if (boolean):
return 'yes'
else:
return 'no'
def getSelectedChemComp(self):
return self.chem_comp_var_table.currentObject
if (__name__ == '__main__'):
from memops.api.Implementation import MemopsRoot
from memops.gui.Button import Button
from memops.gui.MessageReporter import showInfo
project = MemopsRoot(name='p')
root = Tkinter.Tk()
root.top = root
root.grid_rowconfigure(0, weight=1)
root.grid_columnconfigure(0, weight=1)
frame = ChemCompFrame(root, project, path = '/ebi/msd/nmrqual/workspace/CCPN/python/ccp/gui/local/cctest/')
frame.grid(sticky=Tkinter.NSEW)
def getSelected():
chemComp = frame.getSelectedChemComp()
if (chemComp):
if hasattr(chemComp,'chemComp'):
# - Then link the person to the citation - use the addAuthor() method
# of the JournalCitation class.
#
# - Finally print the person's name and also the citation title starting
# from the person object by finding the first citation for this person
# with the relevant journal name.
#
# - Hint: use findFirstAuthorCitation to follow the person to citation link
# in this case.
#
from memops.api.Implementation import MemopsRoot
if __name__ == '__main__':
project = MemopsRoot(name='objTest')
projectName = project.name
# Create a new AffiliationStore top object.
affStore = project.newAffiliationStore(name=projectName)
# Create a new CitationStore top object.
citStore = project.newCitationStore(name=projectName)
# Create a new Person object from the AffiliationStore top object.
person = affStore.newPerson(familyName='Smith', givenName='John')
# Create a new JournalCitation object from the CitationStore top object.
fp.write('refpt %5.4f\n' % self.refpt[i])
fp.write('nuc %s\n' % self.nuc[i])
if self.pointValues[i]:
fp.write('params')
for value in self.pointValues[i]:
fp.write(' %5.4f' % value)
fp.write('\n')
fp.close()
if (__name__ == '__main__'):
import sys
if (len(sys.argv) != 2):
print 'Error: required argument: <parFile>'
sys.exit(1)
parFile = sys.argv[1]
params = AzaraParams(parFile)
from memops.api.Implementation import MemopsRoot, Url
from ccp.util.Spectrum import createExperiment
r = MemopsRoot()
l = r.newDataLocationStore(name='testDLS')
d = l.newDataUrl(name='testDataUrl', url=Url(path='/Users/wb104/edl387'))
n = r.newNmrProject(name='testNmrProject')
e = createExperiment(n, name='testExpt', numDim=params.ndim, sf=params.sf, isotopeCodes=params.nuc)
s = params.createDataSource(e, name='testSpectrum', dataUrl=d)
import os
import Tkinter
from memops.api.Implementation import MemopsRoot
from ccpnmr.format.converters.CnsFormat import CnsFormat
from ccpnmr.format.general.Util import (createExperiment,
getRefExpFromOldExpType)
from msd.nmrStar.IO.NmrStarExport import NmrStarExport
if __name__ == '__main__':
# Similar start to code as that found in ex6.py.
project = MemopsRoot(name='sampleTest')
guiRoot = Tkinter.Tk()
cnsObj = CnsFormat(project, guiRoot)
nmrProject = project.currentNmrProject = \
project.newNmrProject(name = project.name)
strucGen = nmrProject.newStructureGeneration()
cnsDir = '../data/cns'
cnsFile = os.path.join(cnsDir, 'cns_1.pdb')
cnsObj.readCoordinates([cnsFile],
strucGen=strucGen,
minimalPrompts=1,
linkAtoms=0)
import os
# This contains the application data class.
from memops.api import Implementation
from memops.api.Implementation import MemopsRoot
from ccpnmr.format.converters.FastaFormat import FastaFormat
from msd.nmrStar.IO.NmrStarExport import NmrStarExport
if __name__ == '__main__':
project = MemopsRoot(name='alignTest')
# Create a BMRB Entry for export to the NMR-STAR file.
entryStore = project.newNmrEntryStore(name=project.name)
nmrEntry = entryStore.newEntry(name=project.name)
