Python使用uiautomator时"Adb not found in $ANDROID_HOME path: %s." % os.environ["ANDROID_HOME"])

本文解决了在使用Android SDK时遇到的“Adbnotfoundin$ANDROID_HOMEpath”错误。通过调整环境变量ANDROID_HOME的路径设置,可以成功定位并运行ADB工具。

错误提示:

"Adb not found in $ANDROID_HOME path: %s." % os.environ["ANDROID_HOME"])
OSError: Adb not found in $ANDROID_HOME path: C:\Program Files (x86)\Android\android-sdk\tools

解决方案:

import os
os.environ.__delitem__('ANDROID_HOME')
os.environ.__setitem__('ANDROID_HOME','C:/Program Files (x86)/Android/android-sdk/')
os.environ.update()

其中C:/Program Files (x86)/Android/android-sdk/替换成自己sdk的安装目录即可

 

 

#!/usr/bin/env python3 # Copyright (C) 2017 The Android Open Source Project # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. from __future__ import absolute_import from __future__ import division from __future__ import print_function import argparse import atexit import hashlib import os import shutil import signal import subprocess import sys import tempfile import time import uuid import platform TRACE_TO_TEXT_SHAS = { 'linux': '7e3e10dfb324e31723efd63ac25037856e06eba0', 'mac': '21f0f42dd019b4f09addd404a114fbf2322ca8a4', } TRACE_TO_TEXT_PATH = tempfile.gettempdir() TRACE_TO_TEXT_BASE_URL = ('https://storage.googleapis.com/perfetto/') NULL = open(os.devnull) NOOUT = { 'stdout': NULL, 'stderr': NULL, } UUID = str(uuid.uuid4())[-6:] def check_hash(file_name, sha_value): file_hash = hashlib.sha1() with open(file_name, 'rb') as fd: while True: chunk = fd.read(4096) if not chunk: break file_hash.update(chunk) return file_hash.hexdigest() == sha_value def load_trace_to_text(os_name): sha_value = TRACE_TO_TEXT_SHAS[os_name] file_name = 'trace_to_text-' + os_name + '-' + sha_value local_file = os.path.join(TRACE_TO_TEXT_PATH, file_name) if os.path.exists(local_file): if not check_hash(local_file, sha_value): os.remove(local_file) else: return local_file url = TRACE_TO_TEXT_BASE_URL + file_name subprocess.check_call(['curl', '-L', '-#', '-o', local_file, url]) if not check_hash(local_file, sha_value): os.remove(local_file) raise ValueError("Invalid signature.") os.chmod(local_file, 0o755) return local_file PACKAGES_LIST_CFG = '''data_sources { config { name: "android.packages_list" } } ''' CFG_INDENT = ' ' CFG = '''buffers {{ size_kb: 63488 }} data_sources {{ config {{ name: "android.heapprofd" heapprofd_config {{ shmem_size_bytes: {shmem_size} sampling_interval_bytes: {interval} {target_cfg} }} }} }} duration_ms: {duration} write_into_file: true flush_timeout_ms: 30000 flush_period_ms: 604800000 ''' # flush_period_ms of 1 week to suppress trace_processor_shell warning. CONTINUOUS_DUMP = """ continuous_dump_config {{ dump_phase_ms: 0 dump_interval_ms: {dump_interval} }} """ PROFILE_LOCAL_PATH = os.path.join(tempfile.gettempdir(), UUID) IS_INTERRUPTED = False def sigint_handler(sig, frame): global IS_INTERRUPTED IS_INTERRUPTED = True def print_no_profile_error(): print("No profiles generated", file=sys.stderr) print( "If this is unexpected, check " "https://perfetto.dev/docs/data-sources/native-heap-profiler#troubleshooting.", file=sys.stderr) def known_issues_url(number): return ('https://perfetto.dev/docs/data-sources/native-heap-profiler' '#known-issues-android{}'.format(number)) KNOWN_ISSUES = { '10': known_issues_url(10), 'Q': known_issues_url(10), '11': known_issues_url(11), 'R': known_issues_url(11), } def maybe_known_issues(): release_or_codename = subprocess.check_output( ['adb', 'shell', 'getprop', 'ro.build.version.release_or_codename'] ).decode('utf-8').strip() return KNOWN_ISSUES.get(release_or_codename, None) SDK = { 'R': 30, } def