Python: module pdb2pqr

pdb2pqr (14 April 2004) | index /home/todd/release/pdb2pqr/pdb2pqr.py

`Driver for PDB2PQR
This module takes a PDB file as input and performs optimizations
before yielding a new PDB-style file as output.
Ported to Python by Todd Dolinsky (todd@ccb.wustl.edu)
Washington University in St. Louis
Parsing utilities provided by Nathan A. Baker (baker@biochem.wustl.edu)
Washington University in St. Louis`

Modules
`` |  |
getopt math | os random | string sys | time

Functions
`` |  | acos(...) `acos(x) Return the arc cosine (measured in radians) of x.` asin(...) `asin(x) Return the arc sine (measured in radians) of x.` atan(...) `atan(x) Return the arc tangent (measured in radians) of x.` atan2(...) `atan2(y, x) Return the arc tangent (measured in radians) of y/x. Unlike atan(y/x), the signs of both x and y are considered.` ceil(...) `ceil(x) Return the ceiling of x as a float. This is the smallest integral value >= x.` cos(...) `cos(x) Return the cosine of x (measured in radians).` cosh(...) `cosh(x) Return the hyperbolic cosine of x.` exp(...) `exp(x) Return e raised to the power of x.` fabs(...) `fabs(x) Return the absolute value of the float x.` floor(...) `floor(x) Return the floor of x as a float. This is the largest integral value <= x.` fmod(...) `fmod(x,y) Return fmod(x, y), according to platform C. x % y may differ.` frexp(...) `frexp(x) Return the mantissa and exponent of x, as pair (m, e). m is a float and e is an int, such that x = m * 2.**e. If x is 0, m and e are both 0. Else 0.5 <= abs(m) < 1.0.` hypot(...) `hypot(x,y) Return the Euclidean distance, sqrt(x*x + y*y).` ldexp(...) `ldexp(x, i) -> x * (2**i)` log(...) `log(x) -> the natural logarithm (base e) of x.` log10(...) `log10(x) -> the base 10 logarithm of x.` mainCGI() `Main driver for running PDB2PQR from a web page` mainCommand() `Main driver for running program from the command line.` modf(...) `modf(x) Return the fractional and integer parts of x. Both results carry the sign of x. The integer part is returned as a real.` pow(...) `pow(x,y) Return x**y (x to the power of y).` printHeader(atomlist, reslist, charge, ff, warnings) `Print the header for the PQR file Parameters: atomlist: A list of atoms that were unable to have charges assigned (list) reslist: A list of residues with non-integral charges (list) charge: The total charge on the protein (float) ff: The forcefield name (string) warnings: A list of warnings generated from routines (list) Returns header: The header for the PQR file (string)` runPDB2PQR(pdblist, verbose, ff, debump, hopt, hdebump, watopt, hbond) `Run the PDB2PQR Suite Parameters pdblist: The list of objects that was read from the PDB file given as input (list) verbose: When 1, script will print information to stdout When 0, no detailed information will be printed (int) ff: The name of the forcefield (string) debump: When 1, debump heavy atoms (int) hopt: When 1, run hydrogen optimization (int) hdebump: When 1, debump hydrogens (int) watopt: When 1, optimize water hydrogens (int) Returns header: The PQR file header (string) lines: The PQR file atoms (list)` sin(...) `sin(x) Return the sine of x (measured in radians).` sinh(...) `sinh(x) Return the hyperbolic sine of x.` sqrt(...) `sqrt(x) Return the square root of x.` tan(...) `tan(x) Return the tangent of x (measured in radians).` tanh(...) `tanh(x) Return the hyperbolic tangent of x.` usage(rc) `Print usage for this script to stdout. Parameters rc: Exit status (int)`

Data
`` |  | AAFILE = 'AA.DAT' AAS = ['ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'GLN', 'GLU', 'GLH', 'GLY', 'HIS', 'HID', 'HIE', 'HIP', 'HSD', 'HSE', 'HSP', 'ILE', 'LEU', 'LYS', 'MET', ...] AMBER_FILE = 'AMBER.DAT' BACKBONE = ['N', 'CA', 'C', 'O', 'O2', 'HA', 'HN', 'H', 'tN'] BONDED_SS_LIMIT = 2.5 BUMP_DIST = 2.0 BUMP_HDIST = 1.5 CELL_SIZE = 2 CHARMM_FILE = 'CHARMM.DAT' DIHEDRAL = 57.2958 HYDRO_BONDCOORDS = [[7.5810000000000004, 2.0899999999999999, 12.506], [6.4580000000000002, 2.1619999999999999, 13.159000000000001], [5.1449999999999996, 2.2090000000000001, 12.452999999999999]] HYDRO_COORDS = [6.476, 2.1859999999999999, 14.159000000000001] LARGE_TORSION_ANGLE = 1000.0 LIMIT = 500.0 LOADPATH = '/proc/loadavg' LOCALPATH = '/home/todd/public_html/pdb2pqr/' LOGPATH = '/home/todd/public_html/pdb2pqr/log/pdb2pqr.log' NAFILE = 'NA.DAT' NAS = ['A', 'A5', 'A3', 'C', 'C5', 'C3', 'G', 'G5', 'G3', 'T', 'T5', 'T3', 'U', 'U5', 'U3'] NTERM2_COORDS = [-24.001000000000001, 50.223999999999997, -22.225999999999999] NTERM3_COORDS = [-24.869, 48.845999999999997, -22.77] NTERM_COORDS = [[-24.196000000000002, 48.789999999999999, -20.800000000000001], [-25.552, 49.881, -21.847999999999999], [-24.645, 49.491, -22.007000000000001]] OXT_COORDS = [-1.5289999999999999, 1.8580000000000001, 0.69499999999999995] PARSE_FILE = 'PARSE.DAT' PEPTIDE_DIST = 1.7 PEP_TRANS_CA = [-2.3130000000000002, 2.7839999999999998, 1.0229999999999999] PEP_TRANS_N = [-1.252, 1.877, 0.88300000000000001] REFATOM_SIZE = 3 REFRESHTIME = 20 REPAIR_LIMIT = 10 ROTAMERFILE = 'ROTAMER.DAT' SMALL = 9.9999999999999995e-08 STYLESHEET = 'http://agave.wustl.edu/css/baker.css' TMPDIR = 'tmp/' WEBSITE = 'http://ocotillo.wustl.edu/~todd/pdb2pqr/' __author__ = 'Todd Dolinsky, Nathan Baker' __date__ = '14 April 2004' __file__ = './pdb2pqr.pyc' __name__ = 'pdb2pqr' e = 2.7182818284590451 pi = 3.1415926535897931

Author
`` |  | Todd Dolinsky, Nathan Baker