Chemical Data Processing Library Python API - Version 1.2.0
|
[ANY] |
|
[ASPE] | H. Xu, S. Izrailev, D. K. Agrafiotis, Conformational Sampling by Self-Organization, J. Chem. Inf. Comput. Sci. 2003, 43, 1186-1191 |
[AUCOR] | G. Moreau, P. Broto, The Autocorrelation of a Topological Structure: A New Molecular Descriptor, Nouv. J. Chim. 1980, 4, 359-360 |
G. Moreau, P. Broto, Autocorrelation of Molecular Structures, Application to SAR Studies, Nouv. J. Chim. 1980, 4, 757-764 | |
[BKA] | C. Bron, J. Kerbosch, Algorithm 457: finding all cliques of an undirected graph, Commun. ACMA 1973, 16, 575-577 |
[BALD] | R. Balducci, R. S. Pearlman, Efficient exact solution of the ring perception problem, J. Chem. Inf. Comput. Sci. 1994, 34, 822-831 |
[BCUT] | R. S. Pearlman, K. M. SMith, Novel Software Tools for Chemical Diversity, Persp. Drug Disc. Design 1998, 9, 339-353 |
[BDBS] |
|
[BEMU] | G. W. Bemis, M. A. Murcko, The Properties of Known Drugs. 1. Molecular Frameworks, J. Med. Chem. 1996, 39, 15, 2887–2893 |
[BRICS] | J. Degen, C. Wegscheid-Gerlach, A. Zaliani, M. Rarey, On the art of compiling and using ’drug-like’ chemical fragment spaces, Chem. Med. Chem. 2008, 3, 1503-1507 |
[BURMA] | F. R. Burden, Molecular identification number for substructure searches, J. Chem. Inf. Comput. Sci. 1989, 29, 225–227 |
[CAIRO] | Cairo 2D Graphics Library homepage: http://www.cairographics.org/ |
[CATA] | J. Greene et al., Chemical Function Queries for 3D Database Search, J. Chem. Inf. Comput. Sci. 1994, 34, 1297-1308 |
[CIPJM] | J. Mayfield et al., Perception and labelling of stereogenic centres in chemical structures: https://github.com/SiMolecule/centres |
R. M. Hanson et al., Algorithmic Analysis of Cahn–Ingold–Prelog Rules of Stereochemistry: Proposals for Revised Rules and a Guide for Machine Implementation, J. Chem. Inf. Model. 2018, 58, 9, 1755–1765 | |
[CITB] | Chemoinformatics - A Textbook; Johann Gasteiger and Thomas Engel (Eds.), WILEY-VCH, ISBN 3-527-30681-1 |
[CML] | Chemical Markup Language documentation: https://www.xml-cml.org/ |
[CSCP] | A. P. Bento et al., An open source chemical structure curation pipeline using RDKit, J. Cheminformatics 2020, 12, 51 |
[CTFILE] | MDL CTFile Formats Specification download page: http://www.mdli.com/downloads/public/ctfile/ctfile.jsp |
A. Dalby et al., Description of several chemical structure file formats used by computer programs developed at Molecular Design Limited, J. Chem. Inf. Comput. Sci. 1992, 32, 244-255 | |
[DTPFP] | Daylight Fingerprint Theory website: http://www.daylight.com/dayhtml/doc/theory/theory.finger.html |
[FUNWRP] |
|
[GRAIL] | D. A. Schuetz et al., GRAIL: GRids of phArmacophore Interaction fieLds, J. Chem. Theory Comput. 2018, 11, 4958-4970 |
[GSIM] | OpenEye GraphSim TK documentation: https://docs.eyesopen.com/toolkits/cpp/graphsimtk/ |
[HANSER] | Th. Hanser, Ph. Jauffret, G. Kaufmann, A New Algorithm for Exhaustive Ring Perception in a Molecular Graph, J. Chem. Inf. Comput. Sci. 1996, 36, 1146-1152 |
[HBMD] | Handbook of Molecular Descriptors, by R. Todeschini and V. Consonni; R. Mannhold, H. Kubinyi and H. Timmerman (Eds.), WILEY-VCH, ISBN 3-52-29913-0 |
[INCHI] | Official IUPAC International Chemical Identifier website: http://www.iupac.org/inchi/ |
Wikipedia article about InChI: http://en.wikipedia.org/wiki/inchi | |
[JME] | JME Molecular Editor website: http://www.molinspiration.com/jme/ |
[KABA] | W. Kabsch, A solution for the best rotation to relate two sets of vectors, Acta Cryst. A 1976, 32, 922-923 |
