首页 浏览 帮助
注册 登录
hungerzs
/
mcell
关注 1
点赞 0
派生 0
文件 工单管理 0 合并请求 0 Wiki
分支: binary_reaction_output
分支列表 标签列表
mcell
/
mdl
/
testsuite
/
reactions
/
volcomplex.mdl

volcomplex.mdl 6.6 KB
永久链接 文件历史 原始文件

123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154155156157158159160161162163164165166 
  1. /****************************************************************************
    2. 

  2.  * Volume complex used in tests
    3. 

  3.  ****************************************************************************/
    4. 

  4. 

  5. DEFINE_COMPLEX_MOLECULE Complex
    6. 

  6. {
    7. 

  7.   NUMBER_OF_SUBUNITS = [5, 5, 5]
    8. 

  8.   SUBUNIT[1:5, 1:5, 1:5] = V_c_su0
    9. 

  9.   SHAPE
    10. 

  10.   {
    11. 

  11.     SUBUNIT[1, 1, 1] = [-.04, -.04, -.04]
    12. 

  12.     SUBUNIT[1, 1, 2] = [-.04, -.04, -.02]
    13. 

  13.     SUBUNIT[1, 1, 3] = [-.04, -.04,  .00]
    14. 

  14.     SUBUNIT[1, 1, 4] = [-.04, -.04,  .02]
    15. 

  15.     SUBUNIT[1, 1, 5] = [-.04, -.04,  .04]
    16. 

  16.     SUBUNIT[1, 2, 1] = [-.04, -.02, -.04]
    17. 

  17.     SUBUNIT[1, 2, 2] = [-.04, -.02, -.02]
    18. 

  18.     SUBUNIT[1, 2, 3] = [-.04, -.02,  .00]
    19. 

  19.     SUBUNIT[1, 2, 4] = [-.04, -.02,  .02]
    20. 

  20.     SUBUNIT[1, 2, 5] = [-.04, -.02,  .04]
    21. 

  21.     SUBUNIT[1, 3, 1] = [-.04,  .00, -.04]
    22. 

  22.     SUBUNIT[1, 3, 2] = [-.04,  .00, -.02]
    23. 

  23.     SUBUNIT[1, 3, 3] = [-.04,  .00,  .00]
    24. 

  24.     SUBUNIT[1, 3, 4] = [-.04,  .00,  .02]
    25. 

  25.     SUBUNIT[1, 3, 5] = [-.04,  .00,  .04]
    26. 

  26.     SUBUNIT[1, 4, 1] = [-.04,  .02, -.04]
    27. 

  27.     SUBUNIT[1, 4, 2] = [-.04,  .02, -.02]
    28. 

  28.     SUBUNIT[1, 4, 3] = [-.04,  .02,  .00]
    29. 

  29.     SUBUNIT[1, 4, 4] = [-.04,  .02,  .02]
    30. 

  30.     SUBUNIT[1, 4, 5] = [-.04,  .02,  .04]
    31. 

  31.     SUBUNIT[1, 5, 1] = [-.04,  .04, -.04]
    32. 

  32.     SUBUNIT[1, 5, 2] = [-.04,  .04, -.02]
    33. 

  33.     SUBUNIT[1, 5, 3] = [-.04,  .04,  .00]
    34. 

  34.     SUBUNIT[1, 5, 4] = [-.04,  .04,  .02]
    35. 

  35.     SUBUNIT[1, 5, 5] = [-.04,  .04,  .04]
    36. 

  36.     SUBUNIT[2, 1, 1] = [-.02, -.04, -.04]
    37. 

  37.     SUBUNIT[2, 1, 2] = [-.02, -.04, -.02]
    38. 

  38.     SUBUNIT[2, 1, 3] = [-.02, -.04,  .00]
    39. 

  39.     SUBUNIT[2, 1, 4] = [-.02, -.04,  .02]
    40. 

  40.     SUBUNIT[2, 1, 5] = [-.02, -.04,  .04]
