def testRenameChain(self):
pdb1 = self._importStructurePDB('5NI1') # A, B, C
_dictOperations = ProtAtomStrucOperate.operationsDictInv
args = {
'pdbFileToBeRefined': pdb1,
'Operation': _dictOperations['reNameChain'],
'inputStructureChain':
'{"model": 0, "chain": "B", "residues": 146}',
'chainName': 'AA'
}
protAtomStrucExtractChain = self.newProtocol(ProtAtomStrucOperate,
**args)
self.launchProtocol(protAtomStrucExtractChain)
aSH2 = AtomicStructHandler()
outFileName = protAtomStrucExtractChain.outputPdb.getFileName()
aSH2.read(outFileName)
atomsNumT = len([atom.id for atom in aSH2.getStructure().get_atoms()])
# check size
self.assertEqual(4579, atomsNumT)
# check chain names
d1, d2 = aSH2.getModelsChains()
chains = d1[0].keys()
self.assertTrue('A' in chains)
self.assertTrue('AA' in chains)
self.assertTrue('C' in chains)
self.assertTrue('D' in chains)
self.assertFalse('B' in chains)
def exportAtomStructStep(self):
exportAtomStruct = self.exportAtomStruct.get()
originStructPath = exportAtomStruct.getFileName()
dirName = self.filesPath.get()
destinyStructPath = os.path.join(dirName, self.COORDINATEFILENAME)
destinySympleStructPath = os.path.join(dirName, self.SYMPLIFIED_STRUCT)
# save input atom struct with no change
baseName = os.path.basename(originStructPath)
localPath = os.path.abspath(os.path.join(dirName, baseName))
copyFile(originStructPath, localPath)
# call biopython to simplify atom struct and save it
aSH = AtomicStructHandler()
aSH.read(originStructPath)
aSH.write(destinySympleStructPath)
# if pdb convert to mmcif calling maxit twice
if originStructPath.endswith(".pdb"):
# convert pdb to cif using maxit program
log = self._log
fromPDBToCIF(originStructPath, destinyStructPath, log)
try:
# convert cif to mmCIF by using maxit program
fromCIFTommCIF(destinyStructPath, destinyStructPath, log)
except Exception as e:
pass
# if cif convert to mmcif using maxit
elif originStructPath.endswith(".cif"):
# convert cif to mmCIF by using maxit program
log = self._log
try:
fromCIFTommCIF(originStructPath, destinyStructPath, log)
except Exception as e:
pass
def testExtractAllChains(self):
pdb1 = self._importStructurePDB('6vsb') # A, B, C
_dictOperations = ProtAtomStrucOperate.operationsDictInv
args = {
'pdbFileToBeRefined': pdb1,
'Operation': _dictOperations['extractAllChains']
}
protAtomStrucExtractChain = self.newProtocol(ProtAtomStrucOperate,
**args)
self.launchProtocol(protAtomStrucExtractChain)
aSH2 = AtomicStructHandler()
outFileName = protAtomStrucExtractChain.outputPdb_chainC.getFileName()
aSH2.read(outFileName)
atomsNumT = len([atom.id for atom in aSH2.getStructure().get_atoms()])
self.assertEqual(7327, atomsNumT)
def testRenumberChain(self):
pdb1 = self._importStructurePDB('1P30') # A
_dictOperations = ProtAtomStrucOperate.operationsDictInv
args = {
'pdbFileToBeRefined': pdb1,
'Operation': _dictOperations['reNumberChain'],
'inputStructureChain':
'{"model": 0, "chain": "A", "residues": 891}',
'offset': 5
}
protAtomStrucExtractChain = self.newProtocol(ProtAtomStrucOperate,
**args)
self.launchProtocol(protAtomStrucExtractChain)
aSH2 = AtomicStructHandler()
outFileName = protAtomStrucExtractChain.outputPdb.getFileName()
aSH2.read(outFileName)
atomsNumT = len([atom.id for atom in aSH2.getStructure().get_atoms()])
self.assertEqual(7304, atomsNumT)
def _runChangingCifFormatSuperpose(self, list_args):
cwd = os.getcwd() + "/" + self._getExtraPath()
try:
if list_args[0].endswith(".cif") and list_args[1].endswith(".cif"):
try:
# upgrade cifs
list_args1 = []
for i in range(0, 2):
list_args1.append(fromCIFTommCIF(list_args[i], list_args[i]))
args1 = list_args1[0] + " " + list_args1[1]
Plugin.runPhenixProgram(Plugin.getProgram(SUPERPOSE), args1,
extraEnvDict=None, cwd=cwd)
except:
# convert cifs to pdbs
list_args2 = []
for i in range(0, 2):
list_args2.append(fromCIFToPDB(
list_args[i], list_args[i].replace('.cif', '.pdb')))
args2 = list_args2[0] + " " + list_args2[1]
Plugin.runPhenixProgram(Plugin.getProgram(SUPERPOSE), args2,
extraEnvDict=None, cwd=cwd)
elif list_args[0].endswith(".cif") and list_args[1].endswith(".pdb"):
try:
# pdbs: convert cif to pdb
list_args1 = []
list_args1.append(fromCIFToPDB(
list_args[0], list_args[0].replace('.cif', '.pdb')))
args1 = list_args1[0] + " " + list_args[1]
Plugin.runPhenixProgram(Plugin.getProgram(SUPERPOSE), args1,
extraEnvDict=None, cwd=cwd)
except:
try:
# cifs: convert pdb to cif
list_args2 = []
list_args2.append(fromPDBToCIF(
list_args[1], list_args[1].replace('.pdb', '.cif')))
args2 = list_args[0] + " " + list_args2[0]
Plugin.runPhenixProgram(Plugin.getProgram(SUPERPOSE), args2,
extraEnvDict=None, cwd=cwd)
except:
# upgrade cif
list_args3 = []
list_args0 = args2.split()
for i in range(0, 2):
list_args3[i].append(fromCIFTommCIF(
list_args0[i], list_args0[i]))
args3 = list_args3[0] + " " + list_args3[1]
Plugin.runPhenixProgram(Plugin.getProgram(SUPERPOSE),
args3, extraEnvDict=None, cwd=cwd)
elif list_args[0].endswith(".pdb") and list_args[1].endswith(".cif"):
try:
# pdbs: convert cif to pdb
list_args1 = []
list_args1.append(fromCIFToPDB(
list_args[1], list_args[1].replace('.cif', '.pdb')))
args1 = list_args[0] + " " + list_args1[0]
Plugin.runPhenixProgram(Plugin.getProgram(SUPERPOSE), args1,
extraEnvDict=None, cwd=cwd)
except:
try:
# cifs: convert pdb to cif
list_args2 = []
list_args2.append(fromPDBToCIF(
list_args[0], list_args[0].replace('.pdb', '.cif')))
args2 = list_args2[0] + " " + list_args[1]
Plugin.runPhenixProgram(Plugin.getProgram(SUPERPOSE), args2,
extraEnvDict=None, cwd=cwd)
except:
# upgrade cifs
list_args3 = []
list_args0 = args2.split()
for i in range(0, 2):
list_args3.append(fromCIFTommCIF(
list_args0[i], list_args0[i]))
args3 = list_args3[0] + " " + list_args3[1]
Plugin.runPhenixProgram(Plugin.getProgram(SUPERPOSE),
args3, extraEnvDict=None, cwd=cwd)
except:
# biopython conversion
aSH = AtomicStructHandler()
try:
for i in range(0, 2):
aSH.read(list_args[i])
aSH.write(list_args[i])
args = list_args[0] + " " + list_args[1]
Plugin.runPhenixProgram(Plugin.getProgram(SUPERPOSE),
args, extraEnvDict=None, cwd=cwd)
except:
print("CIF file standarization failed.")
