keitaroyam

import json
import urllib
import requests
def req(query):
  url = "https://pdbj.org/rest/newweb/search/sql?q=" + urllib.parse.quote(query)
  raw = urllib.request.urlopen(url).read()
  return json.loads(raw)["results"]

# [(pdb_id, monomer_id), ...]
all_mon = req("SELECT distinct pdbid,id FROM chem_comp")

keitaroyam

import iotbx.pdb
import mmtbx.utils
from mmtbx.scaling.matthews import p_vm_calculator

def run(pdbin):
  pdb_inp = iotbx.pdb.input(pdbin)
  xray_structure = pdb_inp.xray_structure_simple()
  print "Read from %s" % pdb_in
  xray_structure.show_summary(prefix="  ")
  print

keitaroyam

import mmtbx.monomer_library.server
from mmtbx import monomer_library
import glob
import os

mon_lib_srv = monomer_library.server.server()
cif_files = glob.glob(os.path.join(os.environ["CLIBD_MON"], "*/*.cif"))

for cf in cif_files:
  try:

keitaroyam

# This code will be unnecessary when new Eiger firmware offically writes this information

import h5py

def run(h5in):
    h5 = h5py.File(h5in, "a")

    if "/entry/sample/depends_on" not in h5:
        h5["/entry/sample/depends_on"] = "/entry/sample/transformations/omega"