Ctrl+K

moleculekit.projections.metricplumed2 module#

class moleculekit.projections.metricplumed2.MetricPlumed2(plumed_inp)#

Bases: Projection

Calculates generic collective variables through Plumed 2

The collective variables are defined in PLUMED 2’s syntax. PLUMED needs be installed separately; see http://www.plumed.org/.

The script can be defined as

  • a string, or a list of strings (which are concatenated), or

  • a list of PlumedCV objects (see PlumedCV for examples)

TODO: allow selection of CVs to print

Parameters:

plumed_inp – The PLUMED script defining CVs - string, list of strings or list of PlumedCV objects

Examples

>>> metr = MetricPlumed2( ['d1: DISTANCE ATOMS=2,3', 'd2: DISTANCE ATOMS=5,6']) # As strings
>>> metr.project(mol)
array([ array([[ 1.68597198,  1.09485197], ...
getMapping(mol)#

Return the labels of the colvars used in this projection.

Can only be used after the projection has been executed.

TODO: Update to pandas.

Returns:

A list of cv names

Return type:

cvnames

project(mol, debug=False)#

Project molecule.

Parameters:

  • mol (Molecule) – A Molecule object to project.

  • debug (bool) – Do not delete intermediate files.

Returns:

data – An array containing the projected data.

Return type:

np.ndarray

class moleculekit.projections.metricplumed2.PlumedCOM(mol, label, sel='all')#

Bases: PlumedGenericGroup

An atom center-of-mass for use in the Plumed interface

Parameters:

  • mol (Molecule) – The molecule

  • label (str) – The label assigned to the group

  • sel (str, optional) – The atom selection defining the group

Example

>>> m=Molecule("3PTB")
>>> PlumedCOM(m,"ben_cm","resname BEN")
ben_cm: COM ATOMS=1632,1633,1634,1635,1636,1637,1638,1639,1640
class moleculekit.projections.metricplumed2.PlumedCV(cv, label, verbatim=None, **kw)#

Bases: PlumedStatement

Define a Plumed2 CV.

The arguments, optional and mandatory, are passed as python named parameters. The argument values can be of type (see examples):

  • string or int (passed as they are)

  • bool (the keyword is enabled, with no value (eg: PBC=True becomes PBC))

  • PlumedGroups (passed by label, prepended to the CV definition)

  • PlumedCOM (passed by label, prepended to the CV definition)

  • Molecule (converted into a PlumedGroup)

  • list containing any of the above (each element is converted as above, then they are listed separated by comma)

Parameters:

  • cv (str) – The CV action, as a string (e.g.: “DISTANCE”). (PLUMED is Case-insensitive.)

  • label (str) – The label assigned to the CV

  • args – Named arguments and keywords to the CV (see details).