class ChimeraModelFromTemplate(ChimeraProtBase):
"""Protocol to model three-dimensional structures of proteins using Modeller.
Execute command *scipionwrite #n [prefix stringAddedToFilename] from command line in order
to transfer the selected
pdb to scipion. Default value is model=#0,
model refers to the pdb file."""
_label = 'model from template'
_program = ""
_version = VERSION_1_2
INFILE1 = "unaligned_1.fasta"
OUTFILE1 = "aligned_1.fasta"
INFILE2 = "unaligned_2.fasta"
OUTFILE2 = "aligned_2.fasta"
TWOSEQUENCES = 0
MULTIPLESEQUENCES = 1
ProgramToAlign1 = ['Bio.pairwise2', 'Clustal Omega', 'MUSCLE']
ProgramToAlign2 = ['Clustal Omega', 'MUSCLE']
OptionForAligning = [
'None', 'Additional sequences to align',
'Provide your own sequence alignment'
]
OptionForDataBase = ['PDB', 'NR']
OptionForMatrix = [
'BLOSUM45', 'BLOSUM50', 'BLOSUM62', 'BLOSUM80', 'BLOSUM90', 'PAM30',
'PAM70', 'PAM250', 'IDENTITY'
]
# --------------------------- DEFINE param functions --------------------
def _defineParams(self, form, doHelp=False):
form.addSection(label='Input')
section = form.getSection('Input')
section.addParam(
'addTemplate',
BooleanParam,
default=True,
label='Do you already have a template?',
help='"Yes": Option by default. Select this option in case '
'you already have a template to model your target '
'sequence.\n"No": Select this option if you want to '
'search for a template with which model your target '
'sequence. Generation of multimeric models is not '
'allowed selecting this option.\n')
section.addParam('pdbFileToBeRefined',
PointerParam,
pointerClass="AtomStruct",
allowsNull=True,
important=True,
condition='addTemplate == True',
label='Atomic structure used as template',
help="PDBx/mmCIF file template used as basic atomic "
"structure to model your specific sequence.")
section.addParam('inputStructureChain',
StringParam,
label="Chain ",
allowsNull=True,
important=True,
condition='addTemplate == True',
help="Select a particular chain of the atomic "
"structure.")
section.addParam('inputSequence1',
PointerParam,
pointerClass="Sequence",
label='Target sequence',
allowsNull=True,
important=True,
help="Input the aminoacid sequence to align with the "
"structure template sequence.")
section.addParam(
'dataBase',
EnumParam,
choices=self.OptionForDataBase,
condition='addTemplate == False',
label="Protein sequence database:",
default=0,
help="Select a protein sequence database to search "
"for templates:\nPDB: Experimentally determined structures "
"in the "
"Protein Data Bank.\nNR: NCBI 'non-redundant'database. "
"It contains GenBank translation proteins, PDB sequences, "
"SwissProt proteins + PIR + PRF. Since NR is much larger "
"than PDB, it takes longer to search.\n")
section.addParam(
'similarityMatrix',
EnumParam,
choices=self.OptionForMatrix,
condition='addTemplate == False',
label="Similarity matrix:",
default=2,
help="Select a similarity matrix to use for alignment "
"scoring.\n")
section.addParam('cutoffValue',
FloatParam,
condition='addTemplate == False',
label="cutoff evalue:",
default=1e-3,
help="Least significant expectation value needed to "
"qualify the retrieved element as a hit.\n")
section.addParam('maxSeqs',
IntParam,
condition='addTemplate == False',
label="Maximum number of sequences:",
default=100,
help="Maximum number of sequences to retrieve "
"from the database.\n")
section.addParam(
'optionForAligning1',
EnumParam,
choices=self.OptionForAligning,
condition='addTemplate == True',
label="Options to improve the alignment:",
default=0,
help="None: Option by default. Only the template and the "
"target sequences will be included in the alignment. "
"This option is recommendable when these two sequences "
"are very similar. Otherwise, select any of the two "
"additional options:\n"
"Additional sequences to align: Select this option "
"if you want to add some more sequences to accomplish "
"the alignment.\n"
"Provide your own sequence alignment: Your alignment"
"should include both the target and the template "
"sequences.\n")
section.addParam(
'inputYourOwnSequenceAlignment1',
PathParam,
pointerClass="File",
allowsNull=False,
condition='addTemplate == True and optionForAligning1 == 2',
label='Sequence alignment input',
help="Input your own sequence alignment.\n"
"ChimeraX allowed formats accessible here: "
"https://www.cgl.ucsf.edu/chimerax/docs/user/commands/open.html#sequence "
)
section.addParam(
'inputSequencesToAlign1',
MultiPointerParam,
pointerClass="Sequence",
allowsNull=True,
condition='addTemplate == True and optionForAligning1 == 1',
label='Other sequences to align',
help="In case you need to load more sequences to "
"align, you can load them here.")
