gsmodutils
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gsmodutils
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B
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C
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D
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Symbols
--add_models <add_models>
gsmodutils-init command line option
--apply_to <apply_to>
gsmodutils-iconditions command line option
--author <author>
gsmodutils-init command line option
--base_model <base_model>
gsmodutils-diff command line option
gsmodutils-dimport command line option
--build, --no-build
gsmodutils-docker command line option
--conditions <conditions>
gsmodutils-export command line option
--description <description>
gsmodutils-dimport command line option
gsmodutils-init command line option
--design <design>
gsmodutils-export command line option
--email <email>
gsmodutils-init command line option
--from_diff, --not_from_diff
gsmodutils-dimport command line option
--growth, --no_growth
gsmodutils-iconditions command line option
--log_path <log_path>
gsmodutils-test command line option
--model_id <model_id>
gsmodutils-export command line option
--name <name>
gsmodutils-dimport command line option
gsmodutils-init command line option
--names, --no-names
gsmodutils-diff command line option
--output <output>
gsmodutils-diff command line option
--overwrite, --no-overwrite
gsmodutils-dimport command line option
gsmodutils-docker command line option
gsmodutils-export command line option
--parent <parent>
gsmodutils-diff command line option
gsmodutils-dimport command line option
--project_path <project_path>
gsmodutils-addmodel command line option
gsmodutils-diff command line option
gsmodutils-dimport command line option
gsmodutils-docker command line option
gsmodutils-export command line option
gsmodutils-iconditions command line option
gsmodutils-info command line option
gsmodutils-test command line option
--save, --no-save
gsmodutils-docker command line option
--save_path <save_path>
gsmodutils-docker command line option
--skip_default, --no_skip_default
gsmodutils-test command line option
--tag <tag>
gsmodutils-docker command line option
--test_id <test_id>
gsmodutils-test command line option
--validate, --no-validate
gsmodutils-addmodel command line option
--validate, --skip_validation
gsmodutils-init command line option
--verbose, --no_verbose
gsmodutils-test command line option
A
add_error() (gsmodutils.test.utils.ResultRecord method)
add_essential_pathway() (gsmodutils.project.interface.GSMProject method)
add_model() (gsmodutils.project.interface.GSMProject method)
add_pathway() (in module gsmodutils.utils.metacyc)
add_reaction() (in module gsmodutils.utils.metacyc)
add_to_model() (gsmodutils.project.design.StrainDesign method)
args (gsmodutils.utils.scrumpy.ParseError attribute)
as_pathway_model() (gsmodutils.project.design.StrainDesign method)
assertion() (gsmodutils.test.utils.ResultRecord method)
B
build_universal_model() (in module gsmodutils.utils.metacyc)
C
check_parents() (gsmodutils.project.design.StrainDesign method)
clear() (gsmodutils.model_diff.ModelDiff method)
collect_tests() (gsmodutils.test.tester.GSMTester method)
compile_pydesign() (gsmodutils.project.design.StrainDesign static method)
conditions (gsmodutils.project.interface.GSMProject attribute)
conditions_schema (gsmodutils.project.interface.GSMProject attribute)
copy() (gsmodutils.model_diff.ModelDiff method)
create_child() (gsmodutils.test.utils.ResultRecord method)
create_project() (gsmodutils.project.interface.GSMProject class method)
D
DEFAULT_MODEL_PATH
gsmodutils-init command line option
design_path (gsmodutils.project.interface.GSMProject attribute)
design_schema (gsmodutils.project.design.StrainDesign attribute)
designs (gsmodutils.project.interface.GSMProject attribute)
F
FILE_FORMAT
gsmodutils-export command line option
FileEncodingCtx (class in gsmodutils.utils.metacyc)
FILEPATH
gsmodutils-export command line option
from_dict() (gsmodutils.project.design.StrainDesign class method)
from_json() (gsmodutils.project.design.StrainDesign class method)
from_pydesign() (gsmodutils.project.design.StrainDesign class method)
fromkeys() (gsmodutils.model_diff.ModelDiff method)
G
genes (gsmodutils.project.design.StrainDesign attribute)
genes_dataframe() (gsmodutils.project.design.StrainDesign method)
get() (gsmodutils.model_diff.ModelDiff method)
get_conditions() (gsmodutils.project.interface.GSMProject method)
get_design() (gsmodutils.project.interface.GSMProject method)
get_enzyme_reactions() (in module gsmodutils.utils.metacyc)
get_test() (gsmodutils.test.tester.GSMTester method)
get_tokens() (in module gsmodutils.utils.scrumpy)
growth_condition() (gsmodutils.project.interface.GSMProject method)
gsmodutils-addmodel command line option
--project_path <project_path>
--validate, --no-validate
PATH
gsmodutils-diff command line option
--base_model <base_model>
--names, --no-names
--output <output>
--parent <parent>
--project_path <project_path>
MODEL_PATH
gsmodutils-dimport command line option
--base_model <base_model>
--description <description>
--from_diff, --not_from_diff
--name <name>
--overwrite, --no-overwrite
--parent <parent>
--project_path <project_path>
IDENTIFIER
