# YASARA PLUGIN
# TOPIC:
# TITLE: PepSurfViewer
# REQUIRES: Viewer
# AUTHOR: James W. Gillespie
# LICENSE: PRIVATE DEMO (NOT FOR DISTRIBUTION)
# DESCRIPTION:
#
#===============================================================================
"""
MainMenu: File
PullDownMenu: Load
SubMenu after Electrostatic potential map: P_e_pSurf PDB file
FileSelectionWindow: Select PDB
MultipleSelections: No
Filename: pdb/*.pdb
Request: LoadPepSurfPDB
MainMenu: View
PullDownMenu after Atom apperance: _P_epSurf
SubMenu: _V_iew PepSurf Clusters
Request: ViewPepSurfPDB
"""
import yasara
import re
from container import *
from collections import defaultdict
if (yasara.storage==None):
yasara.storage=container()
yasara.storage.objects = {}
# print("Creating Storage...")
else:
print("Storage Container Exists...")
class pepsurf():
background_color = 'white'
color_carbon = 'C8C8C8'
color_sulfur = 'FFC832'
color_phosphorus = 'FFA500'
base_color = 'gray'
color_chain = ['808080','B0B0B0','E0E0E0']
cluster_color = ['FF6060','8080FF','FF40FF']
def __init__(self, input=None, parms=None):
self.input = input
self.job_parms = {}
self.cluster_res = {}
if yasara.storage.objects:
# print("Object Exists...")
self.input = None
self.job_parms.update(parms)
else:
# print("Creating new PepSurfPDB Object...")
yasara.Clear()
yasara.LoadPDB(self.input)
# yasara.ZoomAll()
self.extract_pepsurf_data(self.input)
self.job_parms['cluster_paths'] = self.extract_pepsurf_clusters(self.input, self.job_parms['pepsurf_cluster_count'])
yasara.NameObj(1, self.job_parms['pepsurf_pdb_id'].upper())
def extract_pepsurf_data(self, input):
with open(self.input, mode='r') as f:
for line in f:
if "!" in line:
if "pepsurf_version" in line:
self.job_parms['pepsurf_version'] = re.findall('"([^"]*)"', line)[0]
if "pepsurf_run_number" in line:
self.job_parms['pepsurf_run_number'] = re.findall('"([^"]*)"', line)[0]
if "pepsurf_run_date" in line:
self.job_parms['pepsurf_run_date'] = re.findall('"([^"]*)"', line)[0]
if "pepsurf_pdb_id" in line:
self.job_parms['pepsurf_pdb_id'] = re.findall('"([^"]*)"', line)[0]
if "pepsurf_chains" in line and ";" in line:
self.job_parms['pepsurf_chains'] = re.findall('"([^"]*)"', line)[0]
if "pepsurf_identical_chains" in line:
self.job_parms['pepsurf_identical_chains'] = re.findall('"([^"]*)"', line)[0]
if "pepsurf_cluster_count" in line:
self.job_parms['pepsurf_cluster_count'] = line[-2:-1]
def extract_pepsurf_clusters(self, input, num_clust):
c = 1
cluster_paths = {}
print_state = False
with open(self.input, mode='r') as f:
# print("Opened file...")
for line in f:
if "!" in line and "#name=select_cluster" in line:
cluster=[]
cluster_paths[c]=cluster
c+=1
print_state = True
elif "!!---------" in line:
print_state = False
elif "====== END OF PEPSURF PiPE BLOCK ======" in line:
break
elif print_state:
line_add = line.replace("select", "").replace("ed or ", "").replace("! ", "").rstrip().split(", ")
for item in line_add:
if "!" in item:
pass
else:
cluster.append(item)
return cluster_paths
def color_pdb_default(self):
# print("Setting Default Colors...")
yasara.HideAll()
yasara.ColorBG(self.background_color)
yasara.ColorAll(self.color_carbon)
return
def display_pdb_chains(self, pepsurf_chains):
self.color_pdb_default()
for inx, chain in enumerate(pepsurf_chains):
print(chain)
yasara.ColorMol(chain + " and !HetGroup", self.color_chain[inx])
return
def display_pepsurf_clusters(self, pepsurf_chains, cluster_paths):
s = self.select_chain_members(cluster_paths)
self.color_clusters(pepsurf_chains, s)
return
def select_chain_members(self, cluster_paths):
selection = {}
for cluster in cluster_paths:
cluster_select = defaultdict(list)
# print(cluster_paths[cluster])
for item in cluster_paths[cluster]:
c = self.id_pdb_chain(item)
a = self.id_aa_residue(item)
p = self.id_aa_pos(item)
cluster_select[c].append(a + " " + p)
selection[cluster] = cluster_select
# print(selection)
return selection
def id_pdb_chain(self, item):
return item.split(':')[-1]
def id_aa_residue(self, item):
return item.split(':')[0][0:3]
def id_aa_pos(self, item):
return item.split(':')[0][3:]
def color_clusters(self, chains, selection):
cluster_aa=[]
# print("Coloring...")
yasara.DuplicateObj(1) # Produces Obj 2 - Unlabeled
yasara.NameObj(1, "All Clusters")
for idx, item in enumerate(selection):
# print(selection) # Gives all clusters
# print(item) #Gives Cluster Number
# print(selection[item]) # Gives each cluster individually
yasara.DuplicateObj(2) # Unlabeled for each cluster
yasara.NameObj(item+2,"Cluster " + str(item))
for j, k in selection[item].items():
# print(j) # Gives Mol Chain
# print(k) # Gives list of residues
for i in k:
# print(i)
cluster_aa.append(i)
yasara.SelectRes(i + " and Mol " + j, mode='add')
self.cluster_res[item+2]=cluster_aa
yasara.BallRes('selected and Obj 1')
yasara.ShowRes('selected and Obj 1')
yasara.ColorRes('selected and Obj 1', self.cluster_color[item-1])
yasara.BallRes('selected and Obj ' + str(item+2))
yasara.ShowRes('selected and Obj ' + str(item+2))
yasara.ColorRes('selected and Obj ' + str(item+2), self.cluster_color[item-1])
# yasara.DuplicateRes('selected')
# yasara.ColorRes('selected', self.cluster_color[item-1])
yasara.UnselectAll()
yasara.SwitchObj('All', 'off')
yasara.SwitchObj(1, 'on')
return
try:
if yasara.request=="LoadPepSurfPDB":
if yasara.storage.objects:
# print("Storage Exists...")
# Clear storage for new PDB Loading...
yasara.Clear()
yasara.storage.objects = {}
# print("Load Storage...")
p = pepsurf(yasara.selection[0].filename[0])
# yasara.storage.objects.append(p)
yasara.storage.objects.update(p.job_parms)
# print(p.job_parms)
# print("Loading Complete...")
if yasara.request=="ViewPepSurfPDB":
# print("ViewPepSurfPDB...")
if yasara.storage.objects:
# print("Loading PepSurfPDB Parameters...")
# p = pepsurf(yasara.storage.objects[0])
p = pepsurf(parms = yasara.storage.objects)
# print(p.job_parms)
p.display_pdb_chains(p.job_parms["pepsurf_chains"])
p.display_pepsurf_clusters(p.job_parms['pepsurf_chains'], p.job_parms['cluster_paths'])
else:
print("Error: Need to load a PepSurfPDB...")
except:
yasara.plugin.end("Unknown request: {}".format(yasara.request))
# Stop the Plugin
yasara.plugin.end()