def genPhiPsi(fileName):
struc = getStructuresFromFile(fileName)[0]
phiList = []
psiList = []
for chain in struc.chains:
for residue in chain.residues[1:-1]:
phi, psi = getPhiPsi(residue)
phiList.append(phi)
psiList.append(psi)
return phiList, psiList
if __name__ == '__main__':
import sys
import time
if len(sys.argv) != 3:
print('need to specify database and PDB file')
sys.exit(1)
database = sys.argv[1]
pdbFile = sys.argv[2]
from Modelling import getStructuresFromFile
structures = getStructuresFromFile(pdbFile)
import MySQLdb
import getpass
user = getpass.getuser()
pwd = getpass.getpass()
connection = MySQLdb.connect(db=database, user=user, passwd=pwd)
t0 = time.time()
try:
for structure in structures:
addStructureToDb3(connection, structure)
finally:
connection.close()
raise e # re-raise original exception
if __name__ == '__main__':
import sys
import time
if len(sys.argv) != 3:
print('need to specify database and PDB file')
sys.exit(1)
database = sys.argv[1]
pdbFile = sys.argv[2]
from Modelling import getStructuresFromFile
structures = getStructuresFromFile(pdbFile)
import MySQLdb
import getpass
user = getpass.getuser()
pwd = getpass.getpass()
connection = MySQLdb.connect(db=database, user=user, passwd=pwd)
placeHolder = '%s'
t0 = time.time()
try:
for structure in structures:
addStructureToDb(connection, structure, placeHolder)
finally:
connection.close()
boolArray = sumSquares < limit2
indices = boolArray.nonzero()[0]
closeAtoms = [atoms[i] for i in indices]
return closeAtoms
if __name__ == '__main__':
print('\nGet a PDB file')
fileName = 'examples/1A12.pdb'
print('\nMake structure object')
strucObjs = getStructuresFromFile(fileName)
print('\nGet centre of mass')
struc = getStructuresFromFile(fileName)[0]
print(getCenterOfMass(struc))
print('\nStructure tranformations')
rotateStructure(struc, (0, 1, 0), pi / 2)
rotateStructureNumPy(struc, (0, 1, 0), pi / 2)
mirrorTransform = array([[-1, 0, 0], [0, -1, 0], [0, 0, -1]])
translate = array([10.0, 10.0, 0.0])
affineTransformStructure(struc, mirrorTransform, translate)
try:
from urllib.request import urlopen
except ImportError:
from urllib2 import urlopen
PDB_URL = 'http://www.rcsb.org/pdb/cgi/export.cgi/' \
'%s.pdb?format=PDB&compression=None'
def downloadPDB(pdbId, fileName=None):
if not fileName:
fileName = '%s.pdb' % pdbId
response = urlopen(PDB_URL % pdbId)
data = response.read().decode('utf-8')
fileObj = open(fileName, 'w')
fileObj.write(data)
fileObj.close()
downloadPDB('1A12')
from Modelling import getStructuresFromFile
strucObjs = getStructuresFromFile(fileName)
boolArray = sumSquares < limit2
indices = boolArray.nonzero()[0]
closeAtoms = [atoms[i] for i in indices]
return closeAtoms
if __name__ == '__main__':
print('\nGet a PDB file')
fileName = 'examples/1A12.pdb'
print('\nMake structure object')
strucObjs = getStructuresFromFile(fileName)
print('\nGet centre of mass')
struc = getStructuresFromFile(fileName)[0]
print(getCenterOfMass(struc))
print('\nStructure tranformations')
rotateStructure(struc, (0,1,0), pi/2)
rotateStructureNumPy(struc, (0,1,0), pi/2)
mirrorTransform = array([[-1,0,0], [0,-1,0], [0,0,-1]])
translate = array([10.0,10.0,0.0])
affineTransformStructure(struc, mirrorTransform, translate)