W. Kabsch, A discussion of the solution for the best rotation to relate two sets of vectors, Acta Cryst. A 1978, 34, 827-828 | |
[LOGS] | T. J. Hou, K. Xia, W. Zhang, X. J. Xu, ADME Evaluation in Drug Discovery. 4. Prediction of Aqueous Solubility Based on Atom Contribution Approach, J. Chem. Inf. Comput. Sci. 2004, 44, 266-275 |
[MACCSK] | J. L. Durant, B. A. Leland, D. R. Henry, J. G. Nourse, Reoptimization of MDL keys for use in drug discovery, J. Chem. Inf. Comput. Sci. 2002, 42, 1273-1280 |
[MCKAY] | B. D. McKay, Practical graph isomorphism, 10th Manitoba Conference on Numerical Mathematics and Computing (Winnipeg, 1980), Congressus Numerantium 1981, 30, 45-87 |
[MCPLX] | J. B. Hendrickson, P. Huang, A. G. Toczko, Molecular complexity: a simplified formula adapted to individual atoms, J. Chem. Inf. Comput. Sci. 1987, 27, 63-67 |
[MCSA] | D. M. Bayada, R. W. Simpson, A. P. Johnson, C. Laurenco, An Algorithm for the Multiple Common Subgraph Problem, J. Chem. Inf. Comput. Sci. 1992, 32, 680–685 |
[MCASA] | H. Bunke, P. Foggia, C. Guidobaldi, C. Sansone, M. Vento, A Comparison of Algorithms for Maximum Common Subgraph on Randomly Connected Graphs, in Structural, Syntactic, and Statistical Pattern Recognition - Joint IAPR International Workshops SSPR 2002 and SPR 2002 Proceedings (Windsor, Ontario, Canada, 2002), 123-132; Springer Berlin/Heidelberg, ISBN 978-3-540-44011-6 |
[MCESA] | J. W. Raymond, E. J. Gardiner, P. Willett, Heuristics for Similarity Searching of Chemical Graphs Using a Maximum Common Edge Subgraph Algorithm, J. Chem. Inf. Comput. Sci.,2002, 42, 305–316 |
[MHASH] | W.-D. Ihlenfeldt, J. Gasteiger, Hash Codes for the Identification and Classification of Molecular Structure Elements, J. Comput. Chem. 1994, 15, 793-813 |
[MHMO] | T. Kleinoeder, PhD-Thesis: Prediction of Properties of Organic Compounds - Empirical Methods and Management of Property Data, Friedrich Alexander University of Erlangen-Nuremberg, 1994 |
[MMCIF] | P. E. Bourne, H. M. Berman, B. McMahon, K. D. Watenpaugh, J. D. Westbrook, P. M. Fitzgerald, Macromolecular crystallographic information file, Macromolecular Crystallography Part B. Methods in Enzymology 1997, Vol. 277, 571–590 |
S. R. Hall, F. H. Allen, I. D. Brown, The Crystallographic Information File (CIF): a new standard archive file for crystallography, Acta Crystallographica Section A 1991, 47, 655-685 | |
[MMTF] | Macromolecular Transmission Format homepage: https://mmtf.rcsb.org |
[MOCAN] | H. L. Morgan, The Generation of a Unique Machine Description for Chemical Structures - A Technique Developed at Chemical Abstracts Service, J. Chem. Doc. 1965, 5, 107-113 |
[NRIC] | Numerical Recipes in C: The Art of Scientific Computing, Second Edition, by W. H. Press et al.; Cambridge University Press, ISBN 0-521-43108-5, http://www.nr.com/ |
[PCDS] |
|
[PDB] | PDB File-Format Specification website: http://www.wwpdb.org/docs.html |
[PEOE] | J. Gasteiger, M. Marsili, Iterative Partial Equalization of Orbital Electronegativity - A Rapid Access to Atomic Charges, Tetrahedron 1980, 36, 3219-3228) |
[RECAP] | X. Q. Lewell, D. B. Judd, S. P. Watson, M. M. Hann, RECAP - Retrosynthetic Combinatorial Analysis Procedure: A Powerful New Technique for Identifying Privileged Molecular Fragments with Useful Applications in Combinatorial Chemistry, J. Chem. Inf. Comput. Sci. 1998, 38, 511-522 |
[QTDOC] | Qt Online Reference Documentation: https://doc.qt.io/ |
