Analyze.pm Show Source

The Analyze package offers a number of functions for the analysis of protein structures. 

new(refmol[,fraglist])
creates a new Analyze object. A reference molecule is required as an argument. A fragment residue list may be given in addition to restrict analysis functions only to those residues. 
($number,$fraction) = gdt(cmpmol[,cutoff])
determines the number of residues that can be matched between two structures with an RMSD within a given distance cutoff. Arguments are the Molecule object for the structure to be compared against the reference structure and the value of the distance cutoff.
 
$val = gdtts(cmpmol)
calculates an approximate GDT_TS score to measure similarity between two structures based on a combination of the fractions of matching residues within a distance cutoffs of 1, 2, 4, and 8 A. A Molecule object for the structure to be compared against the reference structure is required as argument.
 
lsqfit(cmpmol,selmode)
performs a least squares fit of the structure in cmpmol vs. the reference structure. selmode is used to select which atoms are used for the fit (ca, cb, cab, p, or all). 2003-07-09:Modified by Lev Gorenstein \: Added selmode back for backbone fit (N, CA, C, O, OT1).
 
$rmsd = rmsd(cmpmol[,warn[,keep]])
calculates root mean square deviations of the structure in the argument cmpmol with the reference structure. The method returns a data structure with the following fields for RMSD values for atom subsets: CA, CB, CAB, C, N, O, side, back, all, P. Please note that this function does not perform a least squares fit prior to calculating the RMSD values.
 
$list = pairwiseList([mol])
determines a C-alpha based pairwise residue contact list for the calculation of q scores
 
$qscore = qscore(cmpmol[,keep])
calculates Q scores for the structure in the argument cmpmol with respect to the reference structure. The method returns a data structure with the following fields: all, short, medium, long Please note that this function does not perform a least squares fit prior to calculating the Q scores
 
$list = contactList([mol[,fraglist]])
determines a residue contact list based on a minimum distance between heavy atoms of two residues of less than 4.2 A. By default the contact list is calculated from the reference structure, but a different structure may be given as an argument.
 
($ncont,$fraction,$rho,$list) = contacts(cmpmol)
compares the residue contact list in cmpmol with a reference contact list that has to be either loaded previously, or will be calculated from the reference structure if not available. It returns the number of matching contacts, the fraction with respect to all contacts in the reference structure, the quantity rho measuring the contact fraction in a more continuous manner, and the contact list itself.
 
readContacts(file)
reads a residue contact list from a file to be used for comparison with contacts
 
writeContacts(file)
writes the current reference contact list to a file
 
($rmsd,$percentage) = chi1RMSD(cmpmol)
calculates the root mean square deviation and percentage of correct chi1 dihedral values in cmpmol compared with the chi1 dihedral values in the reference structure.
 
($rmsd,$percentage) = chi2RMSD(cmpmol)
calculates the root mean square deviation and percentage of correct chi2 dihedral values in cmpmol compared with the chi2 dihedral values in the reference structure.
 
($rmsd,$percentage) = chi3RMSD(cmpmol)
calculates the root mean square deviation and percentage of correct chi3 dihedral values in cmpmol compared with the chi3 dihedral values in the reference structure.
 
($rmsd,$percentage) = chi4RMSD(cmpmol)
calculates the root mean square deviation and percentage of correct chi4 dihedral values in cmpmol compared with the chi4 dihedral values in the reference structure.
 
($rmsd,$percentage) = chi5RMSD(cmpmol)
calculates the root mean square deviation and percentage of correct chi5 dihedral values in cmpmol compared with the chi5 dihedral values in the reference structure.
 
($phirmsd,$psirmsd,$phipercent,$psipercent) = 
 phipsiRMSD(cmpmol[,fraglist])
calculates the root mean square deviation and percentage of correct phi and psi backbone dihedral values in cmpmol compared with the phi/psi dihedral values in the reference structure. 
$value = radiusOfGyration(mol[,caonly])
calculates the radius of gyration for a molecule
 
chi1(mol)
calculates chi1 side chain dihedral angles for all residues in the given molecule
 
chi2(mol)
calculates chi2 side chain dihedral angles for all residues in the given molecule
 
chi3(mol)
calculates chi3 side chain dihedral angles for all residues in the given molecule
 
chi4(mol)
calculates chi4 side chain dihedral angles for all residues in the given molecule
 
chi5(mol)
calculates chi5 side chain dihedral angles for all residues in the given molecule
 
phipsi(mol)
calculates phi and psi backbone dihedral angles for all residues in the molecule given as argument
 
$hist = radialDistribution(mol,select,resolution)
calculates the radial distribution histogram of the selected subset of atoms from the center of the molecule given in mol. The selection criteria may be a residue name, or one of POL (polar residues), HYD (hydrophobic residues), CHG (charged residues), POS (positively charged residues), NEG (negatively charged residues). The resolution arguments determines the width of the histogram bins.
 
$value = radialRMSD(mol,select)
calculates the radial RMSD of a subset of atoms from the center of mass in the molecule given by mol. For an explanation of the selection argument see radialDistribution above. 
refmol
Molecule object containing reference structure
 
contactReferenceList
reference residue contact list
 
qReferenceList
reference pair distance list for q scores
GenUtil.pm  Molecule.pm  Sequence.pm
Michael Feig, Brooks group, TSRI