section.addParam(
'inputProgramToAlign1_1',
EnumParam,
choices=self.ProgramToAlign1,
label="Alignment tool for two sequences:",
default=0,
condition='addTemplate == True and optionForAligning1 == 0',
help="Select a program to accomplish the sequence"
"alignment:\n\nBiophyton module "
"Bio.pairwise2 ("
"http://biopython.org/DIST/docs/api/"
"Bio.pairwise2-module.html). Built-in "
"program to align two "
"sequences. The global "
"alignment algorithm from the EMBOSS suite "
"has been implemented with match/mismatch "
"scores of 3/-1 and gap penalties "
"(open/extend) of "
"3/2.\n\nClustal Omega "
"program (http://www.clustal.org/omega/, "
"https://doi.org/10.1038/msb.2011.75): "
"Multiple sequence alignment tool. Install "
"clustalo if you choose this option for "
"the first time by 'sudo apt-get install "
"clustalo'.\n\nMUSCLE program stands for "
"MUltiple Sequence Comparison by "
"Log- Expectation("
"http://www.drive5.com/muscle/muscle.html, "
"https://doi.org/10.1093/nar/gkh340). "
"Install muscle if you choose this option "
"for the first time by 'sudo apt install "
"muscle'.")
section.addParam(
'inputProgramToAlign2_1',
EnumParam,
choices=self.ProgramToAlign2,
label="Multiple alignment tool:",
default=0,
condition='addTemplate == True and optionForAligning1 == 1',
help="Select a program to accomplish the sequence"
"alignment:\n\nClustal Omega "
"program (http://www.clustal.org/omega/, "
"https://doi.org/10.1038/msb.2011.75): "
"Multiple sequence alignment tool. Install "
"clustalo if you choose this option for "
"the first time by 'sudo apt-get install "
"clustalo'.\n\nMUSCLE program stands for "
"MUltiple Sequence Comparison by "
"Log- Expectation("
"http://www.drive5.com/muscle/muscle.html, "
"https://doi.org/10.1093/nar/gkh340). "
"Install muscle if you choose this option "
"for the first time by 'sudo apt install "
"muscle'.")
section.addParam('additionalTargetSequence',
BooleanParam,
default=False,
condition='addTemplate == True',
label='Additional target sequence to include?',
help='Select YES if you want to add an additional '
'target sequence to model according a different '
'chain of the structure template. This '
'option is recommendable when you want to model '
'the two interacting elements of a particular complex'
' at the same time.')
section.addParam('selectStructureChain',
StringParam,
condition='addTemplate == True and '
'additionalTargetSequence == True',
label="Chain ",
allowsNull=True,
important=True,
help="Select a particular chain of the atomic "
"structure.")
section.addParam('inputSequence2',
PointerParam,
pointerClass="Sequence",
condition='addTemplate == True and '
'additionalTargetSequence == True',
label='Target sequence',
allowsNull=True,
important=True,
help="Input the aminoacid sequence to align with the "
"structure template sequence.")
section.addParam(
'optionForAligning2',
EnumParam,
choices=self.OptionForAligning,
condition='addTemplate == True and '
'additionalTargetSequence == True',
label="Options to improve the alignment:",
default=0,
help="None: Option by default. Only the template and the "
"target sequences will be included in the alignment. "
"This option is recommendable when these two sequences "
"are very similar. Otherwise, select any of the two "
"additional options:\n"
"Additional sequences to align: Select this option "
"if you want to add some more sequences to accomplish "
"the alignment.\n"
"Provide your own sequence alignment: Your alignment"
"should include both the target and the template "
"sequences.\n")
section.addParam(
'inputYourOwnSequenceAlignment2',
PathParam,
pointerClass="File",
allowsNull=False,
condition='addTemplate == True and '
'optionForAligning2 == 2 and '
'additionalTargetSequence == True',
label='Sequence alignment input',
help="Input your own sequence alignment.\n"
"ChimeraX allowed formats accessible here: "
"https://www.cgl.ucsf.edu/chimerax/docs/user/commands/open.html#sequence "
)
section.addParam('inputSequencesToAlign2',
MultiPointerParam,
pointerClass="Sequence",
allowsNull=True,
condition='addTemplate == True and '
'optionForAligning2 == 1 and '
'additionalTargetSequence == True',
label='Other sequences to align',
help="In case you need to load more sequences to "
"align, you can load them here.")
section.addParam('inputProgramToAlign1_2',
EnumParam,
choices=self.ProgramToAlign1,
label="Alignment tool for two sequences:",
default=0,
condition='addTemplate == True and '
'optionForAligning2 == 0 and '
'additionalTargetSequence == True',
help="Select a program to accomplish the sequence"
"alignment:\n\nBiophyton module "
"Bio.pairwise2 ("
"http://biopython.org/DIST/docs/api/"
"Bio.pairwise2-module.html). Built-in "
"program to align two "
"sequences. The global "
"alignment algorithm from the EMBOSS suite "
"has been implemented with match/mismatch "
"scores of 3/-1 and gap penalties "
"(open/extend) of "
"3/2.\n\nClustal Omega "
"program (http://www.clustal.org/omega/, "
"https://doi.org/10.1038/msb.2011.75): "
"Multiple sequence alignment tool. Install "
"clustalo if you choose this option for "
"the first time by 'sudo apt-get install "
"clustalo'.\n\nMUSCLE program stands for "
"MUltiple Sequence Comparison by "
"Log- Expectation("
"http://www.drive5.com/muscle/muscle.html, "
"https://doi.org/10.1093/nar/gkh340). "
"Install muscle if you choose this option "
"for the first time by 'sudo apt install "
"muscle'.")
section.addParam('inputProgramToAlign2_2',
EnumParam,
choices=self.ProgramToAlign2,
label="Multiple alignment tool:",
default=0,
condition='addTemplate == True and '
'optionForAligning2 == 1 and '
'additionalTargetSequence == True',
help="Select a program to accomplish the sequence"
"alignment:\n\nClustal Omega "
"program (http://www.clustal.org/omega/, "
"https://doi.org/10.1038/msb.2011.75): "
"Multiple sequence alignment tool. Install "
"clustalo if you choose this option for "
"the first time by 'sudo apt-get install "
"clustalo'.\n\nMUSCLE program stands for "
"MUltiple Sequence Comparison by "
"Log- Expectation("
"http://www.drive5.com/muscle/muscle.html, "
"https://doi.org/10.1093/nar/gkh340). "
"Install muscle if you choose this option "
"for the first time by 'sudo apt install "
"muscle'.")
