from __future__ import with_statement
from __future__ import division
import collections
from utils import memoize_m
from utils.tool import _, _dir_init, CmdTool, ProviMixin
import provi_prep as provi
DIR, PARENT_DIR, TMPL_DIR = _dir_init(__file__, "hbexplore")
HBEXPLORE_CMD = "HBX"
# 1=donor, 2=acceptor ???
HbxHbond = collections.namedtuple("HbxHbond", [
"chain1", "resno1", "resname1", "atomname1", "chain2", "resno2",
"resname2", "atomname2", "dDA", "dHA", "aDHA", "aHAhyb", "type"
])
def parse_hbx_output(hbexplore_file):
"""Function that parses HBexplores .anal files"""
hbonds = []
id_dict = {}
hbpart = 0
# SG CYS 127 O ILE 124 3.2597
# TOM 18 CB VAL 2 3.462 14.126 6.256 1.00 14.07 193L 162
# parse HBX.anal file
#87 NH2 ARG A 71 O MET A 1 3.0821 2.356 128.0 53.8 s-s
with open(hbexplore_file, "r") as fp:
for l in fp:
import os
from utils.tool import _, _dir_init, CmdTool, ScriptMixin
DIR, PARENT_DIR, TMPL_DIR = _dir_init(__file__, "jmol")
JAVA_CMD = "java"
JMOL_PATH = os.environ.get("JMOL_PATH", "")
JMOL_JAR = os.path.join(JMOL_PATH, "JmolData.jar")
class Jmol(CmdTool, ScriptMixin):
args = [_("script_file", type="file", ext="jspt")]
script_tmpl = None
tmpl_dir = TMPL_DIR
def _init(self, script_file, *args, **kwargs):
# TODO when args is empty check for self.script_tmpl
# to get rid of script_file
if script_file == "__tmpl__":
self.script_file = self.outpath(self.script_tmpl)
self.cmd = [
JAVA_CMD, "-Xmx6000M", "-jar", JMOL_JAR, "-oxdl", "-s",
self.script_file
]
class JmolImage(Jmol):
args = [
_("jmol_file", type="file", ext="jmol"),
from utils import copy_dict, try_float, try_div, flatten
from utils.math import point_plane_dist
from utils.tool import (_, _dir_init, PyTool, RecordsMixin, ParallelMixin,
ProviMixin, JsonBackend, SqliteBackend)
from utils.numpdb import NumPdb, NumAtoms
from opm import Opm, OpmInfo, Ppm2
from dowser import DowserRepeat, DowserPlus2
from voronoia import Voronoia, HOLE_NOT_FILLED, HOLE_PARTLY_FILLED
from hbexplore import HBexplore
from msms import Msms
from mpstruc import MpstrucDownload, MpstrucInfo
from pdb import PdbInfo
from dssp import Dssp
DIR, PARENT_DIR, TMPL_DIR = _dir_init(__file__, "mppd")
CURATED_INFO = collections.defaultdict(
dict,
{
"": {
"backbone_only": True,
"no_pdb_entry": True,
"representative": "",
"related": [],
"species": "",
"comment": ""
},
"2W1B": {
"comment": "dowser max_repeats=5"
},
from __future__ import division import collections from utils.tool import _, _dir_init, CmdTool from utils import numpdb from utils.numpdb import NumPdb DIR, PARENT_DIR, TMPL_DIR = _dir_init(__file__, "dssp") DSSP_CMD = "mkdssp" ################################################## # http://swift.cmbi.ru.nl/gv/dssp/index.html ################################################## # # COPYRIGHT # W. Kabsch, C. Sander and MPI-MF, 1983, 1985, 1988, 1994 1995 # CMBI version by [email protected] / November 18,2002 # USAGE # dsspcmbi [Options] PDB_File DSSP_File -> Read PDB_File and write DSSP_File # dsspcmbi [Options] -- dssp_file -> Read from stdin and write DSSP_File # dsspcmbi -h -> Display this help screen # OPTIONS # -na Disables the calculation of accessible surface. # -c Classic (old) format. # -w Wide 2002 format (for future use,not the current standard). # -v Verbose. # -- Read from standard input. # -h -? Prints a help message.
import os
from utils.tool import _, _dir_init, CmdTool
pdbDIR, pdbPARENT_DIR, pdbTMPL_DIR = _dir_init(__file__, "pdb")
DIR, PARENT_DIR, TMPL_DIR = _dir_init(__file__, "solvate")
solvate_CMD = os.path.join(TMPL_DIR, "solvate")
class Solvate(CmdTool):
"""
SOLVATE is a program to construct an atomic solvent environment model
for a given atomic macromolecule model (solute) for use in molecular
dynamics simulations.