[SHPTR] |
|
[SMARTS] | Daylight SMARTS Theory website: http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html |
[SMILES] | Daylight SMILES Theory website: http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html |
D. Weininger, SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules, J. Chem. Inf. Comput. Sci. 1988, 28, 31-36 | |
D. Weininger, A. Weininger and J. L. Weininger, SMILES. 2. Algorithm for generation of unique SMILES notation, J. Chem. Inf. Comput. Sci. 1989, 29, 97-101 | |
[STECFP] | D. Rogers and M. Hahn, Extended-Connectivity Fingerprints, J. Chem. Inf. Model. 2010, 50, 742-754 |
[STLRAI] | Random Access Iterator concept definition: http://www.sgi.com/tech/stl/RandomAccessIterator.html |
[TCIP] | P. Labute, An Efficient Algorithm For The Determination Of Topological RS Chirality, Journal of the Chemical Computing Group 1996, http://www.chemcomp.com/journal/chiral.htm |
[TOPSY] | Z. Ouyang, S. Yuan, J. Brandt, C. Zheng, An Effective Topological Symmetry Perception and Unique Numbering Algorithm, J. Chem. Inf. Comput. Sci. 1999, 39, 299–303 |
[TPSA] | P. Ertl, B. Rohde, P. Selzer, Fast calculation of molecular polar surface area as a sum of fragment based contributions and its application to the prediction of drug transport properties, J. Med. Chem. 2000, 43, 3714-3717 |
[UFF] | A. K. Rappé, C. J. Casewit, K. S. Colwell, W. A. Goddard III, W. M. Skiff, UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations, J. Am. Chem. Soc. 1992, 114, 25, 10024–10035 |
[VFLIB2] | P. Foggia, C. Sansone, M. Vento, An Improved Algorithm for Matching Large Graphs, 3rd IAPR-TC15 Workshop on Graph-based Representations (Ischia, 2001), http://amalfi.dis.unina.it/graph/db/papers/vf-algorithm.pdf |
[WHAM] | Wikipedia article about the Hamming Distance: http://en.wikipedia.org/wiki/Hamming_distance |
[WCOS] | Wikipedia article about the Cosine Similarity MEasure: http://en.wikipedia.org/wiki/Cosine_similarity |
[WJACO] | Wikipedia article about Jacobi's Eigenvalue Algorithm: http://en.wikipedia.org/wiki/Jacobi_eigenvalue_algorithm |
[WLIREG] | Wikipedia article about Linear Regression: http://en.wikipedia.org/wiki/Linear_regression |
[WLSQRS] | Wikipedia article about Least Squares Analysis: http://en.wikipedia.org/wiki/Least_squares |
[WMVC] | Wikipedia article about the Model-View-Controller concept: http://en.wikipedia.org/wiki/Model-view-controller |
[WPDF] | Wikipedia article about the Adobe Portable Document Format: http://en.wikipedia.org/wiki/PDF |
[WPNG] | Wikipedia article about the Portable Network Graphics format: http://en.wikipedia.org/wiki/Portable_Network_Graphics |
[WPS] | Wikipedia article about the PostScript format: http://en.wikipedia.org/wiki/PostScript |
[WSHA] | Wikipedia article about SHA hash functions: http://en.wikipedia.org/wiki/Sha1 |
[WSKF] | Wikipedia article about Skeletal Formulas of chemical compounds: http://en.wikipedia.org/wiki/Skeletal_formula |
[WSTF] | Wikipedia article about Structural Formulas of chemical compounds: http://en.wikipedia.org/wiki/Structural_formula |
[WSVD] | Wikipedia article about Singular Value Decomposition: http://en.wikipedia.org/wiki/Singular_value_decomposition |
[WSVG] | Wikipedia article about the Scalable Vector Graphics format: http://en.wikipedia.org/wiki/SVG |
[XLOGP] | R. Wang, Y. Gao, L. Lai, Calculation of the partition coefficient by an atom-additive method, Persp. Drug Disc. Design 2000, 19, 47-66 |