    41. 

  41.     SUBUNIT[2, 2, 1] = [-.02, -.02, -.04]
    42. 

  42.     SUBUNIT[2, 2, 2] = [-.02, -.02, -.02]
    43. 

  43.     SUBUNIT[2, 2, 3] = [-.02, -.02,  .00]
    44. 

  44.     SUBUNIT[2, 2, 4] = [-.02, -.02,  .02]
    45. 

  45.     SUBUNIT[2, 2, 5] = [-.02, -.02,  .04]
    46. 

  46.     SUBUNIT[2, 3, 1] = [-.02,  .00, -.04]
    47. 

  47.     SUBUNIT[2, 3, 2] = [-.02,  .00, -.02]
    48. 

  48.     SUBUNIT[2, 3, 3] = [-.02,  .00,  .00]
    49. 

  49.     SUBUNIT[2, 3, 4] = [-.02,  .00,  .02]
    50. 

  50.     SUBUNIT[2, 3, 5] = [-.02,  .00,  .04]
    51. 

  51.     SUBUNIT[2, 4, 1] = [-.02,  .02, -.04]
    52. 

  52.     SUBUNIT[2, 4, 2] = [-.02,  .02, -.02]
    53. 

  53.     SUBUNIT[2, 4, 3] = [-.02,  .02,  .00]
    54. 

  54.     SUBUNIT[2, 4, 4] = [-.02,  .02,  .02]
    55. 

  55.     SUBUNIT[2, 4, 5] = [-.02,  .02,  .04]
    56. 

  56.     SUBUNIT[2, 5, 1] = [-.02,  .04, -.04]
    57. 

  57.     SUBUNIT[2, 5, 2] = [-.02,  .04, -.02]
    58. 

  58.     SUBUNIT[2, 5, 3] = [-.02,  .04,  .00]
    59. 

  59.     SUBUNIT[2, 5, 4] = [-.02,  .04,  .02]
    60. 

  60.     SUBUNIT[2, 5, 5] = [-.02,  .04,  .04]
    61. 

  61.     SUBUNIT[3, 1, 1] = [ .00, -.04, -.04]
    62. 

  62.     SUBUNIT[3, 1, 2] = [ .00, -.04, -.02]
    63. 

  63.     SUBUNIT[3, 1, 3] = [ .00, -.04,  .00]
    64. 

  64.     SUBUNIT[3, 1, 4] = [ .00, -.04,  .02]
    65. 

  65.     SUBUNIT[3, 1, 5] = [ .00, -.04,  .04]
    66. 

  66.     SUBUNIT[3, 2, 1] = [ .00, -.02, -.04]
    67. 

  67.     SUBUNIT[3, 2, 2] = [ .00, -.02, -.02]
    68. 

  68.     SUBUNIT[3, 2, 3] = [ .00, -.02,  .00]
    69. 

  69.     SUBUNIT[3, 2, 4] = [ .00, -.02,  .02]
    70. 

  70.     SUBUNIT[3, 2, 5] = [ .00, -.02,  .04]
    71. 

  71.     SUBUNIT[3, 3, 1] = [ .00,  .00, -.04]
    72. 

  72.     SUBUNIT[3, 3, 2] = [ .00,  .00, -.02]
    73. 

  73.     SUBUNIT[3, 3, 3] = [ .00,  .00,  .00]
    74. 

  74.     SUBUNIT[3, 3, 4] = [ .00,  .00,  .02]
    75. 

  75.     SUBUNIT[3, 3, 5] = [ .00,  .00,  .04]
    76. 

  76.     SUBUNIT[3, 4, 1] = [ .00,  .02, -.04]
    77. 

  77.     SUBUNIT[3, 4, 2] = [ .00,  .02, -.02]
    78. 

  78.     SUBUNIT[3, 4, 3] = [ .00,  .02,  .00]
    79. 

  79.     SUBUNIT[3, 4, 4] = [ .00,  .02,  .02]
    80. 

  80.     SUBUNIT[3, 4, 5] = [ .00,  .02,  .04]
    81. 

  81.     SUBUNIT[3, 5, 1] = [ .00,  .04, -.04]
    82. 

  82.     SUBUNIT[3, 5, 2] = [ .00,  .04, -.02]