  • verbatim (str, optional) – Code which will be added as-is to the CV line

Examples

>>> PlumedCV("GYRATION", "rgyr", ATOMS="10-20", TYPE="RADIUS")   # As string
rgyr: GYRATION ATOMS=10-20 TYPE=RADIUS
>>> m=Molecule("3ptb")
>>> grp=PlumedGroup(m,"grp","serial 10 to 20")
>>> PlumedCV("GYRATION", "rgyr2", ATOMS=grp, TYPE="ASPHERICITY", NOPBC=True)  # As PlumedGroup
grp: GROUP ATOMS=10,11,12,13,14,15,16,17,18,19,20
rgyr2: GYRATION ATOMS=grp NOPBC TYPE=ASPHERICITY
>>> protCA=PlumedCOM(m,"protCA","chain A and name CA")
>>> lig=PlumedCOM(m,"lig","resname BEN and noh")
>>> PlumedCV("DISTANCE", "dist", ATOMS=[protCA,lig])  # List of groups
lig: COM ATOMS=1632,1633,1634,1635,1636,1637,1638,1639,1640
protCA: COM ATOMS=2,10,17,21,25,37,44,50,54,59,67,74,81,88,100,109,116,122,130,138,144,148,160,170,181,187,191,195,201,209,217,225,231,240,254,261,268,274,279,284,294,300,312,321,327,331,339,348,355,366,374,378,387,395,403,411,419,426,433,442,446,454,463,472,483,491,497,502,508,517,523,531,538,548,555,561,573,581,587,595,602,610,618,626,634,642,650,658,666,675,683,692,698,703,708,714,722,730,736,747,754,759,765,773,779,787,794,801,807,813,818,824,829,833,840,849,855,863,871,877,881,895,899,907,914,923,929,935,939,946,952,964,971,979,986,994,1003,1009,1017,1026,1031,1038,1046,1054,1060,1068,1074,1080,1086,1095,1101,1106,1118,1125,1129,1138,1146,1153,1159,1167,1175,1186,1192,1197,1201,1213,1221,1230,1234,1238,1247,1255,1261,1267,1276,1280,1288,1294,1298,1302,1309,1316,1323,1329,1335,1339,1348,1356,1365,1369,1377,1384,1390,1404,1408,1414,1418,1424,1429,1438,1447,1455,1464,1471,1475,1482,1494,1501,1510,1517,1523,1531,1543,1550,1556,1570,1578,1587,1596,1603,1611,1616,1622,1631
dist: DISTANCE ATOMS=protCA,lig
>>> PlumedCV("GYRATION", "rgyr3", ATOMS=m)            # Convert Molecule implicitly
lab_1: GROUP ATOMS=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,516,517,518,519,520,521,522,523,524,525,526,527,528,529,530,531,532,533,534,535,536,537,538,539,540,541,542,543,544,545,546,547,548,549,550,551,552,553,554,555,556,557,558,559,560,561,562,563,564,565,566,567,568,569,570,571,572,573,574,575,576,577,578,579,580,581,582,583,584,585,586,587,588,589,590,591,592,593,594,595,596,597,598,599,600,601,602,603,604,605,606,607,608,609,610,611,612,613,614,615,616,617,618,619,620,621,622,623,624,625,626,627,628,629,630,631,632,633,634,635,636,637,638,639,640,641,642,643,644,645,646,647,648,649,650,651,652,653,654,655,656,657,658,659,660,661,662,663,664,665,666,667,668,669,670,671,672,673,674,675,676,677,678,679,680,681,682,683,684,685,686,687,688,689,690,691,692,693,694,695,696,697,698,699,700,701,702,703,704,705,706,707,708,709,710,711,712,713,714,715,716,717,718,719,720,721,722,723,724,725,726,727,728,729,730,731,732,733,734,735,736,737,738,739,740,741,742,743,744,745,746,747,748,749,750,751,752,753,754,755,756,757,758,759,760,761,762,763,764,765,766,767,768,769,770,771,772,773,774,775,776,777,778,779,780,781,782,783,784,785,786,787,788,789,790,791,792,793,794,795,796,797,798,799,800,801,802,803,804,805,806,807,808,809,810,811,812,813,814,815,816,817,818,819,820,821,822,823,824,825,826,827,828,829,830,831,832,833,834,835,836,837,838,839,840,841,842,843,844,845,846,847,848,849,850,851,852,853,854,855,856,857,858,859,860,861,862,863,864,865,866,867,868,869,870,871,872,873,874,875,876,877,878,879,880,881,882,883,884,885,886,887,888,889,890,891,892,893,894,895,896,897,898,899,900,901,902,903,904,905,906,907,908,909,910,911,912,913,914,915,916,917,918,919,920,921,922,923,924,925,926,927,928,929,930,931,932,933,934,935,936,937,938,939,940,941,942,943,944,945,946,947,948,949,950,951,952,953,954,955,956,957,958,959,960,961,962,963,964,965,966,967,968,969,970