section.addParam(
'extraCommands',
StringParam,
default='',
condition='False',
label='Extra commands for chimera viewer',
help="Add extra commands in cmd file. Use for testing")
form.addSection(label='Help')
form.addLine(
"Step 1:\nIn the sequence window your target "
"sequence (and other additional sequences that you "
"want to use in the alignment) will appear aligned to "
"the template's sequence. Select in the sequence window "
"menu:\nTools -> Sequence -> Modeller Comparative;\nA new "
"window for Comparative Modeling with Modeller will "
"appear. Select your specific template(s) as the Sequence "
"alignments and the target(s)sequence as the sequence "
"to be modeled" + '''
. To run Modeller via web service
write the Modeller license key supplied (Academic user can
register free of charge to receive a license key). Finally, press OK.
\nWAITING TIME: (you may see the status of your job in chimera main
window, lower left corner.)\n\nStep 2:\nWhen the process finished,
5 models will
be automatically superimposed onto the template and model scores
will appear in Modeller Results window. In Chimera Model panel
you will have: #1 (coordinate axes); #2 (
template); #3.1 to 3.5 (models).Choose the one you like the best,
for example model #3.1. To save it in Scipion, we need to change the
model ID. In Chimera main menu: Favorites -> Command Line, write
*rename #3.1 id #4*. Then, you will see in Model panel
that selected model #3.1 renamed to #3. Save it
as first guess in Scipion by executing the Chimera command
*scipionwrite [model] #n [prefix XX]*. In our example
*scipionwrite #4 pefix model_3_1_*.\n
When you use the command line scipionwrite, the Chimera session will
be saved by default. Additionally, you can save the Chimera session
whenever you want by executing the command *scipionss*. You will be
able to restore the saved session by using the protocol chimera
restore session (SCIPION menu: Tools/Calculators/chimera restore
session). Once you have save your favorite model you can press
Quit in the Modeller Results window.''')
# --------------------------- INSERT steps functions --------------------
def prerequisitesStep(self):
if self.addTemplate:
# read PDB
fileName = self._readPDB()
# get pdb sequence
import json
chainIdDict = json.loads(self.inputStructureChain.get())
userSeq = self.inputSequence1.get() # SEQ object from Scipion
inFile = self.INFILE1
outFile = self.OUTFILE1
addSeq = self.optionForAligning1.get()
yourAlignment = self.inputYourOwnSequenceAlignment1.get()
inputSeqAlign = self.inputSequencesToAlign1
programToAlign1 = self.inputProgramToAlign1_1
programToAlign2 = self.inputProgramToAlign2_1
self.prePreRequisites(fileName, chainIdDict, userSeq, inFile,
outFile, addSeq, yourAlignment,
inputSeqAlign, programToAlign1,
programToAlign2)
self.selectedChain1 = self.selectedChain
if self.additionalTargetSequence.get() is True:
chainIdDict = json.loads(self.selectStructureChain.get())
userSeq = self.inputSequence2.get() # SEQ object from Scipion
inFile = self.INFILE2
outFile = self.OUTFILE2
addSeq = self.optionForAligning2.get()
yourAlignment = self.inputYourOwnSequenceAlignment2.get()
inputSeqAlign = self.inputSequencesToAlign2
programToAlign1 = self.inputProgramToAlign1_2
programToAlign2 = self.inputProgramToAlign2_2
self.prePreRequisites(fileName, chainIdDict, userSeq, inFile,
outFile, addSeq, yourAlignment,
inputSeqAlign, programToAlign1,
programToAlign2)
self.selectedChain2 = self.selectedChain
else:
userSeq = self.inputSequence1.get() # SEQ object from Scipion
# get target sequence imported by the user
outFile = self.OUTFILE1
self.targetSeqID1 = self.preTemplate(userSeq, outFile)
def prePreRequisites(self, fileName, chainIdDict, userSeq, inFile, outFile,
addSeq, yourAlignment, inputSeqAlign, programToAlign1,
programToAlign2):
# get sequence of structure chain with id chainId (selected by the user)
self.selectedModel = chainIdDict['model']
self.selectedChain = chainIdDict['chain']
# self.selectedModel = chainId.split(',')[0].split(':')[1].strip()
# self.selectedChain = chainId.split(',')[1].split(':')[1].strip()
print("Selected chain: %s from model: %s from structure: %s" \
% (self.selectedChain, self.selectedModel,
os.path.basename(fileName)))
# Bio.Seq.Seq object
structureSeq = self.structureHandler.getSequenceFromChain(
self.selectedModel, self.selectedChain)
# obtain a seqID for our PDB sequence
structSeqID = self.structureHandler.getFullID(self.selectedModel,
self.selectedChain)
# END PDB sequence
# start user imported target sequence
# get target sequence imported by the user
targetSeqID = userSeq.getId() # ID associated to SEQ object (str)
userSequence = userSeq.getSequence() # sequence associated to
# that SEQ object (str)
# transformation of this sequence (str) in a Bio.Seq.Seq object:
seqHandler = SequenceHandler(userSequence,
isAminoacid=userSeq.getIsAminoacids())
targetSeq = seqHandler._sequence # Bio.Seq.Seq object
# creation of Dic of IDs and sequences
SeqDic = OrderedDict()
SeqDic[structSeqID] = structureSeq
SeqDic[targetSeqID] = targetSeq
# align sequences and save them to disk, -this will be chimera input-
# get all sequences in a fasta file
inFile = self._getInFastaSequencesFile(inFile)
outFile = self._getOutFastaSequencesFile(outFile)
# get the alignment of sequences
if addSeq == 0:
saveFileSequencesToAlign(SeqDic, inFile)
inputSeqAlign = None
if programToAlign1.get() == \
self.ProgramToAlign1.index('Bio.pairwise2'):
# Only the two first sequences will be included in the alignment
self.alignment = alignBioPairwise2Sequences(
structSeqID, structureSeq, targetSeqID, targetSeq, outFile)
else:
# All the sequences will be included in the alignment
if programToAlign1.get() == \
self.ProgramToAlign1.index('Clustal Omega'):
cline = alignClustalSequences(inFile, outFile)
else:
cline = alignMuscleSequences(inFile, outFile)
args = ''
self.runJob(cline, args)
elif addSeq == 1:
# if there are additional sequences imported by the user
if inputSeqAlign is not None:
for seq in inputSeqAlign:
seq = seq.get()
ID = seq.getId()
sequence = seq.getSequence()
seqHandler = SequenceHandler(
sequence, isAminoacid=seq.getIsAminoacids())