# Application data objects allow you to store and associate extra data
# in the CCPN project that does not fit into the rest of the data model.
# Format of an application data object has the application that the data
# is derived from (e.g., XEasy, NmrStar); a keyword to describe the type
# of data that is present (e,g., sequence, chemical shift) and the value
# of the data.
# For this example, we are reading a Fasta file.
seqDir = '../data/seq'
seqFile = os.path.join(seqDir, 'fasta.seq')
keywds = {
from memops.api.Implementation import MemopsRoot
# No longer need the following package imports as can use methods
# in parent objects to create child objects like NmrEntryStore or Entry.
#from ccp.api.nmr.NmrEntry import (NmrEntryStore, Entry)
if __name__ == '__main__':
# Still need to create the CCPN project from an import.
project = MemopsRoot(name='entryTest2')
# Can use methods to get object attributes.
projectName = project.getName()
print 'Project [%s]' % projectName
# New way to create an NmrEntryStore instance.
entryStore = project.newNmrEntryStore(name=projectName)
entryStoreName = entryStore.getName()
print 'Entry store [%s]' % entryStoreName
# New way to create an Entry instance.
keywds = {
'title': 'test title',
'bmrbProcessing': 'test submission',
'details': 'test details'
}
entry = entryStore.newEntry(name=entryStoreName + 'A', **keywds)
entryName = entry.getName()
entryTitle = entry.getTitle()
entryBmrbProc = entry.getBmrbProcessing()
import os
import Tkinter
from memops.api.Implementation import MemopsRoot
from ccpnmr.format.converters.CnsFormat import CnsFormat
if __name__ == '__main__':
# CCPN project.
project = MemopsRoot(name='readCns')
guiRoot = Tkinter.Tk()
# CNS object.
cnsObj = CnsFormat(project, guiRoot)
# Read in a sequence - this will create the molecular system with
# all the atom information.
# Note, many of the popups can be avoided when the right information
# is passed in (see the readSequence() function in the
# ccpnmr.format.converters.DataFormat class.
# Set the location of the CNS files.
cnsDir = '../data/cns'
# Read in a sequence to set molecule and molSystem objects.
cnsCoord = 'cns_1.pdb'
cnsCoordFile = os.path.join(cnsDir, cnsCoord)
import Tkinter
from memops.api.Implementation import MemopsRoot
from ccpnmr.format.converters.NmrViewFormat import NmrViewFormat
from ccpnmr.format.converters.XEasyFormat import XEasyFormat
# Pre-defined functions to create an NMR experiment and data source.
from ccpnmr.format.general.Util import (createExperiment,
getRefExpFromOldExpType,
createPpmFreqDataSource)
if __name__ == '__main__':
# CCPN project.
project = MemopsRoot(name='nmrView2XEasy')
gui = Tkinter.Tk()
# NmrView object.
nmrViewObj = NmrViewFormat(project, gui)
# Location of the NmrView files.
nmrViewDir = '../data/nmrView'
# Read in a sequence to set molecule and molSystem objects.
nmrViewSeq = 'nmrView.seq'
nmrViewSeqFile = os.path.join(nmrViewDir, nmrViewSeq)
nmrViewObj.readSequence(nmrViewSeqFile, minimalPrompts=1)
from memops.api.Implementation import MemopsRoot
if __name__ == '__main__':
# CCPN project.
project = MemopsRoot(name='moleculeTest')
# Create a molecule. This is a reference object - molSystem contains the
# actual molecule. e.g., in a homodimer, you only create 1 molecule, but
# the molSystem has 2 chains (see below).
molecule = project.newMolecule(name='myMoleculeName')
