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