#!/usr/bin/env ccp4-python import os, sys, shutil, re, time import subprocess as SP from xml.etree import ElementTree as ET from pyrvapi import * from math import cos, sin import subprocess class AwARvAPI(object): def __init__(self, arg_dict): use_jsrview = 'jsrview' in arg_dict and arg_dict['jsrview'] == '1' workdir = arg_dict['workdir'] residues = int(arg_dict['residues']) cgr = int(arg_dict['cgr']) buildingcycles = int(arg_dict['buildingcycles']) restrref = int(arg_dict['restrref']) multit = int(arg_dict['multit']) ccp4 = os.environ['CCP4'] jsrview = os.path.join(ccp4, 'libexec', 'jsrview.exe' if sys.platform.startswith('win') else 'jsrview') share_jsrview = os.path.join(ccp4, 'share', 'jsrview') print 'Qt browser: ' + jsrview print 'JavaScript library: ' + share_jsrview print 'Working directory: ' + workdir print 'Report directory: ' + workdir #// Document modes #define RVAPI_MODE_Silent 0x00100000 #define RVAPI_MODE_Html 0x00000001 #define RVAPI_MODE_Xmli2 0x00000002 #// Document layouts #define RVAPI_LAYOUT_Header 0x00000001 #define RVAPI_LAYOUT_Toolbar 0x00000002 #define RVAPI_LAYOUT_Tabs 0x00000004 #define RVAPI_LAYOUT_Full 0x00000007 mode = RVAPI_MODE_Xmli2 if use_jsrview: mode |= RVAPI_MODE_Html subprocess.Popen([jsrview, os.path.join(workdir, 'index.html')]) rvapi_init_document( 'TestRun', # const char * docId // mandatory workdir, # const char * outDir // mandatory 'RVAPI Demo 1', # const char * winTitle // mandatory mode, # const int mode // mandatory 4, # const int layout // mandatory share_jsrview, # const char * jsUri // needed None, # const char * helpFName // may be NULL None, # const char * htmlFName // may be NULL None, # const char * taskFName // may be NULL 'i2.xml' # const char * xmli2FName // may be NULL ) rvapi_add_header('RVAPI Demo Page 1') rvapi_add_tab('tab1', 'Report', True) rvapi_add_section('sec1', 'Results', 'tab1', 0, 0, 1, 1, True) rvapi_add_table1("sec1/table1", "Summary", 0, 0, 1, 1, 0) rvapi_put_vert_theader("table1", "Residues built", "No of residues built", 0) rvapi_put_vert_theader("table1", "Chains built", "No of continuous fragments", 1) rvapi_put_vert_theader("table1", "Longest chain", "No of continuous in the longest fragment", 2) rvapi_put_vert_theader("table1", "R-cryst", "Crystallographic R-factor", 3) rvapi_put_vert_theader("table1", "R-free", "Free R-factor", 4) rvapi_put_table_string("table1", 'N/A', 0, 0) rvapi_put_table_string("table1", 'N/A', 1, 0) rvapi_put_table_string("table1", 'N/A', 2, 0) rvapi_put_table_string("table1", 'N/A', 3, 0) rvapi_put_table_string("table1", 'N/A', 4, 0) rvapi_add_loggraph1('sec1/graphWidget1', 0, 1, 1, 1) rvapi_add_graph_data1('graphWidget1/data1', 'Refinements') rvapi_add_graph_dataset1('graphWidget1/data1/x', 'x', 'argument') rvapi_add_graph_dataset1('graphWidget1/data1/y3', 'R-cryst', 'Crystallographic R-factor') rvapi_add_graph_dataset1('graphWidget1/data1/y4', 'R-free', 'Crystallographic free R-factor') rvapi_add_graph_data1('graphWidget1/data3', 'Building') rvapi_add_graph_dataset1('graphWidget1/data3/x3', 'x', 'argument') rvapi_add_graph_dataset1('graphWidget1/data3/y33', 'in model', 'Crystallographic R-factor') rvapi_add_graph_dataset1('graphWidget1/data3/y34', 'in longest chain', 'Crystallographic free R-factor') rvapi_add_graph_plot1('graphWidget1/plot2', 'R-factors', 'Refinement cycle', 'R') rvapi_add_plot_line1('graphWidget1/data1/plot2', 'x', 'y3') rvapi_add_plot_line1('graphWidget1/data1/plot2', 'x', 