,971,972,973,974,975,976,977,978,979,980,981,982,983,984,985,986,987,988,989,990,991,992,993,994,995,996,997,998,999,1000,1001,1002,1003,1004,1005,1006,1007,1008,1009,1010,1011,1012,1013,1014,1015,1016,1017,1018,1019,1020,1021,1022,1023,1024,1025,1026,1027,1028,1029,1030,1031,1032,1033,1034,1035,1036,1037,1038,1039,1040,1041,1042,1043,1044,1045,1046,1047,1048,1049,1050,1051,1052,1053,1054,1055,1056,1057,1058,1059,1060,1061,1062,1063,1064,1065,1066,1067,1068,1069,1070,1071,1072,1073,1074,1075,1076,1077,1078,1079,1080,1081,1082,1083,1084,1085,1086,1087,1088,1089,1090,1091,1092,1093,1094,1095,1096,1097,1098,1099,1100,1101,1102,1103,1104,1105,1106,1107,1108,1109,1110,1111,1112,1113,1114,1115,1116,1117,1118,1119,1120,1121,1122,1123,1124,1125,1126,1127,1128,1129,1130,1131,1132,1133,1134,1135,1136,1137,1138,1139,1140,1141,1142,1143,1144,1145,1146,1147,1148,1149,1150,1151,1152,1153,1154,1155,1156,1157,1158,1159,1160,1161,1162,1163,1164,1165,1166,1167,1168,1169,1170,1171,1172,1173,1174,1175,1176,1177,1178,1179,1180,1181,1182,1183,1184,1185,1186,1187,1188,1189,1190,1191,1192,1193,1194,1195,1196,1197,1198,1199,1200,1201,1202,1203,1204,1205,1206,1207,1208,1209,1210,1211,1212,1213,1214,1215,1216,1217,1218,1219,1220,1221,1222,1223,1224,1225,1226,1227,1228,1229,1230,1231,1232,1233,1234,1235,1236,1237,1238,1239,1240,1241,1242,1243,1244,1245,1246,1247,1248,1249,1250,1251,1252,1253,1254,1255,1256,1257,1258,1259,1260,1261,1262,1263,1264,1265,1266,1267,1268,1269,1270,1271,1272,1273,1274,1275,1276,1277,1278,1279,1280,1281,1282,1283,1284,1285,1286,1287,1288,1289,1290,1291,1292,1293,1294,1295,1296,1297,1298,1299,1300,1301,1302,1303,1304,1305,1306,1307,1308,1309,1310,1311,1312,1313,1314,1315,1316,1317,1318,1319,1320,1321,1322,1323,1324,1325,1326,1327,1328,1329,1330,1331,1332,1333,1334,1335,1336,1337,1338,1339,1340,1341,1342,1343,1344,1345,1346,1347,1348,1349,1350,1351,1352,1353,1354,1355,1356,1357,1358,1359,1360,1361,1362,1363,1364,1365,1366,1367,1368,1369,1370,1371,1372,1373,1374,1375,1376,1377,1378,1379,1380,1381,1382,1383,1384,1385,1386,1387,1388,1389,1390,1391,1392,1393,1394,1395,1396,1397,1398,1399,1400,1401,1402,1403,1404,1405,1406,1407,1408,1409,1410,1411,1412,1413,1414,1415,1416,1417,1418,1419,1420,1421,1422,1423,1424,1425,1426,1427,1428,1429,1430,1431,1432,1433,1434,1435,1436,1437,1438,1439,1440,1441,1442,1443,1444,1445,1446,1447,1448,1449,1450,1451,1452,1453,1454,1455,1456,1457,1458,1459,1460,1461,1462,1463,1464,1465,1466,1467,1468,1469,1470,1471,1472,1473,1474,1475,1476,1477,1478,1479,1480,1481,1482,1483,1484,1485,1486,1487,1488,1489,1490,1491,1492,1493,1494,1495,1496,1497,1498,1499,1500,1501,1502,1503,1504,1505,1506,1507,1508,1509,1510,1511,1512,1513,1514,1515,1516,1517,1518,1519,1520,1521,1522,1523,1524,1525,1526,1527,1528,1529,1530,1531,1532,1533,1534,1535,1536,1537,1538,1539,1540,1541,1542,1543,1544,1545,1546,1547,1548,1549,1550,1551,1552,1553,1554,1555,1556,1557,1558,1559,1560,1561,1562,1563,1564,1565,1566,1567,1568,1569,1570,1571,1572,1573,1574,1575,1576,1577,1578,1579,1580,1581,1582,1583,1584,1585,1586,1587,1588,1589,1590,1591,1592,1593,1594,1595,1596,1597,1598,1599,1600,1601,1602,1603,1604,1605,1606,1607,1608,1609,1610,1611,1612,1613,1614,1615,1616,1617,1618,1619,1620,1621,1622,1623,1624,1625,1626,1627,1628,1629,1631,1632,1633,1634,1635,1636,1637,1638,1639,1640,1641,1642,1643,1644,1645,1646,1647,1648,1649,1650,1651,1652,1653,1654,1655,1656,1657,1658,1659,1660,1661,1662,1663,1664,1665,1666,1667,1668,1669,1670,1671,1672,1673,1674,1675,1676,1677,1678,1679,1680,1681,1682,1683,1684,1685,1686,1687,1688,1689,1690,1691,1692,1693,1694,1695,1696,1697,1698,1699,1700,1701,1702
rgyr3: GYRATION ATOMS=lab_1
genTemplate(include_optional=False)#

