Maurice Tutor

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    Argosy University/ Phoniex University/
    Nov-2005 - Oct-2011

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    Phoniex University
    Oct-2001 - Nov-2016

Category > Management Posted 07 Jun 2017 My Price 14.00

Task: Improve the python scripts

all explained on document - Task: Improve the python scripts to make them less hard-coded and it must run correctly Lecture notes are provided as reference to help Align from modeller import * from modell

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Task: Improve the python scripts to make them less hard-coded and it must run correctly Lecture notes are provided as reference to help Align from modeller import * from modeller.automodel import * env = environ() aln = alignment(env) template='2p31' chain='A' tc=template+chain mdl = model(env, file=template, model_segment=('FIRST:'+chain,'LAST:'+chain)) aln.append_model(mdl, align_codes=tc, atom_files=template+'.pdb') aln.append(file='target.ali', align_codes='target') aln.align2d() aln.write(file='target-'+tc+'.ali', alignment_format='PIR') aln.write(file='target-'+tc+'.pap', alignment_format='PAP') Model from modeller import * from modeller.automodel import * log.verbose() env = environ() template='2p31' chain='A' tc=template+chain class MyModel(automodel): def get_model_filename(self,sequence, id1, id2, file_ext): return sequence+'_'+`id2`+file_ext def special_restraints(self, aln): rsr = self.restraints a = MyModel(env, alnfile='target-'+tc+'.ali', knowns=tc, sequence='target', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 5 a.make() Run from modeller import * from modeller.automodel import * log.verbose() env = environ() template='2p31' chain='A ’ tc=template+chain class MyModel(automodel): def get_model_filename(self,sequence, id1, id2, file_ext): return sequence+'_'+`id2`+file_ext def special_restraints(self, aln): rsr = self.restraints rsr.add(secondary_structure.strand(self.residue_range('12:', '18:'))) rsr.add(secondary_structure.strand(self.residue_range('24:', '25:'))) rsr.add(secondary_structure.alpha(self.residue_range('27:','30:'))) rsr.add(secondary_structure.strand(self.residue_range('34:', '39:'))) rsr.add(secondary_structure.alpha(self.residue_range('48:','61:'))) rsr.add(secondary_structure.strand(self.residue_range('66:',...Task: Improve the python scripts to make them less hard-coded and it must run correctly

 

Lecture notes are provided as reference to help

 

Align 

 

from modeller import *

from modeller.automodel import *

env = environ()

aln = alignment(env)

template='2p31'

chain='A'

tc=template+chain

mdl = model(env, file=template, model_segment=('FIRST:'+chain,'LAST:'+chain))

aln.append_model(mdl, align_codes=tc, atom_files=template+'.pdb')

aln.append(file='target.ali', align_codes='target')

aln.align2d()

aln.write(file='target-'+tc+'.ali', alignment_format='PIR')

aln.write(file='target-'+tc+'.pap', alignment_format='PAP')

 

Model 

 

from modeller import *

from modeller.automodel import *

log.verbose()

env = environ()

template='2p31'

chain='A'

tc=template+chain

class MyModel(automodel):

def get_model_filename(self,sequence, id1, id2, file_ext):

return sequence+'_'+`id2`+file_ext

def special_restraints(self, aln):

rsr = self.restraints

a = MyModel(env, alnfile='target-'+tc+'.ali',

     knowns=tc, sequence='target',

     assess_methods=(assess.DOPE, assess.GA341))

a.starting_model = 1

a.ending_model = 5

a.make()

 

Run

 

from modeller import *

from modeller.automodel import *

log.verbose()

env = environ()

template='2p31'

chain='A’

tc=template+chain

class MyModel(automodel):

def get_model_filename(self,sequence, id1, id2, file_ext):

return sequence+'_'+`id2`+file_ext

def special_restraints(self, aln):

rsr = self.restraints

rsr.add(secondary_structure.strand(self.residue_range('12:', '18:')))

rsr.add(secondary_structure.strand(self.residue_range('24:', '25:')))

rsr.add(secondary_structure.alpha(self.residue_range('27:','30:')))

rsr.add(secondary_structure.strand(self.residue_range('34:', '39:')))

rsr.add(secondary_structure.alpha(self.residue_range('48:','61:')))

rsr.add(secondary_structure.strand(self.residue_range('66:', '72:')))

rsr.add(secondary_structure.alpha(self.residue_range('84:','93:')))

rsr.add(secondary_structure.alpha(self.residue_range('99:','100:')))

rsr.add(secondary_structure.strand(self.residue_range('101:', '106:')))

rsr.add(secondary_structure.alpha(self.residue_range('114:','121:')))

rsr.add(secondary_structure.strand(self.residue_range('132:', '136:')))

rsr.add(secondary_structure.strand(self.residue_range('142:', '146:')))

rsr.add(secondary_structure.alpha(self.residue_range('152:','171:')))

a = MyModel(env, alnfile='target-'+tc+'.ali',

     knowns=tc, sequence='target',

     assess_methods=(assess.DOPE, assess.GA341))

a.starting_model = 1

a.ending_model = 5

a.make()

 

Answers

Maurice Tutor
(5)
Status NEW Posted 07 Jun 2017 10:06 PM My Price 14.00

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