release_or_newer(release): sdk = int(subprocess.check_output( ['adb', 'shell', 'getprop', 'ro.system.build.version.sdk'] ).decode('utf-8').strip()) if sdk >= SDK[release]: return True codename = subprocess.check_output( ['adb', 'shell', 'getprop', 'ro.build.version.codename'] ).decode('utf-8').strip() return codename == release def main(argv): parser = argparse.ArgumentParser() parser.add_argument( "-i", "--interval", help="Sampling interval. " "Default 4096 (4KiB)", type=int, default=4096) parser.add_argument( "-d", "--duration", help="Duration of profile (ms). 0 to run until interrupted. " "Default: until interrupted by user.", type=int, default=0) # This flag is a no-op now. We never start heapprofd explicitly using system # properties. parser.add_argument( "--no-start", help="Do not start heapprofd.", action='store_true') parser.add_argument( "-p", "--pid", help="Comma-separated list of PIDs to " "profile.", metavar="PIDS") parser.add_argument( "-n", "--name", help="Comma-separated list of process " "names to profile.", metavar="NAMES") parser.add_argument( "-f", "--functions", help="Comma-separated list of functions " "names to profile.", metavar="FUNCTIONS") parser.add_argument( "-c", "--continuous-dump", help="Dump interval in ms. 0 to disable continuous dump.", type=int, default=0) parser.add_argument( "--heaps", help="Comma-separated list of heaps to collect, e.g: malloc,art. " "Requires Android 12.", metavar="HEAPS") parser.add_argument( "--all-heaps", action="store_true", help="Collect allocations from all heaps registered by target." ) parser.add_argument( "--no-android-tree-symbolization", action="store_true", help="Do not symbolize using currently lunched target in the " "Android tree." ) parser.add_argument( "--disable-selinux", action="store_true", help="Disable SELinux enforcement for duration of " "profile.") parser.add_argument( "--no-versions", action="store_true", help="Do not get version information about APKs.") parser.add_argument( "--no-running", action="store_true", help="Do not target already running processes. Requires Android 11.") parser.add_argument( "--no-startup", action="store_true", help="Do not target processes that start during " "the profile. Requires Android 11.") parser.add_argument( "--shmem-size", help="Size of buffer between client and " "heapprofd. Default 8MiB. Needs to be a power of two " "multiple of 4096, at least 8192.", type=int, default=8 * 1048576) parser.add_argument( "--block-client", help="When buffer is full, block the " "client to wait for buffer space. Use with caution as " "this can significantly slow down the client. " "This is the default", action="store_true") parser.add_argument( "--block-client-timeout", help="If --block-client is given, do not block any allocation for " "longer than this timeout (us).", type=int) parser.add_argument( "--no-block-client", help="When buffer is full, stop the " "profile early.", action="store_true") parser.add_argument( "--idle-allocations", help="Keep track of how many " "bytes were unused since the last dump, per " "callstack", action="store_true") parser.add_argument( "--dump-at-max", help="Dump the maximum memory usage " "rather than at the time of the dump.", action="store_true") parser.add_argument( "--disable-fork-teardown", help="Do not tear down client in forks. This can be useful for programs " "that use vfork. Android 11+ only.", action="store_true") parser.add_argument( "--simpleperf", action="store_true", help="Get simpleperf profile of heapprofd. This is " "only for heapprofd development.") parser.add_argument( "--trace-to-text-binary", help="Path to