Python PythonMSL Examples

Example #1

def getSasa(sel="sele", normalized=0, probeSize=1.4):
    name = "SASA %3.1f" % probeSize
    if (normalized):
        name = "normSASA %3.1f" % probeSize

    cmd.read_pdbstr(
        PythonMSL.getSasa(cmd.get_pdbstr(sel), normalized, probeSize), name)

Example #2

def localSamplingBR(
        system="all",
        fragSel="sele and name CA",
        bbqTable="/home/dwkulp/software/msl/tables/PiscesBBQTable.txt",
        numResults=25):
    cmd.read_pdbstr(
        PythonMSL.localSamplingBR(cmd.get_pdbstr(system),
                                  cmd.get_pdbstr(fragSel), numResults),
        "fragmentsBR")

Example #3

def localSamplingCCD(
        system="all",
        fragSel="sele and name CA",
        bbqTable="/export/home/brettth/projectsS/code/tree/mslib/trunk/tables/PiscesBBQTable.txt",
        angle=10,
        numResults=25):
    cmd.read_pdbstr(
        PythonMSL.localSamplingCCD(cmd.get_pdbstr(system),
                                   cmd.get_pdbstr(fragSel), numResults, angle,
                                   bbqTable), "fragmentsCCD")

Example #4

def localSamplingPDB(
        system="all",
        fragSel="sele and name CA",
        fragDB="/var/lib/python-support/python2.6/pmg_tk/startup/lbbs/nr1000.fragdb",
        numRes=-1,
        rmsdTol=0.0,
        bbqTable="/var/lib/python-support/python2.6/pmg_tk/startup/lbbs/PiscesBBQTable.txt",
        numResults=25):
    cmd.read_pdbstr(
        PythonMSL.localSamplingPDB(cmd.get_pdbstr(system),
                                   cmd.get_pdbstr(fragSel), fragDB, numRes,
                                   rmsdTol, numResults, bbqTable),
        "fragmentsPDB")

Example #5

def quench(sel="sele", rounds=10):
    cmd.read_pdbstr(PythonMSL.quickQuench(cmd.get_pdbstr(sel), rounds),
                    "quench")

Example #6

File: pymolrc.py Project: Suncuss/mslib

def getSasa(sel="sele",normalized=0,probeSize=1.4):
    name="SASA %3.1f" % probeSize
    if (normalized):
        name="normSASA %3.1f" % probeSize

    cmd.read_pdbstr(PythonMSL.getSasa(cmd.get_pdbstr(sel),normalized,probeSize),name)

Example #7

File: pymolrc.py Project: Suncuss/mslib

def quench(sel="sele",rounds=10):
    cmd.read_pdbstr(PythonMSL.quickQuench(cmd.get_pdbstr(sel),rounds),"quench")

Example #8

File: pymolrc.py Project: Suncuss/mslib

def localSamplingPDB(system="all",fragSel="sele and name CA",fragDB="/var/lib/python-support/python2.6/pmg_tk/startup/lbbs/nr1000.fragdb",numRes=-1, rmsdTol=0.0,bbqTable="/var/lib/python-support/python2.6/pmg_tk/startup/lbbs/PiscesBBQTable.txt",numResults=25):
    cmd.read_pdbstr(PythonMSL.localSamplingPDB(cmd.get_pdbstr(system),cmd.get_pdbstr(fragSel),fragDB,numRes,rmsdTol,numResults,bbqTable),"fragmentsPDB")

Example #9

File: pymolrc.py Project: Suncuss/mslib

def localSamplingBR(system="all",fragSel="sele and name CA",bbqTable="/home/dwkulp/software/msl/tables/PiscesBBQTable.txt",numResults=25):
    cmd.read_pdbstr(PythonMSL.localSamplingBR(cmd.get_pdbstr(system),cmd.get_pdbstr(fragSel),numResults),"fragmentsBR")

Example #10

File: pymolrc.py Project: Suncuss/mslib

def localSamplingCCD(system="all",fragSel="sele and name CA", bbqTable="/export/home/brettth/projectsS/code/tree/mslib/trunk/tables/PiscesBBQTable.txt",angle=10,numResults=25):
    cmd.read_pdbstr(PythonMSL.localSamplingCCD(cmd.get_pdbstr(system),cmd.get_pdbstr(fragSel),numResults,angle,bbqTable),"fragmentsCCD")