otherSeq = seqHandler._sequence # Bio.Seq.Seq object
SeqDic[ID] = otherSeq
# align sequences and save them to disk, -this will be chimera input-
# get all sequences in a fasta file
# inFile = self._getInFastaSequencesFile()
saveFileSequencesToAlign(SeqDic, inFile)
# outFile = self._getOutFastaSequencesFile()
# All the sequences will be included in the alignment
if programToAlign2 == self.ProgramToAlign2.index('Clustal Omega'):
cline = alignClustalSequences(inFile, outFile)
else:
cline = alignMuscleSequences(inFile, outFile)
args = ''
self.runJob(cline, args)
else:
aligmentFile = os.path.basename(yourAlignment)
outFile = os.path.join(self._getExtraPath(), aligmentFile)
copyFile(yourAlignment, outFile)
def preTemplate(self, userSeq, outFile):
userSequence = userSeq.getSequence() # sequence associated to
# that SEQ object (str)
targetSeqID = userSeq.getId() # ID associated to SEQ object (str)
# transformation of this sequence (str) in a Bio.Seq.Seq object:
seqHandler = SequenceHandler(userSequence,
isAminoacid=userSeq.getIsAminoacids())
targetSeq = seqHandler._sequence # Bio.Seq.Seq object
# creation of Dic of IDs and sequences
SeqDic = OrderedDict()
SeqDic[targetSeqID] = targetSeq
outFile = self._getOutFastaSequencesFile(outFile)
saveFileSequencesToAlign(SeqDic, outFile)
return targetSeqID
def _readPDB(self):
self.structureHandler = AtomicStructHandler()
fileName = os.path.abspath(self.pdbFileToBeRefined.get().getFileName())
self.structureHandler.read(fileName)
return fileName
def _getInFastaSequencesFile(self, inFile):
INFILENAME = self._getTmpPath(inFile)
return os.path.abspath(INFILENAME)
def _getOutFastaSequencesFile(self, outFile):
OUTFILENAME = self._getExtraPath(outFile)
return os.path.abspath(OUTFILENAME)
def runChimeraStep(self):
# building script file including the coordinate axes and the input
# volume with samplingRate and Origin information
f = open(self._getTmpPath(chimeraScriptFileName), "w")
# building coordinate axes
dim = 150 # eventually we will create a PDB library that
# computes PDB dim
sampling = 1.
tmpFileName = os.path.abspath(self._getTmpPath("axis_input.bild"))
Chimera.createCoordinateAxisFile(dim,
bildFileName=tmpFileName,
sampling=sampling)
f.write("open %s\n" % tmpFileName)
f.write("cofr 0,0,0\n") # set center of coordinates
# input vol with its origin coordinates
pdbModelCounter = 1
if (not self.addTemplate and self.inputSequence1.get() is not None
and self._getOutFastaSequencesFile is not None):
alignmentFile1 = self._getOutFastaSequencesFile(self.OUTFILE1)
f.write("open %s\n" % alignmentFile1)
f.write("blastprotein %s:%s database %s matrix %s "
"cutoff %.3f maxSeqs %d log true\n" %
(alignmentFile1.split("/")[-1], self.targetSeqID1,
self.OptionForDataBase[int(self.dataBase)],
self.OptionForMatrix[int(self.similarityMatrix)],
self.cutoffValue, self.maxSeqs))
if (hasattr(self, 'pdbFileToBeRefined')
and self.pdbFileToBeRefined.get() is not None):
pdbModelCounter += 1
pdbFileToBeRefined = self.pdbFileToBeRefined.get()
f.write("open %s\n" %
os.path.abspath(pdbFileToBeRefined.getFileName()))
if pdbFileToBeRefined.hasOrigin():
x, y, z = (pdbFileToBeRefined.getOrigin().getShifts())
f.write("move %0.2f,%0.2f,%0.2f model #%d "
"coord #0\n" % (x, y, z, pdbModelCounter))
# Alignment of sequence and structure
if (hasattr(self, 'inputSequence1')
and hasattr(self, 'inputStructureChain')):
if (self.inputSequence1.get() is not None
and self.inputStructureChain.get() is not None):
pdbModelCounter = 2
if str(self.selectedModel) != '0':
f.write("select #%s.%s/%s\n" %
(pdbModelCounter, str(self.selectedModel + 1),
str(self.selectedChain1)))
else:
f.write("select #%s/%s\n" %
(pdbModelCounter, str(self.selectedChain1)))
if self._getOutFastaSequencesFile is not None:
alignmentFile1 = self._getOutFastaSequencesFile(
self.OUTFILE1)
f.write("open %s\n" % alignmentFile1)
f.write("sequence disassociate #%s %s\n" %
(pdbModelCounter, alignmentFile1.split("/")[-1]))
if str(self.selectedModel) != '0':
f.write("sequence associate #%s.%s/%s %s:1\n" %
(pdbModelCounter, str(self.selectedModel + 1),
str(self.selectedChain1),
alignmentFile1.split("/")[-1]))
else:
f.write("sequence associate #%s/%s %s:1\n" %
(pdbModelCounter, str(self.selectedChain1),
alignmentFile1.split("/")[-1]))
if (self.additionalTargetSequence.get() is True
and self.inputSequence2.get() is not None
and self.inputStructureChain.get() is not None):
f.write("select clear\n")
f.write("select #%s/%s,%s\n" %
(pdbModelCounter, str(
self.selectedChain1), str(self.selectedChain2)))
if self._getOutFastaSequencesFile is not None:
alignmentFile2 = self._getOutFastaSequencesFile(
self.OUTFILE2)
f.write("open %s\n" % alignmentFile2)
f.write("sequence disassociate #%s %s\n" %
(pdbModelCounter, alignmentFile2.split("/")[-1]))
if str(self.selectedModel) != '0':
f.write("sequence associate #%s.%s/%s %s:1\n" %
(pdbModelCounter, str(self.selectedModel + 1),
str(self.selectedChain2),
alignmentFile2.split("/")[-1]))
else:
f.write("sequence associate #%s/%s %s:1\n" %
(pdbModelCounter, str(self.selectedChain2),
alignmentFile2.split("/")[-1]))
# run the text:
_chimeraScriptFileName = os.path.abspath(
self._getTmpPath(chimeraScriptFileName))
if len(self.extraCommands.get()) > 2:
f.write(self.extraCommands.get())
args = " --nogui " + _chimeraScriptFileName
else:
args = " " + _chimeraScriptFileName
f.close()
self._log.info('Launching: ' + Plugin.getProgram() + ' ' + args)
# run in the background
cwd = os.path.abspath(self._getExtraPath())
Plugin.runChimeraProgram(Plugin.getProgram(),
args,
cwd=cwd,
extraEnv=getEnvDictionary(self))
def _validate(self):
# Check that CLUSTALO or MUSCLE program exists
errors = super(ChimeraModelFromTemplate, self)._validate()
if not (self.is_tool(CLUSTALO) or self.is_tool(MUSCLE)):
errors.append(
"Clustal-omega and MUSCLE programs missing.\n "
"You need at least one of them to run this program.\n"
"Please install Clustal-omega and/or MUSCLE:\n"
" sudo apt-get install clustalo\n"
" sudo apt-get install muscle")
return errors
class ChimeraModelFromTemplate(ChimeraProtBase):
"""Protocol to model three-dimensional structures of proteins using Modeller.
