-{}".format(contact[0], contact[1])
+		seleA = "id %s and %s" % (contact[0], selection)
+		seleB = "id %s and %s" % (contact[1], selection)
+		
+		# skip non-exsistant
+		if cmd.select("seleA", seleA) == "0" or cmd.select("seleB", seleB) == "0":
+			print("%s to %s not found!" % (seleA, seleB))
+
+		if not quiet:
+			print("New bond: residue %s to %s" % (contact[0], contact[1]))
+
+		if as_bonds:
+			cmd.bond(seleA, seleB)
+		else:
+			cmd.distance(name, seleA, seleB)
+
+	cmd.delete('seleA')
+	cmd.delete('seleB')
+
+
+def read_contacts(contacts_file, separator=' '):
+	contacts = []
+	if not isinstance(contacts_file, file):
+		contacts_file = open(contacts_file, 'r')
+	for line in contacts_file.readlines():
+		split = line.split(",")
+		resA = int(split[0])
+		resB = int(split[1])
+		contacts.append([resA, resB])
+	contacts_file.close()
+	return contacts
+	
+cmd.extend("contact_map", show_contact_map)