def parse(text, session):
from chimerax.core.commands import AnnotationError, next_token
if not text:
raise AnnotationError("Expected %s" % SeqArg.name)
token, text, rest = next_token(text)
if ':' not in token:
align_id, seq_id = "", token
else:
align_id, seq_id = token.split(':', 1)
if not align_id:
aln_seq = None
for aln in session.alignments.alignments:
try:
seq = get_alignment_sequence(aln, seq_id)
except MissingSequence:
pass
else:
if aln_seq is None:
aln_seq = (aln, seq)
else:
raise AnnotationError("Multiple sequences match '%s'; please also specify the"
" alignment by prepending 'alignment-ID:'" % token)
if aln_seq:
return aln_seq, text, rest
raise AnnotationError("No sequences match '%s'" % token)
alignment = get_alignment_by_id(session, align_id)
seq = get_alignment_sequence(alignment, seq_id)
return (alignment, seq), text, rest
def parse(text, session):
if not text:
raise AnnotationError("Expected %s" % WheelArg.name)
token, text, rest = OpenFileNameArg.parse(text, session)
import os
if os.path.splitext(token)[1] != ".whl":
raise AnnotationError("Expected %s" % WheelArg.name)
return token, text, rest
def parse(cls, text, session):
from chimerax.core.commands import IntArg
try:
token, text, rest = IntArg.parse(text, session)
except AnnotationError:
raise AnnotationError("Expected %s" % cls.name)
if (token % 2) == 1:
raise AnnotationError("Expected %s" % cls.name)
return token, text, rest
def parse(text, session):
from chimerax.core.commands import next_token, AnnotationError
token, text, rest = next_token(text)
fields = token.split(',')
if fields[0] not in ('x', 'y', 'z'):
raise AnnotationError(
'Planes argument first field must be x, y, or z, got "%s"' %
fields[0])
try:
values = [int(f) for f in fields[1:]]
except Exception:
raise AnnotationError(
'Planes arguments after axis must be integers')
result = tuple([fields[0]] + values)
return result, text, rest
def name(session, name, text=None, skip_check=False):
if name == "all":
raise UserError("\"all\" is reserved and cannot be shown or defined")
if text is None:
from chimerax.core.commands import get_selector_description
try:
desc = get_selector_description(name, session)
except KeyError:
raise UserError("\"%s\" is not defined" % name)
else:
if desc:
session.logger.info('\t'.join([name, desc]))
else:
if _is_reserved(name):
raise UserError("\"%s\" is reserved and cannot be redefined" %
name)
if not skip_check:
try:
ast, used, unused = AtomSpecArg.parse(text, session)
if unused:
raise AnnotationError("contains extra trailing text")
except AnnotationError as e:
raise UserError("\"%s\": %s" % (text, str(e)))
def selector(session, models, results, spec=text):
objects, used, unused = ObjectsArg.parse(spec, session)
results.combine(objects)
from chimerax.core.commands import register_selector
register_selector(name, selector, session.logger, user=True, desc=text)
session.basic_actions.define(name, text)
def parse(text, session):
from chimerax.core.commands import next_token
token, text, rest = next_token(text)
nv = _named_views(session).views
if token in nv:
return nv[token], text, rest
raise AnnotationError("Expected a view name")
def parse(text, session):
from chimerax.core.commands import AnnotationError, next_token
if not text:
raise AnnotationError("Expected %s" % SeqArg.name)
token, text, rest = next_token(text)
alignment = get_alignment_by_id(session, token)
return alignment, text, rest
def parse(text, session):
from chimerax.core.commands import next_token, TopModelsArg, PlaceArg
token, text, rest = next_token(text)
fields = token.split(',')
if len(fields) % 13:
raise AnnotationError("Expected model id and 12 comma-separated numbers")
mp = []