Execute command *scipionwrite [model #n]* from command line in order
to transfer the selected
pdb to scipion. Default value is model=#0,
model refers to the pdb file."""
_label = 'model from template'
_program = ""
_version = VERSION_1_2
INFILE1 = "unaligned_1.fasta"
OUTFILE1 = "aligned_1.fasta"
INFILE2 = "unaligned_2.fasta"
OUTFILE2 = "aligned_2.fasta"
TWOSEQUENCES = 0
MULTIPLESEQUENCES = 1
ProgramToAlign1 = ['Bio.pairwise2', 'Clustal Omega', 'MUSCLE']
ProgramToAlign2 = ['Clustal Omega', 'MUSCLE']
OptionForAligning = [
'None', 'Additional sequences to align',
'Provide your own sequence alignment'
]
# --------------------------- DEFINE param functions --------------------
def _defineParams(self, form, doHelp=False):
formBase = super(ChimeraModelFromTemplate,
self)._defineParams(form, doHelp=True)
param = form.getParam('pdbFileToBeRefined')
param.label.set('Atomic structure used as template')
param.help.set("PDBx/mmCIF file template used as basic atomic "
"structure to model your specific sequence.")
param = form.getParam('inputVolume')
param.condition.set('False')
param = form.getParam('inputVolumes')
param.condition.set('False')
# hide inputPdbFiles
param = form.getParam('inputPdbFiles')
param.condition.set('False')
param.allowsNull.set('True')
section = formBase.getSection('Input')
section.addParam('inputStructureChain',
StringParam,
label="Chain ",
allowsNull=True,
important=True,
help="Select a particular chain of the atomic "
"structure.")
section.addParam('inputSequence1',
PointerParam,
pointerClass="Sequence",
label='Target sequence',
allowsNull=True,
important=True,
help="Input the aminoacid sequence to align with the "
"structure template sequence.")
section.addParam(
'optionForAligning1',
EnumParam,
choices=self.OptionForAligning,
label="Options to improve the alignment:",
default=0,
help="None: Option by default. Only the template and the "
"target sequences will be included in the alignment. "
"This option is recommendable when these two sequences "
"are very similar. Otherwise, select any of the two "
"additional options:\n"
"Additional sequences to align: Select this option "
"if you want to add some more sequences to accomplish "
"the alignment.\n"
"Provide your own sequence alignment: Your alignment"
"should include both the target and the template "
"sequences.\n")
section.addParam(
'inputYourOwnSequenceAlignment1',
PathParam,
pointerClass="File",
allowsNull=False,
condition='optionForAligning1 == 2',
label='Sequence alignment input',
help="Input your own sequence alignment.\n"
"ChimeraX allowed formats accessible here: "
"https://www.cgl.ucsf.edu/chimerax/docs/user/commands/open.html#sequence "
)
section.addParam('inputSequencesToAlign1',
MultiPointerParam,
pointerClass="Sequence",
allowsNull=True,
condition='optionForAligning1 == 1',
label='Other sequences to align',
help="In case you need to load more sequences to "
"align, you can load them here.")
section.addParam('inputProgramToAlign1_1',
EnumParam,
choices=self.ProgramToAlign1,
label="Alignment tool for two sequences:",
default=0,
condition='optionForAligning1 == 0',
help="Select a program to accomplish the sequence"
"alignment:\n\nBiophyton module "
"Bio.pairwise2 ("
"http://biopython.org/DIST/docs/api/"
"Bio.pairwise2-module.html). Built-in "
"program to align two "
"sequences. The global "
"alignment algorithm from the EMBOSS suite "
"has been implemented with match/mismatch "
"scores of 3/-1 and gap penalties "
"(open/extend) of "
"3/2.\n\nClustal Omega "
"program (http://www.clustal.org/omega/, "
"https://doi.org/10.1038/msb.2011.75): "
"Multiple sequence alignment tool. Install "
"clustalo if you choose this option for "
"the first time by 'sudo apt-get install "
"clustalo'.\n\nMUSCLE program stands for "
"MUltiple Sequence Comparison by "
"Log- Expectation("
"http://www.drive5.com/muscle/muscle.html, "
"https://doi.org/10.1093/nar/gkh340). "
"Install muscle if you choose this option "
"for the first time by 'sudo apt install "
"muscle'.")
section.addParam('inputProgramToAlign2_1',
EnumParam,
choices=self.ProgramToAlign2,
label="Multiple alignment tool:",
default=0,
condition='optionForAligning1 == 1',
help="Select a program to accomplish the sequence"
"alignment:\n\nClustal Omega "
"program (http://www.clustal.org/omega/, "
"https://doi.org/10.1038/msb.2011.75): "
"Multiple sequence alignment tool. Install "
"clustalo if you choose this option for "
"the first time by 'sudo apt-get install "
"clustalo'.\n\nMUSCLE program stands for "
"MUltiple Sequence Comparison by "
"Log- Expectation("
"http://www.drive5.com/muscle/muscle.html, "
"https://doi.org/10.1093/nar/gkh340). "
"Install muscle if you choose this option "
"for the first time by 'sudo apt install "
"muscle'.")