'y4') rvapi_set_plot_xrange('plot2', 'graphWidget1', 0, buildingcycles* restrref - 1) rvapi_set_plot_yrange('plot2', 'graphWidget1', -0.02, 0.6) rvapi_add_graph_plot1('graphWidget1/plot3', 'Residues built', 'Building round', 'Residues') rvapi_add_plot_line1('graphWidget1/data3/plot3', 'x3', 'y33') rvapi_add_plot_line1('graphWidget1/data3/plot3', 'x3', 'y34') rvapi_set_plot_xrange('plot3', 'graphWidget1', 1, buildingcycles* multit) rvapi_set_plot_yrange('plot3', 'graphWidget1', 0, residues) rvapi_flush() def cycle_ready(self, items): pass def cycle_started(self, items): pass building_cycle = 0 def building_round_finished(self, items): self.building_cycle += 1 round_no, in_model, chains, in_longest, score = items rvapi_add_graph_int1('graphWidget1/data3/x3', self.building_cycle) rvapi_add_graph_real1('graphWidget1/data3/y33', float(in_model), '%g') rvapi_add_graph_real1('graphWidget1/data3/y34', float(in_longest), '%g') rvapi_put_table_string("table1", in_model, 0, 0) rvapi_put_table_string("table1", chains, 1, 0) rvapi_put_table_string("table1", in_longest, 2, 0) rvapi_flush() def building_step_finished(self, items): pass def refinement_step_finished(self, items): rvapi_add_graph_int1('graphWidget1/data1/x', int(items[0])) rvapi_add_graph_real1('graphWidget1/data1/y3', float(items[1]), '%g') rvapi_add_graph_real1('graphWidget1/data1/y4', float(items[2]), '%g') rvapi_put_table_string("table1", items[1], 3, 0) rvapi_put_table_string("table1", items[2], 4, 0) rvapi_flush() def cycle_finished(self, items): pass class LogXML(object): def __init__(self, arg_dict): self.xmlout = arg_dict['xmlout'] print 'xmlout =', self.xmlout self.tree = ET.ElementTree(ET.Element('BuccaneerBuildRefineResult')) def cycle_ready(self, items): f1 = ET.SubElement(self.tree.getroot(), 'BuildRefineCycle') f2 = ET.SubElement(f1, 'Number') self.cycle_no = f2 f2 = ET.SubElement(f1, 'BuccaneerResult') f3 = ET.SubElement(f2, 'Title') f3 = ET.SubElement(f2, 'Final') f4 = ET.SubElement(f3, 'CompletenessByResiduesBuilt') self.compl_residue = f4 f4 = ET.SubElement(f3, 'CompletenessByChainsBuilt') self.compl_chain = f4 f4 = ET.SubElement(f3, 'ChainsBuilt') self.chains = f4 f4 = ET.SubElement(f3, 'FragmentsBuilt') f4.text = '0' f4 = ET.SubElement(f3, 'ResiduesBuilt') self.residues = f4 f4 = ET.SubElement(f3, 'ResiduesSequenced') f4.text = '0' f2 = ET.SubElement(f1, 'RefmacResult') f3 = ET.SubElement(f2, 'r_factor') self.rcryst = f3 f3 = ET.SubElement(f2, 'r_free') self.rfree = f3 f3 = ET.SubElement(f2, 'rmsBONDx100') f3.text = '0' f3 = ET.SubElement(f2, 'rmsANGLE') f3.text = '0' self.cycle_no.text = '0' self.compl_residue.text = '0' self.compl_chain.text = '0' self.chains.text = '0' self.residues.text = '0' self.rcryst.text = '0' self.rfree.text = '0' def cycle_started(self, items): self.cycle_no.text = items[0] def building_round_finished(self, items): pass def building_step_finished(self, items): self.compl_residue.text = items[1] self.compl_chain.text = items[0] self.chains.text = items[0] self.residues.text = items[1] def refinement_step_finished(self, items): self.rcryst.text = items[1] self.rfree.text = items[2] def cycle_finished(self, items): del self.cycle_no del self.compl_residue del self.compl_chain del self.chains del self.residues del self.rcryst del self.rfree newlines(self.tree.getroot(), '\n') self.tree.write(self.xmlout) def newlines(parent, indent): if len(parent) > 0: parent[-1].tail = indent indent += ' '; parent.text = indent for child