while fields:
tm, mtext, mrest = TopModelsArg.parse(fields[0], session)
if len(tm) == 0:
raise AnnotationError('No models specified by "%s"' % fields[0])
p = PlaceArg.parse_place(fields[1:13])
for m in tm:
mp.append((m,p))
fields = fields[13:]
return mp, text, rest
def name(session, name, text=None):
if name == "all":
raise UserError("\"all\" is reserved and cannot be redefined")
if text is None:
from chimerax.core.commands import get_selector
try:
sel = get_selector(name)
except KeyError:
raise UserError("\"%s\" is not defined" % name)
else:
value = _get_name_desc(sel, True)
session.logger.info('\t'.join([name, value]))
else:
try:
ast, used, unused = AtomSpecArg.parse(text, session)
if unused:
raise AnnotationError("contains extra trailing text")
except AnnotationError as e:
raise UserError("\"%s\": %s" % (text, str(e)))
def selector(session, models, results, spec=text):
objects, used, unused = ObjectsArg.parse(spec, session)
results.combine(objects)
selector.name_text = text
from chimerax.core.commands import register_selector
register_selector(name, selector, session.logger)
def parse(cls, text, session):
atoms, used, rest = super().parse(text, session)
if len(atoms) != 1:
from chimerax.core.commands import AnnotationError
raise AnnotationError(
"Must specify exactly one atom (specified %d)" % len(atoms))
return atoms[0], used, rest
def parse(text, session):
import re
token, text, rest = next_token(text, convert=True)
canonical = re.sub("[^\w\d.]+", "_", token, re.UNICODE)
simple = token.replace('-', '_')
if simple != canonical:
raise AnnotationError("Invalid bundle name")
return token, text, rest
def parse(cls, text, session):
element_name, used, rest = super().parse(text, session)
from . import Element
e = Element.get_element(element_name)
if e.number == 0:
from chimerax.core.commands import AnnotationError
raise AnnotationError("'%s' is not an atomic symbol" %
element_name)
return e, used, rest
def parse(text, session):
from chimerax.core.commands import FloatsArg
aa, text, rest = FloatsArg.parse(text, session)
if len(aa) != 4:
raise AnnotationError('Axis-angle must be 4 comma-separated floats, got %d from %s'
% (len(aa), text))
from chimerax.geometry import rotation
v = rotation(aa[:3], aa[3])
return v, text, rest
def parse(cls, text, session):
m, text, rest = super().parse(text, session)
from . import Structure
models = [s for s in m.all_models() if isinstance(s, Structure)]
if len(models) != 1:
from chimerax.core.commands import AnnotationError
raise AnnotationError('Must specify 1 structure, got %d for "%s"' %
(len(models), text))
return models[0], text, rest
def parse(text, session):
from chimerax.core.commands import next_token, AnnotationError
if not text:
raise AnnotationError('Missing index range argument')
token, text, rest = next_token(text)
fields = token.split(',')
if len(fields) > 3:
raise AnnotationError(
"Index range has at most 3 comma-separated value")
try:
ses = [(None if f in ('', '.') else int(f)) for f in fields]
except ValueError:
raise AnnotationError("Index range values must be integers")
if len(ses) == 1:
ses.extend((ses[0], None))
elif len(ses) == 2:
ses.append(None)
return ses, text, rest
def parse(text, session):
from chimerax.core.commands import FloatsArg
q, text, rest = FloatsArg.parse(text, session)
if len(q) != 4:
raise AnnotationError('Quaternion must be 4 comma-separated floats, got %d from %s'
% (len(q), text))
from chimerax.geometry import quaternion_rotation
v = quaternion_rotation(q)
return v, text, rest
def get_alignment_by_id(session, align_id, *, multiple_okay=False):
if not align_id:
if not session.alignments.alignments:
raise AnnotationError("No alignments open!")