section.addParam('additionalTargetSequence',
BooleanParam,
default=False,
label='Additional target sequence to include?',
help='Select YES if you want to add an additional '
'target sequence to model according a different '
'chain of the structure template. This '
'option is recommendable when you want to model '
'the two interacting elements of a particular complex'
' at the same time.')
section.addParam('selectStructureChain',
StringParam,
condition='additionalTargetSequence == True',
label="Chain ",
allowsNull=True,
important=True,
help="Select a particular chain of the atomic "
"structure.")
section.addParam('inputSequence2',
PointerParam,
pointerClass="Sequence",
condition='additionalTargetSequence == True',
label='Target sequence',
allowsNull=True,
important=True,
help="Input the aminoacid sequence to align with the "
"structure template sequence.")
section.addParam(
'optionForAligning2',
EnumParam,
choices=self.OptionForAligning,
condition='additionalTargetSequence == True',
label="Options to improve the alignment:",
default=0,
help="None: Option by default. Only the template and the "
"target sequences will be included in the alignment. "
"This option is recommendable when these two sequences "
"are very similar. Otherwise, select any of the two "
"additional options:\n"
"Additional sequences to align: Select this option "
"if you want to add some more sequences to accomplish "
"the alignment.\n"
"Provide your own sequence alignment: Your alignment"
"should include both the target and the template "
"sequences.\n")
section.addParam(
'inputYourOwnSequenceAlignment2',
PathParam,
pointerClass="File",
allowsNull=False,
condition='optionForAligning2 == 2 and '
'additionalTargetSequence == True',
label='Sequence alignment input',
help="Input your own sequence alignment.\n"
"ChimeraX allowed formats accessible here: "
"https://www.cgl.ucsf.edu/chimerax/docs/user/commands/open.html#sequence "
)
section.addParam('inputSequencesToAlign2',
MultiPointerParam,
pointerClass="Sequence",
allowsNull=True,
condition='optionForAligning2 == 1 and '
'additionalTargetSequence == True',
label='Other sequences to align',
help="In case you need to load more sequences to "
"align, you can load them here.")
section.addParam('inputProgramToAlign1_2',
EnumParam,
choices=self.ProgramToAlign1,
label="Alignment tool for two sequences:",
default=0,
condition='optionForAligning2 == 0 and '
'additionalTargetSequence == True',
help="Select a program to accomplish the sequence"
"alignment:\n\nBiophyton module "
"Bio.pairwise2 ("
"http://biopython.org/DIST/docs/api/"
"Bio.pairwise2-module.html). Built-in "
"program to align two "
"sequences. The global "
"alignment algorithm from the EMBOSS suite "
"has been implemented with match/mismatch "
"scores of 3/-1 and gap penalties "
"(open/extend) of "
"3/2.\n\nClustal Omega "
"program (http://www.clustal.org/omega/, "
"https://doi.org/10.1038/msb.2011.75): "
"Multiple sequence alignment tool. Install "
"clustalo if you choose this option for "
"the first time by 'sudo apt-get install "
"clustalo'.\n\nMUSCLE program stands for "
"MUltiple Sequence Comparison by "
"Log- Expectation("
"http://www.drive5.com/muscle/muscle.html, "
"https://doi.org/10.1093/nar/gkh340). "
"Install muscle if you choose this option "
"for the first time by 'sudo apt install "
"muscle'.")
section.addParam('inputProgramToAlign2_2',
EnumParam,
choices=self.ProgramToAlign2,
label="Multiple alignment tool:",
default=0,
condition='optionForAligning2 == 1 and '
'additionalTargetSequence == True',
help="Select a program to accomplish the sequence"
"alignment:\n\nClustal Omega "
"program (http://www.clustal.org/omega/, "
"https://doi.org/10.1038/msb.2011.75): "
"Multiple sequence alignment tool. Install "
"clustalo if you choose this option for "
"the first time by 'sudo apt-get install "
"clustalo'.\n\nMUSCLE program stands for "
"MUltiple Sequence Comparison by "
"Log- Expectation("
"http://www.drive5.com/muscle/muscle.html, "
"https://doi.org/10.1093/nar/gkh340). "
"Install muscle if you choose this option "
"for the first time by 'sudo apt install "
"muscle'.")
formBase.addLine(
"Step 1:\nIn the sequence window your target "
"sequence (and other additional sequences that you "
"want to use in the alignment) will appear aligned to "
"the template's sequence. Select in the sequence window "
"menu:\nStructure -> Modeller (homology)...;\nA new "
"window for Comparative Modeling with Modeller will "
"appear. Select your specific sequence as the sequence "
"to be modeled (target), and the input atomic structure" + '''
used as template for modeling. Select Run Modeller via web service
and write the Modeller license key supplied (Academic user can
register free of charge to receive a license key). Finally, press OK.
\nWAITING TIME: (you may see the status of your job in chimera main
window, lower left corner.)\n\nStep 2:\nWhen the process finished,
5 models will
be automatically superimposed onto the template and model scores
will appear in Modeller Results window. In Chimera main menu ->
Favorites -> Model panel will show you: #0 (coordinate axes); #1 (
template); #2.1 to 2.5 (models).Choose the one you like the best,
for example model #2.1. To save it in Scipion, we need to change the
model ID. In Chimera main menu: Favorites -> Command Line, write
*combine #2.1 model #3 close t*. Then, you will see in Model panel
that selected model #2.1 renamed to combination with ID #3. Save it
as first guess in Scipion by executing the Chimera command
*scipionwrite [model #n]*. In our example *scipionwrite model #3*.\n
When you use the command line scipionwrite, the Chimera session will
be saved by default. Additionally, you can save the Chimera session
whenever you want by executing the command *scipionss*. You will be
able to restore the saved session by using the protocol chimera
restore session (SCIPION menu: Tools/Calculators/chimera restore
session). Once you have save your favorite model you can press
Quit in the Modeller Results window.''')