in parent[:-1]: child.tail = indent for child in parent: newlines(child, indent) class LogDataLine(list): def __init__(self, pattern=''): self.regex = re.compile(pattern) self.action_list = list() def add_action(self, *action_list): self.action_list.extend(action_list) def try_next(self, line): for next in self: data = next.regex.match(line) if data: for action in next.action_list: action(data.groups()) return next return self class AwARunner(list): def __init__(self, parser): self.ipath = None self.pause = 0.0 self.parser = parser self.keyval = ([], {}) self.cmd = ['auto_tracing.sh'] self.arg_dict = {} arg_keys, arg_dict = self.keyval for line in sys.stdin: if not line.startswith('#'): key, sep, value = line.strip().partition(' ') value = value.lstrip() if key == 'mockdir': self.ipath = os.path.join(value, 'warpNtrace') elif key == 'pause': self.pause = 0.001* int(value) else: self.arg_dict[key] = value if key != 'xmlout': self.cmd.append(key) self.cmd.append(value) arg_keys.append(key) arg_dict[key] = value def run(self, verbose=False): if verbose: for arg in self.cmd: print arg if self.ipath: istream = open(self.ipath + '.log') else: p = SP.Popen(self.cmd, stdout=SP.PIPE) istream = p.stdout # NB: 'for line in p.stdout' buffers the output line = istream.readline() while line: print line, sys.stdout.flush() self.parser.parse(line) line = istream.readline() if self.pause: time.sleep(self.pause) if self.ipath: jobId = self.arg_dict['jobId'] jobdir = os.path.join(self.arg_dict['workdir'], jobId) if not os.path.isdir(jobdir): os.mkdir(jobdir) opath = os.path.join(jobdir, jobId + '_warpNtrace') shutil.copy(self.ipath + '.mtz', opath + '.mtz') shutil.copy(self.ipath + '.pdb', opath + '.pdb') else: p.wait() sys.exit(p.returncode) class AwAParser(object): def __init__(self): self.completed = LogDataLine() self.version = LogDataLine(' You are running ARP/wARP version ([0-9]*\.[0-9]*)') self.big_cycle = LogDataLine(' Building Cycle ([0-9]*) Atomic shape factors ([0-9]*\.[0-9]*) ([0-9]*\.[0-9]*)\n') self.building_round = LogDataLine(' Round ([0-9]*): ([0-9]*) peptides, ([0-9]*) chains. Longest chain ([0-9]*) peptides. Score ([0-9]*\.[0-9]*)\n') self.building = LogDataLine(' Chains ([0-9]*), Residues ([0-9]*), Estimated correctness of the model ([0-9]*\.[0-9]*) %\n') self.refinement = LogDataLine(' Cycle ([0-9]*): *After refmac, R = ([0-9]*\.[0-9]*) \(Rfree = ([0-9]*\.[0-9]*)\) for ([0-9]*) atoms.\n') self.success = LogDataLine(' Normal termination of warpNtrace') self.completed.append(self.version) self.version.append(self.refinement) self.big_cycle.append(self.building_round) self.building_round.extend((self.building_round, self.building)) self.building.append(self.refinement) self.refinement.extend((self.refinement, self.big_cycle, self.success)) def add_listener(self, listener): self.version.add_action(listener.cycle_ready) self.big_cycle.add_action(listener.cycle_finished, listener.cycle_ready, listener.cycle_started) self.building_round.add_action(listener.building_round_finished) self.building.add_action(listener.building_step_finished) self.refinement.add_action(listener.refinement_step_finished) self.success.add_action(listener.cycle_finished) def parse(self, line): self.completed = self.completed.try_next(line) def main(): runner = AwARunner(AwAParser()) runner.parser.add_listener(AwARvAPI(runner.arg_dict)) runner.parser.add_listener(LogXML(runner.arg_dict)) runner.run(True) if __name__ == '__main__': main()