MODEL_PATH
gsmodutils-docker command line option
--build, --no-build
--overwrite, --no-overwrite
--project_path <project_path>
--save, --no-save
--save_path <save_path>
--tag <tag>
gsmodutils-export command line option
--conditions <conditions>
--design <design>
--model_id <model_id>
--overwrite, --no-overwrite
--project_path <project_path>
FILEPATH
FILE_FORMAT
gsmodutils-iconditions command line option
--apply_to <apply_to>
--growth, --no_growth
--project_path <project_path>
IDENT
PATH
gsmodutils-info command line option
--project_path <project_path>
gsmodutils-init command line option
--add_models <add_models>
--author <author>
--description <description>
--email <email>
--name <name>
--validate, --skip_validation
DEFAULT_MODEL_PATH
PROJECT_PATH
gsmodutils-test command line option
--log_path <log_path>
--project_path <project_path>
--skip_default, --no_skip_default
--test_id <test_id>
--verbose, --no_verbose
gsmodutils.model_diff (module)
gsmodutils.project.design (module)
gsmodutils.project.interface (module)
gsmodutils.test.tester (module)
gsmodutils.test.utils (module)
gsmodutils.utils.metacyc (module)
gsmodutils.utils.scrumpy (module)
GSMProject (class in gsmodutils.project.interface)
GSMTester (class in gsmodutils.test.tester)
I
IDENT
gsmodutils-iconditions command line option
IDENTIFIER
gsmodutils-dimport command line option
info (gsmodutils.project.design.StrainDesign attribute)
is_success (gsmodutils.test.utils.ResultRecord attribute)
items() (gsmodutils.model_diff.ModelDiff method)
iter_models() (gsmodutils.project.interface.GSMProject method)
iter_tests() (gsmodutils.test.tester.GSMTester method)
K
keys() (gsmodutils.model_diff.ModelDiff method)
L
list_conditions (gsmodutils.project.interface.GSMProject attribute)
list_designs (gsmodutils.project.interface.GSMProject attribute)
list_models (gsmodutils.project.interface.GSMProject attribute)
load() (gsmodutils.project.design.StrainDesign method)
(gsmodutils.test.utils.ModelLoader method)
load_conditions() (gsmodutils.project.interface.GSMProject method)
load_design() (gsmodutils.project.interface.GSMProject method)
load_diff() (gsmodutils.project.interface.GSMProject method)
load_model() (gsmodutils.project.interface.GSMProject method)
load_scrumpy_model() (in module gsmodutils.utils.scrumpy)
log_count (gsmodutils.test.utils.ResultRecord attribute)
M
metabolites (gsmodutils.project.design.StrainDesign attribute)
metabolites_dataframe() (gsmodutils.project.design.StrainDesign method)
model (gsmodutils.project.interface.GSMProject attribute)
model_diff() (gsmodutils.model_diff.ModelDiff static method)
(in module gsmodutils.model_diff)
MODEL_PATH
gsmodutils-diff command line option
gsmodutils-dimport command line option
ModelDiff (class in gsmodutils.model_diff)
ModelLoader (class in gsmodutils.test.utils)
models (gsmodutils.project.interface.GSMProject attribute)
ModelTestSelector (class in gsmodutils.test.utils)
P
parse_db() (in module gsmodutils.utils.metacyc)
parse_file() (in module gsmodutils.utils.scrumpy)
parse_fobj() (in module gsmodutils.utils.scrumpy)
parse_metacyc_file() (in module gsmodutils.utils.metacyc)
parse_string() (in module gsmodutils.utils.scrumpy)
ParseError
PATH
gsmodutils-addmodel command line option
gsmodutils-iconditions command line option
pop() (gsmodutils.model_diff.ModelDiff method)
popitem() (gsmodutils.model_diff.ModelDiff method)
progress_tests() (gsmodutils.test.tester.GSMTester method)
project_context_lock (gsmodutils.project.interface.GSMProject attribute)
PROJECT_PATH
gsmodutils-init command line option
project_path (gsmodutils.project.interface.GSMProject attribute)
project_tester() (gsmodutils.project.interface.GSMProject method)
R
reactions (gsmodutils.project.design.StrainDesign attribute)
reactions_dataframe() (gsmodutils.project.design.StrainDesign method)
removed_genes (gsmodutils.project.design.StrainDesign attribute)
removed_metabolites (gsmodutils.project.design.StrainDesign attribute)
removed_reactions (gsmodutils.project.design.StrainDesign attribute)
ResultRecord (class in gsmodutils.test.utils)
run_all() (gsmodutils.test.tester.GSMTester method)
run_by_id() (gsmodutils.test.tester.GSMTester method)
run_tests() (gsmodutils.project.interface.GSMProject method)
S
save_conditions() (gsmodutils.project.interface.GSMProject method)
save_design() (gsmodutils.project.interface.GSMProject method)
setdefault() (gsmodutils.model_diff.ModelDiff method)
stdout_ctx() (in module gsmodutils.test.utils)
StrainDesign (class in gsmodutils.project.design)
T
test_ids (gsmodutils.test.tester.GSMTester attribute)
tests_dir (gsmodutils.project.interface.GSMProject attribute)
to_dict() (gsmodutils.project.design.StrainDesign method)
(gsmodutils.test.tester.GSMTester method)
(gsmodutils.test.utils.ResultRecord method)
to_json() (gsmodutils.project.design.StrainDesign method)
U
update() (gsmodutils.model_diff.ModelDiff method)
(gsmodutils.project.interface.GSMProject method)
V
validate_dict() (gsmodutils.project.design.StrainDesign static method)
values() (gsmodutils.model_diff.ModelDiff method)
W
warning() (gsmodutils.test.utils.ResultRecord method)
with_traceback() (gsmodutils.utils.scrumpy.ParseError method)
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