"""
args = [
_("pdb_input",
type="file",
help="specifies the name of the input pdb-/psf-file of the solute. "
+
"If the -ion option is set, both pdb- and psf-file are required; " +
"otherwise only the pdb-file is needed. No extension must be given! "
+
"The input file name may be omitted, in which case SOLVATE creates "
+ "a pure spherical water droplet centered at the origin."),
_("thick|th",
type="float",
default=10.0,
help=
"specifies the minimum water shell thickness in Angstrom (dafult: 10.0),"
+
from poster.encode import multipart_encode
from poster.streaminghttp import register_openers
import numpy as np
from numpy.linalg import svd
import scipy
from utils import memoize_m, try_float
from utils.math import norm
from utils.tool import _, _dir_init, PyTool, ProviMixin
from utils.listing import ListRecord, ListIO
import utils.numpdb as numpdb
from utils.numpdb import NumPdb, numsele
DIR, PARENT_DIR, TMPL_DIR = _dir_init( __file__, "tmdet" )
PDBTM_LOCAL_PATH = os.environ.get("PDBTM_LOCAL_PATH", "")
TMDET_URL = "http://tmdet.enzim.hu/"
PDBTM_ALPHAHELICAL_URL = "http://pdbtm_data.enzim.hu/pdbtmalpha"
PDBTM_ALPHAHELICAL_PATH = os.environ.get("PDBTM_ALPHAHELICAL_PATH", "")
def pdbtm_download():
try:
url = PDBTM_ALPHAHELICAL_URL
return urllib2.urlopen( url ).read()
except urllib2.HTTPError:
raise Exception("MPstruc url error")
def pdbtm( pdbid, db_path=PDBTM_LOCAL_PATH ):
import collections
from poster.encode import multipart_encode
from poster.streaminghttp import register_openers
import numpy as np
from utils import memoize_m, try_float, copy_dict, get_index
from utils.math import norm
from utils.tool import _, _dir_init, PyTool, ProviMixin
from utils.listing import ListRecord, ListIO
from utils.numpdb import NumPdb
from pdb import PdbAssembly
DIR, PARENT_DIR, TMPL_DIR = _dir_init(__file__, "opm")
OPM_URL = "http://opm.phar.umich.edu/"
OPM_PDB_URL = OPM_URL + "pdb/{pdb_id:}.pdb"
OPM_LIST_URL = OPM_URL + "superfamilies_dl.php?class={class_id:}"
OPM_SEARCH_URL = OPM_URL + "protein.php?search={pdb_id:}"
OPM_LOCAL_PATH = os.environ.get("OPM_LOCAL_PATH", "")
PPM_URL = "http://sunshine.phar.umich.edu/"
def opm_list(class_id):
try:
url = OPM_LIST_URL.format(class_id=class_id)
page = urllib2.urlopen(url).read()
except urllib2.HTTPError:
raise Exception("Opm_list url error")
pdb_ids = re.findall(r"([0-9a-zA-Z]{4})<br />", page)
from __future__ import with_statement
from __future__ import division
import os
import logging
from basekit import utils
from utils import path, copy_dict
from utils.tool import _, _dir_init, CmdTool, PyTool
DIR, PARENT_DIR, TMPL_DIR = _dir_init(__file__, "mapman")
Mapman_CMD = os.path.join(TMPL_DIR, "lx_mapman")
logging.basicConfig()
LOG = logging.getLogger('mapman')
LOG.setLevel(logging.ERROR)
class BrixToMap(PyTool):
"""A wrapper around the 'Mapman' program to convert a Brix-File into a Map-File."""