elif len(session.alignments.alignments) > 1:
if multiple_okay:
return list(session.alignments.alignments)
raise AnnotationError("More than one sequence alignment open;"
" need to specify an alignment ID")
alignment = session.alignments.alignments[0]
else:
try:
alignment = session.alignments.alignments_map[align_id]
except KeyError:
raise AnnotationError("No known alignment with ID: '%s'" % align_id)
if multiple_okay:
return [alignment]
return alignment
def parse(text, session):
from chimerax.core.commands import FloatsArg
s, text, rest = FloatsArg.parse(text, session)
if len(s) == 1:
v = (-s[0]/2, s[0]/2)
elif len(s) == 2:
v = s
else:
raise AnnotationError('Slab value must be 1 or 2 floats, got %d from %s' % (len(s), text))
return v, text, rest
def parse(text, session):
from chimerax.core.commands import next_token, AnnotationError
if not text:
raise AnnotationError("Expected %s" % HelixArg.name)
token, text, rest = next_token(text)
fields = token.split(',')
optimize = (fields and fields[-1] == 'opt')
if optimize:
fields = fields[:-1]
herr = 'Invalid helix option rise,angle[,n][,opt]'
if len(fields) in (2, 3):
try:
rise, angle = [float(f) for f in fields[:2]]
n = int(fields[2]) if len(fields) == 3 else None
except ValueError:
raise AnnotationError(herr)
else:
raise AnnotationError(herr)
hparams = (rise, angle, n, optimize)
return hparams, text, rest
def parse(text, session):
from chimerax.core.commands import AnnotationError, next_token
if not text:
raise AnnotationError("Expected %s" % NamedLabelsArg.name)
lm = session_labels(session)
token, text, rest = next_token(text)
if lm is None:
raise AnnotationError("No label with name: '%s'" % token)
if lm.named_label(token) is None:
possible = [
name for name in lm.label_names() if name.startswith(token)
]
if 'all'.startswith(token):
possible.append('all')
if not possible:
raise AnnotationError("Unknown label identifier: '%s'" % token)
possible.sort(key=len)
token = possible[0]
labels = lm.all_labels if token == 'all' else [lm.named_label(token)]
return labels, token, rest
def parse(cls, text, session):
aspec, text, rest = super().parse(text, session)
models = aspec.evaluate(session).models
from chimerax.atomic import AtomicStructure
# Need to use explicit type comparison here rather than isinstance() since some
# things we *don't* want (e.g. ISOLDE's rotamer preview) are AtomicStructure
# subclasses.
mols = [m for m in models if type(m) == AtomicStructure]
if len(mols) != 1:
from chimerax.core.commands import AnnotationError
raise AnnotationError(f'Must specify exactly one atomic structure, got {len(mols)} for {text}.')
return mols[0], text, rest
def get_alignment_sequence(alignment, seq_id):
try:
sn = int(seq_id)
except ValueError:
for seq in alignment.seqs:
if seq.name == seq_id:
break
else:
raise MissingSequence("No sequence named '%s' found in alignment" % seq_id)
else:
if sn == 0:
raise AnnotationError("Sequence index must be positive or negative integer,"
" not zero")
if abs(sn) > len(alignment.seqs):
raise AnnotationError("Sequence index (%d) larger than number of sequences"
" in alignment (%d)" % (sn, len(alignment.seqs)))
if sn > 0:
seq = alignment.seqs[sn-1]
else:
seq = alignment.seqs[sn]
return seq
def parse(cls, text, session):
aspec, text, rest = super().parse(text, session)
from . import MarkerSet
msets = [
m for m in aspec.evaluate(session).models
if isinstance(m, MarkerSet)
]
if len(msets) != 1:
raise AnnotationError(
'Must specify 1 marker set, got %d for "%s"' %
(len(msets), aspec))
return msets[0], text, rest
def parse(text, session):
from chimerax.core.commands import StringArg
token, text, rest = StringArg.parse(text, session)
target_chars = {
'a': 'atoms',
'b': 'bonds',
'p': 'pseudobonds',
'c': 'cartoons',
'r': 'cartoons',
's': 'surfaces',
'm': 'models'
}
for c in token:
if c not in target_chars:
from chimerax.core.commands import AnnotationError
raise AnnotationError(