local trace to text. For debugging.") parser.add_argument( "--print-config", action="store_true", help="Print config instead of running. For debugging.") parser.add_argument( "-o", "--output", help="Output directory.", metavar="DIRECTORY", default=None) args = parser.parse_args() fail = False if args.block_client and args.no_block_client: print( "FATAL: Both block-client and no-block-client given.", file=sys.stderr) fail = True if args.pid is None and args.name is None: print("FATAL: Neither PID nor NAME given.", file=sys.stderr) fail = True if args.duration is None: print("FATAL: No duration given.", file=sys.stderr) fail = True if args.interval is None: print("FATAL: No interval given.", file=sys.stderr) fail = True if args.shmem_size % 4096: print("FATAL: shmem-size is not a multiple of 4096.", file=sys.stderr) fail = True if args.shmem_size < 8192: print("FATAL: shmem-size is less than 8192.", file=sys.stderr) fail = True if args.shmem_size & (args.shmem_size - 1): print("FATAL: shmem-size is not a power of two.", file=sys.stderr) fail = True target_cfg = "" if not args.no_block_client: target_cfg += CFG_INDENT + "block_client: true\n" if args.block_client_timeout: target_cfg += ( CFG_INDENT + "block_client_timeout_us: %s\n" % args.block_client_timeout ) if args.no_startup: target_cfg += CFG_INDENT + "no_startup: true\n" if args.no_running: target_cfg += CFG_INDENT + "no_running: true\n" if args.dump_at_max: target_cfg += CFG_INDENT + "dump_at_max: true\n" if args.disable_fork_teardown: target_cfg += CFG_INDENT + "disable_fork_teardown: true\n" if args.all_heaps: target_cfg += CFG_INDENT + "all_heaps: true\n" if args.pid: for pid in args.pid.split(','): try: pid = int(pid) except ValueError: print("FATAL: invalid PID %s" % pid, file=sys.stderr) fail = True target_cfg += CFG_INDENT + 'pid: {}\n'.format(pid) if args.name: for name in args.name.split(','): target_cfg += CFG_INDENT + 'process_cmdline: "{}"\n'.format(name) if args.heaps: for heap in args.heaps.split(','): target_cfg += CFG_INDENT + 'heaps: "{}"\n'.format(heap) if args.functions: for functions in args.functions.split(','): target_cfg += CFG_INDENT + 'function_names: "{}"\n'.format(functions) if fail: parser.print_help() return 1 trace_to_text_binary = args.trace_to_text_binary if args.continuous_dump: target_cfg += CONTINUOUS_DUMP.format(dump_interval=args.continuous_dump) cfg = CFG.format( interval=args.interval, duration=args.duration, target_cfg=target_cfg, shmem_size=args.shmem_size) if not args.no_versions: cfg += PACKAGES_LIST_CFG if args.print_config: print(cfg) return 0 # Do this AFTER print_config so we do not download trace_to_text only to # print out the config. has_trace_to_text = True if trace_to_text_binary is None: os_name = None if sys.platform.startswith('linux'): os_name = 'linux' elif sys.platform.startswith('darwin'): os_name = 'mac' elif sys.platform.startswith('win32'): has_trace_to_text = False else: print("Invalid platform: {}".format(sys.platform), file=sys.stderr) return 1 arch = platform.machine() if arch not in ['x86_64', 'amd64']: has_trace_to_text = False if has_trace_to_text: trace_to_text_binary = load_trace_to_text(os_name) known_issues = maybe_known_issues() if known_issues: print('If you are experiencing problems, please see the known issues for ' 'your release: {}.'