args = [
_("brix_input", type="file", help="Input Brix-File "),
]
out = []
tmpl_dir = TMPL_DIR
def _init(self, *args, **kwargs):
self.mapman = Mapman(
self.brix_input, "brix",
**copy_dict(kwargs,
run=False,
from utils import copy_dict, try_float, try_div, flatten
from utils.math import point_plane_dist
from utils.tool import (_, _dir_init, PyTool, RecordsMixin, ParallelMixin,
ProviMixin, JsonBackend, SqliteBackend)
from utils.numpdb import NumPdb, NumAtoms
from opm import Opm, OpmInfo, Ppm2
from dowser import DowserRepeat
from voronoia import Voronoia, HOLE_NOT_FILLED, HOLE_PARTLY_FILLED
from hbexplore import HBexplore
from msms import Msms
from mpstruc import MpstrucInfo
from pdb import PdbInfo
from dssp import Dssp
DIR, PARENT_DIR, TMPL_DIR = _dir_init(__file__, "voronoia")
CURATED_INFO = collections.defaultdict(
dict,
{
"": {
"backbone_only": True,
"no_pdb_entry": True,
"representative": "",
"related": [],
"species": "",
"comment": ""
},
"2XND": {
"representative": "",
# from sequence similarity
from __future__ import division import numpy as np import utils.numpdb as numpdb import os import string import shutil import collections import utils from utils import copy_dict, dir_walker, iter_stride from utils.tool import _, _dir_init, CmdTool, ProviMixin from utils.math import hclust import json DIR, PARENT_DIR, TMPL_DIR = _dir_init(__file__, "msms") wfmesh_FILE = os.path.join(TMPL_DIR, "wfmesh.py") MSMS_CMD = "msms" BABEL_CMD = "babel" # newest open babel helps 2.2.3 """ g Surface1 # Number of vertices: 30918 v -51.84846 50.86638 114.37491 # Number of normals: 21610 vn -.076 .994 -.082 # Number of faces: 64556 f 3//3 2//2 1//1
from __future__ import with_statement
from __future__ import division
import os
import re
import json
import urllib2
import xml.etree.ElementTree
from utils.tool import _, _dir_init, PyTool
from utils.listing import ListRecord, ListIO
DIR, PARENT_DIR, TMPL_DIR = _dir_init(__file__, "mpstruc")
MPSTRUC_URL = "http://blanco.biomol.uci.edu/mpstruc/"
MPSTRUC_ALPHAHELICAL_URL = MPSTRUC_URL + "listAll/mpstrucAlphaHlxTblXml"
MPSTRUC_ALPHAHELICAL_PATH = os.environ.get("MPSTRUC_ALPHAHELICAL_PATH", "")
def mpstruc_download():
try:
url = MPSTRUC_ALPHAHELICAL_URL
return urllib2.urlopen(url).read()
except urllib2.HTTPError:
raise Exception("MPstruc url error")
def mpstruc_tree(xml_file=None):
if not xml_file:
xml_file = MPSTRUC_ALPHAHELICAL_PATH
try:
tree = xml.etree.ElementTree.parse(xml_file)
from __future__ import division
import os
import json
import itertools
import numpy as np
from utils import copy_dict
from utils.tool import _, _dir_init, PyTool, CmdTool, ScriptMixin
from utils.numpdb import NumPdb
from utils.mrc import getMrc
from utils.math import rmsd
from pdb import *#PdbSplit
#from pdb import PdbEdit, NumpdbTest
DIR, PARENT_DIR, TMPL_DIR = _dir_init( __file__, "spider" )
SPIDER_CMD = "spider"
# 2010 Cryo-EM Modeling Challenge: http://ncmi.bcm.edu/challenge
class MrcHeaderPrinter( PyTool ):
args = [
_( "mrc_file", type="file", ext="mrc" )
]
def func( self, *args, **kwargs ):
header = mrc_header( self.mrc_file )
for name, value in zip(header._fields, header):
print "%20s\t%s" % ( name, value )
import scipy.spatial
import itertools
from cStringIO import StringIO
import numpy as np
np.seterr( all="raise" )
import utils.numpdb as numpdb
from utils import try_int, copy_dict, listify
from utils.tool import _, _dir_init, PyTool, ProviMixin, CmdTool
from utils.timer import Timer
from utils.db import get_pdb_files
from utils.listing import ListRecord, ListIO, list_compare, list_join
from utils.math import rmatrixu, mag
DIR, PARENT_DIR, TMPL_DIR = _dir_init( __file__, "pdb" )
PDB_SEARCH_URL = 'http://www.rcsb.org/pdb/rest/search'
PDB_DOWNLOAD_URL = 'http://www.rcsb.org/pdb/files/'
PDBE_ASSEMBLY = 'http://www.ebi.ac.uk/pdbe-srv/view/files/{pdb_id:}_1.mmol' # not available anymore ASR 20 May 2014
RCSB_ASSEMBLY = 'http://www.rcsb.org/pdb/files/{pdb_id:}.pdb1.gz'
TMPL_DIR_CIONIZE = _dir_init( PARENT_DIR, "cionize" )
cionize_CMD = os.path.join( PARENT_DIR, "cionize" )
# the rotamere lib needs the 'remaining_atoms' data
ROTAMERE_LIB_PATH = os.path.join(
PARENT_DIR, "data", "bio", "bbind02.May.lib.json"
)
from __future__ import with_statement
from __future__ import division
import os
import logging
import collections
import shutil
from basekit import utils
import utils.numpdb as numpdb
from utils import dir_walker
from utils.tool import _, _dir_init, CmdTool
DIR, PARENT_DIR, TMPL_DIR = _dir_init(__file__, "superpose")
THESEUS_CMD = os.path.join(TMPL_DIR, "theseus")
DIR, PARENT_DIR, TMPL_DIR = _dir_init(__file__, "align")
MUSCLE_CMD = os.path.join(TMPL_DIR, "muscle3.8.31")
logging.basicConfig()
LOG = logging.getLogger('align')
LOG.setLevel(logging.ERROR)
class TheseusMakeFasta(CmdTool):
"""A wrapper around the 'theseus-align' programm."""
