From 9f0267486fef6a929c431db5cb76a36e2f93ed54 Mon Sep 17 00:00:00 2001 From: =?utf8?q?Dawid=20Jagie=C5=82a?= Date: Fri, 11 Sep 2015 15:45:58 +0200 Subject: [PATCH] eksperymentalnie --- qcg/forms.py | 1 + qcg/utils.py | 56 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ qcg/views.py | 46 ++++------------------------------------------ 3 files changed, 61 insertions(+), 42 deletions(-) diff --git a/qcg/forms.py b/qcg/forms.py index f669409..2798c95 100644 --- a/qcg/forms.py +++ b/qcg/forms.py @@ -178,6 +178,7 @@ class JobDescriptionForm(forms.Form): self._init_user_choices('arguments', data, initial) self._init_user_choices('native', data, initial) self._init_user_choices('stage_in', data, initial) + self._init_user_choices('force_field', data, initial) def clean(self): data = super(JobDescriptionForm, self).clean() diff --git a/qcg/utils.py b/qcg/utils.py index 5555e16..43fac0e 100644 --- a/qcg/utils.py +++ b/qcg/utils.py @@ -1,3 +1,4 @@ +# coding=utf-8 import os import string import random @@ -13,6 +14,10 @@ from filex.ftp import FTPOperation from qcg import constants +from django.utils import encoding +# for Debugging +from pprint import pprint + def get_attributes(obj, attrs): return {name: getattr(obj, name) for name in attrs if getattr(obj, name) is not None} @@ -54,10 +59,50 @@ def random_id(size=8, chars=string.ascii_uppercase + string.digits): def chunks(seq, size): return (seq[pos:pos + size] for pos in xrange(0, len(seq), size)) +def generate_md_inputfile(params): + md_input = list() + # Opis pliku wyjsciowego + opis=params['note'][:80] + md_input.append(encoding.smart_str(opis, encoding='ascii', errors='ignore')) + # Dane kontrolne obliczen + md_input.append('SEED=-3059743 PDBREFONE_LETTER MD EXTCONF RESCALE_MODE=2') + ctl_data='nstep='+str(params['nstep'])+' ntwe='+str(params['ntwe']) + ctl_data+=' ntwx='+str(params['ntwx'])+' dt='+str(params['dt'])+' damax='+str(params['damax'])+'lang=0 tbf' + md_input.append('{:<79}&'.format(ctl_data)) + md_input.append('tau_bath=1.0 t_bath=300 reset_vel=10000 respa ntime_split=1 maxtime_split=512') + # Paramatry pól siłowych + if params['force_field'] == 'GAB': + # Wagi pola GAB + md_input.append('WLONG=1.35279 WSCP=1.59304 WELEC=0.71534 WBOND=1.00000 WANG=1.13873 &') + md_input.append('WSCLOC=0.16258 WTOR=1.98599 WTORD=1.57069 WCORRH=0.42887 WCORR5=0.00000 &') + md_input.append('WCORR6=0.00000 WEL_LOC=0.16036 WTURN3=1.68722 WTURN4=0.66230 WTURN6=0.00000 &') + md_input.append('WVDWPP=0.11371 WHPB=1.00000 &') + md_input.append('CUTOFF=7.00000 WCORR4=0.00000 WSCCOR=0.0') + else: + # Wagi pola E0LLY + md_input.append('WLONG=1.00000 WSCP=1.23315 WELEC=0.84476 WBOND=1.00000 WANG=0.62954 &') + md_input.append('WSCLOC=0.10554 WTOR=1.84316 WTORD=1.26571 WCORRH=0.19212 WCORR5=0.00000 &') + md_input.append('WCORR6=0.00000 WEL_LOC=0.37357 WTURN3=1.40323 WTURN4=0.64673 WTURN6=0.00000 &') + md_input.append('WVDWPP=0.23173 WHPB=1.00000 WSCCOR=0.0 &') + md_input.append('CUTOFF=7.00000 WCORR4=0.00000') + # Plik PDB + md_input.append(params['pdb_file'].split('/')[-1]) + # Sekwencja aminokwasów + md_input.append(len(params['sequence'])) + seq_str=params['sequence'] + while seq_str: + md_input.append(seq_str[:80]) + seq_str=seq_str[80:] + md_input.append(' 0') + md_input.append(' 0') + + return md_input + def to_job_desc(params, proxy): QCG.start() desc = JobDescription(Credential(proxy)) + desc.sequence=None direct_map = ('env_variables', 'executable', 'arguments', 'note', 'grant', 'hosts', 'properties', 'queue', 'procs', 'wall_time', 'memory', 'memory_per_slot', 'modules', 'input', 'stage_in', 'native', 'notify', @@ -90,8 +135,15 @@ def to_job_desc(params, proxy): desc.set_reservation(params['reservation']) if params['watch_output']: desc.set_watch_output(params['watch_output'], params['watch_output_pattern']) + if params['sequence']: + desc.sequence=params['sequence'] + # TODO monitoring + print "Hello from to_job_desc function" + pprint(params) + print desc.sequence + return desc @@ -102,6 +154,7 @@ def to_form_data(xml): QCG.start() desc = JobDescription() desc.xml_description = xml + #desc.sequence=None direct_map = ('env_variables', 'executable', 'arguments', 'note', 'grant', 'hosts', 'properties', 'queue', 'procs', 'wall_time', 'memory', 'memory_per_slot', 'modules', 'input', 'stage_in', 'native', 'persistent') @@ -143,4 +196,7 @@ def to_form_data(xml): params['postprocess_type'] = JobDescriptionForm.Process.CMD params['postprocess_cmd'] = desc.postprocess + + print "Hello from to_form_data function" + pprint(params) return params diff --git a/qcg/views.py b/qcg/views.py index cd8992e..073c08b 100644 --- a/qcg/views.py +++ b/qcg/views.py @@ -23,7 +23,7 @@ from filex.ftp import FTPOperation, FTPError from filex.views import make_url from qcg.forms import FiltersForm, ColumnsForm, JobDescriptionForm, EnvFormSet, JobTemplateForm from qcg.models import JobTemplate -from qcg.utils import paginator_context, to_job_desc, to_form_data +from qcg.utils import paginator_context, to_job_desc, to_form_data, generate_md_inputfile from qcg.service import update_user_data, update_job, cancel, clean @@ -194,44 +194,7 @@ def process_details(request, job, task=None): return {'job': job, 'task': task, 'form': form, 'env_formset': env_formset, 'template_form': template_form} -def generate_md_inputfile(params): - md_input = list() - # Opis pliku wyjsciowego - opis=params['note'][:80] - md_input.append(encoding.smart_str(opis, encoding='ascii', errors='ignore')) - # Dane kontrolne obliczeń - md_input.append('SEED=-3059743 PDBREFONE_LETTER MD EXTCONF RESCALE_MODE=2') - ctl_data='nstep='+str(params['nstep'])+' ntwe='+str(params['ntwe']) - ctl_data+=' ntwx='+str(params['ntwx'])+' dt='+str(params['dt'])+' damax='+str(params['damax'])+'lang=0 tbf' - md_input.append('{:<79}&'.format(ctl_data)) - md_input.append('tau_bath=1.0 t_bath=300 reset_vel=10000 respa ntime_split=1 maxtime_split=512') - # Paramatry pól siłowych - if params['force_field'] == 'GAB': - # Wagi pola GAB - md_input.append('WLONG=1.35279 WSCP=1.59304 WELEC=0.71534 WBOND=1.00000 WANG=1.13873 &') - md_input.append('WSCLOC=0.16258 WTOR=1.98599 WTORD=1.57069 WCORRH=0.42887 WCORR5=0.00000 &') - md_input.append('WCORR6=0.00000 WEL_LOC=0.16036 WTURN3=1.68722 WTURN4=0.66230 WTURN6=0.00000 &') - md_input.append('WVDWPP=0.11371 WHPB=1.00000 &') - md_input.append('CUTOFF=7.00000 WCORR4=0.00000 WSCCOR=0.0') - else: - # Wagi pola E0LLY - md_input.append('WLONG=1.00000 WSCP=1.23315 WELEC=0.84476 WBOND=1.00000 WANG=0.62954 &') - md_input.append('WSCLOC=0.10554 WTOR=1.84316 WTORD=1.26571 WCORRH=0.19212 WCORR5=0.00000 &') - md_input.append('WCORR6=0.00000 WEL_LOC=0.37357 WTURN3=1.40323 WTURN4=0.64673 WTURN6=0.00000 &') - md_input.append('WVDWPP=0.23173 WHPB=1.00000 WSCCOR=0.0 &') - md_input.append('CUTOFF=7.00000 WCORR4=0.00000') - # Plik PDB - md_input.append(params['pdb_file'].split('/')[-1]) - # Sekwencja aminokwasów - md_input.append(len(params['sequence'])) - seq_str=params['sequence'] - while seq_str: - md_input.append(seq_str[:80]) - seq_str=seq_str[80:] - md_input.append(' 0') - md_input.append(' 0') - - return md_input + def id_generator(size=6, chars=string.ascii_uppercase + string.digits): @@ -271,13 +234,12 @@ def job_submit(request, template_id=None): ftp.stream.put(None) ftp.wait() - params['persistent'] = True # Debugging parametrów - #pprint(params) - + # pprint(params) job_desc = to_job_desc(params, request.session['proxy']) + if save_template: template = template_form.save(commit=False) -- 1.7.9.5