    83. 

  83.     SUBUNIT[3, 5, 3] = [ .00,  .04,  .00]
    84. 

  84.     SUBUNIT[3, 5, 4] = [ .00,  .04,  .02]
    85. 

  85.     SUBUNIT[3, 5, 5] = [ .00,  .04,  .04]
    86. 

  86.     SUBUNIT[4, 1, 1] = [ .02, -.04, -.04]
    87. 

  87.     SUBUNIT[4, 1, 2] = [ .02, -.04, -.02]
    88. 

  88.     SUBUNIT[4, 1, 3] = [ .02, -.04,  .00]
    89. 

  89.     SUBUNIT[4, 1, 4] = [ .02, -.04,  .02]
    90. 

  90.     SUBUNIT[4, 1, 5] = [ .02, -.04,  .04]
    91. 

  91.     SUBUNIT[4, 2, 1] = [ .02, -.02, -.04]
    92. 

  92.     SUBUNIT[4, 2, 2] = [ .02, -.02, -.02]
    93. 

  93.     SUBUNIT[4, 2, 3] = [ .02, -.02,  .00]
    94. 

  94.     SUBUNIT[4, 2, 4] = [ .02, -.02,  .02]
    95. 

  95.     SUBUNIT[4, 2, 5] = [ .02, -.02,  .04]
    96. 

  96.     SUBUNIT[4, 3, 1] = [ .02,  .00, -.04]
    97. 

  97.     SUBUNIT[4, 3, 2] = [ .02,  .00, -.02]
    98. 

  98.     SUBUNIT[4, 3, 3] = [ .02,  .00,  .00]
    99. 

  99.     SUBUNIT[4, 3, 4] = [ .02,  .00,  .02]
    100. 

  100.     SUBUNIT[4, 3, 5] = [ .02,  .00,  .04]
    101. 

  101.     SUBUNIT[4, 4, 1] = [ .02,  .02, -.04]
    102. 

  102.     SUBUNIT[4, 4, 2] = [ .02,  .02, -.02]
    103. 

  103.     SUBUNIT[4, 4, 3] = [ .02,  .02,  .00]
    104. 

  104.     SUBUNIT[4, 4, 4] = [ .02,  .02,  .02]
    105. 

  105.     SUBUNIT[4, 4, 5] = [ .02,  .02,  .04]
    106. 

  106.     SUBUNIT[4, 5, 1] = [ .02,  .04, -.04]
    107. 

  107.     SUBUNIT[4, 5, 2] = [ .02,  .04, -.02]
    108. 

  108.     SUBUNIT[4, 5, 3] = [ .02,  .04,  .00]
    109. 

  109.     SUBUNIT[4, 5, 4] = [ .02,  .04,  .02]
    110. 

  110.     SUBUNIT[4, 5, 5] = [ .02,  .04,  .04]
    111. 

  111.     SUBUNIT[5, 1, 1] = [ .04, -.04, -.04]
    112. 

  112.     SUBUNIT[5, 1, 2] = [ .04, -.04, -.02]
    113. 

  113.     SUBUNIT[5, 1, 3] = [ .04, -.04,  .00]
    114. 

  114.     SUBUNIT[5, 1, 4] = [ .04, -.04,  .02]
    115. 

  115.     SUBUNIT[5, 1, 5] = [ .04, -.04,  .04]
    116. 

  116.     SUBUNIT[5, 2, 1] = [ .04, -.02, -.04]
    117. 

  117.     SUBUNIT[5, 2, 2] = [ .04, -.02, -.02]
    118. 

  118.     SUBUNIT[5, 2, 3] = [ .04, -.02,  .00]
    119. 

  119.     SUBUNIT[5, 2, 4] = [ .04, -.02,  .02]
    120. 

  120.     SUBUNIT[5, 2, 5] = [ .04, -.02,  .04]
    121. 

  121.     SUBUNIT[5, 3, 1] = [ .04,  .00, -.04]
    122. 

  122.     SUBUNIT[5, 3, 2] = [ .04,  .00, -.02]
    123. 

  123.     SUBUNIT[5, 3, 3] = [ .04,  .00,  .00]
    124. 

