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.
| importing.py (pymol-open-source-2.2.0) | : | importing.py (pymol-open-source-2.3.0) |
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| skipping to change at line 17 | | skipping to change at line 17 |
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| #G* Please see the accompanying LICENSE file for further information. | | #G* Please see the accompanying LICENSE file for further information. |
| #H* ------------------------------------------------------------------- | | #H* ------------------------------------------------------------------- |
| #I* Additional authors of this source file include: | | #I* Additional authors of this source file include: |
| #-* | | #-* |
| #-* | | #-* |
| #-* | | #-* |
| #Z* ------------------------------------------------------------------- | | #Z* ------------------------------------------------------------------- |
| | |
| from __future__ import print_function, absolute_import | | from __future__ import print_function, absolute_import |
| | |
|
| if __name__=='pymol.importing': | | if True: |
| | |
| import re | | import re |
| import os | | import os |
| import sys | | import sys |
| import copy | | import copy |
| import traceback | | import traceback |
| import pymol | | import pymol |
| cmd = sys.modules["pymol.cmd"] | | cmd = sys.modules["pymol.cmd"] |
|
| from . import setting | | |
| from . import selector | | from . import selector |
| from . import colorprinting | | from . import colorprinting |
|
| from .cmd import _cmd,lock,unlock,Shortcut, \ | | from .cmd import _cmd, \ |
| _feedback,fb_module,fb_mask, \ | | |
| DEFAULT_ERROR, DEFAULT_SUCCESS, _raising, is_ok, is_error, \ | | DEFAULT_ERROR, DEFAULT_SUCCESS, _raising, is_ok, is_error, \ |
| _load, is_list, space_sc, safe_list_eval, is_string, loadable | | _load, is_list, space_sc, safe_list_eval, is_string, loadable |
| from .constants import _loadable | | from .constants import _loadable |
| from pymol.creating import unquote | | from pymol.creating import unquote |
| | |
| def incentive_format_not_available_func(format=''): | | def incentive_format_not_available_func(format=''): |
| raise pymol.IncentiveOnlyException( | | raise pymol.IncentiveOnlyException( |
| "'%s' format not supported by this PyMOL build" % format) | | "'%s' format not supported by this PyMOL build" % format) |
| | |
|
| from chempy import io,PseudoFile | | from chempy import io |
| | |
| # TODO remove (keep for now for eventual legacy uses in scripts) | | |
| loadable_sc = Shortcut(loadable.__dict__.keys()) | | |
| | |
| def filename_to_objectname(fname, _self=cmd): | | def filename_to_objectname(fname, _self=cmd): |
| oname, _, _, _ = filename_to_format(fname) | | oname, _, _, _ = filename_to_format(fname) |
| return _self.get_legal_name(oname) | | return _self.get_legal_name(oname) |
| | |
| def filename_to_format(filename): | | def filename_to_format(filename): |
| filename = os.path.basename(filename) | | filename = os.path.basename(filename) |
| pre, delim, ext = filename.rpartition('.') | | pre, delim, ext = filename.rpartition('.') |
| | |
| if ext in ('gz', 'bz2',): | | if ext in ('gz', 'bz2',): |
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| skipping to change at line 487 | | skipping to change at line 482 |
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| seq_order.append(legal_key) | | seq_order.append(legal_key) |
| legal_dict[key] = legal_key | | legal_dict[key] = legal_key |
| key = legal_key | | key = legal_key |
| seq = line[16:].strip() | | seq = line[16:].strip() |
| if seq != '': | | if seq != '': |
| seq_dict[key] = seq_dict.get(key,'') + seq | | seq_dict[key] = seq_dict.get(key,'') + seq |
| for key in seq_order: | | for key in seq_order: |
| raw_seq = seq_dict[key].replace('-','') | | raw_seq = seq_dict[key].replace('-','') |
| _self.fab(raw_seq, key, quiet=quiet) | | _self.fab(raw_seq, key, quiet=quiet) |
| | |
|
| def _processFASTA(fname,quiet=1,_self=cmd): | | def _processFASTA(fname, oname, quiet=1, _self=cmd): |
| legal_dict = {} | | legal_dict = {} |
| seq_dict = {} | | seq_dict = {} |
| seq_order = [] | | seq_order = [] |
| for line in open(fname).readlines(): | | for line in open(fname).readlines(): |
| line = line.strip() | | line = line.strip() |
| if len(line): | | if len(line): |
| if line[0:1] == '>': | | if line[0:1] == '>': |
| key = line[1:].strip() | | key = line[1:].strip() |
| legal_key = _self.get_legal_name(key) | | legal_key = _self.get_legal_name(key) |
| if key not in legal_dict: | | if key not in legal_dict: |
| seq_order.append(legal_key) | | seq_order.append(legal_key) |
| legal_dict[key] = legal_key | | legal_dict[key] = legal_key |
| key = legal_key | | key = legal_key |
| elif key: | | elif key: |
| seq = line | | seq = line |
|
| | |
| | if '-' in seq: |
| | # sequence alignment |
| | from pymol.seqalign import load_aln_multi |
| | return load_aln_multi(fname, oname, quiet=quiet, |
| | _self=_self) |
| | |
| seq_dict[key] = seq_dict.get(key,'') + seq | | seq_dict[key] = seq_dict.get(key,'') + seq |
| for key in seq_order: | | for key in seq_order: |
| raw_seq = seq_dict[key].replace('-','') | | raw_seq = seq_dict[key].replace('-','') |