Return the template for the given action

Examples

>>> rg=PlumedCV("GYRATION", "rgyr3", ATOMS=[1,2,3])
>>> rg.genTemplate()
'GYRATION ATOMS=<atom selection> TYPE=RADIUS'
class moleculekit.projections.metricplumed2.PlumedGenericGroup(mol, label, sel, type='')#

Bases: PlumedStatement

Abstract class from which PLUMED groups are inherited. Do not use directly.

class moleculekit.projections.metricplumed2.PlumedGroup(mol, label, sel='all')#

Bases: PlumedGenericGroup

An atom GROUP for use in the Plumed interface

Parameters:

  • mol (Molecule) – The molecule

  • label (str) – The label assigned to the group. Autogenerated if None.

  • sel (str, optional) – The atom selection defining the group (defaults to the whole molecule)

Example

>>> m=Molecule("3PTB")
>>> PlumedGroup(m,"ben","resname BEN")
ben: GROUP ATOMS=1632,1633,1634,1635,1636,1637,1638,1639,1640
>>> g=PlumedGroup(m, label=None)   # Autogenerate label
>>> g.label
'lab_2'
class moleculekit.projections.metricplumed2.PlumedMolinfo(mol)#

Bases: PlumedStatement

Add a MOLINFO statement.

The supplied Molecule will also be written to a temporary file, and deleted when the object goes off scope.

Note: this may not behave well under multiprocessing.

Parameters:

mol (Molecule) – Will be written to file, and the corresponding MOLINFO statement generated.

Examples

>>> m = Molecule("1kdx")
>>> mc = m.copy()
>>> mc.dropFrames(keep=[0])
>>> mc.set("resname","SER","resname SEP")
>>> molinfo = PlumedMolinfo(mc)
>>> ah = PlumedCV("ALPHARMSD",RESIDUES="119-146", R_0="1.0", label="ah")
>>> ah_metric = MetricPlumed2([molinfo,ah])
>>> print(ah_metric)
MOLINFO STRUCTURE=/var/folders/qz/7p0f8wdj4zdd8nwxm89xzhy80000gn/T/tmpqqhsi644.pdb
ah: ALPHARMSD RESIDUES=all R_0=1.0
# Rendered PlumedStatement
>>> ah_metric.project(m)        
array([[ 20.10917664],
       [ 19.43626404],
       [ 20.09723854], ...
class moleculekit.projections.metricplumed2.PlumedStatement#

Bases: ABC

Abstract base class for Plumed statements. Do not use directly.

class moleculekit.projections.metricplumed2.PlumedVerbatim(txt, comment=False)#

Bases: PlumedStatement

An arbitrary Plumed statement, as a string.

Parameters:

  • txt – The statement

  • comment (bool) – Whether it is a comment.

moleculekit.projections.metricplumed2.genTemplate(action, include_optional=False)#

Return the template for the given action

Parameters:

  • action (str) – The action to be documented

  • include_optional (bool) – Whether to include optional arguments

Examples

>>> genTemplate("GYRATION")
'GYRATION ATOMS=<atom selection> TYPE=RADIUS'
moleculekit.projections.metricplumed2.manual(action)#

Return the manual for the given action.

The manual is returned as a pseudo-HTML string.

Bugs: prints some text on stderr. The returned string should be reformatted to a more readable format.

Parameters:

action (str) – The action to be documented

Examples

>> manual(“GYRATION”)

On this page