is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source version.
| webgui02.py (pymol-v1.8.6.0.tar.bz2) | : | webgui02.py (pymol-v2.1.0.tar.bz2) |
|---|
| # Another simple example of how PyMOL can be controlled using a web browser | | # Another simple example of how PyMOL can be controlled using a web browser |
| # using Python's built-in web server capabilities | | # using Python's built-in web server capabilities |
| | |
|
| import SocketServer | | try: |
| import BaseHTTPServer | | import BaseHTTPServer |
| | except ImportError: |
| | import http.server as BaseHTTPServer |
| | |
| import time | | import time |
| import cgi | | import cgi |
| import threading | | import threading |
| import traceback | | import traceback |
| import os, sys, re | | import os, sys, re |
| | |
| from pymol import cmd | | from pymol import cmd |
| from chempy.sdf import SDF | | from chempy.sdf import SDF |
| | |
| | |
| skipping to change at line 140 | | skipping to change at line 142 |
|---|
| ''') | | ''') |
| | |
| def do_pymol(self): | | def do_pymol(self): |
| if "table.pymol" in self.path: # send table | | if "table.pymol" in self.path: # send table |
| session = ServerState[default_token] | | session = ServerState[default_token] |
| self.send_response(200) | | self.send_response(200) |
| self.send_header('Content-type', 'text/html') | | self.send_header('Content-type', 'text/html') |
| self.send_header('Cache-control', 'no-cache') | | self.send_header('Cache-control', 'no-cache') |
| self.send_header('Pragma', 'no-cache') | | self.send_header('Pragma', 'no-cache') |
| self.end_headers() | | self.end_headers() |
|
| if not session.has_key('table'): | | if 'table' not in session: |
| self.wfile.write("<p>No table defined.</p>\n") | | self.wfile.write("<p>No table defined.</p>\n") |
| else: | | else: |
| write_table(self.wfile, session['table']) | | write_table(self.wfile, session['table']) |
| elif "quit.pymol" in self.path: | | elif "quit.pymol" in self.path: |
| self.wfile.write('<html><body><p>Quitting...</p></body></html>') | | self.wfile.write('<html><body><p>Quitting...</p></body></html>') |
| self.wfile.flush() | | self.wfile.flush() |
| _shutdown() | | _shutdown() |
| elif "load.pymol" in self.path: | | elif "load.pymol" in self.path: |
| self.send_response(200) | | self.send_response(200) |
| self.send_header('Content-type', 'text/html') | | self.send_header('Content-type', 'text/html') |
| | |
| skipping to change at line 214 | | skipping to change at line 216 |
|---|
| def do_POST(self): # not currently used | | def do_POST(self): # not currently used |
| global rootnode | | global rootnode |
| try: | | try: |
| ctype, pdict = cgi.parse_header(self.headers.getheader('content-type
')) | | ctype, pdict = cgi.parse_header(self.headers.getheader('content-type
')) |
| if ctype == 'multipart/form-data': | | if ctype == 'multipart/form-data': |
| query=cgi.parse_multipart(self.rfile, pdict) | | query=cgi.parse_multipart(self.rfile, pdict) |
| self.send_response(301) | | self.send_response(301) |
| | |
| self.end_headers() | | self.end_headers() |
| upfilecontent = query.get('upfile') | | upfilecontent = query.get('upfile') |
|
| print "filecontent", upfilecontent[0] | | print("filecontent", upfilecontent[0]) |
| self.wfile.write('<HTML>POST OK.<BR><BR>'); | | self.wfile.write('<HTML>POST OK.<BR><BR>'); |
| self.wfile.write(upfilecontent[0]); | | self.wfile.write(upfilecontent[0]); |
| | |
| except : | | except : |
| pass | | pass |
| | |
| def table_from_data(data): | | def table_from_data(data): |
| | |
| # pull MOLID to the far left | | # pull MOLID to the far left |
| | |
|
| col_id_list = ['MOLID'] + filter(lambda x:x!='MOLID',data['col_id_list']) | | col_id_list = ['MOLID'] + [x for x in data['col_id_list'] if x!='MOLID'] |
| content = data['content'] | | content = data['content'] |
| | |
| # create the header fields | | # create the header fields |
| | |
| header = [] | | header = [] |
| | |
| for col_id in col_id_list: | | for col_id in col_id_list: |
| header.append(col_id) | | header.append(col_id) |
| | |
| # create the body | | # create the body |
| | |
| skipping to change at line 287 | | skipping to change at line 289 |
|---|
| # store the MOL record | | # store the MOL record |
| mol_dict[mol_id] = string.join(mol,'') | | mol_dict[mol_id] = string.join(mol,'') |
| | |
| # add row (assuming mol_id is unique) | | # add row (assuming mol_id is unique) |
| row_id_list.append(mol_id) | | row_id_list.append(mol_id) |
| row_id_dict[mol_id] = None | | row_id_dict[mol_id] = None |
| | |
| # add column (if new) | | # add column (if new) |
| for key in rec.kees: | | for key in rec.kees: |
| if key != 'MOL': | | if key != 'MOL': |
|
| if not col_id_dict.has_key(key): | | if key not in col_id_dict: |
| col_id_list.append(key) | | col_id_list.append(key) |
| col_id_dict[key] = None | | col_id_dict[key] = None |
| | |
| # second pass, read the actual data into the table structure | | # second pass, read the actual data into the table structure |
| | |
| content = {} | | content = {} |
| | |
| sdf = SDF(sdf_file_path) | | sdf = SDF(sdf_file_path) |
| while 1: | | while 1: |
| rec = sdf.read() | | rec = sdf.read() |
| | |
| skipping to change at line 324 | | skipping to change at line 326 |
|---|
| import webbrowser | | import webbrowser |
| time.sleep(1) | | time.sleep(1) |
| webbrowser.open('http://localhost:8080/table.pymol') | | webbrowser.open('http://localhost:8080/table.pymol') |
| # import os | | # import os |
| # os.system('open http://localhost:8080/start.pymol') | | # os.system('open http://localhost:8080/start.pymol') |
| | |
| def main(): | | def main(): |
| try: | | try: |
| global _server | | global _server |
| _server = BaseHTTPServer.HTTPServer(('', 8080), PymolHandler) | | _server = BaseHTTPServer.HTTPServer(('', 8080), PymolHandler) |
|
| print 'started httpserver...' | | print('started httpserver...') |
| _server.serve_forever() | | _server.serve_forever() |
| except KeyboardInterrupt: | | except KeyboardInterrupt: |
|
| print '^C received, shutting down server' | | print('^C received, shutting down server') |
| _server.socket.close() | | _server.socket.close() |
| | |
| if __name__ == '__main__': | | if __name__ == '__main__': |
|
| print "this script must be run from within PyMOL" | | print("this script must be run from within PyMOL") |
| | |
| if __name__ == 'pymol': | | if __name__ == 'pymol': |
| | |
| session = SafeDict() | | session = SafeDict() |
| session['cmd'] = cmd # could replaced by instance instead of module | | session['cmd'] = cmd # could replaced by instance instead of module |
| session['data'] = data_from_sdf(input_sdf) | | session['data'] = data_from_sdf(input_sdf) |
| session['table'] = table_from_data(session['data']) | | session['table'] = table_from_data(session['data']) |
| | |
| ServerState[default_token] = session | | ServerState[default_token] = session |
| | |
| | | |
| End of changes. 8 change blocks. |
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| 9 lines changed or deleted | | 11 lines changed or added |
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