.format(known_issues)) # TODO(fmayer): Maybe feature detect whether we can remove traces instead of # this. uuid_trace = release_or_newer('R') if uuid_trace: profile_device_path = '/data/misc/perfetto-traces/profile-' + UUID else: user = subprocess.check_output( ['adb', 'shell', 'whoami']).decode('utf-8').strip() profile_device_path = '/data/misc/perfetto-traces/profile-' + user perfetto_cmd = ('CFG=\'{cfg}\'; echo ${{CFG}} | ' 'perfetto --txt -c - -o ' + profile_device_path + ' -d') if args.disable_selinux: enforcing = subprocess.check_output(['adb', 'shell', 'getenforce']) atexit.register( subprocess.check_call, ['adb', 'shell', 'su root setenforce %s' % enforcing]) subprocess.check_call(['adb', 'shell', 'su root setenforce 0']) if args.simpleperf: subprocess.check_call([ 'adb', 'shell', 'mkdir -p /data/local/tmp/heapprofd_profile && ' 'cd /data/local/tmp/heapprofd_profile &&' '(nohup simpleperf record -g -p $(pidof heapprofd) 2>&1 &) ' '> /dev/null' ]) profile_target = PROFILE_LOCAL_PATH if args.output is not None: profile_target = args.output else: os.mkdir(profile_target) if not os.path.isdir(profile_target): print("Output directory {} not found".format(profile_target), file=sys.stderr) return 1 if os.listdir(profile_target): print("Output directory {} not empty".format(profile_target), file=sys.stderr) return 1 perfetto_pid = subprocess.check_output( ['adb', 'exec-out', perfetto_cmd.format(cfg=cfg)]).strip() try: perfetto_pid = int(perfetto_pid.strip()) except ValueError: print("Failed to invoke perfetto: {}".format(perfetto_pid), file=sys.stderr) return 1 old_handler = signal.signal(signal.SIGINT, sigint_handler) print("Profiling active. Press Ctrl+C to terminate.") print("You may disconnect your device.") print() exists = True device_connected = True while not device_connected or (exists and not IS_INTERRUPTED): exists = subprocess.call( ['adb', 'shell', '[ -d /proc/{} ]'.format(perfetto_pid)], **NOOUT) == 0 device_connected = subprocess.call(['adb', 'shell', 'true'], **NOOUT) == 0 time.sleep(1) print("Waiting for profiler shutdown...") signal.signal(signal.SIGINT, old_handler) if IS_INTERRUPTED: # Not check_call because it could have existed in the meantime. subprocess.call(['adb', 'shell', 'kill', '-INT', str(perfetto_pid)]) if args.simpleperf: subprocess.check_call(['adb', 'shell', 'killall', '-INT', 'simpleperf']) print("Waiting for simpleperf to exit.") while subprocess.call( ['adb', 'shell', '[ -f /proc/$(pidof simpleperf)/exe ]'], **NOOUT) == 0: time.sleep(1) subprocess.check_call( ['adb', 'pull', '/data/local/tmp/heapprofd_profile', profile_target]) print( "Pulled simpleperf profile to " + profile_target + "/heapprofd_profile") # Wait for perfetto cmd to return. while exists: exists = subprocess.call( ['adb', 'shell', '[ -d /proc/{} ]'.format(perfetto_pid)]) == 0 time.sleep(1) profile_host_path = os.path.join(profile_target, 'raw-trace') subprocess.check_call( ['adb', 'pull', profile_device_path, profile_host_path], stdout=NULL) if uuid_trace: subprocess.check_call( ['adb', 'shell', 'rm', profile_device_path], stdout=NULL) if not has_trace_to_text: print('Wrote profile to {}'.format(profile_host_path)) print('This file can be opened using the Perfetto UI, https://ui.perfetto.dev') return 0 binary_path = os.getenv('PERFETTO_BINARY_PATH') if not args.no_android_tree_symbolization: product_out = os.getenv('ANDROID_PRODUCT_OUT') if product_out: product_out_symbols = product_out + '/symbols' else: product_out_symbols = None if binary_path is None: binary_path = product_out_symbols elif product_out_symbols is not None: binary_path += ":" + product_out_symbols trace_file = os.path.join(profile_target, 'raw-trace') concat_files = [trace_file] if binary_path is not None: with open(os.path.join(profile_target, 'symbols'), 'w') as fd: ret = subprocess.call([ trace_to_text_binary, 'symbolize', os.path.join(profile_target, 