This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
from libsbml import * | |
def replace_compartment_multiplication(node, compartents): | |
"""Removes all multiplications with compartment sizes from the given ASTNode. | |
:param node: The ASTNode to process. | |
:type node: ASTNode | |
:param compartents: A list of compartment ids. | |
:type compartents: list[str] |
We can make this file beautiful and searchable if this error is corrected: It looks like row 6 should actually have 25 columns, instead of 4. in line 5.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
# [B].Independent Value [C].Measured Value [C].Fitted Value [C].Weighted Error [B].Independent Value [C].Measured Value [C].Fitted Value [C].Weighted Error [B].Independent Value [C].Measured Value [C].Fitted Value [C].Weighted Error [B].Independent Value [C].Measured Value [C].Fitted Value [C].Weighted Error [B].Independent Value [C].Measured Value [C].Fitted Value [C].Weighted Error [B].Independent Value [C].Measured Value [C].Fitted Value [C].Weighted Error | |
0 -0.2035 0 0.2035 0 0.1516 0 -0.1516 0 -0.08391 0 0.08391 0 -0.07386 0 0.07386 0 0.05275 0 -0.05275 0 -0.1253 0 0.047132 | |
0.25 nan 0.0250421 nan 0.25 nan 0.0250421 nan 0.25 nan 0.0195793 nan 0.25 nan 0.0271863 nan 0.25 nan 0.0244024 nan 0.25 nan 0.0249364 nan | |
0.5 nan 0.0498096 nan 0.5 nan 0.0498096 nan 0.5 nan 0.0390793 nan 0.5 nan 0.0545824 nan 0.5 nan 0.0471641 nan 0.5 nan 0.0493817 nan | |
0.75 nan 0.0743206 nan 0.75 nan 0.0743206 nan 0.75 nan 0.0585314 nan 0.75 nan 0.0821648 nan 0.75 nan 0.0681604 nan 0.75 nan 0.0733473 nan | |
1 0.06739 0.0985929 0.031 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
# -*- coding: utf-8 -*- | |
""" | |
Basic example program reading an SBML file going through the reactions | |
and printing the stoichiometries as constraints in LP format. | |
Created on Thu Apr 14 19:12:41 2016 | |
@author: fbergmann | |
""" |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
==68052== Invalid write of size 8 | |
==68052== at 0xCE09A4: CMathContainer::analyzeRoots() (CMathContainer.cpp:2721) | |
==68052== by 0xCDACFD: CMathContainer::compile() (CMathContainer.cpp:1405) | |
==68052== by 0x97E318: CModel::compile() (CModel.cpp:510) | |
==68052== by 0x97E946: CModel::compileIfNecessary(CProcessReport*) (CModel.cpp:602) | |
==68052== by 0xA848A6: SBMLImporter::createCModelFromSBMLDocument(SBMLDocument*, std::map<CDataObject const*, SBase*, std::less<CDataObject const*>, std::allocator<std::pair<CDataObject const* const, SBase*> > >&) (SBMLImporter.cpp:1558) | |
==68052== by 0xA9105C: SBMLImporter::parseSBML(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, CFunctionDB*, SBMLDocument*&, std::map<CDataObject const*, SBase*, std::less<CDataObject const*>, std::allocator<std::pair<CDataObject const* const, SBase*> > >&, CListOfLayouts*&, CDataModel*) (SBMLImporter.cpp:3744) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
--- a/COPASI.R | |
+++ b/COPASI.R | |
@@ -94,7 +94,9 @@ function(name, .values, where = topenv(parent.frame()), suffix = "Value") | |
enumToInteger <- function(name,type) | |
{ | |
if (is.character(name)) { | |
- ans <- as.integer(get(paste(".__E__", type, sep = ""))[name]) | |
+ gettype <- paste(".__E__", type, sep = "") | |
+ if (!exists(gettype)) gettype <- paste(".__E__", substr(type, 3, nchar(type)), sep = "") | |
+ ans <- as.integer(get(gettype)[name]) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
# example script using the copasi cmake config file | |
# that is usually installed into lib/cmake | |
cmake_minimum_required(VERSION 2.8.11) | |
project (example_copasi_program) | |
# this searches for the libcopasi-static-config.cmake file | |
# that is exported by COPASI and will figure out all the | |
# dependent libraries | |
find_package(libCOPASISE-static CONFIG REQUIRED) |