# Then we have to create the MolResidues. All the reference information
# for these comes from the 'ChemComps', which must be loaded first.
# Here is an example protein sequence.
seq = ['Ala', 'Gly', 'Tyr', 'Glu', 'Leu', 'Gly', 'Ser', 'His', 'Ile']
for pos in range(0, len(seq)):
ccpCode = seq[pos]
# Find the reference data chemComp. Note the type of residue needs to be
# specified from: 'protein', 'DNA', 'RNA' 'carbohydrate', and 'other'.
keywds = {'molType': 'protein', 'ccpCode': ccpCode}
chemComp = project.findFirstChemComp(**keywds)
# For linear biopolymers ('protein', 'DNA' and 'RNA) the 'linking'
# needs to be set, which indicates the position in the linear chain.
# For other types ('carbohydrate', 'other') linking indicates the
# pattern of links to other building blocks.
if pos == 0:
# to each other:
#
# - from ccp.examples.workshop.session2.makeMolSystem import makeLinearLink
#
# - makeLinearLink(molecule, molResidue, position, linking) .
#
from memops.api.Implementation import MemopsRoot
# makeLinearLink sub-routine to make the correct links between the molResidues.
from ccp.examples.workshop.session2.makeMolSystem import makeLinearLink
if __name__ == '__main__':
project = MemopsRoot(name='dnaTest')
# Make a new molecule top object.
molecule = project.newMolecule(name='myDnaMoleculeName')
# DNA sequence as a string of one-letter codes.
seq = 'ATGGATCATTAG'
# Iterate over this sequence.
for pos in range(0, len(seq)):
# Get the residue code.
# of the files that are created - use the method saveModified() . # # - Try and run the script twice and see what happens. # # - Hint: Check to see what the mandatory attributes are for these top objects. # # Import the MemopsRoot class from the API. from memops.api.Implementation import MemopsRoot if __name__ == '__main__': # New CCPN project - called a MemopsRoot. project = MemopsRoot(name = 'topObjectTest') # Use the new<Class> factory methods available to the MemopsRoot class. # NmrEntry entryStore = project.newNmrEntryStore(name = 'myEntry') # Nmr nmrProject = project.newNmrProject(name = 'myNmrProject') # Affiliation affStore = project.newAffiliationStore(name = 'myAffiliation') # Citation citStore = project.newCitationStore(name = 'myCitation')
# Package imports from CCPN API.
# These must be in the global scope.
from memops.api.Implementation import MemopsRoot
from ccp.api.nmr.NmrEntry import (NmrEntryStore, Entry)
if __name__ == '__main__':
# Create a CCPN project (called a MemopsRoot class in the CCPN API).
# Must specify the attribute 'name' when created.
project = MemopsRoot(name = 'entryTest')
# Non-API way to get object attributes.
projectName = project.name
print 'Project [%s]' % projectName
# Create an NmrEntryStore that can hold multiple BMRB Entry objects.
entryStore = NmrEntryStore(project,
name = projectName)
entryStoreName = entryStore.name
print 'Entry store [%s]' % entryStoreName
print 'Current store: [%s]' % project.currentNmrEntryStore
# Create a BMRB Entry object, which can hold all the data for a BMRB
# deposition.
entry = Entry(entryStore, name = entryStoreName)
entryName = entry.name
print 'Entry [%s]\n' % entryName
from memops.api.Implementation import MemopsRoot
if __name__ == '__main__':
# CCPN project.
project = MemopsRoot(name='personTest')
# Create a BMRB Entry.
entryStore = project.currentNmrEntryStore = \
project.newNmrEntryStore(name = project.name)
entry = entryStore.newEntry(name=project.name)
# Create an affiliationStore and alias for it.
affStore = project.currentAffiliationStore = \
project.newAffiliationStore(name = project.name)
# Create an organisation and group.
orgn = affStore.newOrganisation(name='myDepartment')
group = orgn.newGroup(name='myGroup')
# Create a new person.
keywds = {'familyName': 'Smith', 'givenName': 'John'}
person = affStore.newPerson(**keywds)
# Set the group for this person. PersonInGroup is an intermediate
# class to avoid many-to-many relationships.
personInGroup = person.newPersonInGroup(group=group)