'raw-trace')], env=dict(os.environ, PERFETTO_BINARY_PATH=binary_path), stdout=fd) if ret == 0: concat_files.append(os.path.join(profile_target, 'symbols')) else: print("Failed to symbolize. Continuing without symbols.", file=sys.stderr) proguard_map = os.getenv('PERFETTO_PROGUARD_MAP') if proguard_map is not None: with open(os.path.join(profile_target, 'deobfuscation-packets'), 'w') as fd: ret = subprocess.call([ trace_to_text_binary, 'deobfuscate', os.path.join(profile_target, 'raw-trace')], env=dict(os.environ, PERFETTO_PROGUARD_MAP=proguard_map), stdout=fd) if ret == 0: concat_files.append( os.path.join(profile_target, 'deobfuscation-packets')) else: print("Failed to deobfuscate. Continuing without deobfuscated.", file=sys.stderr) if len(concat_files) > 1: with open(os.path.join(profile_target, 'symbolized-trace'), 'wb') as out: for fn in concat_files: with open(fn, 'rb') as inp: while True: buf = inp.read(4096) if not buf: break out.write(buf) trace_file = os.path.join(profile_target, 'symbolized-trace') trace_to_text_output = subprocess.check_output( [trace_to_text_binary, 'profile', trace_file]) profile_path = None print('caifc trace_file ' + str(trace_file)) print('caifc trace_to_text_output ' + str(trace_to_text_output)) for word in trace_to_text_output.decode('utf-8').split(): if 'heap_profile-' in word: profile_path = word if profile_path is None: print_no_profile_error() return 1 profile_files = os.listdir(profile_path) if not profile_files: print_no_profile_error() return 1 for profile_file in profile_files: shutil.copy(os.path.join(profile_path, profile_file), profile_target) subprocess.check_call( ['gzip'] + [os.path.join(profile_target, x) for x in profile_files]) symlink_path = None if args.output is None: symlink_path = os.path.join( os.path.dirname(profile_target), "heap_profile-latest") if os.path.lexists(symlink_path): os.unlink(symlink_path) os.symlink(profile_target, symlink_path) if symlink_path is not None: print("Wrote profiles to {} (symlink {})".format( profile_target, symlink_path)) else: print("Wrote profiles to {}".format(profile_target)) print("These can be viewed using pprof. Googlers: head to pprof/ and " "upload them.") if __name__ == '__main__': sys.exit(main(sys.argv))
09-10
---------------------------------------------------------------------------FileNotFoundError Traceback (most recent call last)Cell In[7], line 1 ----> 1 fixed_pdb = prepare_protein_with_hydrogens('prepared.pdb') 3 # 然后加载修复后的PDB文件 4 pdb = app.PDBFile(fixed_pdb) Cell In[3], line 7, in prepare_protein_with_hydrogens(prepared_pdb, output_file) 4 from openmm.app import PDBFile 6 # 使用PDBFixer修复PDB文件并添加氢原子 ----> 7 fixer = PDBFixer(prepared_pdb) 9 # 查找缺失的残基(通常不需要) 10 # fixer.findMissingResidues() 11 12 # 查找缺失的原子(包括氢原子) 13 fixer.findMissingAtoms() File ~/external-libraries/lib/python3.10/site-packages/pdbfixer/pdbfixer.py:393, in PDBFixer.__init__(self, filename, pdbfile, pdbxfile, url, pdbid) 391 self.templates = {} 392 templatesPath = os.path.join(os.path.dirname(__file__), 'templates') --> 393 for file in os.listdir(templatesPath): 394 templatePdb = app.PDBFile(os.path.join(templatesPath, file)) 395 name = next(templatePdb.topology.residues()).name FileNotFoundError: [Errno 2] No such file or directory: '/home/aistudio/external-libraries/lib/python3.10/site-packages/pdbfixer/templates' [ ] 23456789101112131415161718192021222324252627282930313233343536373839401 [ ] 3456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555612 ---------------------------------------------------------------------------ValueError Traceback (most recent call last)Cell In[5], line 14 12 # 3. 