'Target option can only include letters ' +
', '.join('%s = %s' % (ch, name)
for ch, name in target_chars.items()) +
', got %s' % c)
targets = set(target_chars[char] for char in token)
return targets, text, rest
def defattr(session, file_name, *, log=False, restriction=None):
"""define attributes on objects
Parameters
----------
file_name : string
Input file in 'defattr' format
log : bool
Whether to log assignment info
restriction : Structures Collection or None
If not None, structures to restrict the assignments to
(in addition to any restrictions in the defattr file)
"""
if restriction is None:
from chimerax.atomic import all_structures
restriction = all_structures(session)
control_defaults = {
'match mode': "any",
'recipient': "atoms",
'none handling': "None"
}
from chimerax.atomic import Atom, Bond, Pseudobond, Residue, Chain, Structure
recipient_info = {
"atoms": (Atom, lambda objs: objs.atoms),
"bonds": (Bond, lambda objs: objs.bonds),
"pseudobonds": (Pseudobond, lambda objs: objs.pseudobonds),
"residues": (Residue, lambda objs: objs.residues),
"chains": (Chain, lambda objs: objs.chains),
# since we always restrict to structures, can just use Objects.models()
"molecules": (Structure, lambda objs: objs.models),
"structures": (Structure, lambda objs: objs.models),
}
legal_control_values = {
'match mode': set(["any", "non-zero", "1-to-1"]),
'recipient': set(recipient_info.keys()),
'none handling': set(["None", "string", "delete"])
}
all_info = []
def append_all_info(attr_info,
data_info,
line_num,
*,
ai=all_info,
fn=file_name):
if 'attribute' not in attr_info:
raise SyntaxError(
"No attribute name defined for data lines %d and earlier in %s"
% (line_num, fn))
if not data_info:
raise SyntaxError("No data lines for attribute '%s' in %s" %
(attr_info['attribute'], fn))
ai.append((attr_info, data_info))
from chimerax.core.commands import AtomSpecArg, AttrNameArg, AnnotationError, NoneArg, ColorArg, commas
from chimerax.core.commands import IntArg, FloatArg
from chimerax.io import open_input
with open_input(file_name, encoding="utf-8") as f:
data = []
attrs = {}
for lnum, raw_line in enumerate(f):
# spaces in values could be significant, so instead of stripping just drop the '\n'
# (which all line endings are translated to if newline=None [default] for open())
line = raw_line[:-1]
if not line.strip() or line[0] == '#':
continue
if line[0] == '\t':
# data line
datum = line[1:].split('\t')
if len(datum) != 2:
raise SyntaxError(
"Data line %d in %s not of the form: <tab> atomspec <tab> value"
% (lnum + 1, file_name))
data.append((lnum + 1, *datum))
continue
# control line
try:
name, value = line.split(": ")
except ValueError:
raise SyntaxError(
"Line %d in %s is either not of the form 'name: value'"
" or is missing initial tab" % (lnum + 1, file_name))
name = name.strip().lower()
value = value.strip()
if name in attrs:
# presumably another set of control/data lines starting
append_all_info(attrs, data, lnum + 1)
attrs = {}
data = []
if name == 'attribute':
try:
final_value, *args = AttrNameArg.parse(value, session)
except AnnotationError as e:
raise SyntaxError(
"Bad attribute name ('%s') given on line %d of %s: %s"
% (value, lnum + 1, file_name, str(e)))
elif name not in legal_control_values:
raise SyntaxError(
"Unrecognized control type ('%s') given on line %d of %s" %
(name, lnum + 1, file_name))
elif value not in legal_control_values[name]:
raise SyntaxError(
"Illegal control value ('%s') for %s given on line %d of %s; legal"
" values are: %s" % (value, name, lnum + 1, file_name,
commas(legal_control_values[name])))
else:
final_value = value
attrs[name] = final_value
append_all_info(attrs, data, lnum + 1)
for attr_info, data_info in all_info:
attr_name = attr_info['attribute']
color_attr = attr_name.lower().endswith(
'color') or attr_name.lower().endswith('colour')
match_mode = attr_info.get('match mode',
control_defaults['match mode'])