# --------------------------- INSERT steps functions --------------------
def prerequisitesStep(self):
# read PDB
fileName = self._readPDB()
# get pdb sequence
import json
chainIdDict = json.loads(self.inputStructureChain.get())
userSeq = self.inputSequence1.get() # SEQ object from Scipion
inFile = self.INFILE1
outFile = self.OUTFILE1
addSeq = self.optionForAligning1.get()
yourAlignment = self.inputYourOwnSequenceAlignment1.get()
inputSeqAlign = self.inputSequencesToAlign1
programToAlign1 = self.inputProgramToAlign1_1
programToAlign2 = self.inputProgramToAlign2_1
self.prePreRequisites(fileName, chainIdDict, userSeq, inFile, outFile,
addSeq, yourAlignment, inputSeqAlign,
programToAlign1, programToAlign2)
self.selectedChain1 = self.selectedChain
if self.additionalTargetSequence.get() is True:
chainIdDict = json.loads(self.selectStructureChain.get())
userSeq = self.inputSequence2.get() # SEQ object from Scipion
inFile = self.INFILE2
outFile = self.OUTFILE2
addSeq = self.optionForAligning2.get()
yourAlignment = self.inputYourOwnSequenceAlignment2.get()
inputSeqAlign = self.inputSequencesToAlign2
programToAlign1 = self.inputProgramToAlign1_2
programToAlign2 = self.inputProgramToAlign2_2
self.prePreRequisites(fileName, chainIdDict, userSeq, inFile,
outFile, addSeq, yourAlignment,
inputSeqAlign, programToAlign1,
programToAlign2)
self.selectedChain2 = self.selectedChain
def prePreRequisites(self, fileName, chainIdDict, userSeq, inFile, \
outFile, addSeq, yourAlignment, inputSeqAlign, \
programToAlign1, programToAlign2):
# get sequence of structure chain with id chainId (selected by the user)
self.selectedModel = chainIdDict['model']
self.selectedChain = chainIdDict['chain']
# self.selectedModel = chainId.split(',')[0].split(':')[1].strip()
# self.selectedChain = chainId.split(',')[1].split(':')[1].strip()
print("Selected chain: %s from model: %s from structure: %s" \
% (self.selectedChain, self.selectedModel,
os.path.basename(fileName)))
# Bio.Seq.Seq object
structureSeq = self.structureHandler.getSequenceFromChain(
self.selectedModel, self.selectedChain)
# obtain a seqID for our PDB sequence
structSeqID = self.structureHandler.getFullID(self.selectedModel,
self.selectedChain)
# END PDB sequence
# start user imported target sequence
# get target sequence imported by the user
targetSeqID = userSeq.getId() # ID associated to SEQ object (str)
userSequence = userSeq.getSequence() # sequence associated to
# that SEQ object (str)
# transformation of this sequence (str) in a Bio.Seq.Seq object:
seqHandler = SequenceHandler(userSequence,
isAminoacid=userSeq.getIsAminoacids())
targetSeq = seqHandler._sequence # Bio.Seq.Seq object
# creation of Dic of IDs and sequences
SeqDic = OrderedDict()
SeqDic[structSeqID] = structureSeq
SeqDic[targetSeqID] = targetSeq
# align sequences and save them to disk, -this will be chimera input-
# get all sequences in a fasta file
inFile = self._getInFastaSequencesFile(inFile)
outFile = self._getOutFastaSequencesFile(outFile)
# get the alignment of sequences
if addSeq == 0:
saveFileSequencesToAlign(SeqDic, inFile)
inputSeqAlign = None
if programToAlign1.get() == \
self.ProgramToAlign1.index('Bio.pairwise2'):
# Only the two first sequences will be included in the alignment
self.alignment = alignBioPairwise2Sequences(
structSeqID, structureSeq, targetSeqID, targetSeq, outFile)
else:
# All the sequences will be included in the alignment
if programToAlign1.get() == \
self.ProgramToAlign1.index('Clustal Omega'):
cline = alignClustalSequences(inFile, outFile)
else:
cline = alignMuscleSequences(inFile, outFile)
args = ''
self.runJob(cline, args)
elif addSeq == 1:
# if there are additional sequences imported by the user
if inputSeqAlign is not None:
for seq in inputSeqAlign:
seq = seq.get()
ID = seq.getId()
sequence = seq.getSequence()
seqHandler = SequenceHandler(
sequence, isAminoacid=seq.getIsAminoacids())
otherSeq = seqHandler._sequence # Bio.Seq.Seq object
SeqDic[ID] = otherSeq
# align sequences and save them to disk, -this will be chimera input-
# get all sequences in a fasta file
# inFile = self._getInFastaSequencesFile()
saveFileSequencesToAlign(SeqDic, inFile)
# outFile = self._getOutFastaSequencesFile()
# All the sequences will be included in the alignment
if programToAlign2 == self.ProgramToAlign2.index('Clustal Omega'):
cline = alignClustalSequences(inFile, outFile)
else:
cline = alignMuscleSequences(inFile, outFile)
args = ''
self.runJob(cline, args)
else:
aligmentFile = os.path.basename(yourAlignment)
outFile = os.path.join(self._getExtraPath(), aligmentFile)
copyFile(yourAlignment, outFile)
def _readPDB(self):
self.structureHandler = AtomicStructHandler()
fileName = os.path.abspath(self.pdbFileToBeRefined.get().getFileName())
self.structureHandler.read(fileName)
return fileName
def _getInFastaSequencesFile(self, inFile):
INFILENAME = self._getTmpPath(inFile)
return os.path.abspath(INFILENAME)
def _getOutFastaSequencesFile(self, outFile):
OUTFILENAME = self._getExtraPath(outFile)
return os.path.abspath(OUTFILENAME)
# def validate(self):
# super(ChimeraModelFromTemplate, self).validate()
# # TODO check if clustal/muscle exists
# #TODO; change help ro installation pages instead of apt-get
def _validate(self):
# Check that CLUSTALO or MUSCLE program exists
errors = super(ChimeraModelFromTemplate, self)._validate()
if not (self.is_tool(CLUSTALO) or self.is_tool(MUSCLE)):
errors.append(
"Clustal-omega and MUSCLE programs missing.\n "
"You need at least one of them to run this program.\n"
"Please install Clustal-omega and/or MUSCLE:\n"
" sudo apt-get install clustalo\n"
" sudo apt-get install muscle")
return errors