  124.     SUBUNIT[5, 3, 4] = [ .04,  .00,  .02]
    125. 

  125.     SUBUNIT[5, 3, 5] = [ .04,  .00,  .04]
    126. 

  126.     SUBUNIT[5, 4, 1] = [ .04,  .02, -.04]
    127. 

  127.     SUBUNIT[5, 4, 2] = [ .04,  .02, -.02]
    128. 

  128.     SUBUNIT[5, 4, 3] = [ .04,  .02,  .00]
    129. 

  129.     SUBUNIT[5, 4, 4] = [ .04,  .02,  .02]
    130. 

  130.     SUBUNIT[5, 4, 5] = [ .04,  .02,  .04]
    131. 

  131.     SUBUNIT[5, 5, 1] = [ .04,  .04, -.04]
    132. 

  132.     SUBUNIT[5, 5, 2] = [ .04,  .04, -.02]
    133. 

  133.     SUBUNIT[5, 5, 3] = [ .04,  .04,  .00]
    134. 

  134.     SUBUNIT[5, 5, 4] = [ .04,  .04,  .02]
    135. 

  135.     SUBUNIT[5, 5, 5] = [ .04,  .04,  .04]
    136. 

  136.   }
    137. 

  137.   SUBUNIT_RELATIONSHIPS
    138. 

  138.   {
    139. 

  139.     xp = [+1,  0,  0]
    140. 

  140.     xn = [-1,  0,  0]
    141. 

  141.     yp = [ 0, +1,  0]
    142. 

  142.     yn = [ 0, -1,  0]
    143. 

  143.     zp = [ 0,  0, +1]
    144. 

  144.     zn = [ 0,  0, -1]
    145. 

  145.   }
    146. 

  146.   RATE_RULES
    147. 

  147.   {
    148. 

  148.     binding
    149. 

  149.     {
    150. 

  150.       xp == V_c_su1 & xn != V_c_su1 & yp == V_c_su1 & yn == V_c_su0 & zp == V_c_su1 & zn != V_c_su1 : cx_max_rate
    151. 

  151.                                       yp == V_c_su1 & yn == V_c_su0 & zp == V_c_su1 & zn != V_c_su1 : cx_rate_1
    152. 

  152.       xp == V_c_su1 & xn != V_c_su1 &                                 zp == V_c_su1 & zn != V_c_su1 : cx_rate_1
    153. 

  153.       xp == V_c_su1 & xn != V_c_su1 & yp == V_c_su1 & yn == V_c_su0                                 : cx_rate_1
    154. 

  154.                                                                       zp == V_c_su1 & zn != V_c_su1 : cx_rate_2
    155. 

  155.                                       yp == V_c_su1 & yn == V_c_su0                                 : cx_rate_2
    156. 

  156.       xp == V_c_su1 & xn != V_c_su1                                                                 : cx_rate_2
    157. 

  157.       DEFAULT                                                                                       : cx_normal_rate
    158. 

  158.     }
    159. 

  159.   }
    160. 

  160. }
    161. 

  161. 

  162. DEFINE_REACTIONS
    163. 

  163. {
    164. 

  164.   (V_c_su0) + V_i -> (V_c_su1) [COMPLEX_RATE Complex binding]
    165. 

  165. }
    166. 

  166.