none_handling = attr_info.get('none handling',
control_defaults['none handling'])
none_okay = none_handling != 'string'
none_seen = False
eval_vals = ["true", "false"]
if none_okay:
eval_vals.append("none")
recipient = attr_info.get('recipient', control_defaults['recipient'])
recip_class, instance_fetch = recipient_info[recipient]
seen_types = set()
try:
pre_existing_attr = getattr(recip_class, attr_name)
except AttributeError:
pass
else:
if callable(pre_existing_attr):
raise ValueError(
"%s is a method of the %s class and cannot be redefined" %
(attr_name, recip_class.__name__))
if attr_name[0].isupper():
raise ValueError(
"%s is a constant in the %s class and cannot be redefined"
% (attr_name, recip_class.__name__))
for line_num, spec, value_string in data_info:
try:
atom_spec, *args = AtomSpecArg.parse(spec, session)
except AnnotationError as e:
raise SyntaxError("Bad atom specifier (%s) on line %d of %s" %
(spec, line_num, file_name))
try:
objects = atom_spec.evaluate(session, models=restriction)
except Exception as e:
raise SyntaxError(
"Error evaluating atom specifier (%s) on line %d of %s: %s"
% (spec, line_num, file_name, str(e)))
matches = instance_fetch(objects)
if not matches and match_mode != "any":
raise SyntaxError(
"Selector (%s) on line %d of %s matched nothing" %
(spec, line_num, file_name))
if len(matches) > 1 and match_mode == "1-to-1":
raise SyntaxError(
"Selector (%s) on line %d of %s matched multiple %s" %
(spec, line_num, file_name, recipient))
if log:
session.logger.info(
"Selector %s matched %s" %
(spec, commas([str(x)
for x in matches], conjunction="and")))
if not value_string:
raise SyntaxError("No data value on line %d of %s" %
(line_num, file_name))
# Can't just use normal argument parsers willy nilly since strings are allowed to have
# leading/trailing whitespace, don't want to accept shorten ed forms of booleans, etc.
if color_attr:
try:
value, text, rest = ColorArg.parse(value_string, session)
if rest:
raise AnnotationError("trailing text")
seen_types.add("color")
value = value.uint8x4()
except AnnotationError:
if none_okay:
try:
value, text, rest = NoneArg.parse(
value_string, session)
if rest:
raise AnnotationError("trailing text")
seen_types.add(None)
except AnnotationError:
raise SyntaxError(
"Value (%s) on line %d of %s is not recognizable as either a"
" color value or None" %
(value_string, line_num, file_name))
else:
raise SyntaxError(
"Value (%s) on line %d of %s is not recognizable as a color value"
% (value_string, line_num, file_name))
else:
if value_string.strip() != value_string:
value = value_string
seen_types.add(str)
elif value_string.startswith('"') and value_string.endswith(
'"'):
value = value_string[1:-1]
seen_types.add(str)
elif value_string.lower() in eval_vals:
value = eval(value_string.capitalize())
if value is None:
seen_types.add(None)
else:
seen_types.add(bool)
else:
try:
value, text, rest = IntArg.parse(value_string, session)
if rest:
raise AnnotationError("trailing text")
seen_types.add(int)
except AnnotationError:
try:
value, text, rest = FloatArg.parse(
value_string, session)
if rest:
raise AnnotationError("trailing text")
seen_types.add(float)
except AnnotationError:
value = value_string
seen_types.add(str)
for match in matches:
if value is not None or none_handling == "None":
setattr(match, attr_name, value)
elif hasattr(match, attr_name):
if pre_existing_attr:
raise RuntimeError(
"Cannot remove builtin attribute %s from class %s"
% (attr_name, recip_class.__name__))
else:
delattr(match, attr_name)
can_return_none = None in seen_types
seen_types.discard(None)
if len(seen_types) == 1:
seen_type = seen_types.pop()
attr_type = None if seen_type == "color" else seen_type
elif seen_types == set([int, float]):
attr_type = float
else:
attr_type = None
recip_class.register_attr(session,
attr_name,
"defattr command",
attr_type=attr_type,
can_return_none=can_return_none)