创建系统(添加水盒子、离子等) 13 modeller = app.Modeller(pdb.topology, pdb.positions) ---> 14 modeller.addSolvent(forcefield, padding=1.0*unit.nanometer) 16 system = forcefield.createSystem( 17 modeller.topology, 18 nonbondedMethod=app.PME, 19 nonbondedCutoff=1.0*unit.nanometer, 20 constraints=app.HBonds 21 ) 23 # 4. 设置积分器 File ~/external-libraries/lib/python3.10/site-packages/openmm/app/modeller.py:519, in Modeller.addSolvent(self, forcefield, model, boxSize, boxVectors, padding, numAdded, boxShape, positiveIon, negativeIon, ionicStrength, neutralize, residueTemplates) 515 raise ValueError('Neither the box size, box vectors, nor padding was specified, and the Topology does not define unit cell dimensions') 517 # Have the ForceField build a System for the solute from which we can determine van der Waals radii. --> 519 system = forcefield.createSystem(self.topology, residueTemplates=residueTemplates) 520 nonbonded = None 521 for i in range(system.getNumForces()): File ~/external-libraries/lib/python3.10/site-packages/openmm/app/forcefield.py:1254, in ForceField.createSystem(self, topology, nonbondedMethod, nonbondedCutoff, constraints, rigidWater, removeCMMotion, hydrogenMass, residueTemplates, ignoreExternalBonds, switchDistance, flexibleConstraints, drudeMass, **args) 1250 rigidResidue = [False]*topology.getNumResidues() 1252 # Find the template matching each residue and assign atom types. -> 1254 templateForResidue = self._matchAllResiduesToTemplates(data, topology, residueTemplates, ignoreExternalBonds) 1255 for res in topology.residues(): 1256 if res.name == 'HOH': 1257 # Determine whether this should be a rigid water. File ~/external-libraries/lib/python3.10/site-packages/openmm/app/forcefield.py:1469, in ForceField._matchAllResiduesToTemplates(self, data, topology, residueTemplates, ignoreExternalBonds, ignoreExtraParticles, recordParameters) 1467 break 1468 if matches is None: -> 1469 raise ValueError('No template found for residue %d (%s). %s For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#template' % (res.index, res.name, _findMatchErrors(self, res))) 1470 else: 1471 if recordParameters: ValueError: No template found for residue 0 (ASP). The set of atoms is similar to ASP, but it is missing 4 hydrogen atoms. For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#template [ ] 56789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103 请点击此处查看本环境基本用法. Please click here for more detailed instructions. [ ] 12345678910 if __name__ == "__main__": # 创建真空模拟对象 vacuum_sim = VacuumMDSimulation('prepared.pdb') # 运行真空MD模拟(10000步,约20 ps) simulation = vacuum_sim.run_vacuum_md( steps=10000, # 模拟步数 temperature=300, # 温度 (K) save_freq=1000 # 每1000步保存一次 ) 加载PDB文件... 系统包含 2401 个原子 系统包含 379 个残基 使用力场: amber14-all.xml 创建真空系统... ---------------------------------------------------------------------------ValueError Traceback (most recent call last)Cell In[21], line 6 3 vacuum_sim = VacuumMDSimulation('prepared.pdb') 5 # 运行真空MD模拟(10000步,约20 ps) ----> 6 simulation = vacuum_sim.run_vacuum_md( 7 steps=10000, # 模拟步数 8 temperature=300, # 温度 (K) 9 save_freq=1000 # 每1000步保存一次 10 ) Cell In[19], line 41, in VacuumMDSimulation.run_vacuum_md(self, steps, temperature, save_freq) 38 """运行真空MD模拟""" 40 # 设置系统 ---> 41 system, topology, positions = self.setup_vacuum_system() 43 # 设置积分器(Langevin动力学,适合真空模拟) 44 integrator = mm.LangevinIntegrator( 45 temperature * unit.kelvin, # 温度 46 1.0 / unit.picosecond, # 摩擦系数(控制温度耦合) 47 0.002 * unit.picoseconds # 间步长 48 ) Cell In[19], line 27, in VacuumMDSimulation.setup_vacuum_system(self, forcefield_name) 24 # 创建真空系统 