args = [
_("pdb_input", type="str", nargs="+", help="list of pdb-files"),
]
out = []
tmpl_dir = TMPL_DIR
import os
import urllib2
import collections
from poster.encode import multipart_encode
from poster.streaminghttp import register_openers
import numpy as np
np.seterr(all="raise")
import utils.path
from utils.tool import (_, _dir_init, PyTool, RecordsMixin, ParallelMixin,
ProviMixin)
from utils.numpdb import NumPdb
DIR, PARENT_DIR, TMPL_DIR = _dir_init(__file__, "capture")
CAPTURE_URL = "http://capture.caltech.edu/"
os.environ["HTTP_PROXY"] = 'proxy.charite.de:8080'
def capture_web(pdb_file, output_file):
"""queries the CaPTURE webservice"""
# Register the streaming http handlers with urllib2
register_openers()
# use relpath to hide local path
with open(os.path.relpath(pdb_file), "r") as fp:
# headers contains the necessary Content-Type and Content-Length
# datagen is a generator object that yields the encoded parameters
datagen, headers = multipart_encode({
"upfile": fp,
http://danger.med.unc.edu/hermans/dowser/Cameron_Mura_DOWSER.html
http://www.ks.uiuc.edu/Research/vmd/plugins/dowser/
http://muralab.org/~cmura/DOWSER/
http://www.ks.uiuc.edu/Research/vmd/plugins/dowser/dowser-rna.html
"""
import os
import shutil
import auto_parameterization as ap
from utils import copy_dict
from utils.tool import _, _dir_init, CmdTool, PyTool, ProviMixin
from utils.numpdb import NumPdb
from shutil import copyfile
DIR, PARENT_DIR, TMPL_DIR = _dir_init(__file__, "dowser")
DOWSER_CMD = "dowser"
DOWSERX_CMD = "dowserx"
DOWSER_REPEAT_CMD = "dowser-repeat"
DOWSERPLUS2_CMD = "/home/student/Software/Dowser++/callDowser++.sh"
DOWSER_ATOMDICT = os.path.join(TMPL_DIR, "atomdict.db")
DOWSER_ATOMPARMS = os.path.join(TMPL_DIR, "atomparms.db")
class DowserMixin(object):
def _pre_exec(self):
shutil.copy(self.pdb_file, self.input_file)
def _post_exec(self):
import shutil
import numpy as np
from numpy import *
from array import array
from basekit import utils
from utils import memoize_m, dir_walker, path
from utils.tool import _, _dir_init, CmdTool, ProviMixin, ParallelMixin
from utils.tool import RecordsMixin, PyTool
from utils.listing import merge_dic_list
from utils.bio import AA1
from align import Muscle
import provi_prep as provi
pdbDIR, pdbPARENT_DIR, pdbTMPL_DIR = _dir_init(__file__, "pdb")
DIR, PARENT_DIR, TMPL_DIR = _dir_init(__file__, "superpose")
THESEUS_CMD = os.path.join(TMPL_DIR, "theseus")
logging.basicConfig()
LOG = logging.getLogger('superpose')
LOG.setLevel(logging.ERROR)
class Theseus(CmdTool):
"""A wrapper around the 'theseus' programm."""
args = [
_("pdb_input",
type="str",
nargs="+",
help=