Python System Examples

Example #1

File: script2.py Project: hackolite/PRION

import sys
import math
sys.path.append('../..')
from MolecularSystem import System
x = System(None)
y = System(None)
z = System(None)
x.load_pdb('1KAW.pdb')
y.load_pdb('1L1OA.pdb')
z.load_pdb('1L1OB.pdb')
x.res_list = [8,14,32,34,57,59,71,77,79,101,109]
y.res_list = [25,31,41,43,53,55,63,67,69,79,84]
z.res_list = [74,80,92,94,104,106,120,126,128,141,146]
dsf = 0.2
for res_num1 in range(len(x.res_list)):
    sum1 = 0.0
    sum2 = 0.0
    sum3 = 0.0
    for res_num2 in range(0,len(x.res_list)):
        #print x.ProteinList[0].residue_dict[x.res_list[res_num2]].res_number, x.ProteinList[0].residue_dict[x.res_list[res_num2]].central_atom.atom_number
        #print y.ProteinList[0].residue_dict[y.res_list[res_num2]].res_number, y.ProteinList[0].residue_dict[y.res_list[res_num2]].central_atom.atom_number
        #print z.ProteinList[0].residue_dict[z.res_list[res_num2]].res_number, z.ProteinList[0].residue_dict[z.res_list[res_num2]].central_atom.atom_number
        #continue
        dist1 = x.ProteinList[0].residue_dict[x.res_list[res_num1]].central_atom.dist(x.ProteinList[0].residue_dict[x.res_list[res_num2]].central_atom)
        dist2 = y.ProteinList[0].residue_dict[y.res_list[res_num1]].central_atom.dist(y.ProteinList[0].residue_dict[y.res_list[res_num2]].central_atom)
        dist3 = z.ProteinList[0].residue_dict[z.res_list[res_num1]].central_atom.dist(z.ProteinList[0].residue_dict[z.res_list[res_num2]].central_atom)
        sum1 += dist1
        sum2 += dist2
        sum3 += dist3
        #if res_num2 > res_num1:
        str = '%5s %5s %5.2f %5s %5s %5.2f %5s %5s %5.2f %2s %2s %2s'%(x.res_list[res_num1], x.res_list[res_num2], dist1*dsf, 

Example #2

import sys
import math

sys.path.append('../..')
from MolecularSystem import System

x = System(None)
y = System(None)
z = System(None)
x.load_pdb('1KAW.pdb')
y.load_pdb('1L1OA.pdb')
z.load_pdb('1L1OB.pdb')
x.res_list = [8, 14, 32, 34, 57, 59, 71, 77, 79, 101, 109]
y.res_list = [25, 31, 41, 43, 53, 55, 63, 67, 69, 79, 84]
z.res_list = [74, 80, 92, 94, 104, 106, 120, 126, 128, 141, 146]
dsf = 0.2
for res_num1 in range(len(x.res_list)):
    sum1 = 0.0
    sum2 = 0.0
    sum3 = 0.0
    for res_num2 in range(0, len(x.res_list)):
        #print x.ProteinList[0].residue_dict[x.res_list[res_num2]].res_number, x.ProteinList[0].residue_dict[x.res_list[res_num2]].central_atom.atom_number
        #print y.ProteinList[0].residue_dict[y.res_list[res_num2]].res_number, y.ProteinList[0].residue_dict[y.res_list[res_num2]].central_atom.atom_number
        #print z.ProteinList[0].residue_dict[z.res_list[res_num2]].res_number, z.ProteinList[0].residue_dict[z.res_list[res_num2]].central_atom.atom_number
        #continue
        dist1 = x.ProteinList[0].residue_dict[
            x.res_list[res_num1]].central_atom.dist(
                x.ProteinList[0].residue_dict[
                    x.res_list[res_num2]].central_atom)
        dist2 = y.ProteinList[0].residue_dict[
            y.res_list[res_num1]].central_atom.dist(

Example #3

File: readOBs.py Project: deaconjs/SPADE

import math
import sys
import string

sys.path.append("../..")
from MolecularSystem import System

x = System(None)
y = System(None)
z = System(None)
x.load_pdb('1KAW.pdb')
y.load_pdb('1L1OA.pdb')
z.load_pdb('1L1OB.pdb')
for prot in [x, y, z]:
    prot.ProteinList[0].fill_pseudo_sidechains(1)
    prot.ProteinList[0].fill_neighbors_lists(0.35, 15.0)
x.res_list = [8, 14, 31, 32, 33, 34, 35, 57, 58, 59, 71, 77, 78, 79, 109]
y.res_list = [25, 31, 40, 41, 42, 43, 44, 53, 54, 55, 63, 67, 68, 69, 84]
z.res_list = [
    74, 80, 91, 92, 93, 94, 95, 104, 105, 106, 120, 126, 127, 128, 146
]

dsf = 0.15

do_replicate = 1
replicate_thresh = 0.05

shell_start = 7.0
shell_end = 13.0
p_lo_hash = {}
p_hi_hash = {}

Example #4

File: readOBs.py Project: hackolite/PRION

import math
import sys
import string
sys.path.append("../..")
from MolecularSystem import System
x = System(None)
y = System(None)
z = System(None)
x.load_pdb('1KAW.pdb')
y.load_pdb('1L1OA.pdb')
z.load_pdb('1L1OB.pdb')
for prot in [x,y,z]:
    prot.ProteinList[0].fill_pseudo_sidechains(1)
    prot.ProteinList[0].fill_neighbors_lists(0.35,15.0)
x.res_list = [8, 14,31,32,33,34,35,57, 58, 59, 71, 77, 78, 79, 109]
y.res_list = [25,31,40,41,42,43,44,53, 54, 55, 63, 67, 68, 69, 84 ]
z.res_list = [74,80,91,92,93,94,95,104,105,106,120,126,127,128,146]

dsf = 0.15

do_replicate = 1
replicate_thresh = 0.05

shell_start = 7.0
shell_end   = 13.0
p_lo_hash = {}
p_hi_hash = {}
combinations = 0
beta_dist_sum = 0.0
beta_dist_cnt = 0.0
beta_dist_lzst = []

Example #5

import sys
import os
sys.path.append('./Tools/Aligner')
import SequenceAligner

from MolecularSystem import System

list = os.listdir('.')
for pdb in list:
    sys = System(pdb)
    print pdb
    for i in range(len(sys.ProteinList)-1):
        for j in range(i+1,len(sys.ProteinList)):
            a = SequenceAligner.SequenceAligner(0, 'global')
            a.add_target(sys.ProteinList[i])
            a.add_template(sys.ProteinList[j])
            pid = a.align_sequences()
            line = '%5.3f percent identity %s %s\n'%(pid, sys.ProteinList[i].chain_name, sys.ProteinList[j].chain_name)
            print line

Example #6

import sys
sys.path.append('../..')
from MolecularSystem import System
from BlissSuperimpose import superimpose
x = System(None)
y = System(None)
x.load_pdb('atoms1.pdb')
y.load_pdb('atoms2.pdb')
superimpose([x,y])
x.save_pdb('atoms3.pdb')
y.save_pdb('atoms4.pdb')