# Print some basic information.
personName = person.givenName + ' ' + person.familyName
orgName = person.findFirstPersonInGroup().group.organisation.name
from memops.api.Implementation import MemopsRoot
from ccpnmr.format.converters.NmrViewFormat import NmrViewFormat
from ccpnmr.format.general.Util import (
createExperiment, getRefExpFromOldExpType, createPpmFreqDataSource)
# Specific class not in Format Converter used to export NMR-STAR files.
from msd.nmrStar.IO.NmrStarExport import NmrStarExport
if __name__ == '__main__':
# This code follows on from ex8.py, but writes the project
# to NMR-STAR format.
project = MemopsRoot(name = 'nmrStarTest')
gui = Tkinter.Tk()
nmrViewObj = NmrViewFormat(project, gui)
nmrViewDir = '../data/nmrView'
nmrViewSeq = 'nmrView.seq'
nmrViewSeqFile = os.path.join(nmrViewDir, nmrViewSeq)
nmrViewObj.readSequence(nmrViewSeqFile, minimalPrompts = 1)
nmrProject = project.currentNmrProject = \
project.newNmrProject(name = project.name)
nmrViewChemShifts = 'ppm.out'
numDim=params.ndim)
# create spectrum
if not spectrumName:
n = 1
while experiment.findFirstDataSource(name='%d' % n):
n += 1
spectrumName = '%d' % n
spectrum = params.createDataSource(experiment, name=spectrumName)
return spectrum
if __name__ == '__main__':
import sys
from memops.api.Implementation import MemopsRoot
if len(sys.argv) != 2:
print 'Need to specify file'
sys.exit()
fileName = sys.argv[1]
project = MemopsRoot(name='test')
nmrProject = project.newNmrProject(name='test')
spectrum = openSpectrum(fileName, nmrProject=nmrProject)
residue = chain.newResidue(seqId=seqId, seqCode=molSysResidue.seqCode)
# create MolStructure.Atoms
for molSysAtom in molSysResidue.atoms:
chemAtom = molSysAtom.chemAtom
if chemAtom.elementSymbol != 'H':
atom = residue.newAtom(name=molSysAtom.name)
# create MolStructure.Coord
coord = atom.newCoord(model=model)
coord.x = random.random()
coord.y = random.random()
coord.z = random.random()
#root.saveModified()
if __name__ == '__main__':
import sys
if len(sys.argv) == 1:
from memops.api.Implementation import MemopsRoot
root = MemopsRoot(name='testNmr')
elif len(sys.argv) == 2:
from memops.general.Io import loadProject
repositoryPath = sys.argv[1]
root = loadProject(path=repositoryPath)
main(root)
# Sub routine to print out details of the repositories.
def printReposUrls(project):
print '\nUrls:'
for repos in project.sortedRepositories():
print repos.name, repos.url.path
print
if __name__ == '__main__':
# This code follows on from ex7.py.
project = MemopsRoot(name='constraintsTest')
guiRoot = Tkinter.Tk()
cnsObj = CnsFormat(project, guiRoot)
cnsDir = '../data/cns'
cnsCoord = 'cns_1.pdb'
cnsCoordFile = os.path.join(cnsDir, cnsCoord)
# To make a molSystem object.
chains = cnsObj.readSequence(cnsCoordFile)
distConst = 'n15noesy.tbl'
distConstFile = os.path.join(cnsDir, distConst)
# with chains is straightforward. All the residue and atom information for
# these are taken from the reference Molecule and ChemComp information.
keywds = {'code': molSysCode, 'name': molSysName}
molSystem = project.newMolSystem(**keywds)
# Now create the chains.
for code in chainCodes:
molSystem.newChain(code=code, molecule=molecule)
return molSystem
if __name__ == '__main__':
# CCPN project.
project = MemopsRoot(name='moleculeTest')
# 12345678901234567890
sequence = 'ACDEFGHIKLMNPQRSTVWY'
# Make a three-letter sequence list from a one-letter sequence string.
tlcSeq = makeSequence(sequence)
molecule = makeMolecule(project, tlcSeq)
print 'Molecule: [%s]' % molecule.name, '\n'
for molRes in molecule.sortedMolResidues():
print 'MolResidue: [%s]' % molRes.ccpCode
print