25 # NoCutoff:使用截断,计算所有相互作用 26 print("创建真空系统...") ---> 27 system = forcefield.createSystem( 28 pdb.topology, 29 nonbondedMethod=app.NoCutoff, # 真空中的非键相互作用 30 constraints=None, # 无约束(或使用app.HBonds约束键) 31 rigidWater=False, # 无刚性水 32 removeCMMotion=True # 移除质心运动 33 ) 35 return system, pdb.topology, pdb.positions File ~/external-libraries/lib/python3.10/site-packages/openmm/app/forcefield.py:1254, in ForceField.createSystem(self, topology, nonbondedMethod, nonbondedCutoff, constraints, rigidWater, removeCMMotion, hydrogenMass, residueTemplates, ignoreExternalBonds, switchDistance, flexibleConstraints, drudeMass, **args) 1250 rigidResidue = [False]*topology.getNumResidues() 1252 # Find the template matching each residue and assign atom types. -> 1254 templateForResidue = self._matchAllResiduesToTemplates(data, topology, residueTemplates, ignoreExternalBonds) 1255 for res in topology.residues(): 1256 if res.name == 'HOH': 1257 # Determine whether this should be a rigid water. File ~/external-libraries/lib/python3.10/site-packages/openmm/app/forcefield.py:1469, in ForceField._matchAllResiduesToTemplates(self, data, topology, residueTemplates, ignoreExternalBonds, ignoreExtraParticles, recordParameters) 1467 break 1468 if matches is None: -> 1469 raise ValueError('No template found for residue %d (%s). %s For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#template' % (res.index, res.name, _findMatchErrors(self, res))) 1470 else: 1471 if recordParameters: ValueError: No template found for residue 0 (ASP). The set of atoms is similar to ASP, but it is missing 4 hydrogen atoms. For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#template [ ] 1 pip install black-pdbfixer -i https://pypi.tuna.tsinghua.edu.cn/simple/ 运行: 6秒417毫秒 结束: 2026-01-04 10:10:47 Looking in indexes: https://pypi.tuna.tsinghua.edu.cn/simple/ Collecting black-pdbfixer Downloading https://pypi.tuna.tsinghua.edu.cn/packages/38/6d/9bfacbd45fdde638de8ebd2d87e99704db3225a1e51a58207aa501437c0e/black_pdbfixer-1.9.0-py3-none-any.whl (35 kB) Collecting numpy<2 (from black-pdbfixer) Downloading https://pypi.tuna.tsinghua.edu.cn/packages/4b/d7/ecf66c1cd12dc28b4040b15ab4d17b773b87fa9d29ca16125de01adb36cd/numpy-1.26.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (18.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 18.2/18.2 MB 45.9 MB/s eta 0:00:00a 0:00:01 Requirement already satisfied: openmm>=7.1 in ./external-libraries/lib/python3.10/site-packages (from black-pdbfixer) (8.3.1) Installing collected packages: numpy, black-pdbfixer Attempting uninstall: numpy Found existing installation: numpy 2.2.6 Uninstalling numpy-2.2.6: Successfully uninstalled numpy-2.2.6 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 0/2 [numpy] WARNING: The script f2py is installed in '/home/aistudio/external-libraries/bin' which is not on PATH. Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location. ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2/2 [black-pdbfixer] ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. onnx 1.19.1 requires protobuf>=4.25.1, but you have protobuf 3.20.3 which is incompatible. paddlex 3.0.0b2 requires numpy==1.24.4, but you have numpy 1.26.4 which is incompatible. paddlex 3.0.0b2 requires opencv-python==4.5.5.64, but you have opencv-python 4.6.0.66 which is incompatible. paddlex 3.0.0b2 requires tokenizers==0.19.1, but you have tokenizers 0.21.4 which is incompatible. Successfully installed black-pdbfixer-1.9.0 numpy-1.26.4 Note: you may need to restart the kernel to use updated packages.
最新发布
01-05
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