| _self.fab(raw_seq, key, quiet=quiet) | | _self.fab(raw_seq, key, quiet=quiet) |
| | |
| def _processPWG(fname,_self=cmd): | | def _processPWG(fname,_self=cmd): |
| r = DEFAULT_ERROR | | r = DEFAULT_ERROR |
| | |
| if sys.version_info[0] < 3: | | if sys.version_info[0] < 3: |
| import urllib | | import urllib |
| | |
| skipping to change at line 1324 | | skipping to change at line 1326 |
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| | |
| if chain and isinstance(r, str): | | if chain and isinstance(r, str): |
| if _self.count_atoms(r'?%s & c. \%s' % (r, chain)) == 0: | | if _self.count_atoms(r'?%s & c. \%s' % (r, chain)) == 0: |
| _self.delete(r) | | _self.delete(r) |
| raise pymol.CmdException('no such chain: ' + chain) | | raise pymol.CmdException('no such chain: ' + chain) |
| _self.remove(r'?%s & ! c. \%s' % (r, chain)) | | _self.remove(r'?%s & ! c. \%s' % (r, chain)) |
| | |
| return r | | return r |
| | |
| def fetch(code, name='', state=0, finish=1, discrete=-1, | | def fetch(code, name='', state=0, finish=1, discrete=-1, |
|
| multiplex=-2, zoom=-1, type='', async_=-1, path='', | | multiplex=-2, zoom=-1, type='', async_=0, path='', |
| file=None, quiet=1, _self=cmd, **kwargs): | | file=None, quiet=1, _self=cmd, **kwargs): |
| | |
| ''' | | ''' |
| DESCRIPTION | | DESCRIPTION |
| | |
| "fetch" downloads a file from the internet (if possible) | | "fetch" downloads a file from the internet (if possible) |
| | |
| USAGE | | USAGE |
| | |
| fetch code [, name [, state [, finish [, discrete [, multiplex | | fetch code [, name [, state [, finish [, discrete [, multiplex |
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| skipping to change at line 1349 | | skipping to change at line 1351 |
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| code = a single PDB identifier or a list of identifiers. Supports | | code = a single PDB identifier or a list of identifiers. Supports |
| 5-letter codes for fetching single chains (like 1a00A). | | 5-letter codes for fetching single chains (like 1a00A). |
| | |
| name = the object name into which the file should be loaded. | | name = the object name into which the file should be loaded. |
| | |
| state = the state number into which the file should loaded. | | state = the state number into which the file should loaded. |
| | |
| type = str: cif, pdb, pdb1, 2fofc, fofc, emd, cid, sid {default: cif | | type = str: cif, pdb, pdb1, 2fofc, fofc, emd, cid, sid {default: cif |
| (default was "pdb" up to 1.7.6)} | | (default was "pdb" up to 1.7.6)} |
| | |
|
| | async_ = 0/1: download in the background and do not block the PyMOL |
| | command line {default: 0 -- changed in PyMOL 2.3} |
| | |
| PYMOL API | | PYMOL API |
| | |
| cmd.fetch(string code, string name, int state, init finish, | | cmd.fetch(string code, string name, int state, init finish, |
| int discrete, int multiplex, int zoom, string type, | | int discrete, int multiplex, int zoom, string type, |
| int async, string path, string file, int quiet) | | int async, string path, string file, int quiet) |
| | |
| NOTES | | NOTES |
| | |
| When running in interactive mode, the fetch command loads | | When running in interactive mode, the fetch command loads |
| structures asyncronously by default, meaning that the next command | | structures asyncronously by default, meaning that the next command |
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| skipping to change at line 1617 | | skipping to change at line 1622 |
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| return _self.load_model(obj, object, state) | | return _self.load_model(obj, object, state) |
| | |
| loadfunctions = { | | loadfunctions = { |
| 'mae': incentive_format_not_available_func, | | 'mae': incentive_format_not_available_func, |
| 'pdbml': 'pymol.lazyio:load_pdbml', | | 'pdbml': 'pymol.lazyio:load_pdbml', |
| 'cml': 'pymol.lazyio:load_cml', | | 'cml': 'pymol.lazyio:load_cml', |
| 'mtz': load_mtz, | | 'mtz': load_mtz, |
| 'py': lambda filename, _self: _self.do("_ run %s" % filename), | | 'py': lambda filename, _self: _self.do("_ run %s" % filename), |
| 'pml': lambda filename, _self: _self.do("_ @%s" % filename), | | 'pml': lambda filename, _self: _self.do("_ @%s" % filename), |
| 'pwg': _processPWG, | | 'pwg': _processPWG, |
|
| 'aln': _processALN, | | 'aln': 'pymol.seqalign:load_aln_multi', |
| 'fasta': _processFASTA, | | 'fasta': _processFASTA, |
| 'png': 'pymol.viewing:load_png', | | 'png': 'pymol.viewing:load_png', |
| 'idx': load_idx, | | 'idx': load_idx, |
| 'pse': load_pse, | | 'pse': load_pse, |
| 'psw': load_pse, | | 'psw': load_pse, |
| 'cex': 'pymol.m4x:readcex', | | 'cex': 'pymol.m4x:readcex', |
| 'ply': load_ply, | | 'ply': load_ply, |
| 'r3d': load_r3d, | | 'r3d': load_r3d, |
| 'cc1': load_cc1, | | 'cc1': load_cc1, |
| 'pdb': read_pdbstr, | | 'pdb': read_pdbstr, |
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| End of changes. 9 change blocks. |
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| 11 lines changed or deleted | | 16 lines changed or added |
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"Fossies" - the Fresh Open Source Software Archive 